Role of dietary fiber in the recovery of the human gut microbiome and its metabolome

Tanes, Ceylan; Bittinger, Kyle; Gao, Yuan; Friedman, Elliot S.; Nessel, Lisa; Paladhi, Unmesha Roy; Chau, Lillian; Panfen, Erika; Fischbach, Michael A.; Braun, Jonathan; Xavier, Ramnik J.; Clish, Clary B.; Li, Hongzhe; Bushman, Frederic D.; Lewis, James D.; Wu, Gary D.

doi:10.1016/j.chom.2020.12.012

Cited by 160 publications

(149 citation statements)

References 57 publications

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“…In addition, our study sampled microbes residing in the gut, while metabolites were measured directly in the circulation. The effects of microbial abundance on plasma metabolite levels are limited and hold only for certain metabolite classes 59 , which was evident in our joint metagenomic/metabolomic analysis that was skewed toward essential amino acids and their derivatives. Associations between microbes and metabolites can arise from indirect modification, for example in the case sphingolipids, which showed strong immunomodulatory effects, and are produced by host and gut eukaryotes 60 , 61 , but modified by Bacteroides 56 , 57 .…”

Section: Discussionmentioning

confidence: 93%

Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations

et al. 2021

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The human gut microbiota is increasingly recognized as an important factor in modulating innate and adaptive immunity through release of ligands and metabolites that translocate into circulation. Urbanizing African populations harbor large intestinal diversity due to a range of lifestyles, providing the necessary variation to gauge immunomodulatory factors. Here, we uncover a gradient of intestinal microbial compositions from rural through urban Tanzanian, towards European samples, manifested both in relative abundance and genomic variation observed in stool metagenomics. The rural population shows increased Bacteroidetes, led by Prevotella copri, but also presence of fungi. Measured ex vivo cytokine responses were significantly associated with 34 immunomodulatory microbes, which have a larger impact on circulating metabolites than non-significant microbes. Pathway effects on cytokines, notably TNF-α and IFN-γ, differential metabolome analysis and enzyme copy number enrichment converge on histidine and arginine metabolism as potential immunomodulatory pathways mediated by Bifidobacterium longum and Akkermansia muciniphila.

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Section: Discussionmentioning

confidence: 93%

Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations

et al. 2021

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“…We chose to focus on gut metabolites as opposed to microbial community composition as most brain-gut interactions are mediated by microbiota products (such as metabolites) rather than an intrinsic characteristic of the particular microbe itself (such as lipopolysaccharide) ( Osadchiy et al, 2019c ). Previous high-quality studies ( Wu et al, 2011 ; Tanes et al, 2021 ) have underscored the important role of dietary fiber in modulating the gut microbiota and gut-microbiota derived fecal metabolites. Although we controlled for the type of diet consumed in our analysis, we did not quantify the fiber content of our participants’ diets, which may confound our results.…”

Section: Discussionmentioning

confidence: 99%

Early life adversity predicts brain-gut alterations associated with increased stress and mood

Coley

Mayer

Osadchiy

et al. 2021

Neurobiology of Stress

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Alterations in the brain-gut system have been implicated in various disease states, but little is known about how early-life adversity (ELA) impacts development and adult health as mediated by brain-gut interactions. We hypothesize that ELA disrupts components of the brain-gut system, thereby increasing susceptibility to disordered mood. In a sample of 128 healthy adult participants, a history of ELA and current stress, depression, and anxiety were assessed using validated questionnaires. Fecal metabolites were measured using liquid chromatography tandem mass spectrometry-based untargeted metabolomic profiling. Functional brain connectivity was evaluated by magnetic resonance imaging. Sparse partial least squares-discriminant analysis, controlling for sex, body mass index, age, and diet was used to predict brain-gut alterations as a function of ELA. ELA was correlated with four gut-regulated metabolites within the glutamate pathway (5-oxoproline, malate, urate, and glutamate gamma methyl ester) and alterations in functional brain connectivity within primarily sensorimotor, salience, and central executive networks. Integrated analyses revealed significant associations between these metabolites, functional brain connectivity, and scores for perceived stress, anxiety, and depression. This study reveals a novel association between a history of ELA, alterations in the brain-gut axis, and increased vulnerability to negative mood and stress. Results from the study raise the hypothesis that select gut-regulated metabolites may contribute to the adverse effects of critical period stress on neural development via pathways related to glutamatergic excitotoxicity and oxidative stress.

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“…In this study, the abundance of Firmicutes was significantly different ( p < 0.05) between the two diet groups with 66.26% in group F and 54.96% in group G. The five microbiotas were significantly different at the genus level between the two groups, all belonging to Firmicutes phylum. Firmicutes are beneficial bacteria in the intestinal tract, which help the host intestinal tract absorb energy from food [ 21 ]. The intestinal flora of obese mice has a strong ability to release energy from food, while the intestinal Firmicutes richness of obese mice is significantly higher than that of slim mice [ 22 ].…”

Section: Discussionmentioning

confidence: 99%

Composition of Fecal Microbiota in Grazing and Feedlot Angus Beef Cattle

Zhang

Yang

et al. 2021

Animals

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This study is to investigate the difference in bovine fecal microbiota between grazing and feedlot Angus cattle. Fecal samples were collected from six Angus cattle grazed on grassland and six Angus cattle fed on a feedlot. The fecal bacterial community was analyzed by high-throughput sequencing of 16S rRNA gene. Sequencing of the V3–V4 region totally produced 1,113,170 effective tages that were computationally clustered into 775 operational taxonomic units (OTUs). These 775 OTUs were taxonomically assigned to bacterial 12 phyla, 19 classes, 25 orders, 54 families, 141 genera, and 145 species. The dominant phyla were Firmicutes and Bacteroidetes. There was similar species richness between grazing and feedlot Angus beef, while higher species diversity was observed in feedlot Angus beef. The relative abundance of Firmicutes, Cyanobacteria, Elusimicrobia and Patescibacteria was significantly different between grazing and feedlot Angus beef (p < 0.05). At a genus level, five microbiotas were significantly different between the two groups and all belonged to the Firmicutes phylum. These significant differences in microbiota composition between grazing and feedlot Angus beef may have an impact on the meat quality of Angus beef.

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Role of dietary fiber in the recovery of the human gut microbiome and its metabolome

Cited by 160 publications

References 57 publications

Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations

Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations

Early life adversity predicts brain-gut alterations associated with increased stress and mood

Composition of Fecal Microbiota in Grazing and Feedlot Angus Beef Cattle

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