Alberdi A. and Gilbert M. T. P. 2019a A guide to the application of Hill numbers to DNA-based diversity analyses. Mol. Ecol. Resour. 19, 804–817.

Article  PubMed  Google Scholar 

Alberdi A. and Gilbert M. T. P. 2019b hilldiv: an R package for the integral analysis of diversity based on Hill numbers. bioRxiv. 545665.

Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D. R. et al. 2011 Enterotypes of the human gut microbiome. Nature 473, 174–180.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aw W. and Fukuda S. 2018 Understanding the role of the gut ecosystem in diabetes mellitus. J. Diabetes Investig. 9, 5–12.

Article  PubMed  Google Scholar 

Blaser M. J. and Falkow S. 2009 What are the consequences of the disappearing human microbiota? Nat. Rev. Microbiol. 7, 887–894.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Blaser M. J. 2017 The theory of disappearing microbiota and the epidemics of chronic diseases. Nat. Rev. Immunol. 17, 461–463.

Article  CAS  PubMed  Google Scholar 

Cho I. and Blaser M. J. 2012 The human microbiome: at the interface of health and disease. Nat. Rev. Genet. 13, 260–270.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Clemente J. C., Pehrsson E. C., Blaser M. J., Sandhu K., Gao Z., Wang B. et al. 2015 The microbiome of uncontacted Amerindians. Sci. Adv. 1, 1500183.

Article  Google Scholar 

De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J. B., Massart S. et al. 2010 Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. USA 107, 14691–14696.

Article  PubMed  PubMed Central  Google Scholar 

Dethlefsen L., McFall-Ngai M. and Relman D. A. 2007 An ecological and evolutionary perspective on human–microbe mutualism and disease. Nature 449, 811–818.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dubey A. K., Uppadhyaya N., Nilawe P., Chauhan N., Kumar S., Gupta U. A. et al. 2018 LogMPIE, pan-India profiling of the human gut microbiome using 16S rRNA sequencing. Sci. Data. 5, 1–10.

Article  Google Scholar 

Dugas L. R., Fuller M., Gilbert J. and Layden B. T. 2016 The obese gut microbiome across the epidemiologic transition. Emerg. Themes Epidemiol. 13, 2.

Article  PubMed  PubMed Central  Google Scholar 

Duncan S. H., Lobley G. E., Holtrop G., Ince J., Johnstone A. M., Louis P. et al. 2008 Human colonic microbiota associated with diet, obesity, and weight loss. Int. J. Obes. (Lond) 32, 1720–1724.

Article  CAS  PubMed  Google Scholar 

Dwiyanto J., Hussain M. H., Reidpath D., Ong K. S., Qasim A., Lee S. W. H. et al. 2021 Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country. Sci. Rep. 11, 1–10.

Article  Google Scholar 

Echarri P. P., Graciá C. M., Berruezo G. R., Vives I., Ballesta M., Solís G. et al. 2011 Assessment of intestinal microbiota of full-term breastfed infants from two different geographical locations. Early Hum. Dev. 87, 511–513.

Article  PubMed  Google Scholar 

Fallani M., Young D., Scott J., Norin E., Amarri S., Adam R. et al. 2010 Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics. J Pediatr. Gastroenterol. Nutr. 51, 77–84.

Article  PubMed  Google Scholar 

Frank D. N., Amand A. L. S., Feldman R. A., Boedeker E. C., Harpaz N. and Pace N. R. 2007 Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. USA 104, 13780–13785.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fujio-Vejar S., Vasquez Y., Morales P., Magne F., Vera-Wolf P., Ugalde J. A. et al. 2017 The gut microbiota of healthy Chilean subjects reveals a high abundance of the phylum verrucomicrobia. Front. Microbiol. 8, 1221.

Article  PubMed  PubMed Central  Google Scholar 

Gilbert J. A., Blaser M. J., Caporaso J. G., Jansson J. K., Lynch S. V. and Knight R. 2018 Current understanding of the human microbiome. Nat. Med. 24, 392–400.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gomez A., Petrzelkova K. J., Burns M. B., Yeoman C. J., Amato K. R., Vlckova K. et al. 2016 Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 14, 2142–2153.

Article  CAS  PubMed  Google Scholar 

Grześkowiak Ł, Grönlund M. M., Beckmann C., Salminen S., von Berg A. and Isolauri E. 2012 The impact of perinatal probiotic intervention on gut microbiota: double-blind placebo-controlled trials in Finland and Germany. Anaerobe 18, 7–13.

Article  PubMed  Google Scholar 

Gupta V. K., Paul S. and Dutta C. 2017 Geography, ethnicity, or subsistence-specific variations in human microbiome composition and diversity. Front. Microbiol. 8, 1162.

Article  PubMed  PubMed Central  Google Scholar 

Hazarika P., Chattopadhyay I., Umpo M., Choudhury Y. and Sharma I. 2022 Elucidating the gut microbiome alterations of tribal community of Arunachal Pradesh: perspectives on their lifestyle or food habits. Sci. Rep. 12, 18296.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hill M. O. 1973 Diversity and evenness: a unifying notation and its consequences. Ecology 54, 427–432.

Article  Google Scholar 

Hsieh T. C., Ma K. H. and Chao A. 2022 iNEXT: Interpolation and Extrapolation for Species Diversity. R package version 3.0.0, http://chao.stat.nthu.edu.tw/wordpress/software_download/.

Human Microbiome Jumpstart Reference Strains Consortium, Nelson K. E., Weinstock G. M., Highlander S. K., Worley K. C., Creasy H. H., Wortman J. R. et al. 2010 A catalog of reference genomes from the human microbiome. Science 328, 994–999.

Article  Google Scholar 

Huttenhower C., Gevers D., Knight R., Abubucker S., Badger J. H., Chinwalla A. T. et al. 2012 Structure, function, and diversity of the healthy human microbiome. Nature 486, 207.

Article  CAS  Google Scholar 

Jari Oksanen F. G. B., Friendly M., Kindt R., Legendre P., McGlinn D., Minchin P. R. 2018 Vegan: community ecology package. R package version, 2.

Jost L. 2006 Entropy and diversity. Oikos 113, 363–375.

Article  Google Scholar 

Karlsson F. H., Tremaroli V., Nookaew I., Bergström G., Behre C. J., Fagerberg B. et al. 2013 Gut metagenome in European women with normal, impaired, and diabetic glucose control. Nature 498, 99–103.

Article  CAS  PubMed  Google Scholar 

Kemppainen K. M., Ardissone A. N., Davis-Richardson A. G., Fagen J. R., Gano K. A., León-Novelo L. G. et al. 2015 Early childhood gut microbiomes show strong geographic differences among subjects at high risk for type 1 diabetes. Diabetes Care 38, 329–332.

Article  PubMed  Google Scholar 

Kolde R. 2019 pheatmap: Pretty Heatmaps. R package version 1.0.12. https://CRAN.R-project.org/package=pheatmap.

Kostic A. D., Gevers D., Pedamallu C. S., Michaud M., Duke F., Earl A. M. et al. 2012 Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 22, 292–298.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lan D., Ji W., Lin B., Chen Y., Huang C., Xiong X. et al. 2017 Correlations between gut microbiota community structures of Tibetans and geography. Sci. Rep. 7, 1–9.

Article  Google Scholar 

Lewis J. D., Chen E. Z., Baldassano R. N., Otley A. R., Griffiths A. M., Lee D. et al. 2015 Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe 18, 489–500.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ley R. E., Turnbaugh P. J., Klein S. and Gordon J. I. 2006 Human gut microbes associated with obesity. Nature 444, 1022–1023.

Article  CAS  PubMed  Google Scholar 

Li J., Jia H., Cai X., Zhong H., Feng Q., Sunagawa S. et al. 2014 An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–841.

Article  CAS  PubMed  Google Scholar 

Li W. and Ma Z. S. 2020 FBA ecological guild: trio of firmicutes-bacteroidetes alliance against actinobacteria in human oral microbiome. Sci. Rep. 10, 1–11.

Google Scholar 

Ma Z. and Li L. 2018 Measuring metagenome diversity and similarity with Hill numbers. Mol. Ecol. Resour. 18, 1339–1355.

Article  CAS  PubMed  Google Scholar 

Magne F., Gotteland M., Gauthier L., Zazueta A., Pesoa S., Navarrete P. et al. 2020 The firmicutes/bacteroidetes ratio: a relevant marker of gut dysbiosis in obese patients? Nutrients 12, 1474.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Magoč T. and Salzberg S. L. 2011 FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963.

Article  PubMed  PubMed Central  Google Scholar 

Manor O., Dai C. L., Kornilov S. A., Smith B., Price N. D., Lovejoy J. C. et al. 2020 Health and disease markers correlate with gut microbiome composition across thousands of people. Nat. Commun. 11, 1–12.

Article