Culturomics: a new approach to study the human microbiome.

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