What is the Microbiome?

The microbiome is the collection of microorganisms living in and on an organism, such as a human or mouse. Interest in the microbiome is increasing due to a clearer understanding of the its impact on a number of different physiological systems, as well as the realization that microbial communities can vary widely from person-to-person.

the structure of the microbiota across species
Aleksandar D. Kostic et al. Genes Dev. 2013; 27:701-718.
Copyright© 2013 by Cold Spring Harbor Laboratories Press
Although there can be significant inter-individual variation in the composition of the microbiota, broad trends exist within a given species, particularly at the phylum level. Here, phyla are represented by color, and the relative abundance of the lower taxonomic levels is indicated by font size.

While each of us has a unique microbiota, it always fulfills the same physiological functions with direct impact on our health. Disturbances in the microbiome have been noted in many disease states. Is this correlation or causation?

Microbiome and Disease

Researchers report that microbiota train the immune system. The microbiome and host immune system act in concert to induce tolerance where required and mount a protective immune response to threats. Dysbiosis - an imbalance or disturbance in the microbiome - has been implicated in a variety of disease states including:
  • Metabolic Disease
  • Cancer
  • Arthritis
  • Multiple Sclerosis
  • Depression
  • Sepsis
  • Liver Disease
Microbiome Activities Graph

Microbiome by the Numbers

microbiome by the number

Copyright© College of Natural Sciences at The University of Texas Austin

Mice as a Microbiome Research Tool

The laboratory mouse has long been a useful tool for in vivo studies, as it is easy to manipulate their genetics, health and microbiome. But with trillions of microbes in the human gut, and variation from individual to individual, how can mouse microbiome studies provide useful data that translates to human studies?

Microbiome researchers may finally have the tools to address such foundational questions. Scientists at the Technical University of Munich published a study that established the Mouse Intestinal Bacterial Collection (miBC) and made it available to the scientific community. The study looked at mice on both chow and high fat diets in a variety of facilities. This study provided reference data for future studies and will support future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies.

This groundbreaking work is essential for researchers looking at the interplay of microbiota and disease, and developing therapies that manipulate the human microbiome.

Lagkouvardos 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, Article number: 16131 (2016) doi:10.1038/nmicrobiol.2016.131

Studies using mice to model the microbiome often take one of two approaches: starting from germ-free stock which are free of all organisms (except the mouse itself), and antibiotic treatment to knock down the microbiome.

Research AimStatus of Host
Investigate microbial phenotype transfer of manifestations known to be microbiota dependentXX
Investigate microbial phenotype transfer of manifestations not known to be microbiota dependent X
Investigate effect of disrupting the microbiome in certain life stages of the hostX 
Investigate effect of targeting certain groups of bacteriaX 
Investigate effect of monocolonization X
Investigate effect of colonization with a few, defined organisms X
Lastly, here's an informational video about the microbiome from NPR:

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