Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction

Abstract

Whole metagenomic shotgun (WMS) sequencing has dramatically enhanced our ability to study microbial genomics. The possibility to unveil the genetic makeup of bacteria that cannot be easily isolated has significantly expanded our microbiological horizon. Here, we report an approach aimed at uncovering novel bacterial species by the use of targeted WMS sequencing. Employing in silico data retrieved from metabolic modelling to formulate a chemically defined medium (CDM), we were able to isolate and subsequently sequence the genomes of six putative novel species of bacteria from the gut of non-human primates.

Fig. 1

Identification of unique genomic signatures of putative novel strains belonging to the genus Bifidobacterium. Panel A displays the relative abundance of the reconstructed bifidobacterial genomic material at species level obtained from CaPy, SaIm, SaOc, MiAr, LeRo and LeCh samples. The x‐axis shows the number of base pairs (bp) assigned to each species. Only species that display at least 30 kb of the total amount of the assembled data were included in the histogram. Panel B exhibits the distribution of unique COGs identified in putative novel bifidobacterial species. Panel C shows the number of unique genes of putative novel bifidobacterial species correlated with the degradation of carbon sources in each sample. [Color figure can be viewed at wileyonlinelibrary.com]

Fig. 2

Phylogenomic tree of the genus Bifidobacterium based on the concatenation of 130 core protein sequences from genomes of 10 novel strains isolated in this study and the 94 type strains of the genus Bifidobacterium. Different colours show the division into 10 phylogenetic groups, of which B. longum and B. bifidum groups are populated by the novel strains (highlighted in bold). The phylogenetic tree was constructed by the Neighbour‐joining method, with the genome sequence of Scardovia inopinata JCM 12537 as outgroup. Bootstrap percentages above 50 are shown at node points, based on 1000 replicates of the phylogenetic tree. [Color figure can be viewed at wileyonlinelibrary.com]