-
1
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214. http:// dx.doi.org/10.1038/nature11234
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
2
-
-
84896092821
-
The treatment-naive microbiome in new-onset Crohn's disease
-
Gevers D, Kugathasan S, Denson L, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song S, Yassour M, Morgan X, Kostic A, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ. 2014. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 15:382-392. http://dx.doi.org/10.1016/j.chom.2014.02.005
-
(2014)
Cell Host Microbe
, vol.15
, pp. 382-392
-
-
Gevers, D.1
Kugathasan, S.2
Denson, L.3
Vázquez-Baeza, Y.4
Van Treuren, W.5
Ren, B.6
Schwager, E.7
Knights, D.8
Song, S.9
Yassour, M.10
Morgan, X.11
Kostic, A.12
Luo, C.13
González, A.14
McDonald, D.15
Haberman, Y.16
Walters, T.17
Baker, S.18
Rosh, J.19
Stephens, M.20
Heyman, M.21
Markowitz, J.22
Baldassano, R.23
Griffiths, A.24
Sylvester, F.25
Mack, D.26
Kim, S.27
Crandall, W.28
Hyams, J.29
Huttenhower, C.30
Knight, R.31
Xavier, R.J.32
more..
-
3
-
-
84931355745
-
Dynamic changes in short-and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection
-
Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ. 2015. Dynamic changes in short-and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. Microbiome 3:10. http:// dx.doi.org/10.1186/s40168-015-0070-0
-
(2015)
Microbiome
, vol.3
, pp. 10
-
-
Weingarden, A.1
González, A.2
Vázquez-Baeza, Y.3
Weiss, S.4
Humphry, G.5
Berg-Lyons, D.6
Knights, D.7
Unno, T.8
Bobr, A.9
Kang, J.10
Khoruts, A.11
Knight, R.12
Sadowsky, M.J.13
-
4
-
-
53049109276
-
Growth of intensive care unit resource use and its estimated cost in Medicare
-
Milbrandt EB, Kersten A, Rahim MT, Dremsizov TT, Clermont G, Cooper LM, Angus DC, Linde-Zwirble WT. 2008. Growth of intensive care unit resource use and its estimated cost in Medicare. Crit Care Med 36:2504-2510. http://dx.doi.org/10.1097/CCM.0b013e318183ef84
-
(2008)
Crit Care Med
, vol.36
, pp. 2504-2510
-
-
Milbrandt, E.B.1
Kersten, A.2
Rahim, M.T.3
Dremsizov, T.T.4
Clermont, G.5
Cooper, L.M.6
Angus, D.C.7
Linde-Zwirble, W.T.8
-
5
-
-
43349103474
-
The re-emerging role of the intestinal microflora in critical illness and inflammation: why the gut hypothesis of sepsis syndrome will not go away
-
Alverdy JC, Chang EB. 2008. The re-emerging role of the intestinal microflora in critical illness and inflammation: why the gut hypothesis of sepsis syndrome will not go away. J Leukoc Biol 83:461-466. http:// dx.doi.org/10.1189/jlb.0607372
-
(2008)
J Leukoc Biol
, vol.83
, pp. 461-466
-
-
Alverdy, J.C.1
Chang, E.B.2
-
6
-
-
84942801515
-
Microbiome as mediator: does systemic infection start in the gut?
-
Latorre M, Krishnareddy S, Freedberg D. 2015. Microbiome as mediator: does systemic infection start in the gut? World J Gastroenterol 21:10487-10492. http://dx.doi.org/10.3748/wjg.v21.i37.10487
-
(2015)
World J Gastroenterol
, vol.21
, pp. 10487-10492
-
-
Latorre, M.1
Krishnareddy, S.2
Freedberg, D.3
-
7
-
-
84961205577
-
The gut as the motor of multiple organ dysfunction in critical illness
-
Klingensmith NJ, Coopersmith CM. 2016. The gut as the motor of multiple organ dysfunction in critical illness. Crit Care Clin 32:203-212. http://dx.doi.org/10.1016/j.ccc.2015.11.004
-
(2016)
Crit Care Clin
, vol.32
, pp. 203-212
-
-
Klingensmith, N.J.1
Coopersmith, C.M.2
-
8
-
-
84908409938
-
Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness
-
Zaborin A, Smith D, Garfield K, Quensen J, Shakhsheer B, Kade M, Tirrell M, Tiedje J, Gilbert JA, Zaborina O, Alverdy JC. 2014. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. mBio 5:e01361-14. http://dx.doi.org/10.1128/mBio.01361-14
-
(2014)
mBio
, vol.5
-
-
Zaborin, A.1
Smith, D.2
Garfield, K.3
Quensen, J.4
Shakhsheer, B.5
Kade, M.6
Tirrell, M.7
Tiedje, J.8
Gilbert, J.A.9
Zaborina, O.10
Alverdy, J.C.11
-
9
-
-
84951944688
-
Metagenomic analysis reveals dynamic changes of whole gut microbiota in the acute phase of intensive care unit patients
-
Ojima M, Motooka D, Shimizu K, Gotoh K, Shintani A, Yoshiya K, Nakamura S, Ogura H, Iida T, Shimazu T. 2016. Metagenomic analysis reveals dynamic changes of whole gut microbiota in the acute phase of intensive care unit patients. Dig Dis Sci 61:1628-1634. http://dx.doi.org/ 10.1007/s10620-015-4011-3
-
(2016)
Dig Dis Sci
, vol.61
, pp. 1628-1634
-
-
Ojima, M.1
Motooka, D.2
Shimizu, K.3
Gotoh, K.4
Shintani, A.5
Yoshiya, K.6
Nakamura, S.7
Ogura, H.8
Iida, T.9
Shimazu, T.10
-
10
-
-
84959356884
-
The microbiome in critical illness: firm conclusions or bact to square one?
-
Lyons JD, Ford ML, Coopersmith CM. 2016. The microbiome in critical illness: firm conclusions or bact to square one? Dig Dis Sci 61: 1420-1421. http://dx.doi.org/10.1007/s10620-016-4092-7
-
(2016)
Dig Dis Sci
, vol.61
, pp. 1420-1421
-
-
Lyons, J.D.1
Ford, M.L.2
Coopersmith, C.M.3
-
11
-
-
80052301430
-
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. 2011. Bayesian community-wide culture-independent microbial source tracking. Nat Methods 8:761-763. http://dx.doi.org/10.1038/nmeth.1650
-
(2011)
Nat Methods
, vol.8
, pp. 761-763
-
-
Knights, D.1
Kuczynski, J.2
Charlson, E.S.3
Zaneveld, J.4
Mozer, M.C.5
Collman, R.G.6
Bushman, F.D.7
Knight, R.8
Kelley, S.T.9
-
12
-
-
84946878517
-
Analysis of composition of microbiomes: a novel method for studying microbial composition
-
Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. 2015. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis 26:27663. http://dx.doi.org/10.3402/mehd.v26.27663
-
(2015)
Microb Ecol Health Dis
, vol.26
-
-
Mandal, S.1
Van Treuren, W.2
White, R.A.3
Eggesbø, M.4
Knight, R.5
Peddada, S.D.6
-
13
-
-
84865733148
-
Inferring correlation networks from genomic survey data
-
Friedman J, Alm EJ. 2012. Inferring correlation networks from genomic survey data. PLoS Comput Biol 8:e1002687. http://dx.doi.org/10.1371/ journal.pcbi.1002687
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Friedman, J.1
Alm, E.J.2
-
14
-
-
85041514113
-
-
Qiita Development Team. 2015. Qiita: spot patterns. https:// pypi.python.org/pypi/qiita-spots
-
(2015)
Qiita: spot patterns
-
-
-
16
-
-
84862141704
-
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. 2012. Human gut microbiome viewed across age and geography. Nature 486:222-227. http://dx.doi.org/10.1038/nature11053
-
(2012)
Nature
, vol.486
, pp. 222-227
-
-
Yatsunenko, T.1
Rey, F.E.2
Manary, M.J.3
Trehan, I.4
Dominguez-Bello, M.G.5
Contreras, M.6
Magris, M.7
Hidalgo, G.8
Baldassano, R.N.9
Anokhin, A.P.10
Heath, A.C.11
Warner, B.12
Reeder, J.13
Kuczynski, J.14
Caporaso, J.G.15
Lozupone, C.A.16
Lauber, C.17
Clemente, J.C.18
Knights, D.19
Knight, R.20
Gordon, J.I.21
more..
-
17
-
-
84907190237
-
Longitudinal analysis of microbial interaction between humans and the indoor environment
-
Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vazquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA. 2014. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345:1048-1052. http://dx.doi.org/10.1126/science.1254529
-
(2014)
Science
, vol.345
, pp. 1048-1052
-
-
Lax, S.1
Smith, D.P.2
Hampton-Marcell, J.3
Owens, S.M.4
Handley, K.M.5
Scott, N.M.6
Gibbons, S.M.7
Larsen, P.8
Shogan, B.D.9
Weiss, S.10
Metcalf, J.L.11
Ursell, L.K.12
Vazquez-Baeza, Y.13
Van Treuren, W.14
Hasan, N.A.15
Gibson, M.K.16
Colwell, R.17
Dantas, G.18
Knight, R.19
Gilbert, J.A.20
more..
-
18
-
-
84955125742
-
Microbial community assembly and metabolic function during mammalian corpse decomposition
-
Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R. 2016. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science 351:158-162. http:// dx.doi.org/10.1126/science.aad2646
-
(2016)
Science
, vol.351
, pp. 158-162
-
-
Metcalf, J.L.1
Xu, Z.Z.2
Weiss, S.3
Lax, S.4
Van Treuren, W.5
Hyde, E.R.6
Song, S.J.7
Amir, A.8
Larsen, P.9
Sangwan, N.10
Haarmann, D.11
Humphrey, G.C.12
Ackermann, G.13
Thompson, L.R.14
Lauber, C.15
Bibat, A.16
Nicholas, C.17
Gebert, M.J.18
Petrosino, J.F.19
Reed, S.C.20
Gilbert, J.A.21
Lynne, A.M.22
Bucheli, S.R.23
Carter, D.O.24
Knight, R.25
more..
-
19
-
-
0026499429
-
Conservation evaluation and phylogenetic diversity
-
Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biol Conserv 61:1-10. http://dx.doi.org/10.1016/0006-3207(92)91201-3
-
(1992)
Biol Conserv
, vol.61
, pp. 1-10
-
-
Faith, D.P.1
-
20
-
-
29144464937
-
UniFrac: a new phylogenetic method for comparing microbial communities
-
Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235. http://dx.doi.org/10.1128/AEM.71.12.8228-8235.2005
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
21
-
-
55949124035
-
Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
-
Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, Grangette C, Vasquez N, Pochart P, Trugnan G, Thomas G, Blottiere HM, Dore J, Marteau P, Seksik P, Langella P. 2008. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 105:16731-16736. http://dx.doi.org/10.1073/pnas.0804812105
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 16731-16736
-
-
Sokol, H.1
Pigneur, B.2
Watterlot, L.3
Lakhdari, O.4
Bermudez-Humaran, L.G.5
Gratadoux, J.J.6
Blugeon, S.7
Bridonneau, C.8
Furet, J.P.9
Corthier, G.10
Grangette, C.11
Vasquez, N.12
Pochart, P.13
Trugnan, G.14
Thomas, G.15
Blottiere, H.M.16
Dore, J.17
Marteau, P.18
Seksik, P.19
Langella, P.20
more..
-
22
-
-
84959106176
-
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
-
Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R. 2016. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J 10:1669-1681. http://dx.doi.org/10.1038/ismej.2015.235
-
(2016)
ISME J
, vol.10
, pp. 1669-1681
-
-
Weiss, S.1
Van Treuren, W.2
Lozupone, C.3
Faust, K.4
Friedman, J.5
Deng, Y.6
Xia, L.C.7
Xu, Z.Z.8
Ursell, L.9
Alm, E.J.10
Birmingham, A.11
Cram, J.A.12
Fuhrman, J.A.13
Raes, J.14
Sun, F.15
Zhou, J.16
Knight, R.17
-
23
-
-
72249087115
-
International study of the prevalence and outcomes of infection in intensive care units
-
Vincent J, Marshall J, Anzueto A, Martin CD, Gomersall C. 2009. International study of the prevalence and outcomes of infection in intensive care units. JAMA 302:2323-2329. http://dx.doi.org/10.1001/ jama.2009.1754
-
(2009)
JAMA
, vol.302
, pp. 2323-2329
-
-
Vincent, J.1
Marshall, J.2
Anzueto, A.3
Martin, C.D.4
Gomersall, C.5
-
24
-
-
19744371404
-
Strain-specific effects of probiotics on gut barrier integrity following hemorrhagic shock
-
Luyer MD, Buurman WA, Hadfoune M, Speelmans G, Knol J, Jacobs JA, Dejong CHC, Vriesema AJM, Greve JWM. 2005. Strain-specific effects of probiotics on gut barrier integrity following hemorrhagic shock. Infect Immun 73:3686-3692. http://dx.doi.org/10.1128/ IAI.73.6.3686-3692.2005
-
(2005)
Infect Immun
, vol.73
, pp. 3686-3692
-
-
Luyer, M.D.1
Buurman, W.A.2
Hadfoune, M.3
Speelmans, G.4
Knol, J.5
Jacobs, J.A.6
Dejong, C.H.C.7
Vriesema, A.J.M.8
Greve, J.W.M.9
-
25
-
-
34247191280
-
Pretreatment with pro-and synbiotics reduces peritonitis-induced acute lung injury in rats
-
Tok D, Ilkgul O, Bengmark S, Aydede H, Erhan Y, Taneli F, Ulman C, Vatansever S, Kose C, Ok G. 2007. Pretreatment with pro-and synbiotics reduces peritonitis-induced acute lung injury in rats. J Trauma 62:880-885. http://dx.doi.org/10.1097/01.ta.0000236019.00650.00
-
(2007)
J Trauma
, vol.62
, pp. 880-885
-
-
Tok, D.1
Ilkgul, O.2
Bengmark, S.3
Aydede, H.4
Erhan, Y.5
Taneli, F.6
Ulman, C.7
Vatansever, S.8
Kose, C.9
Ok, G.10
-
26
-
-
34250622074
-
Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118
-
Corr SC, Li Y, Riedel CU, O'Toole PW, Hill C, Gahan CGM. 2007. Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118. Proc Natl Acad Sci U S A 104: 7617-7621. http://dx.doi.org/10.1073/pnas.0700440104
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 7617-7621
-
-
Corr, S.C.1
Li, Y.2
Riedel, C.U.3
O'Toole, P.W.4
Hill, C.5
Gahan, C.G.M.6
-
27
-
-
84897463412
-
Redefining the gut as the motor of critical illness
-
Mittal R, Coopersmith CM. 2014. Redefining the gut as the motor of critical illness. Trends Mol Med 20:214-223. http://dx.doi.org/10.1016/ j.molmed.2013.08.004
-
(2014)
Trends Mol Med
, vol.20
, pp. 214-223
-
-
Mittal, R.1
Coopersmith, C.M.2
-
28
-
-
84924264354
-
Successful treatment of severe sepsis and diarrhea after vagotomy utilizing fecal microbiota transplantation: a case report
-
Li Q, Wang C, Tang C, He Q, Zhao X, Li N, Li J. 2015. Successful treatment of severe sepsis and diarrhea after vagotomy utilizing fecal microbiota transplantation: a case report. Crit Care 19:37. http:// dx.doi.org/10.1186/s13054-015-0738-7
-
(2015)
Crit Care
, vol.19
, pp. 37
-
-
Li, Q.1
Wang, C.2
Tang, C.3
He, Q.4
Zhao, X.5
Li, N.6
Li, J.7
-
29
-
-
84906829581
-
The Earth Microbiome Project: successes and aspirations
-
Gilbert JA, Jansson JK, Knight R. 2014. The Earth Microbiome Project: successes and aspirations. BMC Biol 12:69. http://dx.doi.org/10.1186/ s12915-014-0069-1
-
(2014)
BMC Biol
, vol.12
, pp. 69
-
-
Gilbert, J.A.1
Jansson, J.K.2
Knight, R.3
-
30
-
-
84863981120
-
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. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621-1624. http://dx.doi.org/10.1038/ismej.2012.8
-
(2012)
ISME J
, vol.6
, pp. 1621-1624
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
Berg-Lyons, D.4
Huntley, J.5
Fierer, N.6
Owens, S.M.7
Betley, J.8
Fraser, L.9
Bauer, M.10
Gormley, N.11
Gilbert, J.A.12
Smith, G.13
Knight, R.14
-
31
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña 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. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335-336. http://dx.doi.org/10.1038/nmeth.f.303
-
(2010)
Nat Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
Fierer, N.7
Peña, A.G.8
Goodrich, J.K.9
Gordon, J.I.10
Huttley, G.A.11
Kelley, S.T.12
Knights, D.13
Koenig, J.E.14
Ley, R.E.15
Lozupone, C.A.16
McDonald, D.17
Muegge, B.D.18
Pirrung, M.19
Reeder, J.20
Sevinsky, J.R.21
Turnbaugh, P.J.22
Walters, W.A.23
Widmann, J.24
Yatsunenko, T.25
Zaneveld, J.26
Knight, R.27
more..
-
32
-
-
84857122937
-
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. 2012. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610-618. http:// dx.doi.org/10.1038/ismej.2011.139
-
(2012)
ISME J
, vol.6
, pp. 610-618
-
-
McDonald, D.1
Price, M.N.2
Goodrich, J.3
Nawrocki, E.P.4
DeSantis, T.Z.5
Probst, A.6
Andersen, G.L.7
Knight, R.8
Hugenholtz, P.9
|