Quantifying the diversity of sulfate-reducing microbes in the human gut
Abstract/Contents
- Abstract
- Sulfate-reducing microbes (SRM) are a diverse group of bacteria and archaea that utilize sulfate as the terminal electron acceptor in anaerobic respiration and are hypothesized to contribute to gut inflammation in humans. The presence of common SRM have been correlated to chronic gastrointestinal inflammatory diseases such as Crohn’s Disease, Ulcerative Colitis, Inflammatory Bowel Disease, and Irritable Bowel Syndrome in geographically homogeneous, adult, Western populations. However, little is understood of the full diversity of the SRMs within the human gut, especially outside of adult, Western populations. This study aims to characterize the full diversity of the SRMs in the human gut by comprehensively identifying SRM species from a wide set of metagenomic data. This study utilizes a computational approach to search publicly available metagenomes from human gut samples for dsrAB, an SRM-specific gene encoding for dissimilatory sulfite reductase. Using dsrAB genes from a manually curated database, we constructed a profile hidden Markov model (HMM) and applied a commonly used bioinformatics tool, HMMER, to identify homologous sequences from 14,286 gut metagenomes. The returned sequences were then phylogenetically classified using Random Axelerated Maximum Likelihood Evolutionary Placement Algorithm (RAxML-EPA) on a reference dsrAB tree. Phylogenetic analyses of collected dsrAB sequences suggests the presence of diverse SRM in the gut from various taxa, including the Desulfovibrionaceae family, the Firmicutes group sensu lato, and the Archaeoglobus cluster. The analysis showed that most common SRM were Desulfovibrio piger, Bilophila wadsworthia, and an uncultured relative of Desulfovibrio desulfuricans, confirming the widely accepted presumption that Desulfovibrionaceae is the most common family of gut-SRM. Many dsrAB sequences from SRM not previously catalogued in the gut environment were found at lower frequencies. These results indicate the SRMs in the human gut are more diverse than previously hypothesized. The results of this study comprehensively characterize an understudied microbial group with implications in gut health, determine the prevalence of different SRM taxa within the human gut, and inform future studies in assessing causality between SRM and gut inflammation.
Description
| Type of resource | text |
|---|---|
| Date created | June 2021 |
| Date modified | December 5, 2022 |
| Publication date | May 2, 2022 |
Creators/Contributors
| Author | Christensen, Rebecca |
|---|---|
| Degree granting institution | Stanford University, Department of Biology, 2021 |
| Thesis advisor | Spormann, Alfred |
| Thesis advisor | Long, Sharon |
Subjects
| Subject | sulfate-reducing microbes |
|---|---|
| Subject | biology |
| Subject | microbiology |
| Subject | human gut |
| Subject | phylogeny |
| Genre | Text |
| Genre | Thesis |
Bibliographic information
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- User agrees that, where applicable, content will not be used to identify or to otherwise infringe the privacy or confidentiality rights of individuals. Content distributed via the Stanford Digital Repository may be subject to additional license and use restrictions applied by the depositor.
- License
- This work is licensed under a Creative Commons Attribution Share Alike 3.0 Unported license (CC BY-SA).
Preferred citation
- Preferred citation
- Christensen, Rebecca and Spormann, Alfred and Long, Sharon. (2021). Quantifying the diversity of sulfate-reducing microbes in the human gut. Stanford Digital Repository. Available at: https://purl.stanford.edu/qh946fx0883
Collection
Undergraduate Theses, Department of Biology, 2020-2021
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- reb26@stanford.edu
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