Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

Abstract

Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and well-being1,2. Intestinal colonisation begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla2. Culture independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases1. However, due to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown3. Here we describe a novel workflow based on targeted phenotypic culturing linked to large-scale whole genome sequencing, phylogenetic analysis and computational modeling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. Applying this approach to healthy individuals, we isolated 137 bacterial species from characterised and candidate novel families, genera and species that were archived as pure cultures. Whole genome and metagenomic sequencing, combined with computational and phenotypic analysis, suggests that at least 50-60% of the bacterial genera from the intestinal microbiota of a healthy individual produce resilient spores, specialised for host-to-host transmission. Our approach unlocks the human intestinal microbiota for phenotypic analysis and reveals how a significant proportion of oxygen-sensitive intestinal bacteria can transmit between individuals, impacting microbiota heritability.

RETRACTED ARTICLE: Culture of previously uncultured members of the human gut microbiota by culturomics

“…We collected the sequences of the 3,871,657 gene non-redundant gene catalogue from the 396 human gut microbiome samples (https://www.cbs.dtu.dk/projects/ CAG/) 15 . We performed an alignment of 247 16S rRNA sequences against the 3,871,657 gene non-redundant gene catalogue using BLASTN with a threshold of 1e-03 e-value, 100% coverage and 98.7% cutoff.…”

“…Therefore, at least 102 new bacterial species were found but not identified in previous metagenomic studies from the HMP. Third, we searched for our 247 new species in the 239 human gut microbiome samples from healthy individuals described by Browne et al, in which 137 bacterial species were isolated 15 . We captured 150 of our new species in these metagenomics data, representing 60.7% (Supplementary Table 9).…”

The role of gut microbiota in health and disease: In vitro modeling of host-microbe interactions at the aerobe-anaerobe interphase of the human gut

“…84 Although many of the bacteria can survive oxygen by mechanisms such as sporulation; 85 oxygen-free conditions are required for the anaerobic bacteria to grow. 1 Recently, a 86 M A N U S C R I P T…”

Biome engineering‐2020

“…Bacterium–bacterium and bacterium–host interactions were deduced from sophisticated bioinformatics network analyses. Now the Sanger Center after years of systematic bacterial genome sequencing reported the culturing of 137 bacterial species from the stool of six healthy adults, many of them were new bacterial species; even new bacterial families were isolated (Browne et al ., 2016). What was until recently considered an ‘unculturable’ part of the human gut microbiota is now accessible for phenotypic analysis and became tools for intervention studies.…”