Gut Microbiome

You can expect to see an increasing amount of research and opinion coming out about how the millions of inhabitants of our gut affects our health in a myriad of ways  – weight control, liver health, inflammation, mood, brain function and more.

NOTE: this topic is closely wrapped up with other topics and currently it is not clear how much aspect of each of the following is involved. Please consider that these topics are closely entwined with each other:

• gut microbiota
• vagal function and stimulation
• liver function and inflammation
• gut barrier, immune and neurological function
• possible gut tissue infections, not just colonization (e.g. ? viral cause of obesity)

Many people and companies will be jumping the gun, suggesting that they know what best to recommend you do about these findings and theories. There are many related products and testing services on offer and there will be ever more, and soon.

In fact, many books have come out in the past year or so advising different protocols of diet changes, probiotics, prebiotics, fermented foods and a slew of other interventions. There will be important things in this direction that you could do to help your health. The reality is that we know very little of what that is, yet.

There is so little money available for good quality research in so many important areas of nutrition and foods. Yet there is a flood of new research in this area, with frequent international conferences and expert research teams. What Up? Most research in nutrition and foods is not expected to lead to patentable applications. The opposite is true in this topic. The gold rush is on to find useful tests and treatments – and to prove the usefulness of these tests and products by published research. Who is going to come out with the block-buster fibre (fiber) product or pro-biotic combination? Which company can offer truly useful tests and how to interpret them? Which companies will most successfully commercialize fecal transplant therapy?

The possibility of patentable products is not enough. The excitement comes from the recent realization that this is a major area of medicine that is expected to have extremely important and also extremely widely-used applications. One could anticipate that most people in the population would have testing procedures done repeatedly in their lives. One could also anticipate that most people in the population would have reason to consider taking products – whether for prevention or treatment or both – repeatedly or semi-continuously through much of their lives.

While we wait, what to do?

Is more fibrous foods and fibre or resistant starch intake the answer? Probably for most people it will turn out that these steps are important for health. Will this be the right path for all? There is very little (if anything) about the health of people which works this way.

The inescapable rule is that people are different and all interventions must be considered with the individual circumstance in mind, if used must be adapted to the individual and, if used, must initially and long-term be considered a trial-of-therapy and the individual’s response to the therapy evaluated (not take for granted).

For example, consider the problem of C. difficile infection. There, one particular bacteria is over-growing in the intestines. Part of the problem is not enough growth of competing species. This basic model is what we think is going on when we refer to problems with the population of “bugs” of various types in the gut _ that is, the gut microbiome. We think that one or several or many specific bugs are over-growing or over-functioning or have an unfavourable pattern of gene function turned on. Part of this scenario would be that increased growth or function of “benign” or “friendly” bugs would control or limit the bad guys.

The pat answer offered is to (1) increase intake of various high fibre foods and/or intake of resistant starches and (2) intake bacterial species to try to improve the environment of the gut and to try to crowd out the unwanted bugs.

Is this strategy reliably effective? There is much speculation and preliminary research, but not much to stand on. Back to C. difficile. If this feed and re-populate treatment worked universally, it would work on C. difficile. It does not. Even when antibiotics are used first to deplete the population of C. difficile bugs, the feed and re-populate intervention fails. With the best that advanced care can offer, C. difficile can still be persistent and people die. The most effective intervention is fecal transplant.

It is highly unlikely that C. difficile is the only gut microbiome disbalance problem that “feed and re-populate” is ineffective for.

So, I do anticipate that for the vast majority of people it will turn out to be true that

1. a high intake of fibrous foods, perhaps with resistant starches, and
2. when indicated (e.g. after taking an antibiotic or from time to time) adding “beneficial” bugs by supplements or in fermented foods

will be important parts of protecting and recovering health.

Still, it would be very problematic if this came to be taken as a certainty for all people in every circumstance. Just like with C. difficile, there may be some people who have gut microbe problems that will not resolve with any amount or types of probiotics and/or prebiotics. There may be some (likely a small minority) people who get worse with higher fibre and fermentable food intakes, rather than better and we need to keep an eye out for that.

Some interesting articles on this topic:

(1) from work at McMaster University “Link between intestinal bacteria, depression found” reported at ScienceDaily July 28/15  LINK Note this is animal research and far from providing answers of what to do about all this.

• “We have shown for the first time in an established mouse model of anxiety and depression that bacteria play a crucial role in inducing this abnormal behaviour,” said Premysl Bercik, senior author of the paper and an associate professor of medicine with McMaster’s Michael G. DeGroote School of Medicine.
• “But it’s not only bacteria, it’s the altered bi-directional communication between the stressed host — mice subjected to early life stress — and its microbiota, that leads to anxiety and depression.”
• “However, if we transfer the bacteria from stressed mice into non stressed germ-free mice, no abnormalities are observed. This suggests that in this model, both host and microbial factors are required for the development of anxiety and depression-like behavior. Neonatal stress leads to increased stress reactivity and gut dysfunction that changes the gut microbiota which, in turn, alters brain function,” said Bercik.
• G. De Palma, P. Blennerhassett, J. Lu, Y. Deng, A. J. Park, W. Green, E. Denou, M. A. Silva, A. Santacruz, Y. Sanz, M. G. Surette, E. F. Verdu, S. M. Collins, P. Bercik. Microbiota and host determinants of behavioural phenotype in maternally separated mice. Nature Communications, 2015; 6: 7735 DOI: 10.1038/ncomms8735

(2) “The Sum of Our Parts”
“Putting the microbiome front and center in health care, in preventive strategies, and in health-risk assessments could stem the epidemic of noncommunicable diseases.” From The Scientist, by Janice Dietert, and Rodney Dietert, July 1, 2015  LINK

• “Commensal microbes that live on and in us are critical for our health. By cell numbers, we are approximately 90 percent microbial, and the vast majority of the genes expressed in our superorganism are not on our mammalian chromosomes but in the bacteria, archaea, and single-celled eukaryotes that call the human body home.
• Normally, a robust microbiome would be part of our inheritance, a legacy passed, largely maternally, from generation to generation. But recently that chain has been broken, usually more than once.
• The increase in cesarean deliveries, the reduced prevalence and duration of breastfeeding, overuse of antibiotics both as prescription drugs and in agriculture, modern urban living surrounded by sanitizers, and a general tendency to limit contact with the environment have changed our relationship with the microbes that are an integral part of our biology.”