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Applying Advanced In Vitro Culturing Technology to Study the Human Gut Microbiota

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Published on: February 15, 2019

Towards the human intestinal microbiota phylogenetic core.

Julien Tap¹, Stanislas Mondot, Florence Levenez

¹INRA, UEPSD, UR910, 78350 Jouy en Josas, France.

Environmental Microbiology

|July 16, 2009

Summary

A small group of dominant bacterial operational taxonomic units (OTUs) form a core phylogenetic structure in the human fecal microbiota, despite high individual variation. This core microbiota plays a crucial role in human health.

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Area of Science:

Microbiology
Human Microbiome Research
Genetics

Background:

The human fecal microbiota exhibits global functionalities conserved across individuals.
A paradox exists between host specificity and conserved microbiota functions.
The presence of a stable phylogenetic core in the human gut microbiota is hypothesized.

Purpose of the Study:

To investigate the existence of a dominant and prevalent set of bacterial molecular species within the healthy human fecal microbiota.
To identify a potential phylogenetic core shared among individuals.

Main Methods:

Analysis of 10,456 non-chimeric bacterial 16S ribosomal RNA (rRNA) sequences from 17 human fecal DNA samples.
Identification of 3,180 operational taxonomic units (OTUs) using alignment and tetranucleotide frequency-based methods.
Statistical modeling to confirm OTU prevalence across multiple datasets and experimental procedures.

Main Results:

The human fecal microbiota is primarily composed of Firmicutes (79.4%) and Bacteroidetes (16.9%).
While most OTUs are individual-specific, 2.1% of OTUs were prevalent in over 50% of samples, accounting for 35.8% of sequences.
These 66 dominant and prevalent OTUs include key genera like Faecalibacterium, Ruminococcus, Bacteroides, and Bifidobacterium, and show consistency across different studies.

Conclusions:

A limited number of shared OTUs constitute a potential phylogenetic core of the human intestinal microbiota.
This core microbiota exists despite significant species richness and high individual specificity.
The functional role of this identified phylogenetic core in human health warrants further investigation.