Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

Abstract

Background Bacteria within family S24-7 (phylum Bacteroidetes ) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had not been cultured until recently and the family classification is still ambiguous, interaction with their host was difficult to study and confusion still exists regarding sequence data annotation. Methods We investigated family S24-7 by combining data from large-scale 16S rRNA gene analysis and from functional and taxonomic studies of metagenomic and cultured species. Results A total of 685 species was inferred by full-length 16S rRNA gene sequence clustering. While many species could not be assigned ecological habitats (93,045 samples analyzed), the mouse was the most commonly identified host (average of 20% relative abundance and nine co-occurring species). Shotgun metagenomics allowed reconstruction of 59 molecular species, of which 34 were representative of the 16S rRNA gene-derived species clusters. In addition, cultivation efforts allowed isolating five strains representing three species, including two novel taxa. Genome analysis revealed that S24-7 spp. are functionally distinct from neighboring families and versatile with respect to complex carbohydrate degradation. Conclusions We provide novel data on the diversity, ecology, and description of bacterial family S24-7, for which the name Muribaculaceae is proposed. Electronic supplementary material The online version of this article (10.1186/s40168-019-0637-2) contains supplementary material, which is available to authorized users.

Changes in the Solid-, Liquid-, and Epithelium-Associated Bacterial Communities in the Rumen of Hu Lambs in Response to Dietary Urea Supplementation

“…These bacteria have also been observed in the solid and liquid fractions of dairy cattle (De Mulder et al, 2017;Schären et al, 2017) and yak (Ren et al, 2019). The bacteria within the family Muribaculaceae encode enzymes that degrade plant glycans (hemicellulose and pectin) and host-derived glycans; they also exhibit specificity in nitrogen utilization and harbor a specific urease (Ormerod et al, 2016;Lagkouvardos et al, 2019). Members of the Christensenellaceae family contain enzymes, such as α-arabinosidase, β-galactosidase, and β-glucosidase (Perea et al, 2017).…”

Respiratory viral infection alters the gut microbiota by inducing inappetence

“…There was no change in these phyla in control or single housed ad libitum fed mice. At the family level, the major change seen was an increase in the abundance of the S24_7 family (also known as Muribaculaceae (Lagkouvardos et al, 2019): Fig.1G). This pattern was very similar to that previously observed after RSV infection (Groves et al, 2018).…”

Shift of maternal gut microbiome of Tibetan antelope (Pantholops hodgsonii) during the perinatal period

“…We only started to decipher the functions of the gut microbiome in the perinatal period and many unknowns remain to be explored. For example, the family Muribaculaceae is recently classified (Lagkouvardos et al, 2019) and we are not sure about their precise roles in the transition from late pregnancy to the postpartum period. The same applies to other taxa, such as Christensenellaceae_R-7_ group, Ruminococcaceae_UCG-010, Ruminococcaceae_UCG-014, Alistipes, and Lachnospiraceae_NK4A136_ group.…”