ArticlePLoS computational biology2010
Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed, 72 citations in OpenAlex.
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- Novel genes arise from genomic deletions across the bacterial tree of life.bioRxiv : the preprint server for biology · 2026Article
- Polysaccharide utilization loci encoded DUF1735 likely functions as membrane-bound spacer for carbohydrate active enzymes.FEBS open bio · 2024Article
- Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences.Genome biology and evolution · 2023Article
- PathFams: statistical detection of pathogen-associated protein domains.BMC genomics · 2021Article
- Structures of single-layer β-sheet proteins evolved from β-hairpin repeats.Protein science : a publication of the Protein Society · 2019Article
- Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach.Frontiers in microbiology · 2019Review
- Chemical transformation of xenobiotics by the human gut microbiota.Science (New York, N.Y.) · 2017Review
- A prominent glycyl radical enzyme in human gut microbiomes metabolizesScience (New York, N.Y.) · 2017Article
- NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.The FEBS journal · 2016Article
- The Sus operon: a model system for starch uptake by the human gut Bacteroidetes.Cellular and molecular life sciences : CMLS · 2016Review
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- Determining microbial products and identifying molecular targets in the human microbiome.Cell metabolism · 2014Review
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- Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase.BMC bioinformatics · 2014Article
- Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities.Frontiers in microbiology · 2014Article
- Interactions in the microbiome: communities of organisms and communities of genes.FEMS microbiology reviews · 2014Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
The microbes that inhabit particular environments must be able to perform molecular functions that provide them with a competitive advantage to thrive in those environments. As most molecular functions are performed by proteins and are conserved between related proteins, we can expect that organisms successful in a given environmental niche would contain protein families that are specific for functions that are important in that environment. For instance, the human gut is rich in polysaccharides from the diet or secreted by the host, and is dominated by Bacteroides, whose genomes contain highly expanded repertoire of protein families involved in carbohydrate metabolism. To identify other protein families that are specific to this environment, we investigated the distribution of protein families in the currently available human gut genomic and metagenomic data. Using an automated procedure, we identified a group of protein families strongly overrepresented in the human gut. These not only include many families described previously but also, interestingly, a large group of previously unrecognized protein families, which suggests that we still have much to discover about this environment. The identification and analysis of these families could provide us with new information about an environment critical to our health and well being.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.