Subspecies in the global human gut microbiome

Area of Science:

• Microbiology
• Genomics
• Human Microbiome Research

Background:

• Population genomics is limited to a few pathogenic bacteria due to a lack of diverse isolate genomes.
• Understanding the population structure of prevalent human gut microbes is crucial for microbiome research.

Purpose of the Study:

• To conduct a large-scale survey of population structure in prevalent human gut microbial species using a culture-independent metagenomic approach.
• To identify and characterize subspecies within abundant gut prokaryotes and investigate their functional and ecological significance.

Main Methods:

• Analyzed 2,144 human fecal metagenomes to examine the variation landscape of 71 microbial species.
• Utilized single-nucleotide variation to identify subspecies within species.
• Identified subspecies-specific genes and associated them with microbial community and host properties.

Main Results:

• Found evidence of subspecies in 44 out of 71 abundant gut prokaryotic species (72% of total microbial abundance).
• Observed distinct geographic distributions for subspecies, with Firmicutes subspecies being more restricted.
• Identified functional differences, such as a pro-inflammatory flagellum operon in *Eubacterium rectale* subspecies linked to lower gut diversity and altered host metabolic markers.
• Demonstrated niche specialization of subspecies in the oral cavity using 676 oral samples.

Conclusions:

• The majority of abundant gut prokaryotes harbor distinct subspecies.
• Subspecies exhibit unique genetic and ecological characteristics, influencing the human gut microbiome and host.
• This research provides a deeper functional and ecological understanding of the human gut microbiome and its host interactions.