The microbiome and its influence on evolution

The interaction between a microbiome and its host species, and the impact of this interaction on both bacterium and host organism evolution, is a fascinating subject.  Known as the hologenome theory of evolution, it has been widely understood that microbiome communities and their animal hosts undergo natural selection in concert.  In other words, human and microbiome evolutionary processes are not mutually exclusive.  In the hope of gaining a deeper understanding of this relationship, a recent study published in Nature Communications examined the exact role of the microbiome in host speciation of a vertebrate organism.  Researchers explored evolutionary divergence within two subspecies of mice and examined to what extent genetic loci played a role in regulating intestinal microbiota populations. 

Four strains of mice were used to develop a unique mouse model paradigm.  Researchers collected two naturally occurring and genetically distinct mouse populations – M.m. musculus and M.m. domesticus –that are geographically isolated in Europe (see map).  Interestingly, a small “hybrid zone” exists in which both subspecies interbreed.  Researchers examined these three distinct populations and added a fourth by artificially producing a hybrid strain between both subspecies under strict laboratory conditions.  The purpose of the laboratory-bred hybrid was to control for any confounding influence from environmental factors (it has been demonstrated that environment can influence microbiome populations and gene expression).  A subsequent analysis was performed to investigate intestinal microbiome genetic profiles for both pure species and hybrid species in addition to gene expression with potential connection to pathological indications in host species. 

Pyrosequencing techniques of a bacterial rRNA gene were used to identify genetic differences between pure species and “naturally occurring” wild-hybrid species.  Bacteria community structure varied significantly in hybrid generations, both those obtained from the hybrid zone and bred in the lab.  The most significant differences were observed in the laboratory-bred hybrid generation.  Furthermore, there was a significant decrease in bacterium species richness in both wild and lab hybrid mice.  QTL mapping, a technique used to assess underlying genetic factors, displayed a low number of microbiota genomic loci present in both hybrid strains.  This finding was thought to explain a 14.1% variation in bacterial community structure, ultimately suggesting that genetic deficiencies disrupted microbiome communities. 

QTL profiling of microbiota also indicated a high frequency of genes implicated in immune system regulation.  Laboratory hybrid generations were shown to have imbalanced T-cell subset populations at various immune sites (e.g. spleen, mesenteric lymph nodes) in combination with the aforementioned alterations in bacterium community structure.  Additionally, histological analysis of intestinal mucosa revealed significant increases in inflammatory cell infiltrates and epithelial ulcerations in both wild and lab hybrid mice as compared to both purebred wild species.  The investigators suggest a discrepancy in communication between microbiome populations and the host immune cells. 

The data from this study suggest abnormal genetic architecture and irregular immune function result in an altered intestinal microbiome due to cross-breeding between two vertebrate subspecies.  The hybrid species displayed poor fitness for survival.  As suggested by the authors, species divergence, and the consequentially genetic disruptions resulting in an altered microbiota population, is perhaps responsible for generating subspecies population isolation.  This theory offers a possible explanation or contributing factor as to why M.m. musculus and M.m. domesticus populations are geographically distinct.  Obviously, evolutionary biology is an enormously complex process with many diverse and distinct influences.  However, as this article proposes, perhaps the microbiome has had a much more profound influence on evolutionary fate than we previously realized.


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The views expressed in the blog are solely those of the author of the blog and not necessarily the American Microbiome Institute or any of our scientists, sponsors, donors, or affiliates.

Probiotics may help fight the flu

The influenza viruses are the devastating viruses that cause the flu.  They highly communicable and can cause pneumonia, ear infections, sinus infections, asthma and even diabetes.  Basically, they are really nasty bugs that people have been suffering from, and trying to get rid of, for at least the last 2000 years.  One possible treatment, which is now being explored, is the use of probiotics to prevent flu and its virulence.  Scientists in Japan recently tested how one type of probiotic, Bifidobacterium longum, could combat the flu in mice.  They published their results in Microbiology and Immunology.

Mice were divided into two groups, one which received the B. longum for 17 consecutive days in their drinking water, and one which did not.  On day 14 of the study all the mice were infected with flu via injection.  The researchers then monitored all of the mice to see the effect of the probiotics.  Surprisingly, the mice which received the probiotics had improved clinical symptoms as compared to those that did not.  For example, the mortality rate dropped from 70% to 35% after 12 days in those mice that had been given probiotics.  In addition, the probiotics seemed to help with breathing and general activity as well as kept mice from losing as much weight as the control mice.  Beyond this, the probiotics appeared to decrease the proliferation of the influenza in the respiratory tract, which resulted in a suppression of overall inflammation as compared to the mice without probiotics.  Finally the researchers presented evidence for several possible pathways by which the probiotics were helping the mice.

This study is fascinating in that it shows a simple, yet powerful tool to alleviate the flu in mice.  It also begs for a follow-up study to see if the same type of probiotic response would be observed in mice infected with rhinoviruses, the cause of the common cold.  While we here at the AMI encourage everyone to get vaccinated for the flu, if for whatever reason you cannot, perhaps consider eating a bit more yogurt this winter.

Please email blog@MicrobiomeInstitute.org for any comments, news, or ideas for new blog posts.

The views expressed in the blog are solely those of the author of the blog and not necessarily the American Microbiome Institute or any of our scientists, sponsors, donors, or affiliates.