Biology subjects

Turnbaugh, P. J.

Publications and source records attributed to Turnbaugh, P. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters

Bacteriophages are a promising tool for microbiome editing, yet their development has been constrained by limited insights into bacteriophage-host interactions within their shared mammalian body habitat. We isolated a lytic phage {Phi}KL11 that efficiently targets a disease-associated member of the human gut microbiota, Eggerthella lenta, during in vitro growth. However, {Phi}KL11 selects for a pre-existing and reversible bacteriophage-resistant sub-population in mice. Long-read sequencing revealed a massive genomic inversion event, representing >50% of the E. lenta genome, enriched in response to bacteriophage infection. Transcriptomics linked this inversion to the altered expression of three capsular polysaccharide synthesis (CPS) gene clusters and transmission electron microscopy confirmed differential capsule production. Finally, we show that {Phi}KL11 has a broad host range attributable to CPS and other strain-variable genes. These findings suggest a previously unrecognized strategy for phage evasion in the gut, involving megabase-scale genomic inversions and reversible capsule variation driving phage resistance.

microbiology↗

bioRxiv2026

Inhibitors of gut bacterial L-dopa decarboxylation with reduced susceptibility to host metabolism

Microorganisms in the human gut influence the efficacy and metabolism of host-targeted small molecule therapeutics, including the frontline Parkinson's disease drug levodopa (L-dopa). Previous work has identified a mechanism-based inhibitor of gut bacterial decarboxylases that degrade L-dopa, -fluoromethyltyrosine (AFMT). However, early experiments with AFMT in rodent models suggested undesirable in vivo metabolism by host tyrosine hydroxylase, producing -fluoromethyldopa, a metabolite likely to worsen Parkinson's phenotypes and prevent application as an L-dopa co-treatment. Here, we demonstrate oxidation of AFMT to -fluoromethyldopa in vitro by recombinant human tyrosine hydroxylase. We then develop AFMT analogs that retain activity against bacterial decarboxylases but have reduced susceptibility to host hydroxylation. Suitable arenes for inhibitor design were identified using assays with commercially available noncanonical amino acids, which revealed aryl difluorination as a promising modification. Difluoroaryl AFMT derivatives are less prone to degradation by tyrosine hydroxylase in vitro yet still inhibit L-dopa metabolism by bacterial decarboxylases. This work exemplifies how substrate reactivity can streamline design of mechanism-based enzyme inhibitors, as well as how constraints posed by the host can be incorporated during development of microbiome-targeted therapeutics. The compounds reported here are promising starting points for future studies in animal models and further exploration of gut bacterial effects on L-dopa treatment efficacy.

microbiology↗

bioRxiv2026

A widespread gut bacterial lineage distinguished by redox metabolism and phage defense

Genomic variation within gut microbial species can have consequences for host health and disease. However, for low abundance species, these variations can be difficult to capture by both culture-dependent and -independent approaches. Here, we focus on the prevalent but low abundance gut Actinomycetota Eggerthella lenta. We developed a selective media for sensitive and specific isolation of E. lenta from human stool. Genomes from 87 new E. lenta isolates were combined with prior high-quality assemblies, shedding light on within-species functional diversity. Phylogenetic analysis revealed a broadly distributed subclade, which we refer to as E. lenta Group B. This lineage was differentiated by its metabolic potential and bacteriophage defense, though mobile elements were shared broadly across the species. Notably, Group B was positively associated with intestinal inflammation in subjects with inflammatory bowel disease. Overall, these results emphasize the importance of bacterial population structure in host-microbiome interactions and provide a framework to study low-abundance gut taxa. HIGHLIGHTSO_LISelective media enables E. lenta isolation and reveals high prevalence in humans C_LIO_LIDiscovery of a distinctive lineage within E. lenta undergoing genome reduction C_LIO_LIE. lenta Group B has altered metabolism, phage defense, and disease associations C_LIO_LIA widespread conjugative plasmid could enable improved genetics C_LI

microbiology↗

bioRxiv2026

Multi-cohort Analysis Reveals Microbiome Signatures Associated with Drug Response in New-Onset Rheumatoid Arthritis

The human gut microbiome influences treatment outcomes, but whether microbiome signatures of drug response generalize across cohorts remains unclear. Here, we perform a multi-cohort analysis (3 cohorts, N=100 patients) to determine whether cross-cohort microbial signatures are associated with methotrexate (MTX) response in new-onset rheumatoid arthritis (RA) patients. Pre-treatment gut microbiome community structure and function differed by future MTX response status, with MTX-nonresponders (MTX-NR) showing Bacteroides caccae depletion and Ruminococcus bromii enrichment. Multiple microbial functions were depleted in MTX-NR, including nucleotide metabolism, one-carbon pool by folate, and histidine metabolism. Notably, candidate MTX-degrading genes were enriched in MTX-NR. Microbiome functional profiles outperformed clinical metrics in predicting future MTX response. These results show that consistent microbiome signatures are associated with MTX response across different RA cohorts and pave the way for microbiome-based precision medicine in newly diagnosed RA patients.

microbiology↗

bioRxiv2026

Female-enriched Eggerthella lenta drives neuroinflammation and IFN-γ via host receptor TLR2

Women are at increased risk of autoimmune diseases, including multiple sclerosis (MS); however, the degree to which sex differences in the gut microbiota impact autoimmunity remains largely unexplored. Our 27-cohort meta-analysis revealed 60 sex-associated gut bacterial species. Leveraging an independent clinical cohort, we demonstrate that female-enriched species significantly associate with MS status and clinical disability (EDSS). Top female-enriched species Eggerthella lenta drove disease in the experimental autoimmune encephalomyelitis (EAE) MS model, consistent with brain and gut lamina propria T cell infiltration and MS-associated T helper (Th) signatures. E. lenta induced intestinal Th1 and Th17 in healthy mice, independent of bacterial viability. Mechanistically, we demonstrate that TLR2 directly drives E. lenta-induced IFN-{gamma} production in Th cells and is necessary for exacerbation of EAE. Together, we identify a causal host-microbe axis contributing to sex differences in autoimmunity and provide a framework for evaluating sex as a biological variable in human microbiome research. HIGHLIGHTSO_LI27-cohort meta-analysis identifies a robust sex-signature in human gut microbiota. C_LIO_LIFemale-enriched species are associated with MS risk and severity. C_LIO_LIFemale-enriched Eggerthella lenta exacerbates the EAE model. C_LIO_LIE. lenta impacts neuroinflammation via toll-like receptor 2. C_LI

microbiology↗

bioRxiv2025

Shifts in the human gut microbiome during cancer chemotherapy are diet-dependent

Numerous studies have implicated both dietary intake and the human gut microbiome in colorectal cancer (CRC) treatment outcomes. However, little is known about how patients adjust their dietary intake during cancer chemotherapy or if these dietary changes contribute to treatment-associated alterations in the gut microbiome. We performed paired longitudinal diet and microbiome analysis during CRC treatment with oral fluoropyrimidines (NCT04054908) and validated key associations using cell culture assays. At each timepoint, diet was measured by averaging up to 3 consecutive days of 24-hour dietary records (NCI ASA24; 35 patients; 2.5{+/-}1.1 timepoints per patient), while microbiome composition was measured from stool (16S rRNA gene sequencing, metagenomics, qPCR; 40 patients; 5.6{+/-}1.4 timepoints per patient). Diet quality significantly decreased during chemotherapy. Carbohydrate and refined grain intake increased, accompanied by decreased consumption of fats, nuts and seeds, and fat-soluble micronutrients. Multiple individual dietary components were strongly linked to the gut microbiome. Decreases in theobromine intake correlated with decreases in overall microbial diversity and more gastrointestinal toxicities. Diet shifts partly explained changes in bacterial abundance during chemotherapy, including more severe depletion of Faecalibacterium prausnitzii in patients with decreased vitamin K1 intake. Changes in diet were correlated with multiple bacterial gene families involved in micronutrient metabolism and drug sensitivity. Increased copper intake was linked to decreased Fusobacterium nucleatum in patients and inhibited F. nucleatum in cell assays. Together, these data suggest that changes in diet during chemotherapy contribute to changes in gut bacterial diversity, taxonomic composition, and gene abundance. Our approach may generalize to other cancer therapies and emphasizes the need for collecting more robust dietary data in clinical microbiome studies.

microbiology↗

bioRxiv2025

The gut microbiome shapes pharmacology and treatment outcomes for a key anti-inflammatory therapy

The human gut microbiome encodes a formidable metabolic repertoire that harvests nutrients from the diet, but these same pathways may also metabolize medications. Indeed, large screens have revealed extensive microbial metabolism of drugs in vitro, but the pharmacologic and clinical repercussions of microbiota-mediated metabolism in vivo remain to be discerned. As a proof-of-concept, we investigate how human gut microbes contribute to in vivo pharmacology and efficacy of a key anti-inflammatory drug, methotrexate (MTX). Specifically, we demonstrate that the gut microbiome shapes drug pharmacology in vivo in mice, both by directly metabolizing the drug and by inducing host pathways that promote drug metabolism. Moreover, interindividual variation in the human gut microbiome contributes to variation in pharmacokinetic (PK) profiles. When we quantified metabolites produced by microbes, we unexpectedly identified novel MTX metabolites, one of which, p-methylaminobenzoyl-L-glutamic acid (pMABG), was a major byproduct of microbial metabolism both in vitro and in vivo. Further, we find that a large proportion of patient-associated microbes are capable of metabolizing MTX. Finally, we show that microbial metabolism of MTX is linked to PK profiles and disease outcomes in a mouse model of inflammatory arthritis. Taken together, these findings provide evidence that the human gut microbiome causally contributes to drug pharmacology in vivo for a key anti-inflammatory drug through known and novel mechanisms. Our studies provide a framework for elucidating the clinical relevance of drug microbial metabolism in the context of treatment response. These results are a first step towards understanding and manipulating the human gut microbiome in the treatment of autoimmunity and the advancement of precision medicine for millions of patients taking MTX for immune or inflammatory conditions. HighlightsO_LIThe gut microbiome impacts methotrexate (MTX) pharmacology in mice C_LIO_LIThe human gut microbiome contributes to interindividual variation in MTX pharmacology C_LIO_LIHuman gut microbes produce novel MTX metabolites, pMABG and 6-MPDA C_LIO_LIMicrobial metabolism of MTX is linked to treatment outcomes C_LI

pharmacology and toxicology↗

bioRxiv2025

Comprehensive Cross-Domain Taxonomic Classification of Microbiotas using Partitioned Amplification Multiplexed Amplicon Sequencing (PAMA-seq)

Microbial communities encompass diverse bacteria, archaea, and eukaryotes that play vital roles in ecosystems and host health. Comprehensive analysis of these communities requires accurate, quantitative, and cross-domain profiling, yet current sequencing methods--metagenome shotgun sequencing (MGS) and ribosomal RNA (rRNA) amplicon sequencing--struggle to achieve these goals in a single assay. MGS provides broad functional insights but suffers from high cost, computational burden, and reliance on incomplete reference databases. rRNA amplicon sequencing, while more taxonomically targeted, typically profiles either prokaryotes or eukaryotes separately, depending on the chosen primer sets, and thus lacks simultaneous cross-domain resolution. To address these limitations, we developed PAMA-seq, a droplet-digital multiplex PCR technique. PAMA-seq partitions DNA sample from microbial communities into nanoliter droplets, each containing a single template molecule, and independently amplifies both the 16S and 18S rRNA genes, resulting in uniform amplification efficiency and accurate quantification. We validated PAMA-seq on a synthetic microbial community, a stool sample from a patient with colorectal cancer, and a coastal seawater sample. The method provided stable, cross-domain taxonomic profiles at sequencing depths as low as 104 reads--one to two orders of magnitude fewer than comparable shotgun metagenomics approaches--while significantly reducing variability between replicates. By combining comprehensive domain coverage with low sequencing depth requirements, PAMA-seq offers an efficient, cost-effective, and scalable method for monitoring microbial communities across diverse ecosystems, from clinical samples to global marine environments.

microbiology↗

bioRxiv2025

Gut bacterial lactate stimulates lung epithelial mitochondria and exacerbates acute lung injury

Acute respiratory distress syndrome (ARDS) is an often fatal critical illness where lung epithelial injury leads to intrapulmonary fluid accumulation. ARDS became widespread during the COVID-19 pandemic, motivating a renewed effort to understand the complex etiology of this disease. Rigorous prior work has implicated lung endothelial and epithelial injury in response to an insult such as bacterial infection; however, the impact of microorganisms found in other organs on ARDS remains unclear. Here, we use a combination of gnotobiotic mice, cell culture experiments, and re-analyses of a large metabolomics dataset from ARDS patients to reveal that gut bacteria impact lung cellular respiration by releasing metabolites that alter mitochondrial activity in lung epithelium. Colonization of germ-free mice with a complex gut microbiota stimulated lung mitochondrial gene expression. A single human gut bacterial species, Bifidobacterium adolescentis, was sufficient to replicate this effect, leading to a significant increase in mitochondrial membrane potential in lung epithelial cells. We then used genome sequencing and mass spectrometry to confirm that B. adolescentis produces L-lactate, which was sufficient to increase mitochondrial activity in lung epithelial cells. Finally, we found that serum lactate was significantly associated with disease severity in patients with ARDS from the Early Assessment of Renal and Lung Injury (EARLI) cohort. Together, these results emphasize the importance of more broadly characterizing the microbial etiology of ARDS and other lung diseases given the ability of gut bacterial metabolites to remotely control lung cellular respiration. Our discovery of a single bacteria-metabolite pair provides a proof-of-concept for systematically testing other microbial metabolites and a mechanistic biomarker that could be pursued in future clinical studies. Furthermore, our work adds to the growing literature linking the microbiome to mitochondrial function, raising intriguing questions as to the bidirectional communication between our endo- and ecto-symbionts.

molecular biology↗

bioRxiv2025

A20's Linear Ubiquitin Binding Motif Restrains Pathogenic Activation of TH17/22 cells and IL-22 Driven Enteritis

A20, encoded by the TNFAIP3 gene, is a protein linked to Crohns disease and celiac disease in humans. We now find that mice expressing point mutations in A20s M1 ubiquitin binding motif (ZF7) spontaneously develop proximate enteritis that requires both luminal microbes and T cells. Cellular and transcriptomic profiling reveal expansion of TH17/22 cells and aberrant expression of IL-17A and IL-22 in intestinal lamina propria of A20ZF7 mice. While deletion of IL-17A from A20ZF7/ZF7 mice exacerbates enteritis, deletion of IL-22 abrogates intestinal epithelial cell hyperproliferation, barrier dysfunction, and alarmin expression. A20ZF7/ZF7 TH17/22 cells autonomously express more ROR{psi}t and IL-22 after differentiation in vitro. ATAC sequencing identified an enhancer region upstream of the Il22 gene in A20ZF7/ZF7 T cells, and this enhancer demonstrated increased activating histone acetylation coupled with exaggerated Il22 transcription. Finally, CRISPR/Cas9-mediated ablation of A20ZF7 in human T cells increases ROR{psi}t expression and IL22 transcription. These studies link A20s M1 ubiquitin binding function with ROR{psi}t expression, epigenetic activation of TH17/22 cells, and IL-22 driven enteritis.

immunology↗

bioRxiv2024

Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states

Human immune systems are highly variable, with most variation attributable to non-genetic sources. The gut microbiome crucially shapes the immune system; however, its relationship with the baseline immune states of healthy humans remains incompletely understood. Therefore, we performed multi-omic profiling of 110 healthy participants through the ImmunoMicrobiome study. A factor-based integrative approach identified coordinated variation, revealing that the tonic interferon response was amongst the most variable immune features in healthy participants. Microbiome composition, pathways, and stool metabolites varied concomitantly with interferon response pathways. Distinct transcriptional programs involving inflammation and TGF-{beta} in SIGLEC-1high monocytes and CD69high activated MAIT and NK cells were representative of these programs. Our study provides extensive data to examine the relationship between the immune states and microbiomes of healthy individuals at steady state, which paves the way for delineating inter-individual differences relevant for disease susceptibility and responses to therapy.

immunology↗

bioRxiv2024

Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome

Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some cases by homologous enzymes. We conducted a systematic search for all human proteins with gut microbial homologs. Because gene fusion and fission can obscure homology detection, we built a pipeline to identify not only full-length homologs, but also cases where microbial homologs were split across multiple adjacent genes in the same neighborhood or operon ("split homologs"). We found that human proteins with full-length gut microbial homologs disproportionately participate in xenobiotic metabolism. While this included many different enzyme classes, short-chain and aldo-keto reductases were the most frequently detected, especially in prevalent gut microbes, while cytochrome P450 homologs were largely restricted to lower-prevalence facultative anaerobes. In contrast, human proteins with split homologs tended to play roles in central metabolism, especially of nucleobase-containing compounds. We identify twelve specific drugs that gut microbial split homologs may metabolize; two of these, 6-mercaptopurine by xanthine dehydrogenase (XDH) and 5-fluorouracil by dihydropyrimidine dehydrogenase (DPYD), have been recently confirmed in mouse models. This work provides a comprehensive map of homology between the human and gut microbial proteomes, indicates which human xenobiotic enzyme classes are most likely to be shared by gut microorganisms, and finally demonstrates that split homology may be an underappreciated explanation for microbial contributions to drug metabolism. Article SummaryWe develop a pipeline to systematically find human proteins with gut microbial homologs, including those split across multiple microbial genes (e.g., operons). This reveals thousands of proteins with full-length gut homologs, especially reductases and hydrolases that metabolize xenobiotics. Nearly two dozen split homologs are also observed for central metabolic enzymes, many of which can transform substrate analogs; in two cases, previous studies verify that microbial split homologs enable the expected drug to be metabolized in vivo. These results, which we provide as a resource, map out homology and shed light on parallel drug metabolism between host and microbiome.

genomics↗

bioRxiv2024

Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity

Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Herein, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal study of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. 16S rRNA gene sequencing revealed significant shifts in gut microbial community structure during oral fluoropyrimidine treatment across multiple patient cohorts, in mouse small and large intestinal contents, and in patient-derived ex vivo communities. Metagenomic sequencing revealed marked shifts in pyrimidine-related gene abundance during oral fluoropyrimidine treatment, including enrichment of the preTA operon, which is sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). preTA+ bacteria depleted 5-FU in gut microbiota grown ex vivo and the mouse distal gut. Germ-free and antibiotic-treated mice experienced increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA+ E. coli, or preTA-high CRC patient stool. Finally, preTA abundance was negatively associated with fluoropyrimidine toxicity in patients. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach is generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease. One Sentence Summary: Gut microbial enzymes can be used to predict and prevent anticancer drug toxicity.

systems biology↗

bioRxiv2024

Effects of long-term high dose aspartame on body mass, bone strength, femoral geometry, and microbiota composition in a young and aged cohort of male and female mice

BackgroundRecent reassessment of the safety of aspartame has prompted increased evaluation of its effect on the health of a range of tissues. The gut microbiome is altered by oral aspartame. One prior study suggested that changes in the microbiome caused by aspartame could influence the strength of bone in young skeletally developing mice. Here we ask how aspartame influences bone in mice of different age and sex. ObjectiveThe objective of this study was to determine the effect of aspartame on the bone strength and gut microbiota of young and aged mice. MethodsMale and female C57Bl/6J mice were untreated or treated with a high dose of aspartame in their drinking water from 1 month of age until 4 (young cohort; n = 80) or 22 months (aged cohort; n = 52). ResultsIn aged males, mice treated with aspartame had greater body mass, whole bone strength, and femoral geometry relative to untreated. Specifically, in aged males, aspartame led to 9% increase in body mass (p < 0.001), 22% increase in whole bone strength (p = 0.006), and 17% increase in section modulus (p < 0.001) relative to untreated mice. Aged males and females receiving aspartame had a different microbiota than untreated mice and a decreased abundance of Odoribacter. No differences in body mass, whole bone strength, or femoral geometry were associated with aspartame dosing in young males or young or aged females. ConclusionsAspartame treated aged males had greater whole bone strength and the effect appeared to be explained by greater body mass. Aspartame treatment did not alter whole bone strength in young males or young or aged females despite the aspartame having a similar effect on the microbiota of both aged males and females.

bioengineering↗

bioRxiv2023

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity

Diet can protect from autoimmune disease; however, whether diet acts via the host and/or microbiome remains unclear. Here, we use a ketogenic diet (KD) as a model to dissect these complex interactions. A KD rescued the experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis in a microbiota-dependent fashion. Dietary supplementation with a single KD-dependent host metabolite ({beta}-hydroxybutyrate, {beta}HB) rescued EAE whereas transgenic mice unable to produce {beta}HB in the intestine developed more severe disease. Transplantation of the {beta}HB-shaped gut microbiota was protective. Lactobacillus sequence variants were associated with decreased T helper 17 (Th17) cell activation in vitro. Finally, we isolated a L. murinus strain that protected from EAE, which was phenocopied by the Lactobacillus metabolite indole lactic acid. Thus, diet alters the immunomodulatory potential of the gut microbiota by shifting host metabolism, emphasizing the utility of taking a more integrative approach to study diet-host-microbiome interactions.

microbiology↗

bioRxiv2023

Microbiome single cell atlases generated with a commercial instrument

Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, we present EASi-seq (Easily Accessible Single microbe sequencing). By adapting the single cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbes genomes. EASi-seq allows thousands of microbes to be sequenced per run and, as we show, can generate detailed atlases of human and environmental microbiomes. The ability to capture large shotgun genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, we develop a companion bioinformatic pipeline that clusters genome by sequence similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, we demonstrate integration of metagenomic contigs with the EASi-seq datasets to reduce capture bias and increase coverage. Overall, EASi-seq enables high quality single cell genomic data for microbiome samples using an accessible workflow that can be run on a commercially available platform.

bioengineering↗

bioRxiv2022

Mild SARS-CoV-2 infection results in long-lasting microbiota instability

Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2 positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls, as long as 154 days after their positive test. These results were confirmed and extended in the K18-hACE2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila. Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCETaken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2 it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.

microbiology↗

bioRxiv2022

The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli

The microbiome is an underappreciated contributor to intestinal drug metabolism with broad implications for drug efficacy and toxicity. While considerable progress has been made towards identifying the gut bacterial genes and enzymes involved, the role of environmental factors in shaping their activity remains poorly understood. Here, we focus on the gut bacterial reduction of azo bonds (R-N=N-R), found in diverse chemicals in both food and drugs. Surprisingly, the canonical azoR gene in Escherichia coli was dispensable for azo bond reduction. Instead, azo reductase activity was controlled by the fumarate and nitrate reduction (fnr) regulator, consistent with a requirement for the anoxic conditions found within the gastrointestinal tract. Paired transcriptomic and proteomic analysis of the fnr regulon revealed that in addition to altering the expression of multiple reductases, FNR is necessary for the metabolism of L-Cysteine to hydrogen sulfide, enabling the degradation of azo bonds. Taken together, these results show how gut bacteria sense and respond to their intestinal environment to enable the metabolism of chemical motifs found in both dietary and pharmaceutical compounds. IMPORTANCEThis work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and non-enzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen and cysteine, control the ability of E. coli to degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.

microbiology↗