Different taxonomic levels are used in mono-gastric animal feeding experiments which report changes in intestinal microbial diversity indexes and relative abundance caused by dietary treatments. For example, paper report changes in diversity indexes and relative abundance of fecal microbiol in phylum level, family level or genus level for studying effects of buytric acid (a feed additive) supplementation. And sometimes researchers relate the changes in intestinal microbial diversity indexes and relative abundance to the improvements in growth performance and incidence of diarrhea of experimental animals. Can someone experienced in this field explain the criteria for choosing the correct taxonomic level for comparing microbial diversity following dietary treatments? What factors should be considered? Thank you.
Wakita et al. showed that family-, genus-, and species-level analyses are appropriate to correlate the fecal microbiome and the fecal metabolome [1]. Even though the amplification of short 16S rDNA variable regions can result in the inability to determine the species-level with a high level of confidence, genus- and family-levels are still reachable and valid.
Meanwhile, due to the easiness of classifying sequences to phylum-level, the Firmicutes/Bacteroidetes ratio is frequently used in the scientific literature. However, the biological meaning of this is limited, especially if you are interested in the metabolome changes induced by diet. The popular index, Firmicutes/Bacteroidetes ratio, is based on the phylum level and was initially associated with obesity and certain health states. Interestingly, new data refuted its validity [2].
References:
Article Taxonomic classification for microbiome analysis, which corr...
Article The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut...
This question has two scopes to be mentioned:
- Similar things were said in the reference 2 in the post above that Firmicutes/Bacteroidetes ratio is not a convincing criteria to describe the health. Phylum Firmicutes is huge and so does the phylum Bacteroidetes. And there are so many different factors which affect some members of these phyla while other members do not get affected.
- Short chain fatty acid supplementation and its effect on gut microbiota is not easy to understand in gut systems and need extensive studies. In such cases, higher taxa and use of 16S as a marker is not very informative either.
>> What factors should be considered? To answer your question in short, it depends on your marker and the community you want to analyse.
The nutrient composition of feed ingredients itself should undergo chemical evaluation in terms of its taxonomic level.
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