Microbiology Meets Big Data: The Case of Gut Microbiota–Derived Trimethylamine
Open accessAbstract
During the past decade, meta-omics approaches have revolutionized microbiology, allowing for a cultivation-free assessment of the composition and functional properties of entire microbial ecosystems. On the one hand, a phylogenetic and functional interpretation of such data relies on accumulated genetic, biochemical, metabolic, and phenotypic characterization of microbial variation. On the other hand, the increasing availability of extensive microbiome data sets and corresponding metadata provides a vast, underused resource for the microbiology field as a whole. To demonstrate the potential for integrating big data into a functional microbiology workflow, we review literature on trimethylamine (TMA), a microbiota-generated metabolite linked to atherosclerosis development. Translating recently elucidated microbial pathways resulting in TMA production into genomic orthologs, we demonstrate how to mine for their presence in public (meta-) genomic databases and link findings to associated metadata. Reviewing pathway abundance in public data sets shows that TMA production potential is associated with symptomatic atherosclerosis and allows identification of currently uncharacterized TMA-producing bacteria.
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Orthologs and homologs of CntA/CntB and YeaW/YeaX occur in diverse gut microbiota, including Gammaproteobacteria, Betaproteobacteria, Firmicutes, and Actinobacteria, and appear absent in Bacteroidetes.
“Orthologs and homologs of the CntA/CntB and YeaW/YeaX gene pairs are found in a variety of gut microbiota: Gammaproteobacteria (Klebsiella pneumoniae, E. coli, Citrobacter, Providencia, and Shigella), Betaproteobacteria (Achromobacter), Firmicutes (Sporosarcina), and Actinobacteria; they appear to be absent in Bacteroidetes (41).”
From Trimethylamine <i>N</i> -Oxide, the Microbiome, and Heart and Kidney Disease (2017) · cites this paper as [41]
A microbial pathway that produces TMA and malic semialdehyde from L-carnitine hydroxylation is active in human colon isolates of Acinetobacter and Serratia.
“A microbial metabolic pathway generating TMA and malic semialdehyde from L-carnitine hydroxylation are active in human colon isolates belonging to the genera Acinetobacter and Serratia (41).”
From Trimethylamine <i>N</i> -Oxide, the Microbiome, and Heart and Kidney Disease (2017) · cites this paper as [41]
Some microbial metabolism that produces TMA remains undiscovered.
“The elucidation of microbial TMA-generating pathways is ongoing, and it is likely that part of TMAproducing microbial metabolism remains undiscovered (41).”
From Trimethylamine <i>N</i> -Oxide, the Microbiome, and Heart and Kidney Disease (2017) · cites this paper as [41]
Little information on the abundance and taxonomic composition of TMA-producing bacteria in vivo is available.
“Despite this multitude of knowledge on TMA-producing bacteria and their importance for human health, little information on their abundance and taxonomic composition in vivo is available.”
From Uncovering the trimethylamine-producing bacteria of the human gut microbiota (2017) · cites this paper as [11]
Only one study estimates the overall potential of intestinal communities to produce TMA.
“So far, only one study estimates the overall potential of intestinal communities to produce TMA [11], and specific structural insights into this functional community are largely lacking.”
From Uncovering the trimethylamine-producing bacteria of the human gut microbiota (2017) · cites this paper as [11]
The database developed in this study unequivocally shows that the vast amount of genomes exhibits a single copy of the cntA/yeaW gene group.
“Importantly, a recent report based on a genome-screening approach suggesting that numerous taxa contain both cntA/B and yeaW/X is misleading [11] as the database developed in this study unequivocally shows that the vast amount of genomes exhibits a single copy of this gene group.”
From Uncovering the trimethylamine-producing bacteria of the human gut microbiota (2017) · cites this paper as [11]
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- Authors
- Falony, G., Vieira-Silva, S., & Raes, J.
- Affiliations
- KU Leuven (BE)
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium;
- Vrije Universiteit Brussel (BE)
- Venue
- Annual Review of Microbiology
- Publisher
- Annual Reviews
- Published
- 2015-10-15
- Volume
- 69
- Issue
- 1
- Pages
- 305-321
- ISSN
- 0066-4227 (ISSN-L)
- 1545-3251
- OpenAlex
- W1883624133
- Cited by
- 187
- References
- 17
- Citations by year
- 2026: 4 · 2025: 23 · 2024: 18 · 2023: 18 · 2022: 34 · 2021: 24 · 2020: 14 · 2019: 16 · 2018: 14 · 2017: 12 · 2016: 7 · 2015: 2
- FWCI
- 1.13
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Annual Review of Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion)
- Lirias (KU Leuven) (submittedVersion)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Funders
- European Commission (100016, 305312, 267139)
- Fonds Wetenschappelijk Onderzoek
- KU Leuven
- Vlaamse regering
- FP7 People: Marie-Curie Actions
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- trimethylamine, gut microbiota, atherosclerosis, meta-omics, genomic databases, metadata mining, microbial metabolites
- MeSH terms
- Gastrointestinal Microbiome, Animals, Humans, Methylamines, Atherosclerosis, Metagenomics, Dysbiosis
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