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Digestive Health Blog

The Rise of the Omes:

Updated: Sep 18, 2022

We’ve previously given a technical description of how microbes were “mapped”, and how detection of conserved genetics can tell us which organisms are present inside the human gut. We’ve also described the limitations of this “16s rRNA” mapping. So how are scientists solving the problem of determining cause and effect? In a long list of ways! These “omes” include the metagenome, proteome, transcriptome, immunome, epigenome, metabolome and microbiome.

In relation to the microbiome, metagenomics is a term for the mechanisms used to investigate more than the presence of organisms, but how they may function generally compared to other known organisms and situations.




This includes techniques like “shotgun sequencing”, which for matters of clarity I won’t get into much here, but most of the newest commercial at home microbiome tests are sent to a few labs that perform this analysis. Suffice to say these techniques only infer function by a looking for genes already known from other studies to have different protein and molecular functions. By identifying the presence of those known genes and their expression in a stool sample, scientists can compare to established knowledge and begin to conjecture about meaning and possible causation for health and diseases. However, it may not identify mechanisms, provide treatment targets or a simple “good bacteria/bad bacteria” answer. The most honest companies will convey these generalizations and uncertainties in their microbiome test interpretation information. If you are interested, this is a great review: https://www.researchgate.net/publication/263585285_An_Introduction_to_the_Analysis_of_Shotgun_Metagenomic_Data





One benefit of metagenomics over 16S rRNA mapping? Better assessment of non-bacterial organisms. Indeed, the role of such organisms is highly intriguing in and of itself. For example, fungi can modulate and regulate some immune functions that interact with bacterial microbes! Yes, this has yet another term: the mycobiome. We’ve previously described how bacteriophage (viruses that infect bacteria) may play a role in treating C. difficile. We didn't know that a fecal transplant worked for reasons we didn't even think about! These unintended consequences have been both good and bad, of course, because we didn't understand the systems. Now, that knowledge is leading to CRISPR derived treatments with specific bacteriophage that someday may replace antibiotics Crazy, huh? But also an example of caution. Most superficial recommendations about the microbiome and all things related to it fail to understand the deeper science such as these complex interactions and unknowns. If you simply give a concoction of stool hoping for benefit, not understanding what is in it or the recipient, you may deliver as much harm as good. Have a look at these concepts evaluating non-bacterial microbes as they relate to irritable bowel here: https://www.mdpi.com/2072-6651/14/9/596/htm


Now, this also isn’t to say that yeast such as candida can be “overgrown” into a pathogen. Recall studies that implied this in the past simply used cultures to see what grows (“culturomics"). Candida grows a lot, easily. It’s much more complicated, in that dysbiosis and altered physiology from it are seen but no single organism is shown to be the “pathogen”. And many of the ways to study causation are only recently becoming cheap and robust.



Cross-talk between gut mycobiota and host immunity. Host immunity is then responsible for bacterial monitoring and regulation.



Given the complexity of organisms, their interactions and links to health and disease let’s look at some of the other research tools used to determine causation.

The end result of expressing genes can be the production of proteins. This process is called transcription. The transcriptome has some advantages in researching for causation, certainly. This is because it can elucidate gene expression, but also because it’s very complex to attempt to find causation via novel proteins. Proteomics is the “ome” of protein research. Also recall that not all of the impacts of a microbiome are likely via protein interactions, such as the many already identified to be biochemical or molecular. Thus, it’s becoming more clear that we can and indeed should use multiple “omes”, or multi-omic, methods to identify potential disease mechanisms related to the microbiome. Here is a great overview of combining the different multi-omics: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990367


A few fascinating and recent examples related to the gut microbes include the presence of proteases. These are proteins called enzymes that degrade other proteins into amino acids, and we’ve identified many that are human and microbe derived. In studies of irritable bowel and ulcerative colitis, there are now measures showing altered proteases to be potential causes in some patients. Read the discussion of the first paper to see how “omics” were used to attempt to derive causation: https://microbiologycommunity.nature.com/posts/irritable-bowel-syndrome-a-story-of-missing-microbes


In the case of IBS, microbial derived β-glucuronidase (GUS) enzymes play an important role in deconjugation of bilirubin glucuronides produced by the liver and to use glucuronic acid as a carbon source. High human derived proteolytic activity (PA) was seen in IBS patients who had lower fecal GUS activity and end-products of bilirubin metabolism. “Missing” bacteria did not produce enough GUS to suppress PA, and therefore levels of bilirubin metabolism were altered. Like most microbiome research, these links lead to further study and not an immediate clinical solution. But unraveling these complex systems is how medicine works. Which dovetails into the other study about proteases in the gut: those that might be directly causing ulcerative colitis (UC):


In the case of UC, this study supports a specific microbe driving ulcerative colitis, the protein class it expresses, and a promising solution all via research conducted with “multi-omics”. Taking what we’ve discussed about the altered microbiome, the interactions between nutrition, hosts and organisms and those interactions with the immune system and barrier function of intestinal cells…we can start to tie things together. Up to 40% of UC patients have increased bacterial protease levels. This may be a secondary phenomenon to nutrient unavailability (such as altered short chain fatty acid metabolism), but bacteria such as Bacteroides vulgatus were shown to produce proteases that when blocked, improved the mouse model of UC.



I hope this introduction to the history and concepts of research into the great unknown inside our guts has been helpful. You can now understand how oversimplification of research findings is used inappropriately in the wellness industry. Yet, let’s be clear: when there is a great unknown there is a great need for humility. Giving early theories space to be vetted is important, and when there is a broad range of interesting ideas without extensive data I appreciate this concept:

1. Is it safe, well supported, inexpensive and effective?

2. Is it potentially harmful, lacking much data, expensive and hard to measure effectiveness?

When you see claims about the microbiome/nutrition do they claim to have effectiveness in conditions that are measurable? Typically, no. Have a look at the first google search result for microbiome and wellness which suggests the microbiome is related to the following:

· Weakened immune response

· Constipation, diarrhea, or irritable bowel syndrome

· Gas and bloating

· Poor absorption of nutrients

· Brain fog and reduced cognitive function

· Unhealthy skin

· Faster aging

· Stress management issues

· Mood disorders

· Chronic inflammation

So while there is strong data about clinically applicable microbiome research in a small number of areas, there is a much larger area of study, that while intriguing, has only just begun to unravel causation. Here is an overview discussing how to best study the microbiome: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391518/


Want to test your knowledge? Read this 2019 article about a digestive condition termed small intestinal bacterial overgrowth that rightly shows that gastroenterologists have learned from microbiome theories and research. What are the problems with this discussion? From what you’ve learned from our posts, how might the concepts presented here be too superficial or lack clear causation? How do you think our Digestive Health program approaches this topic differently (we do!) The knowledge in 2019 referenced here was only the tip of the iceberg. https://acpinternist.org/archives/2019/05/rethinking-sibo-in-the-microbiome-era.htm


The future of medicine will move faster into understanding these complexities, I’m sure of it! The progress and use of artificial intelligence is rapidly altering the world of precision medicine, complex physiology and ecology while providing new opportunities. Here is a great review: https://www.nature.com/articles/s41591-022-01981-2





I realize there is so, so much information out there about what the microbiome may or may not cause, and how to test and treat based on superficial knowledge. Instead of trying to cover every single claim, I think we should instead first look at an example that has the most promise. So what is an objective and measurable disease state which has supportive data regarding the microbiome and nutrition? Well, next we’ll move into an example that is near and dear to Pearl Health Partners Digestive Health: Weight Loss and Fatty Liver Disease. I’ve been egging you all along so that you’ll understand the program we are undertaking to effectively treat one of the largest “quiet pandemics” in the world. Ready?

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