Human Gastrointestinal Microbes Vary Throughout the Day

Abstract

BackgroundHuman health is intricately intertwined with the composition and function of the trillions of microorganisms that make up the gastrointestinal (GI) microbiota. Habitual diet patterns, rapid changes in dietary fat and fiber composition, and consumption of dietary fibers and prebiotics have all been shown to impact the GI microbiota. Intriguingly, the impact of diet on the microbiota may not only be related to what we eat, but also to when we eat. Emerging research suggests gut microbes experience diurnal rhythms, and that the health effects of eating patterns, such as time‐restricted feeding and meal frequency, may also be related to the GI microbiota.ObjectiveWe aimed to investigate the relationship between time of day and the composition and function of the gastrointestinal microbiota in healthy adults.MethodsHealthy adult male and female participants (n=29) provided up to 9 fecal samples (189 total samples) within 15 minutes of defecation over the course of a 15 week trial. Fecal DNA extracts were subjected to 16S ribosomal RNA amplicon‐based high‐throughput sequencing to assess the composition of the microbiota. Sequences were clustered into operational taxonomic units (OTUs) using the Greengenes 13‐8 reference OTU database (97% similarity). Fecal short‐chain fatty acids (SCFA), products of microbial metabolism, were measured by gas chromatography mass spectroscopy. Dietary records were kept throughout the sample collection period and analyzed using the Nutrition Data System for Research (NDSR). Correlations were performed between sample time and bacterial OTUs, and partial correlations between sample time and SCFA concentration were performed with total dietary fiber intake normalized by energy intake as the controlling variable.ResultsTime of defecation ranged from 07:30 to 22:00, median=10:40. Concentrations of acetate, butyrate, and propionate decreased over the course of the day (r=−0.35, −0.31, −0.33, respectively, p<0.0001 for all). The abundance of Clostridium spp. also decreased throughout the day (r=− 0.20, p<0.01). Conversely, Dorea (r=0.18, p=0.01), Oscillospira (r=0.36, p<0.0001), Ruminococcus (r=0.19, p=0.01) and Butyricimonas (r=0.16, p=0.03) increased over the course of the day.ConclusionsThese novel results support and expand preclinical research findings—Oscillospira and Ruminococcus, as well as members of the Lachnospiraceae family and Clostridiales order, have been shown to exhibit diurnal oscillations in rodent models. Our findings also reveal functional changes in the microbiota over the course of the day, as evidenced by reductions in SCFA concentrations with time. In summary, these results suggest that diurnal patterns are also relevant factors for assessments and interventions aimed at modulating the GI microbiota.Support or Funding InformationSupported in part by the USDA National Institute of Food and Agriculture, Hatch project ILLU‐668‐902.