-
1
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Meta HIT Consortium
-
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; Meta HIT Consortium, Bork P, Ehrlich SD, Wang J. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59-65. https://doi.org/10.1038/nature08821.
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
Manichanh, C.6
Nielsen, T.7
Pons, N.8
Levenez, F.9
Yamada, T.10
Mende, D.R.11
Li, J.12
Xu, J.13
Li, S.14
Li, D.15
Cao, J.16
Wang, B.17
Liang, H.18
Zheng, H.19
Xie, Y.20
Tap, J.21
Lepage, P.22
Bertalan, M.23
Batto, J.M.24
Hansen, T.25
Le Paslier, D.26
Linneberg, A.27
Nielsen, H.B.28
Pelletier, E.29
Renault, P.30
Sicheritz-Ponten, T.31
Turner, K.32
Zhu, H.33
Yu, C.34
Li, S.35
Jian, M.36
Zhou, Y.37
Li, Y.38
Zhang, X.39
Li, S.40
Qin, N.41
Yang, H.42
Wang, J.43
Brunak, S.44
Dore, J.45
Guarner, F.46
Kristiansen, K.47
Pedersen, O.48
Parkhill, J.49
Weissenbach, J.50
Bork, P.51
Ehrlich, S.D.52
Wang, J.53
more..
-
2
-
-
84858376593
-
The impact of the gut microbiota on human health: An integrative view
-
Clemente JC, Ursell LK, Parfrey LW, Knight R. 2012. The impact of the gut microbiota on human health: an integrative view. Cell 148:1258-1270. https://doi.org/10.1016/j.cell.2012.01.035.
-
(2012)
Cell
, vol.148
, pp. 1258-1270
-
-
Clemente, J.C.1
Ursell, L.K.2
Parfrey, L.W.3
Knight, R.4
-
3
-
-
84978062955
-
The microbiome in early life: Implications for health outcomes
-
Tamburini S, Shen N, Wu HC, Clemente JC. 2016. The microbiome in early life: implications for health outcomes. Nat Med 22:713-722. https://doi.org/10.1038/nm.4142.
-
(2016)
Nat Med
, vol.22
, pp. 713-722
-
-
Tamburini, S.1
Shen, N.2
Wu, H.C.3
Clemente, J.C.4
-
4
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium
-
Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214. https://doi.org/10.1038/nature11234.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
5
-
-
15544369658
-
Host-bacterial mutualism in the human intestine
-
Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. 2005. Host-bacterial mutualism in the human intestine. Science 307: 1915-1920. https://doi.org/10.1126/science.1104816.
-
(2005)
Science
, vol.307
, pp. 1915-1920
-
-
Bäckhed, F.1
Ley, R.E.2
Sonnenburg, J.L.3
Peterson, D.A.4
Gordon, J.I.5
-
6
-
-
84952324827
-
Immune-microbiota interactions in health and disease
-
Palm NW, de Zoete MR, Flavell RA. 2015. Immune-microbiota interactions in health and disease. Clin Immunol 159:122-127. https://doi.org/10.1016/j.clim.2015.05.014.
-
(2015)
Clin Immunol
, vol.159
, pp. 122-127
-
-
Palm, N.W.1
De Zoete, M.R.2
Flavell, R.A.3
-
7
-
-
79551687271
-
Mechanisms controlling pathogen colonization of the gut
-
Stecher B, Hardt WD. 2011. Mechanisms controlling pathogen colonization of the gut. Curr Opin Microbiol 14:82-91. https://doi.org/10.1016/j.mib.2010.10.003.
-
(2011)
Curr Opin Microbiol
, vol.14
, pp. 82-91
-
-
Stecher, B.1
Hardt, W.D.2
-
8
-
-
84905027614
-
Reset of a critically disturbed microbial ecosystem: Faecal transplant in recurrent Clostridium difficile infection
-
Fuentes S, van Nood E, Tims S, Heikamp-de Jong I, ter Braak CJ, Keller JJ, Zoetendal EG, de Vos WM. 2014. Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection. ISME J 8:1621-1633. https://doi.org/10.1038/ismej.2014.13.
-
(2014)
ISME J
, vol.8
, pp. 1621-1633
-
-
Fuentes, S.1
Van Nood, E.2
Tims, S.3
Heikamp-De Jong, I.4
Ter Braak, C.J.5
Keller, J.J.6
Zoetendal, E.G.7
De Vos, W.M.8
-
9
-
-
77951700268
-
Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea
-
Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ. 2010. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol 44:354-360. https://doi.org/10.1097/MCG.0b013e3181c87e02.
-
(2010)
J Clin Gastroenterol
, vol.44
, pp. 354-360
-
-
Khoruts, A.1
Dicksved, J.2
Jansson, J.K.3
Sadowsky, M.J.4
-
10
-
-
84898771460
-
Role of the intestinal microbiota in resistance to colonization by Clostridium difficile
-
Britton RA, Young VB. 2014. Role of the intestinal microbiota in resistance to colonization by Clostridium difficile. Gastroenterology 146: 1547-1553. https://doi.org/10.1053/j.gastro.2014.01.059.
-
(2014)
Gastroenterology
, vol.146
, pp. 1547-1553
-
-
Britton, R.A.1
Young, V.B.2
-
11
-
-
84929297936
-
Dynamics and stabilization of the human gut microbiome during the first year of life
-
Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, Li Y, Xia Y, Xie H, Zhong H, Khan MT, Zhang J, Li J, Xiao L, Al-Aama J, Zhang D, Lee YS, Kotowska D, Colding C, Tremaroli V, Yin Y, Bergman S, Xu X, Madsen L, Kristiansen K, Dahlgren J, Wang J, Jun W. 2015. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17:690-703. https://doi.org/10.1016/j.chom.2015.04.004.
-
(2015)
Cell Host Microbe
, vol.17
, pp. 690-703
-
-
Bäckhed, F.1
Roswall, J.2
Peng, Y.3
Feng, Q.4
Jia, H.5
Kovatcheva-Datchary, P.6
Li, Y.7
Xia, Y.8
Xie, H.9
Zhong, H.10
Khan, M.T.11
Zhang, J.12
Li, J.13
Xiao, L.14
Al-Aama, J.15
Zhang, D.16
Lee, Y.S.17
Kotowska, D.18
Colding, C.19
Tremaroli, V.20
Yin, Y.21
Bergman, S.22
Xu, X.23
Madsen, L.24
Kristiansen, K.25
Dahlgren, J.26
Wang, J.27
Jun, W.28
more..
-
12
-
-
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. https://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..
-
13
-
-
34547129847
-
Development of the human infant intestinal microbiota
-
Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. 2007. Development of the human infant intestinal microbiota. PLoS Biol 5:e177. https://doi.org/10.1371/journal.pbio.0050177.
-
(2007)
PLoS Biol
, vol.5
, pp. e177
-
-
Palmer, C.1
Bik, E.M.2
DiGiulio, D.B.3
Relman, D.A.4
Brown, P.O.5
-
14
-
-
77955386857
-
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
-
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. 2010. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 107:11971-11975. https://doi.org/10.1073/pnas.1002601107.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 11971-11975
-
-
Dominguez-Bello, M.G.1
Costello, E.K.2
Contreras, M.3
Magris, M.4
Hidalgo, G.5
Fierer, N.6
Knight, R.7
-
15
-
-
84875150368
-
Gut microbiota of healthy Canadian infants: Profiles by mode of delivery and infant diet at 4 months
-
Azad MB, Konya T, Maughan H, Guttman DS, Field CJ, Chari RS, Sears MR, Becker AB, Scott JA, Kozyrskyj AL, CHILD Study Investigators. 2013. Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ 185:385-394. https://doi.org/10.1503/cmaj.121189.
-
(2013)
CMAJ
, vol.185
, pp. 385-394
-
-
Azad, M.B.1
Konya, T.2
Maughan, H.3
Guttman, D.S.4
Field, C.J.5
Chari, R.S.6
Sears, M.R.7
Becker, A.B.8
Scott, J.A.9
Kozyrskyj, A.L.10
-
16
-
-
84943327494
-
Exploring vertical transmission of bifidobacteria from mother to child
-
Milani C, Mancabelli L, Lugli GA, Duranti S, Turroni F, Ferrario C, Mangifesta M, Viappiani A, Ferretti P, Gorfer V, Tett A, Segata N, van Sinderen D, Ventura M. 2015. Exploring vertical transmission of bifidobacteria from mother to child. Appl Environ Microbiol 81:7078-7087. https://doi.org/10.1128/AEM.02037-15.
-
(2015)
Appl Environ Microbiol
, vol.81
, pp. 7078-7087
-
-
Milani, C.1
Mancabelli, L.2
Lugli, G.A.3
Duranti, S.4
Turroni, F.5
Ferrario, C.6
Mangifesta, M.7
Viappiani, A.8
Ferretti, P.9
Gorfer, V.10
Tett, A.11
Segata, N.12
Van Sinderen, D.13
Ventura, M.14
-
17
-
-
84906679880
-
Patterned progression of bacterial populations in the premature infant gut
-
La Rosa PS, Warner BB, Zhou Y, Weinstock GM, Sodergren E, Hall-Moore CM, Stevens HJ, Bennett WE, Jr., Shaikh N, Linneman LA, Hoffmann JA, Hamvas A, Deych E, Shands BA, Shannon WD, Tarr PI. 2014. Patterned progression of bacterial populations in the premature infant gut. Proc Natl Acad Sci U S A 111:12522-12527. https://doi.org/10.1073/pnas.1409497111.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 12522-12527
-
-
La Rosa, P.S.1
Warner, B.B.2
Zhou, Y.3
Weinstock, G.M.4
Sodergren, E.5
Hall-Moore, C.M.6
Stevens, H.J.7
Bennett, W.E.8
Shaikh, N.9
Linneman, L.A.10
Hoffmann, J.A.11
Hamvas, A.12
Deych, E.13
Shands, B.A.14
Shannon, W.D.15
Tarr, P.I.16
-
18
-
-
84903383222
-
Early empiric antibiotic use in preterm infants is associated with lower bacterial diversity and higher relative abundance of Enterobacter
-
Greenwood C, Morrow AL, Lagomarcino AJ, Altaye M, Taft DH, Yu Z, Newburg DS, Ward DV, Schibler KR. 2014. Early empiric antibiotic use in preterm infants is associated with lower bacterial diversity and higher relative abundance of Enterobacter. J Pediatr 165:23-29. https://doi.org/10.1016/j.jpeds.2014.01.010.
-
(2014)
J Pediatr
, vol.165
, pp. 23-29
-
-
Greenwood, C.1
Morrow, A.L.2
Lagomarcino, A.J.3
Altaye, M.4
Taft, D.H.5
Yu, Z.6
Newburg, D.S.7
Ward, D.V.8
Schibler, K.R.9
-
19
-
-
84862209519
-
A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy
-
Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J. 2012. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One 7:e36466. https://doi.org/10.1371/journal.pone.0036466.
-
(2012)
PLoS One
, vol.7
, pp. e36466
-
-
Aagaard, K.1
Riehle, K.2
Ma, J.3
Segata, N.4
Mistretta, T.A.5
Coarfa, C.6
Raza, S.7
Rosenbaum, S.8
Van Den Veyver, I.9
Milosavljevic, A.10
Gevers, D.11
Huttenhower, C.12
Petrosino, J.13
Versalovic, J.14
-
20
-
-
79959247053
-
Characterization of the diversity and temporal stability of bacterial communities in human milk
-
Hunt KM, Foster JA, Forney LJ, Schütte UM, Beck DL, Abdo Z, Fox LK, Williams JE, McGuire MK, McGuire MA. 2011. Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS One 6:e21313. https://doi.org/10.1371/journal.pone.0021313.
-
(2011)
PLoS One
, vol.6
, pp. e21313
-
-
Hunt, K.M.1
Foster, J.A.2
Forney, L.J.3
Schütte, U.M.4
Beck, D.L.5
Abdo, Z.6
Fox, L.K.7
Williams, J.E.8
McGuire, M.K.9
McGuire, M.A.10
-
21
-
-
84865336911
-
The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery
-
Cabrera-Rubio R, Collado MC, Laitinen K, Salminen S, Isolauri E, Mira A. 2012. The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. Am J Clin Nutr 96:544-551. https://doi.org/10.3945/ajcn.112.037382.
-
(2012)
Am J Clin Nutr
, vol.96
, pp. 544-551
-
-
Cabrera-Rubio, R.1
Collado, M.C.2
Laitinen, K.3
Salminen, S.4
Isolauri, E.5
Mira, A.6
-
22
-
-
84965187800
-
Temporal variability is a personalized feature of the human microbiome
-
Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, Leff JW, Vázquez-Baeza Y, Gonzalez A, Knight R, Dunn RR, Fierer N. 2014. Temporal variability is a personalized feature of the human microbiome. Genome Biol 15:531. https://doi.org/10.1186/s13059-014-0531-y.
-
(2014)
Genome Biol
, vol.15
, pp. 531
-
-
Flores, G.E.1
Caporaso, J.G.2
Henley, J.B.3
Rideout, J.R.4
Domogala, D.5
Chase, J.6
Leff, J.W.7
Vázquez-Baeza, Y.8
Gonzalez, A.9
Knight, R.10
Dunn, R.R.11
Fierer, N.12
-
23
-
-
84881484788
-
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. 2013. Cohabiting family members share microbiota with one another and with their dogs. Elife 2:e00458. https://doi.org/10.7554/eLife.00458.
-
(2013)
Elife
, vol.2
, pp. e00458
-
-
Song, S.J.1
Lauber, C.2
Costello, E.K.3
Lozupone, C.A.4
Humphrey, G.5
Berg-Lyons, D.6
Caporaso, J.G.7
Knights, D.8
Clemente, J.C.9
Nakielny, S.10
Gordon, J.I.11
Fierer, N.12
Knight, R.13
-
24
-
-
84996559882
-
The first microbial environment of infants born by C-section: The operating room microbes
-
Shin H, Pei Z, Martinez KA, II, Rivera-Vinas JI, Mendez K, Cavallin H, Dominguez-Bello MG. 2015. The first microbial environment of infants born by C-section: the operating room microbes. Microbiome 3:59. https://doi.org/10.1186/s40168-015-0126-1.
-
(2015)
Microbiome
, vol.3
, pp. 59
-
-
Shin, H.1
Pei, Z.2
Martinez, K.A.3
Rivera-Vinas, J.I.4
Mendez, K.5
Cavallin, H.6
Dominguez-Bello, M.G.7
-
25
-
-
84906944200
-
Vertical motherneonate transfer of maternal gut bacteria via breastfeeding
-
Jost T, Lacroix C, Braegger CP, Rochat F, Chassard C. 2014. Vertical motherneonate transfer of maternal gut bacteria via breastfeeding. Environ Microbiol 16:2891-2904. https://doi.org/10.1111/1462-2920.12238.
-
(2014)
Environ Microbiol
, vol.16
, pp. 2891-2904
-
-
Jost, T.1
Lacroix, C.2
Braegger, C.P.3
Rochat, F.4
Chassard, C.5
-
26
-
-
78650847143
-
Mode of delivery affects the bacterial community in the newborn gut
-
Biasucci G, Rubini M, Riboni S, Morelli L, Bessi E, Retetangos C. 2010. Mode of delivery affects the bacterial community in the newborn gut. Early Hum Dev 86(Suppl 1):13-15. https://doi.org/10.1016/j.earlhumdev.2010.01.004.
-
(2010)
Early Hum Dev
, vol.86
, pp. 13-15
-
-
Biasucci, G.1
Rubini, M.2
Riboni, S.3
Morelli, L.4
Bessi, E.5
Retetangos, C.6
-
27
-
-
84978619185
-
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer
-
Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC. 2016. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med 22: 250-253. https://doi.org/10.1038/nm.4039.
-
(2016)
Nat Med
, vol.22
, pp. 250-253
-
-
Dominguez-Bello, M.G.1
De Jesus-Laboy, K.M.2
Shen, N.3
Cox, L.M.4
Amir, A.5
Gonzalez, A.6
Bokulich, N.A.7
Song, S.J.8
Hoashi, M.9
Rivera-Vinas, J.I.10
Mendez, K.11
Knight, R.12
Clemente, J.C.13
-
28
-
-
82955178526
-
Transmission of intestinal Bifidobacterium longum subsp. Longum strains from mother to infant, determined by multilocus sequencing typing and amplified fragment length polymorphism
-
Makino H, Kushiro A, Ishikawa E, Muylaert D, Kubota H, Sakai T, Oishi K, Martin R, Ben Amor K, Oozeer R, Knol J, Tanaka R. 2011. Transmission of intestinal Bifidobacterium longum subsp. longum strains from mother to infant, determined by multilocus sequencing typing and amplified fragment length polymorphism. Appl Environ Microbiol 77:6788-6793. https://doi.org/10.1128/AEM.05346-11.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 6788-6793
-
-
Makino, H.1
Kushiro, A.2
Ishikawa, E.3
Muylaert, D.4
Kubota, H.5
Sakai, T.6
Oishi, K.7
Martin, R.8
Ben Amor, K.9
Oozeer, R.10
Knol, J.11
Tanaka, R.12
-
29
-
-
84866146940
-
Diversity, stability and resilience of the human gut microbiota
-
Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489:220-230. https://doi.org/10.1038/nature11550.
-
(2012)
Nature
, vol.489
, pp. 220-230
-
-
Lozupone, C.A.1
Stombaugh, J.I.2
Gordon, J.I.3
Jansson, J.K.4
Knight, R.5
-
30
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. 2009. A core gut microbiome in obese and lean twins. Nature 457:480-484. https://doi.org/10.1038/nature07540.
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
Hamady, M.2
Yatsunenko, T.3
Cantarel, B.L.4
Duncan, A.5
Ley, R.E.6
Sogin, M.L.7
Jones, W.J.8
Roe, B.A.9
Affourtit, J.P.10
Egholm, M.11
Henrissat, B.12
Heath, A.C.13
Knight, R.14
Gordon, J.I.15
-
31
-
-
84961392884
-
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
-
Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, Truong DT, Tett A, Morrow AL, Segata N. 2016. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat Methods 13: 435-438. https://doi.org/10.1038/nmeth.3802.
-
(2016)
Nat Methods
, vol.13
, pp. 435-438
-
-
Scholz, M.1
Ward, D.V.2
Pasolli, E.3
Tolio, T.4
Zolfo, M.5
Asnicar, F.6
Truong, D.T.7
Tett, A.8
Morrow, A.L.9
Segata, N.10
-
32
-
-
84871732071
-
Genomic variation landscape of the human gut microbiome
-
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P. 2013. Genomic variation landscape of the human gut microbiome. Nature 493:45-50. https://doi.org/10.1038/nature11711.
-
(2013)
Nature
, vol.493
, pp. 45-50
-
-
Schloissnig, S.1
Arumugam, M.2
Sunagawa, S.3
Mitreva, M.4
Tap, J.5
Zhu, A.6
Waller, A.7
Mende, D.R.8
Kultima, J.R.9
Martin, J.10
Kota, K.11
Sunyaev, S.R.12
Weinstock, G.M.13
Bork, P.14
-
33
-
-
77952158672
-
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
-
Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI. 2010. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A 107:7503-7508. https://doi.org/10.1073/pnas.1002355107.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 7503-7508
-
-
Turnbaugh, P.J.1
Quince, C.2
Faith, J.J.3
McHardy, A.C.4
Yatsunenko, T.5
Niazi, F.6
Affourtit, J.7
Egholm, M.8
Henrissat, B.9
Knight, R.10
Gordon, J.I.11
-
34
-
-
84872535919
-
Xenobiotics shape the physiology and gene expression of the active human gut microbiome
-
Maurice CF, Haiser HJ, Turnbaugh PJ. 2013. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152:39-50. https://doi.org/10.1016/j.cell.2012.10.052.
-
(2013)
Cell
, vol.152
, pp. 39-50
-
-
Maurice, C.F.1
Haiser, H.J.2
Turnbaugh, P.J.3
-
35
-
-
84861708688
-
Metagenomics of human microbiome: Beyond 16S rDNA
-
Gosalbes MJ, Abellan JJ, Durbán A, Pérez-Cobas AE, Latorre A, Moya A. 2012. Metagenomics of human microbiome: beyond 16S rDNA. Clin Microbiol Infect 18(Suppl 4):47-49. https://doi.org/10.1111/j.1469-0691.2012.03865.x.
-
(2012)
Clin Microbiol Infect
, vol.18
, pp. 47-49
-
-
Gosalbes, M.J.1
Abellan, J.J.2
Durbán, A.3
Pérez-Cobas, A.E.4
Latorre, A.5
Moya, A.6
-
36
-
-
84946746270
-
Strand-specific community RNAseq reveals prevalent and dynamic antisense transcription in human gut microbiota
-
Bao G, Wang M, Doak TG, Ye Y. 2015. Strand-specific community RNAseq reveals prevalent and dynamic antisense transcription in human gut microbiota. Front Microbiol 6:896. https://doi.org/10.3389/fmicb.2015.00896.
-
(2015)
Front Microbiol
, vol.6
, pp. 896
-
-
Bao, G.1
Wang, M.2
Doak, T.G.3
Ye, Y.4
-
37
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M. 2007. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14:169-181. https://doi.org/10.1093/dnares/dsm018.
-
(2007)
DNA Res
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
Itoh, T.2
Kuwahara, T.3
Oshima, K.4
Toh, H.5
Toyoda, A.6
Takami, H.7
Morita, H.8
Sharma, V.K.9
Srivastava, T.P.10
Taylor, T.D.11
Noguchi, H.12
Mori, H.13
Ogura, Y.14
Ehrlich, D.S.15
Itoh, K.16
Takagi, T.17
Sakaki, Y.18
Hayashi, T.19
Hattori, M.20
more..
-
38
-
-
79952763661
-
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. 2011. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A 108(Suppl 1):4578-4585. https://doi.org/10.1073/pnas.1000081107.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 4578-4585
-
-
Koenig, J.E.1
Spor, A.2
Scalfone, N.3
Fricker, A.D.4
Stombaugh, J.5
Knight, R.6
Angenent, L.T.7
Ley, R.E.8
-
39
-
-
0030070873
-
Polymerase chain reaction (PCR) detection of Listeria monocytogenes in diluted milk and reversal of PCR inhibition caused by calcium ions
-
Bickley J, Short JK, McDowell DG, Parkes HC. 1996. Polymerase chain reaction (PCR) detection of Listeria monocytogenes in diluted milk and reversal of PCR inhibition caused by calcium ions. Lett Appl Microbiol 22:153-158. https://doi.org/10.1111/j.1472-765X.1996.tb01131.x.
-
(1996)
Lett Appl Microbiol
, vol.22
, pp. 153-158
-
-
Bickley, J.1
Short, J.K.2
McDowell, D.G.3
Parkes, H.C.4
-
40
-
-
30844434554
-
Technical note: Improved method for rapid DNA extraction of mastitis pathogens directly from milk
-
Cremonesi P, Castiglioni B, Malferrari G, Biunno I, Vimercati C, Moroni P, Morandi S, Luzzana M. 2006. Technical note: improved method for rapid DNA extraction of mastitis pathogens directly from milk. J Dairy Sci 89:163-169. https://doi.org/10.3168/jds.S0022-0302(06)72080-X.
-
(2006)
J Dairy Sci
, vol.89
, pp. 163-169
-
-
Cremonesi, P.1
Castiglioni, B.2
Malferrari, G.3
Biunno, I.4
Vimercati, C.5
Moroni, P.6
Morandi, S.7
Luzzana, M.8
-
41
-
-
84867711039
-
PCR inhibitors - Occurrence, properties and removal
-
Schrader C, Schielke A, Ellerbroek L, Johne R. 2012. PCR inhibitors - occurrence, properties and removal. J Appl Microbiol 113:1014-1026. https://doi.org/10.1111/j.1365-2672.2012.05384.x.
-
(2012)
J Appl Microbiol
, vol.113
, pp. 1014-1026
-
-
Schrader, C.1
Schielke, A.2
Ellerbroek, L.3
Johne, R.4
-
42
-
-
84878007093
-
Human milk metagenome: A functional capacity analysis
-
Ward TL, Hosid S, Ioshikhes I, Altosaar I. 2013. Human milk metagenome: a functional capacity analysis. BMC Microbiol 13:116. https://doi.org/10.1186/1471-2180-13-116.
-
(2013)
BMC Microbiol
, vol.13
, pp. 116
-
-
Ward, T.L.1
Hosid, S.2
Ioshikhes, I.3
Altosaar, I.4
-
43
-
-
0842303407
-
Ultrasound imaging of milk ejection in the breast of lactating women
-
Ramsay DT, Kent JC, Owens RA, Hartmann PE. 2004. Ultrasound imaging of milk ejection in the breast of lactating women. Pediatrics 113: 361-367. https://doi.org/10.1542/peds.113.2.361.
-
(2004)
Pediatrics
, vol.113
, pp. 361-367
-
-
Ramsay, D.T.1
Kent, J.C.2
Owens, R.A.3
Hartmann, P.E.4
-
44
-
-
84875254461
-
Human milk: A source of more life than we imagine
-
Jeurink PV, van Bergenhenegouwen J, Jiménez E, Knippels LM, Fernández L, Garssen J, Knol J, Rodríguez JM, Martín R. 2013. Human milk: a source of more life than we imagine. Benef Microbes 4:17-30. https://doi.org/10.3920/BM2012.0040.
-
(2013)
Benef Microbes
, vol.4
, pp. 17-30
-
-
Jeurink, P.V.1
Van Bergenhenegouwen, J.2
Jiménez, E.3
Knippels, L.M.4
Fernández, L.5
Garssen, J.6
Knol, J.7
Rodríguez, J.M.8
Martín, R.9
-
45
-
-
84861992014
-
The application of ecological theory toward an understanding of the human microbiome
-
Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, Relman DA. 2012. The application of ecological theory toward an understanding of the human microbiome. Science 336:1255-1262. https://doi.org/10.1126/science.1224203.
-
(2012)
Science
, vol.336
, pp. 1255-1262
-
-
Costello, E.K.1
Stagaman, K.2
Dethlefsen, L.3
Bohannan, B.J.4
Relman, D.A.5
-
46
-
-
84879744885
-
The long-term stability of the human gut microbiota
-
Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, Gordon JI. 2013. The long-term stability of the human gut microbiota. Science 341:1237439. https://doi.org/10.1126/science.1237439.
-
(2013)
Science
, vol.341
, pp. 1237439
-
-
Faith, J.J.1
Guruge, J.L.2
Charbonneau, M.3
Subramanian, S.4
Seedorf, H.5
Goodman, A.L.6
Clemente, J.C.7
Knight, R.8
Heath, A.C.9
Leibel, R.L.10
Rosenbaum, M.11
Gordon, J.I.12
-
47
-
-
79551622954
-
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant
-
Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, Banfield JF. 2011. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A 108:1128-1133. https://doi.org/10.1073/pnas.1010992108.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 1128-1133
-
-
Morowitz, M.J.1
Denef, V.J.2
Costello, E.K.3
Thomas, B.C.4
Poroyko, V.5
Relman, D.A.6
Banfield, J.F.7
-
48
-
-
84871956840
-
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
-
Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. 2013. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res 23:111-120. https://doi.org/10.1101/gr.142315.112.
-
(2013)
Genome Res
, vol.23
, pp. 111-120
-
-
Sharon, I.1
Morowitz, M.J.2
Thomas, B.C.3
Costello, E.K.4
Relman, D.A.5
Banfield, J.F.6
-
49
-
-
84946740229
-
The human gut virome: A multifaceted majority
-
Ogilvie LA, Jones BV. 2015. The human gut virome: a multifaceted majority. Front Microbiol 6:918. https://doi.org/10.3389/fmicb.2015.00918.
-
(2015)
Front Microbiol
, vol.6
, pp. 918
-
-
Ogilvie, L.A.1
Jones, B.V.2
-
50
-
-
84905041075
-
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
-
Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA. 2014. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun 5:4498. https://doi.org/10.1038/ncomms5498.
-
(2014)
Nat Commun
, vol.5
, pp. 4498
-
-
Dutilh, B.E.1
Cassman, N.2
McNair, K.3
Sanchez, S.E.4
Silva, G.G.5
Boling, L.6
Barr, J.J.7
Speth, D.R.8
Seguritan, V.9
Aziz, R.K.10
Felts, B.11
Dinsdale, E.A.12
Mokili, J.L.13
Edwards, R.A.14
-
51
-
-
66149101252
-
Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis
-
Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, Wang C, Naeem A, Zaidi S, Delwart E. 2009. Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol 83:4642-4651. https://doi.org/10.1128/JVI.02301-08.
-
(2009)
J Virol
, vol.83
, pp. 4642-4651
-
-
Victoria, J.G.1
Kapoor, A.2
Li, L.3
Blinkova, O.4
Slikas, B.5
Wang, C.6
Naeem, A.7
Zaidi, S.8
Delwart, E.9
-
52
-
-
77954627922
-
Viruses in the faecal microbiota of monozygotic twins and their mothers
-
Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. 2010. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466:334-338. https://doi.org/10.1038/nature09199.
-
(2010)
Nature
, vol.466
, pp. 334-338
-
-
Reyes, A.1
Haynes, M.2
Hanson, N.3
Angly, F.E.4
Heath, A.C.5
Rohwer, F.6
Gordon, J.I.7
-
53
-
-
31144459030
-
RNA viral community in human feces: Prevalence of plant pathogenic viruses
-
Zhang T, Breitbart M, Lee WH, Run JQ, Wei CL, Soh SW, Hibberd ML, Liu ET, Rohwer F, Ruan Y. 2006. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 4:e3. https://doi.org/10.1371/journal.pbio.0040003.
-
(2006)
PLoS Biol
, vol.4
, pp. e3
-
-
Zhang, T.1
Breitbart, M.2
Lee, W.H.3
Run, J.Q.4
Wei, C.L.5
Soh, S.W.6
Hibberd, M.L.7
Liu, E.T.8
Rohwer, F.9
Ruan, Y.10
-
54
-
-
12844269824
-
Expression of a viral polymerase-bound host factor turns human cell lines permissive to a plant-and insect-infecting virus
-
de Medeiros RB, Figueiredo J, Resende RDO, De Avila AC. 2005. Expression of a viral polymerase-bound host factor turns human cell lines permissive to a plant-and insect-infecting virus. Proc Natl Acad Sci U S A 102:1175-1180. https://doi.org/10.1073/pnas.0406668102.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 1175-1180
-
-
De Medeiros, R.B.1
Figueiredo, J.2
Resende, R.D.O.3
De Avila, A.C.4
-
55
-
-
84873854916
-
Tobacco mosaic virus in the lungs of mice following intra-tracheal inoculation
-
Balique F, Colson P, Barry AO, Nappez C, Ferretti A, Moussawi KA, Ngounga T, Lepidi H, Ghigo E, Mege JL, Lecoq H, Raoult D. 2013. Tobacco mosaic virus in the lungs of mice following intra-tracheal inoculation. PLoS One 8:e54993. https://doi.org/10.1371/journal.pone.0054993.
-
(2013)
PLoS One
, vol.8
, pp. e54993
-
-
Balique, F.1
Colson, P.2
Barry, A.O.3
Nappez, C.4
Ferretti, A.5
Moussawi, K.A.6
Ngounga, T.7
Lepidi, H.8
Ghigo, E.9
Mege, J.L.10
Lecoq, H.11
Raoult, D.12
-
56
-
-
77956332518
-
Pepper mild mottle virus, a plant virus associated with specific immune responses, fever, abdominal pains, and pruritus in humans
-
Colson P, Richet H, Desnues C, Balique F, Moal V, Grob JJ, Berbis P, Lecoq H, Harlé JR, Berland Y, Raoult D. 2010. Pepper mild mottle virus, a plant virus associated with specific immune responses, fever, abdominal pains, and pruritus in humans. PLoS One 5:e10041. https://doi.org/10.1371/journal.pone.0010041.
-
(2010)
PLoS One
, vol.5
, pp. e10041
-
-
Colson, P.1
Richet, H.2
Desnues, C.3
Balique, F.4
Moal, V.5
Grob, J.J.6
Berbis, P.7
Lecoq, H.8
Harlé, J.R.9
Berland, Y.10
Raoult, D.11
-
57
-
-
84865169911
-
Going viral: Next-generation sequencing applied to phage populations in the human gut
-
Reyes A, Semenkovich NP, Whiteson K, Rohwer F, Gordon JI. 2012. Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol 10:607-617. https://doi.org/10.1038/nrmicro2853.
-
(2012)
Nat Rev Microbiol
, vol.10
, pp. 607-617
-
-
Reyes, A.1
Semenkovich, N.P.2
Whiteson, K.3
Rohwer, F.4
Gordon, J.I.5
-
58
-
-
64749109065
-
Laboratory procedures to generate viral metagenomes
-
Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. 2009. Laboratory procedures to generate viral metagenomes. Nat Protoc 4:470-483. https://doi.org/10.1038/nprot.2009.10.
-
(2009)
Nat Protoc
, vol.4
, pp. 470-483
-
-
Thurber, R.V.1
Haynes, M.2
Breitbart, M.3
Wegley, L.4
Rohwer, F.5
-
59
-
-
80054886353
-
Bacteroides in the infant gut consume milk oligosaccharides via mucusutilization pathways
-
Marcobal A, Barboza M, Sonnenburg ED, Pudlo N, Martens EC, Desai P, Lebrilla CB, Weimer BC, Mills DA, German JB, Sonnenburg JL. 2011. Bacteroides in the infant gut consume milk oligosaccharides via mucusutilization pathways. Cell Host Microbe 10:507-514. https://doi.org/10.1016/j.chom.2011.10.007.
-
(2011)
Cell Host Microbe
, vol.10
, pp. 507-514
-
-
Marcobal, A.1
Barboza, M.2
Sonnenburg, E.D.3
Pudlo, N.4
Martens, E.C.5
Desai, P.6
Lebrilla, C.B.7
Weimer, B.C.8
Mills, D.A.9
German, J.B.10
Sonnenburg, J.L.11
-
60
-
-
84923570274
-
Mucin glycan foraging in the human gut microbiome
-
Tailford LE, Crost EH, Kavanaugh D, Juge N. 2015. Mucin glycan foraging in the human gut microbiome. Front Genet 6:81. https://doi.org/10.3389/fgene.2015.00081.
-
(2015)
Front Genet
, vol.6
, pp. 81
-
-
Tailford, L.E.1
Crost, E.H.2
Kavanaugh, D.3
Juge, N.4
-
61
-
-
80051707062
-
Genetic strategies for mucin metabolism in Bifidobacterium bifidum PRL2010: An example of possible human-microbe co-evolution
-
Turroni F, Milani C, van Sinderen D, Ventura M. 2011. Genetic strategies for mucin metabolism in Bifidobacterium bifidum PRL2010: an example of possible human-microbe co-evolution. Gut Microbes 2:183-189. https://doi.org/10.4161/gmic.2.3.16105.
-
(2011)
Gut Microbes
, vol.2
, pp. 183-189
-
-
Turroni, F.1
Milani, C.2
Van Sinderen, D.3
Ventura, M.4
-
62
-
-
84874963999
-
Bacteria as vitamin suppliers to their host: A gut microbiota perspective
-
LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M. 2013. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol 24:160-168. https://doi.org/10.1016/j.copbio.2012.08.005.
-
(2013)
Curr Opin Biotechnol
, vol.24
, pp. 160-168
-
-
LeBlanc, J.G.1
Milani, C.2
De Giori, G.S.3
Sesma, F.4
Van Sinderen, D.5
Ventura, M.6
-
63
-
-
84863871551
-
Microbial degradation of complex carbohydrates in the gut
-
Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. 2012. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 3:289-306. https://doi.org/10.4161/gmic.19897.
-
(2012)
Gut Microbes
, vol.3
, pp. 289-306
-
-
Flint, H.J.1
Scott, K.P.2
Duncan, S.H.3
Louis, P.4
Forano, E.5
-
64
-
-
84910107735
-
Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life
-
Brown CT, Sharon I, Thomas BC, Castelle CJ, Morowitz MJ, Banfield JF. 2013. Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome 1:30. https://doi.org/10.1186/2049-2618-1-30.
-
(2013)
Microbiome
, vol.1
, pp. 30
-
-
Brown, C.T.1
Sharon, I.2
Thomas, B.C.3
Castelle, C.J.4
Morowitz, M.J.5
Banfield, J.F.6
-
65
-
-
84926420111
-
Why is initial bacterial colonization of the intestine important to infants' and children's health?
-
Houghteling PD, Walker WA. 2015. Why is initial bacterial colonization of the intestine important to infants' and children's health? J Pediatr Gastroenterol Nutr 60:294-307. https://doi.org/10.1097/MPG.0000000000000597.
-
(2015)
J Pediatr Gastroenterol Nutr
, vol.60
, pp. 294-307
-
-
Houghteling, P.D.1
Walker, W.A.2
-
66
-
-
84861011960
-
Diversity of bifidobacteria within the infant gut microbiota
-
Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, Claesson MJ, Kerr C, Hourihane J, Murray D, Fuligni F, Gueimonde M, Margolles A, De Bellis G, O'Toole PW, van Sinderen D, Marchesi JR, Ventura M. 2012. Diversity of bifidobacteria within the infant gut microbiota. PLoS One 7:e36957. https://doi.org/10.1371/journal.pone.0036957.
-
(2012)
PLoS One
, vol.7
, pp. e36957
-
-
Turroni, F.1
Peano, C.2
Pass, D.A.3
Foroni, E.4
Severgnini, M.5
Claesson, M.J.6
Kerr, C.7
Hourihane, J.8
Murray, D.9
Fuligni, F.10
Gueimonde, M.11
Margolles, A.12
De Bellis, G.13
O'Toole, P.W.14
Van Sinderen, D.15
Marchesi, J.R.16
Ventura, M.17
-
67
-
-
82955205923
-
Ability of Bifidobacterium breve to grow on different types of milk: Exploring the metabolism of milk through genome analysis
-
Turroni F, Foroni E, Serafini F, Viappiani A, Montanini B, Bottacini F, Ferrarini A, Bacchini PL, Rota C, Delledonne M, Ottonello S, van Sinderen D, Ventura M. 2011. Ability of Bifidobacterium breve to grow on different types of milk: exploring the metabolism of milk through genome analysis. Appl Environ Microbiol 77:7408-7417. https://doi.org/10.1128/AEM.05336-11.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 7408-7417
-
-
Turroni, F.1
Foroni, E.2
Serafini, F.3
Viappiani, A.4
Montanini, B.5
Bottacini, F.6
Ferrarini, A.7
Bacchini, P.L.8
Rota, C.9
Delledonne, M.10
Ottonello, S.11
Van Sinderen, D.12
Ventura, M.13
-
68
-
-
78751580602
-
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
-
Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze XL, Brown D, Stares MD, Scott P, Bergerat A, Louis P, McIntosh F, Johnstone AM, Lobley GE, Parkhill J, Flint HJ. 2011. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 5:220-230. https://doi.org/10.1038/ismej.2010.118.
-
(2011)
ISME J
, vol.5
, pp. 220-230
-
-
Walker, A.W.1
Ince, J.2
Duncan, S.H.3
Webster, L.M.4
Holtrop, G.5
Ze, X.L.6
Brown, D.7
Stares, M.D.8
Scott, P.9
Bergerat, A.10
Louis, P.11
McIntosh, F.12
Johnstone, A.M.13
Lobley, G.E.14
Parkhill, J.15
Flint, H.J.16
-
69
-
-
84930531205
-
Manipulating the gut microbiota to maintain health and treat disease
-
Scott KP, Antoine JM, Midtvedt T, van Hemert S. 2015. Manipulating the gut microbiota to maintain health and treat disease. Microb Ecol Health Dis 26:25877. https://doi.org/10.3402/mehd.v26.25877.
-
(2015)
Microb Ecol Health Dis
, vol.26
, pp. 25877
-
-
Scott, K.P.1
Antoine, J.M.2
Midtvedt, T.3
Van Hemert, S.4
-
70
-
-
79951995822
-
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak
-
Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, Tang P. 2011. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 364:730-739. https://doi.org/10.1056/NEJMoa1003176.
-
(2011)
N Engl J Med
, vol.364
, pp. 730-739
-
-
Gardy, J.L.1
Johnston, J.C.2
Ho Sui, S.J.3
Cook, V.J.4
Shah, L.5
Brodkin, E.6
Rempel, S.7
Moore, R.8
Zhao, Y.9
Holt, R.10
Varhol, R.11
Birol, I.12
Lem, M.13
Sharma, M.K.14
Elwood, K.15
Jones, S.J.16
Brinkman, F.S.17
Brunham, R.C.18
Tang, P.19
-
71
-
-
84875921666
-
A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4
-
Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ, Quick J, Weir JC, Quince C, Smith GP, Betley JR, Aepfelbacher M, Pallen MJ. 2013. A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 309:1502-1510. https://doi.org/10.1001/jama.2013.3231.
-
(2013)
JAMA
, vol.309
, pp. 1502-1510
-
-
Loman, N.J.1
Constantinidou, C.2
Christner, M.3
Rohde, H.4
Chan, J.Z.5
Quick, J.6
Weir, J.C.7
Quince, C.8
Smith, G.P.9
Betley, J.R.10
Aepfelbacher, M.11
Pallen, M.J.12
-
72
-
-
84968880438
-
Durable coexistence of donor and recipient strains after fecal microbiota transplantation
-
Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P. 2016. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science 352:586-589. https://doi.org/10.1126/science.aad8852.
-
(2016)
Science
, vol.352
, pp. 586-589
-
-
Li, S.S.1
Zhu, A.2
Benes, V.3
Costea, P.I.4
Hercog, R.5
Hildebrand, F.6
Huerta-Cepas, J.7
Nieuwdorp, M.8
Salojärvi, J.9
Voigt, A.Y.10
Zeller, G.11
Sunagawa, S.12
De Vos, W.M.13
Bork, P.14
-
73
-
-
84858990515
-
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
-
Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A. 2012. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol 13:R23. https://doi.org/10.1186/gb-2012-13-3-r23.
-
(2012)
Genome Biol
, vol.13
, pp. R23
-
-
Giannoukos, G.1
Ciulla, D.M.2
Huang, K.3
Haas, B.J.4
Izard, J.5
Levin, J.Z.6
Livny, J.7
Earl, A.M.8
Gevers, D.9
Ward, D.V.10
Nusbaum, C.11
Birren, B.W.12
Gnirke, A.13
-
74
-
-
84875098273
-
Comparison of sequencing utility programs
-
Aronesty E. 2013. Comparison of sequencing utility programs. Open Bioinforma J 7:1-8. https://doi.org/10.2174/1875036201307010001.
-
(2013)
Open Bioinforma J
, vol.7
, pp. 1-8
-
-
Aronesty, E.1
-
75
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357-359. https://doi.org/10.1038/nmeth.1923.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
76
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: Improved data processing and Web-based tools
-
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and Web-based tools. Nucleic Acids Res 41:D590-D596. https://doi.org/10.1093/nar/gks1219.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D590-D596
-
-
Quast, C.1
Pruesse, E.2
Yilmaz, P.3
Gerken, J.4
Schweer, T.5
Yarza, P.6
Peplies, J.7
Glöckner, F.O.8
-
77
-
-
84964994621
-
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
-
Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N. 2015. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods 12:902-903. https://doi.org/10.1038/nmeth.3589.
-
(2015)
Nat Methods
, vol.12
, pp. 902-903
-
-
Truong, D.T.1
Franzosa, E.A.2
Tickle, T.L.3
Scholz, M.4
Weingart, G.5
Pasolli, E.6
Tett, A.7
Huttenhower, C.8
Segata, N.9
-
78
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797. https://doi.org/10.1093/nar/gkh340.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
79
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313. https://doi.org/10.1093/bioinformatics/btu033.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
80
-
-
84901847186
-
Relating the metatranscriptome and metagenome of the human gut
-
Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C. 2014. Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci U S A 111:E2329-E2338. https://doi.org/10.1073/pnas.1319284111.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. E2329-E2338
-
-
Franzosa, E.A.1
Morgan, X.C.2
Segata, N.3
Waldron, L.4
Reyes, J.5
Earl, A.M.6
Giannoukos, G.7
Boylan, M.R.8
Ciulla, D.9
Gevers, D.10
Izard, J.11
Garrett, W.S.12
Chan, A.T.13
Huttenhower, C.14
-
81
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079. https://doi.org/10.1093/bioinformatics/btp352.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
82
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841-842. https://doi.org/10.1093/bioinformatics/btq033.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
83
-
-
80555140075
-
Scikit-learn: Machine learning in Python
-
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J, Passos A, Cournapeau D, Brucher M, Perrot M, Duchesnay E. 2011. Scikit-learn: machine learning in Python. J Mach Learn Res 12:2825-2830.
-
(2011)
J Mach Learn Res
, vol.12
, pp. 2825-2830
-
-
Pedregosa, F.1
Varoquaux, G.2
Gramfort, A.3
Michel, V.4
Thirion, B.5
Grisel, O.6
Blondel, M.7
Prettenhofer, P.8
Weiss, R.9
Dubourg, V.10
Vanderplas, J.11
Passos, A.12
Cournapeau, D.13
Brucher, M.14
Perrot, M.15
Duchesnay, E.16
-
84
-
-
79959383523
-
Metagenomic biomarker discovery and explanation
-
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. 2011. Metagenomic biomarker discovery and explanation. Genome Biol 12:R60. https://doi.org/10.1186/gb-2011-12-6-r60.
-
(2011)
Genome Biol
, vol.12
, pp. R60
-
-
Segata, N.1
Izard, J.2
Waldron, L.3
Gevers, D.4
Miropolsky, L.5
Garrett, W.S.6
Huttenhower, C.7
-
85
-
-
84937442075
-
Compact graphical representation of phylogenetic data and metadata with GraPhlAn
-
Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N. 2015. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 3:e1029. https://doi.org/10.7717/peerj.1029.
-
(2015)
PeerJ
, vol.3
, pp. e1029
-
-
Asnicar, F.1
Weingart, G.2
Tickle, T.L.3
Huttenhower, C.4
Segata, N.5
|