Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns
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 diversi...
Main Authors: | , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2021-09-01
|
Series: | Frontiers in Genetics |
Subjects: | |
Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.724661/full |
id |
doaj-e9842b99a40b4b5d94bdf2b8574999a6 |
---|---|
record_format |
Article |
spelling |
doaj-e9842b99a40b4b5d94bdf2b8574999a62021-09-24T06:09:30ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-09-011210.3389/fgene.2021.724661724661Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual PatternsHongju (Daisy) Chen0Hongju (Daisy) Chen1Hongju (Daisy) Chen2Bin Yi3Qiang Liu4Xia Xu5Lin Dai6Zhanshan (Sam) Ma7Zhanshan (Sam) Ma8Zhanshan (Sam) Ma9Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, ChinaCollege of Mathematics, Honghe University, Mengzi, ChinaCollege of Mathematics, Honghe University, Mengzi, ChinaCollege of Mathematics, Honghe University, Mengzi, ChinaCollege of Mathematics, Honghe University, Mengzi, ChinaFaculty of Science, Kunming University of Science and Technology, Kunming, ChinaComputational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, ChinaKunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, ChinaCenter for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, ChinaThe 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.https://www.frontiersin.org/articles/10.3389/fgene.2021.724661/fullInter-individual microbiome heterogeneityIntra-DT microbiome heterogeneityDiversity-area relationship (DAR)Potential diversityDiversity scaling |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hongju (Daisy) Chen Hongju (Daisy) Chen Hongju (Daisy) Chen Bin Yi Qiang Liu Xia Xu Lin Dai Zhanshan (Sam) Ma Zhanshan (Sam) Ma Zhanshan (Sam) Ma |
spellingShingle |
Hongju (Daisy) Chen Hongju (Daisy) Chen Hongju (Daisy) Chen Bin Yi Qiang Liu Xia Xu Lin Dai Zhanshan (Sam) Ma Zhanshan (Sam) Ma Zhanshan (Sam) Ma Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns Frontiers in Genetics Inter-individual microbiome heterogeneity Intra-DT microbiome heterogeneity Diversity-area relationship (DAR) Potential diversity Diversity scaling |
author_facet |
Hongju (Daisy) Chen Hongju (Daisy) Chen Hongju (Daisy) Chen Bin Yi Qiang Liu Xia Xu Lin Dai Zhanshan (Sam) Ma Zhanshan (Sam) Ma Zhanshan (Sam) Ma |
author_sort |
Hongju (Daisy) Chen |
title |
Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns |
title_short |
Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns |
title_full |
Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns |
title_fullStr |
Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns |
title_full_unstemmed |
Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns |
title_sort |
diversity scaling of human digestive tract (dt) microbiomes: the intra-dt and inter-individual patterns |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2021-09-01 |
description |
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. |
topic |
Inter-individual microbiome heterogeneity Intra-DT microbiome heterogeneity Diversity-area relationship (DAR) Potential diversity Diversity scaling |
url |
https://www.frontiersin.org/articles/10.3389/fgene.2021.724661/full |
work_keys_str_mv |
AT hongjudaisychen diversityscalingofhumandigestivetractdtmicrobiomestheintradtandinterindividualpatterns AT hongjudaisychen diversityscalingofhumandigestivetractdtmicrobiomestheintradtandinterindividualpatterns AT hongjudaisychen diversityscalingofhumandigestivetractdtmicrobiomestheintradtandinterindividualpatterns AT binyi diversityscalingofhumandigestivetractdtmicrobiomestheintradtandinterindividualpatterns AT qiangliu diversityscalingofhumandigestivetractdtmicrobiomestheintradtandinterindividualpatterns AT xiaxu diversityscalingofhumandigestivetractdtmicrobiomestheintradtandinterindividualpatterns AT lindai diversityscalingofhumandigestivetractdtmicrobiomestheintradtandinterindividualpatterns AT zhanshansamma diversityscalingofhumandigestivetractdtmicrobiomestheintradtandinterindividualpatterns AT zhanshansamma diversityscalingofhumandigestivetractdtmicrobiomestheintradtandinterindividualpatterns AT zhanshansamma diversityscalingofhumandigestivetractdtmicrobiomestheintradtandinterindividualpatterns |
_version_ |
1717370153726902272 |