American Gut: an Open Platform for Citizen Science Microbiome Research

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, et al. (2018)
mSystems 3(3): e00031-18.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
McDonald, Daniel; Hyde, Embriette; Debelius, Justine W.; Morton, James T.; Gonzalez, Antonio; Ackermann, Gail; Aksenov, Alexander A.; Behsaz, Bahar; Brennan, Caitriona; Chen, Yingfeng; DeRight Goldasich, Lindsay; Dorrestein, Pieter C.
Alle
Einrichtung
Erscheinungsjahr
2018
Zeitschriftentitel
mSystems
Band
3
Ausgabe
3
Seite(n)
e00031-18
ISSN
2379-5077
Page URI
https://pub.uni-bielefeld.de/record/2921267

Zitieren

McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3):e00031-18.
McDonald, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., et al. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems, 3(3), e00031-18. https://doi.org/10.1128/msystems.00031-18
McDonald, Daniel, Hyde, Embriette, Debelius, Justine W., Morton, James T., Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A., et al. 2018. “American Gut: an Open Platform for Citizen Science Microbiome Research”. mSystems 3 (3): e00031-18.
McDonald, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., et al. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems 3, e00031-18.
McDonald, D., et al., 2018. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems, 3(3), p e00031-18.
D. McDonald, et al., “American Gut: an Open Platform for Citizen Science Microbiome Research”, mSystems, vol. 3, 2018, pp. e00031-18.
McDonald, D., Hyde, E., Debelius, J.W., Morton, J.T., Gonzalez, A., Ackermann, G., Aksenov, A.A., Behsaz, B., Brennan, C., Chen, Y., DeRight Goldasich, L., Dorrestein, P.C., Dunn, R.R., Fahimipour, A.K., Gaffney, J., Gilbert, J.A., Gogul, G., Green, J.L., Hugenholtz, P., Humphrey, G., Huttenhower, C., Jackson, M.A., Janssen, S., Jeste, D.V., Jiang, L., Kelley, S.T., Knights, D., Kosciolek, T., Ladau, J., Leach, J., Marotz, C., Meleshko, D., Melnik, A.V., Metcalf, J.L., Mohimani, H., Montassier, E., Navas-Molina, J., Nguyen, T.T., Peddada, S., Pevzner, P., Pollard, K.S., Rahnavard, G., Robbins-Pianka, A., Sangwan, N., Shorenstein, J., Smarr, L., Song, S.J., Spector, T., Swafford, A.D., Thackray, V.G., Thompson, L.R., Tripathi, A., Vázquez-Baeza, Y., Vrbanac, A., Wischmeyer, P., Wolfe, E., Zhu, Q., Knight, R., Mann, A.E., Amir, A., Frazier, A., Martino, C., Lebrilla, C., Lozupone, C., Lewis, C.M., Raison, C., Zhang, C., Lauber, C.L., Warinner, C., Lowry, C.A., Callewaert, C., Bloss, C., Willner, D., Galzerani, D.D., Gonzalez, D.J., Mills, D.A., Chopra, D., Gevers, D., Berg-Lyons, D., Sears, D.D., Wendel, D., Lovelace, E., Pierce, E., TerAvest, E., Bolyen, E., Bushman, F.D., Wu, G.D., Church, G.M., Saxe, G., Holscher, H.D., Ugrina, I., German, J.B., Caporaso, J.G., Wozniak, J.M., Kerr, J., Ravel, J., Lewis, J.D., Suchodolski, J.S., Jansson, J.K., Hampton-Marcell, J.T., Bobe, J., Raes, J., Chase, J.H., Eisen, J.A., Monk, J., Clemente, J.C., Petrosino, J., Goodrich, J., Gauglitz, J., Jacobs, J., Zengler, K., Swanson, K.S., Lewis, K., Mayer, K., Bittinger, K., Dillon, L., Zaramela, L.S., Schriml, L.M., Dominguez-Bello, M.G., Jankowska, M.M., Blaser, M., Pirrung, M., Minson, M., Kurisu, M., Ajami, N., Gottel, N.R., Chia, N., Fierer, N., White, O., Cani, P.D., Gajer, P., Strandwitz, P., Kashyap, P., Dutton, R., Park, R.S., Xavier, R.J., Mills, R.H., Krajmalnik-Brown, R., Ley, R., Owens, S.M., Klemmer, S., Matamoros, S., Mirarab, S., Moorman, S., Holmes, S., Schwartz, T., Eshoo-Anton, T.W., Vigers, T., Pandey, V., Treuren, W.V., Fang, X., Zech Xu, Z., Jarmusch, A., Geier, J., Reeve, N., Silva, R., Kopylova, E., Nguyen, D., Sanders, K., Salido Benitez, R.A., Heale, A.C., Abramson, M., Waldispühl, J., Butyaev, A., Drogaris, C., Nazarova, E., Ball, M., Gunderson, B.: American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 3, e00031-18 (2018).
McDonald, Daniel, Hyde, Embriette, Debelius, Justine W., Morton, James T., Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A., Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, DeRight Goldasich, Lindsay, Dorrestein, Pieter C., Dunn, Robert R., Fahimipour, Ashkaan K., Gaffney, James, Gilbert, Jack A., Gogul, Grant, Green, Jessica L., Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A., Janssen, Stefan, Jeste, Dilip V., Jiang, Lingjing, Kelley, Scott T., Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua, Leach, Jeff, Marotz, Clarisse, Meleshko, Dmitry, Melnik, Alexey V., Metcalf, Jessica L., Mohimani, Hosein, Montassier, Emmanuel, Navas-Molina, Jose, Nguyen, Tanya T., Peddada, Shyamal, Pevzner, Pavel, Pollard, Katherine S., Rahnavard, Gholamali, Robbins-Pianka, Adam, Sangwan, Naseer, Shorenstein, Joshua, Smarr, Larry, Song, Se Jin, Spector, Timothy, Swafford, Austin D., Thackray, Varykina G., Thompson, Luke R., Tripathi, Anupriya, Vázquez-Baeza, Yoshiki, Vrbanac, Alison, Wischmeyer, Paul, Wolfe, Elaine, Zhu, Qiyun, Knight, Rob, Mann, Allison E., Amir, Amnon, Frazier, Angel, Martino, Cameron, Lebrilla, Carlito, Lozupone, Catherine, Lewis, Cecil M., Raison, Charles, Zhang, Chi, Lauber, Christian L., Warinner, Christina, Lowry, Christopher A., Callewaert, Chris, Bloss, Cinnamon, Willner, Dana, Galzerani, Daniela Domingos, Gonzalez, David J., Mills, David A., Chopra, Deepak, Gevers, Dirk, Berg-Lyons, Donna, Sears, Dorothy D., Wendel, Doug, Lovelace, Elijah, Pierce, Emily, TerAvest, Emily, Bolyen, Evan, Bushman, Frederic D., Wu, Gary D., Church, George M., Saxe, Gordon, Holscher, Hanna D., Ugrina, Ivo, German, J. Bruce, Caporaso, J. Gregory, Wozniak, Jacob M., Kerr, Jacqueline, Ravel, Jacques, Lewis, James D., Suchodolski, Jan S., Jansson, Janet K., Hampton-Marcell, Jarrad T., Bobe, Jason, Raes, Jeroen, Chase, John H., Eisen, Jonathan A., Monk, Jonathan, Clemente, Jose C., Petrosino, Joseph, Goodrich, Julia, Gauglitz, Julia, Jacobs, Julian, Zengler, Karsten, Swanson, Kelly S., Lewis, Kim, Mayer, Kris, Bittinger, Kyle, Dillon, Lindsay, Zaramela, Livia S., Schriml, Lynn M., Dominguez-Bello, Maria G., Jankowska, Marta M., Blaser, Martin, Pirrung, Meg, Minson, Michael, Kurisu, Mike, Ajami, Nadim, Gottel, Neil R., Chia, Nicholas, Fierer, Noah, White, Owen, Cani, Patrice D., Gajer, Pawel, Strandwitz, Philip, Kashyap, Purna, Dutton, Rachel, Park, Rachel S., Xavier, Ramnik J., Mills, Robert H., Krajmalnik-Brown, Rosa, Ley, Ruth, Owens, Sarah M., Klemmer, Scott, Matamoros, Sébastien, Mirarab, Siavash, Moorman, Stephanie, Holmes, Susan, Schwartz, Tara, Eshoo-Anton, Tifani W., Vigers, Tim, Pandey, Vineet, Treuren, Will Van, Fang, Xin, Zech Xu, Zhenjiang, Jarmusch, Alan, Geier, Justin, Reeve, Nicolai, Silva, Ricardo, Kopylova, Evguenia, Nguyen, Dominic, Sanders, Karenina, Salido Benitez, Rodolfo Antonio, Heale, Arthur Cole, Abramson, Max, Waldispühl, Jérôme, Butyaev, Alexander, Drogaris, Chris, Nazarova, Elena, Ball, Madeleine, and Gunderson, Beau. “American Gut: an Open Platform for Citizen Science Microbiome Research”. mSystems 3.3 (2018): e00031-18.

28 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.
Tito RY, Chaffron S, Caenepeel C, Lima-Mendez G, Wang J, Vieira-Silva S, Falony G, Hildebrand F, Darzi Y, Rymenans L, Verspecht C, Bork P, Vermeire S, Joossens M, Raes J., Gut 68(7), 2019
PMID: 30171064
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.
Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, Knight R., Clin Gastroenterol Hepatol 17(2), 2019
PMID: 30240894
You are what you eat: diet, health and the gut microbiota.
Zmora N, Suez J, Elinav E., Nat Rev Gastroenterol Hepatol 16(1), 2019
PMID: 30262901
Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease.
Mills RH, Vázquez-Baeza Y, Zhu Q, Jiang L, Gaffney J, Humphrey G, Smarr L, Knight R, Gonzalez DJ., mSystems 4(1), 2019
PMID: 30801026
Feed Restriction Modifies Intestinal Microbiota-Host Mucosal Networking in Chickens Divergent in Residual Feed Intake.
Metzler-Zebeli BU, Siegerstetter SC, Magowan E, Lawlor PG, Petri RM, O Connell NE, Zebeli Q., mSystems 4(1), 2019
PMID: 30701192
Calour: an Interactive, Microbe-Centric Analysis Tool.
Xu ZZ, Amir A, Sanders J, Zhu Q, Morton JT, Bletz MC, Tripathi A, Huang S, McDonald D, Jiang L, Knight R., mSystems 4(1), 2019
PMID: 30701193
Systematic Review of Gut Microbiota and Major Depression.
Cheung SG, Goldenthal AR, Uhlemann AC, Mann JJ, Miller JM, Sublette ME., Front Psychiatry 10(), 2019
PMID: 30804820
Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults.
de la Cuesta-Zuluaga J, Kelley ST, Chen Y, Escobar JS, Mueller NT, Ley RE, McDonald D, Huang S, Swafford AD, Knight R, Thackray VG., mSystems 4(4), 2019
PMID: 31098397
Open Humans: A platform for participant-centered research and personal data exploration.
Greshake Tzovaras B, Angrist M, Arvai K, Dulaney M, Estrada-Galiñanes V, Gunderson B, Head T, Lewis D, Nov O, Shaer O, Tzovara A, Bobe J, Price Ball M., Gigascience 8(6), 2019
PMID: 31241153
Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome.
Rodionov DA, Arzamasov AA, Khoroshkin MS, Iablokov SN, Leyn SA, Peterson SN, Novichkov PS, Osterman AL., Front Microbiol 10(), 2019
PMID: 31275260
Quantifying and Understanding Well-to-Well Contamination in Microbiome Research.
Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R., mSystems 4(4), 2019
PMID: 31239396
Gut microbiota phenotypes of obesity.
Stanislawski MA, Dabelea D, Lange LA, Wagner BD, Lozupone CA., NPJ Biofilms Microbiomes 5(), 2019
PMID: 31285833
Crowdsourcing Our National Gut.
Grieneisen LE, Blekhman R., mSystems 3(3), 2018
PMID: 29795799
Designer microbiomes.
Gleeson A, Sawyer A., Biotechniques 65(1), 2018
PMID: 30014735
Are microbiome studies ready for hypothesis-driven research?
Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R., Curr Opin Microbiol 44(), 2018
PMID: 30059804
Regional variation limits applications of healthy gut microbiome reference ranges and disease models.
He Y, Wu W, Zheng HM, Li P, McDonald D, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Knight R, Ma WJ, Zhou HW., Nat Med 24(10), 2018
PMID: 30150716
Clinician Guide to Microbiome Testing.
Staley C, Kaiser T, Khoruts A., Dig Dis Sci 63(12), 2018
PMID: 30267172
Daylight exposure modulates bacterial communities associated with household dust.
Fahimipour AK, Hartmann EM, Siemens A, Kline J, Levin DA, Wilson H, Betancourt-Román CM, Brown GZ, Fretz M, Northcutt D, Siemens KN, Huttenhower C, Green JL, Van Den Wymelenberg K., Microbiome 6(1), 2018
PMID: 30333051
High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity.
Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R., mSystems 3(6), 2018
PMID: 30417111
Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria.
Cekanaviciute E, Pröbstel AK, Thomann A, Runia TF, Casaccia P, Katz Sand I, Crabtree E, Singh S, Morrissey J, Barba P, Gomez R, Knight R, Mazmanian S, Graves J, Cree BAC, Zamvil SS, Baranzini SE., mSystems 3(6), 2018
PMID: 30417113
Identifying and Predicting Novelty in Microbiome Studies.
Su X, Jing G, McDonald D, Wang H, Wang Z, Gonzalez A, Sun Z, Huang S, Navas J, Knight R, Xu J., MBio 9(6), 2018
PMID: 30425147
Military-Related Exposures, Social Determinants of Health, and Dysbiosis: The United States-Veteran Microbiome Project (US-VMP).
Brenner LA, Hoisington AJ, Stearns-Yoder KA, Stamper CE, Heinze JD, Postolache TT, Hadidi DA, Hoffmire CA, Stanislawski MA, Lowry CA., Front Cell Infect Microbiol 8(), 2018
PMID: 30510919
A Phylogeny-Regularized Sparse Regression Model for Predictive Modeling of Microbial Community Data.
Xiao J, Chen L, Yu Y, Zhang X, Chen J., Front Microbiol 9(), 2018
PMID: 30619188

120 References

Daten bereitgestellt von Europe PubMed Central.

A communal catalogue reveals Earth's multiscale microbial diversity.
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vazquez-Baeza Y, Gonzalez A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium, Rivera JLA, Al-Moosawi L, Alverdy J, Amato KR, Andras J, Angenent LT, Antonopoulos DA, Apprill A, Armitage D, Ballantine K, Barta J, Baum JK, Berry A, Bhatnagar A, Bhatnagar M, Biddle JF, Bittner L, Boldgiv B, Bottos E, Boyer DM, Braun J, Brazelton W, Brearley FQ, Campbell AH, Caporaso JG, Cardona C, Carroll J, Cary SC, Casper BB, Charles TC, Chu H, Claar DC, Clark RG, Clayton JB, Clemente JC, Cochran A, Coleman ML, Collins G, Colwell RR, Contreras M, Crary BB, Creer S, Cristol DA, Crump BC, Cui D, Daly SE, Davalos L, Dawson RD, Defazio J, Delsuc F, Dionisi HM, Dominguez-Bello MG, Dowell R, Dubinsky EA, Dunn PO, Ercolini D, Espinoza RE, Ezenwa V, Fenner N, Findlay HS, Fleming ID, Fogliano V, Forsman A, Freeman C, Friedman ES, Galindo G, Garcia L, Garcia-Amado MA, Garshelis D, Gasser RB, Gerdts G, Gibson MK, Gifford I, Gill RT, Giray T, Gittel A, Golyshin P, Gong D, Grossart HP, Guyton K, Haig SJ, Hale V, Hall RS, Hallam SJ, Handley KM, Hasan NA, Haydon SR, Hickman JE, Hidalgo G, Hofmockel KS, Hooker J, Hulth S, Hultman J, Hyde E, Ibanez-Alamo JD, Jastrow JD, Jex AR, Johnson LS, Johnston ER, Joseph S, Jurburg SD, Jurelevicius D, Karlsson A, Karlsson R, Kauppinen S, Kellogg CTE, Kennedy SJ, Kerkhof LJ, King GM, Kling GW, Koehler AV, Krezalek M, Kueneman J, Lamendella R, Landon EM, Lane-deGraaf K, LaRoche J, Larsen P, Laverock B, Lax S, Lentino M, Levin II, Liancourt P, Liang W, Linz AM, Lipson DA, Liu Y, Lladser ME, Lozada M, Spirito CM, MacCormack WP, MacRae-Crerar A, Magris M, Martin-Platero AM, Martin-Vivaldi M, Martinez LM, Martinez-Bueno M, Marzinelli EM, Mason OU, Mayer GD, McDevitt-Irwin JM, McDonald JE, McGuire KL, McMahon KD, McMinds R, Medina M, Mendelson JR, Metcalf JL, Meyer F, Michelangeli F, Miller K, Mills DA, Minich J, Mocali S, Moitinho-Silva L, Moore A, Morgan-Kiss RM, Munroe P, Myrold D, Neufeld JD, Ni Y, Nicol GW, Nielsen S, Nissimov JI, Niu K, Nolan MJ, Noyce K, O'Brien SL, Okamoto N, Orlando L, Castellano YO, Osuolale O, Oswald W, Parnell J, Peralta-Sanchez JM, Petraitis P, Pfister C, Pilon-Smits E, Piombino P, Pointing SB, Pollock FJ, Potter C, Prithiviraj B, Quince C, Rani A, Ranjan R, Rao S, Rees AP, Richardson M, Riebesell U, Robinson C, Rockne KJ, Rodriguezl SM, Rohwer F, Roundstone W, Safran RJ, Sangwan N, Sanz V, Schrenk M, Schrenzel MD, Scott NM, Seger RL, Seguin-Orlando A, Seldin L, Seyler LM, Shakhsheer B, Sheets GM, Shen C, Shi Y, Shin H, Shogan BD, Shutler D, Siegel J, Simmons S, Sjoling S, Smith DP, Soler JJ, Sperling M, Steinberg PD, Stephens B, Stevens MA, Taghavi S, Tai V, Tait K, Tan CL, Tas N, Taylor DL, Thomas T, Timling I, Turner BL, Urich T, Ursell LK, van der Lelie D, Van Treuren W, van Zwieten L, Vargas-Robles D, Thurber RV, Vitaglione P, Walker DA, Walters WA, Wang S, Wang T, Weaver T, Webster NS, Wehrle B, Weisenhorn P, Weiss S, Werner JJ, West K, Whitehead A, Whitehead SR, Whittingham LA, Willerslev E, Williams AE, Wood SA, Woodhams DC, Yang Y, Zaneveld J, Zarraonaindia I, Zhang Q, Zhao H., Nature 551(7681), 2017
PMID: 29088705
Population-level analysis of gut microbiome variation.
Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J., Science 352(6285), 2016
PMID: 27126039
A human gut microbial gene catalogue established by metagenomic sequencing.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J, Antolin M, Artiguenave F, Blottiere H, Borruel N, Bruls T, Casellas F, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Forte M, Friss C, van de Guchte M, Guedon E, Haimet F, Jamet A, Juste C, Kaci G, Kleerebezem M, Knol J, Kristensen M, Layec S, Le Roux K, Leclerc M, Maguin E, Minardi RM, Oozeer R, Rescigno M, Sanchez N, Tims S, Torrejon T, Varela E, de Vos W, Winogradsky Y, Zoetendal E., Nature 464(7285), 2010
PMID: 20203603
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA; LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J., Science 352(6285), 2016
PMID: 27126040
Structure, function and diversity of the healthy human microbiome.
Human Microbiome Project Consortium, Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, FitzGerald MG, Fulton RS, Giglio MG, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, Martin JC, Mitreva M, Muzny DM, Sodergren EJ, Versalovic J, Wollam AM, Worley KC, Wortman JR, Young SK, Zeng Q, Aagaard KM, Abolude OO, Allen-Vercoe E, Alm EJ, Alvarado L, Andersen GL, Anderson S, Appelbaum E, Arachchi HM, Armitage G, Arze CA, Ayvaz T, Baker CC, Begg L, Belachew T, Bhonagiri V, Bihan M, Blaser MJ, Bloom T, Bonazzi V, Brooks J, Buck GA, Buhay CJ, Busam DA, Campbell JL, Canon SR, Cantarel BL, Chain PS, Chen IM, Chen L, Chhibba S, Chu K, Ciulla DM, Clemente JC, Clifton SW, Conlan S, Crabtree J, Cutting MA, Davidovics NJ, Davis CC, DeSantis TZ, Deal C, Delehaunty KD, Dewhirst FE, Deych E, Ding Y, Dooling DJ, Dugan SP, Dunne WM, Durkin A, Edgar RC, Erlich RL, Farmer CN, Farrell RM, Faust K, Feldgarden M, Felix VM, Fisher S, Fodor AA, Forney LJ, Foster L, Di Francesco V, Friedman J, Friedrich DC, Fronick CC, Fulton LL, Gao H, Garcia N, Giannoukos G, Giblin C, Giovanni MY, Goldberg JM, Goll J, Gonzalez A, Griggs A, Gujja S, Haake SK, Haas BJ, Hamilton HA, Harris EL, Hepburn TA, Herter B, Hoffmann DE, Holder ME, Howarth C, Huang KH, Huse SM, Izard J, Jansson JK, Jiang H, Jordan C, Joshi V, Katancik JA, Keitel WA, Kelley ST, Kells C, King NB, Knights D, Kong HH, Koren O, Koren S, Kota KC, Kovar CL, Kyrpides NC, La Rosa PS, Lee SL, Lemon KP, Lennon N, Lewis CM, Lewis L, Ley RE, Li K, Liolios K, Liu B, Liu Y, Lo CC, Lozupone CA, Lunsford R, Madden T, Mahurkar AA, Mannon PJ, Mardis ER, Markowitz VM, Mavromatis K, McCorrison JM, McDonald D, McEwen J, McGuire AL, McInnes P, Mehta T, Mihindukulasuriya KA, Miller JR, Minx PJ, Newsham I, Nusbaum C, O'Laughlin M, Orvis J, Pagani I, Palaniappan K, Patel SM, Pearson M, Peterson J, Podar M, Pohl C, Pollard KS, Pop M, Priest ME, Proctor LM, Qin X, Raes J, Ravel J, Reid JG, Rho M, Rhodes R, Riehle KP, Rivera MC, Rodriguez-Mueller B, Rogers YH, Ross MC, Russ C, Sanka RK, Sankar P, Sathirapongsasuti J, Schloss JA, Schloss PD, Schmidt TM, Scholz M, Schriml L, Schubert AM, Segata N, Segre JA, Shannon WD, Sharp RR, Sharpton TJ, Shenoy N, Sheth NU, Simone GA, Singh I, Smillie CS, Sobel JD, Sommer DD, Spicer P, Sutton GG, Sykes SM, Tabbaa DG, Thiagarajan M, Tomlinson CM, Torralba M, Treangen TJ, Truty RM, Vishnivetskaya TA, Walker J, Wang L, Wang Z, Ward DV, Warren W, Watson MA, Wellington C, Wetterstrand KA, White JR, Wilczek-Boney K, Wu Y, Wylie KM, Wylie T, Yandava C, Ye L, Ye Y, Yooseph S, Youmans BP, Zhang L, Zhou Y, Zhu Y, Zoloth L, Zucker JD, Birren BW, Gibbs RA, Highlander SK, Methe BA, Nelson KE, Petrosino JF, Weinstock GM, Wilson RK, White O., Nature 486(7402), 2012
PMID: 22699609
Human gut microbiome viewed across age and geography.
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI., Nature 486(7402), 2012
PMID: 22699611
Temporal variability is a personalized feature of the human microbiome.
Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, Leff JW, Vazquez-Baeza Y, Gonzalez A, Knight R, Dunn RR, Fierer N., Genome Biol. 15(12), 2014
PMID: 25517225
Cohabiting family members share microbiota with one another and with their dogs.
Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R., Elife 2(), 2013
PMID: 23599893
Conservation evaluation and phylogenetic diversity
Faith DP., 1992
Balance Trees Reveal Microbial Niche Differentiation.
Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vazquez-Baeza Y, Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, Knight R., mSystems 2(1), 2017
PMID: 28144630
The microbiome of uncontacted Amerindians.
Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcon O, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG., Sci Adv 1(3), 2015
PMID: 26229982
Subsistence strategies in traditional societies distinguish gut microbiomes.
Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, Zech Xu Z, Van Treuren W, Knight R, Gaffney PM, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Warinner C, Ozga AT, Lewis CM., Nat Commun 6(), 2015
PMID: 25807110
UniFrac: a new phylogenetic method for comparing microbial communities.
Lozupone C, Knight R., Appl. Environ. Microbiol. 71(12), 2005
PMID: 16332807
UniFrac: an effective distance metric for microbial community comparison.
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R., ISME J 5(2), 2010
PMID: 20827291
Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping.
Amir A, McDonald D, Navas-Molina JA, Debelius J, Morton JT, Hyde E, Robbins-Pianka A, Knight R., mSystems 2(2), 2017
PMID: 28289733
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns.
Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, Kightley EP, Thompson LR, Hyde ER, Gonzalez A, Knight R., mSystems 2(2), 2017
PMID: 28289731
Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies.
Song SJ, Amir A, Metcalf JL, Amato KR, Xu ZZ, Humphrey G, Knight R., mSystems 1(3), 2016
PMID: 27822526
Worlds within worlds: evolution of the vertebrate gut microbiota.
Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI., Nat. Rev. Microbiol. 6(10), 2008
PMID: 18794915
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P., ISME J 6(3), 2011
PMID: 22134646
SEPP: SATé-enabled phylogenetic placement
Mirarab S, Nguyen N, Warnow T., 2012
Dynamics of the human gut microbiome in inflammatory bowel disease.
Halfvarson J, Brislawn CJ, Lamendella R, Vazquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK., Nat Microbiol 2(), 2017
PMID: 28191884
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania.
Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, Knight R, Manjurano A, Changalucha J, Elias JE, Dominguez-Bello MG, Sonnenburg JL., Science 357(6353), 2017
PMID: 28839072
Global marine bacterial diversity peaks at high latitudes in winter.
Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS., ISME J 7(9), 2013
PMID: 23514781
Extreme Dysbiosis of the Microbiome in Critical Illness.
McDonald D, Ackermann G, Khailova L, Baird C, Heyland D, Kozar R, Lemieux M, Derenski K, King J, Vis-Kampen C, Knight R, Wischmeyer PE., mSphere 1(4), 2016
PMID: 27602409
Diet rapidly and reproducibly alters the human gut microbiome.
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ., Nature 505(7484), 2013
PMID: 24336217
movie_s1.mp4
McDonald D, Robbins-Pianka A, Mann AE, Vrbanac A, Amir A, Frazier A, Gonzalez A, Tripathi A, Fahimipour AK, Brennen C, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Huttenhower C, Knights D, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Wolfe E, Lovelace E, Hyde ER, Pierce E, TerAvest E, Montassier E, Bolyen E, Bushman FD, Ackermann G, Wu GD, Church GM, Rahnavard G, Saxe G, Gogul G, Humphrey G, Holscher HD, Ugrina I, German JB, Caporaso JG, Gilbert J, Wozniak JM, Kerr J, Ravel J, Gaffney J, Lewis JD, Morton JT, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Leach J, Raes J, Green JL, Metcalf JL, Chase JH, Eisen JA, Monk J, Navas-Molina JA, Clemente JC., 2018
Oscillospira and related bacteria - From metagenomic species to metabolic features.
Gophna U, Konikoff T, Nielsen HB., Environ. Microbiol. 19(3), 2017
PMID: 28028921
The carbohydrate-active enzymes database (CAZy) in 2013.
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24270786
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota.
El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B., Nat. Rev. Microbiol. 11(7), 2013
PMID: 23748339
The control and consequences of bacterial fermentation in the human colon.
Cummings JH, Macfarlane GT., J. Appl. Bacteriol. 70(6), 1991
PMID: 1938669
Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range.
Henderson G, Cox F, Ganesh S, Jonker A, Young W; Global Rumen Census Collaborators, Janssen PH, Abecia L, Angarita E, Aravena P, Nora Arenas G, Ariza C, Attwood GT, Mauricio Avila J, Avila-Stagno J, Bannink A, Barahona R, Batistotti M, Bertelsen MF, Brown-Kav A, Carvajal AM, Cersosimo L, Vieira Chaves A, Church J, Clipson N, Cobos-Peralta MA, Cookson AL, Cravero S, Cristobal Carballo O, Crosley K, Cruz G, Ceron Cucchi M, de la Barra R, De Menezes AB, Detmann E, Dieho K, Dijkstra J, Dos Reis WL, Dugan ME, Hadi Ebrahimi S, Eythorsdottir E, Nde Fon F, Fraga M, Franco F, Friedeman C, Fukuma N, Gagic D, Gangnat I, Javier Grilli D, Guan le L, Heidarian Miri V, Hernandez-Sanabria E, Gomez AX, Isah OA, Ishaq S, Jami E, Jelincic J, Kantanen J, Kelly WJ, Kim SH, Klieve A, Kobayashi Y, Koike S, Kopecny J, Nygaard Kristensen T, Julie Krizsan S, LaChance H, Lachman M, Lamberson WR, Lambie S, Lassen J, Leahy SC, Lee SS, Leiber F, Lewis E, Lin B, Lira R, Lund P, Macipe E, Mamuad LL, Cuquetto Mantovani H, Marcoppido GA, Marquez C, Martin C, Martinez G, Eugenia Martinez M, Lucia Mayorga O, McAllister TA, McSweeney C, Mestre L, Minnee E, Mitsumori M, Mizrahi I, Molina I, Muenger A, Munoz C, Murovec B, Newbold J, Nsereko V, O'Donovan M, Okunade S, O'Neill B, Ospina S, Ouwerkerk D, Parra D, Pereira LG, Pinares-Patino C, Pope PB, Poulsen M, Rodehutscord M, Rodriguez T, Saito K, Sales F, Sauer C, Shingfield K, Shoji N, Simunek J, Stojanovic-Radic Z, Stres B, Sun X, Swartz J, Liang Tan Z, Tapio I, Taxis TM, Tomkins N, Ungerfeld E, Valizadeh R, van Adrichem P, Van Hamme J, Van Hoven W, Waghorn G, John Wallace R, Wang M, Waters SM, Keogh K, Witzig M, Wright AD, Yamano H, Yan T, Yanez-Ruiz DR, Yeoman CJ, Zambrano R, Zeitz J, Zhou M, Wei Zhou H, Xia Zou C, Zunino P., Sci Rep 5(), 2015
PMID: 26449758
Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals.
O' Donnell MM, Harris HMB, Ross RP, O'Toole PW., Microbiologyopen 6(5), 2017
PMID: 28834331
Physiological and microbial adjustments to diet quality permit facultative herbivory in an omnivorous lizard.
Kohl KD, Brun A, Magallanes M, Brinkerhoff J, Laspiur A, Acosta JC, Bordenstein SR, Caviedes-Vidal E., J. Exp. Biol. 219(Pt 12), 2016
PMID: 27307545
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.
Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crusemann M, Boudreau PD, Esquenazi E, Sandoval-Calderon M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodriguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Muller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutierrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N., Nat. Biotechnol. 34(8), 2016
PMID: 27504778
Mass spectral molecular networking of living microbial colonies.
Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC., Proc. Natl. Acad. Sci. U.S.A. 109(26), 2012
PMID: 22586093
Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI).
Sumner LW, Amberg A, Barrett D, Beale MH, Beger R, Daykin CA, Fan TW, Fiehn O, Goodacre R, Griffin JL, Hankemeier T, Hardy N, Harnly J, Higashi R, Kopka J, Lane AN, Lindon JC, Marriott P, Nicholls AW, Reily MD, Thaden JJ, Viant MR., Metabolomics 3(3), 2007
PMID: 24039616
Polyunsaturated fatty acid saturation by gut lactic acid bacteria affecting host lipid composition.
Kishino S, Takeuchi M, Park SB, Hirata A, Kitamura N, Kunisawa J, Kiyono H, Iwamoto R, Isobe Y, Arita M, Arai H, Ueda K, Shima J, Takahashi S, Yokozeki K, Shimizu S, Ogawa J., Proc. Natl. Acad. Sci. U.S.A. 110(44), 2013
PMID: 24127592
Conjugated linoleic acid biosynthesis by human-derived Bifidobacterium species.
Coakley M, Ross RP, Nordgren M, Fitzgerald G, Devery R, Stanton C., J. Appl. Microbiol. 94(1), 2003
PMID: 12492934
Commensal bacteria make GPCR ligands that mimic human signalling molecules.
Cohen LJ, Esterhazy D, Kim SH, Lemetre C, Aguilar RR, Gordon EA, Pickard AJ, Cross JR, Emiliano AB, Han SM, Chu J, Vila-Farres X, Kaplitt J, Rogoz A, Calle PY, Hunter C, Bitok JK, Brady SF., Nature 549(7670), 2017
PMID: 28854168
Trends in GPCR drug discovery: new agents, targets and indications.
Hauser AS, Attwood MM, Rask-Andersen M, Schioth HB, Gloriam DE., Nat Rev Drug Discov 16(12), 2017
PMID: 29075003
Minireview: Gut microbiota: the neglected endocrine organ.
Clarke G, Stilling RM, Kennedy PJ, Stanton C, Cryan JF, Dinan TG., Mol. Endocrinol. 28(8), 2014
PMID: 24892638
Challenges of self-reported medical conditions and electronic medical records among members of a large military cohort.
Smith B, Chu LK, Smith TC, Amoroso PJ, Boyko EJ, Hooper TI, Gackstetter GD, Ryan MA; Millennium Cohort Study Team, Gray GC, Riddle JR, Wells TS., BMC Med Res Methodol 8(), 2008
PMID: 18644098
Altered fecal microbiota composition in patients with major depressive disorder.
Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L, Ruan B., Brain Behav. Immun. 48(), 2015
PMID: 25882912
Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder.
Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y, Li Q., J Affect Disord 207(), 2016
PMID: 27741466
The WHO World Health Report 2001 on mental health.
Saraceno B., Epidemiol Psichiatr Soc 11(2), 2002
PMID: 12212469
Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host's metabolism.
Zheng P, Zeng B, Zhou C, Liu M, Fang Z, Xu X, Zeng L, Chen J, Fan S, Du X, Zhang X, Yang D, Yang Y, Meng H, Li W, Melgiri ND, Licinio J, Wei H, Xie P., Mol. Psychiatry 21(6), 2016
PMID: 27067014
Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.
Weingarden A, Gonzalez A, Vazquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ., Microbiome 3(), 2015
PMID: 25825673
Succession of microbial consortia in the developing infant gut microbiome.
Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE., Proc. Natl. Acad. Sci. U.S.A. 108 Suppl 1(), 2010
PMID: 20668239
movie_s2.mp4
McDonald D, Robbins-Pianka A, Mann AE, Vrbanac A, Amir A, Frazier A, Gonzalez A, Tripathi A, Fahimipour AK, Brennen C, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Huttenhower C, Knights D, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Wolfe E, Lovelace E, Hyde ER, Pierce E, TerAvest E, Montassier E, Bolyen E, Bushman FD, Ackermann G, Wu GD, Church GM, Rahnavard G, Saxe G, Gogul G, Humphrey G, Holscher HD, Ugrina I, German JB, Caporaso JG, Gilbert J, Wozniak JM, Kerr J, Ravel J, Gaffney J, Lewis JD, Morton JT, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Leach J, Raes J, Green JL, Metcalf JL, Chase JH, Eisen JA, Monk J, Navas-Molina JA, Clemente JC., 2018
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R., ISME J 6(8), 2012
PMID: 22402401
Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton
Apprill A, McNally S, Parsons R, Weber L., 2015
Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees.
Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T., Science 324(5934), 2009
PMID: 19541996
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664
QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R., Nat. Methods 7(5), 2010
PMID: 20383131
Normalization and microbial differential abundance strategies depend upon data characteristics.
Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vazquez-Baeza Y, Birmingham A, Hyde ER, Knight R., Microbiome 5(1), 2017
PMID: 28253908

Ryan CL, Bauman K., 2016

Howden LM, Meyer JA., 2011
Table 58
AUTHOR UNKNOWN, 2016
Prevalence of and trends in diabetes among adults in the United States, 1988-2012.
Gao HX, Regier EE, Close KL., J Diabetes 8(1), 2016
PMID: 27144261

AUTHOR UNKNOWN, 2015

AUTHOR UNKNOWN, 2018

Flores AR, Herman JL, Gates GJ, Brown TNT., 2016
A new method for non-parametric multivariate analysis of variance
Anderson MJ., 2001
PLS-regression: a basic tool of chemometrics
Wold S, Sjöström M, Eriksson L., 2001
EMPeror: a tool for visualizing high-throughput microbial community data.
Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R., Gigascience 2(1), 2013
PMID: 24280061
An ordination of the upland forest communities of southern Wisconsin
Bray JR, Curtis JT., 1957
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Benjamini Y, Hochberg Y., 1995
Notes on continuous stochastic phenomena.
MORAN PA., Biometrika 37(1-2), 1950
PMID: 15420245
Marked seasonal variation in the wild mouse gut microbiota.
Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ., ISME J 9(11), 2015
PMID: 26023870

Cramér H., 1946
A power primer.
Cohen J., Psychol Bull 112(1), 1992
PMID: 19565683
Molecular networking as a dereplication strategy.
Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, de Felicio R, Fenner A, Wong WR, Linington RG, Zhang L, Debonsi HM, Gerwick WH, Dorrestein PC., J. Nat. Prod. 76(9), 2013
PMID: 24025162
Bringing the Dynamic Microbiome to Life with Animations.
Vazquez-Baeza Y, Gonzalez A, Smarr L, McDonald D, Morton JT, Navas-Molina JA, Knight R., Cell Host Microbe 21(1), 2017
PMID: 28081445
Strains, functions and dynamics in the expanded Human Microbiome Project.
Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C., Nature 550(7674), 2017
PMID: 28953883
OpenMS: a flexible open-source software platform for mass spectrometry data analysis.
Rost HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmstrom L, Aebersold R, Reinert K, Kohlbacher O., Nat. Methods 13(9), 2016
PMID: 27575624
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T., Genome Res. 13(11), 2003
PMID: 14597658
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides.
Nguyen DD, Melnik AV, Koyama N, Lu X, Schorn M, Fang J, Aguinaldo K, Lincecum TL Jr, Ghequire MG, Carrion VJ, Cheng TL, Duggan BM, Malone JG, Mauchline TH, Sanchez LM, Kilpatrick AM, Raaijmakers JM, De Mot R, Moore BS, Medema MH, Dorrestein PC., Nat Microbiol 2(), 2016
PMID: 27798598
Searching molecular structure databases with tandem mass spectra using CSI:FingerID.
Duhrkop K, Shen H, Meusel M, Rousu J, Bocker S., Proc. Natl. Acad. Sci. U.S.A. 112(41), 2015
PMID: 26392543

AUTHOR UNKNOWN, 2016

AUTHOR UNKNOWN, 2016

AUTHOR UNKNOWN, 2017

AUTHOR UNKNOWN, 2017
Neue Begründung der Theorie quadratischer Formen von unendlichvielen Veränderlichen
Hellinger E., 1909
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data.
Pluskal T, Castillo S, Villar-Briones A, Oresic M., BMC Bioinformatics 11(), 2010
PMID: 20650010
Evaluation of normalization methods to pave the way towards large-scale LC-MS-based metabolomics profiling experiments.
Ejigu BA, Valkenborg D, Baggerman G, Vanaerschot M, Witters E, Dujardin JC, Burzykowski T, Berg M., OMICS 17(9), 2013
PMID: 23808607
Filtering for increased power for microarray data analysis.
Hackstadt AJ, Hess AM., BMC Bioinformatics 10(), 2009
PMID: 19133141
Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis.
Xia J, Wishart DS., Curr Protoc Bioinformatics 55(), 2016
PMID: 27603023
Random forests
Breiman L., 2001
Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities.
Lozupone CA, Hamady M, Kelley ST, Knight R., Appl. Environ. Microbiol. 73(5), 2007
PMID: 17220268
Colicin E2 production and release by Escherichia coli K12 and other Enterobacteriaceae.
Pugsley AP, Goldzahl N, Barker RM., J. Gen. Microbiol. 131(10), 1985
PMID: 3934329
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA., J. Comput. Biol. 19(5), 2012
PMID: 22506599
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood DE, Salzberg SL., Genome Biol. 15(3), 2014
PMID: 24580807
Escherichia coli induces DNA double-strand breaks in eukaryotic cells.
Nougayrede JP, Homburg S, Taieb F, Boury M, Brzuszkiewicz E, Gottschalk G, Buchrieser C, Hacker J, Dobrindt U, Oswald E., Science 313(5788), 2006
PMID: 16902142
Genetic structure and distribution of the colibactin genomic island among members of the family Enterobacteriaceae.
Putze J, Hennequin C, Nougayrede JP, Zhang W, Homburg S, Karch H, Bringer MA, Fayolle C, Carniel E, Rabsch W, Oelschlaeger TA, Oswald E, Forestier C, Hacker J, Dobrindt U., Infect. Immun. 77(11), 2009
PMID: 19720753
Escherichia coli producing colibactin triggers premature and transmissible senescence in mammalian cells.
Secher T, Samba-Louaka A, Oswald E, Nougayrede JP., PLoS ONE 8(10), 2013
PMID: 24116215
Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra.
Gurevich A, Mikheenko A, Shlemov A, Korobeynikov A, Mohimani H, Pevzner PA., Nat Microbiol 3(3), 2018
PMID: 29358742
HMMER web server: interactive sequence similarity searching.
Finn RD, Clements J, Eddy SR., Nucleic Acids Res. 39(Web Server issue), 2011
PMID: 21593126
Fitting linear mixed-effects models using lme4
Bates D, Mächler M, Bolker B, Walker S., 2015
Atropos: specific, sensitive, and speedy trimming of sequencing reads.
Didion JP, Martin M, Collins FS., PeerJ 5(), 2017
PMID: 28875074
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
Bracken: estimating species abundance in metagenomics data
Lu J, Breitwieser FP, Thielen P, Salzberg SL., 2017
metaSPAdes: a new versatile metagenomic assembler.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA., Genome Res. 27(5), 2017
PMID: 28298430
Prokka: rapid prokaryotic genome annotation.
Seemann T., Bioinformatics 30(14), 2014
PMID: 24642063
FragGeneScan: predicting genes in short and error-prone reads.
Rho M, Tang H, Ye Y., Nucleic Acids Res. 38(20), 2010
PMID: 20805240
Accelerated Profile HMM Searches.
Eddy SR., PLoS Comput. Biol. 7(10), 2011
PMID: 22039361
Functional Metagenomics to Study Antibiotic Resistance.
Boolchandani M, Patel S, Dantas G., Methods Mol. Biol. 1520(), 2017
PMID: 27873261
Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes.
Jiang L, Amir A, Morton JT, Heller R, Arias-Castro E, Knight R., mSystems 2(6), 2017
PMID: 29181446
American Gut Project fecal sOTU counts table
McDonald D, Robbins-Pianka A, Mann AE, Vrbanac A, Amir A, Frazier A, Gonzalez A, Tripathi A, Fahimipour AK, Brennen C, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Huttenhower C, Knights D, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Wolfe E, Lovelace E, Hyde ER, Pierce E, TerAvest E, Montassier E, Bolyen E, Bushman FD, Ackermann G, Wu GD, Church GM, Rahnavard G, Saxe G, Gogul G, Humphrey G, Holscher HD, Ugrina I, German JB, Gregory JG, Gilbert J, Wozniak JM, Kerr J, Ravel J, Gaffney J, Lewis JD, Morton JT, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Leach J, Raes J, Green JL, Metcalf JL, Chase JH, Eisen JA, Monk J, Navas-Molina JA., 2018
American Gut Project fecal sOTU relative abundance table
McDonald D, Robbins-Pianka A, Mann AE, Vrbanac A, Amir A, Frazier A, Gonzalez A, Tripathi A, Fahimipour AK, Brennen C, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Huttenhower C, Knights D, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Wolfe E, Lovelace E, Hyde ER, Pierce E, TerAvest E, Montassier E, Bolyen E, Bushman FD, Ackermann G, Wu GD, Church GM, Rahnavard G, Saxe G, Gogul G, Humphrey G, Holscher HD, Ugrina I, German JB, Caporaso JG, Gilbert J, Wozniak JM, Kerr J, Ravel J, Gaffney J, Lewis JD, Morton JT, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Leach J, Raes J, Green JL, Metcalf JL, Chase JH, Eisen JA, Monk J, Navas-Molina JA., 2018
ag_tree.tre
McDonald D, Robbins-Pianka A, Mann AE, Vrbanac A, Amir A, Frazier A, Gonzalez A, Tripathi A, Fahimipour AK, Brennen C, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Huttenhower C, Knights D, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Wolfe E, Lovelace E, Hyde ER, Pierce E, TerAvest E, Montassier E, Bolyen E, Bushman FD, Ackermann G, Wu GD, Church GM, Rahnavard G, Saxe G, Gogul G, Humphrey G, Holscher HD, Ugrina I, German JB, Caporaso JG, Gilbert J, Wozniak JM, Kerr J, Ravel J, Gaffney J, Lewis JD, Morton JT, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Leach J, Raes J, Green JL, Metcalf JL, Chase JH, Eisen JA, Monk J, Navas-Molina JA., 2018
Full American Gut Project mapping file
McDonald D, Robbins-Pianka A, Mann AE, Vrbanac A, Amir A, Frazier A, Gonzalez A, Tripathi A, Fahimipour AK, Brennen C, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Huttenhower C, Knights D, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Wolfe E, Lovelace E, Hyde ER, Pierce E, TerAvest E, Montassier E, Bolyen E, Bushman FD, Ackermann G, Wu GD, Church GM, Rahnavard G, Saxe G, Gogul G, Humphrey G, Holscher HD, Ugrina I, German JB, Caporaso JG, Gilbert J, Wozniak JM, Kerr J, Ravel J, Gaffney J, Lewis JD, Morton JT, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Leach J, Raes J, Green JL, Metcalf JL, Chase JH, Eisen JA, Monk J, Navas-Molina JA., 2018
American Gut collated alpha diversities
McDonald D, Robbins-Pianka A, Mann AE, Vrbanac A, Amir A, Frazier A, Gonzalez A, Tripathi A, Fahimipour AK, Brennen C, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Huttenhower C, Knights D, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Wolfe E, Lovelace E, Hyde ER, Pierce E, TerAvest E, Montassier E, Bolyen E, Bushman FD, Ackermann G, Wu GD, Church GM, Rahnavard G, Saxe G, Gogul G, Humphrey G, Holscher HD, Ugrina I, German JB, Caporaso JG, Gilbert J, Wozniak JM, Kerr J, Ravel J, Gaffney J, Lewis JD, Morton JT, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Leach J, Raes J, Green JL, Metcalf JL, Chase JH, Eisen JA, Monk J, Navas-Molina JA., 2018
Unweighted UniFrac distances
McDonald D, Robbins-Pianka A, Mann AE, Vrbanac A, Amir A, Frazier A, Gonzalez A, Tripathi A, Fahimipour AK, Brennen C, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Huttenhower C, Knights D, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Wolfe E, Lovelace E, Hyde ER, Pierce E, TerAvest E, Montassier E, Bolyen E, Bushman FD, Ackermann G, Wu GD, Church GM, Rahnavard G, Saxe G, Gogul G, Humphrey G, Holscher HD, Ugrina I, German JB, Caporaso JG, Gilbert J, Wozniak JM, Kerr J, Ravel J, Gaffney J, Lewis JD, Morton JT, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Leach J, Raes J, Green JL, Metcalf JL, Chase JH, Eisen JA, Monk J, Navas-Molina JA., 2018
Weighted normalized UniFrac distances
McDonald D, Robbins-Pianka A, Mann AE, Vrbanac A, Amir A, Frazier A, Gonzalez A, Tripathi A, Fahimipour AK, Brennen C, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Huttenhower C, Knights D, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Wolfe E, Lovelace E, Hyde ER, Pierce E, TerAvest E, Montassier E, Bolyen E, Bushman FD, Ackermann G, Wu GD, Church GM, Rahnavard G, Saxe G, Gogul G, Humphrey G, Holscher HD, Ugrina I, German JB, Caporaso JG, Gilbert J, Wozniak JM, Kerr J, Ravel J, Gaffney J, Lewis JD, Morton JT, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Leach J, Raes J, Green JL, Metcalf JL, Chase JH, Eisen JA, Monk J, Navas-Molina JA., 2018
Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist.
Cohen LJ, Kang HS, Chu J, Huang YH, Gordon EA, Reddy BV, Ternei MA, Craig JW, Brady SF., Proc. Natl. Acad. Sci. U.S.A. 112(35), 2015
PMID: 26283367
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 29795809
PubMed | Europe PMC

Suchen in

Google Scholar