The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Abstract

Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

Functional Intestinal Bile Acid 7α-Dehydroxylation by Clostridium scindens Associated with Protection from Clostridium difficile Infection in a Gnotobiotic Mouse Model

“…All Oligo-MM 12 strains are available at http://www.dsmz.de/miBC. In-depth description of the Oligo-MM 12 consortium species and description of novel taxa are provided elsewhere (Brugiroux et al, 2016; Lagkouvardos et al, 2016). SPF mice were purchased from Envigo (formerly Harlan, The Netherlands).…”

“…The bacterial strains combined in the Oligo-MM 12 consortium were recently described in detail and are openly available from the DSMZ repository (Lagkouvardos et al, 2016). Gnotobiotic Oligo-MM 12 -associated mice (henceforth referred to as “stable defined moderately diverse microbiota, murine 2,” short sDMDMm2 mice) were originally generated by colonization of germ-free mice with a cocktail of cultured bacteria.…”

Nlrp3-dependent IL-1β inhibits CD103+ dendritic cell differentiation in the gut

“…Raw read files were processed using IMNGS (www.imngs. org) (43). OTUs were picked at a threshold of 97 % sequence similarity.…”

“…Only those with a relative abundance above 0.5% total sequences per sample were kept. Readouts and statistics were generated in R using Rhea (https://lagkouvardos.github.io/Rhea/) (43).…”

Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health

“…Efforts are already underway to establish a comprehensive collection of mouse gut bacteria with associated genome sequences. The preliminary data suggest that a minimal consortium of 18 strains can cover up to 75% of the known functional potential of the mouse microbial metagenome (Lagkouvardos et al, 2016). …”