Prebiotics: Yet Another Layer of Biome Complexity

I regularly receive FB messages and emails from people asking me what probiotic or prebiotic they should be taking.  If I knew the answer, I’d be rich.  The answer is…no one knows.  We are so at the tip of the iceberg on all this, it’s mind boggling.

Over the weekend, I read a paper that took an in-depth met-analysis look at the differences in bacterial content between control and autistic children’s guts.  These scientists reviewed 9 studies, with a total of 254 patients, and found “…that children with ASD had lower percentages of Akkermansia, Bacteroides, Bifidobacterium, and Parabacteroides and a higher percentage of Faecalibacterium in the total detected microflora compared to controls. In contrast, children with ASD had lower abundance of Enterococcus, Escherichia coli, Bacteroides, and Bifidobacterium and higher abundance of Lactobacillus.”[i] The differences were highly statistically significant.

How many illnesses now have been shown to have bacterial microbiome differences?  On this blog alone I’ve talked at length about not just autism, but everything from obesity to chronic fatigue syndrome to depression, etc. etc. etc.  The list feels endless somedays. And this is just the bacterial microbiome.  Don’t forget that differences have also been found in the mycobiome (yeasts)…and the virome (viruses)…and in the metabolome (the secretions from all these various organisms)…and I still haven’t even touched on the parts played by the macrobiome, protozoa, and so on.

As though this is not all complex enough, as it turns out, even prebiotic fiber is unbelievably complex.

So back to the question:  what probiotic and/or prebiotic should I take?  Well…obviously, that is ultimately going to come down to what is already in your gut.  I’ve already written, more than once, about how some day in the not-terribly-distant-future, we will know enough to individualize treatments using diet, probiotics, prebiotics, and so forth that are tailored to the exact needs of each person.  I think we took one step closer to that, in research just out Washington University in St. Louis, wherein scientists began the laborious process of figuring out just which prebiotic fiber (and individual components of a prebiotic fibers) affect which bacterial species, and how.[ii]

These scientists took sterile rats, without microbiomes, and colonized them with 20 strains of the common gut bacterial strain, Bacteroides. They had the rats eat a “westernized” diet for 4 weeks, with high saturated fat and low fiber (fruit and vegetables) content, but to this they added one of 34 different kinds of prebiotic fiber, including pea protein, citrus peel, pectin, apple fiber, oat hull fiber, chia seeds, and many more. In total, they tested 144 different diet combinations as to how they affected those 20 bacterial strains.  21 of those 144 combinations had significant effect:  citrus pectin and pea fiber enormously increased B. thetaiotaomicron while B. ovatus levels increased dramatically from barley bran.  Some kinds of inulin, resistant maltodextrin and psyllium also had significant effects on certain strains.

As I mentioned previously, they also analyzed what it was in the fiber’s carbohydrate content that had the bioactive properties.  Pea fiber, for example has a polysaccharide called arabinan that seems to affect bacteria, whereas in citrus pectin, it was something called homogalacturonan that led to the increase in specific bacterial strains.

Says Dr. Gordon, the lead researcher on this study, …fiber is actually a very complicated mixture of many different components. Moreover, fibers from different plant sources that are processed in different ways during food manufacturing have different constituents…Unfortunately, we lack detailed knowledge of these differences and their biological significance.”[iii]

 They also found that there were interactions between species as they fed on the fiber, leading to a distinct hierarchy of bacteria.  Some species were stronger competitors than others, in their fight for the nutrients:  “…it’s important to understand how the presence of a particular organism affects the dining behavior of other organisms — in this case, with regard to different fibers. If we are going to develop microbiota-directed foods aimed at providing benefits to human health, it’s important to find ways to determine which food staples will be the best source of nutrients and how the microbiota will respond.”[iv]

While obviously we’re not there yet, you can imagine how someday soon, we may be able to easily analyze the bacterial content of each person’s gut, and then have a tailor-made prebiotic that address their specific needs.   I’m looking forward to the day I won’t have to respond with “I don’t know” again.


 [i] Xu, M, Xuefeng, X, Li, J, Li, F. Association between gut microbiota and autism spectrum disorder: a systematic review and meta-analysis.  Frontiers in Psychiatry. 2019.   doi: 10.3389/fpsyt.2019.00473

[ii] Michael L. Patnode, Zachary W. Beller, Nathan D. Han, Jiye Cheng, Samantha L. Peters, Nicolas Terrapon, Bernard Henrissat, Sophie Le Gall, Luc Saulnier, David K. Hayashi, Alexandra Meynier, Sophie Vinoy, Richard J. Giannone, Robert L. Hettich, Jeffrey I. Gordon. Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans. Cell, 2019; 179 (1): 59 DOI: 10.1016/j.cell.2019.08.011



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