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Proteobacteria explain significant functional variability in the human gut microbiome.

Patrick H Bradley1, Katherine S Pollard2,3

  • 1Gladstone Institutes, San Francisco, CA, USA.

Microbiome
|March 24, 2017
PubMed
Summary
This summary is machine-generated.

Human gut microbiomes show surprising functional redundancy, but a new test reveals thousands of variable genes. These gene differences may explain individual physiological variations.

Keywords:
BacteroidetesEnterotypesFirmicutesFunctional redundancyHuman gut microbiomeProteobacteriaShotgun metagenomicsStatistical methodsVariance

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Human gut microbiome taxonomic composition varies greatly between individuals.
  • Despite taxonomic variation, biological pathway abundance appears functionally redundant across hosts.
  • This apparent functional redundancy may obscure underlying differences in gene abundance.

Purpose of the Study:

  • To develop a method to identify gene abundance variations in the human gut microbiome.
  • To investigate the extent of functional redundancy and identify variable genes.
  • To explore the association of variable genes with specific taxa.

Main Methods:

  • Developed CCoDA (Comparative analysis of Co-varying gene الداta), a novel test for gene variability in shotgun metagenomes.
  • Applied CCoDA to analyze healthy human fecal metagenomes from three independent cohorts.
  • Integrated data from multiple studies to enhance the robustness of the analysis.

Main Results:

  • Identified thousands of genes with significant and consistent abundance differences between individuals.
  • Found variability in glycolytic enzymes, lipopolysaccharide biosynthesis genes, and secretion systems.
  • Observed that variable genes are often associated with Proteobacteria, distinct from enterotype-defining taxa.

Conclusions:

  • Functional redundancy in the human gut microbiome has limits.
  • Specific genes and taxa exhibiting variability can be predicted.
  • These findings may elucidate physiological differences observed between individual gut microbiomes.