Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome.
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome.
复制标题
DOI:
10.1186/s13059-015-0611-7
复制
发表时间:
2015-03-25
期刊:
影响因子:
12.3
通讯作者:
Pollard KS
中科院分区:
文献类型:
--
作者:
Nayfach S;Pollard KS
Average genome size is an important, yet often overlooked, property of microbial communities. We developed MicrobeCensus to rapidly and accurately estimate average genome size from shotgun metagenomic data and applied our tool to 1,352 human microbiome samples. We found that average genome size differs significantly within and between body sites and tracks with major functional and taxonomic differences. In the gut, average genome size is positively correlated with the abundance of Bacteroides and genes related to carbohydrate metabolism. Importantly, we found that average genome size variation can bias comparative analyses, and that normalization improves detection of differentially abundant genes. The online version of this article (doi:10.1186/s13059-015-0611-7) contains supplementary material, which is available to authorized users.
登录
查看更多内容
影响因子:
4.4
作者:
Frank, Jeremy A.;Sorensen, Soren J.
通讯作者:
Sorensen, Soren J.
DOI:
10.1111/j.2517-6161.1995.tb02031.x
发表时间:
1995-01-01
影响因子:
5.8
作者:
BENJAMINI, Y;HOCHBERG, Y
通讯作者:
HOCHBERG, Y
DOI:
10.1073/pnas.1116053109
发表时间:
2012-01-10
影响因子:
11.1
作者:
Greenblum, Sharon;Turnbaugh, Peter J.;Borenstein, Elhanan
通讯作者:
Borenstein, Elhanan
影响因子:
4.3
作者:
Angly FE;Willner D;Prieto-Davó A;Edwards RA;Schmieder R;Vega-Thurber R;Antonopoulos DA;Barott K;Cottrell MT;Desnues C;Dinsdale EA;Furlan M;Haynes M;Henn MR;Hu Y;Kirchman DL;McDole T;McPherson JD;Meyer F;Miller RM;Mundt E;Naviaux RK;Rodriguez-Mueller B;Stevens R;Wegley L;Zhang L;Zhu B;Rohwer F
通讯作者:
Rohwer F
影响因子:
64.8
作者:
Methe, Barbara A.;Nelson, Karen E.;Pop, Mihai;Creasy, Heather H.;Giglio, Michelle G.;Huttenhower, Curtis;Gevers, Dirk;Petrosino, Joseph F.;Abubucker, Sahar;Badger, Jonathan H.;Chinwalla, Asif T.;Earl, Ashlee M.;FitzGerald, Michael G.;Fulton, Robert S.;Hallsworth-Pepin, Kymberlie;Lobos, Elizabeth A.;Madupu, Ramana;Magrini, Vincent;Martin, John C.;Mitreva, Makedonka;Muzny, Donna M.;Sodergren, Erica J.;Versalovic, James;Wollam, Aye M.;Worley, Kim C.;Wortman, Jennifer R.;Young, Sarah K.;Zeng, Qiandong;Aagaard, Kjersti M.;Abolude, Olukemi O.;Allen-Vercoe, Emma;Alm, Eric J.;Alvarado, Lucia;Andersen, Gary L.;Anderson, Scott;Appelbaum, Elizabeth;Arachchi, Harindra M.;Armitage, Gary;Arze, Cesar A.;Ayvaz, Tulin;Baker, Carl C.;Begg, Lisa;Belachew, Tsegahiwot;Bhonagiri, Veena;Bihan, Monika;Blaser, Martin J.;Bloom, Toby;Bonazzi, Vivien R.;Brooks, Paul;Buck, GregoryA.;Buhay, Christian J.;Busam, Dana A.;Campbell, Joseph L.;Canon, Shane R.;Cantarel, Brandi L.;Chain, Patrick S.;Chen, I-Min A.;Chen, Lei;Chhibba, Shaila;Chu, Ken;Ciulla, Dawn M.;Clemente, Jose C.;Clifton, Sandra W.;Conlan, Sean;Crabtree, Jonathan;Cutting, Mary A.;Davidovics, Noam J.;Davis, Catherine C.;DeSantis, Todd Z.;Deal, Carolyn;Delehaunty, Kimberley D.;Dewhisrst, Floyd E.;Deych, Elena;Ding, Yan;Dooling, David J.;Dugan, Shannon P.;Dunne, W. Michael, Jr.;Durkin, A. Scott;Edgar, Robert C.;Erlich, Rachel L.;Farmer, Candace N.;Farrell, Ruth M.;Faust, Karoline;Feldgarden, Michael;Felix, Victor M.;Fisher, Sheila;Fodor, Anthony A.;Forney, Larry;Foster, Leslie;Di Francesco, Valentina;Friedman, Jonathan;Friedrich, Dennis C.;Fronick, Catrina C.;Fulton, Lucinda L.;Gao, Hongyu;Garcia, Nathalia;Giannoukos, Georgia;Giblin, Christina;Giovanni, Maria Y.;Goldberg, Jonathan M.;Goll, Johannes;Gonzalez, Antonio;Griggs, Allison;Gujja, Sharvari;Haas, Brian J.;Hamilton, Holli A.;Harris, Emily L.;Hepburn, Theresa A.;Herter, Brandi;Hoffmann, Diane E.;Holder, Michael E.;Howarth, Clinton;Huang, Katherine H.;Huse, Susan M.;Izard, Jacques;Jansson, Janet K.;Jiang, Huaiyang;Jordan, Catherine;Joshi, Vandita;Katancik, JamesA.;Keitel, WendyA.;Kelley, Scott T.;Kells, Cristyn;Kinder-Haake, Susan;King, Nicholas B.;Knight, Rob;Knights, Dan;Kong, Heidi H.;Koren, Omry;Koren, Sergey;Kota, Karthik C.;Kovar, Christie L.;Kyrpides, Nikos C.;La Rosa, Patricio S.;Lee, Sandra L.;Lemon, Katherine P.;Lennon, Niall;Lewis, Cecil M.;Lewis, Lora;Ley, Ruth E.;Li, Kelvin;Liolios, Konstantinos;Liu, Bo;Liu, Yue;Lo, Chien-Chi;Lozupone, Catherine A.;Lunsford, R. Dwayne;Madden, Tessa;Mahurkar, Anup A.;Mannon, Peter J.;Mardis, Elaine R.;Markowitz, Victor M.;Mavrommatis, Konstantinos;McCorrison, Jamison M.;McDonald, Daniel;McEwen, Jean;McGuire, Amy L.;McInnes, Pamela;Mehta, Teena;Mihindukulasuriya, Kathie A.;Miller, Jason R.;Minx, Patrick J.;Newsham, Irene;Nusbaum, Chad;O'Laughlin, Michelle;Orvis, Joshua;Pagani, Ioanna;Palaniappan, Krishna;Patel, Shital M.;Pearson, Matthew;Peterson, Jane;Podar, Mircea;Pohl, Craig;Pollard, Katherine S.;Priest, Margaret E.;Proctor, Lita M.;Qin, Xiang;Raes, Jeroen;Ravel, Jacques;Reid, Jeffrey G.;Rho, Mina;Rhodes, Rosamond;Riehle, Kevin P.;Rivera, Maria C.;Rodriguez-Mueller, Beltran;Rogers, Yu-Hui;Ross, Matthew C.;Russ, Carsten;Sanka, Ravi K.;Sankar, Pamela;Sathirapongsasuti, J. Fah;Schloss, Jeffery A.;Schloss, Patrick D.;Schmidt, Thomas M.;Scholz, Matthew;Schriml, Lynn;Schubert, Alyxandria M.;Segata, Nicola;Segre, Julia A.;Shannon, William D.;Sharp, Richard R.;Sharpton, Thomas J.;Shenoy, Narmada;Sheth, Nihar U.;Simone, Gina A.;Singh, Indresh;Smillie, Chris S.;Sobel, Jack D.;Sommer, Daniel D.;Spicer, Paul;Sutton, Granger G.;Sykes, Sean M.;Tabbaa, Diana G.;Thiagarajan, Mathangi;Tomlinson, Chad M.;Torralba, Manolito;Treangen, Todd J.;Truty, Rebecca M.;Vishnivetskaya, Tatiana A.;Walker, Jason;Wang, Lu;Wang, Zhengyuan;Ward, Doyle V.;Warren, Wesley;Watson, Mark A.;Wellington, Christopher;Wetterstrand, Kris A.;White, James R.;Wilczek-Boney, Katarzyna;Wu, Yuan Qing;Wylie, Kristine M.;Wylie, Todd;Yandava, Chandri;Ye, Liang;Ye, Yuzhen;Yooseph, Shibu;Youmans, Bonnie P.;Zhang, Lan;Zhou, Yanjiao;Zhu, Yiming;Zoloth, Laurie;Zucker, Jeremy D.;Birren, Bruce W.;Gibbs, Richard A.;Highlander, Sarah K.;Weinstock, George M.;Wilson, Richard K.;White, Owen
通讯作者:
White, Owen