AUTHOR=Chen Hongju , Yi Bin , Qiao Yuting , Peng Kunbao , Zhang Jianmei , Li Jinsong , Zheng Kun-Wen , Ning Ping , Li Wendy 

TITLE=Diversity-scaling analysis of human breast milk microbiomes from population perspective

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 13 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.940412

DOI=10.3389/fmicb.2022.940412

ISSN=1664-302X

ABSTRACT=Most existing studies of human microbiomes have been focused on gut microbiomes and on individual level, i.e., measuring and reporting the alpha diversity of individual samples. This de facto standard analysis missed some population or cohort level insights such as potential total diversity in a cohort (population), the scaling level (change rate) of diversity across individuals or inter-individual heterogeneity in diversity, and comparison of an “averaged” individual with total population diversity in diversity. Quantitative measuring these population-level or individual-population relationship characteristics is of obvious significance. Here we reanalyze a dozen datasets of 2115 human breast milk microbiome (BMM) samples with diversity-area relationship (DAR) to tackle the previous questions. Our focus on BMM is aimed to offer insights for supplementing the gut microbiome research from nutritional perspective. DAR is an extension to classic species-area relationship, which was discovered in the 19th century and established as one of a handful fundamental laws in community ecology. Our DAR modeling revealed the following numbers, all approximately: (i) The population-level potential diversity of BMM is 1108 in terms of species richness (number of total species), and 67 in terms of typical species (ii) On average, an individual carries 17% of population-level diversity in terms of species richness, and 61% in terms of typical species. (iii) The similarity (overlap) between individuals according to pair-wise diversity overlap (PDO) should be approximately 76% in terms of total species, and 92% in terms of typical species, which symbolizes the inter-individual heterogeneity.  (iv) The average individual (alpha-) diversity of BMM is approximately 188 (total-species) and 37 (typical-species). (v) To deal with the potential difference among 12 BMM datasets, we conducted DAR modeling separately for each dataset, and then performed permutation tests for DAR parameters. It was found that the DAR scaling parameter that measures inter-individual heterogeneity in diversity is invariant (constant), but the population potential diversity is different among 30% of the pair-wise comparison between 12 BMM datasets.  These results offer quantitative measures on the alpha, beta- and gamma-diversity of the BMM from biodiversity perspective, corresponding to diversity analysis at individual, inter-individual and population levels, respectively, from host scale perspective.