昼夜节律紊乱下的肠道菌群与胆汁酸代谢：从结构失调到功能互作

The disruption of the diurnal rhythm has been recognized as a significant contributing factor to metabolic dysregulation. The important role of gut microbiota and bile acid metabolism has attracted extensive attention. However, the function of the gut microbiota-bile acid axis in regulating the diurnal rhythms of metabolic homeostasis remains largely unknown. Herein, we aimed to investigate the interplay between rhythmicity of host metabolism and gut microbiota-bile acid axis, as well as to assess the impact of obesity on them. We found that high fat diet feeding and Leptin gene deficiency (ob/ob) significantly disturbed the rhythmic patterns of insulin sensitivity and serum total cholesterol levels. The bile acid profiling unveiled a conspicuous diurnal rhythm oscillation of ursodeoxycholic acid (UDCA) in lean mice, concomitant with fluctuations in insulin sensitivity, whereas it was absent in obese mice. The aforementioned diurnal rhythm oscillations were largely desynchronized by gut microbiota depletion, suggesting the indispensable role of gut microbiota in diurnal regulation of insulin sensitivity and bile acid metabolism. Consistently, 16S rRNA sequencing revealed that UDCA-associated bacteria exhibited diurnal rhythm oscillations that paralleled the fluctuation in insulin sensitivity. Collectively, the current study provides compelling evidence regarding the association between diurnal rhythm of insulin sensitivity and gut microbiota-bile acid axis. Moreover, we have elucidated the deleterious effects of obesity on gut microbiome-bile acid metabolism in both the genetic obesity model and the diet-induced obesity model.

Circadian rhythms are biological systems that synchronize cellular circadian oscillators with the organism's daily feeding-fasting or rest-activity cycles in mammals. Circadian rhythms regulate nutrient absorption and utilization at the cellular level, and are closely related to obesity and metabolic disorders. Bile acids are important modulators that facilitate nutrient absorption and regulate energy metabolism. Here, we provide an overview of the current connections and future perspectives between the circadian clock and bile acids metabolism as well as related metabolic diseases. Feeding and fasting cycles influence bile acid pool size and composition, and bile acid signaling can respond to acute lipid and glucose utilization and mediate energy balance. Disruption of circadian rhythms, such as shift work, irregular diet, and gene mutations can contribute to altered bile acid metabolism and heighten obesity risk. High-fat diets, alcohol and gene mutations related to bile acid signaling result in desynchronized circadian rhythms. Gut microbiome also plays a role in connecting circadian rhythms with bile acids metabolism. The underlying mechanism of how circadian rhythms interact with bile acids metabolism has not been fully explored. Sustaining bile acids homeostasis based on circadian rhythms may be potential therapies to alleviate metabolic disturbance.

Fasting/feeding cycles regulate clock-lipid-bile acid (BA) metabolic homeostasis, and gut microbiota also participates in connecting circadian rhythms with BA metabolism. To investigate the cyclical nature of microbial-metabolism-host interactions, sixty male C57BL/6 mice were randomized into three feeding regimens with a chow diet: 24 h ad libitum (AC), 12 h nighttime feeding (NC) or 12 h daytime feeding (DC). Five weeks later, the mice were sacrificed at six-hour intervals over 24 hours. Daytime feeding abolished hepatic rhythmic expressions of Per1, Cry1/2 and Rev-erbα or changed the acrophase of Clock, Bmal1 and Per2, also the rhythmic expression of genes Hsl, Fas, Acc, Srebp-1c in lipid homeostasis and Cyp7a1, Cyp7b1, Cyp8b1, Lrh-1 and Shp in bile acid metabolism compared with their ad libitum and dark-fed companions. Furthermore, daytime feeding upregulated the levels of fecal primary BA, secondary BA and unconjugated BA at ZT0 and decreased their levels at ZT12. Meanwhile, daytime feeding altered the diversity of gut microbiota and microbiota compositions, with obviously higher abundance of Firmicutes and F/B ratio, and significantly lower abundance of Verrucomicrobia, as well as altered fluctuations of Akkermansia, Lactobacillus and Parabacteroides. In conclusion, shifting food intake to the rest phase caused a desynchronization in the liver between circadian rhythm and metabolism, as well as abnormal circadian variations in fecal BA profiles and gut microbiota.

The homeostasis of circadian clock linked to bile acid (BA) metabolism and gut microbiota has profound benefits in maintaining the health status of the host. The aim of this study was to investigate the prevention and regulation of apple polyphenol extract (APE) on BA metabolism and gut microbiota by means of modulation of circadian rhythms in mice. Eighty male C57BL/6 mice were randomized into four groups: 24-hour ad libitum standard chow group (AC), ad libitum HFD group (AF), restricted 12 h daytime HFD feeding group (DF), and daytime HFD feeding with APE treatment group (DP). Five weeks later, the mice were sacrificed at 6 h intervals over a 24 h period. The results showed that APE decreased body weight and induced daily rhythms of Cry1 and Rorα in the suprachiasmatic nucleus (SCN) and Clock, Cry1 and Cry2 in the ileum in daytime HFD mice. APE significantly increased the expression of hepatic FXR at ZT0 and BSEP at ZT12 and inhibited the expression of ileac FXR at ZT12, reduced levels of fecal TBAs, secondary BAs, and unconjugated BAs at ZT0. Meanwhile, APE regulated the diversity and composition of the gut microbiota, and increased the abundance of probiotics. Therefore, our work revealed that APE as a clock-regulating natural compound could modulate BA metabolism and gut microbiota and protect against circadian disruption in a clock-dependent manner.

Background Hepatic lipid metabolism regulates biliary composition and influences the formation of cholesterol gallstones. The genes Hmgcr and Cyp7a1, which encode key liver enzymes, are regulated by circadian rhythm-related transcription factors. We aimed to investigate the effect of circadian rhythm disruption on hepatic cholesterol and bile acid metabolism and the incidence of cholesterol stone formation. Methods Adult male C57BL/6J mice were fed either a lithogenic diet (LD) only during the sleep phase (time-restricted lithogenic diet feeding, TRF) or an LD ad libitum (non-time-restricted lithogenic diet feeding, nTRF) for 4 weeks. Food consumption, body mass gain, and the incidence of gallstones were assessed. Circulating metabolic parameters, lipid accumulation in the liver, the circadian expression of hepatic clock and metabolic genes, and the gut microbiota were analyzed. Results TRF caused a dysregulation of the circadian rhythm in the mice, characterized by significant differences in the circadian expression patterns of clock-related genes. In TRF mice, the circadian rhythms in the expression of genes involved in bile acid and cholesterol metabolism were disrupted, as was the circadian rhythm of the gut microbiota. These changes were associated with high biliary cholesterol content, which promoted gallstone formation in the TRF mice. Conclusion Disordered circadian rhythm is associated with abnormal hepatic bile acid and cholesterol metabolism in mice, which promotes gallstone formation.

Host circadian signaling, feeding, and the gut microbiome are tightly interconnected. Changes in the gut microbial community can affect the expression of core clock genes, but the specific metabolites and molecular mechanisms that mediate this relationship remain largely unknown. Here, we sought to identify gut microbial metabolites that impact circadian signaling. Through a phenotypic screen of a focused library of gut microbial metabolites, we identified a bile acid metabolite, lithocholic acid (LCA), as a circadian modulator. LCA lengthened the circadian period of core clock gene hPer2 transcription in a dose-responsive manner in human colonic cells. We found evidence that LCA modulates the casein kinase 1 δ/ε (CK1δ/ε)-protein phosphatase 1 (PP1) feedback loop and stabilizes core clock protein cryptochrome 2 (CRY2). Furthermore, we showed that LCA feeding alters circadian transcription in mouse distal ileum and colon. Taken together, our work identifies LCA as a molecular link between host circadian biology and the microbiome. Because bile acids are secreted in response to feeding, our work provides potential mechanistic insight into the molecular nature of the food-entrainable oscillator (FEO) by which peripheral clocks adapt to the timing of food intake. Given the association between circadian rhythm, feeding, and metabolic disease, our insights may offer an avenue for modulating host health.

ABSTRACT Circadian rhythms are prominent in nearly all living organisms and regulated by an endogenous central circadian clock that synchronizes physiological and behavioral processes to the external environment. The circadian clock is driven by the transcriptional-translational negative feedback loop that plays important role in the control of liver function and metabolism. As crucial signaling molecules, bile acids participate in regulating the metabolisms of glucose, lipids, energy, medications, and bile acids themselves. Bile acid synthesis, as well as bile acid-activated key enzymes and nuclear receptors involved in bile acid regulation, also displays distinct circadian variations. Circadian deregulation, such as the consequence of circadian clock disruption, restricted feeding and sleep disruption, can disrupt bile acid homeostasis, resulting in cholestatic and metabolic diseases. This review addresses the circadian rhythms in bile acid synthesis and transport and potential consequences of abnormal disrupted circadian rhythm of bile acid homeostasis.

… conjugated bile acids (BAs) that act in an antagonistic manner on intestinal farnesoid X … by CRD, and suggest that the gut microbiota-bile acid-FXR axis may be potential therapies. …

The gut microbiome and circadian rhythms (CRs) both exhibit unique influence on mammalian hosts and have been implicated in the context of many diseases, particularly metabolic disorders. It has become increasingly apparent that these systems also interact closely to alter host physiology and metabolism. However, the mechanisms that underlie these observations remain largely unknown. Recent findings have implicated microbially derived mediators as potential signals between the gut microbiome and host circadian clocks; two specific mediators are discussed in this review: short-chain fatty acids (SCFAs) and bile acids (BAs). Key gaps in knowledge and major challenges that remain in the circadian and microbiome fields are also discussed, including animal versus human models and the need for precise timed sample collection.

Disruptions to circadian rhythm in mice and humans have been associated with an increased risk of obesity and metabolic syndrome. The gut microbiota is known to be essential for the maintenance of circadian rhythm in the host suggesting a role for microbe-host interactions in the regulation of the peripheral circadian clock. Previous work suggested a role for gut bacterial bile salt hydrolase (BSH) activity in the regulation of host circadian gene expression. Here we demonstrate that unconjugated bile acids, known to be generated through the BSH activity of the gut microbiota, are potentially chronobiological regulators of host circadian gene expression. We utilised a synchronised Caco-2 epithelial colorectal cell model and demonstrated that unconjugated bile acids, but not the equivalent tauro-conjugated bile salts, enhance the expression levels of genes involved in circadian rhythm. In addition oral administration of mice with unconjugated bile acids significantly altered expression levels of circadian clock genes in the ileum and colon as well as the liver with significant changes to expression of hepatic regulators of circadian rhythm (including Dbp) and associated genes (Per2, Per3 and Cry2). The data demonstrate a potential mechanism for microbe-host crosstalk that significantly impacts upon host circadian gene expression.

The circadian clock and gut microbiome play integral roles in preserving metabolic homeostasis. Circadian rhythms represent an endogenous time-keeping system that regulates cell and organ functions and synchronizes physiology with external cues to establish metabolic homeostasis. A variety of functions throughout the gastrointestinal tract and liver are under circadian control, including nutrient transport, processing, and detoxification. The gut microbiota also plays an essential role in host metabolism, regulating processes such as digestion, inflammatory modulation, and bile acid metabolism. Both the circadian clock and the gut microbiota influence each other in a reciprocal fashion, as gut dysbiosis can precipitate circadian asynchrony, and vice-versa. Disruption of either system impacts homeostasis in a bidirectional manner and can contribute to metabolic dysfunction. Evidence suggests such disruptions can lead to the development of metabolic diseases, including obesity, diabetes, nonalcoholic fatty liver disease, cirrhosis, and hepatocellular carcinoma. This review will provide a basic overview of the circadian and gut microbial systems, how they are intertwined, and their impact on the liver and gastrointestinal tract and in the development of metabolic disease. Particular areas of discussion include epigenetic regulation of circadian pathways as well as a mechanistic overview of microbial dysbiosis. In addition, therapeutic targets of these systems, including dietary modifications, behavioral modifications, and microbial-directed therapies, will be explored.

Simple Summary There is a growing consensus that the gut microbiota exhibits diurnal oscillation. The rhythmicity of gut microbiota has fundamental implications for host physiology, metabolism, and health. Further, the gut microbiota rhythmicity can regulate the host’s circadian rhythm. Therefore, in this review, we aimed to highlight the rhythmic phenomenon of the gut microbiota and elucidate its fundamental roles in host physiology, metabolism, and health, and illuminate the possible interactions between the gut microbiota rhythmicity and host circadian rhythm. Insights into these questions facilitate the development of chronotherapy. Abstract Unlike the strictly hierarchical organization in the circadian clock system, the gut microbiota rhythmicity has a more complex multilayer network of all taxonomic levels of microbial taxa and their metabolites. However, it is worth noting that the functionality of the gut microbiota rhythmicity is highly dependent on the host circadian clock and host physiological status. Here, we discussed the diurnal rhythmicity of the gut microbiota; its crucial role in host physiology, health, and metabolism; and the crosstalk between the gut microbial rhythmicity and host circadian rhythm. This knowledge lays the foundation for the development of chronotherapies targeting the gut microbiota. However, the formation mechanism, its beneficial effects on the host of gut microbial rhythmicity, and the dynamic microbial–host crosstalk are not yet clear and warrant further research.

ABSTRACT Life for meta-organisms is based on a strong relationship between gut bacteria and body cells. This review summarizes to what extent the microbiota can influence host circadian rhythms via a literature review on the topic. The results show that microbiota can influence the host’s circadian gene expression through direct interactions via immunoreceptors and microbiota-derived metabolites, especially in peripheral tissues. Noteworthy metabolites that are only attributable to the microbiota are short-chain fatty acids and unconjugated bile acids. The microbiota also serves as a mediator for the interplay between the host’s diet and circadian rhythmicity. This work furthermore displays that the microbiota is subject to diurnal variations in terms of structure and function and that the host and the host’s diet influence these fluctuations. As most of these results originate in mouse models, we hope this work stimulates further research in human derived tissue to verify these conclusions.

ABSTRACT Desynchronization between the master clock in the brain, which is entrained by (day) light, and peripheral organ clocks, which are mainly entrained by food intake, may have negative effects on energy metabolism. Bile acid metabolism follows a clear day/night rhythm. We investigated whether in rats on a normal chow diet the daily rhythm of plasma bile acids and hepatic expression of bile acid metabolic genes is controlled by the light/dark cycle or the feeding/fasting rhythm. In addition, we investigated the effects of high caloric diets and time-restricted feeding on daily rhythms of plasma bile acids and hepatic genes involved in bile acid synthesis. In experiment 1 male Wistar rats were fed according to three different feeding paradigms: food was available ad libitum for 24 h (ad lib) or time-restricted for 10 h during the dark period (dark fed) or 10 h during the light period (light fed). To allow further metabolic phenotyping, we manipulated dietary macronutrient intake by providing rats with a chow diet, a free choice high-fat-high-sugar diet or a free choice high-fat (HF) diet. In experiment 2 rats were fed a normal chow diet, but food was either available in a 6-meals-a-day (6M) scheme or ad lib. During both experiments, we measured plasma bile acid levels and hepatic mRNA expression of genes involved in bile acid metabolism at eight different time points during 24 h. Time-restricted feeding enhanced the daily rhythm in plasma bile acid concentrations. Plasma bile acid concentrations are highest during fasting and dropped during the period of food intake with all diets. An HF-containing diet changed bile acid pool composition, but not the daily rhythmicity of plasma bile acid levels. Daily rhythms of hepatic Cyp7a1 and Cyp8b1 mRNA expression followed the hepatic molecular clock, whereas for Shp expression food intake was leading. Combining an HF diet with feeding in the light/inactive period annulled CYp7a1 and Cyp8b1 gene expression rhythms, whilst keeping that of Shp intact. In conclusion, plasma bile acids and key genes in bile acid biosynthesis are entrained by food intake as well as the hepatic molecular clock. Eating during the inactivity period induced changes in the plasma bile acid pool composition similar to those induced by HF feeding.

This integrated review synthesizes current evidence on the molecular interplay between the gut microbiome and circadian rhythms, emphasizing a sophisticated bidirectional communication system crucial for maintaining metabolic, immune, and neurological homeostasis. The host circadian clock orchestrates microbial composition and function through rhythmic changes in feeding-fasting cycles, hormone secretion, immune responses, and bile acid metabolism. In return, microbial metabolites, including short-chain fatty acids such as butyrate, secondary bile acids like lithocholic acid, and tryptophan derivatives, act as timing cues that influence core clock gene expression via epigenetic mechanisms, receptor-mediated signaling (GPR41/43, FXR), and neuroendocrine pathways. Disruption of this finely tuned dialogue, known as chronodisruption, often driven by modern lifestyles, predisposes individuals to a range of pathologies, including metabolic syndrome, inflammatory bowel disease (IBD), neurodegenerative disorders, and cancer. The review also evaluates promising chronotherapeutic interventions such as time-restricted eating (TRE), targeted probiotic use, and chronopharmacology, which aim to resynchronize host-microbe rhythms and restore physiological balance. Elucidating these mechanisms provides a foundational framework for developing personalized health strategies that target the gut-clock axis.

This article reviews the current evidence associating gut microbiota with factors that impact host circadian-metabolic axis, such as light/dark cycles, sleep/wake cycles, diet, and eating patterns. We examine how gut bacteria possess their own daily rhythmicity in terms of composition, their localization to intestinal niches, and functions. We review evidence that gut bacteria modulate host rhythms via microbial metabolites such as butyrate, polyphenolic derivatives, vitamins, and amines. Lifestyle stressors such as altered sleep and eating patterns that may disturb the host circadian system also influence the gut microbiome. The consequent disruptions to microbiota-mediated functions such as decreased conjugation of bile acids or increased production of hydrogen sulfide and the resultant decreased production of butyrate, in turn affect substrate oxidation and energy regulation in the host. Thus, disturbances in microbiome rhythms may at least partially contribute to an increased risk of obesity and metabolic syndrome associated with insufficient sleep and circadian misalignment. Good sleep and a healthy diet appear to be essential for maintaining gut microbial balance. Manipulating daily rhythms of gut microbial abundance and activity may therefore hold promise for a chrononutrition-based approach to consolidate host circadian rhythms and metabolic homeorhesis.

Insufficient sleep and circadian misalignment are associated with adverse metabolic health outcomes. Alterations in gut microbial diversity occur with insufficient sleep and circadian misalignment, which can lead to modifications in microbial structure and function. Changes in microbially produced and modified metabolites such as short chain fatty acids and secondary bile acids may contribute to chronic inflammation, positive energy balance and endocrine changes, and represent potential mechanisms linking insufficient sleep and circadian misalignment with metabolic dysregulation. Literature primarily from the last two years is reviewed here, examining the impact of sleep and circadian rhythms and their disruption on the gut microbiome in human and non-human models, with an emphasis on the hypothesis that the altered gut microbiome may be one pathway by which insufficient sleep and circadian misalignment dysregulate metabolism.

Background & Aims Bile acids are physiologic detergents that also activate nuclear receptors to regulate glucose and lipid homeostasis. Cholesterol 7α-hydroxylase (Cyp7a1), the rate-limiting enzyme that converts cholesterol to bile acids, is transcriptionally regulated by bile acids and circadian rhythms. Fasting, nutrients, and the circadian clock critically control hepatic bile acid and lipid homeostasis, and circadian misalignment is associated with the metabolic syndrome in humans. To delineate these interactions, we employed a sleep disruption model to induce circadian disruption and examined hepatic metabolism with respect to bile acids, lipids, and clock gene expression. Methods B6xC57 mice were maintained on chow or Western diet and were sleep disrupted for 6 hours/day for 5 days. Mice were sacrificed at 4-hour intervals over 24 hours. Hepatic metabolic genes were examined, and bile acid pool and lipid profiles were measured over 24 hours. Results Sleep disruption significantly suppressed circadian expression of core clock genes, genes involved in lipid metabolism, and key regulators of Cyp7a1 as well as Cyp7a1 expression itself. Sleep disruption abolished the peak in serum cholesterol and increased liver and serum free fatty acids. Bile acid pool size was increased while liver bile acids were decreased. Chromatin immunoprecipitation assay revealed that hepatocyte nuclear factor 4α (HNF4α) and D-site binding protein (Dbp) occupancies were suppressed at the Cyp7a1 promoter in sleep-disrupted mice. When coupled with Western diet, sleep disruption abolished liver clock rhythms and elevated free fatty acids. Conclusions Even short-term circadian disruption dramatically alters hepatic clock gene expression, bile acid metabolism, and lipid homeostasis to contribute to dyslipidemia.

Background Bile acids are potentially toxic compounds and their levels of hepatic production, uptake and export are tightly regulated by many inputs, including circadian rhythm. We tested the impact of disrupting the peripheral circadian clock on integral steps of bile acid homeostasis. Methodology/Principal Findings Both restricted feeding, which phase shifts peripheral clocks, and genetic ablation in Per1−/−/Per2−/− (PERDKO) mice disrupted normal bile acid control and resulted in hepatic cholestasis. Restricted feeding caused a dramatic, transient elevation in hepatic bile acid levels that was associated with activation of the xenobiotic receptors CAR and PXR and elevated serum aspartate aminotransferase (AST), indicative of liver damage. In the PERDKO mice, serum bile acid levels were elevated and the circadian expression of key bile acid synthesis and transport genes, including Cyp7A1 and NTCP, was lost. This was associated with blunted expression of a primary clock output, the transcription factor DBP, which transactivates the promoters of both genes. Conclusions/Significance We conclude that disruption of the circadian clock results in dysregulation of bile acid homeostasis that mimics cholestatic disease.

… the strong link between circadian rhythm disruption and aging, … bile acid to non-conjugated bile acid in stool(n = 5). K The mRNA expression levels of key enzymes in bile acid synthesis …

Background: Disturbance of circadian rhythm leads to abnormalities in bile acid (BA) and lipid metabolism, and it is of great significance to explore the relationship between them. This study explored the effects of circadian dysregulation on the rhythms of intestinal BA metabolism. Method: Period circadian clock 1/period circadian clock 2 (Per1/Per2) double gene knockout (DKO) and wild-type (WT) male C57BL/6 mice were fed with a control or high-fat diet for 16 weeks. We measure plasma parameters of mice. Pathological changes including those in liver and intestine were detected by hematoxylin and eosin (H&E) and oil O staining. Western blot was used to detect the intestinal core rhythm protein clock circadian regulator (CLOCK), nuclear receptor subfamily 1, group D, member 1 (REV-ERBα), Farnesoid X receptor (FXR), Small heterodimer partner (SHP), and Fibroblast growth factor 15 (FGF15) expressions. We analyzed the bile acid and intestinal flora profile in the mice intestine tissues by BA-targeted metabolomics detection and high-throughput sequencing. Results: Rhythmic chaos affected lipid metabolism and lipid accumulation in mice liver and intestine, and diurnal fluctuations of plasma triglycerides (TGs) were absent in normal-feeding DKO mice. The normal circadian fluctuations of the CLOCK and REV-ERBα observed in wild mice disappeared (normal diet) or were reversed (high-fat diet) in DKO mice. In WT mice intestine, total BA and conjugated BA were affected by circadian rhythm under both normal and high-fat diets, while these circadian fluctuations disappeared in DKO mice. Unconjugated BA seemed to be affected exclusively by diet (significantly increased in the high-fat group) without obvious fluctuations associated with circadian rhythm. Correlation analysis showed that the ratio of conjugated/unconjugated BA was positively correlated with the presence of Bacteroidetes and displayed a circadian rhythm. The expression levels of BA receptor pathway protein FXR, SHP, and FGF15 were affected by the ratio of conjugated/unconjugated BA. Conclusion: Bacteroidetes-related diurnal changes to intestinal ratios of conjugated/unconjugated BA have the potential to regulate diurnal fluctuations in liver BA synthesis via FXR-FGF15. The inverted intestinal circadian rhythm observed in DKO mice fed with a high-fat diet may be an important reason for their abnormal circadian plasma TG rhythms and their susceptibility to lipid metabolism disorders.  

The bidirectional interplay between sleep and metabolic homeostasis is fundamental to physiological health. While the roles of glucose and lipid metabolism in sleep regulation have been extensively characterized, bile acids (BAs), which are traditionally viewed as digestive surfactants, are emerging as critical metabolic messengers with distinct circadian rhythmicity and pleiotropic signaling functions. This review systematically elucidates the signaling network of the gut–liver–brain axis mediated by BAs through the nuclear Farnesoid X receptor and the membrane Takeda G protein‐coupled receptor 5. Accumulating evidence suggests that BAs are not only precisely regulated by the hepatic circadian clock but also modulate the central nervous system function by crossing the blood–brain barrier or via vagal afferent pathways. Specifically, recent findings highlight that aberrantly elevated BAs can infiltrate the central nervous system to disrupt the master circadian clock and modulate neurocircuitry governing arousal, thereby contributing to sleep fragmentation and circadian misalignment. Furthermore, this review discusses the potential of BA profiles as systemic biomarkers in obstructive sleep apnea, chronic insomnia, and related metabolic comorbidities. Finally, we propose that targeting BA metabolic receptors and the gut microbiota represents a promising translational strategy for the management of sleep disorders and their metabolic consequences.

Chronic disruption of rhythms (CDR) impacts sleep and can result in circadian misalignment of physiological systems, which in turn is associated with increased disease risk. Exposure to repeated or severe stressors also disturbs sleep and diurnal rhythms. Prebiotic nutrients produce favorable changes in gut microbial ecology, the gut metabolome, and reduce several negative impacts of acute severe stressor exposure, including disturbed sleep, core body temperature rhythmicity, and gut microbial dysbiosis. This study tested the hypothesis whether prebiotics can also reduce the negative impacts of CDR by facilitating light/dark realignment of sleep/wake, core body temperature, and locomotor activity; and whether prebiotic-induced changes in bacteria and bile acid profiles are associated with these effects. Male, Sprague Dawley rats were fed diets enriched in prebiotic substrates or calorically matched control chow. After 5 weeks on diet, rats were exposed to CDR (12h light/dark reversal, weekly for 8 weeks) or remained on undisturbed normal light/dark cycles (NLD). Sleep EEG, core body temperature, and locomotor activity were recorded via biotelemetry in freely moving rats. Fecal samples were collected on experimental days -33, 0 (day of onset of CDR), and 42. Taxonomic identification and relative abundances of gut microbes were measured in fecal samples using 16S rRNA gene sequencing and shotgun metagenomics. Fecal primary, bacterially-modified secondary, and conjugated bile acids were measured using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Prebiotic diet produced rapid and stable increases in the relative abundances of Parabacteroides distasonis and Ruminiclostridium 5. Shotgun metagenomics analyses confirmed reliable increases in relative abundances of Parabacteroides distasonis and Clostridium leptum, a member of the Ruminiclostridium genus. Prebiotic diet also modified fecal bile acid profiles; and based on correlational and step-wise regression analyses, Parabacteroides distasonis and Ruminiclostridium 5 were positively associated with each other and negatively associated with secondary and conjugated bile acids. Prebiotic diet, but not CDR, impacted beta diversity. Measures of alpha diversity evenness were decreased by CDR and prebiotic diet prevented that effect. Rats exposed to CDR while eating prebiotic, compared to control diet, more quickly realigned NREM sleep and core body temperature (ClockLab) diurnal rhythms to the altered light/dark cycle. Finally, both cholic acid and Ruminiclostridium 5 prior to CDR were associated with time to realign CBT rhythms to the new light/dark cycle after CDR; whereas both Ruminiclostridium 5 and taurocholic acid prior to CDR were associated with NREM sleep recovery after CDR. These results suggest that ingestion of prebiotic substrates is an effective strategy to increase the relative abundance of health promoting microbes, alter the fecal bile acid profile, and facilitate the recovery and realignment of sleep and diurnal rhythms after circadian disruption.

… regulating bile acid metabolism that impacts circadian clock genes. Additionally, gut microbes … position the gut microbiota as a key regulator of host circadian rhythms and sleep patterns, …

Diurnal (i.e., 24-hour) oscillations of the gut microbiome have been described in various species including mice and humans. However, the driving force behind these rhythms remains less clear. In this study, we differentiate between endogenous and exogenous time cues driving microbial rhythms. Our results demonstrate that fecal microbial oscillations are maintained in mice kept in the absence of light, supporting a role of the host’s circadian system rather than representing a diurnal response to environmental changes. Intestinal epithelial cell-specific ablation of the core clock gene Bmal1 disrupts rhythmicity of microbiota. Targeted metabolomics functionally link intestinal clock-controlled bacteria to microbial-derived products, in particular branched-chain fatty acids and secondary bile acids. Microbiota transfer from intestinal clock-deficient mice into germ-free mice altered intestinal gene expression, enhanced lymphoid organ weights and suppressed immune cell recruitment. These results highlight the importance of functional intestinal clocks for microbiota composition and function, which is required to balance the host’s gastrointestinal homeostasis. Here, Heddes et al. demonstrate a major role for the intestinal circadian clock in driving microbiome dynamics. Microbiota transfer from intestinal clock-deficient mice promotes altered intestinal phenotypes, highlighting the importance of functional intestinal clocks for gastrointestinal homeostasis of the host.

Cholesterol and bile acid (BA) homeostasis plays a central role in systemic metabolism. Accumulating evidence suggests a key regulatory function of the circadian clock, our biological timer, in lipid metabolism, particularly cholesterol and bile acid flux. Previously, we showed that Nobiletin (NOB), a natural compound targeting the ROR (Retinoic acid receptor-related orphan receptor) nuclear receptors in the circadian oscillator, strongly protects lipid homeostasis, including normal serum cholesterol levels in high-fat (HF) fed mice at both young and old ages. In this study, we further examined the role of NOB in cholesterol metabolism in HF-fed aged mice, and found that NOB lowered the serum LDL/VLDL cholesterol levels and consequently the LDL/HDL ratio. BA levels in the serum were markedly reduced in the HF.NOB group, and examination of additional hepatic markers further indicate a protective role of NOB in the liver. At the molecular level, whereas HF feeding downregulated hepatic expression of several ROR target genes involved in bile acid synthesis, NOB treatment (HF.NOB) was able to rescue it. In accordance, fecal BA excretion was enhanced by NOB, and microbial 16S sequencing revealed alteration of several taxa known to be involved in secondary BA production in the gut. Together, these results demonstrate concerted effects of the clock-modulating compound NOB in cholesterol and BA metabolism, suggesting pharmacological manipulation of the clock as a novel therapeutic strategy against metabolic disorders and age-related decline.

Bile acids are trans-genomic molecules arising from the concerted metabolism of the human host and the intestinal microbiota and are important for digestion, energy homeostasis and metabolic regulation. While diurnal variation has been demonstrated in the enterohepatic circulation and the gut microbiota, existing human data are poorly resolved, and the influence of the host circadian system has not been determined. Using entrained laboratory protocols, we demonstrate robust daily rhythms in the circulating bile acid pool in healthy male participants. We identify temporal relationships between bile acids and plasma lipids and show that these relationships are lost following sleep deprivation. We also highlight that bile acid rhythmicity is predominantly lost when environmental timing cues are held constant. Here we show that the environment is a stronger determinant of these temporal dynamics than the intrinsic circadian system of the host. This has significance for the intimate relationship between circadian timing and metabolism. Bile acids are important for digestion, energy homeostasis and metabolic regulation. Here the authors show daily rhythms in the circulating bile acid pool which are lost when environmental timing cues are held constant indicating that environment is a stronger determinant of these dynamics than the circadian system.

… Together, these findings suggest that altered microbial composition under circadian–disrupted … Complex interaction between circadian rhythm and diet on bile acid homeostasis in male …

People with obstructive sleep apnea, identified by loud snoring and breathing irregularly while sleeping, are at a higher risk of high blood pressure, type 2 diabetes, cardiac arrhythmias, stroke, and sudden cardiac death. We wanted to understand whether the gut microbiome changes induced by obstructive sleep apnea could potentially explain some of these medical problems. ABSTRACT Obstructive sleep apnea (OSA), characterized by intermittent hypoxia and hypercapnia (IHC), affects the composition of the gut microbiome and metabolome. The gut microbiome has diurnal oscillations that play a crucial role in regulating circadian and overall metabolic homeostasis. Thus, we hypothesized that IHC adversely alters the gut luminal dynamics of key microbial families and metabolites. The objective of this study was to determine the diurnal dynamics of the fecal microbiome and metabolome of Apoe−/− mice after a week of IHC exposure. Individually housed, 10-week-old Apoe−/− mice on an atherogenic diet were split into two groups. One group was exposed to daily IHC conditions for 10 h (Zeitgeber time 2 [ZT2] to ZT12), while the other was maintained in room air. Six days after the initiation of the IHC conditions, fecal samples were collected every 4 h for 24 h (6 time points). We performed 16S rRNA gene amplicon sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in the microbiome and metabolome. IHC induced global changes in the cyclical dynamics of the gut microbiome and metabolome. Ruminococcaceae, Lachnospiraceae, S24-7, and Verrucomicrobiaceae had the greatest shifts in their diurnal oscillations. In the metabolome, bile acids, glycerolipids (phosphocholines and phosphoethanolamines), and acylcarnitines were greatly affected. Multi-omic analysis of these results demonstrated that Ruminococcaceae and tauro-β-muricholic acid (TβMCA) cooccur and are associated with IHC conditions and that Coriobacteriaceae and chenodeoxycholic acid (CDCA) cooccur and are associated with control conditions. IHC significantly change the diurnal dynamics of the fecal microbiome and metabolome, increasing members and metabolites that are proinflammatory and proatherogenic while decreasing protective ones. IMPORTANCE People with obstructive sleep apnea are at a higher risk of high blood pressure, type 2 diabetes, cardiac arrhythmias, stroke, and sudden cardiac death. We wanted to understand whether the gut microbiome changes induced by obstructive sleep apnea could potentially explain some of these medical problems. By collecting stool from a mouse model of this disease at multiple time points during the day, we studied how obstructive sleep apnea changed the day-night patterns of microbes and metabolites of the gut. Since the oscillations of the gut microbiome play a crucial role in regulating metabolism, changes in these oscillations can explain why these patients can develop so many metabolic problems. We found changes in microbial families and metabolites that regulate many metabolic pathways contributing to the increased risk for heart disease seen in patients with obstructive sleep apnea.

Background The interaction between the host and microbiota is influenced by host circadian rhythm. However, it is unknown what the changes of gut microbiota and metabolites. Methods We conducted a cross-sectional study (n=72) in which participants’ fecal DNA was detected by macrogenomic sequencing analysis. The feces, urine and blood were analyzed by widely targeted metabolomics analysis. Results Pearson correlation analysis showed that most of the clinical symptoms of people with circadian rhythm disorders were moderately positively correlated with gastrointestinal symptoms. By distilling the results of multinomic analysis, we reported a variety of different species (19 species in the gut) and metabolites. In our results, the correlation of multiomics is mostly concentrated in Lachnospiraceae bacterium and Streptococcus mitis oralis pneumoniae. Bile acid-related metabolites are the most significant metabolites associated with these species. Discussion Our study demonstrates the severity of clinical manifestations caused by circadian rhythm disorder is closely related to microbiota and metabolism. In the future, personalized interventions targeting specific microbial species or metabolites may help alleviate the physical and psychological discomfort induced by circadian rhythm disturbances.

The accelerated pace of life at present time has resulted in tremendous alterations in living patterns. Changes in diet and eating patterns, in particular, coupled with irregular light–dark (LD) cycles will further induce circadian misalignment and lead to disease. Emerging data has highlighted the regulatory effects of diet and eating patterns on the host‐microbe interactions with the circadian clock (CC), immunity, and metabolism. Herein, we studied how LD cycles regulate the homeostatic crosstalk among the gut microbiome (GM), hypothalamic and hepatic CC oscillations, and immunity and metabolism using multiomics approaches. Our data demonstrated that central CC oscillations lost rhythmicity under irregular LD cycles, but LD cycles had minimal effects on diurnal expression of peripheral CC genes in the liver including Bmal1. We further demonstrated that the GM could regulate hepatic circadian rhythms under irregular LD cycles, the candidate bacteria including Limosilactobacillus, Actinomyces, Veillonella, Prevotella, Campylobacter, Faecalibacterium, Kingella, and Clostridia vadinBB60 et al. A comparative transcriptomic study of innate immune genes indicated that different LD cycles had varying effects on immune functions, while irregular LD cycles had greater impacts on hepatic innate immune functions than those in the hypothalamus. Extreme LD cycle alterations (LD0/24 and LD24/0) had worse impacts than slight alterations (LD8/16 and LD16/8), and led to gut dysbiosis in mice receiving antibiotics. Metabolome data also demonstrated that hepatic tryptophan metabolism mediated the homeostatic crosstalk among GM‐liver–brain axis in response to different LD cycles. These research findings highlighted that GM could regulate immune and metabolic disorders induced by circadian dysregulation. Further, the data provided potential targets for developing probiotics for individuals with circadian disruption such as shift workers.

AIMS Over the past years, interest in chrono-nutrition has grown enormously as the fundamental role of circadian rhythms in regulating most physiological and metabolic processes has become clearer. Recently, the influence of circadian rhythms on the gut microbiota (GM) composition has also emerged, as more than half of the total microbial composition fluctuates rhythmically throughout the day. At the same time, other studies have observed that the GM itself synchronises the host's circadian biological clock through signals of a different nature. Therefore, it has been hypothesised that there is a two-way communication between the circadian rhythms of the host and the GM, but researchers have only just begun to identify some of its action mechanisms. The manuscript aim is, therefore, to gather and combine the latest evidence in the field of chrono-nutrition with the more recent research on the GM, in order to investigate their relationship and their potential impact on human health. DATA SYNTHESIS Considering current evidence, a desynchronization of circadian rhythms is closely associated with an alteration in the abundance and functionality of the gut microbiota with consequent deleterious effects on health, such as increased risk of numerous pathologies, including cardiovascular disease, cancer, irritable bowel disease, and depression. A key role in maintaining the balance between circadian rhythms and GM seems to be attributed to meal-timing and diet quality, as well as to certain microbial metabolites, in particular short-chain fatty acids. CONCLUSIONS Future studies are needed to decipher the link between the circadian rhythms and specific microbial patterns in relation to different disease frameworks.

… genes, Per1 and Per2, was further shown to abrogate compositional, functional, biogeographical and metabolomic fluctuations of the gut microbiome in mice 31,34 . The influence of …

Our hypothesis is that diabetes leads to loss of diurnal oscillatory rhythms in gut microbiota altering circulating metabolites. We performed an observational study where we compared diurnal changes of the gut microbiota with temporal changes of plasma metabolites. Metadata analysis from bacterial DNA from fecal pellets collected from 10-month old control (db/m) and type 2 diabetic (db/db) mice every 4 h for a 24-h period was used for prediction analysis. Blood plasma was collected at a day and night time points and was used for untargeted global metabolomic analysis. Feeding and activity behaviors were recorded. Our results show that while diabetic mice exhibited feeding and activity behavior similar to control mice, they exhibited a loss of diurnal oscillations in bacteria of the genus Akkermansia, Bifidobacterium, Allobaculum, Oscillospira and a phase shift in the oscillations of g.Prevotella, proteobacteria, and actinobacteria. Analysis of the circulating metabolites showed alterations in the diurnal pattern of metabolic pathways where bacteria have been implicated, such as the histidine, betaine, and methionine/cysteine pathway, mitochondrial function and the urea cycle. Functional analysis of the differential microbes revealed that during the day, when mice are asleep, the microbes of diabetic mice were enriched in processing carbon and pyruvate metabolic pathways instead of xenobiotic degradation as was observed for control mice. Altogether, our study suggests that diabetes led to loss of rhythmic oscillations of many gut microbiota with possible implications for temporal regulation of host metabolic pathways.

The molecular circadian clock and symbiotic host-microbe relationships both evolved as mechanisms that enhance metabolic responses to environmental challenges. The gut microbiome benefits the host by breaking down diet-derived nutrients indigestible by the host and generating microbiota-derived metabolites that support host metabolism. Similarly, cellular circadian clocks optimize organismal physiology to the environment by influencing the timing and coordination of metabolic processes. Host-microbe interactions are influenced by dietary quality and timing, as well as daily light/dark cycles that entrain circadian rhythms in the host. Together, the gut microbiome and the molecular circadian clock play a coordinated role in neural processing, metabolism, adipogenesis, inflammation, and disease initiation and progression. This review examines the bidirectional interactions between the circadian clock, gut microbiota, and host metabolic systems and their effects on obesity and energy homeostasis. Directions for future research and the development of therapies that leverage these systems to address metabolic disease are highlighted.

Bile acid synthesis is the most significant pathway for catabolism of cholesterol and for maintaining whole body cholesterol homeostasis. Bile acids are physiological detergents that absorb, distribute, metabolize and excrete nutrients, drugs and xenobiotics. Bile acids also are signal molecules and metabolic integrators that activate nuclear farnesoid X receptor (FXR) and membrane Takeda G protein-coupled receptor 5 (TGR5, aka G protein-coupled bile acid receptor-1) to regulate glucose, lipid and energy metabolism. The gut-to-liver axis plays a critical role in the transformation of primary bile acids to secondary bile acids and in the regulation of bile acid synthesis to maintain composition within the bile acid pool and metabolic homeostasis to prevent hyperglycemia, dyslipidemia, obesity and diabetes. High fat and high calorie diets, dysbiosis, alcohol, drugs and disruption of sleep and circadian rhythms cause metabolic diseases including alcoholic and non-alcoholic fatty liver diseases, obesity, diabetes, and cardiovascular disease. Bile acid-based drugs targeting bile acid receptors are being developed for the treatment of metabolic diseases of the liver.

… of the nuclear receptors FXR and TGR5. Expression of … Here we show that acute circadian disruption (simulating jet-… In summary, FXR may play an important role in protecting the …

Circadian misalignment induced by a high-fat diet (HFD) increases the risk of metabolic diseases. Methionine restriction (MR) is known to have the potential of alleviating obesity by improving insulin sensitivity. However, the role of the circadian clock in mediating the effects of MR on obesity-related metabolic disorders remains unclear. Ten-week-old male C57BL/6J mice were fed with a low-fat diet (LFD) or a HFD for 4 wk, followed with a full diet (0.86 % methionine, w/w) or a methionine-restricted diet (0.17 % methionine, w/w) for 8 wk. Our results showed that MR attenuated insulin resistance triggered by HFD, especially at ZT12. Moreover, MR led to a time-specific enhancement of the expression of FGF21 and activated the AMPK/PGC-1α signaling. Notably, MR upregulated the cyclical levels of cholic acid (CA) and chenodeoxycholic acid (CDCA), and downregulated the cyclical level of deoxycholic acid (DCA) in the dark phase. MR restored the HFD-disrupted cyclical fluctuations of lipidolysis genes and BAs synthetic genes and improved the circulating lipid profile. Also, MR improved the expressions of clock-controlled genes (CCGs) in the liver and the brown adipose tissue throughout one day. In conclusion, MR exhibited the lipid-lowering effects on HFD-induced obesity and restored the diurnal metabolism of lipids and BAs, which could be partly explained by improving the expression of CCGs. These findings suggested that MR could be a potential nutritional intervention for attenuating obesity-induced metabolic misalignment.

The gut microbiota is strongly shaped by a high-fat diet, and obese humans and animals are characterized by low gut microbial diversity and impaired gut microbiota compositions. Comprehensive data on mammalian gut metagenomes shows gut microbiota exhibit circadian rhythms, which is disturbed by a high-fat diet. On the other hand, melatonin is a natural and ubiquitous molecule showing multiple mechanisms of regulating the circadian clock and lipid metabolism, while the role of melatonin in the regulation of the diurnal patterns of gut microbial structure and function in obese animals is not yet known. This study delineates an intricate picture of melatonin-gut microbiota circadian rhythms and may provide insight for obesity intervention. ABSTRACT Melatonin, a circadian hormone, has been reported to improve host lipid metabolism by reprogramming the gut microbiota, which also exhibits rhythmicity in a light/dark cycle. However, the effect of the administration of exogenous melatonin on the diurnal variation in the gut microbiota in mice fed a high-fat diet (HFD) is unclear. Here, we further confirmed the antiobesogenic effect of melatonin on mice fed an HFD for 2 weeks. Samples were collected every 4 h within a 24-h period, and diurnal rhythms of clock gene expression (Clock, Cry1, Cry2, Per1, and Per2) and serum lipid indexes varied with diurnal time. Notably, Clock and triglycerides (TG) showed a marked rhythm in the control in melatonin-treated mice but not in the HFD-fed mice. The rhythmicity of these parameters was similar between the control and melatonin-treated HFD-fed mice compared with that in the HFD group, indicating an improvement caused by melatonin in the diurnal clock of host metabolism in HFD-fed mice. Moreover, 16S rRNA gene sequencing showed that most microbes exhibited daily rhythmicity, and the trends were different for different groups and at different time points. We also identified several specific microbes that correlated with the circadian clock genes and serum lipid indexes, which might indicate the potential mechanism of action of melatonin in HFD-fed mice. In addition, effects of melatonin exposure during daytime or nighttime were compared, but a nonsignificant difference was noticed in response to HFD-induced lipid dysmetabolism. Interestingly, the responses of microbiota-transplanted mice to HFD feeding also varied at different transplantation times (8:00 and 16:00) and with different microbiota donors. In summary, the daily oscillations in the expression of circadian clock genes, serum lipid indexes, and the gut microbiota appeared to be driven by short-term feeding of an HFD, while administration of exogenous melatonin improved the composition and diurnal rhythmicity of some specific gut microbiota in HFD-fed mice. IMPORTANCE The gut microbiota is strongly shaped by a high-fat diet, and obese humans and animals are characterized by low gut microbial diversity and impaired gut microbiota compositions. Comprehensive data on mammalian gut metagenomes shows gut microbiota exhibit circadian rhythms, which is disturbed by a high-fat diet. On the other hand, melatonin is a natural and ubiquitous molecule showing multiple mechanisms of regulating the circadian clock and lipid metabolism, while the role of melatonin in the regulation of the diurnal patterns of gut microbial structure and function in obese animals is not yet known. This study delineates an intricate picture of melatonin-gut microbiota circadian rhythms and may provide insight for obesity intervention.

The prevalence of gestational obesity has reached epidemic proportions. Evidence supported that the interactions between the gut microbiota and circadian clocks far reached, affecting host metabolism. Our study aimed to investigate the effect of a high-fat diet (HF) on the hepatic and adipose circadian rhythms in gestational mice and to explore the role of gut microbiota-derived short-chain fatty acids (SCFAs) in mediating the effects. C57BL/6 female mice were randomly fed a standard chow diet (Ctr) or HF prior to and during pregnancy. Samples were collected every 4 h over 24 h (six time points), and 16S rRNA and metabonomics were carried out. Rhythmic patterns were identified and compared using CircaCompare. The results showed that the HF before and during pregnancy significantly induced obesity and worsen glucose tolerance, insulin sensitivity, and lipid metabolism in the gestational mice. Furthermore, the HF significantly disrupted the rhythmic pattern of hepatic and adipose circadian clock genes and downstream metabolic genes. Importantly, our results revealed that the HF altered the diurnal rhythm of the gut microbiota in a diverse manner, which was assessed across three categories: phase shift, loss rhythmicity, and gained rhythmicity. We report here, for the first time, a parallel alteration of the rhythmic phase of butyric acid and butyrate-producing Clostridiaceae_1, which was confirmed by a positive correlation between them. Overall, our research emphasized the importance of the rhythmicity of gut microbiota-derived SCFAs in mediating circadian disruption in response to the HF in gestational mice, which may provide novel insights into the prevention and treatment of gestational obesity.

Several epidemiological studies suggest a correlation between eating time and obesity. Night eating syndrome characterized by a time-delayed eating pattern is positively associated with obesity in humans as well as in experimental animals. Here, we show that oil intake at night significantly makes more fat than that at day in wild-type mice, and circadian Period 1 (Per1) contributes to this day–night difference. Per1-knockout mice are protected from high-fat diet–induced obesity, which is accompanied by a reduction in the size of the bile acid pool, and the oral administration of bile acids restores fat absorption and accumulation. We identify that PER1 directly binds to the major hepatic enzymes involved in bile acid synthesis such as cholesterol 7alpha-hydroxylase and sterol 12alpha-hydroxylase. A biosynthesis rhythm of bile acids is accompanied by the activity and instability of bile acid synthases with PER1/PKA-mediated phosphorylation pathways. Both fasting and high fat stress enhance Per1 expression, increasing the fat absorption and accumulation. Our findings reveal that Per1 is an energy regulator and controls daily fat absorption and accumulation. Circadian Per1 controls daily fat absorption and accumulation, suggesting Per1 is a potential candidate of a key regulator in stress response and the relevant obesity risk.

The intestinal microbiota undergoes diurnal compositional and functional oscillations within a day, which affect the metabolic homeostasis of the host and exacerbate the occurrence of obesity. TB has the effect of reducing body weight and lipid accumulation, but the mechanism of improving obesity caused by a high-fat diet based on the circadian rhythm of intestinal microorganisms has not been clarified. In this study, we used multi-omics and imaging approaches to investigate the mechanism of TB in alleviating obesity in mice based on the circadian rhythm of gut microbiota. The results showed that TB could significantly regulate the levels and rhythmic expression of serum lipid indicators (TG, TC, LDL) and serum hormones (MT, FT3, LEP, CORT). The number of intestinal microbiota colonizing the colonic epithelium underwent daily fluctuations. TB remodeled the rhythmic oscillation of gut microbes (i.e., Lachnospiraceae_NK4A136_group, Alistipes, etc.), including the number, composition, abundance and rhythmic expression of the biogeographic localization of microbes. TB notably reduced the levels of 16 bile acids (TCA, THDCA, TCDA, GHDCA, T-α-MCA, etc.) and restored the balance of bile acid metabolism. It was found that TB may mitigate high-fat diet-induced obesity in mice by reshaping the circadian rhythm of the gut microbiome and regulating bile acid metabolism.

Our previous studies have found that fish oil rich in ω-3 polyunsaturated fatty acids (ω-3 PUFA) protects against non-alcoholic fatty liver disease (NAFLD) in mice. This study was aimed to explore the effects of fish oil on high fat diet (HFD)-induced circadian bile composition chaos. Male C57BL/6 mice were randomly divided into three groups, a control group (CON), a HFD group and a fish oil (FO) group, which were fed a normal chow diet, a HFD, and a HFD supplemented with FO, respectively for 12 weeks. At the end of the experiment, liver tissue, blood and bile samples were processed at 12-h intervals with the first one at zeitgeber time 0 (ZT0) and the second at zeitgeber time 12 (ZT12). Metabolites in bile were determined using UPLC-QTOF-MS, screened using multivariate statistical analysis, and analyzed using KEGG database and Metaboanalyst. The expression levels of key proteins in bile acid metabolism were examined using western blot. Results of biochemical analysis and H&E staining illustrated that feeding of HFD induced NAFLD, which was ameliorated in FO group. The bile content of each group at ZT0 (CON, HFD, or FO group) was respectively higher than that at ZT12 (P<.05). The metabolic pathway analysis of differential metabolites showed that these differences were correlated with amino acid metabolism, fatty acid biosynthesis and primary bile acid synthesis at ZT0. FO supplement could modify bile composition, which was related to the influence of its ω-3 PUFA on liver metabolism. ω-3 PUFA may also regulate the circadian rhythm of bile metabolism.

BACKGROUND Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by circadian rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Circadian rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems. RESULTS Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes-including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1-that are regulated by the hepatic circadian clock and modulate metabolites via the gut-liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism. DISCUSSION Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the circadian rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut-liver axis-a key mechanism in hyperlipidemia pathogenesis. CONCLUSIONS This study identifies critical temporal windows and core microbial taxa involved in microbiota-metabolite-gene crosstalk via the gut-liver axis, offering a theoretical foundation for circadian rhythm-targeted interventions in metabolic diseases.

Simple Summary Circadian rhythms serve as the body’s internal metronome, driving responses to environmental cues over a 24-h period. Essential to nearly all life forms, the core circadian clock gene network drives physiological outputs associated with metabolic and immune responses. Modern-day disruptions to host circadian rhythms, such as shift work and jet lag, result in aberrant metabolic responses and development of complex diseases, including obesity and Type 2 Diabetes. These complex diseases are also impacted by interactions between gut microbes and the host immune system, driving a chronic low-grade inflammatory response. Gut microbes exhibit circadian dynamics that are closely tied to host circadian networks and disrupting microbial rhythmicity contributes to metabolic diseases. The underlying mediators that drive communication between host metabolism, the immune system, gut microbes, and circadian networks remain unknown, particularly in humans. Here, we explore the current state of knowledge regarding the transkingdom control of circadian networks and discuss gaps and challenges to overcome to push the field forward from the preclinical to clinical setting. Abstract Circadian rhythms are essential for nearly all life forms, mediated by a core molecular gene network that drives downstream molecular processes involved in immune function and metabolic regulation. These biological rhythms serve as the body’s metronome in response to the 24-h light:dark cycle and other timed stimuli. Disrupted circadian rhythms due to drastic lifestyle and environmental shifts appear to contribute to the pathogenesis of metabolic diseases, although the mechanisms remain elusive. Gut microbiota membership and function are also key mediators of metabolism and are highly sensitive to environmental perturbations. Recent evidence suggests rhythmicity of gut microbes is essential for host metabolic health. The key molecular mediators that transmit rhythmic signals between microbes and host metabolic networks remain unclear, but studies suggest the host immune system may serve as a conduit between these two systems, providing homeostatic signals to maintain overall metabolic health. Despite this knowledge, the precise mechanism and communication modalities that drive these rhythms remain unclear, especially in humans. Here, we review the current literature examining circadian dynamics of gut microbes, the immune system, and metabolism in the context of metabolic dysregulation and provide insights into gaps and challenges that remain.

Metabolic dysfunction-associated fatty liver disease (MASLD), previously known as non-alcoholic fatty liver disease (NAFLD), has become the most common chronic liver disease worldwide. Although excessive lipid accumulation, insulin resistance, and chronic low-grade inflammation are recognized as the main pathophysiological drivers, an increasing body of research indicates that the relationship between circadian rhythms, gut microbiota, and liver metabolism is far more complex than previously imagined, forming a systemic regulatory network. Disruption of circadian rhythms can affect the temporal coordination of metabolic pathways in the liver and other surrounding tissues. At the same time, the gut microbiota itself also exhibits circadian rhythm variations. The dysregulation of these rhythms, leading to microbial imbalance, intestinal permeability defects, and imbalances in microbial metabolites, can exacerbate lipid deposition and inflammatory responses in the liver. Research shows that important microorganisms can produce short-chain fatty acids, regulate bile acid balance, and enhance intestinal barrier function, creating a synergistic effect with the host's circadian rhythms. Conversely, during circadian disruption, the proliferation of harmful symbionts can exacerbate the entry of lipopolysaccharides into the bloodstream, oxidative stress, and the development of steatohepatitis. This relationship among the three establishes the ' circadian rhythm-gut microbiota-liver axis' as a new model for understanding the mechanisms underlying MASLD and for developing temporal therapies and microbiome interventions. This review systematically explores how circadian rhythms regulate the relationship between the gut microbial ecology and liver metabolism, focusing on the microbial species closely related to the interaction between circadian rhythms and MASLD. It also introduces emerging therapeutic strategies, including time-restricted feeding, circadian probiotics, postbiotics supplementation, and circadian rhythm drugs. These findings collectively suggest that targeting the temporal dimension of the interactions between the host and microbiota holds clinical potential for the prevention and treatment of MASLD.

… peripheral circadian rhythm, in addition to cuing bile acid release … Additionally, prior metagenomic and metatranscriptomic … different bile acid metabolites fluctuate with different …