Button KS, Ioannidis JP, Mokrysz C, Nosek BA, Flint J, Robinson ES, Munafò MR. Power failure: why small sample size undermines the reliability of neuroscience. Nat Rev Neurosci. 2013;14:365.
Article
CAS
Google Scholar
Jervis-Bardy J, Leong LE, Marri S, Smith RJ, Choo JM, Smith-Vaughan HC, Nosworthy E, Morris PS, O’Leary S, Rogers GB. Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. Microbiome. 2015;3:19.
Article
Google Scholar
Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J. KatharoSeq enables high-throughput microbiome analysis from low-biomass samples. MSystems. 2018;3:e00218–7.
CAS
PubMed
PubMed Central
Google Scholar
Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotech. 2013;31:814–21.
Article
CAS
Google Scholar
Aßhauer KP, Wemheuer B, Daniel R, Meinicke P. Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics. 2015;31:2882–4.
Article
Google Scholar
Louca S, Parfrey LW, Doebeli M. Decoupling function and taxonomy in the global ocean microbiome. Science. 2016;353:1272–7.
Article
CAS
Google Scholar
Douglas GM, Maffei VJ, Zaneveld J, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MG. PICRUSt2: an improved and extensible approach for metagenome inference. BioRxiv. 2019;672295.
Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014;15:382–92.
Article
CAS
Google Scholar
Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT. Human genetics shape the gut microbiome. Cell. 2014;159:789–99.
Article
CAS
Google Scholar
Carmody RN, Gerber GK, Luevano JM Jr, Gatti DM, Somes L, Svenson KL, Turnbaugh PJ. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe. 2015;17:72–84.
Article
CAS
Google Scholar
De Palma G, Blennerhassett P, Lu J, Deng Y, Park A, Green W, Denou E, Silva M, Santacruz A, Sanz Y. Microbiota and host determinants of behavioural phenotype in maternally separated mice. Nat Commun. 2015;6:7735.
Article
Google Scholar
Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Org E, Parks B, Lusis AJ, Knight R, Caporaso JG, Svanbäck R. Individual diet has sex-dependent effects on vertebrate gut microbiota. Nat commun. 2014;5:4500.
Ainsworth TD, Krause L, Bridge T, Torda G, Raina J-B, Zakrzewski M, Gates RD, Padilla-Gamiño JL, Spalding HL, Smith C. The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts. ISME J. 2015;9:2261.
Article
CAS
Google Scholar
Revetta R, Gomez-Alvarez V, Gerke T, Santo Domingo J, Ashbolt N. Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system. Journal of applied microbiology. 2016;121:294–305.
Article
CAS
Google Scholar
Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich NA, Mills DA, Martin G, Taghavi S. The soil microbiome influences grapevine-associated microbiota. MBio. 2015;6:e02527–14.
Article
Google Scholar
Li X, Sun S, Yuan H, Badgley BD, He Z. Mainstream upflow nitritation-anammox system with hybrid anaerobic pretreatment: long-term performance and microbial community dynamics. Water research. 2017;125:298–308.
Article
CAS
Google Scholar
Ling N, Zhu C, Xue C, Chen H, Duan Y, Peng C, Guo S, Shen Q. Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis. Soil Biol Biochem. 2016;99:137–49.
Article
CAS
Google Scholar
Choi J, Yang F, Stepanauskas R, Cardenas E, Garoutte A, Williams R, Flater J, Tiedje JM, Hofmockel KS, Gelder B. Strategies to improve reference databases for soil microbiomes. ISME J. 2017;11:829.
Article
Google Scholar
Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, FitzGerald MG, Fulton RS. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207.
Article
CAS
Google Scholar
Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C. Sequencing and beyond: integrating molecular‘omics’ for microbial community profiling. Nat Rev Microbiol. 2015;13:360.
Article
CAS
Google Scholar
Ortiz-Álvarez R, Fierer N, de los Ríos A, Casamayor EO, Barberán A. Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession. ISME J. 2018;12:1658.
Article
Google Scholar
Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017;550:61.
Article
CAS
Google Scholar
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505:559.
Article
CAS
Google Scholar
Mao S, Zhang M, Liu J, Zhu W. Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function. Sci Rep. 2015;5:16116.
Article
CAS
Google Scholar
Loudon AH, Woodhams DC, Parfrey LW, Archer H, Knight R, McKenzie V, Harris RN. Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus). ISME J. 2014;8:830.
Article
CAS
Google Scholar
Grice EA, Segre JA. The human microbiome: our second genome. Annual review of genomics and human genetics. 2012;13:151–70.
Article
CAS
Google Scholar
Vartoukian SR, Palmer RM, Wade WG. Strategies for culture of ‘unculturable’bacteria. FEMS Microbiol Lett. 2010;309:1–7.
CAS
PubMed
Google Scholar
Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol. 2005;3:679.
Article
CAS
Google Scholar
Wilkinson TJ, Huws SA, Edwards JE, Kingston-Smith AH, Siu-Ting K, Hughes M, Rubino F, Friedersdorff M, Creevey CJ. CowPI: a rumen microbiome focussed version of the PICRUSt functional inference software. Front Microbiol. 2018;9:1095.
Article
Google Scholar
Winglee K, Howard AG, Sha W, Gharaibeh RZ, Liu J, Jin D, Fodor AA, Gordon-Larsen P. Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes. Microbiome. 2017;5:121.
Article
Google Scholar
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP. Human gut microbiome viewed across age and geography. Nature. 2012;486:222.
Article
CAS
Google Scholar
Hicks AL, Lee KJ, Couto-Rodriguez M, Patel J, Sinha R, Guo C, Olson SH, Seimon A, Seimon TA, Ondzie AU. Gut microbiomes of wild great apes fluctuate seasonally in response to diet. Nat Commun. 2018;9:1786.
Article
Google Scholar
Wang J, Linnenbrink M, Künzel S, Fernandes R, Nadeau M-J, Rosenstiel P, Baines JF. Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice. Proc Natl Acad Sci. 2014:201402342.
Hou Q, Kwok L-Y, Zheng Y, Wang L, Guo Z, Zhang J, Huang W, Wang Y, Leng L, Li H. Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits. Sci Rep. 2016;6:37376.
Article
CAS
Google Scholar
Mendes LW, Raaijmakers JM, de Hollander M, Mendes R, Tsai SM. Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. ISME J. 2017;12:212.
Article
Google Scholar
Navarrete AA, Tsai SM, Mendes LW, Faust K, de Hollander M, Cassman NA, Raes J, van Veen JA, Kuramae EE. Soil microbiome responses to the short-term effects of Amazonian deforestation. Molecular ecology. 2015;24:2433–48.
Article
CAS
Google Scholar
Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods. 2018;15:962.
Article
CAS
Google Scholar