Deciphering individual bacterial strains in the gut is important to understanding the microbiome

Phylogenetic trees go beyond just genus and species, but also to strains.

When scientists determine the bacterial population of one’s microbiome using genetic sequencing they are forced to make determinations of the populations’ phylogeny.  Some scientists will determine the abundance of each genus, like all the bacteria that belong to the Clostridium genus, while others will narrow their scope to specific species, like all the bacteria that belong to the Clostridium difficile versus Clostridium scindens species.  These distinctions can be immensely important.  For example, C difficile can cause colitis, but C. scindens can prevent colitis, so measuring the amount of Clostridium in the gut does not paint as clear a picture as measuring the amount of C. difficile (potentially harmful) and C. scindens (potentially helpful).  There is, however, a deeper level of differentiation within species: the strain (e.g. C. difficile A90 vs. C. difficile AA1).  These strains are very similar genetically, especially in the genomic regions most important to determining phylogeny, there are however, potentially important genetic differences. 

Scientists have long realized and understood that by characterizing the species population of the microbiome they were neglecting possible important strain-specific effects.  There have even been specific examples within the microbiome that differences in strains are important, like strains within the Staphylococcus aureus that differ in their antibiotic resistance (e.g. MRSA).  Just how important these strain-specific differences are is unknown, but there is mounting evidence they need to be taken into account.  Last week in the journal Cell, researchers from the University of Washington published results that showed strain-specific differences can be vast and immense, and that this is even more so true in the microbiome where genetic mutations and genetic transfers happen at a high rate.

The researchers used metagenomics data from patients with IBD from a previously published data set.  They took this data, compared it with previously published species’ genomes, and did a lot of fancy bioinformatics to measure strain-specific genetic differences within species.  I don’t mean to neglect the bioinformatics aspect of the paper, which is critically important their results, but the details of their ‘pipeline’ are beyond the scope of this short blog.  In any event, they learned that there were many examples of different strains that coded for as much as 20% more copies of specific genes.  As it turns out, these differences were prevalent in genes that coded for important functions, like transport, signaling, biosynthesis, motility, secretion, and virulence.  These are important processes in the gut environment, and each may have important impacts on the host.

Before this paper, the level of genomic resolution and bioinformatics needed to make strain specific determinations was difficult, and beyond the expertise of most labs.  Now that these researchers have published their methods, this type of strain analysis can be incorporated into many more experiments.  It does have its drawbacks, as full genomes are needed for each species that is analyzed, and inserted/deleted genes are not analyzed, but overall it is a very important paper.  As we move forward in microbiome research, this type of analysis that incorporates specific strains will become critical in associating diseases and phenotypes with the microbiome.

The oral microbiome of the medieval man

Plaque that forms on teeth, also called calculus, can be preserved for a very long time, and traps all types of biomolecules and bacteria that are found in our mouths. An article published by Nature Genetics explores a study conducted to observe the oral microbiome on calculi of ancient human teeth and its differences from the oral microbiome that exists today. In this study, the ancient calculi showed the historical importance of gene transfer in the microbiome, which has been, and still is a rich consortium of bacteria that readily and rapidly exchange gene. 

The researchers studied the teeth of four adult human skeletons from the medieval city of Dalheim, Germany, who showed signs of mild to severe periodontal disease, as well as the current teeth of nine people. Interestingly, the same bacteria, proteins, and pathogens were identified in both the ancient and modern calculus, despite the differences in oral hygiene and diet between each time period. Researchers also found evidence of antibiotic resistance genes, like efflux pumps, in many members of the ancient plaque.  This means that horizontal gene transfer was clearly occurring between members of the oral microbiome, and the genes for some forms of antibiotic resistance have ancient roots.  However, other genetic adaptations for antibiotic resistance against modern drugs were not identified, even those that are ubiquitous in the oral microbiome today.  This should be no surprise, as modern antibiotics were not in use in the Middle Ages.

Medieval dental calculi, and fecal samples for that matter, give us a peak at what the ancient microbiome looked like.  By studying it, we can learn how the human oral microbiome has adapted over time in response to changes in human behavior, diets, hygiene, and antibiotic use.  

Altering the microbiome, diet, probiotics, and FMT

I recently had the pleasure of hearing a lecture by Eric Alm, an associate professor at MIT.  During the lecture he described a number of studies his group has performed, and I would like to share some of his conclusions.

In his first study he and his student sampled their own microbiome every day over the course of one year, while cataloging every minute detail of their lives over the same time frame.  They were investigating what activities have real effects on the microbiome, and as they discovered, unsurprisingly, what one eats is the most important.  They found that the amount of fiber in the diet perturbed the microbiome most, in addition to things like orange juice, yogurt, fruits, and soup.  They also discovered that after flossing, a certain bacteria from their mouth, would show up in their stool.  More importantly, they confirmed that the microbiome is robust, and rebounds after drastic changes like vacationing in foreign countries.  In addition, they learned that perturbations occur within 24 hours.  Most of the results of the study can be found here.

In another study, Eric discovered that the microbiome is a hotbed for horizontal gene transfer.  With so many genetically different bacteria living and evolving in close quarters there has been a great amount of genes passed around.  He also discovered that the microbiome of farm animals (which are given antibiotics to gain weight), develop antibiotic resistance, which is then transferred to our own guts' microbiomes through this lateral gene transfer.  The results from this study are published here.  

Another study focused on mice that were fed Lactobacillus in their drinking water versus those control mice that were not.  The mice that were given the probiotic were skinnier than control mice, and had shinier coats and healthier skin.  They then discovered that it was alterations to the immune system, rather than the Lactobacillus themselves, that were causing these changes.  These results are not yet published.

Finally, Eric talked about his stool bank, OpenBiome, which we previously discussed in a separate blog post.  OpenBiome is dristributing fecal material to be used in fecal microbiota transplants (FMTs).  We have talked about FMTs in this blog extensively, and even touched on some studies that showed mice lose weight, or become less stressed, when given the microbiome of a healthy donor.  I asked Eric if any additional phenotypes were being transferred with FMTs in humans.  He mentioned in one case a patient with alopecia suddenly grew hair after the FMT, but eventually lost the hair again.  In another case he mentioned a skinny woman that became obese after treatment with FMT.  We will leave the reader to decide how these things play into the overall ethical controversy surrounding FMTs.