Exploring the universal healthy human gut microbiota around the World

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• The human gut microbiota is crucial for host health, but knowledge is limited by Western-centric data and databases.
• Existing studies often lack comprehensive representation of global gut microbial diversity.

Purpose of the Study:

• To address limitations in gut microbiome research, particularly database bias.
• To identify core bacterial taxa consistently found in the human gut worldwide.
• To evaluate database enrichment strategies for improved microbiome analysis.

Main Methods:

• Enrichment of the National Center for Biotechnology Information (NCBI) NT database with human microbiota-specific datasets.
• Analysis of 545 whole-genome shotgun sequencing datasets from fecal samples across Westernization gradients.
• Examination of the impact of incomplete-taxonomy metagenome-assembled genomes on database enrichment.

Main Results:

• Database enrichment significantly improved classification capacity across diverse populations and lifestyles.
• Incomplete genomes are useful but require cautious application at specific taxonomic levels.
• A conserved set of bacterial taxa was identified in healthy human gut microbiomes globally.

Conclusions:

• Database enrichment is a viable strategy to enhance microbiome analysis and overcome data biases.
• A core group of universally prevalent gut bacteria exists, suggesting co-evolution with humans.
• These core taxa possess conserved traits and metabolic functions, potentially forming a mutualistic phylogenetic core.