gut microbiome balance

The stability of the gut microbiome (part 1)

In this fully referenced blog series on the human microbiome, our expert Miguel Toribio-Mateas discusses why the stability of our gut flora is as important to its diversity and shares his evidence-based clinical approach to gut health.

The role of the gut flora in health and disease is as crucial as is complex. Ample evidence from both human and animal studies describes the impact of dietary interventions on the idiosyncrasies the gut microbiota, the tens of trillions of microorganisms1,2 that inhabit our gastrointestinal system in quantities and diversity increasing from stomach to small intestine to colon3,4. Under natural conditions, intestinal bacteria share their habitat with a dynamic community of viruses, protozoa, helminths and fungi5-7, many of which exhibit parasitic behaviour8 . Every unique community of microorganisms interacts with their human host through immune, neuroendocrine and neural pathways9, thereby casting local as well as systemic effects on the host’s health as well as their disease risks. In turn, the gut microbiota modulates disease risks by means of their ability to ferment non-digestible substrates such as dietary fibres10 and polyphenols11,12. This fermentation supports the growth of specialist microbes that produce short chain fatty acids (SCFAs, e.g. butyrate, acetate and propionate)13, as well as gases like methane and hydrogen14-16, modulating and supporting the symbiotic relationship between microbiobial communities and the host. Additionally, some commensals like Akkermansia muciniphila17 are able to degrade various molecules present within the intestinal mucus18-20, thereby supporting tissue barrier function21 and alleviating inflammation22, 23.

Defining a healthy gut. Can it be done?

Ongoing development of microbiome assessment tools, particularly sequencing platforms that integrate multi-omic technologies such as shotgun metagenomics / metatranscriptomics (aka “next generation sequencing”) have enabled scientists to identify, measure and describe in ever-increasing detail the nature, function and abundance of individual microbes, as well as the diversity of entire microbial communities24.  Moreover, technological advancements are resulting in emerging evidence pointing to a larger degree of uniqueness in microbial signatures from person to person than previously anticipated. In amongst this level of detail and complexity, the “elephant in the room” is the lack of a definition of “normal” or “healthy” microbiota. The existence of idiosyncratic microbial signatures pertaining to certain conditions is a well-known phenomenon characterised by microbial imbalance or maladaptation and typically referred to as dysbiosis25-28, a reported as a contributor to the multiple system dysregulation observed in the pathogenesis of a number of diseases, including cardiovascular29-31, metabolic32-35, neuroimmune36-39, neuropsychiatric40-42 and neurodegenerative43-46 conditions. However, intriguing new findings recently published by Zeevi and colleagues at the Weizmann Institute of Science47 provides support to a new status quo in microbiome research: a situation where the same microbe might engage differently with different people, regulating its own adaptation as well as that other microbes in its community differently from person to person, in addition to contributing to different health outcomes in every individual.

Translating the science into clinical practice

In addition to all of the areas explored so far, the diversity of your microbiome, determined by the number of species present in your gut, is also a key marker of how healthy a person’s microbiome is. Also to be taken into consideration is the ability of these microbes to synthesise valuable nutrients such as B vitamins and butyrate, a short-chain fatty acid that helps maintain the integrity of your gut lining. In fact, I would say that it is more important to know about the abundance of butyrate-producing bugs, such as several species in the Roseburia and Faecalibacterium genii, as I’ll explain in a moment.

This practically overwhelming level of complexity in current lines of inquiry in microbiome research, makes it increasingly difficult for practitioners to apply science in clinical practice. Having worked in development of microbiome assessment tools for years, I would always apply a few very simple rules:

  • The only way to know about the state of your gut microbiome is by testing it. Period. That is the plain reality. If you try to figure out what levels of Firmicutes you may have or if you are experiencing dysbiosis without looking at the results of a stool test, you might as well try to answer that question by doing the Tarot or using a crystal ball. Of course you can use methods such as validated scales to ask your client / patient about specific areas such as bloating, bowel motion frequency, etc. or use a tool like the Bristol stool chart to find out what the consistency of their stool looks like. That can give you some insight into what might be going on, but it’s never going to answer specific questions.
  • Try not to answer too specific questions. Why? Because microbiome science advances at such as rate that it is almost impossible to have very precise answers to clinical problems by looking into the microbiome. This applies in particular to trying to be too specific in recommendations with things like expecting that they will have a very specific effect. Like “eat more red berries to increase your Akkermansia levels”. Everyone’s microbiome is likely to have a slightly different response to the same intervention, so keep an open mind and keep testing.
  • Repeat. Then test again. Many practitioners expect to find all the answers they need in a single microbiome test. If you’re one of them, you’re set to be disappointed. Why? Because you will only start figuring out the stability of your client’s microbiome after you’ve repeated a test at least 3 times. In my experience, this means 3 times at 3-intervals. That’s when you start realising that whatever you do, your client Lactobacilli might be low, or that they tend to have abundant levels of Prevotella, typically seen in those who eat plenty of fruit and vegetables. That is what scientists refer to as a “stable microbial signature” which should give you a much deeper understanding of the kind of advice to suggest for that particular person. Asking your client how they feel, and trying to identify patterns that may coincide with changes in their microbiome is key. Being a good listener and taking thorough consultation notes will help you capture their narrative so that you can provide them with more precise, more individualised advice.
  • Last, but not least, do not underestimate the value of common sense. You can try very hard at applying a complex approach or one of many “protocols” that are around. Nutrition is a science, but its application is an art. So do listen to your gut as much as you follow an evidence-based approach.

I have developed a special collaboration between microbiome assessment company Atlas Biomed and BANT that will enable you to put some of the insights I’ve share with you in this article in your own clinical practice. So if you are a BANT member, please look out for an announcement via the usual channels, Facebook, LinkedIn and eNews.

About Miguel

Miguel Toribio-Mateas is a clinical neuroscientist and nutrition practitioner, currently working towards a professional doctorate in health neuroscience, using health-related quality of life outcome measures alongside biomarkers from microbiome analysis to assess the complex effects of food on cognitive function and mental health via the gut brain axis.

With many thanks to Miguel for this blog. If you have any questions regarding the health topics that have been raised, please don’t hesitate to get in touch with Amanda via e-mail or phone:
01684 310099

Amanda Williams and the Cytoplan Editorial Team


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Last updated on 8th March 2021 by cytoffice


4 thoughts on “The stability of the gut microbiome (part 1)

  1. Thank you I found this article very interesting. I suffered over a year ago with helicobacter pylori and the treatment is quite hard core and I am still suffering a year on. I know my gut health is not great, but am at a loss as to what to do. So this was a good read.

  2. Please can you provide best supplements for stress and anxiety related to a very busy Goy divorce and supplements for post cancer. I’ve had my ovaries removed at 51 and am on Letrozole. I need to be mindful of my bone health and also my stress levels. Thank you

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