Culturomics: a new approach to study the human microbiome.

Humans are heavily colonized by approximately 10 bacteria, and the composition of our microbiota has been shown to be associated with various diseases, such as obesity, diabetes, atopic dermatitis, and bacterial vaginosis [1]. The medical importance of our microbiota, which has even been considered as a ‘human organ’[2], has thus led to a growing number of descriptive studies, mainly comparing the microbiomes of healthy and ill individuals. As the large majority of microbial communities are located in the gut, an especially high number of studies have tried to define the composition of its core microbiota, as well as to identify specific alterations that might be associated with various pathologies, such as ulcerative colitis, colorectal cancer, and necrotizing enterocolitis [3–5]. During the last 10 years, most of these studies have been performed with metagenomic approaches, which allow relatively fast assessment of the microbial composition by highthroughput sequencing (Table 1). Despite completely missing the microbial species present in the studied ecosystems at a low concentration (<10–10 mL), direct metagenomics has progressively replaced molecular techniques based on PCR amplification steps, such as sequencing libraries of cloned ribosomal amplicons or pyrosequencing of 16S rRNA amplicons, as these PCR-based approaches were limited to eubacteria, and did not provide any information on the metabolic capacities of the studied microbiota. Microarrays have also been used to define the microbial composition of the intestinal human microbiota; however, this approach also has major limitations, including a low depth of analysis, and the fact that it only identifies the known bacterial species, for which corresponding sequences are present on the chip [6]. Thus, ‘culturomics’, the new approach depicted in the article by Lagier et al. [7], represents a completely new approach to the study of complex microbial ecosystems, such as the human intestinal tract, that: (i) has the potential to detect minority populations; (ii) is not restricted to eubacteria; and (iii) provides strains that allow extensive characterization of new species and allows the study of interactions between different bacterial strains present in a given microbiota (Table 1). Another additional advantage of using culture instead of molecular approaches is the additional information on the viability of detected microorganisms. Providing strains for downstream studies is not trivial. Indeed, as metagenomics only provides sequencing data, metagenomic-based research investigating the impact of the microbiome on a given disease (e.g. obesity) had to be split in two parts: first, bacterial species that are probably involved in weight gain were identified by metagenomics; then, animal experiments were performed with a strain of the same species, but generally recovered from completely different ecosystems, and thus possibly not containing the bacterial genes that are important in triggering obesity. In contrast, with culturomics, it is possible to directly test the strain originating from the patient microbiota presenting the disease of interest. Culturomics may be defined—by analogy with metagenomics—as an approach allowing an extensive assessment of the microbial composition by high-throughput culture (Table 1). Thus, Lagier et al. have identified as many as 32 500 different colonies recovered from three human stools [7]. Such very high-throughput identification was only possible because of the availability of matrix-assisted laser desorption ionization time-of-flight mass spectrometry, which not only represents a revolution in clinical diagnostic laboratories [8,9], but also represents a revolution in microbial ecology, especially when it is coupled to smart incubators and automated colony-picking systems to constitute the next generation of culturomic approaches. Indeed, culturomics will further improve, thanks to automation, miniaturization, and improved technology. It is noteworthy that Lagier et al. not only propose a new concept, i.e. ‘culturomics’, but also, more importantly, they provide in this milestone article a proof-of-concept. They applied 212 different culture conditions, and successfully cultured 340 different bacterial species, as well as five fungi and the largest virus ever found in a human sample [7]. Moreover, 32 new species have been discovered. This