Biology subjects

Dodd, D.

Publications and source records attributed to Dodd, D..

9 recordsLinked to original sources

bioRxiv2026

Indole-3-acetic acid production is rare among gut bacteria and reflects OFOR-driven amino acid oxidation in acetogens

Indole-3-acetic acid (IAA) is a tryptophan-derived gut microbial metabolite with reported anti-inflammatory activities, but the organisms and anaerobic pathways that support robust production remain unclear. Screening 206 human gut bacterial isolates by LC-MS revealed that IAA production is rare: only five strains exceeded the limit of quantitation, and high-capacity production was confined to the acetogens Blautia hydrogenotrophica and Intestinibacter bartlettii. Across growth conditions, IAA was a minor product that rose alongside carbohydrate-sensitive, OFOR-linked catabolism of multiple amino acids, generating abundant branched-chain and aromatic organic acids. In gnotobiotic mice mono-colonized with I. bartlettii, these metabolites were produced in vivo but showed distinct host handling, with branched-chain fatty acids largely extracted between portal and peripheral plasma, whereas aromatic acids and their glycine conjugates appeared in plasma and urine. Genomic analyses and heterologous enzyme assays identified expanded repertoires of 2-oxoacid:ferredoxin oxidoreductases (OFORs) with activities spanning pyruvate/oxaloacetate, branched-chain, and aromatic 2-oxoacids, including indolepyruvate conversion to indoleacetyl-CoA, a putative intermediate en route to IAA. Finally, position-specific 13C tracing showed that CO2 released during amino acid oxidation is reassimilated into acetate via reductive acetogenesis, indicating that gut acetogens can maintain redox balance without fermenting partner strains. Together, these findings show that high IAA output is restricted to select gut acetogens and linked to a broader OFOR-driven anaerobic metabolism that generates additional metabolites that are absorbed by the host.

microbiology↗

bioRxiv2025

IsoPairFinder: A tool for biochemical pathway discovery using stable isotope tracing metabolomics

SummaryThe functional annotation of microbial genes lags far behind genome sequencing, leaving critical gaps in our knowledge of metabolic pathways. While integrating genetic manipulation with stable isotope tracing (SIT) metabolomics holds promise for pathway discovery, existing tools lack specialized capabilities for gene perturbation experiments. To address this need, we developed IsoPairFinder, a computational tool that identifies pathway intermediates by analyzing paired unlabeled (12C) and isotope-labeled (13C) metabolomics data from gene-edited microbes. By prioritizing substrate-specific feature pairs, IsoPairFinder efficiently prioritizes biologically relevant intermediates. Implemented as an open-source R package and integrated into the GNPS2 ecosystem, IsoPairFinder provides an accessible platform for the research community to accelerate novel pathway discovery and validation. Availability and implementationIsoPairFinder is freely available as an open-source R package (https://github.com/DoddLab/IsoPairFinder) and as a web-based workflow in the GNPS2 ecosystem (https://gnps2.org/workflowinput?workflowname=isopairfinder_nextflow_workflow). Comprehensive tutorials are provided at https://doddlab.github.io/IsoPairFinder_Tutorials. These implementations support both command-line and graphical analysis workflows. Contactddodd2@stanford.edu Supplementary informationSupplementary information is available at Bioinformatics online.

bioinformatics↗

bioRxiv2025

Gut bacteria degrade purines via the 2,8-dioxopurine pathway

The loss of uricase during hominid evolution has predisposed humans to hyperuricemia and gout, conditions with high global prevalence. In healthy individuals, approximately one-third of urate is excreted into the intestinal tract1 where bacteria consume this purine aiding in its elimination2,3. However, the molecular details of purine metabolism in the gut microbiome remain unknown. Here we uncover the 2,8-dioxopurine pathway, a previously unrecognized anaerobic route for purine degradation in gut bacteria. This pathway uses a novel selenium-dependent enzyme, 2,8-dioxopurine dehydrogenase (DOPDH), and seven additional enzymes that together link purine metabolism to ATP generation and short chain fatty acid production. Competition experiments in gnotobiotic mice demonstrate that bacteria harboring this pathway exhibit a fitness advantage, with wild-type bacteria rapidly outcompeting a DOPDH-deficient strain. These findings highlight a host-microbe symbiosis, where host-secreted urate fosters a metabolic niche for bacteria that break it down. By elucidating this pathway, our study provides new avenues to modify and enhance intestinal elimination of urate, which has therapeutic implications for treating hyperuricemia and gout, conditions that affect millions of adults worldwide.

microbiology↗

bioRxiv2022

Systems biology illuminates alternative metabolic niches in the human gut microbiome

Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem.

microbiology↗

bioRxiv2022

A widely distributed gene cluster compensates for uricase loss in hominids

Approximately 15% of US adults have circulating levels of uric acid above its solubility limit, which is causally linked to the disease gout. In most mammals, uric acid elimination is facilitated by the enzyme uricase. However, human uricase is a pseudogene, having been inactivated early in hominid evolution. Though it has long been known that uric acid is eliminated in the gut, the role of the gut microbiota in hyperuricemia has not been studied. Here we identify a widely distributed bacterial gene cluster that encodes a pathway for uric acid degradation. Stable isotope tracing demonstrates that gut bacteria metabolize uric acid to xanthine or short chain fatty acids. Ablation of the microbiota in uricase-deficient mice causes severe hyperuricemia, and anaerobe-targeted antibiotics increase the risk of gout in humans. These data reveal a role for the gut microbiota in uric acid excretion and highlight the potential for microbiome-targeted therapeutics in hyperuricemia.

microbiology↗

bioRxiv2021

A metabolomics pipeline enables mechanistic interrogation of the gut microbiome

Gut microbes modulate host phenotypes and are associated with numerous health effects in humans, ranging from cancer immunotherapy response to metabolic disease and obesity. However, difficulty in accurate and high-throughput functional analysis of human gut microbes has hindered defining mechanistic connections between individual microbial strains and host phenotypes. One key way the gut microbiome influences host physiology is through the production of small molecules1-3, yet progress in elucidating this chemical interplay has been hindered by limited tools calibrated to detect products of anaerobic biochemistry in the gut. Here we construct a microbiome-focused, integrated mass-spectrometry pipeline to accelerate the identification of microbiota-dependent metabolites (MDMs) in diverse sample types. We report the metabolic profiles of 178 gut microbe strains using our library of 833 metabolites. Leveraging this metabolomics resource we establish deviations in the relationships between phylogeny and metabolism, use machine learning to discover novel metabolism in Bacteroides, and employ comparative genomics-based discovery of candidate biochemical pathways. MDMs can be detected in diverse biofluids in gnotobiotic and conventional mice and traced back to corresponding metabolomic profiles of cultured bacteria. Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microbe and microbe-host interactions.

microbiology↗

bioRxiv2021

A systematic analysis of metabolic pathways in the human gut microbiota

The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here, we systematically profile primary metabolic genes from the gut microbiome, identifying 19,885 gene clusters in 4,240 high-quality microbial genomes. We find marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 subjects from a Dutch population-based cohort shows that the level of 14 microbiome-derived metabolites in plasma is almost completely uncorrelated with the metagenomic abundance of the corresponding biosynthetic genes, revealing a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.

bioinformatics↗

bioRxiv2019

Electron transfer complexes in the gut dictate high abundance circulating metabolites

It has long been known that proteolytic Clostridia obtain their energy by coupling oxidative and reductive pathways for amino acid metabolism - the Stickland reaction1. The oxidation of one amino acid is coupled with reduction of another, yielding energy in the former step and re-achieving redox balance with the latter. Here, we find that the gut bacterium, Clostridium sporogenes metabolizes amino acids through reductive pathways to produce metabolites that circulate within the host. Measurements in vitro indicate that reductive Stickland pathways are coupled to ATP formation, revealing their role in energy capture by gut bacteria. By probing the genetics of C. sporogenes, we find that the Rnf complex is involved in reductive amino acid metabolism. Rnf complex mutants are attenuated for growth in the mouse gut, demonstrating the importance of energy capture during reductive metabolism for gut colonization. Our findings reveal that the production of high-abundance molecules by a commensal bacterium within the host gut is linked to an energy yielding redox process.

microbiology↗

bioRxiv2018

Depletion of microbiome-derived molecules in the host using Clostridium genetics

The gut microbiota produce hundreds of molecules that are present at high concentrations in circulation and whose levels vary widely among humans. In most cases, molecule production has not been linked to specific bacterial strains or metabolic pathways, and unraveling the contribution of each molecule to host biology remains difficult. A general system to toggle molecules in this pool on/off in the host would enable interrogation of the mechanisms by which they modulate host biology and disease processes. Such a system has been elusive due to limitations in the genetic manipulability of Clostridium and its relatives, the source of many molecules in this pool. Here, we describe a method for reliably constructing clean deletions in a model commensal Clostridium, C. sporogenes (Cs), including multiply mutated strains. We demonstrate the utility of this method by using it to toggle off the production of ten Cs-derived molecules that accumulate in host tissues. By comparing mice colonized by wild-type Cs versus a mutant deficient in the production of branched short-chain fatty acids, we discover a previously unknown IgA-modulatory activity of these abundant microbiome-derived molecules. Our method opens the door to interrogating and sculpting a highly concentrated pool of chemicals from the microbiome.

microbiology↗