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Updated: Dec 7, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?
Matteo Soverini1, Simone Rampelli2, Silvia Turroni2
1Department of Pharmacy and Biotechnology, Unit of Microbial Ecology of Health, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy. matteo.soverini5@unibo.it.
Background:
Advances in bioinformatics recently allowed for the recovery of 'metagenomes assembled genomes' from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits.
Results:
In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.
Conclusions:
The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.
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