Creating a 3D microbial and chemical snapshot of a human habitat

Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, et al. (2018)
Scientific Reports 8(1).

Zeitschriftenaufsatz | Veröffentlicht| Englisch
 
Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Autor*in
Kapono, Clifford A.; Morton, James T.; Bouslimani, Amina; Melnik, Alexey V.; Orlinsky, Kayla; Knaan, Tal Luzzatto; Garg, Neha; Vázquez-Baeza, Yoshiki; Protsyuk, Ivan; Janssen, StefanUniBi ; Zhu, Qiyun; Alexandrov, Theodore
Alle
Einrichtung
Erscheinungsjahr
2018
Zeitschriftentitel
Scientific Reports
Band
8
Ausgabe
1
ISSN
2045-2322
Page URI
https://pub.uni-bielefeld.de/record/2921273

Zitieren

Kapono CA, Morton JT, Bouslimani A, et al. Creating a 3D microbial and chemical snapshot of a human habitat. Scientific Reports. 2018;8(1).
Kapono, C. A., Morton, J. T., Bouslimani, A., Melnik, A. V., Orlinsky, K., Knaan, T. L., Garg, N., et al. (2018). Creating a 3D microbial and chemical snapshot of a human habitat. Scientific Reports, 8(1). doi:10.1038/s41598-018-21541-4
Kapono, C. A., Morton, J. T., Bouslimani, A., Melnik, A. V., Orlinsky, K., Knaan, T. L., Garg, N., Vázquez-Baeza, Y., Protsyuk, I., Janssen, S., et al. (2018). Creating a 3D microbial and chemical snapshot of a human habitat. Scientific Reports 8.
Kapono, C.A., et al., 2018. Creating a 3D microbial and chemical snapshot of a human habitat. Scientific Reports, 8(1).
C.A. Kapono, et al., “Creating a 3D microbial and chemical snapshot of a human habitat”, Scientific Reports, vol. 8, 2018.
Kapono, C.A., Morton, J.T., Bouslimani, A., Melnik, A.V., Orlinsky, K., Knaan, T.L., Garg, N., Vázquez-Baeza, Y., Protsyuk, I., Janssen, S., Zhu, Q., Alexandrov, T., Smarr, L., Knight, R., Dorrestein, P.C.: Creating a 3D microbial and chemical snapshot of a human habitat. Scientific Reports. 8, (2018).
Kapono, Clifford A., Morton, James T., Bouslimani, Amina, Melnik, Alexey V., Orlinsky, Kayla, Knaan, Tal Luzzatto, Garg, Neha, Vázquez-Baeza, Yoshiki, Protsyuk, Ivan, Janssen, Stefan, Zhu, Qiyun, Alexandrov, Theodore, Smarr, Larry, Knight, Rob, and Dorrestein, Pieter C. “Creating a 3D microbial and chemical snapshot of a human habitat”. Scientific Reports 8.1 (2018).

4 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Updates in Rhea: SPARQLing biochemical reaction data.
Lombardot T, Morgat A, Axelsen KB, Aimo L, Hyka-Nouspikel N, Niknejad A, Ignatchenko A, Xenarios I, Coudert E, Redaschi N, Bridge A., Nucleic Acids Res 47(d1), 2019
PMID: 30272209
Comparative genomics of Bacteria commonly identified in the built environment.
Merino N, Zhang S, Tomita M, Suzuki H., BMC Genomics 20(1), 2019
PMID: 30691394
The impact of skin care products on skin chemistry and microbiome dynamics.
Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim JN, Humphrey G, Schwartz T, Sanders K, Brennan C, Luzzatto-Knaan T, Ackermann G, McDonald D, Zengler K, Knight R, Dorrestein PC., BMC Biol 17(1), 2019
PMID: 31189482
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

44 References

Daten bereitgestellt von Europe PubMed Central.

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.
Petras D, Nothias LF, Quinn RA, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcon G, Chen L, Dang T, Floros DJ, Hook V, Garg N, Hoffner N, Jiang Y, Kapono CA, Koester I, Knight R, Leber CA, Ling TJ, Luzzatto-Knaan T, McCall LI, McGrath AP, Meehan MJ, Merritt JK, Mills RH, Morton J, Podvin S, Protsyuk I, Purdy T, Satterfield K, Searles S, Shah S, Shires S, Steffen D, White M, Todoric J, Tuttle R, Wojnicz A, Sapp V, Vargas F, Yang J, Zhang C, Dorrestein PC., Anal. Chem. 88(22), 2016
PMID: 27732780
Indoor ecosystems.
Humphries C., Science 335(6069), 2012
PMID: 22323793
Home life: factors structuring the bacterial diversity found within and between homes.
Dunn RR, Fierer N, Henley JB, Leff JW, Menninger HL., PLoS ONE 8(5), 2013
PMID: 23717552
Lifestyle chemistries from phones for individual profiling.
Bouslimani A, Melnik AV, Xu Z, Amir A, da Silva RR, Wang M, Bandeira N, Alexandrov T, Knight R, Dorrestein PC., Proc. Natl. Acad. Sci. U.S.A. 113(48), 2016
PMID: 27849584
Origin, Analytical Characterization, and Use of Human Odor in Forensics.
Cuzuel V, Cognon G, Rivals I, Sauleau C, Heulard F, Thiebaut D, Vial J., J. Forensic Sci. 62(2), 2017
PMID: 28120328
Microbiome Tools for Forensic Science.
Metcalf JL, Xu ZZ, Bouslimani A, Dorrestein P, Carter DO, Knight R., Trends Biotechnol. 35(9), 2017
PMID: 28366290
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
Partial least squares: a versatile tool for the analysis of high-dimensional genomic data.
Boulesteix AL, Strimmer K., Brief. Bioinformatics 8(1), 2006
PMID: 16772269
Bayesian community-wide culture-independent microbial source tracking.
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST., Nat. Methods 8(9), 2011
PMID: 21765408
3D molecular cartography using LC-MS facilitated by Optimus and 'ili software.
Protsyuk I, Melnik AV, Nothias LF, Rappez L, Phapale P, Aksenov AA, Bouslimani A, Ryazanov S, Dorrestein PC, Alexandrov T., Nat Protoc 13(1), 2017
PMID: 29266099
Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy.
Quinn RA, Nothias LF, Vining O, Meehan M, Esquenazi E, Dorrestein PC., Trends Pharmacol. Sci. 38(2), 2016
PMID: 27842887
Molecular cartography of the human skin surface in 3D.
Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, Gonzalez A, Berg-Lyon D, Ackermann G, Moeller Christensen GJ, Nakatsuji T, Zhang L, Borkowski AW, Meehan MJ, Dorrestein K, Gallo RL, Bandeira N, Knight R, Alexandrov T, Dorrestein PC., Proc. Natl. Acad. Sci. U.S.A. 112(17), 2015
PMID: 25825778

AUTHOR UNKNOWN, 0
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

JA, Stand Genomic Sci. 3(3), 2010
Acinetobacter infection--an emerging threat to human health.
Visca P, Seifert H, Towner KJ., IUBMB Life 63(12), 2011
PMID: 22006724
Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L.
Erlacher A, Cernava T, Cardinale M, Soh J, Sensen CW, Grube M, Berg G., Front Microbiol 6(), 2015
PMID: 25713563
OpenMS - an open-source software framework for mass spectrometry.
Sturm M, Bertsch A, Gropl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O., BMC Bioinformatics 9(), 2008
PMID: 18366760

AUTHOR UNKNOWN, 0

AA, Nat. Rev. Chem. 1(7), 2017

Z, IJMS. 40(10), 2005
Forensic applications of isotope ratio mass spectrometry--a review.
Benson S, Lennard C, Maynard P, Roux C., Forensic Sci. Int. 157(1), 2006
PMID: 15919168

MR, Crime Lab Digest. 20(4), 1993
Validation of mitochondrial DNA sequencing for forensic casework analysis.
Wilson MR, DiZinno JA, Polanskey D, Replogle J, Budowle B., Int. J. Legal Med. 108(2), 1995
PMID: 8547161
Using mug shots to find suspects.
Lindsay RC, Nosworthy GJ, Martin R, Martynuck C., J Appl Psychol 79(1), 1994
PMID: 8200869

MV, J Forensic Investigation. 2941(), 1997

AUTHOR UNKNOWN, 0

AK, IEEE Trans. 14(1), 2004

E, J. Appl. Psychol. 62(3), 1977
Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons.
Shepherd ML, Swecker WS Jr, Jensen RV, Ponder MA., FEMS Microbiol. Lett. 326(1), 2011
PMID: 22092776
Experimental and analytical tools for studying the human microbiome.
Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R., Nat. Rev. Genet. 13(1), 2011
PMID: 22179717
An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform.
Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J., Microbiome 2(1), 2014
PMID: 24558975

M, BMC Mol Biol. 17(1), 2017
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
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

S, Microbiome. 3(1), 2015
Identifying personal microbiomes using metagenomic codes.
Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C., Proc. Natl. Acad. Sci. U.S.A. 112(22), 2015
PMID: 25964341

A, mSystems. 2(2), 2017
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

AUTHOR UNKNOWN, 0

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 29487294
PubMed | Europe PMC

Suchen in

Google Scholar