Expansion of the protein repertoire in newly explored environments

human gut microbiome specific protein families.

Kyle Ellrott, Lukasz Jaroszewski, Weizhong Li, John C. Wooley, Adam Godzik

Research output: Contribution to journalArticle

43 Citations (Scopus)

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.

Original languageEnglish (US)
JournalPLoS Computational Biology
Volume6
Issue number6
DOIs
StatePublished - 2010
Externally publishedYes

Fingerprint

Microbiota
digestive system
Proteins
Protein
protein
proteins
Metagenomics
Polysaccharides
Bacteroides
Gastrointestinal Microbiome
microbiome
Family
Human
family
Niche
Carbohydrates
Carbohydrate Metabolism
carbohydrate metabolism
Nutrition
polysaccharide

ASJC Scopus subject areas

  • Cellular and Molecular Neuroscience
  • Ecology
  • Molecular Biology
  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Computational Theory and Mathematics

Cite this

Expansion of the protein repertoire in newly explored environments : human gut microbiome specific protein families. / Ellrott, Kyle; Jaroszewski, Lukasz; Li, Weizhong; Wooley, John C.; Godzik, Adam.

In: PLoS Computational Biology, Vol. 6, No. 6, 2010.

Research output: Contribution to journalArticle

@article{76c5709037314ddb8f01b59fb09d3030,
title = "Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families.",
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.",
author = "Kyle Ellrott and Lukasz Jaroszewski and Weizhong Li and Wooley, {John C.} and Adam Godzik",
year = "2010",
doi = "10.1371/journal.pcbi.1000798",
language = "English (US)",
volume = "6",
journal = "PLoS Computational Biology",
issn = "1553-734X",
publisher = "Public Library of Science",
number = "6",

}

TY - JOUR

T1 - Expansion of the protein repertoire in newly explored environments

T2 - human gut microbiome specific protein families.

AU - Ellrott, Kyle

AU - Jaroszewski, Lukasz

AU - Li, Weizhong

AU - Wooley, John C.

AU - Godzik, Adam

PY - 2010

Y1 - 2010

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=77956223931&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77956223931&partnerID=8YFLogxK

U2 - 10.1371/journal.pcbi.1000798

DO - 10.1371/journal.pcbi.1000798

M3 - Article

VL - 6

JO - PLoS Computational Biology

JF - PLoS Computational Biology

SN - 1553-734X

IS - 6

ER -