Research Highlights

Culturomics in action

Published online 27 November 2016

This novel technique can extend our knowledge of the human gut microbiota.

Lakshini Mendis

A host of international researchers used culturomics to identify new microorganisms, including a host of bacterial species in the human gut. 

The researchers utilized culturomics, first introduced in 20121. The technique was developed to address shortcomings of metagenomics, which studies genetic material recovered from natural samples. Metagenomics has revolutionized this field of research, but its limitation was the yield of a large number of sequences that could not be assigned to a known microorganism.

Now, Jean-Christophe Lagier and researchers from France, French Polynesia, Saudi Arabia, Senegal, and French Guiana, identified 1,057 prokaryotic species. Their research extends the known human gut repertoire by 531 species: 146 bacteria known in humans but not in the gut, 187 bacteria and one archaea not previously isolated in humans, and 197 potentially new species, which made up 20% of the species identified in this study2.

Humans are heavily colonized by approximately 1014 bacteria, of which the majority is located in the human gut. Studies have previously focused on defining the composition of the core microbiota of the human gut, and investigating links between alterations therein and various diseases such as ulcerative colitis, colorectal cancer, and necrotizing enterocolitis. 

To identify the growing human microbiota colonies, the scientists used microbial culturomics, in which high-throughput culture conditions are applied, in combination with matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF) or 16S rRNA amplification and sequencing 

“We have provided a gift for the community… an opportunity to not only understands the microbiota, but also how they function,” says Didier Raoult, senior principal research scientist, Aix Marseille Université. 


  1. Lagier, J.-C. et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin. Microbiol. Infect. 18, 1185–1193 (2012).
  2. Lagier, J.-C. et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat. Microbiol. 1, 16203 (2016).