2022
Hanes D, Nowinski B, Lamb JJ, Larson IA, McDonald D, Knight R, Song S and Patno N (2022) The gastrointestinal and microbiome impact of a resistant starch blend from potato, banana, and apple fibers: A randomized clinical trial using smart caps. Front. Nutr. 9:987216. doi: 10.3389/fnut.2022.987216
Hakim D, Wandro S, Zengler K, Zaramela LS, Nowinski B, Swafford A, Zhu Q, Song S, Gonzalez A, McDonald D, Knight R (2022) Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References. Msystems. Sep 8:e00758-22.
Orchanian SB, Gauglitz JM, Wandro S, Weldon KC, Doty M, Stillwell K, Hansen S, Jiang L, Vargas F, Rhee KE, Lumeng JC, Dorrestein PC, Knight R, Kim JH, Song S, and Swafford AD. (2022) Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention. Advanced Biology. Aug;6(8):2101313.
Martino C, McDonald D, Cantrell K, Dilmore AH, Vázquez-Baeza Y, Shenhav L, Shaffer JP, Rahman G, Armstrong G, Allaband C, Song SJ, and Knight R. (2022) Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype. Msystems. Apr 28:e00050-22.
Bai-Tong SS, Thoemmes MS, Weldon KC, Motazavi D, Kitsen J, Hansen S, Furst A, Geng B, Song S, Gilbert JA, Bode L, Dorrestein PC, Knight R, Leibel SA, and Leibel SL. (2022) The impact of maternal asthma on the preterm infants' gut metabolome and microbiome (MAP study). Scientific reports. Apr 19;12(1):1-2.
Cotillard A, Cartier-Meheust A, Litwin NS, Chaumont S, Saccareau M, Lejzerowicz F, Tap J, Koutnikova H, Lopez DG, McDonald D, Song S, Knight R, Derrien M, Veiga P. (2022) A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project. The American journal of clinical nutrition. Feb;115(2):432-43.
2021
Song S, Wang J, Martino C, Jiang L, Thompson WK, Shenhav L, McDonald D, Marotz C, Harris PR, Hernandez CD, Henderson N, ... and Dominguez-Bello MG. (2021) Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding. Med. Aug 13;2(8):951-64.
Sabey KA, Song S, Jolles A, Knight R, Ezenwa VO. (2021) Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota. The ISME journal. May;15(5):1359-71.
Marotz C, Cavagnero KJ, Song S, McDonald D, Wandro S, Humphrey G, Bryant M, Ackermann G, Diaz E, Knight R. (2021) Evaluation of the effect of storage methods on fecal, saliva, and skin microbiome composition. Msystems. Apr 27;6(2):e01329-20.
Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, ... Song S, ...and Knight R. (2021) EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets. Msystems. 2021 Mar 16;6(2):e01216-20.
2020
Videvall E, Song S, Bensch HM, Strandh M, Engelbrecht A, Serfontein N, Hellgren O, Olivier A, Cloete S, Knight R, Cornwallis CK (2020) Early-life gut dysbiosis linked to juvenile mortality in ostriches. Microbiome 8:147.
Poore GD, Kopylova E, Zhu Q, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf J, Song S, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Knight R (2020) Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature 579:567–574.
Song S, Sanders JG, Delsuc F, Metcalf J, Amato K, Taylor MW, Mazel F, Lutz HL, Winker K, Graves GR, Humphrey G, Gilbert JA, Hackett SJ, White KP, Skeen HR, Kurtis SM, Withrow J, Braile T, Miller M, McCracken KG, Maley JM, Ezenwa VO, Williams A, Blanton JM, McKenzie VJ, Knight R (2020) Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats. MBio. doi: 10.1128/mBio.02901-19
Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song S, McDonald D, Derrien M, Knight R (2020) Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems. doi: 10.1128/mSystems.00901-19
Casals-Pascual C, González A, Vázquez-Baeza Y, Song S, Jiang L, Knight R (2020) Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations. Gastroenterology 158:1524–1528.
2019
McCall L-I, Callewaert C, Zhu Q, Song S, Bouslimani A, Minich JJ, Ernst M, Ruiz-Calderon JF, Cavallin H, Pereira HS, Novoselac A, Hernandez J, Rios R, Branch OH, Blaser MJ, Paulino LC, Dorrestein PC, Knight R, Dominguez-Bello MG. 2019. Home chemical and microbial transitions across urbanization. Nat Microbiol. doi: 10.1038/s41564-019-0593-4.
Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song S, Bonneau R, Dorrestein PC, Knight R, 2019. Learning representations of microbe-metabolite interactions. Nat Methods. doi: 10.1038/s41592-019-0616-3.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu Y-X, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song S, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:1091.
Song S, Sanders J, Baldassarre D, Chaves J, Johnson N, Piaggio A, Stuckey M, Novakova E, Metcalf JL, Chomel B, Aguilar-Setien A, Knight R, McKenzie V. 2019. Is there convergence of gut microbes in blood-feeding vertebrates? Philosophical Transactions of the Royal Society B.
Song S, Woodhams DC, Martino C, Allaband C, Mu A, Javorschi-Miller-Montgomery S, Suchodolski JS, Knight R. 2019. Engineering the microbiome for animal health and conservation. Exp Biol Med 1535370219830075. epub ahead of print.
Kodama WA, Xu Z, Metcalf JL, Song S, Harrison N, Knight R, Carter DO, Happy CB. 2018. Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. J Forensic Sci. doi: 10.1111/1556-4029.13949
Videvall E, Song S, Bensch HM, Strandh M, Engelbrecht A, Serfontein N, Hellgren O, Olivier A, Cloete S, Knight R, Cornwallis CK. 2019. Major shifts in gut microbiota during development and its relationship to growth in ostriches. Mol Ecol. doi: 10.1111/mec.15087
Amato KR, G Sanders J, Song S, Nute M, Metcalf JL, Thompson LR, Morton JT, Amir A, J McKenzie V, Humphrey G, Gogul G, Gaffney J, L Baden A, A O Britton G, P Cuozzo F, Di Fiore A, J Dominy N, L Goldberg T, Gomez A, Kowalewski MM, J Lewis R, Link A, L Sauther M, Tecot S, A White B, E Nelson K, M Stumpf R, Knight R, R Leigh S. 2019. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J 13:576–587.
2018
Kodama WA, Xu Z, Metcalf JL, Song S, Harrison N, Knight R, Carter DO, Happy CB. 2018. Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. J Forensic Sci. doi: 10.1111/1556-4029.13949
Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song S, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R (2018) Are microbiome studies ready for hypothesis-driven research? Curr Opin Microbiol 44:61–69.
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song S, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, American Gut Consortium, Knight R. 2018. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. doi: 10.1128/mSystems.00031-18.
2017
Davenport ER, JG Sanders, S Song, KR Amato, AG Clark, R Knight. 2017. The human microbiome in evolution. BMC biology 15(1): 127
Metcalf JL, S Song, JT Morton, S Weiss, A Seguin-Orlando, F Joly, C Feh, P Taberlet, E Coissac, A Amir, E Willerslev, R Knight, V McKenzie, L Orlando. 2017. Evaluating the impact of domestication and captivity on the horse gut microbiome. Scientific reports 7(1):15497.
Thompson LR, JG Sanders, D McDonald, A Amir, J Ladau, KJ Locey, RJ Prill, A Tripathi, SM Gibbons, G Ackermann, JA Navas- Molina, E Kopylova, Y Vázquez-Baeza, S Janssen, JT Morton, S Mirarab, ZZ Xu, MF Haroon, J Kanbar, Q Zhu, A Gonzalez, S Song, T Kosciolek, NA Bokulich, J Lefler, CJ Brislawn, GC Humphrey, SM Owens, J Hampton-Marcell, D Berg-Lyons, V McKenzie, N Fierer, JA Fuhrman, A Clauset, RL Stevens, A Shade, KS Pollard, KD Goodwin, JK Jansson, JA Gilbert, R Knight, and The Earth Microbiome Project Consortium. 2017. A communal catalogue reveals Earth's multiscale microbial diversity. Nature 551 (7681):457.
Mandeville E, T Parchman, K Thompson, R Compton, K Gelwicks, S Song, and CA Buerkle. 2017. Inconsistent reproductive isolation revealed by interactions between Catostomus fish species. Evolution Letters 1(5):255-268.
McKenzie VJ, S Song, F Delsuc, TL Prest, AM Oliverio, TM Korpita, A Alexiev, KR Amato, JL Metcalf, M Kowalewski, NL Avenant, A Link, T Di Fiore, A Seguin-Orlando, C Feh, L Orlando, J Mendelson, J Sanders, and R Knight. The effects of captivity on the mammalian gut microbiome. Integrative and Comparative Biology 57(4):690–704. doi:10.1093/icb/icx090.
Morton JT, J Sanders, RA Quinn, D McDonald, A González, Y Vasquez-Baeza, JA Navas-Molina, S Song, JL Metcalf, ER Hyde, M Lladser, PC Dorrestein, and R Knight. 2017. Balance trees reveal microbial niche differentiation. mSystems 2(1):e00162-16. doi:10.1128/mSystems.00162-16.
2016
Debelius J, S Song, Y Vasquez-Baeza, ZZ Xu, A Gonzalez, and R Knight. 2016. Tiny microbes, enormous impacts: what matters in gut microbiome studies? Genome Biology. 17:217.
PD Scanlan, R Knight, S Song, GL Ackermann, and PD Cotter. 2016. Prevalence, genetic diversity and potential for Blastocystis human-human transmission within family units living in the United States. 2016. Infection, Genetics and Evolution. 45:95-97. doi:10.1016/j.meegid.2016.08.018.
Hyde E, J Navas-Molina, S Song, J Kueneman, G Ackermann, C Cardona, G Humphrey, D Boyer, T Weaver, J Mendelson III, V McKenzie, J Gilbert, and R Knight. 2016. The oral and skin microbiomes of captive Komodo Dragons are significantly shared with their habitat. mSystems 1(4):e00046-16. doi:10.1128/mSystems.00046-16.
Amato KR, JL Metcalf, S Song, VL Hale, J Clayton, G Ackermann, G Humphrey, K Niu, D Cui, H Zhao, MD Schrenzel, CL Tan, R Knight, and J Braun. 2016. Using the gut microbiota as a novel tool for examining colobine primate GI health. Global Ecology and Conservation 7:225–237. doi:10.1016/j.gecco.2016.06.004.
Levin I, DM Zonana, BK Fosdick, S Song, R Knight, and RJ Safran. 2016. Stress response, gut microbial diversity, and sexual signals correlate with social interactions. 2016. Biology Letters 12: 20160352. doi:10.1098/rsbl.2016.0352.
Quinn RA, JA Navas-Molina, ER Hyde , S Song, Y Vázquez-Baeza, G Humphrey, J Gaffney, JJ Minich, AV Melnik, J Herschend, J DeReus, A Durant, RJ Dutton, M Khosroheidari, C Green, R da Silva, PC Dorrestein, and R Knight. 2016. From sample to multi-omics conclusions in under 48 hours. mSystems 1(2):e00038-16. doi:10.1128/mSystems.00038-16.
Song S, A Amir, JL Metcalf, KR Amato, ZZ Xu, G Humphrey, and R Knight. 2016. Preservation methods differ in fecal microbiome stability, affecting suitability for field studies. mSystems 1(3):e00021-16. doi:10.1128/mSystems.00021-16.
Engel P, WK Kwong, Q McFrederick, KE Anderson, SM Barribeau, JA Chandler, RS Cornman, J Dainat, JR de Miranda, V Doublet, O Emery, JD Evans, L Farinelli, ML Flenniken, F Granberg, JA Grasis, L Gauthier, J Hayer, H Koch, S Kocher, V Martinson, N Moran, M Munoz-Torres, I Newton, RJ Paxton, E Powell, B Sadd, P Schmid‐Hempel, R Schmid-Hempel, S Song, RS Schwarz, D vanEngelsdorp, and B Dainat. 2016. The Bee Microbiome: Impact on bee health and model for evolution and ecology of host-microbe interactions. mBio 7(2):e02164-15. doi:10.1128/mBio.02164-15.
Ruiz-Calderon* JF, Cavallin* H, Song* S, A Novoselac, LR Pericchi, JN Hernandez, R Rios, OH Branch, H Pereira, LC Paulino, MJ Blaser, R Knight, and MG Dominguez-Bello. 2016. Walls talk: Microbial biogeography of homes spanning urbanization. Science Advances. 2(2): e1501061.
doi: 10.1126/sciadv.1501061. *Authors contributed equally.
Dominguez-Bello MG, KM De Jesus-Laboy, N Shen, LM Cox, A Amir, A Gonzalez, NA Bokulich, S Song, M Hoashi, JI Rivera-Vina, K Mendez, R Knight, and JC Clemente. 2016. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine. doi:10.1038/nm.4039.
Metcalf JL, ZZ Xu, S Weiss, S Lax, W Van Treuren, ER Hyde, S Song, A Amir, P Larsen, N Sangwan, D Haarmann, GC Humphrey, G Ackermann, LR Thompson, C Lauber, A Bibat, C Nicholas, MJ Gebert, JF Petrosino, SC Reed, JA Gilbert, AM Lynne, SR Bucheli, DO Carter, R Knight. 2016. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science 2016 Jan 8;351(6269):158-62.
2015
Clemente JC, EC Pehrsson, MJ Blaser, K Sandhu, Z Gao, B Wang, M Magris, G Hidalgo, M Contreras, O Noya-Alarcon, O Lander, J McDonald, M Cox, J Walter, PL Oh, JF Ruiz, S Rodriguez, N Shen, S Song, J Metcalf, R Knight, G Dantas, and MG Dominguez-Bello. 2015. The microbiome of uncontacted Amerindians. Science Advances. 1(3): e1500183-e1500183.
2014
Weiss S, A Amir, ER Hyde, JL Metcalf, S Song, and R Knight. 2014. Tracking down the sources of experimental contamination in microbiome studies. Genome Biology. 15(12):564.
Gevers D, S Kugathasan, LA Denson, Y Vázquez-Baeza, W Van Treuren, B Ren, E Schwager, D Knights, S Song, M Yassour, XC Morgan, AD Kostic, C Luo, A González, D McDonald, Y Haberman, T Walters, S Baker, J Rosh, M Stephens, M Heyman, J Markowitz, R Baldassano, A Griffiths, F Sylvester, D Mack, S Kim, W Crandall, J Hyams, C Huttenhower, R Knight, and RJ Xavier. 2014. The treatment-naïve microbiome in new-onset Crohn’s disease. Cell Host & Microbe. 15(3):382-392.
2013
Delsuc F, JL Metcalf, L Parfrey, S Song, and R Knight. 2013. Convergent evolution of gut microbiomes in myrmecophagous mammals. Molecular Ecology 23(6):1301-1317.
Navas-Molina JA, JM Peralta-Sánchez, A González, PJ McMurdie, Y Vázquez-Baeza, Z Xu, LK Ursell, C Lauber, H Zhou, S Song, J Huntley, GL Ackermann, D Berg-Lyons, S Holmes, JG Caporaso, and R Knight. 2013. Advancing our understanding of the human microbiome using QIIME. Methods Enzymology 531:371-444.
Song S, C Lauber, EK Costello, CA Lozupone, G Humphrey, D Berg-Lyons, JG Caporaso, D Knights, JC Clemente, S Nakielny, JI Gordon, N Fierer, and R Knight. 2013. Cohabiting family members sharemicrobiota with one another and with their dogs. eLife 2:e00458.
Song S, MG Dominguez-Bello, and R Knight. 2013. Commentary: How delivery mode and feeding can shape the bacterial community in the infant gut. Canadian Medical Association Journal. 185(5):373-4.
2012
Fierer N, S Ferrenberg, GE Flores, A González, J Kueneman, T Legg, RC Lynch, D McDonald, JR Mihaljevic, SP O’Neill, ME Rhodes, S Song, and WA Walters. 2012. From animalcules to an ecosystem: application of ecological concepts to the human microbiome. Annual Review of Ecology, Evolution, and Systematics. 43(1):137-155.
Paull SH, S Song, K McClure, LC Sackett, AM Kilpatrick, and PTJ Johnson. 2012. Disease superspreaders and hotspots: linking elevated transmission across hosts and space. Frontiers in Ecology and Environment. 10: 75–82.
2011
González A, A King, M Robeson, S Song, JL Metcalf, A Shade, and R Knight. 2011. Characterizing microbial communities through space and time. Current Opinion in Biotechnology. 23(3):431-436.
González A, JC Clemente, A Shade, JL Metcalf, S Song, B Prithiviraj, BE Palmer, and R Knight. 2011. Our microbial selves: what ecology can teach us. EMBO Reports. 12:775-784.
Hanes D, Nowinski B, Lamb JJ, Larson IA, McDonald D, Knight R, Song S and Patno N (2022) The gastrointestinal and microbiome impact of a resistant starch blend from potato, banana, and apple fibers: A randomized clinical trial using smart caps. Front. Nutr. 9:987216. doi: 10.3389/fnut.2022.987216
Hakim D, Wandro S, Zengler K, Zaramela LS, Nowinski B, Swafford A, Zhu Q, Song S, Gonzalez A, McDonald D, Knight R (2022) Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References. Msystems. Sep 8:e00758-22.
Orchanian SB, Gauglitz JM, Wandro S, Weldon KC, Doty M, Stillwell K, Hansen S, Jiang L, Vargas F, Rhee KE, Lumeng JC, Dorrestein PC, Knight R, Kim JH, Song S, and Swafford AD. (2022) Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention. Advanced Biology. Aug;6(8):2101313.
Martino C, McDonald D, Cantrell K, Dilmore AH, Vázquez-Baeza Y, Shenhav L, Shaffer JP, Rahman G, Armstrong G, Allaband C, Song SJ, and Knight R. (2022) Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype. Msystems. Apr 28:e00050-22.
Bai-Tong SS, Thoemmes MS, Weldon KC, Motazavi D, Kitsen J, Hansen S, Furst A, Geng B, Song S, Gilbert JA, Bode L, Dorrestein PC, Knight R, Leibel SA, and Leibel SL. (2022) The impact of maternal asthma on the preterm infants' gut metabolome and microbiome (MAP study). Scientific reports. Apr 19;12(1):1-2.
Cotillard A, Cartier-Meheust A, Litwin NS, Chaumont S, Saccareau M, Lejzerowicz F, Tap J, Koutnikova H, Lopez DG, McDonald D, Song S, Knight R, Derrien M, Veiga P. (2022) A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project. The American journal of clinical nutrition. Feb;115(2):432-43.
2021
Song S, Wang J, Martino C, Jiang L, Thompson WK, Shenhav L, McDonald D, Marotz C, Harris PR, Hernandez CD, Henderson N, ... and Dominguez-Bello MG. (2021) Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding. Med. Aug 13;2(8):951-64.
Sabey KA, Song S, Jolles A, Knight R, Ezenwa VO. (2021) Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota. The ISME journal. May;15(5):1359-71.
Marotz C, Cavagnero KJ, Song S, McDonald D, Wandro S, Humphrey G, Bryant M, Ackermann G, Diaz E, Knight R. (2021) Evaluation of the effect of storage methods on fecal, saliva, and skin microbiome composition. Msystems. Apr 27;6(2):e01329-20.
Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, ... Song S, ...and Knight R. (2021) EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets. Msystems. 2021 Mar 16;6(2):e01216-20.
2020
Videvall E, Song S, Bensch HM, Strandh M, Engelbrecht A, Serfontein N, Hellgren O, Olivier A, Cloete S, Knight R, Cornwallis CK (2020) Early-life gut dysbiosis linked to juvenile mortality in ostriches. Microbiome 8:147.
Poore GD, Kopylova E, Zhu Q, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf J, Song S, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Knight R (2020) Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature 579:567–574.
Song S, Sanders JG, Delsuc F, Metcalf J, Amato K, Taylor MW, Mazel F, Lutz HL, Winker K, Graves GR, Humphrey G, Gilbert JA, Hackett SJ, White KP, Skeen HR, Kurtis SM, Withrow J, Braile T, Miller M, McCracken KG, Maley JM, Ezenwa VO, Williams A, Blanton JM, McKenzie VJ, Knight R (2020) Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats. MBio. doi: 10.1128/mBio.02901-19
Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song S, McDonald D, Derrien M, Knight R (2020) Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems. doi: 10.1128/mSystems.00901-19
Casals-Pascual C, González A, Vázquez-Baeza Y, Song S, Jiang L, Knight R (2020) Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations. Gastroenterology 158:1524–1528.
2019
McCall L-I, Callewaert C, Zhu Q, Song S, Bouslimani A, Minich JJ, Ernst M, Ruiz-Calderon JF, Cavallin H, Pereira HS, Novoselac A, Hernandez J, Rios R, Branch OH, Blaser MJ, Paulino LC, Dorrestein PC, Knight R, Dominguez-Bello MG. 2019. Home chemical and microbial transitions across urbanization. Nat Microbiol. doi: 10.1038/s41564-019-0593-4.
Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song S, Bonneau R, Dorrestein PC, Knight R, 2019. Learning representations of microbe-metabolite interactions. Nat Methods. doi: 10.1038/s41592-019-0616-3.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu Y-X, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song S, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:1091.
Song S, Sanders J, Baldassarre D, Chaves J, Johnson N, Piaggio A, Stuckey M, Novakova E, Metcalf JL, Chomel B, Aguilar-Setien A, Knight R, McKenzie V. 2019. Is there convergence of gut microbes in blood-feeding vertebrates? Philosophical Transactions of the Royal Society B.
Song S, Woodhams DC, Martino C, Allaband C, Mu A, Javorschi-Miller-Montgomery S, Suchodolski JS, Knight R. 2019. Engineering the microbiome for animal health and conservation. Exp Biol Med 1535370219830075. epub ahead of print.
Kodama WA, Xu Z, Metcalf JL, Song S, Harrison N, Knight R, Carter DO, Happy CB. 2018. Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. J Forensic Sci. doi: 10.1111/1556-4029.13949
Videvall E, Song S, Bensch HM, Strandh M, Engelbrecht A, Serfontein N, Hellgren O, Olivier A, Cloete S, Knight R, Cornwallis CK. 2019. Major shifts in gut microbiota during development and its relationship to growth in ostriches. Mol Ecol. doi: 10.1111/mec.15087
Amato KR, G Sanders J, Song S, Nute M, Metcalf JL, Thompson LR, Morton JT, Amir A, J McKenzie V, Humphrey G, Gogul G, Gaffney J, L Baden A, A O Britton G, P Cuozzo F, Di Fiore A, J Dominy N, L Goldberg T, Gomez A, Kowalewski MM, J Lewis R, Link A, L Sauther M, Tecot S, A White B, E Nelson K, M Stumpf R, Knight R, R Leigh S. 2019. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J 13:576–587.
2018
Kodama WA, Xu Z, Metcalf JL, Song S, Harrison N, Knight R, Carter DO, Happy CB. 2018. Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. J Forensic Sci. doi: 10.1111/1556-4029.13949
Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song S, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R (2018) Are microbiome studies ready for hypothesis-driven research? Curr Opin Microbiol 44:61–69.
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song S, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, American Gut Consortium, Knight R. 2018. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. doi: 10.1128/mSystems.00031-18.
2017
Davenport ER, JG Sanders, S Song, KR Amato, AG Clark, R Knight. 2017. The human microbiome in evolution. BMC biology 15(1): 127
Metcalf JL, S Song, JT Morton, S Weiss, A Seguin-Orlando, F Joly, C Feh, P Taberlet, E Coissac, A Amir, E Willerslev, R Knight, V McKenzie, L Orlando. 2017. Evaluating the impact of domestication and captivity on the horse gut microbiome. Scientific reports 7(1):15497.
Thompson LR, JG Sanders, D McDonald, A Amir, J Ladau, KJ Locey, RJ Prill, A Tripathi, SM Gibbons, G Ackermann, JA Navas- Molina, E Kopylova, Y Vázquez-Baeza, S Janssen, JT Morton, S Mirarab, ZZ Xu, MF Haroon, J Kanbar, Q Zhu, A Gonzalez, S Song, T Kosciolek, NA Bokulich, J Lefler, CJ Brislawn, GC Humphrey, SM Owens, J Hampton-Marcell, D Berg-Lyons, V McKenzie, N Fierer, JA Fuhrman, A Clauset, RL Stevens, A Shade, KS Pollard, KD Goodwin, JK Jansson, JA Gilbert, R Knight, and The Earth Microbiome Project Consortium. 2017. A communal catalogue reveals Earth's multiscale microbial diversity. Nature 551 (7681):457.
Mandeville E, T Parchman, K Thompson, R Compton, K Gelwicks, S Song, and CA Buerkle. 2017. Inconsistent reproductive isolation revealed by interactions between Catostomus fish species. Evolution Letters 1(5):255-268.
McKenzie VJ, S Song, F Delsuc, TL Prest, AM Oliverio, TM Korpita, A Alexiev, KR Amato, JL Metcalf, M Kowalewski, NL Avenant, A Link, T Di Fiore, A Seguin-Orlando, C Feh, L Orlando, J Mendelson, J Sanders, and R Knight. The effects of captivity on the mammalian gut microbiome. Integrative and Comparative Biology 57(4):690–704. doi:10.1093/icb/icx090.
Morton JT, J Sanders, RA Quinn, D McDonald, A González, Y Vasquez-Baeza, JA Navas-Molina, S Song, JL Metcalf, ER Hyde, M Lladser, PC Dorrestein, and R Knight. 2017. Balance trees reveal microbial niche differentiation. mSystems 2(1):e00162-16. doi:10.1128/mSystems.00162-16.
2016
Debelius J, S Song, Y Vasquez-Baeza, ZZ Xu, A Gonzalez, and R Knight. 2016. Tiny microbes, enormous impacts: what matters in gut microbiome studies? Genome Biology. 17:217.
PD Scanlan, R Knight, S Song, GL Ackermann, and PD Cotter. 2016. Prevalence, genetic diversity and potential for Blastocystis human-human transmission within family units living in the United States. 2016. Infection, Genetics and Evolution. 45:95-97. doi:10.1016/j.meegid.2016.08.018.
Hyde E, J Navas-Molina, S Song, J Kueneman, G Ackermann, C Cardona, G Humphrey, D Boyer, T Weaver, J Mendelson III, V McKenzie, J Gilbert, and R Knight. 2016. The oral and skin microbiomes of captive Komodo Dragons are significantly shared with their habitat. mSystems 1(4):e00046-16. doi:10.1128/mSystems.00046-16.
Amato KR, JL Metcalf, S Song, VL Hale, J Clayton, G Ackermann, G Humphrey, K Niu, D Cui, H Zhao, MD Schrenzel, CL Tan, R Knight, and J Braun. 2016. Using the gut microbiota as a novel tool for examining colobine primate GI health. Global Ecology and Conservation 7:225–237. doi:10.1016/j.gecco.2016.06.004.
Levin I, DM Zonana, BK Fosdick, S Song, R Knight, and RJ Safran. 2016. Stress response, gut microbial diversity, and sexual signals correlate with social interactions. 2016. Biology Letters 12: 20160352. doi:10.1098/rsbl.2016.0352.
Quinn RA, JA Navas-Molina, ER Hyde , S Song, Y Vázquez-Baeza, G Humphrey, J Gaffney, JJ Minich, AV Melnik, J Herschend, J DeReus, A Durant, RJ Dutton, M Khosroheidari, C Green, R da Silva, PC Dorrestein, and R Knight. 2016. From sample to multi-omics conclusions in under 48 hours. mSystems 1(2):e00038-16. doi:10.1128/mSystems.00038-16.
Song S, A Amir, JL Metcalf, KR Amato, ZZ Xu, G Humphrey, and R Knight. 2016. Preservation methods differ in fecal microbiome stability, affecting suitability for field studies. mSystems 1(3):e00021-16. doi:10.1128/mSystems.00021-16.
Engel P, WK Kwong, Q McFrederick, KE Anderson, SM Barribeau, JA Chandler, RS Cornman, J Dainat, JR de Miranda, V Doublet, O Emery, JD Evans, L Farinelli, ML Flenniken, F Granberg, JA Grasis, L Gauthier, J Hayer, H Koch, S Kocher, V Martinson, N Moran, M Munoz-Torres, I Newton, RJ Paxton, E Powell, B Sadd, P Schmid‐Hempel, R Schmid-Hempel, S Song, RS Schwarz, D vanEngelsdorp, and B Dainat. 2016. The Bee Microbiome: Impact on bee health and model for evolution and ecology of host-microbe interactions. mBio 7(2):e02164-15. doi:10.1128/mBio.02164-15.
Ruiz-Calderon* JF, Cavallin* H, Song* S, A Novoselac, LR Pericchi, JN Hernandez, R Rios, OH Branch, H Pereira, LC Paulino, MJ Blaser, R Knight, and MG Dominguez-Bello. 2016. Walls talk: Microbial biogeography of homes spanning urbanization. Science Advances. 2(2): e1501061.
doi: 10.1126/sciadv.1501061. *Authors contributed equally.
Dominguez-Bello MG, KM De Jesus-Laboy, N Shen, LM Cox, A Amir, A Gonzalez, NA Bokulich, S Song, M Hoashi, JI Rivera-Vina, K Mendez, R Knight, and JC Clemente. 2016. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine. doi:10.1038/nm.4039.
Metcalf JL, ZZ Xu, S Weiss, S Lax, W Van Treuren, ER Hyde, S Song, A Amir, P Larsen, N Sangwan, D Haarmann, GC Humphrey, G Ackermann, LR Thompson, C Lauber, A Bibat, C Nicholas, MJ Gebert, JF Petrosino, SC Reed, JA Gilbert, AM Lynne, SR Bucheli, DO Carter, R Knight. 2016. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science 2016 Jan 8;351(6269):158-62.
2015
Clemente JC, EC Pehrsson, MJ Blaser, K Sandhu, Z Gao, B Wang, M Magris, G Hidalgo, M Contreras, O Noya-Alarcon, O Lander, J McDonald, M Cox, J Walter, PL Oh, JF Ruiz, S Rodriguez, N Shen, S Song, J Metcalf, R Knight, G Dantas, and MG Dominguez-Bello. 2015. The microbiome of uncontacted Amerindians. Science Advances. 1(3): e1500183-e1500183.
2014
Weiss S, A Amir, ER Hyde, JL Metcalf, S Song, and R Knight. 2014. Tracking down the sources of experimental contamination in microbiome studies. Genome Biology. 15(12):564.
Gevers D, S Kugathasan, LA Denson, Y Vázquez-Baeza, W Van Treuren, B Ren, E Schwager, D Knights, S Song, M Yassour, XC Morgan, AD Kostic, C Luo, A González, D McDonald, Y Haberman, T Walters, S Baker, J Rosh, M Stephens, M Heyman, J Markowitz, R Baldassano, A Griffiths, F Sylvester, D Mack, S Kim, W Crandall, J Hyams, C Huttenhower, R Knight, and RJ Xavier. 2014. The treatment-naïve microbiome in new-onset Crohn’s disease. Cell Host & Microbe. 15(3):382-392.
2013
Delsuc F, JL Metcalf, L Parfrey, S Song, and R Knight. 2013. Convergent evolution of gut microbiomes in myrmecophagous mammals. Molecular Ecology 23(6):1301-1317.
Navas-Molina JA, JM Peralta-Sánchez, A González, PJ McMurdie, Y Vázquez-Baeza, Z Xu, LK Ursell, C Lauber, H Zhou, S Song, J Huntley, GL Ackermann, D Berg-Lyons, S Holmes, JG Caporaso, and R Knight. 2013. Advancing our understanding of the human microbiome using QIIME. Methods Enzymology 531:371-444.
Song S, C Lauber, EK Costello, CA Lozupone, G Humphrey, D Berg-Lyons, JG Caporaso, D Knights, JC Clemente, S Nakielny, JI Gordon, N Fierer, and R Knight. 2013. Cohabiting family members sharemicrobiota with one another and with their dogs. eLife 2:e00458.
Song S, MG Dominguez-Bello, and R Knight. 2013. Commentary: How delivery mode and feeding can shape the bacterial community in the infant gut. Canadian Medical Association Journal. 185(5):373-4.
2012
Fierer N, S Ferrenberg, GE Flores, A González, J Kueneman, T Legg, RC Lynch, D McDonald, JR Mihaljevic, SP O’Neill, ME Rhodes, S Song, and WA Walters. 2012. From animalcules to an ecosystem: application of ecological concepts to the human microbiome. Annual Review of Ecology, Evolution, and Systematics. 43(1):137-155.
Paull SH, S Song, K McClure, LC Sackett, AM Kilpatrick, and PTJ Johnson. 2012. Disease superspreaders and hotspots: linking elevated transmission across hosts and space. Frontiers in Ecology and Environment. 10: 75–82.
2011
González A, A King, M Robeson, S Song, JL Metcalf, A Shade, and R Knight. 2011. Characterizing microbial communities through space and time. Current Opinion in Biotechnology. 23(3):431-436.
González A, JC Clemente, A Shade, JL Metcalf, S Song, B Prithiviraj, BE Palmer, and R Knight. 2011. Our microbial selves: what ecology can teach us. EMBO Reports. 12:775-784.