You are the Chosen One, at least by your bacteria

Host genomics is not the main decision-making factor for bacteria immigrating into human body, but  it is an important factor. Two papers recently published in the Proceedings of the National Academy of Sciences help to understand why you are chosen and how the choosers make their decisions.

Benson et al studied microbes of mice C57BL/6J, HR and their offspring. BL6 is a common inbred line prone to diet-induced obesity, type 2 diabetes, and atherosclerosis. They also develop age-related hearing loss, if are not following recommended dietary allowance. High runner (HR) mice is lean and fit and loves to exercise - it's in the genes.

Noninvasive 16S RNA sequencing (Roche 454) showed that the abundance of microbes in "core measurable microbiota" depended on 530 host SNPs, mostly those located in 13 quantitative trait loci and was influenced by 5 more QTLs.

Some of the genetic regions appear to determine what kind of bacteria immigrate and strive in the host, other regions influence the immigration rate, attracting a wide variety pf or specific nationalities. Supplementary material elaborates on  sources of variation and genotype frequencies at given SNP locations. 

How are bacteria making their decisions to colonize or not to colonize?

In another PNAS article, Ben-Jacob and Schultz explain why microbes could be smarter than humans. We may think that our decisions are well thought and sophisticated, but we are, indeed, influenced by other people and our over-interpretations of other people's reactions. Bacteria can assess the noisy and stressful environment around them more objectively and rationally. They anticipate possible drastic changes in the environment and find the best decisions by providing every bacterium with the freedom to choose its own fate. This may look like throwing dice, but the colony manages the odds and effectively programs the effect of the noise on the gene circuit performance.

Our genes may be shaping microbial communities that could, in their turn, control our physical and mental health. Yet our lifestyle choices could break the patterns and let us decide what types of bacteria we want to live with.

And for those whose fight against unwanted microbes is too hard, there may be light in the end of the tunnel: Personal Genomes project has just announced a new collaboration with Rob Knight and Noah Fierer that will enable to explore the microbial diversity of various habitats of the human body and correlate it to the genotype.

References

• Andrew K. Benson,, Scott A. Kelly,, Ryan Legge,, Fangrui Ma,, Soo Jen Low,, Jaehyoung Kim,, Min Zhang,, Phaik Lyn Oh,, Derrick Nehrenberg,, Kunjie Hu,, Stephen D. Kachman,, Etsuko N. Moriyama,, Jens Walter,, Daniel A. Peterson,, & Daniel Pomp10.1073/pnas.1007028107 (2010). Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors Proceedings of the National Academy of Sciences of the United States of America, Published online before print October 11, 2010
• Ben-Jacob E, &; Schultz D (2010). Bacteria determine fate by playing dice with controlled odds. Proceedings of the National Academy of Sciences of the United States of America, 107 (30), 13197-8 PMID: 20660309

Human Body: A map of where Bacteria live

Who's The True You? A collaboration of our body and 100 trillion of microbes (bacteria, algae, yeast, protists and more) colonizing it.

Microbiota is specific to every individual, and varies systematically across body habitats and time, as well as geographical location, preventing or causing a disease after exposures to infectious agents.

Some human skin locations harbor even more diverse bacterial communities than the gut that we were thoughtfully nourishing with probiotics.

New analysis published in Science Express adds more information to the earlier results (from May 2009, for example), showing how diverse the microbiota is and how easy it is to re-colonize the skin.

We mapped some of the findings as shown in the Figure (on the right; the figure on the left maps bacteria in GI tract, from Dr. Richard Lord’s presentation at the 2008 Functional Medicine Symposium in Carlsbad, CA). Moist sites are shown with blue arrows, such as inside the nose, the armpits, the navel, dry areas are shown with green arrows, such as the forearm and oily sites are shown with yellow arrows: inside the ear, between the eyebrows, forehead, the back of the scalp.
Sites of most bacterial diversity were : The index finger, back of knee, forearm, palm and sole of foot.The forehead displayed the least diversity (with bacterial populations strongly preffering this site and not letting other bacteria to co-habit the space), but there were individual differences between different people. The mouth cavity showed the least variation in diversity both within individuals and between people. Studies of other microbes such as viruses and bacteriophages show low diversity in the airways as well, even though the human respiratory tract is constantly exposed to a wide variety of microbes and environmental agents. There is a difference between diseased and non-diseased individuals though - in Cystic Fibrosis (CF). for example, viromes are enriched in aromatic amino acid metabolism. Note that this disease causes a distinct acidic breath - the more severe the condition is in an individual, the more acidic his breath becomes. The microbes were especially sensitive to amino-acid starvation indicating that therapeutic measures may be more effective if used to change the respiratory environment, as opposed to shifting the taxonomic composition of resident microbiota.
Altered breath resulting from changed micrflora is a known phenomenon and it can be detected not only by complex mass spec machines, but also by devices used in QA testing of foods (e.g. Cyranose pick up the scent of penzane, isoprene acetone, and benzene in the breath of lung cancer patients) and car air quality sensors to study human "fermentome". (See also ongoing clinical trials on chemicals in human breath for diagnostics of diseases).

Altered bacterial populations could, indeed, be studied by metabonomic profiling. At present, however, the most accurate analysis, was performed based on microbial DNA or 16S RNA.
The study subjects were sampled four times each over a three-month period, typically after showering an hour or two earlier. Microbial DNA was then isolated directly from swabs used for sampling each body site. To recover bacteria from the skin surface, it was enough to swab it once by a wet cotton swab in 30s.