Cultured microbes represent a substantial fraction of the human and mouse gut microbiota

Abstract

During the last 15 years, molecular techniques have been preferred over culture-based approaches for the study of mammalian gut microbiota, i.e. the communities of microorganisms dwelling in the intestine of mammals. The main reason is the belief that the majority of gut bacteria, especially strict anaerobes, escape cultivation. Despite numerous such statements in publications, the literature does not provide a clear overview on the subject. In the present manuscript, we highlight recent work on the cultivation of bacteria from the intestine of mammals, review the literature and provide novel data pertaining to cultured fractions of mammalian gut microbiota. These data show that, despite marked inter-sample variations, 35 to 65% of molecular species detected by sequencing have representative strains in culture.

Keywords: 16S rRNA gene; anaerobic cultivation; cultured fraction; dark matter; gut microbiota; intestinal bacteria; microbial diversity; minimal microbiome.

Figure 1.

Estimates of the cultured fraction of human and mouse gut bacteria and archaea as detected by high-throughput sequencing of 16S rRNA amplicons. The analysis was based on 14,734 full-length sequences of isolates and 26,036 complex gut microbial profiles (16,667 from human and 9,369 from mouse). Single OTUs from these profiles were matched to the isolate sequences, and those with similarities above the conservative species- (97%) and genus- (95%) specific levels were considered to originate from cultured bacteria. Results were expressed either as percentage of OTU richness or corresponding cumulative relative abundance of sequences. The figure illustrates data obtained when considering OTUs that occurred at a relative abundance > 0.5%. For estimates based on all OTUs, readers are referred to Supplemental Figure S1.