Belkaid Y, Naik S. Compartmentalized and systemic control of tissue immunity by commensals. Nat Immunol. 2013;14(7):646–53.
Article
PubMed
CAS
Google Scholar
Sender R, Fuchs S, Milo R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell. 2016;164(3):337–40.
Article
PubMed
CAS
Google Scholar
Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009;9(5):313–23.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ghaisas S, Maher J, Kanthasamy A. Gut microbiome in health and disease: linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases. Pharmacol Ther. 2015;158:52–62.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tojo R, Suarez A, Clemente MG, de los Reyes-Gavilan CG, Margolles A, Gueimonde M, et al. Intestinal microbiota in health and disease: role of bifidobacteria in gut homeostasis. World J Gastroenterol. 2014;20(41):15163–76.
Article
PubMed
PubMed Central
Google Scholar
Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012;13(4):260–70.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R. The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. J Allergy Clin Immunol. 2012;129(5):1204–8.
Article
PubMed
PubMed Central
Google Scholar
Caporaso G, Lauber C, Costello E, Berg-Lyons D, Gonzalez A, Stombaugh J, et al. Moving pictures of the human microbiome. Genome Biol. 2011;12(5):R50.
Article
PubMed
PubMed Central
Google Scholar
Marti JM, Martinez-Martinez D, Rubio T, Gracia C, Pena M, Latorre A, et al. Health and disease imprinted in the time variability of the human microbiome. mSystems. 2017;2(2):e00144-16.
Monda V, Villano I, Messina A, Valenzano A, Esposito T, Moscatelli F, et al. Exercise modifies the gut microbiota with positive health effects. Oxidative Med Cell Longev. 2017;2017:3831972.
Article
CAS
Google Scholar
Bressa C, Bailen-Andrino M, Perez-Santiago J, Gonzalez-Soltero R, Perez M, Montalvo-Lominchar MG, et al. Differences in gut microbiota profile between women with active lifestyle and sedentary women. PLoS One. 2017;12(2):e0171352.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010;107(26):11971–5.
Article
PubMed
PubMed Central
Google Scholar
Adlerberth I, Wold AE. Establishment of the gut microbiota in western infants. Acta Paediatr. 2009;98(2):229–38.
Article
PubMed
CAS
Google Scholar
Lee SA, Lim JY, Kim BS, Cho SJ, Kim NY, Kim OB, et al. Comparison of the gut microbiota profile in breast-fed and formula-fed Korean infants using pyrosequencing. Nutr Res Pract. 2015;9(3):242–8.
Article
PubMed
Google Scholar
Mueller NT, Bakacs E, Combellick J, Grigoryan Z, Dominguez-Bello MG. The infant microbiome development: mom matters. Trends Mol Med. 2015;21(2):109–17.
Article
PubMed
Google Scholar
Walker AW, Lawley TD. Therapeutic modulation of intestinal dysbiosis. Pharmacol Res. 2013;69(1):75–86.
Article
PubMed
CAS
Google Scholar
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457(7228):480–4.
Article
PubMed
CAS
Google Scholar
Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One. 2010;5(2):e9085.
Article
PubMed
PubMed Central
CAS
Google Scholar
Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M, Zheng Z, et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology. 2010;139(6):1844–54. e1
Article
PubMed
Google Scholar
Michail S, Durbin M, Turner D, Griffiths AM, Mack DR, Hyams J, et al. Alterations in the gut microbiome of children with severe ulcerative colitis. Inflamm Bowel Dis. 2012;18(10):1799–808.
Article
PubMed
Google Scholar
Parracho HM, Bingham MO, Gibson GR, McCartney AL. Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J Med Microbiol. 2005;54(Pt 10):987–91.
Article
PubMed
Google Scholar
Spear GT, Sikaroodi M, Zariffard MR, Landay AL, French AL, Gillevet PM. Comparison of the diversity of the vaginal microbiota in HIV-infected and HIV-uninfected women with or without bacterial vaginosis. J Infect Dis. 2008;198(8):1131–40.
Article
PubMed
PubMed Central
Google Scholar
Alekseyenko AV, Perez-Perez GI, De Souza A, Strober B, Gao Z, Bihan M, et al. Community differentiation of the cutaneous microbiota in psoriasis. Microbiome. 2013;1(1):31.
Article
PubMed
PubMed Central
Google Scholar
Wang Y, Kasper LH. The role of microbiome in central nervous system disorders. Brain Behav Immun. 2014;38:1–12.
Article
PubMed
CAS
Google Scholar
Dinan TG, Cryan JF. The microbiome-gut-brain Axis in health and disease. Gastroenterol Clin N Am. 2017;46(1):77–89.
Article
Google Scholar
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2012;40:D115–22.
Article
PubMed
CAS
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222–30.
Article
PubMed
CAS
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Article
PubMed
CAS
Google Scholar
Karp PD, Riley M, Paley SM, Pelligrini-Toole A. EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 1996;24(1):32–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Cade S, Doherty R, et al. EuPathDB: the eukaryotic pathogen database. Nucleic Acids Res. 2013;41:D684–91.
Article
PubMed
CAS
Google Scholar
Saier MH Jr, Reddy VS, Tamang DG, Vastermark A. The transporter classification database. Nucleic Acids Res. 2014;42:D251–8.
Article
PubMed
CAS
Google Scholar
Ulrich LE, Zhulin IB. MiST: a microbial signal transduction database. Nucleic Acids Res. 2007;35:D386–90.
Article
PubMed
CAS
Google Scholar
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386.
Article
PubMed
PubMed Central
CAS
Google Scholar
Codd EF. A relational model of data for large shared data banks. Commun ACM. 1970;13(6):377–87.
Article
Google Scholar
Strawn G, Strawn C. Relational databases: Codd, Stonebraker, and Ellison. IT Prof. 2016;18(2):63–5.
Article
Google Scholar
Verstichel S KW, Dupont T, Volckaert B, Ongenae F, De Turck F and Demeester P. LimeDS and the TraPIST project: a case study. 7th International Joint Conference on Knowledge Discovery, Knowledge Engineering, and Knowledge Management; 12/11/2015–14/11/2015; Lisbon, Portugal. 2015. p. 501–508.
Tedjo DI, Jonkers DM, Savelkoul PH, Masclee AA, van Best N, Pierik MJ, et al. The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects. PLoS One. 2015;10(5):e0126685.
Article
PubMed
PubMed Central
CAS
Google Scholar
(ICH): MedDRA. Available from: http://www.meddra.org/how-to-use/basics/hierarchy. Accessed 11 Apr 2017.
Federhen S. The NCBI taxonomy database. Nucleic Acids Res. 2012;40:D136–43.
Article
PubMed
CAS
Google Scholar
Balvociute M, Huson DH. SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare? BMC Genomics. 2017;18(Suppl 2):114.
Article
PubMed
PubMed Central
Google Scholar
Wang WL, Xu SY, Ren ZG, Tao L, Jiang JW, Zheng SS. Application of metagenomics in the human gut microbiome. World J Gastroenterol. 2015;21(3):803–14.
Article
PubMed
PubMed Central
Google Scholar
Ranjbar R, Behzadi P, Najafi A, Roudi R. DNA microarray for rapid detection and identification of food and water borne Bacteria: from dry to wet lab. Open Microbiol J. 2017;11:330–8.
Article
PubMed
PubMed Central
Google Scholar
Siqueira JF Jr, Sakamoto M, Rosado AS. Microbial community profiling using terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Methods Mol Biol. 2017;1537:139–52.
Article
PubMed
CAS
Google Scholar
Sjoberg F, Nowrouzian F, Rangel I, Hannoun C, Moore E, Adlerberth I, et al. Comparison between terminal-restriction fragment length polymorphism (T-RFLP) and quantitative culture for analysis of infants’ gut microbiota. J Microbiol Methods. 2013;94(1):37–46.
Article
PubMed
CAS
Google Scholar
Ansorge WJ. Next-generation DNA sequencing techniques. New Biotechnol. 2009;25(4):195–203.
Article
CAS
Google Scholar
Samarajeewa AD, Hammad A, Masson L, Khan IU, Scroggins R, Beaudette LA. Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia. J Microbiol Methods. 2015;108:103–11.
Article
PubMed
CAS
Google Scholar
Hahn A, Sanyal A, Perez GF, Colberg-Poley AM, Campos J, Rose MC, et al. Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum. J Microbiol Methods. 2016;130:95–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kodama Y, Shumway M, Leinonen R. The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res. 2012;40:D54–6.
Article
PubMed
CAS
Google Scholar
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Res. 2017;45:D37–42.
Article
PubMed
CAS
Google Scholar
Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tarraga A, Cheng Y, et al. The European nucleotide archive. Nucleic Acids Res. 2011;39:D28–31.
Article
PubMed
CAS
Google Scholar
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007;449(7164):804–10.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schulz KF. The quest for unbiased research: randomized clinical trials and the CONSORT reporting guidelines. Ann Neurol. 1997;41(5):569–73.
Article
PubMed
CAS
Google Scholar
von Elm E, Altman DG, Egger M, Pocock SJ, Gotzsche PC, Vandenbroucke JP. The Strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies. PLoS Med. 2007;4(10):e296.
Article
PubMed
PubMed Central
Google Scholar
Vesterinen HM, Egan K, Deister A, Schlattmann P, Macleod MR, Dirnagl U. Systematic survey of the design, statistical analysis, and reporting of studies published in the 2008 volume of the journal of cerebral blood flow and metabolism. J Cereb Blood Flow Metab. 2011;31(4):1064–72.
Article
PubMed
Google Scholar
Kilkenny C, Parsons N, Kadyszewski E, Festing MF, Cuthill IC, Fry D, et al. Survey of the quality of experimental design, statistical analysis and reporting of research using animals. PLoS One. 2009;4(11):e7824.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kilkenny C, Browne WJ, Cuthi I, Emerson M, Altman DG. Improving bioscience research reporting: the ARRIVE guidelines for reporting animal research. Vet Clin Pathol. 2012;41(1):27–31.
Article
PubMed
Google Scholar