Diversity scaling of human digestive tract (DT) microbiomes: the intra-DT and inter-individual patterns

Abstract The human gut microbiome has been extensively studied, but its diversity scaling (changes) along the DT ( digestive tract ) as well as their inter-individual heterogeneities have not been adequately addressed in our opinion. 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 the 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 scaling parameter —all sites possessing the same diversity change rate across individuals, but most sites have different potential diversities. 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 vs . 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 is larger—suggesting that the intra-DT biodiversity changes are more dramatic than inter-individual changes. On average, each site contains 21%-36% of genus diversity of the whole DT, and the percentages are even higher at the higher taxon levels.

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Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-Individual Patterns

10.21203/rs.3.rs-41491/v1 ◽

2020 ◽

Author(s):

Hongju Chen ◽

Bin Yi ◽

Xia xu ◽

Qiang Liu ◽

Lin Dai ◽

...

Keyword(s):

Digestive Tract ◽

Bacterial Species ◽

Population Level ◽

Change Rate ◽

Scaling Parameter ◽

Genus Richness ◽

Species Area ◽

Human Digestive Tract ◽

Biodiversity Changes ◽

Recent Extension

Abstract The human gut microbiome has been extensively studied, but its diversity scaling (changes) along the DT (digestive tract) as well as their inter-individual heterogeneities have not been adequately addressed in our opinion. 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 the 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 scaling parameter—all sites possessing the same diversity change rate across individuals, but most sites have different potential diversities. 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 vs. 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 is larger—suggesting that the intra-DT biodiversity changes are more dramatic than inter-individual changes. On average, each site contains 21%-36% of genus diversity of the whole DT, and the percentages are even higher at the higher taxon levels.

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Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns

Frontiers in Genetics ◽

10.3389/fgene.2021.724661 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hongju (Daisy) Chen ◽

Bin Yi ◽

Qiang Liu ◽

Xia Xu ◽

Lin Dai ◽

...

Keyword(s):

Digestive Tract ◽

Bacterial Species ◽

Population Level ◽

Individual Heterogeneity ◽

Scaling Parameter ◽

Genus Richness ◽

Species Area ◽

The Difference ◽

Human Digestive Tract ◽

Biodiversity Changes

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.

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Diversity Scaling Analysis of Chinese Gut Microbiomes Across Ethnicities and Lifestyles

Frontiers in Microbiology ◽

10.3389/fmicb.2021.736393 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wanmeng Xiao ◽

Depei Gao ◽

Hongju (Daisy) Chen ◽

Yuting Qiao ◽

Zhanshan (Sam) Ma ◽

...

Keyword(s):

Population Level ◽

Pairwise Comparisons ◽

Scaling Analysis ◽

Human Gut ◽

Rapid Urbanization ◽

Chinese Populations ◽

Rural And Urban ◽

Scaling Parameters ◽

Species Area ◽

Recent Extension

Diversity scaling (changes) of human gut microbiome is important because it measures the inter-individual heterogeneity of diversity and other important parameters of population-level diversity. Understanding the heterogeneity of microbial diversity can be used as a reference for the personalized medicine of microbiome-associated diseases. Similar to diversity per se, diversity scaling may also be influenced by host factors, especially lifestyles and ethnicities. Nevertheless, this important topic regarding Chinese populations has not been addressed, to our best knowledge. Here, we fill the gap by applying a recent extension to the classic species–area relationship (SAR), i.e., diversity–area relationship (DAR), to reanalyze a large dataset of Chinese gut microbiomes covering the seven biggest Chinese ethnic groups (covering > 95% Chinese) living rural and urban lifestyles. Four DAR profiles were constructed to investigate the diversity scaling, diversity overlap, potential maximal diversity, and the ratio of local to global diversity of Chinese gut microbiomes. We discovered the following: (i) The diversity scaling parameters (z) at various taxon levels are little affected by either ethnicity or lifestyles, as exhibited by less than 0.5% differences in pairwise comparisons. (ii) The maximal accrual diversity (potential diversity) exhibited difference in only about 5% of pairwise comparisons, and all of the differences occurred in ethnicity comparisons (i.e., lifestyles had no effects). (iii) Ethnicity seems to have stronger effects than lifestyles across all taxon levels, and this may reflect the reality that China has been experiencing rapid urbanization in the last few decades, while the ethnic-related genetic background may change relatively little during the same period.

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Inter-Individual Diversity Scaling Analysis of the Human Virome With Classic Diversity-Area Relationship (DAR) Modeling

Frontiers in Genetics ◽

10.3389/fgene.2021.627128 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wanmeng Xiao ◽

Zhanshan (Sam) Ma

Keyword(s):

Bacterial Communities ◽

Human Microbiome ◽

Population Level ◽

Scaling Analysis ◽

Global Diversity ◽

Local Diversity ◽

Species Area ◽

Viral Communities ◽

Recent Extension ◽

Area Law

The human virome is a critical component of the human microbiome, and it is believed to hold the richest diversity within human microbiomes. Yet, the inter-individual scaling (changes) of the human virome has not been formally investigated to the best of our knowledge. Here we fill the gap by applying diversity-area relationship (DAR) modeling (a recent extension to the classic species-area law in biodiversity and biogeography research) for analyzing four large datasets of the human virome with three DAR profiles: DAR scaling (z)—measuring the inter-individual heterogeneity in virome diversity, MAD (maximal accrual diversity: Dmax) and LGD ratio (ratio of local diversity to global diversity)—measuring the percentage of individual to population level diversity. Our analyses suggest: (i) The diversity scaling parameter (z) is rather resilient against the diseases as indicated by the lack of significant differences between the healthy and diseased treatments. (ii) The potential maximal accrual diversity (Dmax) is less resilient and may vary between the healthy and diseased groups or between different body sites. (iii) The LGD ratio of bacterial communities is much smaller than for viral communities, and relates to the comparatively greater heterogeneity between local vs. global diversity levels found for bacterial-biomes.

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DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

Revista Fitotecnia Mexicana ◽

10.35196/rfm.2018.3.255-264 ◽

2018 ◽

Vol 41 (3) ◽

pp. 255-264 ◽

Cited By ~ 1

Author(s):

J. Abraham Pérez-Pérez ◽

David Espinosa-Victoria ◽

Hilda V. Silva-Rojas ◽

Lucía López-Reyes

Keyword(s):

Bacterial Diversity ◽

Digestive Tract ◽

Bacterial Species ◽

Brain Heart Infusion ◽

Rrna Gene ◽

Eisenia Foetida ◽

Bacterial Isolates ◽

Bacterial Microbiota ◽

Decomposition Of Organic Matter ◽

Earthworm Gut

Bacteria are an unavoidable component of the natural earthworm diet; thus, bacterial diversity in the earthworm gut is directly linked to decomposition of organic matter and development of the surrounding plants. The aim of this research was to isolate and to identify biochemically and molecularly the culturable bacterial microbiota of the digestive tract of Eisenia foetida. Earthworms were sourced from Instituto de Reconversión Productiva y Bioenergética (IRBIO) and Colegio de Postgraduados (COLPOS), México. Bacterial isolation was carried out on plates of Brain Heart Infusion (BHI) culture medium. Fifty six and 44 bacterial isolates were obtained from IRBIO and COLPOS, respectively. The population was composed of 44 Gram-negative and 56 Gram-positive isolates. Over 50 % of the bacterial isolates were rod-shaped cells. The 16S rRNA gene was sequenced and nine genera were identified in worms from IRBIO (Bacillus, Paenibacillus, Solibacillus, Staphylococcus, Arthrobacter, Pantoea, Stenotrophomonas, Acinetobacter and Aeromonas) and six in worms from COLPOS (Bacillus, Paenibacillus, Stenotrophomonas, Staphylococcus, Acinetobacter and Aeromonas). Bacillus was the predominant genus, with eight and six species in the oligochaetes from IRBIO and COLPOS, respectively. The most represented bacteria in the worms from both sites were Bacillus sp. and B. subtilis. The predominance of Bacillus was probably due to spore formation, a reproductive strategy that ensures survival and dispersion in the soil and oligochaetes digestive tract. The gut of E. foetida not only harbored bacterial species of agronomic importance but also species potentially pathogenic for humans (Staphylococcus warneri, Pantoea agglomerans and Stentrophomonas sp.). The larger bacterial diversity in worms from IRBIO could be due to their feeding on cattle manure, which is a rich source of bacteria.

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Gluten-degrading bacteria: availability and applications

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11263-5 ◽

2021 ◽

Author(s):

Viia Kõiv ◽

Tanel Tenson

Keyword(s):

Microbial Communities ◽

Digestive Tract ◽

Storage Proteins ◽

Gluten Free Diet ◽

Natural Food ◽

Gluten Free ◽

Efficient Treatment ◽

Gluten Intolerance ◽

Degrading Bacteria ◽

Human Digestive Tract

Abstract Gluten is a mixture of storage proteins in wheat and occurs in smaller amounts in other cereal grains. It provides favorable structure to bakery products but unfortunately causes disease conditions with increasing prevalence. In the human gastrointestinal tract, gluten is cleaved into proline and gluten rich peptides that are not degraded further. These peptides trigger immune responses that might lead to celiac disease, wheat allergy, and non-celiac gluten sensitivity. The main treatment option is a gluten-free diet. Alternatively, using enzymes or microorganisms with gluten-degrading properties might alleviate the disease. These components can be used during food production or could be introduced into the digestive tract as food supplements. In addition, natural food from the environment is known to enrich the microbial communities in gut and natural environmental microbial communities have high potential to degrade gluten. It remains to be investigated if food and environment-induced changes in the gut microbiome could contribute to the triggering of gluten-related diseases. Key points • Wheat proteins, gluten, are incompletely digested in human digestive tract leading to gluten intolerance. • The only efficient treatment of gluten intolerance is life-long gluten-free diet. • Environmental bacteria acquired together with food could be source of gluten-degrading bacteria detoxifying undigested gluten peptides.

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Influx of Enterococci and Associated Antibiotic Resistance and Virulence Genes from Ready-To-Eat Food to the Human Digestive Tract

Applied and Environmental Microbiology ◽

10.1128/aem.01444-07 ◽

2007 ◽

Vol 73 (21) ◽

pp. 6740-6747 ◽

Cited By ~ 25

Author(s):

Lilia Macovei ◽

Ludek Zurek

Keyword(s):

Antibiotic Resistance ◽

Digestive Tract ◽

Fast Food ◽

Virulence Genes ◽

Food Contamination ◽

Gene Copy ◽

Marker Genes ◽

Enterococcus Casseliflavus ◽

Fast Food Restaurants ◽

Human Digestive Tract

ABSTRACT The influx of enterococcal antibiotic resistance (AR) and virulence genes from ready-to-eat food (RTEF) to the human digestive tract was assessed. Three RTEFs (chicken salad, chicken burger, and carrot cake) were sampled from five fast-food restaurants five times in summer (SU) and winter (WI). The prevalence of enterococci was significantly higher in SU (92.0% of salad samples and 64.0% of burger samples) than in WI (64.0% of salad samples and 24.0% of burger samples). The overall concentrations of enterococci during the two seasons were similar (∼103 CFU/g); the most prevalent were Enterococcus casseliflavus (41.5% of isolates) and Enterococcus hirae (41.5%) in WI and Enterococcus faecium (36.8%), E. casseliflavus (27.6%), and Enterococcus faecalis (22.4%) in SU. Resistance in WI was detected primarily to tetracycline (50.8%), ciprofloxacin (13.8%), and erythromycin (4.6%). SU isolates were resistant mainly to tetracycline (22.8%), erythromycin (22.1%), and kanamycin (13.0%). The most common tet gene was tet(M) (35.4% of WI isolates and 11.9% of SU isolates). The prevalence of virulence genes (gelE, asa1, cylA, and esp) and marker genes for clinical isolates (EF_0573, EF_0592, EF_0605, EF_1420, EF_2144, and pathogenicity island EF_0050) was low (≤12.3%). Genotyping of E. faecalis and E. faecium using pulsed-field gel electrophoresis revealed that the food contamination likely originated from various sources and that it was not clonal. Our conservative estimate (single AR gene copy per cell) for the influx of tet genes alone to the human digestive tract is 3.8 Ã¯Â¿Â½ 105 per meal (chicken salad). This AR gene influx is frequent because RTEFs are commonly consumed and that may play a role in the acquisition of AR determinants in the human digestive tract.

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