MicrobiotaMi Comment 21_21  by Martina Morandi

Related Journal Article:  Role of dietary fiber in the recovery of the human gut microbiome and its metabolome.

This article was published in the: Cell Host Microbe. 2021 Mar 10;29(3):394-407.e5. doi: 10.1016/j.chom.2020.12.012. Epub 2021 Jan 12. PMID: 33440171

The importance of fiber in the maintenance of human gut microbiota health

Food is one of the most singularly important factors in overall health and a healthy diet is the cornerstone for a healthier life. Generally speaking, a diverse gut microbiota is considered to be more beneficial for the host, this is because the more species of bacteria you have, the greater number of benefits they may be able to contribute to. A diet rich of different food types can lead to a diverse microbiota. Gut microbes are able, from their metabolism, to produce a large range of bioactive small molecules, such as short chain fatty acids (SCFAs), amino acid metabolites and modified bile acids. All these little molecules play an important role in the maintenance of host health. There are specific foods that boost the production of these metabolites and those are principally fibres. A daily portion of fiber is highly recommended in all diets, nevertheless the typical American diet is relatively poor. In contrast, vegetarians and vegans consume typically more fiber.

In this Food and Resulting Microbial Metabolites (FARMM) study published on Cell Host & Microbes, Tanes C. and colleagues, have compared the microbiome and metabolome of adults that followed three different diets: vegan, typical American (here referred as omnivore) and a liquid diet with no fiber identified as an exclusive enteral nutrition diet (EEN). These three diets were followed for 5 days (dietary phase). They also included an antibiotic and polyethylene glycol (Abx/PEG) treatment (for 3 days) to evaluate the ability of the diet and the produced-associated metabolites, on the recovery of microbiota depletion (recovery phase: 7 days).

Compared to the vegan and omnivore diets, the EEN diet results in a substantial change of microbiota composition within 3 days of the dietary phase, including an increase of two Romincoccus genera, respectively R. gnavus, and R.torques and some other Clostridia clades.

The Abx/PEG intervention reduced viable bacteria by approximately 5 logs and the recovery of bacteria load was slower in the EEN group compared to the vegan (that was the most resilient) and omnivore ones. Moreover, after the recovery phase, the EEG group showed higher levels of Proteobacteria than Bacteroidetes or Firmicutes, while the microbiota of vegan and omnivore groups quickly recovered to Bacteroidetes and Firmicutes levels, observed in the pre-treatment phase. The absence of fiber within the EEN diet was hypothesized to be the reason of the largest difference in gut microbiota composition observed between people who followed a EEN diet and those who followed a vegan or omnivore diet.

Starting from this hypothesis, the researchers have examined those genes involved in the degradation of fiber, (such as hydrolase genes) and the production of SCFAs. EEN showed lower levels of glycoside hydrolases, enzymes responsible for the degradation of structural plant carbohydrates and in particular, during the third phase, the recovery of the keystone gene that produces butyrate, was slower than in omnivore group. These results suggest that the absence of fiber in the dietary intake, affects both carbohydrate- and amino acid-based production of butyrate. Contrary, those subjects who followed an omnivore o vegan diet, showed an increase of fecal butyrate levels.

Metabolomic analysis was performed both in stool and plasma samples. They observed a consistent increase of fecal amino acids levels (including tryptophan, tyrosine, phenylalanine) during the Abx/PEG intervention that was independent of diet, consequence of the purge of dietary nutrients from the gut before their absorption. During the early recovery phase, it was observed a decrease of the same amino acids in vegan and omnivore groups, but not in the EEN group, possibly due to the lack of bacterial consumption. Metabolomic analysis in the plasma samples did not reflect the results obtained in stool samples, indicating that the impact of gut microbiota on human plasma is less visible.

To conclude, in this study the researchers showed the importance of consuming dietary fiber which has a broad impact on both the composition and metabolite production of human gut microbiota. In fact, a diet free of fiber in combination with an antibiotic treatment, altered consistently the human gut microbiome configuration with an increase of Proteobacteria, in particular Clostridium taxa. This is explained by the involvement of fiber in preserving microbial biomass and diversity. Moreover, the impact of dietary fiber on the generation of metabolites from both carbohydrate and amino acid components, suggest the importance of their role in the maintenance of gut microbiota health.

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