Understanding the pieces of all those meeces: characterizing mice gut microbiota

tom and jerry

Image from Google image commons

In an age where a tremendous amount of data is generated, this week has seen some moves towards providing open access to extensive data sets. These attempts have been in the realm of chemistry as well as microbiology, where in a recent paper by Lagkouvardos and colleagues, access was provided to a set of isolates and their respective genomes, characterizing the microbial diversity of mice intestines.
It’s evident that human microbiomes are linked to both physical and mental health, and it’s also essential to understand how gut fauna might also affect mice. Since mice models are used extensively to predict how drugs might impact humans, it’s only logical we characterize the diversity and overlap humans share with the microbiomes of our furry little friends.

Last week, Lagkouvardos et al., delved into the world of gut microbes using an extensive culture-based approach coupled with whole genome sequencing. The study also focused on determining host-specificity of species diversity and if culture-based techniques accurately reflect diversity in an ecosystem.
In total they cultured 1,500 isolates, and then, using morphological observations as well as 16s rRNA gene sequences, selected a sub-sample of 100 strains to represent the collection, which then deposited in the DSMZ. For good measure, they also threw 8 species they had cultured before and 4 other labs had previously reported, into the analysis.

Lagkouvardos et al., Figure 1.

Whole genomes were obtained from the 100 strains made publically available, which is a substantial effort, even if it might be nice to have access to a bigger proportion of the 1,500 originally cultures. As a side note, even though the cost of one or two strains is nominal, buying the whole set of 100 could run up a price tag of about 13,000 USD. These 100 isolates represent 76 different species, encompassing a broad swath of microbial diversity.

Modified from Lagkouvardos et al., Supplemntal Figure 3.

They also identified 15 strains with 16S sequences that were significantly divergent (<97% ID) from those currently reported.

Lagkouvardos et al., Figure 2.

The authors ultimately demonstrated the utility of both classical methods as well as recently developed sequencing technology to characterize the mouse microbiome. They also emphasize that their research lays the groundwork for future genetic studies of the mouse gut microbiome, as well as provides an essential tool for the general research community (miBC), by providing access to mouse-enriched taxa and strains relevant to ecological and health related studies.

Lagkouvardos et al., Supplemental Figure 2.

As the authors acknowledged, the 16S is not the most definitive measure of genome diversity, and it would be great to have more info on the diversity of strains classified as the same species. However, this study represents the foundation for further research and in order to fully exploit the potential of this database, it will require collaboration from the broader community. There has already been interesting research looking at the coevolution of microbiomes in humans and mice, as our ability to share and fully exploit data advances there’s no telling what else might be in store.
Cho, Ilseung, and Martin J. Blaser. “The human microbiome: at the interface of health and disease.” Nature Reviews Genetics 13.4 (2012): 260-270.
Goodrich, Julia K., et al. “Cross-species comparisons of host genetic associations with the microbiome.” Science 352.6285 (2016): 532-535.
Lagkouvardos, Ilias, et al. “The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.” Nature Microbiology 1 (2016): 16131.
Wang, Mingxun, et al. “Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.” Nature Biotechnology 34.8 (2016): 828-837.

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