Microbial Feast or Famine: dietary carbohydrate composition and gut microbiota metabolic function

Background

There are many facets that contribute to overall human health. A physically small yet important one, is the diverse community of microorganisms living inside our gut, known as the microbiome. Our gut microbial community plays a role not only in digestion but has been linked to health concerns including diabetes, inflammatory diseases, and obesity.

The food that we consume influences our gut microbiome: high fibre diets are more beneficial compared to low fibre diets. Low fibre diets, typically associated with Western countries, are often absorbed almost entirely in the upper gastrointestinal tract (GI), leaving the microorganisms in the lower GI tract without any fuel. When this occurs, the microorganisms begin to consume mucin, which is the mucus lining that protects our GI tract, leading to inflammation and other health issues.

In this preprinted study, Dirks and collaborators conducted clinical trials to compare the functional activities of microbial gut communities when eating a low fibre, Western Diets (WD), compared to a high fibre, Microbiome Enhancer Diet (MBD). Participants were assigned to either the WD or MBD for 22 days straight, then given 14 days to resume their normal diet, followed by another 22 days of eating the opposite diet to the one they were first assigned. Throughout the study, participants were closely monitored and fecal samples were collected to measure differences in microbial composition and function for 11 days during each diet. Metatranscriptomic techniques were used to quantify the active gene expression of the microbial communities.

 

Key Findings

1) The overall diversity and composition of enzymes expressed by the microbial communities were similar between the WD and MBD.

This suggests functional redundancy of the gut microbiota, meaning many microbes can perform the same tasks. As a result, the gut community stays stable even when the available nutrients change, since its members can adjust their gene expression to keep key metabolic functions going.

2) The MBD microbiota expressed transcripts used for growth and digesting a variety of nutrients, whereas the WD expressed transcripts mostly for amino acid degradation.

This suggests that the microbes in the WD diet lack carbohydrates since amino acids are generally consumed once carbohydrates have been exhausted.

3) Transcripts indicated that MBD microbiota express CAZymes used to break down complex carbohydrates, whereas the WD CAZymes are used to degrade host-derived carbohydrates.

Out of a large group of enzymes important for breaking down and modifying carbohydrates (CAZymes) the difference in expression suggests that MBD delivered a rich source of polysaccharides to the microbiota to consume, while those polysaccharides were much lower in the WD. It can be speculated that, as a result, the WD microbiota turn to alternative, non-dietary carbohydrate sources, such as host tissue.

4) MBD microbiota expressed protein-degrading transcripts with a diversity of functions compared to the WD where enzymes were more focused on protein degradation (Fig. 1).

MBD transcripts are used for building cell walls, synthesizing new proteins, disposing of misfolded proteins. While these activities were still occurring under the WD, microbiota were more focused on protein degradation.

5) MBD microbiota protein degradation produces products important for maintaining the gut barrier, while WD microbiota produce toxin.

MDB produce polyamines (e.g., cadaverine, putrescine, and spermidine) important for the gut barrier while WD microbiota protein degradation produce uremic toxins, biogenic monoamine, and tryamine, which have been linked to gastrointestinal disorder (e.g. irritable bowel syndrome, Crohn’s disease).

 

 

Why I highlight this preprint

Although my primary field of study is marine biology, I have a personal interest in human health and wanted to highlight this study because it offers findings that may contribute to improving human well-being. Additionally, dietary modifications represent a relatively accessible intervention that many individuals can adopt to support gut health.

 

Questions for the authors

1) What were some of the high fibre foods the MBD participants were eating, and would you recommend these foods to support gut microbial health?

2) How quickly can the function and composition of our gut microbiota change after introducing a fibre rich diet similar to the MBD?

 

Tags: gastrointestinal tract, human health, metatranscriptomics, microbiome

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