Microbiota and Their Genes

cartoon-detective

As humans, we all have resident bacteria messing around with our insides, interfering with our genes for better or worse. It’s like the tenants in the basement are in charge of the circuit breaker box, and can affect any light fixture, garage door, or electric can opener, by switching it on or off at will.

Their will, not ours. So it behooves us to figure out what they are doing, and what they call themselves doing, because their actions and motives are both are important if we are to coexist.

The eventual goal is to manipulate the microbial consortia “by altering their ecology and gearing them towards desirable outcomes…” Meanwhile, we have to put up with them and their ways. Not only is it an arranged marriage we can’t get out of but the microbiota can decide to give us Type 1 diabetes.

The hope of diagnosing this illness sooner is one of the motivations that people in the field are driven by. Researchers want to know, for instance, how diabetes is related to the ways in which the bugs synthesize thiamine, because a cause-and-effect relationship seems to be happening there.

What causes type 1 diabetes mellitus, or T1DM? There can be a genetic predisposition to it, but other things are going on too. Insulin is produced by beta cells in the pancreas — except when something stops this from happening. What is that something?

Possibly, interference from gastrointestinal microbes who for some reason mis-identify insulin as a dangerous foreign substance. As Paul Wilmes, Associate Professor, University of Luxembourg, puts it in an article for Nature Microbiology, “gene-environment interactions are at play such that external factors may trigger the auto-immune destruction of insulin-producing beta cells of the endocrine pancreas which results in T1DM.”

Detective agency

Like clumsy burglars, the microbiota can’t help leaving evidence, known as biomarker organism signatures. That is how we deduce what they are up to. Wilmes wrote:

Microbes are ubiquitous and their importance with respect to human health and the environment is now universally accepted. However, their actions in the wild are much less well understood.

His team first explored biological wastewater treatment systems and the ecology of lipid-accumulating bacteria therein. He explains their research protocols in great detail, and how “activities depend on many factors and cannot be inferred by conjecture based solely on information about presence/absence and/or genetic potential.”

In another publication, Wilmes clarifies the very substantial advance that has been made in understanding the microbiome:

While we had been able to determine the species composition in the gut ecosystem by conventional DNA analyses, we were in the dark as to what was actually going on there at a given point in time. To use the analogy of human society: We were able to carry out a census of different individuals without knowing what they might do as a profession. Now we know who does what and when.

This was achieved by combining several analytical techniques, to track the activities of DNA, RNA, and proteins. In what sounds like a fantastically complicated game of three-dimensional chess, the research has provided “an entirely new picture of the functional processes occurring in the gut, for example in relation to metabolism.”

The research team discovered that “only by simultaneously looking at genetic repertoire, transcripts, proteins and metabolites will we really understand the function of distinct microbial populations in their native environments.”

Your responses and feedback are welcome!

Source: “Integrating multiple ‘omes’ from the microbiome: ‘small is beautiful’,” NatureMicrobiologyCommunity.com, 10/10/16
Source: “Sick or healthy? Bacterial metabolism tells us which — and why,” uni.lu, 10/11/16
Photo credit: olarte.ollie via Visualhunt/CC BY-SA

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