Research just published sheds more light to the role of gut bacteria in autoimmune diseases


Research just published sheds more light to the role of gut bacteria in autoimmune diseases


Author: Dimitri Dimitriou


The implication of the human microbiome in disease has been suspected on and off for a long time and sayings passed on from generation to generation like “you are what you eat”, “an apple a day keeps the doctor away”, going back to dates BC, when Hippocrates was quoted to say “all disease begins in the gut”.

Whereas this is likely to be not 100% the case, thankfully the efforts of the scientific community in the last few years have helped advance our knowledge of the human microbiome and the role it plays in health and disease.

A publication last April in the journal Nature entitled “A new genomic blueprint of the human gut microbiota”, identified almost 2,000 new species of bacteria, previously “unknown”. Knowing which individual species is in present and in which relative quantities, is likely to help decipher their roles in diseases. The researchers used an advanced method using metagenomics to “re-create” potential likely bacteria species.  It is very hard to isolate individual live species from each other using manual methods in a lab, much like it’s impossible to see many stars with telescopes but more can be detected using energy waves.

The study is available at

Just recently (the past August), a publication from researchers at Harvard Medical School, in Cell Host & Microbe, with the title “The Landscape of Genetic Content in the Gut and Oral Human Microbiome”, presenting the results of an analysis of over 3,500 samples from 13 studies found that around half of the people have a very individual composition of their microbiome, a little bit like a “fingerprint”. While this is an interesting finding, it makes it more complicated to identify sets of bacteria in diseased individuals who share common characteristics.

The publication can be viewed at

In parallel, also last August another group of researchers published a paper in Nature Communications with the title “Genetic risk for autoimmunity is associated with distinct changes in the human gut microbiome”.  Based on a big project in Sweden (the ABIS cohort), where over 17,000 young children gave samples at different time points, there is an apparent link between autoimmune disease (e.g. Type 1 diabetes and coeliac disease) and a genetic marker (HLA or class II human leukocyte antigen).  One of the exciting findings was the discovery of a couple of particular bacterial genera, Intestinibacter and Romboutsia, the presence of which seems to be associated with lower risk of these diseases.  The paper is available at

The authors also describe past research that showed that the common probiotics (incl. Lactobacillus) are associated with an increase of the new Romboutsia species (which by the way used to be thought to be a type of Clostridium

What is interesting is whether HLA is a causative factor in changes in the microbiome or the opposite.  Bacteria produce gigantic numbers of simple and complicated substances which may elicit directly or indirectly a number of diseases, some (if not most) of which are mediated through changes in our genes.  The new field of epigenetics is an exciting one, with a promise to help identify nutritional and lifestyle influences on our genes, some of which are undoubtedly mediated by bacterial secretions and interactions with our immune cells.

So, what does all this novel science mean for someone involved in natural methods of healing? Whilst reinforcing the importance of a healthy diet based on vegetables, fruits, nuts, seeds, etc that our “good” gut bacteria need, it should soon provide more specific knowledge on particular nutritional ways of modulating the gut bacteria to help disease.  The use of probiotics has been associated with improvement in the microbiome, although the effect on a disease would take longer and most probably requires the modification of other factors.

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