Abstract
The human gut microbiome has been extensively studied, but its diversity scaling (changes or heterogeneities) along the digestive tract (DT) as well as their inter-individual heterogeneities have not been adequately addressed to the best of our knowledge. Here we fill the gap by applying the diversity-area relationship (DAR), a recent extension to the classic species-area relationship (SAR) in biogeography, by reanalyzing a dataset of over 2000 16s-rRNA microbiome samples obtained from 10 DT sites of over 200 individuals. We sketched out the biogeography “maps” for each of the 10 DT sites by cross-individual DAR analysis, and the intra-DT distribution pattern by cross-DT-site DAR analysis. Regarding the inter-individual biogeography, it was found that all DT sites have the invariant (constant) scaling parameter—all sites possessing the same diversity change rate across individuals, but most sites have different potential diversities, which include the portions of diversity that may be absent locally but present regionally. In the case of this study, the potential diversity of each DT site covers the total diversity of the respective site from all individuals in the cohort. In terms of the genus richness, an average individual hosts approximately 20% of the population-level genus richness (total bacterial genus of a human population). In contrast, in terms of community biodiversity, the percentages of individual over population may exceed 90%. This suggests that the differences between individuals in their DT microbiomes are predominantly in the composition of bacterial species, rather than how their abundances are distributed (i.e., biodiversity). Regarding the intra-DT patterns, the scaling parameter (z) is larger—suggesting that the intra-DT biodiversity changes are larger than inter-individual changes. The higher intra-DT heterogeneity of bacteria diversity, as suggested by larger intra-DT z than the inter-individual heterogeneity, should be expected since the intra-DT heterogeneity reflects the functional differentiations of the DT tract, while the inter-individual heterogeneity (z) reflects the difference of the same DT site across individuals. On average, each DT site contains 21–36% of the genus diversity of the whole DT, and the percentages are even higher in terms of higher taxon levels.
Highlights
There have been extensive studies on various aspects of human gut microbiomes over the last decade or so, on their diversities (for example, HMP Consortium (Human Microbiome Project Consortium), 2012a; HMP Consortium (Human Microbiome Project Consortium), 2012b; Lozupone et al, 2012; Segata et al, 2012)
The digestive tract (DT) microbiome dataset we reanalyzed in this study was first reported by Segata et al (2012), which is part of the Human Microbiome Project (HMP)
A total of 2078 DT microbiome samples were collected from 242 healthy adults aged from 18 to 40 years old, who were enrolled in the HMP
Summary
There have been extensive studies on various aspects of human gut microbiomes over the last decade or so, on their diversities (for example, HMP Consortium (Human Microbiome Project Consortium), 2012a; HMP Consortium (Human Microbiome Project Consortium), 2012b; Lozupone et al, 2012; Segata et al, 2012). One of the most well-known ecological laws in the field is the sotermed species-area relationship (SAR), which was first discovered in the 19th century (Watson, 1835) and has been extensively investigated since the 1960s (Preston, 1960; Connor and McCoy, 1979; Rosenzweig, 1995; Lomolino, 2000; Drakare et al, 2006; Tjørve and Tjørve, 2008, 2009; Harte et al, 2009; He and Hubbell 2011; Sizling et al, 2011; Storch et al, 2012; Triantis et al, 2012; Helmus et al, 2014) It is considered as “ecology’s most general, yet protean pattern” by Lomolino (2000) and Whittaker and Triantis (2012). The dataset provides an ideal opportunity for us achieve the objective of this study—analyzing the inter-individual and intra-individual diversity scaling of the human DT microbiomes
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