Gut microbiome diversity measures for metabolic conditions: a systematic scoping review

Abstract

Background Evidence on the association between the gut microbiome and metabolic conditions has been increasing during the past decades. Unlike the straightforward identification of beneficial non-pathogenic bacteria as a potential probiotic for clinical use, the analysis of gut microbiome diversity is more complex and required a better understanding of various measures.

Aim To summarize an elaborated list of gut microbiome diversity measures and to analyze the benefits and drawbacks of each measure.

Design and setting Systematic scoping review.

Method Systematic search was conducted in three databases: PubMed, Embase, and Cochrane Central Register of Clinical Trials for the relationship between gut microbiota and metabolic diseases published in 2019.

Results Of 5929 potential studies, 47 were included in the systematic review (14632 patients). Of 13 alpha diversity measures, the Shannon index was the most commonly used in 37 studies (78.7%), followed by Chao1 index (19 studies) and Operational Taxonomic Unit (OTU) richness (15 studies). The advantages of Shannon diversity are simplicity and appropriateness for the community dominant by two or three species. Of 2 beta diversity measures, the UniFrac was the most commonly used in 24 studies (unweighted 17 studies and weighted 16 studies), followed by Bray-Curtis dissimilarity (16 studies). There is no predilection for beta diversity.

Conclusion Various measurements of gut microbiome diversity have been used in the literature. They have unique characteristics, advantages, and disadvantages which lead to different usage frequency. The measures were chosen considering cost, simplicity, and types of research.