Distinct maternal microbiota clusters are associated with diet during pregnancy: impact on neonatal microbiota and infant growth during the first 18 months of life

References

• Nauta A, Amor K, Knol J, Garssen J, Van Der Beek E. Relevance of pre- and postnatal nutrition to development and interplay between the microbiota and metabolic and immune systems. Am J Clin Nutr. [Internet]. 2013;98:586S–593S. http://www.embase.com/search/results?subaction=viewrecord&from=export&id=L369512071%0Ahttp://ajcn.nutrition.org/content/98/2/586S.full.pdf+html%0Ahttp://dx.doi.org/10.3945/ajcn.112.039644.
   Google Scholar
• Lucas C, Charlton KE, Yeatman H. Nutrition advice during pregnancy: do women receive it and can health professionals provide it? Matern Child Health J. [Internet]. 2014;18:2465–2478. doi:10.1007/s10995-014-1485-0.
   Google Scholar
• Amarasekara R, Jayasekara RW, Senanayake H, Dissanayake VHW. Microbiome of the placenta in pre-eclampsia supports the role of bacteria in the multifactorial cause of pre-eclampsia. J Obstet Gynaecol Res. [Internet]. 2015 accessed 2019 Jun 3;41:662–669. doi:10.1111/jog.12619.
   Google Scholar
• Bhutta ZA, Lassi ZS. Preconception care and nutrition interventions in low- and middle-income countries. [Internet]. S. Karger AG; 2014. [ accessed 2018 May 30]. p. 15–26. https://www.karger.com/Article/FullText/360246.
   Google Scholar
• García-Mantrana I, Bertua B, Martínez-Costa C, Collado MC. Perinatal nutrition: how to take care of the gut microbiota? Clin Nutr Exp. [Internet]. 2016 accessed 2017 Aug 10;6:3–16. http://linkinghub.elsevier.com/retrieve/pii/S2352939316000063.
   Google Scholar
• Mokkala K, Röytiö H, Munukka E, Pietilä S, Ekblad U, Rönnemaa T, Eerola E, Laiho A, Laitinen K. Gut microbiota richness and composition and dietary intake of overweight pregnant women are related to serum zonulin concentration, a marker for intestinal permeability. J Nutr. [Internet]. 2016 accessed 2019 Oct 16;146:1694–1700. http://www.ncbi.nlm.nih.gov/pubmed/27466607.
   Google Scholar
• Mandal S, Godfrey KM, McDonald D, Treuren WV, Bjørnholt JV, Midtvedt T, Moen B, Rudi K, Knight R, Brantsæter AL, et al. Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intake. Microbiome. [Internet]. 2016 accessed 2019 Oct 16;4:55. http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0200-3.
   Google Scholar
• Gomez-Arango LF, Barrett HL, Wilkinson SA, Callaway LK, McIntyre HD, Morrison M, Dekker Nitert M. Low dietary fiber intake increases Collinsella abundance in the gut microbiota of overweight and obese pregnant women. Gut Microbes. [Internet]. 2018 accessed 2019 Oct 16;9:189–201. https://www.tandfonline.com/doi/full/10.1080/19490976.2017.1406584.
   Google Scholar
• Ferrocino I, Ponzo V, Gambino R, Zarovska A, Leone F, Monzeglio C, Goitre I, Rosato R, Romano A, Grassi G, et al. Changes in the gut microbiota composition during pregnancy in patients with gestational diabetes mellitus (GDM). Sci Rep. [Internet]. 2018 accessed 2019 Oct 16;8:12216. http://www.ncbi.nlm.nih.gov/pubmed/30111822.
   Google Scholar
• Barrett H, Gomez-Arango L, Wilkinson S, McIntyre H, Callaway L, Morrison M, Dekker Nitert M. A vegetarian diet is a major determinant of gut microbiota composition in early pregnancy. Nutrients. [Internet]. 2018 accessed 2019 Oct 16;10:890. http://www.ncbi.nlm.nih.gov/pubmed/30002323.
   Google Scholar
• Savage JH, Lee-Sarwar KA, Sordillo JE, Lange NE, Zhou Y, O’Connor GT, Sandel M, Bacharier LB, Zeiger R, Sodergren E, et al. Diet during pregnancy and infancy and the infant intestinal microbiome. J Pediatr. [Internet]. 2018 accessed 2019 Oct 16;203:47–54.e4. http://www.ncbi.nlm.nih.gov/pubmed/30173873.
   Google Scholar
• Cox LM, Blaser MJ. Antibiotics in early life and obesity. Nat Rev Endocrinol.[Internet]. 2015 accessed 2019 Oct 16;11:182–190. http://www.ncbi.nlm.nih.gov/pubmed/25488483.
   Google Scholar
• Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci. [Internet]. 2010 accessed 2017 Oct 2;107:11971–11975. http://www.ncbi.nlm.nih.gov/pubmed/20566857.
   Google Scholar
• Ajslev TA, Andersen CS, Gamborg M, Sørensen TIA, Jess T. Childhood overweight after establishment of the gut microbiota: the role of delivery mode, pre-pregnancy weight and early administration of antibiotics. Int J Obes. [Internet]. 2011 accessed 2019 Jul 11;35:522–529. http://www.nature.com/articles/ijo201127.
   Google Scholar
• Kalliomäki M, Carmen Collado M, Salminen S, Isolauri E. Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr. [Internet]. 2008 accessed 2019 Jul 11;87:534–538. https://academic.oup.com/ajcn/article/87/3/534/4633266.
   Google Scholar
• Collado MC, Isolauri E, Laitinen K, Salminen S. Effect of mother’s weight on infant’s microbiota acquisition, composition, and activity during early infancy: a prospective follow-up study initiated in early pregnancy. Am J Clin Nutr. [Internet]. 2010 accessed 2018 May 30;92:1023–1030. http://www.ncbi.nlm.nih.gov/pubmed/20844065.
   Google Scholar
• Garcia-Mantrana I, Collado MC. Obesity and overweight: impact on maternal and milk microbiome and their role for infant health and nutrition. Mol Nutr Food Res. [Internet]. 2016 accessed 2017 Aug 10;60:1865–1875. http://www.ncbi.nlm.nih.gov/pubmed/27159888.
   Google Scholar
• Singh SB, Madan J, Coker M, Hoen A, Baker ER, Karagas MR, Mueller NT. Does birth mode modify associations of maternal pre-pregnancy BMI and gestational weight gain with the infant gut microbiome? Int J Obes. [Internet]. 2019 accessed 2019 Oct 16. http://www.ncbi.nlm.nih.gov/pubmed/30765892.
   Google Scholar
• Kovatcheva-Datchary P, Nilsson A, Akrami R, Lee YS, De Vadder F, Arora T, Hallen A, Martens E, Björck I, Bäckhed F. Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of prevotella. Cell Metab. [Internet]. 2015 accessed 2019 Dec 16;22:971–982. https://linkinghub.elsevier.com/retrieve/pii/S1550413115005173.
   Google Scholar
• Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BAH, Forslund K, Hildebrand F, Prifti E, Falony G, et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. [Internet]. 2016 accessed 2019 Dec 16;535:376–381. http://www.nature.com/articles/nature18646.
   Google Scholar
• David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. Internet. 2014;505:559–563. https://www.ncbi.nlm.nih.gov/pubmed/24336217.
   Google Scholar
• Walker AW, Duncan SH, Harmsen HJM, Holtrop G, Welling GW, Flint HJ. The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities. Environ Microbiol. Internet. 2008;10:3275–3283. doi:10.1111/j.1462-2920.2008.01717.x.
   Google Scholar
• Miquel S, Martín R, Rossi O, Bermúdez-Humarán L, Chatel J, Sokol H, Thomas M, Wells J, Langella P. Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol. Internet. 2013 accessed 2019 Jun 6;16:255–261. https://www.sciencedirect.com/science/article/pii/S1369527413000775.
   Google Scholar
• Zhang M, Zhou L, Wang Y, Dorfman RG, Tang D, Xu L, Pan Y, Zhou Q, Li Y, Yin Y, et al. Faecalibacterium prausnitzii produces butyrate to decrease c-Myc-related metabolism and Th17 differentiation by inhibiting histone deacetylase 3. Int Immunol. Internet. 2019 accessed 2019 Jun 6;31:499–514. https://academic.oup.com/intimm/advance-article/doi/10.1093/intimm/dxz022/5365732.
   Google Scholar
• Rivière A, Selak M, Lantin D, Leroy F, De Vuyst L. Bifidobacteria and butyrate-producing colon bacteria: importance and strategies for their stimulation in the human gut. Front Microbiol. Internet. 2016 accessed 2017 Jul 21;7:979. http://www.ncbi.nlm.nih.gov/pubmed/27446020.
   Google Scholar
• Garcia-Mantrana I, Selma-Royo M, Alcantara C, Collado MC. Shifts on gut microbiota associated to mediterranean diet adherence and specific dietary intakes on general adult population. Front Microbiol. Internet. 2018 accessed 2019 Jun 5;9. http://journal.frontiersin.org/article/10.3389/fmicb.2018.00890/full.
   Google Scholar
• Maeda N, Okamoto M, Kondo K, Ishikawa H, Osada R, Tsurumoto A, Fujita H. Incidence of Prevotella intermedia and Prevotella nigrescens in periodontal health and disease. Microbiol Immunol. Internet. 1998 accessed 2019 Jun 3;42:583–589. doi:10.1111/j.1348-0421.1998.tb02328.x.
   Google Scholar
• Riggio MP, Lennon A. Identification of oral peptostreptococcus isolates by PCR-restriction fragment length polymorphism analysis of 16S rRNA genes. J Clin Microbiol. Internet. 2003 cited 2019 Jun 3;41:4475–4479. http://www.ncbi.nlm.nih.gov/pubmed/12958299.
   Google Scholar
• Szafrański SP, Deng Z-L, Tomasch J, Jarek M, Bhuju S, Meisinger C, Kühnisch J, Sztajer H, Wagner-Döbler I. Functional biomarkers for chronic periodontitis and insights into the roles of Prevotella nigrescens and Fusobacterium nucleatum; a metatranscriptome analysis. NPJ Biofilms Microbiomes. Internet. 2015 accessed 2019 Jun 3;1:15017. http://www.ncbi.nlm.nih.gov/pubmed/28721234.
   Google Scholar
• Hansen TH, Kern T, Bak EG, Kashani A, Allin KH, Nielsen T, Hansen T, Pedersen O. Impact of a vegan diet on the human salivary microbiota. Sci Rep. Internet. 2018;8:5847. https://www.ncbi.nlm.nih.gov/pubmed/29643500.
   Google Scholar
• Lourenςo TGB, Spencer SJ, Alm EJ, Colombo APV. Defining the gut microbiota in individuals with periodontal diseases: an exploratory study. J Oral Microbiol. Internet. 2018 cited 2019 Jun 3;10:1487741. http://www.ncbi.nlm.nih.gov/pubmed/29988721.
   Google Scholar
• Vonaesch P, Morien E, Andrianonimiadana L, Sanke H, Mbecko J-R, Huus KE, Naharimanananirina T, Gondje BP, Nigatoloum SN, Vondo SS, et al. Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa. Proc Natl Acad Sci. Internet. 2018 accessed 2019 Jun 3;115:E8489–98. http://www.ncbi.nlm.nih.gov/pubmed/30126990.
   Google Scholar
• Olsen I, Yamazaki K. Can oral bacteria affect the microbiome of the gut? J Oral Microbiol. Internet. 2019 accessed 2019 Jun 3;11:1586422. http://www.ncbi.nlm.nih.gov/pubmed/30911359.
   Google Scholar
• Schmidt TS, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, et al. Extensive transmission of microbes along the gastrointestinal tract. Elife. Internet. 2019 accessed 2019 Jun 3;8. http://www.ncbi.nlm.nih.gov/pubmed/30747106.
   Google Scholar
• Borgo PV, Rodrigues VAA, Feitosa ACR, Xavier KCB, Avila-Campos MJ, BORGO PV, RODRIGUES VAA, FEITOSA ACR, XAVIER KCB, AVILA-CAMPOS MJ. Association between periodontal condition and subgingival microbiota in women during pregnancy: a longitudinal study. J Appl Oral Sci. Internet. 2014 accessed 2019 Jun 3;22:528–533. http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-77572014000600528&lng=en&tlng=en.
   Google Scholar
• Merchant AT, Pitiphat W, Franz M, Joshipura KJ. Whole-grain and fiber intakes and periodontitis risk in men. Am J Clin Nutr. Internet. 2006;83:1395–1400. doi:10.1093/ajcn/83.6.1395.
   Google Scholar
• Nielsen SJ, Trak-Fellermeier MA, Joshipura K, Dye BA. Dietary fiber intake is inversely associated with periodontal disease among US adults. J Nutr. Internet. 2016;146:2530–2536. https://www.ncbi.nlm.nih.gov/pubmed/27798338.
   Google Scholar
• Rombaldi Bernardi J, de Souza Escobar R, Ferreira CF, Pelufo Silveira P. Fetal and neonatal levels of omega-3: effects on neurodevelopment, nutrition, and growth. Sci World J. Internet. 2012 accessed 2019 Oct 16;2012:202473. http://www.ncbi.nlm.nih.gov/pubmed/23125553.
   Google Scholar
• Coletta JM, Bell SJ, Roman AS. Omega-3 fatty acids and pregnancy. Rev Obstet Gynecol. Internet. 2010;3:163–171. https://www.ncbi.nlm.nih.gov/pubmed/21364848.
   Google Scholar
• Ciesielski TH, Bartlett J, Williams SM. Omega-3 polyunsaturated fatty acid intake norms and preterm birth rate: a cross-sectional analysis of 184 countries. BMJ Open. Internet. 2019;9:e027249. http://bmjopen.bmj.com/content/9/4/e027249.abstract.
   Google Scholar
• Tortosa-Caparrós E, Navas-Carrillo D, Marín F, Orenes-Piñero E. Anti-inflammatory effects of omega 3 and omega 6 polyunsaturated fatty acids in cardiovascular disease and metabolic syndrome. Crit Rev Food Sci Nutr. Internet. 2017 accessed 2019 Dec 17;57:3421–3429. http://www.ncbi.nlm.nih.gov/pubmed/26745681.
   Google Scholar
• Costantini L, Molinari R, Farinon B, Merendino N. Impact of omega-3 fatty acids on the gut microbiota. Int J Mol Sci. Internet. 2017;18:2645. https://www.ncbi.nlm.nih.gov/pubmed/29215589.
   Google Scholar
• Duda-Chodak A, Tarko T, Satora P, Sroka P. Interaction of dietary compounds, especially polyphenols, with the intestinal microbiota: a review. Eur J Nutr. Internet. 2015 accessed 2019 Jun 28;54:325–341. http://www.ncbi.nlm.nih.gov/pubmed/25672526.
   Google Scholar
• Ozdal T, Sela DA, Xiao J, Boyacioglu D, Chen F, Capanoglu E. The reciprocal interactions between polyphenols and gut microbiota and effects on bioaccessibility. Nutrients. Internet. 2016 accessed 2019 Jun 28;8:78. http://www.ncbi.nlm.nih.gov/pubmed/26861391.
   Google Scholar
• Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, et al. Human genetics shape the gut microbiome. Cell. Internet. 2014 accessed 2017 Jul 21;159:789–799. http://www.ncbi.nlm.nih.gov/pubmed/25417156.
   Google Scholar
• Chan YK, Brar MS, Kirjavainen PV, Chen Y, Peng J, Li D, Leung F-C-C, El-Nezami H. High fat diet induced atherosclerosis is accompanied with low colonic bacterial diversity and altered abundances that correlates with plaque size, plasma A-FABP and cholesterol: a pilot study of high fat diet and its intervention with Lactobacillus rhamno. BMC Microbiol. Internet. 2016;16:264. https://www.ncbi.nlm.nih.gov/pubmed/27821063.
   Google Scholar
• Louis P, Flint HJ. Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol. Internet. 2017 accessed 2019 Jun 6;19:29–41. http://www.ncbi.nlm.nih.gov/pubmed/27928878.
   Google Scholar
• Wyatt SB, Winters KP, Dubbert PM. Overweight and obesity: prevalence, consequences, and causes of a growing public health problem. Am J Med Sci. Internet. 2006 accessed 2019 Jun 28;331:166–174. https://www.sciencedirect.com/science/article/abs/pii/S0002962915328032.
   Google Scholar
• Hassink SG, Daniels SR, Abrams SA, Corkins MR, De Ferranti SD, Golden NH, Magge SN, Schwarzenberg SJ. The role of the pediatrician in primary prevention of obesity. Pediatrics. 2015;136:e275–92. doi:10.1542/peds.2015-1558.
   Google Scholar
• Roy SM, Spivack JG, Faith MS, Chesi A, Mitchell JA, Kelly A, Grant SFA, McCormack SE, Zemel BS. Infant BMI or weight-for-length and obesity risk in early childhood. Pediatrics. 2016;137:e20153492–e20153492. doi:10.1542/peds.2015-3492.
   Google Scholar
• Silverwood RJ, De Stavola BL, Cole TJ, Leon DA. BMI peak in infancy as a predictor for later BMI in the uppsala family study. Int J Obes. Internet. 2009 accessed 2019 Oct 16;33:929–937. http://www.ncbi.nlm.nih.gov/pubmed/19564879.
   Google Scholar
• Sovio U, Kaakinen M, Tzoulaki I, Das S, Ruokonen A, Pouta A, Hartikainen A-L, Molitor J, Järvelin M-R. How do changes in body mass index in infancy and childhood associate with cardiometabolic profile in adulthood? Findings from the Northern Finland Birth Cohort 1966 study. Int J Obes. Internet. 2014 accessed 2019 Oct 16;38:53–59. http://www.ncbi.nlm.nih.gov/pubmed/24080793.
   Google Scholar
• Roy SM, Fields DA, Mitchell JA, Hawkes CP, Kelly A, Wu GD, DeRusso PA, Elovitz MA, Ford E, Drigo D, Zemel BS, McCormack SE. Body Mass Index Is a Better Indicator of Body Composition than Weight-for-Length at Age 1 Month. J Pediatr. 2019; 204:77–83. doi:10.1016/j.jpeds.2018.08.007.
   Google Scholar
• de Onis M, Lobstein T. Defining obesity risk status in the general childhood population: which cut-offs should we use? Int J Pediatr Obes. Internet. 2010 accessed 2019 Oct 16;5:458–460. http://www.ncbi.nlm.nih.gov/pubmed/20233144.
   Google Scholar
• Stanislawski MA, Dabelea D, Wagner BD, Sontag MK, Lozupone CA, Eggesbø M. Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants. Microbiome. Internet. 2017 accessed 2019 Dec 16;5:113. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0332-0.
   Google Scholar
• Koleva P, Bridgman S, Kozyrskyj A. the infant gut microbiome: evidence for obesity risk and dietary intervention. Nutrients. Internet. 2015 accessed 2017 Oct 27;7:2237–2260. http://www.ncbi.nlm.nih.gov/pubmed/25835047.
   Google Scholar
• Stanislawski MA, Dabelea D, Wagner BD, Iszatt N, Dahl C, Sontag MK, Knight R, Lozupone CA, Eggesbø M. Gut microbiota in the first 2 years of life and the association with body mass index at age 12 in a Norwegian Birth Cohort. MBio. 2018;9:1–14. doi:10.1128/mBio.01751-18.
   Google Scholar
• Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, Lieber AD, Wu F, Perez-Perez GI, Chen Y, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med. Internet] 2016 accessed 2019 Oct 16;8:343ra82–343ra82. http://www.ncbi.nlm.nih.gov/pubmed/27306664.
   Google Scholar
• Azad MB, Moossavi S, Owora A, Sepehri S. Early-life antibiotic exposure, gut microbiota development, and predisposition to obesity. Internet. In: Nestle Nutrition Institute workshop series. 2017 [accessed 2019 Oct 16]. p. 67–79. http://www.ncbi.nlm.nih.gov/pubmed/28346924.
   Google Scholar
• Dutton H, Doyle M-A, Buchan CA, Mohammad S, Adamo KB, Shorr R, Fergusson DA. Antibiotic exposure and risk of weight gain and obesity: protocol for a systematic review. Syst Rev. Internet. 2017 accessed 2019 Oct 16;6:169. http://www.ncbi.nlm.nih.gov/pubmed/28837004.
   Google Scholar
• García-Mantrana I, Alcántara C, Selma-Royo M, Boix-Amorós A, Dzidic M, Gimeno-Alcañiz J, Úbeda-Sansano I, Sorribes-Monrabal I, Escuriet R, Gil-Raga F, et al. MAMI: a birth cohort focused on maternal-infant microbiota during early life. BMC Pediatr. 2019;19:140. doi:10.1186/s12887-019-1502-y.
   Google Scholar
• Fernández-Ballart JD, Piñol JL, Zazpe I, Corella D, Carrasco P, Toledo E, Perez-Bauer M, Ngel Martínez-González M, Salas-Salvadó J, Martín-Moreno JM. Relative validity of a semi-quantitative food-frequency questionnaire in an elderly Mediterranean population of Spain. Br J Nutr. Internet. 2010 accessed 2017 Nov 29;103:1808–1816. https://www.cambridge.org/core/services/aop-cambridge-core/content/view/AE602565052BA7B01EE799B4D9B3E8C4/S0007114509993837a.pdf/relative_validity_of_a_semiquantitative_foodfrequency_questionnaire_in_an_elderly_mediterranean_population_of_spain.pdf.
   Google Scholar
• Cervera P, Farran A, Zamora-Ros R. Tablas de composición de alimentos CESNID = Taules de composició d’aliments del CESNID. New York: McGraw-Hill, Universitat de Barcelona; 2004.
   Google Scholar
• Marlett J, Cheung T. Database and quick methods of assessing typical dietary fiber intakes using data for 228 commonly consumed foods. J Am Diet Assoc. Internet. 1997 accessed 2019 Jun 6;97:1139–1151. http://www.ncbi.nlm.nih.gov/pubmed/9336561.
   Google Scholar
• Neveu V, Perez-Jiménez J, Vos F, Crespy V, Du Chaffaut L, Mennen L, Knox C, Eisner R, Cruz J, Wishart D, et al. Phenol-Explorer: an online comprehensive database on polyphenol contents in foods. Database (Oxford). Internet. 2010 accessed 2019 Oct 16;2010:bap024. http://www.ncbi.nlm.nih.gov/pubmed/20428313.
   Google Scholar
• Martinez-Gonzalez MA, Corella D, Salas-Salvado J, Ros E, Covas MI, Fiol M, Warnberg J, Aros F, Ruiz-Gutierrez V, Lamuela-Raventos RM, et al. Cohort Profile: design and methods of the PREDIMED study. Int J Epidemiol. Internet. 2012 accessed 2017 Jul 21;41:377–385. http://www.ncbi.nlm.nih.gov/pubmed/21172932.
   Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. Internet. 2010 accessed 2017 Sep 29;7:335–336. http://www.ncbi.nlm.nih.gov/pubmed/20383131.
   Google Scholar
• Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J-M, et al. Enterotypes of the human gut microbiome. Nature. Internet. 2011 accessed 2019 Jun 3;473:174–180. http://www.nature.com/articles/nature09944.
   Google Scholar
• McMurdie PJ, Holmes S. phyloseq: an r package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217. doi:10.1371/journal.pone.0061217.
   Google Scholar
• Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K. cluster: cluster analysis basics and extensions. R package version 2.0.9; 2019.
   Google Scholar
• Venables WN, Ripley BD. Modern applied statistics with S. Fourth. New York: Springer; 2002. ISBN 0-387-95457-0.
   Google Scholar
• Walesiak M, Dudek A. clusterSim: searching for optimal clustering procedure for a data set.R package version 0.47-3. 2018. Available from: https://CRAN.R-project.org/package=clusterSim (accessed 2019 Feb 12).
   Google Scholar
• Bougeard S, Dray S. Supervised multiblock analysis in R with the ade4 package. J Stat Softw. 2018;86(1):1–17. doi:10.18637/jss.v086.i01.
   Google Scholar
• IBM Corp. IBM SPSS statistics for windows.
   Google Scholar
• R Studio Team. RStudio: integrated development for R. RStudio, Inc; Boston (MA); 2016.
   Google Scholar
• Warners GR, Bolker B, Bonebakker L, Gentleman W, Liaw HA, Lumley T, Maechler M, Magrusson A, Moeller S, Schwartz M, et al. gplots: various R programming tools for plotting data. 2019.
   Google Scholar