Xenobiotics shape the physiology and gene expression of the active human gut microbiome

By Corinne F. Maurice, Henry J. Haiser, Peter J. Turnbaugh. Cell, 2013

786 citations recorded by the source corpus.

SUMMARY The human gut contains trillions of microorganisms that influence our health by metabolizing xenobiotics, including host-targeted drugs and antibiotics. Recent efforts have characterized the diversity of this host-associated community, but it remains unclear which microorganisms are active and what perturbations influence this activity. Here, we combine flow cytometry, 16S rRNA gene sequencing, and metatranscriptomics to demonstrate that the gut contains a distinctive set of active microorganisms, primarily Firmicutes. Short-term exposure to a panel of xenobiotics significantly affected the physiology, structure, and gene expression of this active gut microbiome. Xenobiotic-responsive genes were found across multiple bacterial phyla, encoding antibiotic resistance, drug metabolism, and stress response pathways. These results demonstrate the power of moving beyond surveys of microbial diversity to better understand metabolic activity, highlight the unintended consequences of xenobiotics, and suggest that attempts at personalized medicine should consider inter-individual variations in the active human gut microbiome.

Subfields: Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b15f114ce99fe136d6133d7fc234165db809e642

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Citations in the corpus

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Host genetic variation impacts microbiome composition across human body sites (2015, background): “In addition, intake of drugs and antibiotics can modulate the gut microbiome [16, 17].”
The gut microbiome: Relationships with disease and opportunities for therapy (2018, background): “, 2016), xenobiotics (Maurice et al., 2013), environmental toxicants (Lu et al.”
The gut microbiota: a major player in the toxicity of environmental pollutants? (2016, background): “This is of particular importance because some xenobiotics might impact the GI microbiota physiology without inducing dysbiosis: indeed, when fresh human faecal samples were incubated with antibiotics or with host-targeted drugs, all host-targeted drugs resulted in significant alterations of microbia”
Human gut microbiome: hopes, threats and promises (2018, background): “64 65 More recently, Schirmer et al profiled the gut microbiomes of more than a hundred individuals, including patients with Crohn’s disease, ulcerative colitis and non-IBD control patients and analysed both the metagenomes and the metatranscriptomes of these individuals.”
Conducting a Microbiome Study (2014, background): “Each antibiotic can affect the microbiome differently, and microbiome responses to a single antibiotic can also vary substantially between individuals (Dethlefsen et al., 2008; Dethlefsen and Relman, 2011; Maurice et al., 2013).”
Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances (2016, background): “…with different antibiotics, there was an increase in the proportion of gut microbiota cells with damaged membranes, the active populations of the microbiota changed, and genes involved in antibiotic resistance, stress response and phage induction augmented in expression (Maurice et al., 2013).”
Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease (2014, neutral): “Importantly, as was observed in other recent studies using FACS to sort fecal bacteria (Ben-Amor et al., 2005; Maurice et al., 2013; Peris-Bondia et al., 2011), sorting itself did not artificially alter microbial composition (p > 0.05, PERMANOVA).”
Diet dominates host genotype in shaping the murine gut microbiota (2014, background): “See also Figure S1 and Tables S1 and S2. overall microbial community structure corresponded to rapid shifts in the relative abundance of the two major bacterial orders in the distal gut, the Bacteroidales (phylum: Bacteroidetes) and Clostridiales (phylum: Firmicutes) (Figures 6C and 6D).”