微生物

No abstract available

The human gut microbiome is highly personal. However, the contribution of gut physiology and environment to variations in the gut microbiome remains understudied. Here we performed an observational trial using multi-omics to profile microbiome composition and metabolism in 61 healthy adults for 9 consecutive days. We assessed day-to-day changes in gut environmental factors and measured whole-gut and segmental intestinal transit time and pH using a wireless motility capsule in a subset of 50 individuals. We observed substantial daily fluctuations, with intra-individual variations in gut microbiome and metabolism associated with changes in stool moisture and faecal pH, and inter-individual variations accounted for by whole-gut and segmental transit times and pH. Metabolites derived from microbial carbohydrate fermentation correlated negatively with the gut passage time and pH, while proteolytic metabolites and breath methane showed a positive correlation. Finally, we identified associations between segmental transit time/pH and coffee-, diet-, host- and microbial-derived metabolites. Our work suggests that gut physiology and environment are key to understanding the individuality of the human gut microbial composition and metabolism. An observational longitudinal clinical trial, incorporating a SmartPill and metabolomics, reveals the role of host factors in shaping the gut microbiome in healthy human adults.

Diet is a major determinant of gut microbiome composition, and variation in diet-microbiome interactions may contribute to variation in their health consequences. To mechanistically understand these relationships, here we map interactions between ∼150 small-molecule dietary xenobiotics and the gut microbiome, including the impacts of these compounds on community composition, the metabolic activities of human gut microbes on dietary xenobiotics, and interindividual variation in these traits. Microbial metabolism can toxify and detoxify these compounds, producing emergent interactions that explain community-specific remodeling by dietary xenobiotics. We identify the gene and enzyme responsible for detoxification of one such dietary xenobiotic, resveratrol, and demonstrate that this enzyme contributes to interindividual variation in community remodeling by resveratrol. Together, these results systematically map interactions between dietary xenobiotics and the gut microbiome and connect toxification and detoxification to interpersonal differences in microbiome response to diet.

“Normal” for the gut microbiota For the benefit of future clinical studies, it is critical to establish what constitutes a “normal” gut microbiome, if it exists at all. Through fecal samples and questionnaires, Falony et al. and Zhernakova et al. targeted general populations in Belgium and the Netherlands, respectively. Gut microbiota composition correlated with a range of factors including diet, use of medication, red blood cell counts, fecal chromogranin A, and stool consistency. The data give some hints for possible biomarkers of normal gut communities. Science, this issue pp. 560 and 565 Two large-scale studies in Western Europe establish environment-diet-microbe-host interactions. Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions.

Variation in the human gut microbiome can reflect host lifestyle and behaviors and influence disease biomarker levels in the blood. Understanding the relationships between gut microbes and host phenotypes are critical for understanding wellness and disease. Here, we examine associations between the gut microbiota and ~150 host phenotypic features across ~3,400 individuals. We identify major axes of taxonomic variance in the gut and a putative diversity maximum along the Firmicutes-to-Bacteroidetes axis. Our analyses reveal both known and unknown associations between microbiome composition and host clinical markers and lifestyle factors, including host-microbe associations that are composition-specific. These results suggest potential opportunities for targeted interventions that alter the composition of the microbiome to improve host health. By uncovering the interrelationships between host diet and lifestyle factors, clinical blood markers, and the human gut microbiome at the population-scale, our results serve as a roadmap for future studies on host-microbe interactions and interventions. Variation in the gut microbiome can reflect host lifestyle, behaviour, and influence blood-based biomarkers. Here the authors examine associations between the microbiota and 150 host phenotypic features in a large cohort of >3,000 individuals.

Fear-related psychiatric disorders including posttraumatic stress disorder are more prevalent in women, yet most mechanistic research on fear and extinction using animal models has been conducted in males (1). Activational effects of estrogens shape the response of neural circuits underlying extinction learning and recall (2), but the pathways through which peripheral physiology influences these cognitive processes remain poorly understood. Meanwhile, research on the gut-brain axis has revealed that intestinal microbes influence emotional behavior and stress responses (3,4). In a recent study published in Biological Psychiatry: Global Open Science , Hartsgrove et al. (5) bring these 2 fields together by asking whether acute estradiol treatment alters the gut microbiome in parallel with its well-known effects on fear extinction memory in female rats. Their findings reveal that estradiol enhances recent but not remote extinction recall while enriching specific microbial taxa previously associated with hormone metabolism and anxiety regulation. This study provides an important starting point for integrating hormonal, microbial, and cognitive dimensions of female-specific vulnerability to stress at a systems level (Figure 1). Hartsgrove et al. (5) used a carefully controlled design that considered both behavioral phase and estrous cycle stage. Naturally cycling female rats underwent auditory fear conditioning during estrus, as estrogen levels decreased, followed by extinction training and recall during metestrus/diestrus when estrogen levels were low. Thirty minutes prior to extinction, animals received a subcutaneous injection of 17 β - estradiol (E2) (15 μ g/kg) or sesame oil vehicle. Recent recall was tested 24 hours later and remote recall 1 to 2 weeks later, both tested in the same cycle phase. Estradiol-treated females froze less than the control group during the 24-hour recall test, replicating prior findings that estrogen supports cognitive flexibility by enhancing the consolidation of extinction learning. However, this behavioral advantage was not maintained at the remote recall test. It should be noted that at the remote recall time point, the estradiol group’s freezing seemed to remain stable,

Alzheimer’s disease (AD) pathology is thought to progress from normal cognition through preclinical disease and ultimately to symptomatic AD with cognitive impairment. Recent work suggests that the gut microbiome of symptomatic patients with AD has an altered taxonomic composition compared with that of healthy, cognitively normal control individuals. However, knowledge about changes in the gut microbiome before the onset of symptomatic AD is limited. In this cross-sectional study that accounted for clinical covariates and dietary intake, we compared the taxonomic composition and gut microbial function in a cohort of 164 cognitively normal individuals, 49 of whom showed biomarker evidence of early preclinical AD. Gut microbial taxonomic profiles of individuals with preclinical AD were distinct from those of individuals without evidence of preclinical AD. The change in gut microbiome composition correlated with β-amyloid (Aβ) and tau pathological biomarkers but not with biomarkers of neurodegeneration, suggesting that the gut microbiome may change early in the disease process. We identified specific gut bacterial taxa associated with preclinical AD. Inclusion of these microbiome features improved the accuracy, sensitivity, and specificity of machine learning classifiers for predicting preclinical AD status when tested on a subset of the cohort (65 of the 164 participants). Gut microbiome correlates of preclinical AD neuropathology may improve our understanding of AD etiology and may help to identify gut-derived markers of AD risk. Description The gut microbiome is an indicator of preclinical Alzheimer’s disease (AD) and may improve machine learning prediction of AD status. Editor’s summary Individuals with Alzheimer’s disease (AD) may have an altered gut microbiome, and these changes may occur early in the disease course. Now, Ferreiro et al. show that the gut microbiomes of people with preclinical AD (indicated by altered brain amyloid and tau proteins) had a different composition from that of healthy individuals. Gut microbial taxa correlated with amyloid and tau markers of preclinical AD, but not with signatures of neurodegeneration. Specific gut bacteria were identified as being associated with preclinical AD, and their inclusion improved machine learning predictions of preclinical AD status. —Orla Smith

No abstract available

No abstract available

BACKGROUND & AIMS The gut microbiome has been suggested to play a role in gut barrier hemostasis, but data are scarce and limited to animal studies. Therefore, we aimed to assess if alterations in gut microbial composition and functional pathways are associated with gut barrier function in a cohort of healthy first-degree relatives of patients with Crohn's disease. METHODS We utilized the Genetic Environmental Microbial (CCC-GEM) cohort of healthy first-degree relatives of patients with Crohn's disease. Gut barrier function was assessed using urinary fractional excretion ratio of lactulose to mannitol (LMR). Microbiome composition was assessed by sequencing fecal 16S rRNA. The cohort was divided into a discovery cohort (n=2,472) and a validation cohort (n=655). A regression model was used to assess microbial associations with LMR. A Random Forest classifier algorithm was performed to assess microbial community contribution to barrier function. RESULTS Subjects with impaired barrier function (LMR>0.025) had reduced alpha-diversity (Chao1 index, p=4.0e-4) and altered beta-diversity (Bray-Curtis dissimilarity index, R2=0.001, p=1.0e-3) compared to subjects with LMR≤0.025. When taxa were assessed individually, we identified eight genera and 52 microbial pathways associated with LMR>0.025 (q<0.05). Four genera (decreased prevalence of Adlercreutzia, Clostridia UCG 014, and Clostridium sensu stricto 1 and increased abundance of Colidextribacter) and eight pathways (including decreased biosynthesis of glutamate, tryptophan and threonine) were replicated in the validation cohort. Random forest approach revealed that bacterial community is associated with gut barrier function (p= 1.4e-6, area under the curve 0.63). CONCLUSIONS Gut microbiome community and pathways are associated with changes in gut barrier function. These findings may identify potential microbial targets to modulate gut barrier.

The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 women diagnosed with diverticulitis requiring antibiotics or hospitalizations (cases), matched to 121 women without diverticulitis (controls) according to age and race. Overall microbial community structure and metabolomic profiles differed in diverticulitis cases compared to controls, including enrichment of pro-inflammatory Ruminococcus gnavus, 1,7-dimethyluric acid, and histidine-related metabolites, and depletion of butyrate-producing bacteria and anti-inflammatory ceramides. Through integrated multi-omic analysis, we detected covarying microbial and metabolic features, such as Bilophila wadsworthia and bile acids, specific to diverticulitis. Additionally, we observed that microbial composition modulated the protective association between a prudent fiber-rich diet and diverticulitis. Our findings offer insights into the perturbations in inflammation-related microbial and metabolic signatures associated with diverticulitis, supporting the potential of microbial-based diagnostics and therapeutic targets. Here, the authors present a multi-omics examination of stool samples obtained from individuals with diverticulitis and controls, uncovering disruptions in the balance of microbial composition and metabolites, as well as co-occurring microbe-metabolite associations relevant to the disease.

Abstract Human taeniasis, caused by Taenia tapeworms, is a global parasitic disease with significant implications for public health and food safety. These tapeworms can grow to considerable sizes and potentially impact the microecology of the host gut. Despite their importance, the effects of Taenia infection on host gut microbiota haven’t been thoroughly investigated. In this study, we conducted a cross-sectional analysis of the gut microbiome in patients infected with Taenia asiatica (n = 87) compared to healthy controls (n = 79) in the Dali cohort, China. We also performed a longitudinal assessment of microbial changes following deworming in a subset of patients (n = 24). Our findings reveal a significant shift in gut microbial composition, characterized by increased alpha-diversity and an enrichment of Prevotella-driven enterotypes in infected patients compared to healthy controls. The stability of these microbial features post-deworming varied widely among individuals and was lower in those with lower initial alpha diversity and Prevotella-enterotype before deworming. We observed a significant depletion of Bifidobacterium species in infected individuals, regardless of enterotypes, and these prebiotics did not recover post-deworming. Metabolic network analysis and in vitro experiments suggest that the reduction of Bifidobacterium was linked to metabolic competition for ecological niches or nutrients, particularly stachyose, from other microbes rather than the parasitism itself. Furthermore, our machine learning analysis demonstrated that taxa associated with Bifidobacterium in stachyose metabolism could robustly predict infection but could not predict deworming. This study highlights the substantial impact of taeniasis on the human gut microbiome and overall gut health.

Background Understanding how the host’s microbiome shapes phenotypes and participates in the host response to selection is fundamental for evolutionists and animal and plant breeders. Currently, selection for resilience is considered a critical step in improving the sustainability of livestock systems. Environmental variance ( V _E), the within-individual variance of a trait, has been successfully used as a proxy for animal resilience. Selection for reduced V _E could effectively shift gut microbiome composition; reshape the inflammatory response, triglyceride, and cholesterol levels; and drive animal resilience. This study aimed to determine the gut microbiome composition underlying the V _E of litter size (LS), for which we performed a metagenomic analysis in two rabbit populations divergently selected for low ( n  = 36) and high ( n  = 34) V _E of LS. Partial least square-discriminant analysis and alpha- and beta-diversity were computed to determine the differences in gut microbiome composition among the rabbit populations. Results We identified 116 KEGG IDs, 164 COG IDs, and 32 species with differences in abundance between the two rabbit populations studied. These variables achieved a classification performance of the V _E rabbit populations of over than 80%. Compared to the high V _E population, the low V _E (resilient) population was characterized by an underrepresentation of Megasphaera sp., Acetatifactor muris , Bacteroidetes rodentium , Ruminococcus bromii , Bacteroidetes togonis , and Eggerthella sp. and greater abundances of Alistipes shahii , Alistipes putredinis , Odoribacter splanchnicus , Limosilactobacillus fermentum , and Sutterella , among others . Differences in abundance were also found in pathways related to biofilm formation, quorum sensing, glutamate, and amino acid aromatic metabolism. All these results suggest differences in gut immunity modulation, closely related to resilience. Conclusions This is the first study to show that selection for V _E of LS can shift the gut microbiome composition. The results revealed differences in microbiome composition related to gut immunity modulation, which could contribute to the differences in resilience among rabbit populations. The selection-driven shifts in gut microbiome composition should make a substantial contribution to the remarkable genetic response observed in the V _E rabbit populations. Video Abstract

Background Feed efficiency is a crucial parameter in swine production, given both its economic and environmental impact. The gut microbiota plays an essential role in nutrient digestibility and is, therefore, likely to affect feed efficiency. This study aimed to characterize feed efficiency, fatness traits, and gut microbiome composition in three major breeds of domesticated swine and investigate a possible link between feed efficiency and gut microbiota composition. Results Average daily feed intake (ADFI), average daily gain (ADG), feed conversion ratio (FCR), residual feed intake (RFI), backfat, loin depth, and intramuscular fat of 615 pigs belonging to the Duroc (DR), Landrace (LR), and Large White (LW) breeds were measured. Gut microbiota composition was characterized by 16S rRNA gene sequencing. Orthogonal contrasts between paternal line (DR) and maternal lines (LR+LW) and between the two maternal lines (LR versus LW) were performed. Average daily feed intake and ADG were statistically different with DR having lower ADFI and ADG compared to LR and LW. Landrace and LW had a similar ADG and RFI, with higher ADFI and FCR for LW. Alpha diversity was higher in the fecal microbial communities of LR pigs than in those of DR and LW pigs for all time points considered. Duroc communities had significantly higher proportional representation of the Catenibacterium and Clostridium genera compared to LR and LW, while LR pigs had significantly higher proportions of Bacteroides than LW for all time points considered. Amplicon sequence variants from multiple genera (including Anaerovibrio , Bacteroides , Blautia , Clostridium , Dorea , Eubacterium , Faecalibacterium , Lactobacillus , Oscillibacter , and Ruminococcus ) were found to be significantly associated with feed efficiency, regardless of the time point considered. Conclusions In this study, we characterized differences in the composition of the fecal microbiota of three commercially relevant breeds of swine, both over time and between breeds. Correlations between different microbiome compositions and feed efficiency were established. This suggests that the microbial community may contribute to shaping host productive parameters. Moreover, our study provides important insights into how the intestinal microbial community might influence host energy harvesting capacity. A deeper understanding of this process may allow us to modulate the gut microbiome in order to raise more efficient animals. Video Abstract

Human gut microbiota produce a variety of molecules, some of which enter the bloodstream and impact health. Conversely, dietary or pharmacological compounds may affect the microbiota before entering the circulation. Characterization of these interactions is an important step towards understanding the effects of the gut microbiota on health. In this cross-sectional study, we used deep metagenomic sequencing and ultra-high-performance liquid chromatography linked to mass spectrometry for a detailed characterization of the gut microbiota and plasma metabolome, respectively, of 8583 participants invited at age 50 to 64 from the population-based Swedish CArdioPulmonary bioImage Study. Here, we find that the gut microbiota explain up to 58% of the variance of individual plasma metabolites and we present 997 associations between alpha diversity and plasma metabolites and 546,819 associations between specific gut metagenomic species and plasma metabolites in an online atlas ( https://gutsyatlas.serve.scilifelab.se/ ). We exemplify the potential of this resource by presenting novel associations between dietary factors and oral medication with the gut microbiome, and microbial species strongly associated with the uremic toxin p -cresol sulfate. This resource can be used as the basis for targeted studies of perturbation of specific metabolites and for identification of candidate plasma biomarkers of gut microbiota composition. Here, Dekkers et al. characterize associations of 1528 gut metagenomic species with the plasma metabolome in 8583 participants of the SCAPIS Study, and find that gut microbiota explain up to 58% of the variance of individual plasma metabolites.

Highlights • Investigation of gut microbiome composition and diversity with respect to human personality.• Analyses targeted bacterial genera linked to behaviour in animal and human psychiatric studies.• Bacterial genera were modelled (using negative binomial regression) with respect to personality.• Genera linked to autism are also related to social behaviour in the general population.• Sociability is associated with higher diversity, and anxiety and stress with reduced diversity.

OBJECTIVE: To examine the previously unknown long-term association between gut microbiome composition and incident type 2 diabetes in a representative population cohort. RESEARCH DESIGN AND METHODS: We collected fecal samples of 5 572 Finns (mean age 48.7 years, 54.1% women) in 2002 who were followed up for incident type 2 diabetes until Dec 31 st , 2017. The samples were sequenced using shotgun metagenomics. We examined associations between gut microbiome compositions and incident diabetes using multivariable- adjusted Cox regression models. We first used the Eastern Finland sub-population to obtain initial findings and validated these in the Western Finland sub-population. RESULTS: Altogether 432 cases of incident diabetes occurred over the median follow-up of 15.8 years. We detected 4 species and 2 clusters consistently associated with incident diabetes in the validation models. These 4 species were Clostridium citroniae (HR, 1.21; 95% CI, 1.04- 1.42), C. bolteae (HR, 1.20; 95% CI, 1.04-1.39), Tyzzerella nexilis (HR, 1.17; 95% CI, 1.01- 1.36), and Ruminococcus gnavus (HR = 1.17; 95% CI, 1.01-1.36). The positively associated clusters, cluster 1 (HR, 1.18; 95% CI, 1.02-1.38) and cluster 5 (HR, 1.18; 95% CI, 1.02-1.36), mostly consisted of these same species. CONCLUSIONS: We observed robust species-level taxonomic features predictive of incident type 2 diabetes over a long-term follow-up. These findings build on and extend previous mainly cross-sectional evidence and further support links between dietary habits, metabolic diseases, and type 2 diabetes that are modulated by the gut microbiome. The gut microbiome could potentially be used to improve risk prediction and to uncover novel therapeutic targets for diabetes.

Dystonia is a movement disorder in which patients have involuntary abnormal movements or postures. Non-motor symptoms, such as psychiatric symptoms, sleep problems and fatigue, are common. We hypothesise that the gut microbiome might play a role in the pathophysiology of the (non-)motor symptoms in dystonia via the gut–brain axis. This exploratory study investigates the composition of the gut microbiome in dystonia patients compared to healthy controls. Furthermore, the abundance of neuro-active metabolic pathways, which might be implicated in the (non-)motor symptoms, was investigated. We performed both metagenomic and 16S rRNA sequencing on the stool samples of three subtypes of dystonia (27 cervical dystonia, 20 dopa-responsive dystonia and 24 myoclonus-dystonia patients) and 25 controls. While microbiome alpha and beta diversity was not different between dystonia patients and controls, dystonia patients had higher abundances of Ruminococcus torques and Dorea formicigenerans, and a lower abundance of Butyrivibrio crossotus compared to controls. For those with dystonia, non-motor symptoms and the levels of neurotransmitters in plasma explained the variance in the gut microbiome composition. Several neuro-active metabolic pathways, especially tryptophan degradation, were less abundant in the dystonia patients compared to controls. This suggest that the gut–brain axis might be involved in the pathophysiology of dystonia. Further studies are necessary to confirm our preliminary findings.

Emerging evidence has suggested the association of the gut microbiome with some human diseases, including type 2 diabetes (T2D). In this study, we analyzed the gut microbiota from a cohort of healthy and diabetic Chinese individuals from Northern China. Pyrosequencing of the V4V5 region of 16S rRNA genes revealed a significant decrease in the gut microbiota diversity of diabetic patients as compared to healthy individuals. Butyrate-producing bacteria such as Bifidobacterium and Akkermansia were significantly decreased in diabetic patients. Furthermore, the abundance of Dorea was significantly increased in T2D individuals and negatively correlated with the abundance of butyrate-producing bacteria. The increase of Dorea could play a role in the development of T2D and has been previously overlooked. Importantly, functional analysis of the gut microbiome revealed for the first time that increased levels of butyrate production via transferases and the degradation of several amino acids due to gut microbial metabolism have strong correlations with T2D in Northern China. Moreover, the potential of gut microbiota-based classifiers to identify individuals with a high risk for T2D has been demonstrated in this study. Taken together, our findings have revealed a previously unappreciated association of the gut microbiome with T2D and have also suggested that changes in gut microbiota may be used to identify individuals at high risk for T2D.

Experimental manipulation of gut microbes in animal models alters fear behavior and relevant neurocircuitry. In humans, the first year of life is a key period for brain development, the emergence of fearfulness, and the establishment of the gut microbiome. Variation in the infant gut microbiome has previously been linked to cognitive development, but its relationship with fear behavior and neurocircuitry is unknown. In this pilot study of 34 infants, we find that 1-year gut microbiome composition (Weighted Unifrac; lower abundance of Bacteroides, increased abundance of Veillonella, Dialister, and Clostridiales) is significantly associated with increased fear behavior during a non-social fear paradigm. Infants with increased richness and reduced evenness of the 1-month microbiome also display increased non-social fear. This study indicates associations of the human infant gut microbiome with fear behavior and possible relationships with fear-related brain structures on the basis of a small cohort. As such, it represents an important step in understanding the role of the gut microbiome in the development of human fear behaviors, but requires further validation with a larger number of participants. Experimental manipulation of the gut microbiome in animal models impacts fear behaviours. Here, the authors show in a pilot study that features of the human infant gut microbiome are associated with non-social fear behaviours during a laboratory based assessment.

Intestinal microbiome and gut-brain axis have been receiving increasing attention for their role in the regulation of brain/behavior and possible biological basis of psychiatric disorders. Several recent clinical studies have linked the microbiome with neuropsychiatric conditions, although the literature on schizophrenia is quite limited. This study investigated gut microbiome composition in 50 individuals, including 25 persons with chronic schizophrenia and 25 demographically-matched non-psychiatric comparison subjects (NCs). Stool samples were collected and assayed using 16S rRNA sequencing of the V4 region. Examination of unweighted UniFrac and Bray-Curtis dissimilarity revealed significant community-level separation in microbiome composition between the two subject groups. At the phylum level, Proteobacteria were found to be relatively decreased in schizophrenia subjects compared to NCs. At the genus level, Anaerococcus was relatively increased in schizophrenia while Haemophilus, Sutterella, and Clostridium were decreased. Within individuals with schizophrenia, abundance of Ruminococcaceae was correlated with lower severity of negative symptoms; Bacteroides was associated with worse depressive symptoms; and Coprococcus was related to greater risk for developing coronary heart disease. Our findings provide evidence of altered gut microbial composition in persons with chronic schizophrenia and suggest a need for larger and longitudinal studies of microbiome in schizophrenia.

Background The potential role of the gut microbiome (GM) in heart failure (HF) had recently been revealed. However, the underlying mechanisms of the GM and fecal metabolome in HF have not been characterized. The Dahl salt-sensitive rat model of hypertensive heart failure (H-HF) was used to study the clinical symptoms and characteristics. To elucidate the pathogenesis of HF, we combined 16S rRNA gene sequencing and metabolomics to analyze gut microbial compositions and fecal metabolomic profiles of rats with H-HF. Results PCoA of beta diversity shown that the gut microbiome composition profiles among the three groups were separated. Gut microbial composition was significantly altered in H-HF rats, the ratio of Firmicutes to Bacteroidetes (F/B) increased and the abundance of Muribaculaceae , Lachnospiraceae , and Lactobacillaceae decreased. Significantly altered levels of 17 genera and 35 metabolites were identified as the potential biomarker of H-HF. Correlation analysis revealed that specific altered genera were strongly correlated with changed fecal metabolites. The reduction in short-chain fatty acids (SCFA)-producing bacteria and trimethylamine N-oxide (TMAO) might be a notable characteristic for H-HF. Conclusions This is the first study to characterize the fecal microbiome of hypertensive heart failure by integrating 16S rRNA gene sequencing and LC–MS-based metabolomics approaches. Collectively, the results suggesting changes of gut microbiome composition and metabolites are associated with hypertensive heart failure rats.

Berberine and metformin, both established pharmaceutical agents with herbal origins, have incidental beneficial effects on multiple diseases, including diabetes. These effects have been speculated to occur via the gut microbiome. In this study, we administered either berberine or metformin to db/db mice and investigated changes in body weight, food intake, and blood glucose levels. Fresh stool samples were analyzed using 16 s rDNA high-throughput sequencing to evaluate the gut microbiome. Short-chain fatty acids (SCFA) in the stool were quantified using gas chromatography. The expression of NF-κB signaling pathway and tight junction (ZO1 and occludin) proteins in the intestinal epithelium was determined using qPCR and western blotting. The intestinal barrier structure was examined using transmission electron microscopy and serum lipopolysaccharide (LPS) was measured using a commercial kit. Both berberine and metformin reduced food intake, body weight, and blood glucose and HbA1c levels. Both treatments effectively restored the intestinal SCFA content, reduced the level of serum LPS, relieved intestinal inflammation, and repaired intestinal barrier structure. Intervention with metformin or berberine modified the gut microbiome in db/db mice, increasing the number of SCFA-producing bacteria (e.g., Butyricimonas, Coprococcus, Ruminococcus) and reducing opportunistic pathogens (e.g., Prevotella, Proteus). An increased abundance of other probiotics including Lactobacillus and Akkermansia was also observed. Berberine and metformin can modulate the composition of the gut microbiome and reduce body weight, blood glucose levels, and intestinal inflammation in db/db mice, which demonstrates their effectiveness in the reduction of diabetic complications in this model.

Diets rich in animal source foods vs plant-based diets have different macronutrient composition, and they have been shown to have differential effects on the gut microbiome. In this study, we hypothesized that diets with very different nutrient composition are able to change gut microbiome composition and metabolites in a very short period. We compared a fast food (FF) diet (ie, burgers and fries) with a Mediterranean (Med) diet, which is rich in vegetables, whole grains, olive oil, nuts, and fish. Ten healthy subjects participated in a controlled crossover study in which they consumed a Med diet and FF diet in randomized order for 4 days each, with a 4-day washout between treatments. Fecal DNA was extracted and the 16S V4 region amplified using polymerase chain reaction followed by sequencing on an Illumina MiSeq. Plasma metabolites and bile acids were analyzed using liquid chromatography-mass spectrometry. Certain bile-tolerant microbial genera and species including Collinsella, Parabacteroides, and Bilophila wadsworthia significantly increased after the FF diet. Some fiber-fermenting bacteria, including Lachnospiraceae and Butyricicoccus, increased significantly after the Med diet and decreased after the FF diet. Bacterially produced metabolites indole-3-lactic acid and indole-3-propionic acid, which have been shown to confer beneficial effects on neuronal cells, increased after the Med diet and decreased after the FF diet. Interindividual variability in response to the treatments may be related to differences in background diet, for example as shown by differences in Bilophila response in relationship to the saturated fat content of the baseline diet. In conclusion, an animal fat-rich, low-fiber FF diet v. a high-fiber Med diet altered human gut microbiome composition and its metabolites after just 4 days.

Alteration of gut microbiome composition has been linked to cardiovascular diseases. To identify specific bacterial communities associated with coronary artery diseases (CAD), we conducted a case-control study with 53 advanced CAD patients and 53 age-, sex-, race-, and BMI-matched controls. V3-V5 regions of the 16S rDNA from the fecal gut material were analyzed to compare the gut microbiome composition between CAD patients and controls. The alpha diversity, including Chao-1, Shannon-index, and the number of observed taxonomy units were significantly decreased in CAD patients indicating, decreased richness and evenness of gut microbiome. Among 23 different abundant taxa at the genus level, 12 taxa belonged to Lachnospiraceae family, which are known to produce butyrate. Further, we identified five taxa which showed more than two log-fold changes with maximum proportion >0.002, including Ruminococcus gnavus, Lachnospiraceae anaerosporobacter, Lachnospiraceae NK4B4 group, Lachnospiraceae UCG-004, and Ruminococcus gauvreauii. After adjustment for coronary risk factors (diabetes mellitus and dyslipidemia), decreased relative abundance of Lachnospiraceae NK4B4 group and Ruminococcus Gauvreauii and increased relative abundance of Ruminococcus gnavus were associated with the presence of advanced CAD. The observed differences in taxa between CAD patients and controls in this study may provide insight into the link between the gut microbiome and CAD.

OBJECTIVES The microbiota-gut-brain axis is an intricate communication network that is emerging as a key modulator of psychological and physiological wellbeing. Recent pioneering work in the field has suggested a possible link between gut microbiome composition with sleep, an evolutionarily conserved behavior demonstrated to play a critical role in health. This study is the first to address relationships between self-reported sleep habits and gut microbiome composition in young, healthy individuals. METHODS A total of 28 young, healthy subjects (17 males/11 females; 29.8 ± 10.4 years) that were free of metabolic or cardiovascular disease, and that did not take sleep medication or antibiotics within the past six months were included in the study. Relationships between self-reported sleep quality, obtained using the Pittsburgh Sleep Quality Index (PSQI), with microbial diversity (Shannon Index), the Firmicutes/Bacteroidetes (F/B) ratio, and select bacterial taxa were assessed. RESULTS Alpha diversity (r = -0.50) and F/B ratio (r = -0.47) were inversely associated (P < 0.05) with the PSQI score. Ten bacterial taxa were associated (P < 0.05) with the PSQI score, including genus-level Blautia (r = -0.57), Ruminococcus (r = -0.39), and Prevotella (r = 0.39). CONCLUSIONS In young healthy individuals, self-reported sleep quality was positively associated with microbial diversity. We also observed a positive association between sleep quality with F/B ratio, seemingly due to a greater relative abundance of Blautia and Ruminococcus (Firmicutes) and lower proportions of Prevotella (Bacteroidetes) in individuals reporting superior sleep quality. Future studies are encouraged to evaluate mechanistic links between the gut microbiome with sleep, as well as the health implications of this relationship.

ABSTRACT Background Vogt-Koyanagi-Harada (VKH) disease is a multisystemic autoimmune disorder characterized by granulomatous panuveitis. Gut microbiome has been considered to play a role in the pathogenesis of this disease but whether the alternation of gut microbiome was involved is unclear. This study was set up to identify abnormalities of gut microbiome composition in VKH disease. Results Depleted butyrate-producing bacteria, lactate-producing bacteria and methanogens as well as enriched Gram-negative bacteria were identified in the active VKH patients, as well as in VKH patients of Mix enterotype and Bacteroides enterotype. Changes of gut microbiome in the VKH patients were partially restored after an immunosuppressive treatment. The disease susceptibility genotype HLA-DRA was associated with Bacteroides sp.2.1.33B, Paraprevotella clara, Alistipes finegoldii and Eubacterium eligens. A microbial marker profile including 40 disease-associated species was established to differentiate patients from controls. Another microbial marker profile including 37 species was found to be associated with the response to treatment. An animal experiment showed that transfer of gut microbiome from VKH patients could significantly exacerbate disease activity clinically and pathologically in the recipient mice. Conclusion Our results revealed a distinct gut microbiome signature in VKH patients and showed an exacerbating effect of this gut microbiome on experimental autoimmune uveitis (EAU). We also developed two microbial marker profiles in differentiating VKH patients from healthy controls as well as predicting the effectiveness of treatment.

Background African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon. Subjects followed pastoralist, agropastoralist, and hunter-gatherer lifestyles and were compared to an urban US population from Philadelphia. Results We observe significant differences in gut microbiome composition across populations that correlate with subsistence strategy and country. After these, the variable most strongly associated with gut microbiome structure in Cameroonians is the presence of gut parasites. Hunter-gatherers have high frequencies of parasites relative to agropastoralists and pastoralists. Ascaris lumbricoides , Necator americanus , Trichuris trichiura , and Strongyloides stercoralis soil-transmitted helminths (“ANTS” parasites) significantly co-occur, and increased frequency of gut parasites correlates with increased gut microbial diversity. Gut microbiome composition predicts ANTS positivity with 80% accuracy. Colonization with ANTS, in turn, is associated with elevated levels of TH1, TH2, and proinflammatory cytokines, indicating an association with multiple immune mechanisms. The unprecedented size of this dataset allowed interrogation of additional questions—for example, we find that Fulani pastoralists, who consume high levels of milk, possess an enrichment of gut bacteria that catabolize galactose, an end product of lactose metabolism, and of bacteria that metabolize lipids. Conclusions These data document associations of bacterial microbiota and eukaryotic parasites with each other and with host immune responses; each of these is further correlated with subsistence practices.

Simple Summary The intestinal tract affects the brain through metabolites produced by gut-inhabiting bacteria. In this study, we show that the number of errors the dogs commit in a short-term memory test and also their age is linked to the gut microbiome composition. The proportion of Fusobacteria is lower in older animals. Dogs with better memory performance (i.e., fewer mistakes) have relatively fewer Actinobacteria in their fecal samples collected right after the behavior test. This result is in agreement with the high abundance of some Actinobacteria in the gastrointestinal tract of persons living with Alzheimer’s disease. Links between memory performance and gut microbiota have been reported on rodents but not on dogs before. The research opens up new venues in canine aging and neurodevelopmental research. Abstract Gut microbiota can crucially influence behavior and neurodevelopment. Dogs show unique similarities to humans in their physiology and may naturally develop dementia-like cognitive decline. We assessed 29 pet dogs’ cognitive performance in a memory test and analyzed the bacterial 16S rRNA gene from fecal samples collected right after the behavioral tests. The major phyla identified in the dog microbiomes were Bacteroidetes, Firmicutes, and Fusobacteria, each represented by >20% of the total bacterial community. Fewer Fusobacteria were found in older dogs and better memory performance was associated with a lower proportion of Actinobacteria. Our preliminary findings support the existence of links between gut microbiota, age, and cognitive performance in pet dogs.

ABSTRACT Fatty liver disease is the most common liver disease in the world. Its connection with the gut microbiome has been known for at least 80 y, but this association remains mostly unstudied in the general population because of underdiagnosis and small sample sizes. To address this knowledge gap, we studied the link between the Fatty Liver Index (FLI), a well-established proxy for fatty liver disease, and gut microbiome composition in a representative, ethnically homogeneous population sample of 6,269 Finnish participants. We based our models on biometric covariates and gut microbiome compositions from shallow metagenome sequencing. Our classification models could discriminate between individuals with a high FLI (≥60, indicates likely liver steatosis) and low FLI (<60) in internal cross-region validation, consisting of 30% of the data not used in model training, with an average AUC of 0.75 and AUPRC of 0.56 (baseline at 0.30). In addition to age and sex, our models included differences in 11 microbial groups from class Clostridia, mostly belonging to orders Lachnospirales and Oscillospirales. Our models were also predictive of the high FLI group in a different Finnish cohort, consisting of 258 participants, with an average AUC of 0.77 and AUPRC of 0.51 (baseline at 0.21). Pathway analysis of representative genomes of the positively FLI-associated taxa in (NCBI) Clostridium subclusters IV and XIVa indicated the presence of, e.g., ethanol fermentation pathways. These results support several findings from smaller case–control studies, such as the role of endogenous ethanol producers in the development of the fatty liver.

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OBJECTIVE The aim of this study was to investigate the characteristics and composition of intestinal microbiota in children with refractory epilepsy after ketogenic diet (KD) therapy and to explore the bacterial biomarkers related to clinical efficacy. METHODS We prospectively analyzed 20 patients (14 males, 6 females) treated with KD. Clinical efficacy, electroencephalogram (EEG) changes, and laboratory tests were evaluated, and fecal specimens were obtained prior to and 6 months after therapy. The composition of gut microbiota was analyzed by 16S rDNA sequencing, and we screened the possible flora associated with efficacy of the KD. RESULTS After 6 months of treatment, 2 patients were seizure free, 3 had ≥ 90% seizure reduction, 5 had a reduction of 50-89%, and 10 had < 50% reduction. All 10 responders showed an improvement in EEG. Compared with baseline, fecal microbial profiles showed lower alpha diversity after KD therapy and revealed significantly decreased abundance of Firmicutes and increased levels of Bacteroidetes. We also observed that Clostridiales, Ruminococcaceae, Rikenellaceae, Lachnospiraceae, and Alistipes were enriched in the non-responsive group. CONCLUSIONS The results show that the KD can reduce the species richness and diversity of intestinal microbiota. The changes of gut microbiota may be associated with different efficacy after KD, and specific gut microbiota may serve as an efficacy biomarker and a potential therapeutic target in patients with refractory epilepsy.

Background Polycystic ovary syndrome (PCOS) is a common female endocrinopathy of unclear origin characterized by hyperandrogenism, oligo-/anovulation, and ovarian cysts. Women with PCOS frequently display overweight, insulin resistance, and systemic low-grade inflammation. We hypothesized that endotoxemia resulting from a leaky gut is associated with inflammation, insulin resistance, fat accumulation, and hyperandrogenemia in PCOS. In this pilot study, we compared the stool microbiome, gut permeability, and inflammatory status of women with PCOS and healthy controls. Methods 16S rRNA gene amplicon sequencing was performed on stool samples from 24 PCOS patients and 19 healthy controls. Data processing and microbiome analysis were conducted in mothur and QIIME using different relative abundance cut-offs. Gut barrier integrity, endotoxemia, and inflammatory status were evaluated using serum and stool markers and associations with reproductive, metabolic, and anthropometric parameters were investigated. Results The stool microbiome of PCOS patients showed a lower diversity and an altered phylogenetic composition compared to controls. We did not observe significant differences in any taxa with a relative abundance>1%. When looking at rare taxa, the relative abundance of bacteria from the phylum Tenericutes, the order ML615J-28 (phylum Tenericutes) and the family S24-7 (phylum Bacteroidetes) was significantly lower and associated with reproductive parameters in PCOS patients. Patients showed alterations in some, but not all markers of gut barrier function and endotoxemia. Conclusion Patients with PCOS have a lower diversity and an altered phylogenetic profile in their stool microbiome, which is associated with clinical parameters. Gut barrier dysfunction and endotoxemia were not driving factors in this patient cohort, but may contribute to the clinical phenotype in certain PCOS patients.

Effects of metformin, the first-line drug for type 2 diabetes therapy, on gut microbiome composition in type 2 diabetes have been described in various studies both in human subjects and animals. However, the details of the molecular mechanisms of metformin action have not been fully understood. Moreover, there is a significant lack of information on how metformin affects gut microbiome composition in female mice models, as most of the existing studies have focused on males only. Our study aimed to examine metformin-induced alterations in gut microbiome diversity and composition of high-fat diet-induced type 2 diabetes mouse model, employing a randomized block, factorial study design, and including 24 experimental units allocated to 8 treatment groups. We performed shotgun metagenomic sequencing using DNA obtained from fecal samples representing gut microbiome before and after ten weeks-long metformin treatment. We identified 100 metformin-related differentially abundant species in high-fat diet-fed mice before and after the treatment, with most of the species abundances increased. In contrast, no significant changes were observed in control diet-fed mice.We also observed sex-specific differences in response to metformin treatment. Males experienced more pronounced changes in metabolic markers, while, in females, the extent of changes in gut microbiome representatives was more marked, indicated by 53 differentially abundant species with more remarkable Log fold changes compared to the combined-sex analysis. Our results suggest that both sexes of animals should be included in future studies focusing on metformin effects on the gut microbiome.

Staphylococcus aureus is a notorious pathogen responsible for significant morbidity and mortality in both human society and animal husbandry. The presence of S. aureus persisters is also one of the leading causes of recurrent and chronic diseases. Persisters are a subset of growth-arrested bacteria within a susceptible bacterial population that are able to tolerate antibiotic treatment and resuscitate after stress removal. Consequently, investigating their formation and characteristics is of crucial importance to provide mechanism-based options for their eradication. However, one challenge in mechanistic research on persisters is the enrichment of pure persisters. In this work, we validated a proposed method to isolate persisters from vancomycin and enrofloxacin generated persistent populations. With this, we analyzed the proteome profile of pure persisters and revealed the distinct mechanisms associated with vancomycin and enrofloxacin induced persisters. Furthermore, morphological and metabolic characterizations were performed, indicating further differences between these two persister populations. Finally, we assessed the effect of ATP repression, protein synthesis inhibition and reactive oxygen species (ROS) level on persister formation. In conclusion, this work provides a comprehensive understanding of S. aureus vancomycin and enrofloxacin induced persisters at the molecular, single cell and population levels, facilitating a better understanding of persisters and the development of effective strategies to combat them.

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Abstract This study was conducted to understand the dynamics of microbial communities of soil microorganisms, and their distribution and abundance in the indigenous microorganisms (IMOs) manipulated from humus collected from the forest near the crop field. The soil microorganisms originated from humus and artificially cultured microbial-based soil amendments were characterized by molecular and biochemical analyses. The bacterial population (2 × 106∼13 × 106 CFU/g sample) was approximately 100-fold abundant than the fungal population (2 × 104∼8 × 104 CFU/g sample). The 16S rDNA and ITS sequence analyses showed that the bacterial and fungal communities in humus and IMOs were mainly composed of Bacillus and Pseudomonas, and Trichoderma and Aspergillus species, respectively. Some of the bacterial isolates from the humus and IMOs showed strong inhibitory activity against soil-borne pathogenic fungi Fusarium oxysporum and Sclerotinia sclerotiorum. These bacteria also showed the siderophore production activity as well as phosphate solubilizing activity, which are requisite traits for biological control of plant pathogenic fungi. These results suggest that humus and IMOs could be a useful resource for sustainable agriculture.

Carbapenem resistant Acinetobacter baumannii has evolved as the most troublesome microorganism with multiple virulence factors. Biofilm formation, porins, micronutrient capturing mechanism and quorum sensing, provide protection against desiccation, host-pathogen killing and enhance its persistence. The conservation of these factors between colonizing and pathogenic carbapenem resistant A. baumannii has been barely investigated. We studied biofilm formation, desiccation survival, motility and hemolysis in pathogenic carbapenem resistant A. baumannii and colonizer carbapenem resistant A. baumannii from the hospital environment. The virulent genes pgaA, csuE, bap, ompA, abaI, pilA and bauA were detected by simplex-PCR and Quantitative Real-Time PCR was done for expressional studies. In-vivo survival percentage was studied by Galleria mellonella (wax moth) killing assay. Phenotypic characterization revealed that the biofilm formation and desiccation survival proportion was significantly higher in colonizer carbapenem resistant A. baumannii (p < 0.05). Twitching motility was found comparable (mean 0.5 to 1.5 cm). Surface associated motility varied widely. None showed hemolysis. The csuE, bap, ompA, abaI, pilA and bauA genes were detected in almost all the pathogenic and colonizer carbapenem resistant A. baumannii isolates while none harboured pgaA gene. The expression of bap, ompA and bauA gene was found significantly higher in pathogenic carbapenem resistant A. baumannii while expression of csuE and abaI gene was comparable in both. Overexpression of pilA gene was seen in those with higher surface associated motility. Pathogenic carbapenem resistant A. baumannii showed significantly higher pathogenicity in-vivo, as 100% of larvae died on 4th day post-infection. In conclusion high level expression of outer membrane proteins (ompA) and siderophores is significantly associated with the pathogenicity in carbapenem resistant A. baumannii isolated from infections, which can be a differentiating point from the colonizers. Not Applicable

The pangenome of Escherichia coli is composed of a conserved core and variable genomic regions. The constant genetic component allows to determine the phylogeny of the microorganism, while genetic variability promoted the emergence of intestinal pathogenic strains and extraintestinal strains. In this study we characterized 85 extraintestinal pathogenic isolates genetically isolated from canines and felines. We used the Clermont scheme that includes intestinal (A and B1) and extraintestinal (B2 and D) phylogroups, virulence markers (pap1-2, pap3-4, sfa, afa, hlyA, aer and cnf) and hybrid pathogens. A percentage of 69.4% of the isolates belonged to phylogroup A; 1.2% to phylogroup B1; 16.5% to phylogroup B2 and 12.9% to phylogroup D. The most commonly found gene was sfa (21/85), followed by pap1-2 and cnf (20/85) and pap3-4 (19/85). No hybrids were detected. Animal isolates should be studied due to the zoonotic potential of the microorganism.

Mycoplasma gallisepticum (M. gallisepticum) is a significant pathogenic microorganism contaminating poultry hatchery environments. During intensive hatching, M. gallisepticum significantly impairs embryonic health and development, ultimately reducing embryonic vitality. Clinically, it is common for affected embryos to exhibit incomplete pipping of eggshell, a condition referred to as pipping failure embryos (PFEs). Critically, live PFEs exhibit high M. gallisepticum shedding, substantially increasing the risk of M. gallisepticum transmission to healthy chicks at early-stage within the same space. These asymptomatic infected chicks often develop chronic respiratory disease (CRD) under stress during subsequent growth. This study investigated M. gallisepticum contamination in hatchery environments and isolated M. gallisepticum strains from live PFEs. A total of 1,200 environmental samples collected from 16 hatcheries across eight provinces in China showed M. gallisepticum positivity rates exceeding 80 % in both dust and feather samples. Among 888 live PFEs, the M. gallisepticum positivity rate was 79.62 %, with a 100 % positivity rate observed in Sichuan Province. Molecular typing of 29 M. gallisepticum isolates using partial mgc2 revealed four distinct clusters: China I Clade, China II Clade, R Clade, and 685 Clade. Notably, China I Clade strains formed a unique cluster distinct from isolates obtained from 12 other countries. Subsequently, one isolate from each of 4 clusters was selected for pathogenicity tests. The result suggested the China I Clade GDya_38 isolate demonstrated significantly higher virulence in 8-day-old specific-pathogen-free (SPF) chicken embryos yolk sac inoculation experiments, inducing severe incomplete pipping. Additionally, tracheal challenge in 15-day-old SPF chicks revealed that GDya_38 caused more severe airsacculitis compared to other isolates. In conclusion, severe M. gallisepticum contamination has been identified in hatchery environments across China, with the unique China I Clade GDya_38 isolate exhibiting heightened pathogenic potential. This strain's capacity for vertical transmission, leading to embryonic vitality impairment, and horizontal transmission, causing CRD symptoms, underscores its substantial threat to poultry production.

Levan is a biopolymer with many different uses. Temperature is an important parameter in biopolymer synthesis. Herein, levan production was carried out from Bacillus haynesii, a thermophilic microorganism, in the temperature range of 4 °C-95 °C. The highest levan production was measured as 10.9 g/L at 37 °C. The synthesized samples were characterized by FTIR and NMR analysis. The particle size of the levan samples varied between 153 and 824.4 nm at different temperatures. In levan samples produced at high temperatures, the water absorption capacity is higher in accordance with the particle size. Irregularities were observed in the surface pores at temperatures of 60 °C and above. The highest emulsion capacity of 83.4 % was measured in the sample synthesized at 4 °C. The antioxidant activity of all levan samples synthesized at different temperatures was measured as 84 % on average. All synthesized levan samples showed antibacterial effect on pathogenic bacteria. In addition, levan synthesized at 45 °C showed the highest antimicrobial effect on E. coli ATCC 35218 with an inhibition zone of 21.3 ± 1.82 mm. Antimicrobial activity against yeast sample C. albicans, was measured only in levan samples synthesized at 80 °C, 90 °C, 95 °C temperatures. Levan synthesized from Bacillus haynesii at low and high temperatures showed differences in characterization and bioactivity.

Candidatus Liberibacter asiaticus (CLas) has been associated with Huanglongbing, a lethal vector-borne disease affecting citrus crops worldwide. While comparative genomics has provided preliminary insights into the metabolic capabilities of this uncultured microorganism, a comprehensive functional characterization is currently lacking. Here, we reconstructed and manually curated genome-scale metabolic models for the six CLas strains A4, FL17, gxpsy, Ishi-1, psy62, and YCPsy, in addition to a model of the closest related culturable microorganism, L. crescens BT-1. Predictions about nutrient requirements and changes in growth phenotypes of CLas were confirmed using in vitro hairy root-based assays, while the L. crescens BT-1 model was validated using cultivation assays. Host-dependent metabolic phenotypes were revealed using expression data obtained from CLas-infected citrus trees and from the CLas-harboring psyllid Diaphorina citri Kuwayama. These results identified conserved and unique metabolic traits, as well as strain-specific interactions between CLas and its hosts, laying the foundation for the development of model-driven Huanglongbing management strategies.

Arcobacter (A.) butzleri is an emerging pathogenic microorganism, whose taxonomy has been recently suggested to be emended to the Aliarcobacter (Al.) butzleri comb. nov. Despite extensive taxonomic analysis, only few fragmented studies have investigated the occurrence and the prevalence of virulence and antibiotic resistance determinants of this species in strains isolated from shellfish. Herein we report for the first time the whole genome sequencing and genomic characterization of two A. butzleri strains isolated from shellfish, with particular reference to the antibiotic, heavy metals and virulence determinants. This study supported the taxonomic assignment of these strains to the Al. butzleri species, and allowed us to identify antibiotic and metal resistance along with virulence determinants, also additional to those previously reported for the only two A. butzleri strains from different environments genomically characterized. Moreover, both strains showed resistance to β-lactams, vanocomycin, tetracycline and erythromycin and susceptibility to aminoglycosides and ciprofloxacin. Beside enlarging the availability of genomic data to perform comparative studies aimed at correlating phenotypic differences associated with ecological niche and geographic distribution with the genetic diversity of A. butzleri spp., this study reports the endowment of antibiotic and heavy metal resistance and virulence determinants of these shellfish-isolated strains. This leads to hypothesize a relatively high virulence of A. butzleri isolated from shellfish and prompt the need for a wider genomic analysis and for in vitro and in vivo studies of more strains isolated from this and other ecological niches, to unravel the mechanism of pathogenicity of this species, and the potential risk associated to their consumption.

Many pathogenic bacteria can use heme compounds as a source of iron. Pathogenic Escherichia coli strains are capable of using hemoglobin as an iron source. However, the mechanism of heme acquisition from hemoglobin is not understood for this microorganism. We present the first molecular characterization of a hemoglobin protease (Hbp) from a human pathogenic E. coli strain. The enzyme also appeared to be a heme-binding protein. Affinity purification of this bifunctional protein enabled us to identify the extracellular gene product, and to clone and analyze its gene. A purification procedure developed for Hbp allowed us to perform functional studies. The protein interacted with hemoglobin, degraded it and subsequently bound the released heme. These results suggest that the protein is involved in heme acquisition by this human pathogen. Hbp belongs to the so-called IgA1 protease-like proteins, as indicated by the kinetics of its membrane transfer and DNA sequence similarity. The gene of this protein appears to be located on the large pColV-K30 episome, that only has been isolated from human and animal pathogens. All these characteristics indicate that Hbp may be an important virulence factor that may play a significant role in the pathogenesis of E. coli infections.

“Hongtuozhusun” (Phallus rubrovolvatus) is an important edible and medicinal mushroom endemic to Southwest China. However, yellow rot disease is a severe disease of P. rubrovolvatus that occurs extensively in Guizhou Province. It has caused major economic losses and hinders the development of the P. rubrovolvatus industry. In this study, 28 microorganism strains were isolated from diseased fruiting bodies of P. rubrovolvatus at various stages, two of which were confirmed to be pathogenic based on Koch’s postulates. These two strains are introduced herein as Saccharomycopsis phalluae sp. nov. based on morphological, physiological, and molecular analysis. We reported a high-quality de novo sequencing and assembly of the S. phalluae genome using single-molecule real-time sequencing technology. The whole genome was approximately 14.148 Mb with a G+C content of 43.55%. Genome assembly generated 8 contigs with an N50 length of 1,822,654 bp. The genome comprised 5966 annotated protein-coding genes. This is the first report of mushroom disease caused by Saccharomycopsis species. We expect that the information on genome properties, particularly in pathogenicity-related genes, assist in developing effective control measures in order to prevent severe losses and make amendments in management strategies.

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Leptospirosis is a zoonotic disease caused by pathogenic Leptospira. However, understanding of the pathogenic mechanism of Leptospira is still elusive due to the limited number of genetic tools available for this microorganism. Currently, the reason for the genetic inaccessibility of Leptospira is still unknown. It is well known that as an acquired immunity of bacteria, Clustered Regularly Interspaced Short Palindromic Repeat‐CRISPR‐associated gene (CRISPR‐Cas) systems can help bacteria against invading mobile genetic elements. In this study, the occurrence and diversity of CRISPR‐Cas systems in 41 genomes of Leptospira strains were investigated. Three subtypes (subtype I‐B, subtype I‐C and subtype I‐E) of CRISPR‐Cas systems were identified in both pathogenic and intermediate Leptospira species but not in saprophytic species. Noteworthy, the majority of pathogenic species harbor two different types of CRISPR‐Cas systems (subtype I‐B and subtype I‐E). Furthermore, Cas2 protein of subtype I‐C in L. interrogans exhibited a metal‐dependent DNase activity in a nonspecific manner. CRISPR spacers in subtype I‐B are highly conserved within the same serovars and hypervariable across different serovars of L. interrogans. Based on the subtype I‐B CRISPR arrays, the serotypes of different L. interrogans strains were easily identified. Investigation of the origin of CRISPR spacers showed that 192 spacers (23.5%) matched to mobile genetic elements, indicating CRISPR‐Cas systems may play an important role in the defense of foreign invading DNA.

The abuse of antibiotics and following rapidly increasing of antibiotic-resistant pathogens is the serious threat to our society. Natural products from microorganism are regarded as the important substitution antimicrobial agents of antibiotics. We isolated a new strain, Bacillus sp. GFP-2, from the Chiloscyllium plagiosum (Whitespotted bamboo shark) intestine, which showed great inhibitory effects on the growth of both Gram-positive and Gram-negative bacteria. Additionally, the growth of salmon was effectively promoted when fed with inactivated strain GFP-2 as the inhibition agent of pathogenic bacteria. The genes encoding antimicrobial peptides like LCI, YFGAP and hGAPDH and gene clusters for secondary metabolites and bacteriocins, such as difficidin, bacillibactin, bacilysin, surfactin, butirosin, macrolactin, bacillaene, fengycin, lanthipeptides and LCI, were predicted in the genome of Bacillus sp. GFP-2, which might be expressed and contribute to the antimicrobial activities of this strain. The gene encoding β-1,3-1,4-glucanase was successfully cloned from the genome and this protein was detected in the culture supernatant of Bacillus sp. GFP-2 by the antibody produced in rabbit immunized with the recombinant β-1,3-1,4-glucanase, indicating that this strain could express β-1,3-1,4-glucanase, which might partially contribute to its antimicrobial activities. This study can enhance a better understanding of the mechanism of antimicrobial activities in genus Bacillus and provide a useful material for the biotechnology study in antimicrobial agent development.

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The increasing prevalence and dissemination of multidrug-resistant bacteria represent a serious concern for public health. Aeromonas caviae is a pathogenic microorganism that causes a wide spectrum of diseases in fish and humans and is often associated with aquatic environments and isolated from foods and animals. Here, we present the isolation and characterization of the V15T strain isolated from a drinking water storage tank in Rio de Janeiro, Brazil. The V15T strain has a genome length of 4,443,347 bp with an average G + C content of 61.78% and a total of 4028 open reading frames. Its genome harbors eight types of antibiotic resistance genes (ARGs) involving resistance to beta-lactamases, macrolides, and quinolones. The presence of blaMOX-6, blaOXA-427/blaOXA-504, and mutations in parC were detected. In addition, other ARGs (macA, macB, opmH, and qnrA) and multidrug efflux pumps (such as MdtL), along with several resistance determinants and 106 genes encoding virulence factors, including adherence (polar and lateral flagella), secretion (T2SS, T6SS), toxin (hlyA), and stress adaptation (katG) systems, were observed. The genome sequence reported here provides insights into antibiotic resistance, biofilm formation, evolution, and virulence in Aeromonas strains, highlighting the need for more public health attention and the further monitoring of drinking water systems. Also, the results of physiological and phylogenetic data, average nucleotide identity (ANI) calculation, and digital DNA–DNA hybridization (dDDH) analysis support the inclusion of the strain V15T in the genus Aeromonas as a new subspecies with the proposed name Aeromonas caviae subsp. aquatica subsp. nov. (V15T = P53320T). This study highlights the genomic plasticity and pathogenic potential of Aeromonas within household drinking water systems, calling for the revision of water treatment protocols to address biofilm-mediated resistance and the implementation of routine genomic surveillance to mitigate public health risks.

BackgroundAmong all species of Listeria, Listeria monocytogenes (L. monocytogenes) is a major pathogenic microorganism of humans and animals and L. ivanovii is rarely pathogenic for humans. The objective of this study was to isolate and characterize Listeria species and to determine the frequencies of virulence genes in L. monocytogenes serotypes in fresh fish, shrimp, crab and lobster in Isfahan and Shahrekord, Iran.MethodsFrom September 2010 to April 2011, a total of 300 marine food samples were purchased from supermarkets of Isfahan and Shahrekord cities, Iran. All samples were cultured and the positive samples for L. monocytogenes were analyzed for presence of serotypes and virulence genes.ResultsFrom the total 300 samples, 23 (10.45%) fresh fish and 1 (2.5%) shrimp samples were positive for Listeria spp., but there were no positive lobster and crab samples for Listeria species. Only L. monocytogenes was isolated from 17 fish (7.25%) and 1 shrimp (2.5%) samples while L. innocua, L. ivanovii and L. seeligeri only detected in fish samples (2 (0.9%), 3 (1.36%) and 1 (0.45%)), respectively. The plcA, prfA, actA, hlyA and iap virulence genes were detected in all of the 18 L. monocytogenes isolates. Totally, the 4b, 1/2a and 1/2b serotypes were detected in 66.66%, 5.55% and 27.77% bacterial isolates, respectively.ConclusionsConsumption of these sea foods, either raw or undercooked, may contribute to food-borne illness due to L. monocytogenes in Iran. The hygienic quality of sea food products should be observe.Virtual slidesThe virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/3422944359800606

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Microorganisms have provided a bounty of bioactive secondary metabolites with very exciting biological activities such as antibacterial, antifungal antiviral, and anticancer, etc. The present study aims at the optimization of culture conditions for improved antimicrobial production of Paenibacillus elgii obtained from Wayanad forest of Western Ghats region of Kerala, India. A bacterial strain isolated from the Western Ghats forest soil of Wayanad, Kerala, India was identified as P. elgii by 16S rRNA gene sequencing. P. elgii recorded significant board spectrum activity against all human and plant pathogenic microorganism tested except Candida albicans. It has been well known that even minor variations in the fermentation medium may impact not only the quantity of desired bioactive metabolites but also the general metabolic profile of the producing microorganisms. Thus, further studies were carried out to assess the impact of medium components on the antimicrobial production of P. elgii and to optimize an ideal fermentation medium to maximize its antimicrobial production. Out of three media [nutrient broth (NA), Luria broth (LB) and Trypticase soy broth (TSB)] used for fermentation, TSB medium recorded significant activity. Glucose and meat peptone were identified as the best carbon and nitrogen sources, which significantly affected the antibiotic production when supplemented with TSB medium. Next the effect of various fermentation conditions such as temperature, pH, and incubation time on the production of antimicrobial compounds was studied on TSB + glucose + meat peptone and an initial pH of 7 and a temperature of 30°C for 3 days were found to be optimum for maximum antimicrobial production. The results indicate that medium composition in the fermentation media along with cultural parameters plays a vital role in the enhanced production of antimicrobial substances.

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Pink/red discoloration encompasses a series of relatively common spoilage defects of commercial dairy products. In this study, we used shotgun proteomics to identify the microorganism responsible for the production of intensely red-coloured slimes found on the surface of freshly opened commercial spreadable cheese and yogurt samples. Proteome-wide characterization of microbial proteins allowed to identify 1042 and 687 gene products from Rhodotorula spp. in spreadable cheese and yogurt samples, respectively, while no significant protein scores from other microorganisms were recorded. Subsequent microbiological analyses and sequencing of the 26S rRNA gene region supported the proteomic results demonstrating that the microorganism involved was Rhodotorula mucilaginosa, a carotenoid - producing basidiomycetous that can be potentially pathogenic to humans, especially for immunocompromised individuals. This is the first time that shotgun proteomics has been used to identify a microorganism responsible for spoilage in dairy products, proposing it as a relatively fast, sensitive, and reliable alternative or complement to conventional methods for microbial identification.

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Background Massa Medicata Fermentata (MMF) is a traditional medicinal/edible fermented product; however, comprehensive research on the fermentation process from a microscopic perspective remains limited. In this study, we aimed to investigate the dynamic changes and correlations of physicochemical properties, microbial communities, and metabolite profiles in different fermentation stages (0, 48, 72, and 96 h) of MMF. Methods Standard analytical tests, microbiome sequencing, broad-target metabolism, mixed standard-based mass spectrometry, and fine structure analysis were integrated to elucidate fluctuations in physicochemical, microbial, and metabolic levels during MMF fermentation. Results During the fermentation process, bacterial diversity generally shows an increasing trend, whereas fungal diversity generally shows a decreasing trend. Revealing that the differentially abundant metabolites were primarily categorized into lipids, amino acids and derivatives, phenolic acids, organic acids, flavonoids, lignans and coumarins, nucleotides and derivatives, and alkaloids. Structural equation modeling and correlation analysis indicated that two species of bacteria (Bacillus velezensis, Bacillus safensis) and four species of fungi (Apiotrichum montevideense, Geotrichum bryndzae, f_Dipodascaceae, Saccharomycopsis fibuligera) showed significant positive correlations with five types of differential metabolites, including lipids, flavonoids, phenolic acids, lignans and coumarins, and organic acids. These differential metabolites are essential components responsible for the therapeutic effects of MMF, particularly those that reach peak concentrations at 72 h of fermentation. Conclusion These findings are expected to provide a reference for developing strategies to strengthen the quality of MMF and promote its modern application.

Electroactive bacteria (EAB) hold great promise for the development of electrochemical biosensors given their unique ability to transfer electrons extracellularly via specialized pathways, a process termed extracellular electron transfer (EET). Ongoing research aims to overcome current limitations and fully harness the potential of EABs for high-performance biosensing applications. Herein, we report the fabrication of an electrochemical microsensor based on biomineralized electroactive bacteria, specifically Shewanella oneidensis MR-1. We exploited the EET capability of S. oneidensis to mineralize gold nanoparticles (AuNPs) in situ, thereby enhancing the EET efficiency and improving the electrochemical performance. With lactate serving as the sole electron donor, S. oneidensis functions as a whole-cell electrical transducer, converting the metabolism of lactate into detectable electrical signals. The resulting microsensor, designated AuNPs@S. oneidensis@CFE, exhibited enhanced sensitivity, a broad linear detection range, and high specificity for lactate detection, along with relatively good stability and reproducibility. Furthermore, when integrated into a three-in-one microelectrode, it enabled online monitoring of lactate fermentation. Thus, this work highlights the potential of combining the EET reduction capacity and sensory ability of EABs with miniaturized devices, demonstrating the feasibility of integrating biomineralization with EET pathways of EABs to develop robust electrochemical microbial biosensors.

Luzhou-flavoured liquor is one of Chinese most popular distilled liquors. Hundreds of flavoured components have been detected from this liquor, with esters as its primary flavouring substance. Among these esters, ethyl hexanoate was the main component. As an essential functional microbe that produces ethyl hexanoate, yeast is an important functional microorganism that produces ethyl hexanoate. The synthesis of ethyl hexanoate in yeast mainly involves the lipase/esterase synthesis pathway, alcohol transferase pathway and alcohol dehydrogenase pathway. In this study, whole-genome sequencing of W. anomalus Y-1 isolated from a Chinese liquor fermentation starter, a fermented wheat starter containing brewing microorganisms, was carried out using the Illumina HiSeq X Ten platform. The sequence had a length of 15,127,803 bp with 34.56% GC content, encoding 7,024 CDS sequences, 69 tRNAs and 1 rRNA. Then, genome annotation was performed using three high-quality databases, namely, COG, KEGG and GO databases. The annotation results showed that the ko7019 pathway of gene 6,340 contained the Eht1p enzyme, which was considered a putative acyltransferase similar to Eeb1p and had 51.57% homology with two known medium-chain fatty acid ethyl ester synthases, namely, Eht1 and Eeb1. Ethyl hexanoate in W. anomalus was found to be synthesised through the alcohol acyltransferase pathway, while acyl-coenzyme A and alcohol were synthesised under the catalytic action of Eht1p. The results of this study are beneficial to the exploration of key genes of ester synthesis and provide reference for the improvement of liquor flavoured.

Despite the recognized capacity of the gut microbiota to regulate intestinal lipid metabolism, the role of specific commensal species remains undefined. Here, we aimed to understand the bacterial effectors and molecular mechanisms by which Lactobacillus paracasei and Escherichia coli regulate lipid metabolism in enterocytes. We show that L-lactate produced by L. paracasei inhibits chylomicron secretion from enterocytes and promotes lipid storage by a mechanism involving L-lactate absorption by enterocytes, its conversion to malonyl-CoA, and the subsequent inhibition of lipid beta-oxidation. In contrast, acetate produced by E. coli also inhibits chylomicron secretion by enterocytes but promotes lipid oxidation by a mechanism involving acetate absorption by enterocytes, its metabolism to acetyl-CoA and AMP, and the subsequent upregulation of the AMPK/PGC-1α/PPARα pathway. Our study opens perspectives for developing specific bacteria- and metabolite-based therapeutic interventions against obesity, atherosclerosis, and malnutrition by targeting lipid metabolism in enterocytes.

Intestinal epithelial absorption of dietary lipids is a major determinant of animal energy balance and metabolic health. Recent studies uncovered significant roles for intestinal microbiota in this process, but underlying mechanisms remain unresolved. Araújo et al. (2020) identify two end-products of bacterial fermentation that regulate intestinal lipid absorption and metabolism.

Disease tolerance is a host response to infection that limits collateral damage to host tissues while having a neutral effect on pathogen fitness. Previously, we found that the pathogenic lactic acid bacterium Streptococcus pyogenes manipulates disease tolerance using its aerobic mixed-acid fermentation pathway via the enzyme pyruvate dehydrogenase, but the microbe-derived molecules that mediate communication with the host’s disease tolerance pathways remain elusive. Here we show in a murine model that aerobic mixed-acid fermentation inhibits the accumulation of inflammatory cells including neutrophils and macrophages, reduces the immunosuppressive cytokine interleukin-10, and delays bacterial clearance and wound healing. In infected macrophages, the aerobic mixed-acid fermentation end-products acetate and formate from streptococcal upregulate host acetyl-CoA metabolism and reduce interleukin-10 expression. Inhibiting aerobic mixed-acid fermentation using a bacterial-specific pyruvate dehydrogenase inhibitor reduces tissue damage during murine infection, correlating with increased interleukin-10 expression. Our results thus suggest that reprogramming carbon flow provides a therapeutic strategy to mitigate tissue damage during infection. Disease tolerance helps avoid inflammatory damages when immune system is trying to clear infection, but the mechanisms are still unclear. Here the authors show that the bacteria tap into disease tolerance by altering host cell acetyl-CoA metabolism to suppress innate cell function and cytokine production.

How enteric pathogens adapt their metabolism to a dynamic gut environment is not yet fully understood. To investigate how Salmonella enterica Typhimurium (S.Tm) colonizes the gut, we conducted an in vivo transposon mutagenesis screen in a gnotobiotic mouse model. Our data implicate mixed-acid fermentation in efficient gut-luminal growth and energy conservation throughout infection. During initial growth, the pathogen utilizes acetate fermentation and fumarate respiration. After the onset of gut inflammation, hexoses appear to become limiting, as indicated by carbohydrate analytics and the increased need for gluconeogenesis. In response, S.Tm adapts by ramping up ethanol fermentation for redox balancing and supplying the TCA cycle with α-ketoglutarate for additional energy. Our findings illustrate how S.Tm flexibly adapts mixed fermentation and its use of the TCA cycle to thrive in the changing gut environment. Similar metabolic wiring in other pathogenic Enterobacteriaceae may suggest a broadly conserved mechanism for gut colonization.

Ethyl carbamate (EC) poses a potential public health risk; the reduction efficiency is limited by high ethanol and acidic conditions during fermentation. This study identified fungi as key EC-degrading microbes from Baijiu fermented grains. Aspergillus recifensis. EC-1 isolated from Baijiu fermented grains degraded 50.7% EC (5 g·L-1) in 7 days. Transcriptomics and metabolomics revealed EC hydrolysis via amidase into ammonia and ethanol: ammonia entered arginine biosynthesis, while ethanol fueled central carbon metabolism. TR3859 was identified as degrading enzyme. It remained highly active under 20% ethanol and 15% NaCl conditions (9.1 U·mg-1 and 38.8 U·mg-1), and the enzyme's affinity for EC was Km = 6.0 mM. When coculture with strain EC-1 and Daqu, EC degradation reached 81.5% within 3 days, and the relative abundance of the genera Thermoascus and Thermomyces exceeds 65%. The objective of this study was to provide an efficient method for EC elimination in fermented foods by microbes and enzymes.

This study integrates metagenomic and metabolomic data to systematically analyze the microbial community succession and carbon source metabolism transitions during the third fermentation cycle of Agaricus bisporus, with the aim of optimizing fermentation efficiency and lignocellulose degradation strategies. Principal Coordinate Analysis (PcoA) based on Bray–Curtis dissimilarity reveals significant microbial community separation across the stages of the first mushroom fruiting cycle. The overall pattern of “stage-specific differentiation” is consistent with the “cellulose hydrolysis” turn to the degradation of complex polysaccharides via carbohydrate-active enzymes (CAZymes). In the microbial network analysis showed that different microbe group controlled the stage-specific differentiation. These findings highlight a phase-dependent metabolic shift during the fermentation process: the early stages of fruiting rely more on cellulose-degrading microbes and their enzymatic systems, while later stages are driven by the degradation of complex polysaccharides and lignin derivatives, with Planctomycetota leading the degradation. This provides new mechanistic insights into agricultural waste resource utilization and the directional regulation of fermentation processes.

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This study integrated metabolomic and metatranscriptomic techniques to examine how the endogenous microbe, Staphylococcus succinus, influenced the essential flavor of fermented chili peppers. The mechanisms governing spontaneous fermentation and S. succinus-inoculated fermentation were also elucidated. Esters (e.g., ethyl undecanoate, isoamyl acetate, and methyl salicylate), terpenes (e.g., terpinen-4-ol), and alcohols (e.g., α-terpineol, linalool, and 4-methyl-3-heptanol) were found to be the key aroma-active compounds, aspartic acid (Asp) and glutamic acid (Glu) were identified as primary flavoring free amino acids. Notably, during the early stages of S. succinus-inoculated fermentation, the production of these essential metabolites was abundant, while their gradual increase over time was observed in the case of spontaneous fermentation. Metatranscriptomic analysis revealed that S. succinus inoculation could up-regulate genes related to glycolysis, amino acid metabolism, and aroma compound synthesis. These changes sequentially boosted the production of sweet and umami free amino acids, enhanced organic acid levels, increased unique aroma compound generation, and further improved the flavor and quality of the fermented chili peppers. Therefore, S. succinus inoculation can augment the sensory quality of fermented chili peppers, making this strain a promising candidate for Sichuan pickle fermentation starters.

Saccharomyces cerevisiae is the most common microbe used for the industrial production of bioethanol, and it encounters various stresses that inhibit cell growth and metabolism during fermentation. However, little is currently known about the physiological changes that occur in individual yeast cells during ethanol fermentation. Therefore, in this work, Raman spectroscopy and chemometric techniques were employed to monitor the metabolic changes of individual yeast cells at distinct stages during high gravity ethanol fermentation. Raman tweezers was used to acquire the Raman spectra of individual yeast cells. Multivariate curve resolution-alternating least squares (MCR-ALS) and principal component analysis were employed to analyze the Raman spectra dataset. MCR-ALS extracted the spectra of proteins, phospholipids, and triacylglycerols and their relative contents in individual cells. Changes in intracellular biomolecules showed that yeast cells undergo three distinct physiological stages during fermentation. In addition, heterogeneity among yeast cells significantly increased in the late fermentation period, and different yeast cells may respond to ethanol stress via different mechanisms. Our findings suggest that the combination of Raman tweezers and chemometrics approaches allows for characterizing the dynamics of molecular components within individual cells. This approach can serve as a valuable tool in investigating the resistance mechanism and metabolic heterogeneity of yeast cells during ethanol fermentation.

It has been demonstrated that the gut microbiota may play an important intermediary role in anthocyanins' beneficial impacts on obesity. However, the microbe-related anti-obesity mechanism of blueberry anthocyanins remains unclear. In this study, the interactions between blueberry anthocyanin extracts (BAE) and gut microbiota from obese humans were explored using an in vitro fermentation model. Due to hydrolysis and metabolism by the microbiota, the contents of blueberry anthocyanins are reduced during fermentation. It was demonstrated that both aglycones and glycosides affected the degradation rate. The microbial composition evaluation revealed that BAE could alleviate obesity by promoting the colonization of probiotics such as Lachnospiraceae_UCG-004 and Bacteroides, as well as inhibiting the proliferation of harmful bacteria including Escherichia-Shigella, Clostridium_sensu_stricto_1, and Klebsiella. Blueberry anthocyanin extracts facilitate the production of short-chain fatty acids (SCFAs), which is beneficial for obesity control. The relationship between blueberry anthocyanins, gut microbiota, and SCFAs was further investigated. Overall, this data provides new insights into the positive interaction between blueberry anthocyanins and gut microbiota in obese humans.

Microbiota consisting of various fungi and bacteria have a significant impact on the physiological functions of the host. However, it is unclear which species are essential to this impact and how they affect the host. This study analyzed and isolated microbes from natural food sources of Drosophila larvae, and investigated their functions. Hanseniaspora uvarum is the predominant yeast responsible for larval growth in the earlier stage of fermentation. As fermentation progresses, Acetobacter orientalis emerges as the key bacterium responsible for larval growth, although yeasts and lactic acid bacteria must coexist along with the bacterium to stabilize this host-bacterial association. By providing nutrients to the larvae in an accessible form, the microbiota contributes to the upregulation of various genes that function in larval cell growth and metabolism. Thus, this study elucidates the key microbial species that support animal growth under microbial transition.

Adherent-invasive E. coli (AIEC) are enriched in the intestinal microbiota of patients with Crohn's disease (CD) and promote intestinal inflammation. Yet, how AIEC metabolism of nutrients impacts intestinal homeostasis is poorly defined. Here, we show that AIEC encoding the large subunit of propanediol dehydratase (PduC), which facilitates the utilization of fucose fermentation product 1,2-propanediol, are increased in the microbiome of CD patients and drive AIEC-induced intestinal T cell inflammation. In murine models, CX3CR1+ mononuclear phagocytes (MNP) are required for PduC-dependent induction of T helper 17 (Th17) cells and interleukin-1β (IL-1β) production that leads to AIEC-induced inflammatory colitis. Activation of this inflammatory cascade requires the catalytic activity of PduC to generate propionate, which synergizes with lipopolysaccharide (LPS) to induce IL-1β by MNPs. Disrupting fucose availability limits AIEC-induced propionate production and intestinal inflammation. These findings identify MNPs as metabolic sensors linking AIEC metabolism with intestinal inflammation and identify microbial metabolism as a potential therapeutic target in Crohn's disease treatment.

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Recycling waste gases from industry is vital for the transition toward a circular economy. The model microbe Clostridium ljungdahlii reduces carbon from syngas and primarily produces acetate and ethanol. Here, a gas fermentation experiment is presented in chemostats with C. ljungdahlii and pure carbon monoxide (CO) as feedstock while entirely omitting yeast extract. A maximum ethanol production rate of 0.07 ± 0.01 g L-1 h-1 and a maximum average ethanol/acetate ratio of 1.41 ± 0.39 was observed under steady-state conditions. This confirmed that CO as the sole feedstock pushes the metabolism toward more reduced fermentation products. This effect was even more pronounced when 15 mM sodium acetate was added to the feed medium. An ethanol production rate of 0.23 ± 0.01 g L-1 h-1 was achieved, representing an increase of more than 240%. This increase was accompanied by an increase in cell density and selectivity toward ethanol, with a maximum average ethanol/acetate ratio of 92.96 ± 28.39. Oxygen contaminations voided this effect, although the cultures were still able to maintain a stable biomass concentration and ethanol production rate. These findings highlight the potential of CO-fermentation with acetate augmentation and the importance of preventing oxygen contaminations.

Eubacterium hallii is considered an important microbe in regard to intestinal metabolic balance due to its ability to utilize glucose and the fermentation intermediates acetate and lactate, to form butyrate and hydrogen. Recently, we observed that E. hallii is capable of metabolizing glycerol to 3-hydroxypropionaldehyde (3-HPA, reuterin) with reported antimicrobial properties. The key enzyme for glycerol to 3-HPA conversion is the cobalamin-dependent glycerol/diol dehydratase PduCDE which also utilizes 1,2-propanediol (1,2-PD) to form propionate. Therefore our primary goal was to investigate glycerol to 3-HPA metabolism and 1,2-PD utilization by E. hallii along with its ability to produce cobalamin. We also investigated the relative abundance of E. hallii in stool of adults using 16S rRNA and pduCDE based gene screening to determine the contribution of E. hallii to intestinal propionate formation. We found that E. hallii utilizes glycerol to produce up to 9 mM 3-HPA but did not further metabolize 3-HPA to 1,3-propanediol. Utilization of 1,2-PD in the presence and absence of glucose led to the formation of propanal, propanol and propionate. E. hallii formed cobalamin and was detected in stool of 74% of adults using 16S rRNA gene as marker gene (n = 325). Relative abundance of the E. hallii 16S rRNA gene ranged from 0 to 0.59% with a mean relative abundance of 0.044%. E. hallii PduCDE was detected in 63 to 81% of the metagenomes depending on which subunit was investigated beside other taxons such as Ruminococcus obeum, R. gnavus, Flavonifractor plautii, Intestinimonas butyriciproducens, and Veillonella spp. In conclusion, we identified E. hallii as a common gut microbe with the ability to convert glycerol to 3-HPA, a step that requires the production of cobalamin, and to utilize 1,2-PD to form propionate. Our results along with its ability to use a broad range of substrates point at E. hallii as a key species within the intestinal trophic chain with the potential to highly impact the metabolic balance as well as the gut microbiota/host homeostasis by the formation of different short chain fatty acids.

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Gut microbiota acts as a barrier against intestinal pathogens, but species-specific protection of the host from infection remains relatively unexplored. Although lactobacilli and bifidobacteria produce beneficial lactic and short-chain fatty acids in the mammalian gut, the significance of intestinal Escherichia coli producing these acids is debatable. Taking a Koch’s postulates approach in reverse, we define Escherichia coli as health-promoting for naturally colonizing the gut of healthy mice and protecting them against intestinal colonization and concomitant mortality by Pseudomonas aeruginosa. Reintroduction of faecal bacteria and E. coli in antibiotic-treated mice establishes a high titre of E. coli in the host intestine and increases defence against P. aeruginosa colonization and mortality. Strikingly, high sugar concentration favours E. coli fermentation to lactic and acetic acid and inhibits P. aeruginosa growth and virulence in aerobic cultures and in a model of aerobic metabolism in flies, while dietary vegetable fats - not carbohydrates or proteins - favour E. coli fermentation and protect the host in the anaerobic mouse gut. Thus E. coli metabolic output is an important indicator of resistance to infection. Our work may also suggest that the lack of antimicrobial bacterial metabolites in mammalian lungs and wounds allows P. aeruginosa to be a formidable microbe at these sites.

High-grain (HG) diets are known to alter the rumen microbiome. However, the responses of the hindgut microbiota and its epithelial function need further investigation in ruminants. ABSTRACT The cecum serves as an additional fermentation site for ruminants, but it lacks buffering capacity and has a relatively simple epithelial structure compared to the rumen. The role of high-grain (HG) diets in manipulating the rumen microbiome has been well elucidated, yet the microbial response to such diets in the cecum and the subsequent microbe-host interactions remain largely unexplored. Here, we describe the modification of the cecal microbiome and host epithelial gene expression based on data from 20 sheep grouped to feed an HG diet for 7, 14, and 28 days. Our data indicate that the alteration of cecal microbial fermentation was manifested by a decrease in luminal pH and an increase in acetate and butyrate concentrations following the diet change to HG. We further demonstrate that the alteration of the microbiome was driven by microbes that are likely acetate producers (e.g., Blautia spp. and Akkermansia spp.) and butyrate producers (e.g., Anaerostipes spp. and Roseburia spp.). Moreover, the core microbiota in the cecal microbiome was predominantly maintained after HG diet feeding, while the specific populations of the cecal microbiomes adaptively varied at the species and genomic levels time dependently. Association analysis suggests that the perturbations of the cecal microbiome under the HG diet were closely linked to the variations in the two key enzymes that catalyze the conversion of pyruvate to acetyl-CoA and urease enzymes that hydrolyze urea into ammonia, alongside mucosal inflammatory responses. Overall, our findings here provide novel insights into understanding microbiome-host interactions in the hindgut of ruminants. IMPORTANCE High-grain (HG) diets are known to alter the rumen microbiome. However, the responses of the hindgut microbiota and its epithelial function need further investigation in ruminants. Using 20 sheep as the experimental model, we found that the microbial fermentation pattern of the cecum changed after switching to the HG diet. The taxa of the acetate and butyrate producers increased with the feeding time. Moreover, enzymes engaged in carbon and nitrogen metabolisms of the cecal microbiome are altered. The expression of epithelial genes related to volatile fatty acid (VFA) absorption and metabolism, cytokines, and tight junction proteins, alongside light microscopy visualization of epithelial tissue, suggested that the HG diet may induce cecal mucosal inflammatory responses. Our findings reveal cecal microbial and metabolic perturbations in response to HG diets in sheep and provide a new reference for the research on hindgut microbial homeostasis and host health in ruminants.

Abstract Epigenetic regulation may play an important role in mediating microbe–host interactions and adaptation of intestinal gene expression to bacterial colonization just after birth. This is particularly important after preterm birth because the immature intestine is hypersensitive to invading bacteria. We compared the intestinal DNA methylome and microbiome between conventional (CON) and antibiotics-treated (AB) preterm pigs, used as a model for preterm infants. Oral AB treatment reduced bacterial density (∼100-fold), diversity and fermentation, improved the resistance to necrotizing enterocolitis (NEC) and changed the genome-wide DNA methylation in the distal small intestine. Integration of epigenome data with previously obtained proteome data showed that intestinal immune–metabolic pathways were affected by the AB-induced delay in bacterial colonization. DNA methylation and expression of intestinal genes, related to innate immune response, phagocytosis, endothelial homeostasis and tissue metabolism (e.g. CPN1, C3, LBP, HIF1A, MicroRNA-126, PTPRE), differed between AB and CON pigs even before any evidence of NEC lesions. Our findings document that the newborn immature intestine is influenced by bacterial colonization via DNA methylation changes. Microbiota-dependent epigenetic programming of genes related to gut immunity, vascular integrity and metabolism may be critical for short- and long-term intestinal health in preterm neonates.

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Secondary bile acids (BAs) and short chain fatty acids (SCFAs), two major types of bacterial metabolites in the colon, cause opposing effects on colonic inflammation at chronically high physiological levels. Primary BAs play critical roles in cholesterol metabolism, lipid digestion, and host–microbe interaction. Although BAs are reabsorbed via enterohepatic circulation, primary BAs serve as substrates for bacterial biotransformation to secondary BAs in the colon. High-fat diets increase secondary BAs, such as deoxycholic acid (DCA) and lithocholic acid (LCA), which are risk factors for colonic inflammation and cancer. In contrast, increased dietary fiber intake is associated with anti-inflammatory and anticancer effects. These effects may be due to the increased production of the SCFAs acetate, propionate, and butyrate during dietary fiber fermentation in the colon. Elucidation of the molecular events by which secondary BAs and SCFAs regulate colonic cell proliferation and inflammation will lead to a better understanding of the anticancer potential of dietary fiber in the context of high-fat diet-related colon cancer. This article reviews the current knowledge concerning the effects of secondary BAs and SCFAs on the proliferation of colon epithelial cells, inflammation, cancer, and the associated microbiome.

The composition and function of the gut microbiota are intimately tied to nutrient acquisition strategies and metabolism, with significant implications for host health. Both dietary and host-intrinsic factors influence community structure and the basic modes of bacterial energy metabolism. The intestinal tract is rich in carbon and nitrogen sources; however, limited access to oxygen restricts energy-generating reactions to fermentation. By contrast, increased availability of electron acceptors during episodes of intestinal inflammation results in phylum-level changes in gut microbiota composition, suggesting that bacterial energy metabolism is a key driver of gut microbiota function. In this review article, we will illustrate diverse examples of microbial nutrient acquisition strategies in the context of habitat filters and anatomical location and the central role of energy metabolism in shaping metabolic strategies to support bacterial growth in the mammalian gut.

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Rumen microbiota drive fermentation and contribute to variation in feed efficiency among ruminants, yet the underlying host–microbe mechanisms remain poorly understood. This study explores how rumen microbes shape feed conversion efficiency (FCR) through integrated interactions with multiple host organs. We applied a multi-omics strategy—combining rumen metagenomics and host multi-organ transcriptomics—in Hu sheep with divergent FCR. From a uniform cohort of 150 weaned male Hu lambs, 13 low-FCR (LFCR) and 13 high-FCR (HFCR) individuals were selected for integrated analyses. LFCR sheep exhibited greater growth performance and higher ruminal propionate concentrations compared with HFCR animals. The ruminal microbiomes were enriched in Saccharofermentans and Succinivibrionaceae_UBA2804, and showed functional convergence on amino acid biosynthesis, central carbon metabolism, and propionate-oriented fermentation in LFCR sheep. Carbohydrate-active enzyme profiles indicated that LFCR animals favored fiber- and starch-associated modules (GH126, CBM27, EPS-GT), whereas HFCR animals were enriched in host-glycan and uronic acid–degrading families (CE14, GH89, PL15). Hydrogen metabolism highlighted a clear dichotomy: LFCR animals redirected H₂ toward propionate and sulfate reduction, while HFCR animals retained greater butyrate-producing and methanogenic capacity. Transcriptomic profiling across rumen epithelium, liver, and muscle identified tissue-specific regulatory modules. Only the liver showed strong enrichment of carbohydrate metabolism, with a complete glycogen turnover and glucose export system (GYS2, PYGL, PGM2, G6PC1) and pathways linking microbial short-chain fatty acids to gluconeogenesis. In contrast, muscle efficiency modules were dominated by contractile and cytoskeletal genes (e.g., MYL2, TNNC1, TPM3), reflecting optimized energy expenditure rather than substrate metabolism. No efficiency-associated modules were detected in the rumen epithelium, consistent with its role in propionate absorption rather than metabolism. The rumen microbiota of LFCR sheep possess highly efficient capacities for volatile fatty acid and amino acid synthesis, thereby enhancing energy utilization at its source. The resulting propionate further promotes hepatic gluconeogenesis, directly supplying energy for muscle cell growth and ultimately improving FCR. Thus, co-metabolism between rumen microbiota and the liver provides energy for muscle cell growth and is a key determinant of improved feed efficiency.

The microbiome-gut-brain axis plays a role in anxiety, the stress response and social development, and is of growing interest in neuropsychiatric conditions. The gut microbiota shows compositional alterations in a variety of psychiatric disorders including depression, generalised anxiety disorder (GAD), autism spectrum disorder (ASD) and schizophrenia but studies investigating the gut microbiome in social anxiety disorder (SAD) are very limited. Using whole-genome shotgun analysis of 49 faecal samples (31 cases and 18 sex- and age-matched controls), we analysed compositional and functional differences in the gut microbiome of patients with SAD in comparison to healthy controls. Overall microbiota composition, as measured by beta-diversity, was found to be different between the SAD and control groups and several taxonomic differences were seen at a genus- and species-level. The relative abundance of the genera Anaeromassillibacillus and Gordonibacter were elevated in SAD, while Parasuterella was enriched in healthy controls. At a species-level, Anaeromassilibacillus sp An250 was found to be more abundant in SAD patients while Parasutterella excrementihominis was higher in controls. No differences were seen in alpha diversity. In relation to functional differences, the gut metabolic module 'aspartate degradation I' was elevated in SAD patients. In conclusion, the gut microbiome of patients with SAD differs in composition and function to that of healthy controls. Larger, longitudinal studies are warranted to validate these preliminary results and explore the clinical implications of these microbiome changes.

Irritable bowel syndrome (IBS) is a heterogeneous condition with multifactorial pathogenesis. We studied deeply phenotyped individuals with microbiota sequencing enrolled in the American Gut Project. The IBS subjects were matched by age, gender, body mass index, geography, and dietary patterns with non-IBS controls. A total of 942 subjects with IBS-Diarrhea (IBS-D), IBS-Constipation (IBS-C), unclassified IBS (IBS-U), and 942 non-IBS controls were included. We compared taxonomic and functional composition of gut microbiota based on 16S sequencing data and linked them with clinical characteristics and dietary factors. Subjects with IBS-D or IBS-U but not IBS-C showed significantly reduced bacterial diversity (Shannon; p < .01). Distinct bacterial signatures were associated with different IBS subtypes, and the related functional changes were related to IBS pathogenesis, such as the increased hydrogen sulfide production pathway in IBS-D and the increased palmitoleate biosynthesis pathway in IBS-C. IBS subjects with depression showed lower abundance of

Complex regional pain syndrome is a chronic pain syndrome typically affecting a limb. It is characterized by severe spontaneous and evoked pain, along with vasomotor, autonomic, and motor signs and symptoms. Although dysregulation in several physiologic systems has been suggested in complex regional pain syndrome (CRPS), including aberrant inflammatory and immune responses, vasomotor dysfunction, and nervous system changes, the pathophysiologic mechanisms underlying the syndrome remain elusive. Effective treatment options are also limited. Previous research has highlighted the role of the gut microbiome in chronic pain, prompting us to investigate the composition and function of the gut microbiome in CRPS. The gut microbiomes of individuals with CRPS to age-, sex-, and ethnicity-matched pain-free control participants were compared using 16S rRNA gene amplification. To minimize environmental confounders, participants were recruited from two geographically independent regions. To explore potential changes in gut bacteria-derived metabolites, targeted metabolomic analysis of feces and plasma was performed. Finally, machine learning algorithms were trained to identify the gut microbiome composition specific to CRPS patients and were tested on a validation cohort. In this study, differential abundance analysis revealed significant differences in several bacterial taxa when comparing 53 CRPS patients to 52 unrelated controls, including alterations in short-chain fatty acid-metabolizing species. Targeted stool and plasma metabolite analysis confirmed differences in fecal and plasma short-chain fatty acid levels between CRPS patients and controls. Notably, the microbiome composition alone allowed accurate classification of patients and controls in a geographically independent test cohort. These findings highlight unique compositional and functional changes in the gut microbiome of individuals with CRPS, thus contributing to the growing body of evidence supporting the role of the gut microbiome in chronic pain syndromes. Furthermore, they pave the way for further studies elucidating the pathophysiology of CRPS and exploring new diagnostic aids and treatment modalities.

During the last decades, the incidence of diabetes and a variety of complications such as diabetic retinopathy (DR) and cardiovascular diseases have been increased exponentially. Gut bacterial composition -microbiota - has been associated with the pathobiology of many inflammatory and metabolic disorders such as diabetes. Gut microbiota plays a crucial role in preserving the metabolic and immune homeostasis, protecting against pathogens and regulating host immunity; however, gut microbiome ecosystem can be altered by lifestyle, cigarette smoking, dietary patterns, and oxidative stress.Herein, we present a hypothesis on the potential complex association between gut microbiota and DR as one of the microvascular complications of diabetes.

Chronic unpredictable mild stress (CUMS) can not only lead to depression-like behavior but also change the composition of the gut microbiome. Regulating the gut microbiome can have an antidepressant effect, but the mechanism by which it improves depressive symptoms is not clear. Short-chain fatty acids (SCFAs) are small molecular compounds produced by the fermentation of non-digestible carbohydrates. SFCAs are ubiquitous in intestinal endocrine and immune cells, making them important mediators of gut microbiome-regulated body functions. The balance between the pro- and anti-inflammatory microglia plays an important role in the occurrence and treatment of depression caused by chronic stress. Non-absorbable antibiotic rifaximin can regulate the structure of the gut microbiome. We hypothesized that rifaximin protects against stress-induced inflammation and depression-like behaviors by regulating the abundance of fecal microbial metabolites and the microglial functions. We administered 150 mg/kg rifaximin intragastrically to rats exposed to CUMS for 4 weeks and investigated the composition of the fecal microbiome, the content of short-chain fatty acids in the serum and brain, the functional profiles of microglia and hippocampal neurogenesis. Our results show that rifaximin ameliorated depressive-like behavior induced by CUMS, as reflected by sucrose preference, the open field test and the Morris water maze. Rifaximin increased the relative abundance of Ruminococcaceae and Lachnospiraceae, which were significantly positively correlated with the high level of butyrate in the brain. Rifaximin increased the content of anti-inflammatory factors released by microglia, and prevented the neurogenic abnormalities caused by CUMS. These results suggest that rifaximin can regulate the inflammatory function of microglia and play a protective role in pubertal neurodevelopment during CUMS by regulating the gut microbiome and short-chain fatty acids.

In the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.

The gut microbiome is now viewed as a tissue that interacts bidirectionally with the gastrointestinal, immune, endocrine and nervous systems, affecting the cellular responses in numerous organs. Evidence is accumulating of gut microbiome involvement in a growing number of pathophysiological processes, many of which are linked to inflammatory responses. More specifically, data acquired over the last decade point to effects of the gut microbiome on bone mass regulation and on the development of bone diseases (such as osteoporosis) and of inflammatory joint diseases characterized by bone loss. Mice lacking a gut microbiome have bone mass alteration that can be reversed by gut recolonization. Changes in the gut microbiome composition have been reported in mice with estrogen-deficiency osteoporosis and have also been found in a few studies in humans. Probiotic therapy decreases bone loss in estrogen-deficient animals. The effect of the gut microbiome on bone tissue involves complex mechanisms including modulation of CD4

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Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of approximately 470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World-Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.

Biofilms are a community of surface-associated microorganisms characterized by the presence of different cell types in terms of physiology and phenotype [...].

Allotransplantation and xenotransplantation may be associated with the transmission of pathogens from the donor to the recipient. Whereas in the case of allotransplantation the transmitted microorganisms and their pathogenic effect are well characterized, the possible influence of porcine microorganisms on humans is mostly unknown. Porcine circoviruses (PCVs) are common in pig breeds and they belong to porcine microorganisms that still have not been fully addressed in terms of evaluating the potential risk of xenotransplantation using pig cells, tissues, and organs. Two types of PCVs are known: porcine circovirus (PCV) 1 and PCV2. Whereas PCV1 is apathogenic in pigs, PCV2 may induce severe pig diseases. Although most pigs are subclinically infected, we do not know whether this infection impairs pig transplant functionality, particularly because PCV2 is immunosuppressive. In addition, vaccination against PCV2 is able to prevent diseases, but in most cases not transmission of the virus. Therefore, PCV2 has to be eliminated to obtain xenotransplants from uninfected healthy animals. Although there is evidence that PCV2 does not infect-at least immunocompetent-humans, animals should be screened using sensitive methods to ensure virus elimination by selection, Cesarean delivery, vaccination, or embryo transfer.

Free radicals are often described as chemical compounds characterized by unpaired electrons in their outer orbital rendering them highly reactive species. In mammalians, studies on free radicals were focused on reactive oxygen species (ROS) or reactive nitrogen species (RNS) due to their relative importance in physiological as well as in pathological processes. These cellular compounds are produced by different physiological systems such as the aerobic metabolism and play a major role in cell signaling pathways but also in the host immune defenses against pathogenic microorganisms. ROS and RNS are highly reactive species with potentially harmful effects on any cellular components (lipids, proteins and nucleic acids) when produced with a high level. To maintain ROS and RNS at a non-toxic concentration, enzymatic and non-enzymatic cellular antioxidants coordinate the balance between their production and their degradation. Superoxide dismutases, catalases, glutathione system, thioredoxin system, peroxidase systems, flavohemoglobins and nitrate or nitrite reductases represent the prominent enzymatic antioxidants used to scavenge excess of internal as well as external ROS and RNS. Bacteria, fungi and parasites also display similar enzymatic activities to escape the host oxidative defenses during the immune response against infectious processes. Here we summarize current knowledge on the enzymatic systems that allow microorganisms to fight against ROS and RNS, and shed light on the role that take some of them in microbial infections. Such microbial protective systems are considered as virulence factors, and therefore represent key targets for diagnosis of the infections or development of anti-infectious drugs.

Refractory apical periodontitis (RAP) is an oral infectious disease characterised by persistent inflammation, progressive alveolar bone destruction, and delayed bone healing. RAP has received increasing attention, because it cannot be cured after repeated root canal therapies. The aetiology of RAP is related to the complex interplay between the pathogen and its host. However, the exact pathogenesis of RAP remains unclarified and includes several factors, such as microorganism immunogenicity, host immunity and inflammation, and tissue destruction and repair. Enterococcus faecalis is the dominant pathogen involved in RAP, and has evolved multiple strategies to ensure survival, which cause persistent intraradicular and extraradicular infections. To review the crucial role of E. faecalis in the pathogenesis of RAP, and open new avenues for prevention and treatment of RAP. The PubMed and Web of Science databases were searched for pertinent publications, employing the search terms "Enterococcus faecalis", "refractory apical periodontitis", "persistent periapical periodontitis", "pathogenicity", "virulence", "biofilm formation", "dentine tubule", "immune cell", "macrophage", and "osteoblast". Besides its high pathogenicity due to various virulence mechanisms, E. faecalis modulates the macrophage and osteoblast responses, including regulated cell death, cell polarisation, cell differentiation, and inflammatory response. An in-depth understanding of the multifaceted host cell responses modulated by E. faecalis will help to design potential future therapeutic strategies and overcome the challenges of sustained infection and delayed tissue healing in RAP.

The lipid bilayer of the plasma membrane is thought to be compartmentalized by the presence of lipid-protein microdomains. In eukaryotic cells, microdomains composed of sterols and sphingolipids, commonly known as lipid rafts, are believed to exist, and reports on the presence of sterol- or protein-mediated microdomains in bacterial cell membranes are also appearing. Despite increasing attention, little is known about microdomains in the plasma membrane of pathogenic microorganisms. This review attempts to provide an overview of the current state of knowledge of lipid rafts in pathogenic fungi and bacteria. The current literature on characterization of microdomains in pathogens is reviewed, and their potential role in growth, pathogenesis, and drug resistance is discussed. Better insight into the structure and function of membrane microdomains in pathogenic microorganisms might lead to a better understanding of their pathogenesis and development of raft-mediated approaches for therapy.

For decades, Aggregatibacter actinomycetemcomitans has been considered the most likely etiologic agent in aggressive periodontitis. Implementation of DNA-based microbiologic methodologies has considerably improved our understanding of the composition of subgingival biofilms, and advanced open-ended molecular techniques even allow for genome mapping of the whole bacterial spectrum in a sample and characterization of both the cultivable and not-yet-cultivable microbiota associated with periodontal health and disease. Currently, A. actinomycetemcomitans is regarded as a minor component of the resident oral microbiota and as an opportunistic pathogen in some individuals. Its specific JP2 clone, however, shows properties of a true exogenous pathogen and has an important role in the development of aggressive periodontitis in certain populations. Still, limited data exist on the impact of other microbes specifically in aggressive periodontitis. Despite a wide heterogeneity of bacteria, especially in subgingival samples collected from patients, bacteria of the red complex in particular, and those of the orange complex, are considered as potential pathogens in generalized aggressive periodontitis. These types of bacterial findings closely resemble those found for chronic periodontitis, representing a mixed polymicrobial infection without a clear association with any specific microorganism. In aggressive periodontitis, the role of novel and not-yet-cultivable bacteria has not yet been elucidated. There are geographic and ethnic differences in the carriage of periodontitis-associated microorganisms, and they need to be taken into account when comparing study reports on periodontal microbiology in different study populations. In the present review, we provide an overview on the colonization of potential periodontal pathogens in childhood and adolescence, and on specific microorganisms that have been suspected for their role in the initiation and progression of aggressive forms of periodontal disease.

Most of the human gene homologs are found in Caenorhabditis elegans. As a wide variety of micro-organisms present in the environment is pathogens, so, C. elegans could be a useful model to track future infectious disease. With this knowledge, in this study, we isolated Acinetobacter courvalinii from the soil and characterized its pathogenicity for the first time. For the isolation, we used Glucose-Yeast extract-Ethanol-Calcium carbonate medium. To this aim, we evaluated the resistivity of bacteria against several stressful microenvironments. As we observed, A. courvalinii JP_A1001 shown highly tolerance against the acidic environment (pH 3-7), resistant against up to 0.2% of phenol content, and survived in the medium supplemented with 0.3% of bile salt. In addition, the bacteria were also resistant against several antibiotics showing the property of multidrug-resistant bacteria. Moreover, the isolated bacteria have shown the biofilm formation ability within 60 h. Further, we found that incubation of C. elegans with A. courvalinii JP_A1001 decreased the body movement and increased the free radical generation which remarkably influenced the life expectancy of C. elegans compared to E. coli OP50. Therefore, we concluded that A. courvalinii JP_A1001 found in the soil could be a future threat as a pathogen to public health.

Bacteria of the genus

Adaptation to any undesirable change in the environment dictates the survivability of many microorganisms, with such changes generating a quick and suitable response, which guides the physiology of bacteria. During nutritional deprivation, bacteria show a stringent response, as characterized by the accumulation of (p)ppGpp, resulting in the repression of stable RNA species, such as rRNA and tRNA, with a concomitant change in colony morphology. However, genes involved in amino acid biosynthesis become over-expressed to help bacteria survive under such conditions. The survivability of pathogenic bacteria inside a host cell also depends upon the stringent response demonstrated. Therefore, an understanding of the physiology of stringent conditions becomes very interesting in regulation of the growth and persistence of such invading pathogens.

After decades marked by a decrease in the incidence and severity of scarlet fever and streptococcal soft-tissue infections, invasive infections with group A streptococci have reemerged as a global public health problem. Sporadic outbreaks of a rapidly progressive disorder characterized by fever, shock, desquamating rash, and multiorgan system failure often associated with severe suppurative soft-tissue infection have recently been recognized in young, otherwise-healthy adults. Referred to as streptococcal toxic shock-like syndrome, this acute, progressive, often fatal illness appears to be related to an overall change in the virulence of group A streptococci and the reappearance of highly mucoid exotoxin-producing strains. However, the relationship between virulence factors, epidemiological features, and precise pathogenesis of these infections remains unclear. The 80% incidence of soft-tissue involvement in streptococcal toxic shock-like syndrome and the high frequency of progression to necrotizing fasciitis, myositis, or even death are unprecedented. The type and extent of tissue injury, systemic toxicity, and multiorgan system failure associated with this syndrome appear to be mediated by streptococcal pyrogenic exotoxins via the induction of biologically potent endogenous cytokines. The observed increase in the incidence and severity of invasive group A streptococcal infections coincides with the resurgence of genetically related, highly virulent strains of Staphylococcus pyogenes that express an invasive phenotype and carry a specific gene for pyrogenic exotoxin A. The changing spectrum of invasive group A streptococcal infections has prompted a reexamination of the microorganism and its diverse clinical manifestations. A clonal basis for increased virulence expression is supported epidemiologically. As the incidence of streptococcal toxic shock-like syndrome appears to be increasing, it is imperative that clinicians become familiar with the presentation of this syndrome so they can diagnose and treat it in a timely and effective manner.

Pathogenic microorganisms, such as pathogenic mycobacteria, pose a global health burden. Studying these organisms is crucial for gaining detailed knowledge about the pathogens and the diseases they cause. To handle pathogenic organisms, specific biosafety measures appropriate to the virulence of the organism must be fulfilled, most importantly ensuring that all manipulations of pathogenic material are performed within a confined environment. Atomic force microscopy (AFM) is a powerful technique to study biological samples at nanometer-scale resolution, yielding also mechanical properties, all while maintaining physiological conditions. However, standard AFM sample holders do not meet stringent biosafety requirements since they do not constitute a confined system. AFM imaging relies on direct contact between the cantilever and the sample and is sensitive to mechanical interference, rendering conventional containment systems for handling infectious substances inapplicable. Here, we introduce a hermetically sealed AFM sample chamber that meets biosafety demands while satisfying the mechanical and optical constraints of correlated optical microscopy and AFM. We imaged various pathogenic mycobacteria to demonstrate the chamber's versatility and effectiveness in containing biohazardous materials. This sample chamber enables high-resolution, time-lapse correlated imaging and biomechanical characterization of pathogenic microorganisms

Vibrio parahaemolyticus is a marine microorganism that causes acute gastroenteritis associated with the consumption of contaminated raw or under cooked seafood. During infection, the bacterium utilizes a wide variety of virulence factors, including adhesins, toxins and type III secretion systems, to cause both cytotoxicity in cultured cells and enterotoxicity in animal models. Herein, we describe recent discoveries on the regulation and characterization of the virulence factors from V. para. Determining how this bacterial pathogen uses virulence factors to mediate pathogenicity improves our understanding of V. para. infections and more generally, host-pathogen interactions.

Functional traits are characteristics that affect the fitness and metabolic function of a microorganism. There is growing interest in using high-throughput methods to characterize bacterial pathogens based on functional virulence traits. Traditional methods that phenotype a single organism for a single virulence trait can be time consuming and labor intensive. Alternatively, machine learning of whole-genome sequences (WGS) has shown some success in predicting virulence. However, relying solely on WGS can miss functional traits, particularly for organisms lacking classical virulence factors. We propose that high-throughput assays for functional virulence trait identification should become a prominent method of characterizing bacterial pathogens on a population scale. This work is critical as we move from compiling lists of bacterial species associated with disease to pathogen-agnostic approaches capable of detecting novel microbes. We discuss six key areas of functional trait testing and how advancing high-throughput methods could provide a greater understanding of pathogens.

The field of microbial pathogenesis seeks to identify the agents and mechanisms responsible for disease causation. Since Robert Koch introduced postulates that were used to guide the characterization of microbial pathogens, technological advances have substantially increased the capacity to rapidly identify a causative infectious agent. Research efforts currently focus on causation at the molecular level with a search for virulence factors (VFs) that contribute to different stages of the infectious process. We note that the quest to identify and characterize VFs sometimes lacks scientific rigor, and this suggests a need to examine the epistemology of VF characterization. We took this premise as an opportunity to explore the epistemology of VF characterization. In this perspective, we discuss how the characterization of various gene products that evolved to facilitate bacterial survival in the broader environment have potentially been prematurely mischaracterized as VFs that contribute to pathogenesis in the context of human biology. Examples of the reasoning that can affect misinterpretation, or at least a premature assignment of mechanistic causation, are provided. Our aim is to refine the categorization of VFs by emphasizing a broader biological view of their origin.

Oomycetes form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms, of which several hundred organisms are considered among the most devastating plant pathogens-especially members of the genus

Agrobacterium species are plant-associated relatives of the rhizobia. Several species cause plant diseases such as crown gall and hairy root, although there are also avirulent species. A. tumefaciens is the most intensively studied species and causes crown gall, a neoplastic disease that occurs on a variety of plants. Virulence is specified by large plasmids, and in the case of A. tumefaciens this is called the Ti (tumor-inducing) plasmid. During pathogenesis virulent agrobacteria copy a segment of the Ti plasmid and transfer it to the plant, where it subsequently integrates into the plant genome, and expresses genes that result in the disease symptoms. A. tumefaciens has been used extensively as a plant genetic engineering tool and is also a model microorganism that has been well studied for host-microbe associations, horizontal gene transfer, cell-cell communication, and biofilm formation. This unit describes standard protocols for simple phenotypic characterizations of A. tumefaciens.

The human gut microbiota ferments dietary non-digestible carbohydrates into short-chain fatty acids (SCFA). These microbial products are utilized by the host and propionate and butyrate in particular exert a range of health-promoting functions. Here an overview of the metabolic pathways utilized by gut microbes to produce these two SCFA from dietary carbohydrates and from amino acids resulting from protein breakdown is provided. This overview emphasizes the important role played by cross-feeding of intermediary metabolites (in particular lactate, succinate and 1,2-propanediol) between different gut bacteria. The ecophysiology, including growth requirements and responses to environmental factors, of major propionate and butyrate producing bacteria are discussed in relation to dietary modulation of these metabolites. A detailed understanding of SCFA metabolism by the gut microbiota is necessary to underpin effective strategies to optimize SCFA supply to the host.

Food is an integral part of our civilization. It is a cultural phenomenon that, while having evolved, is associated with societal traditions and identity. This work analyzes studies conducted to highlight the health properties of the most common ethnic foods. Although these foods were originally created from the need to preserve perishable produce, presently, we know that the fermentation process makes them nutritionally more complete. The basis of these transformations lies in that vast range of prokaryotic and eukaryotic microorganisms that, similar to small biochemical factories, can transform the initial nutrients into metabolically more active biomolecules through fermentation. Although naturally occurring microbes work together for mutual benefit, environmental conditions enhance or inhibit their development. Starting from a selection of microorganisms naturally present on a substrate, we attempt to select the most suitable species to obtain a fermented food with the best nutritional qualities and the richest in nutraceuticals.

Increased consumption of yogurt, kefir, and other fermented foods has been driven, in part, by the health benefits these products may confer. Epidemiological studies have shown that the consumption of fermented foods is associated with reduced risks of type 2 diabetes, metabolic syndrome, and heart disease, along with improved weight management. The microorganisms present in these foods are suggested to contribute to these health benefits. Among these are the yogurt starter culture organisms Streptococcus thermophilus and Lactobacillus delbrueckii subsp bulgaricus as well as Bifidobacterium and Lactobacillus strains that are added for their probiotic properties. In contrast, for other fermented foods, such as sauerkraut, kimchi, and miso, fermentation is initiated by autochthonous microbes present in the raw material. In both cases, for these fermentation-associated microbes to influence the gut microbiome and contribute to host health, they must overcome, at least transiently, colonization resistance and other host defense factors. Culture and culture-independent methods have now clearly established that many of these microbes present in fermented dairy and nondairy foods do reach the gastrointestinal tract. Several studies have shown that consumption of yogurt and other fermented foods may improve intestinal and extraintestinal health and might be useful in improving lactose malabsorption, treating infectious diarrhea, reducing the duration and incidence of respiratory infections, and enhancing immune and anti-inflammatory responses.

This infographic on Bacteroides thetaiotaomicron (Bt) explores the ability of this microbe to digest a broad array of complex carbohydrates, alter its surface features, and its emerging role in gastrointestinal diseases. The infographic of Bacteroides thetaiotaomicron (Bt) illustrates two key facets of its symbiotic lifestyle in the human gut: a broad ability to digest dietary fiber polysaccharides and host glycans, and a dynamic cell-surface architecture that promotes both interactions with and evasion of the host immune system. The starch-utilization system (Sus) is a cell-surface and periplasmic system involved in starch cleavage and transport. Over 80 additional Sus-like systems utilize substrates ranging from host glycans to plant cell wall pectins. Bt has evolved intricate strategies to interact with other microbes or its host, including modification of its surface. Some nutrient utilization pathways select for or directly trigger changes in capsular polysaccharide (CPS) expression. Like other fermentative members of the gut microbiome, Bt produces host absorbable short-chain and organic acids, which can all be absorbed by the host as a source of energy.

Soy sauce is a traditional Japanese fermented seasoning that contains various constituents such as amino acids, organic acids, and volatiles that are produced during the long fermentation process. Although studies regarding the correlation between microbes and aroma constituents have been performed, there are no reports about the influences of the microbial products, such as lactic acid, acetic acid, and ethanol, during fermentation. Because it is known that these compounds contribute to microbial growth and to changes in the constituent profile by altering the moromi environment, understanding the influence of these compounds is important. Metabolomics, the comprehensive study of low molecular weight metabolites, is a promising strategy for the deep understanding of constituent contributions to food characteristics. Therefore, the influences of microbes and their products such as lactic acid, acetic acid, and ethanol on aroma profiles were investigated using gas chromatography/mass spectrometry (GC/MS)-based metabolic profiling. The presence of aroma constituents influenced by microbes and chemically influenced by lactic acid, acetic acid, and ethanol were proposed. Most of the aroma constituents were not produced by adding ethanol alone, confirming the participation of yeast in aroma production. It was suggested that lactic acid bacterium relates to a key aromatic compound, 2,5-dimethyl-4-hydroxy-3(2H)-furanone. However, most of the measured aroma constituents changed similarly in both samples with lactic acid bacterium and acids. Thus, it was clear that the effect of lactic acid and acetic acid on the aroma profile was significant.

Golden pomfret (Trachinotus ovatus) is an important farmed fish in Asia, often consumed following salting and natural microbial fermentation. Flavor development in fermented foods depends on the metabolism of fermenting microbes, especially amino acid metabolism. However, the microbes involved in golden pomfret fermentation and the mechanism by which they regulate flavor development are largely unknown. Accordingly, in this study, we investigated the microbial community and volatile and non-volatile compounds during the traditional fermentation of golden pomfret, focusing on amino acid metabolism. Thirty-five volatile compounds were detected. Glutamate, alanine, and leucine were the main amino acids responsible for the development of the characteristic taste of fermented golden pomfret. Metagenomic analyses were performed, and microbial genes for amino acid metabolism were functionally annotated, revealing the underlying mechanisms of flavor development during fish fermentation. Halobacterium, Clostridium, Natrinema, Alkalibacillus, Natrialba, and Vibrio were the dominant microbial genera with a major contribution to amino acid metabolism during fermentation and were strongly correlated with the majority of volatile compounds. The study provides a theoretical reference for the mechanism of flavor formation and important information on the microbial sources of volatile compounds derived from amino acids.

Xylo-oligosaccharide (XOS), a prebiotic oligosaccharide, has been reported to exert the beneficial effects on the host, primarily by modulating the gut microbiota and associated metabolism. However, the specific microbes, their metabolic interactions and mechanistic insights remain understudied. In this study, we aim to investigate the response of gut microbiota to XOS at the fine-grained level using combined approaches of microbiome sequencing, genomic analyses, and metabolomic analyses based on in vitro fecal fermentation using healthy human fecal samples. The results showed that XOS significantly altered the composition of the gut microbiota and enriched numerous bacterial taxa, such as Blautia, Bifidobacterium longum subsp. longum, and Faecalibacterium prausnitzii. Functional genomic analyses further confirmed that specifically identified XOS-responsive bacteria harbored varied XOS-utilizing capacities, consistent with the levels of their abundance elevation. The fecal metabolomics analysis revealed that XOS intervention significantly altered the metabolic profile (γ-aminobutyric acid, serotonin, and inosine). The microbe-microbe and microbe-metabolite interaction networks consistently identified three independent groups, potentially representing different levels of XOS degradation and/or other response mechanisms. Finally, the beneficial effects of XOS on the gut microbiota and metabolism were confirmed by the alleviation D-galactose-induced aging in mouse model. This study supports the role of XOS as prebiotics and highlights the potential of XOS in alleviating host aging-associated phenotypes in a D-galactose-induced aging mouse model in terms of improvements on cognitive function, inflammatory markers, and oxidative stress levels.

Volatile sulfur compounds play a crucial role in fermented foods, however, their metabolism during spontaneous food fermentation remains underexplored. With 3-(methylthio)-1-propanal as a case, we revealed the effect of initial acidity on the sulfur metabolism during sesame flavor-type baijiu fermentation. Results showed that the content of 3-(methylthio)-1-propanal reached 383.29 μg/kg with 1.8 mmol/10 g of the initial acidity, and it decreased to 320.54 μg/kg when the initial acidity increased to 2.4 mmol/10 g. Metagenomic analysis identified 11 core microbes associated with sulfur metabolism, characterized by gene abundance (> 0.5 %) and catalytic enzyme distribution frequency (> 10 %). Saccharomyces was the main producer of sulfur compounds. Lactobacillus was an important player in the methyl cycle pathway of sulfur metabolism. Low initial acidity increased the abundance of Lactobacillus and the content of genes associated with the methyl cycle pathway (P < 0.05). This resulted in a significant increase of methionine (253.26 mg/kg) (P < 0.05) and 3-(methylthio)-1-propanal contents (383.29 μg/kg) (P < 0.05). In simulated fermentation, the content of 3-(methylthio)-1-propanal significantly increased by 2.91 folds when Saccharomyces cerevisiae was cocultured with Lactobacillus acetotolerans (P < 0.05), and the transcription of genes related to sulfur metabolism significantly increased by 33.71 folds (P < 0.05). Results indicated that low initial acidity increased the abundance of Lactobacillus, which mediates the methyl cycle pathway in the sulfur metabolism, thereby increasing the contents of methionine and volatile sulfur compounds. This work provided insight into the regulation of metabolic mechanisms of volatile sulfur compounds in baijiu fermentation.

Microbial sulfur metabolism plays crucial roles in various food and alcoholic beverage fermentations. 3-(Methylthio)-1-propanol and dimethyl disulfide are important sulfur compounds in fermented foods and alcoholic beverages. Here, we studied the dynamics of these two compounds during spontaneous Chinese liquor fermentation. The two compounds reached the maximum concentration at day 10 and the maximum production rate at day 3. Metatranscriptomic analysis at days 3 and 10 revealed a total of 354 metabolically active microorganisms.

Most known natural and industrial food fermentation processes are driven by either simple or complex communities of microorganisms. Obviously, these fermenting microbes will not only interact with the fermentable substrate but also with each other. These microbe-microbe interactions are complex but thought to be crucial for obtaining the desired product characteristics. Microbial interactions are mediated through a variety of molecular and physiological mechanisms. Examples of interaction mechanisms which have an impact on the outcome of food fermentation processes will be discussed. Finally, the technological and scientific challenges associated with the production and propagation of complex mixed starter cultures are briefly addressed. Research on the composition and functionality of complex microbial consortia is gaining momentum and will open new avenues for controlling and improving food fermentation processes, and developing new applications for mixed cultures.

Diet composition and microbiota play a crucial role in animal health and productivity. The study aimed to explore the effects of different fermentation substrates on rumen microbiota and their extracellular vesicles (EVs). Straw (fiber), corn starch (starch), and casein (protein) were used as substrates for in vitro fermentation. After 24 h of fermentation, samples were collected and subjected to 16 S rRNA gene sequencing to analyze rumen microbiota. Microbe-derived EVs were extracted and their morphology and particle size were determined. Results showed that fiber increased the diversity of rumen microorganisms, protein increased richness, and starch decreased both diversity and richness of the microbes. Rumen microbiota was dominated by Firmicutes in the protein group, Bacteroidota in the fiber group and Prevotella in the starch group. Principal co-ordinates analysis (PCoA) revealed significant differences in microbial community structure among the three groups. LEfSe analysis at the genus level identified that Prevotella, Succinivibrio, Clostridia_UCG_014 were enriched in the starch group, whereas Acidaminococcus, Muribaculaceae, Pyramidobacter were enriched in the protein group. For the fiber group, the enriched genera included F082 and Rikenellaceae_RC9_gut_group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis showed that the top ten microbial functions were mainly involved in signaling and cellular processes (K06142, K03310, K02030, K06147, K01990, K02004, K01992, K02014) and genetic information processing (K06180, K03088), with the fiber group showing better performance in these processes compared to other two groups. Additionally, the particle sizes of extracellular vesicles ranged from 20 to 400 nm, with an average particle distribution coefficients (PDI) close to 0.3 in each group, indicating uniform particle size. Overall, different fermentation substrates significantly affected the diversity of rumen microbes, without affecting the morphology and particle size of microbial EVs.

Plant-based fermentations and their microbes provide an underexplored source for novel biotechnological applications. Recent advances in DNA sequencing technologies and analyses of sequencing data highlight that a diverse array of lactic acid bacteria (LAB) frequently dominate these plant fermentations. Because of the long history of safe LAB use in fermented foods, we argue here that various novel probiotic, synbiotic and a range of other industrial applications can be produced based on new insights in the functional and genetic potential of these LAB. To aid in this quest, comparative genomics tools are increasingly available enabling a more rational design of wet-lab experiments to screen for the most relevant properties. This is also true for the exploration of useful enzymatic and (secondary) metabolic production capacities of the LAB that can be isolated from these plant-based fermentations, such as the recent discovery of a cellulase enzyme in specific Lactobacillus plantarum group members.

The understanding of microbial diversity and their metabolic activities inside the oil reservoir is not well understood. The microbial community of the oil reservoir plays diversified roles from souring to microbial enhanced oil recovery. Therefore, studying community dynamics, phylogenetic diversity and ecological roles of the community inside the reservoir is crucial. This chapter discussed different microbial processes taking place in petroleum reservoirs. The study showed the crude oil being the major electron donor inside the reservoir supporting major life forms. The major metabolic reactions taking place are nitrate and nitrite reduction, sulfur and sulfate reduction, iron reduction, fermentation, and methanogenesis. Many of the thermo-tolerant strains that are capable of exploiting numerous energy sources and electron acceptors are among the most often cultured on functional groups, which include sulfate and sulfur reducing bacteria like Desulfacinum infernum, Desulfacinum subterraneum, iron reducing, fermentative such as Thermococcus, Thermotoga, and Thermoanaerobacter species, and methanogenic microorganisms like Methanothermobacter thermautotrophicus. The stimulated growth of microbes could also enhance the oil recovery from the reservoir by 66 percent as proved in some experimental studies. The microbial growth could be increased by injection of nitrate which could also control sulfide production, or nutrients such as sugar molasses that increases fermentative microbial growth, which could improve volumetric sweep efficiency and thus oil recovery. Microbial growth also has the potential for corrosion and souring due to the presence of microbes such as Desulfovibrio¸ Clostridium etc. It could be concluded that the scope of microbial diversity is far more extensive than what is known till date.

The gut microbiota ferments dietary fibers, producing short-chain fatty acids (SCFA). Enhanced SCFA production in the distal colon has been linked to improved cardiometabolic health. However, most fibers are fermented proximally, resulting in increased protein fermentation distally, producing metabolites putatively harmful to metabolic health. This 12-week randomized, placebo-controlled trial aimed to improve metabolic health through increasing distal SCFA production while inhibiting proteolytic fermentation using a fiber supplement that increased distal SCFA production