The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species

Abstract

After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in describing new prokaryotic species and filling metagenomic gaps. In 2015, only 2172 different prokaryotic species were reported to have been isolated at least once from the human body as pathogens or commensals. In this review, we update the previous repertoire by reporting the different species isolated from the human body to date, increasing it by 28% to reach a total of 2776 species associated with human beings. They have been classified into 11 different phyla, mostly the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Finally, culturomics contributed up to 66.2% towards updating this repertoire by reporting 400 species, of which 288 were novel. This demonstrates the need to continue the culturing work, which seems essential in order to decipher the hidden human microbial content.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0485-5) contains supplementary material, which is available to authorized users.

The microbiome of pest insects: it is not just bacteria

“…We now need to expand this research on the role of the microbiome and more explicitly include the non-bacterial components of the microbiome and their various interactions, as well as their functioning. Given that the field of microbiome is progressing in metagenomics, emphasis on culturomics (Bilen et al, 2018) is the need of the hour to get a better grasp about what is actually going on in this network where all the microbial partners are interconnected. In closing, we highlight three openstanding questions that we consider of primary importance for understanding the ecology of the microbiome associated with pests.…”

Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut

“…The latter proved its efficiency in describing the human gut microbiota by reporting a significant number of previously uncultured and novel bacterial species (Lagier et al, ). Nevertheless, we are still far from understanding the human microbiome since only around 2,776 human bacterial species have been isolated, knowing that up to 1,012 bacteria are estimated to be present in only 1 g of stool (Bilen et al, ; Hugon et al, ). In the present work, the two studied organisms, strains Marseille‐P2849 T and Marseille‐P3277 T , were isolated from the stool samples of a 19‐year‐old healthy Saudi Bedouin and an 11‐year‐old Congolese pygmy female, respectively.…”

Antioxidants maintain Butyrate production by Human GutClostridiain the presence of Oxygen

“…Serendipitously, we observed an absence of unpleasant odor when anaerobes were grown aerobically with antioxidants. To test what might explain a better smell, we selected 3 strains of the human gut isolated by microbial culturomics [17][18][19][20] , that produced the strongest smells in our anaerobic culture laboratory: Clostridium sporogenes, Clostridium subterminale and Romboutsia lituseburensis. We compared the volatile organic compounds (VOCs) of these 3 strains grown under standard anaerobic condition or in ambient air thanks to antioxidants (uric acid, ascorbate, glutathione) [14][15][16] using gas chromatography coupled with mass spectrometry.…”