|Credit: Dana C. Thomas/University of Washington|
Here's the headline of a recent paper: "Extensive strain-level variation is detected in the human gut microbiome, with differences in gene copy-number impacting specific adaptive functions and linked to obesity and inflammatory bowel disease."
It's not the species of gut microbe...it's the strain.
Professor Art Ayers of Cooling Inflammation blog has been hammering this home to us for years. He once compared the colon to a 3-D printer, making a new copy if itself with each meal. Dr. Ayers once remarked:
Just a thought: I think of the gut, clinging biofilms and churning mixtures of food and bacteria as a 3D nanobioprinter, aka "Lamarck." Based on a niche description, Lamarck produces complementarily approximate bacteria.
Lamarck, of course, is a reference to the theories of evolution and the adaptations that occur on a very quick timescale in the human gut. To further clarify, Art says:
By providing niches with selective advantage to particular phenotypes among prodigious genomic diversity, the gut establishes genotypes with phenotypes that fit the niches. There is continuous flow of food and bacteria through the gut, and the only bacterial genotypes to persist are those that increase in numbers relative to others. At the same time, the genomes are very dynamic, since dozens of replications errors, mutations, occur during each bacterial division and bacteria from unrelated species exchange genes. So, though this appears to be Lamarckian evolution with the niche defining the adaptations, it is actually just exaggerated selection within outrageous diversity that makes it look like instructions were given to a bioprinter.
A paper released January 29th, 2015 in Cell magazine further explains and clarifies some of the mysteries of the gut biome:
...researchers at the University of Washington show that even when people share microbes in common, the exact strains each carries might be very different.
The implications of this paper are huge, but hardly new to science. Even though we have extensive libraries showing the taxonomic characteristics of our gut flora, and can accurately identify the species occupying the niches we provide and fermenting the food we eat, we cannot really say that X microbe is better than Y. As described by the researchers:
Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously sequenced strains, and accordingly, the prevalence of intra-species variation, its functional role, and its relation to host health remain unclear.
Your Unique Microbes
|Cite for Picture|
While studying the variations present in normal human commensal bacteria, lots of variability was seen in genes encoding for movement. Bacteria need to move, usually, and have evolved ways of doing so. For instance, in the ever-present Eubacterium rectale, they discovered seven different genes for movement: four for "flagellation," two for "chemotaxis," and one for 'twitching.' Depending on which genes are 'turned-on' the bacteria can act in radically different way. While E. rectale is a normally harmless bacteria, the implication of these different modes of movement in a species like E. coli can make a world of difference in the outcome of an infection. But not only is "movement" variable, similar genetics determine the food they use.
Similar differences in genes are seen in bacteria that ferment galactose, starch, sucrose, fructose and mannose, as well as other sugars. So the appearance of key microbes on a stool test only tell part of the story. And bacteria that are thought to produce butyrate may actually be manufacturing a wide variety of compounds depending on their individual genes. Again, Dr. Ayers was being very insightful when he quipped:
People are sick because of life style corruption of their gut printer. They literally make themselves sick and print pathogens that are selected for their ability to spread. The larger the population of ebola infected people, for example, the greater the chance it will spread by casual contact, since the Ebola virus mutates a thousand times faster than bacteria and selection for aerial transmission is very high.
Each microbe we harbor can vary greatly in its genes...the genes they have, the genes they use, and the number of each gene they possess. Just like humans, there may be blue-eyed Bifidobacterium breve, brown-eyed, or green!
Same Microbes, Different Personalities
These genetic differences within a species have a major impact on that microbes capabilities. Its drug resistance, virulence, the food it desires, and the chemicals (or smells) it produces can all be different depending on "how it was born." These differences, as the authors explain:
These different capabilities among strains can obviously affect the microbe's lifestyle, yet many may also translate to consequences for the health of the human host.
This research is vital to our understanding of the gut microbiome and why it's important that people partake in uBiome and American Gut. This is all a numbers game! The more data available, the better our understanding becomes. Already they've identified "over 5,000 genes in dozens of species" with significant genetic differences, and that some individual microbes have variations in almost 25% of their genes.
Does this mean we throw our hands in the air and stop worrying about our microbiome? Not really. But it should give us pause when self-proclaimed "gut gurus" tell us they know exactly what a healthy microbiome looks like, especially when they then offer to sell us all we need to test for and grow these magical microbes.
In the end, our microbiome is going to do what it has done for billions of years...adapt to our food source and try to keep us healthy. If a microbe could "want" something, it would probably be that its host remains healthy, happy, and horny. Individual variations in your own genetics as well as the genetics of the microbiome ensure that each persons "perfect blend" of gut bugs will be vastly different.
The perfect microbiome, though different for each person, will undoubtedly come about from eating a wide variety of plant fibers, fermented foods, and avoiding inflammatory modern foods along with a good routine involving sleep, exercise, sun exposure and a low-stress life.
[Hattip Gemma and Dr. Ayers]