-
1
-
-
84878004134
-
Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)
-
Ottesen AR, González Peña A, White JR, Pettengill JB, Li C, Allard S, Rideout S, Allard M, Hill T, Evans P, Strain E, Musser S, Knight R, Brown E. 2013. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol 13:114. http://dx.doi.org/10.1186/1471-2180-13-114.
-
(2013)
BMC Microbiol
, vol.13
, pp. 114
-
-
Ottesen, A.R.1
González Peña, A.2
White, J.R.3
Pettengill, J.B.4
Li, C.5
Allard, S.6
Rideout, S.7
Allard, M.8
Hill, T.9
Evans, P.10
Strain, E.11
Musser, S.12
Knight, R.13
Brown, E.14
-
2
-
-
84879743032
-
Season, irrigation, leaf age, and Escherichia coli inoculation influence the bacterial diversity in the lettuce phyllosphere
-
Williams TR, Moyne AL, Harris LJ, Marco ML. 2013. Season, irrigation, leaf age, and Escherichia coli inoculation influence the bacterial diversity in the lettuce phyllosphere. PLoS One 8:e68642. http://dx.doi.org/10.1371/journal.pone.0068642.
-
(2013)
Plos One
, vol.8
-
-
Williams, T.R.1
Moyne, A.L.2
Harris, L.J.3
Marco, M.L.4
-
3
-
-
84908262674
-
Phyllosphere microbiota composition and microbial community transplantation on lettuce plants grown indoors
-
Williams TR, Marco ML. 2014. Phyllosphere microbiota composition and microbial community transplantation on lettuce plants grown indoors. mBio 5:e01564-14. http://dx.doi.org/10.1128/mBio.01564-14.
-
(2014)
Mbio
, vol.5
, pp. e01e14-e01564
-
-
Williams, T.R.1
Marco, M.L.2
-
4
-
-
84875430559
-
Bacterial communities associated with the surfaces of fresh fruits and vegetables
-
Leff JW, Fierer N. 2013. Bacterial communities associated with the surfaces of fresh fruits and vegetables. PLoS One 8:e59310. http://dx.doi.org/10.1371/journal.pone.0059310.
-
(2013)
Plos One
, vol.8
-
-
Leff, J.W.1
Fierer, N.2
-
5
-
-
84880599158
-
The microbial content of raw and pasteurized cow milk as determined by molecular approaches
-
Quigley L, McCarthy R, O’Sullivan O, Beresford TP, Fitzgerald GF, Ross RP, Stanton C, Cotter PD. 2013. The microbial content of raw and pasteurized cow milk as determined by molecular approaches. J Dairy Sci 96:4928–4937. http://dx.doi.org/10.3168/jds.2013-6688.
-
(2013)
J Dairy Sci
, vol.96
, pp. 4928-4937
-
-
Quigley, L.1
McCarthy, R.2
O’Sullivan, O.3
Beresford, T.P.4
Fitzgerald, G.F.5
Ross, R.P.6
Stanton, C.7
Cotter, P.D.8
-
6
-
-
84866184346
-
High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses
-
Quigley L, O’Sullivan O, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD. 2012. High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Appl Environ Microbiol 78:5717–5723. http://dx.doi.org/10.1128/AEM.00918-12.
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 5717-5723
-
-
Quigley, L.1
O’Sullivan, O.2
Beresford, T.P.3
Ross, R.P.4
Fitzgerald, G.F.5
Cotter, P.D.6
-
7
-
-
84881261838
-
The complex microbiota of raw milk
-
Quigley L, O’Sullivan O, Stanton C, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD. 2013. The complex microbiota of raw milk. FEMS Microbiol Rev 37:664–698. http://dx.doi.org/10.1111/1574-6976.12030.
-
(2013)
FEMS Microbiol Rev
, vol.37
, pp. 664-698
-
-
Quigley, L.1
O’Sullivan, O.2
Stanton, C.3
Beresford, T.P.4
Ross, R.P.5
Fitzgerald, G.F.6
Cotter, P.D.7
-
8
-
-
36849038919
-
Molting in Salmonella enteritidis-challenged laying hens fed alfalfa crumbles. IV. Immune and stress protein response
-
Dunkley CS, McReynolds JL, Dunkley KD, Njongmeta LN, Berghman LR, Kubena LF, Nisbet DJ, Ricke SC. 2007. Molting in Salmonella enteritidis-challenged laying hens fed alfalfa crumbles. IV. Immune and stress protein response. Poult Sci 86:2502–2508. http://dx.doi.org/10.3382/ps.2006-00401.
-
(2007)
Poult Sci
, vol.86
, pp. 2502-2508
-
-
Dunkley, C.S.1
McReynolds, J.L.2
Dunkley, K.D.3
Njongmeta, L.N.4
Berghman, L.R.5
Kubena, L.F.6
Nisbet, D.J.7
Ricke, S.C.8
-
9
-
-
84882647373
-
Boardinvited review: Rumen microbiology: Leading the way in microbial ecology
-
Krause DO, Nagaraja TG, Wright AD, Callaway TR. 2013. Boardinvited review: rumen microbiology: leading the way in microbial ecology. J Anim Sci 91:331–341. http://dx.doi.org/10.2527/jas.2012-5567.
-
(2013)
J Anim Sci
, vol.91
, pp. 331-341
-
-
Krause, D.O.1
Nagaraja, T.G.2
Wright, A.D.3
Callaway, T.R.4
-
10
-
-
79954531771
-
Cultivable microbial communities in raw cow milk and potential transfers from stables of sixteen French farms
-
Vacheyrou M, Normand AC, Guyot P, Cassagne C, Piarroux R, Bouton Y. 2011. Cultivable microbial communities in raw cow milk and potential transfers from stables of sixteen French farms. Int J Food Microbiol 146: 253–262. http://dx.doi.org/10.1016/j.ijfoodmicro.2011.02.033.
-
(2011)
Int J Food Microbiol
, vol.146
, pp. 253-262
-
-
Vacheyrou, M.1
Normand, A.C.2
Guyot, P.3
Cassagne, C.4
Piarroux, R.5
Bouton, Y.6
-
11
-
-
33947355835
-
Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses
-
Delbès C, Ali-Mandjee L, Montel MC. 2007. Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses. Appl Environ Microbiol 73:1882–1891. http://dx.doi.org/10.1128/AEM.01716-06.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 1882-1891
-
-
Delbès, C.1
Ali-Mandjee, L.2
Montel, M.C.3
-
12
-
-
84938979544
-
Pseudomonas spp. And Serratia liquefaciens as predominant spoilers in cold raw milk
-
Machado SG, da Silva FL, Bazzolli DM, Heyndrickx M, Costa PM, Vanetti MC. 2015. Pseudomonas spp. and Serratia liquefaciens as predominant spoilers in cold raw milk. J Food Sci 80:M1842–M1849. http://dx.doi.org/10.1111/1750-3841.12957.
-
(2015)
J Food Sci
, vol.80
, pp. M1842-M1849
-
-
Machado, S.G.1
da Silva, F.L.2
Bazzolli, D.M.3
Heyndrickx, M.4
Costa, P.M.5
Vanetti, M.C.6
-
13
-
-
33746101830
-
Changes in the spoilage-related microbiota of beef during refrigerated storage under dif-ferent packaging conditions
-
Ercolini D, Russo F, Torrieri E, Masi P, Villani F. 2006. Changes in the spoilage-related microbiota of beef during refrigerated storage under dif-ferent packaging conditions. Appl Environ Microbiol 72:4663–4671. http://dx.doi.org/10.1128/AEM.00468-06.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 4663-4671
-
-
Ercolini, D.1
Russo, F.2
Torrieri, E.3
Masi, P.4
Villani, F.5
-
14
-
-
84949906876
-
Impact of nisin-activated packaging on microbiota of beef burgers during storage
-
Ferrocino I, Greppi A, La Storia A, Rantsiou K, Ercolini D, Cocolin L. 2016. Impact of nisin-activated packaging on microbiota of beef burgers during storage Appl Environ Microbiol 82:549–559. http://dx.doi.org/10.1128/AEM.03093-15
-
(2016)
Appl Environ Microbiol
, vol.82
, pp. 549-559
-
-
Ferrocino, I.1
Greppi, A.2
La Storia, A.3
Rantsiou, K.4
Ercolini, D.5
Cocolin, L.6
-
15
-
-
84986626543
-
Food balance
-
Food and Agriculture Organization of the United Nations (FAOSTAT). 2013. Food balance, domestic utilization data. http://faostat3.fao.org/compare/E.
-
(2013)
Domestic Utilization Data
-
-
-
16
-
-
84986610800
-
-
United States Department of Agriculture Economic Research Service, Washington, DC
-
Hoskin R, Cessna J. 2016. From raw milk to dairy products. United States Department of Agriculture Economic Research Service, Washington, DC. http://www.ers.usda.gov/topics/animal-products/dairy/background.aspx.
-
(2016)
From Raw Milk to Dairy Products
-
-
Hoskin, R.1
Cessna, J.2
-
17
-
-
0031792931
-
An ecological study of lactococci isolated from raw milk in the Camembert cheese registered designation of origin area
-
Corroler D, Mangin I, Desmasures N, Gueguen M. 1998. An ecological study of lactococci isolated from raw milk in the Camembert cheese registered designation of origin area. Appl Environ Microbiol 64:4729–4735.
-
(1998)
Appl Environ Microbiol
, vol.64
, pp. 4729-4735
-
-
Corroler, D.1
Mangin, I.2
Desmasures, N.3
Gueguen, M.4
-
18
-
-
84904578387
-
Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity
-
Wolfe BE, Button JE, Santarelli M, Dutton RJ. 2014. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158:422–433. http://dx.doi.org/10.1016/j.cell.2014.05.041.
-
(2014)
Cell
, vol.158
, pp. 422-433
-
-
Wolfe, B.E.1
Button, J.E.2
Santarelli, M.3
Dutton, R.J.4
-
19
-
-
0041804948
-
Causes and control of culture-related flavor defects in cultured dairy-products
-
Sandine WE, Daly C, Elliker PR, Vedamuthu ER. 1972. Causes and control of culture-related flavor defects in cultured dairy-products. J Dairy Sci 55:1031–1039. http://dx.doi.org/10.3168/jds.S0022-0302(72)85617-0.
-
(1972)
J Dairy Sci
, vol.55
, pp. 1031-1039
-
-
Sandine, W.E.1
Daly, C.2
Elliker, P.R.3
Vedamuthu, E.R.4
-
20
-
-
84860228687
-
Microbiological spoilage of dairy products
-
Sperber WH, Doyle MP, Springer, New York, NY
-
Ledenbach LH, Marshall RT. 2009. Microbiological spoilage of dairy products, p 41–67. In Sperber WH, Doyle MP (ed), Compendium of the microbiological spoilage of foods and beverages. Springer, New York, NY. http://dx.doi.org/10.1007/978-1-4419-0826-1_2.
-
(2009)
Compendium of the Microbiological Spoilage of Foods and Beverages
, pp. 41-67
-
-
Ledenbach, L.H.1
Marshall, R.T.2
-
21
-
-
44349145955
-
Comparative analysis of the diversity of aerobic spore-forming bacteria in raw milk from organic and conventional dairy farms
-
Coorevits A, De Jonghe V, Vandroemme J, Reekmans R, Heyrman J, Messens W, De Vos P, Heyndrickx M. 2008. Comparative analysis of the diversity of aerobic spore-forming bacteria in raw milk from organic and conventional dairy farms. Syst Appl Microbiol 31:126–140. http://dx.doi.org/10.1016/j.syapm.2008.03.002.
-
(2008)
Syst Appl Microbiol
, vol.31
, pp. 126-140
-
-
Coorevits, A.1
De Jonghe, V.2
Vandroemme, J.3
Reekmans, R.4
Heyrman, J.5
Messens, W.6
De Vos, P.7
Heyndrickx, M.8
-
22
-
-
0024698259
-
Isolation and identification of coagulase-negative Staphylococcus species from bovine body sites and streak canals of nulliparous heifers
-
White DG, Harmon RJ, Matos JE, Langlois BE. 1989. Isolation and identification of coagulase-negative Staphylococcus species from bovine body sites and streak canals of nulliparous heifers. J Dairy Sci 72: 1886–1892. http://dx.doi.org/10.3168/jds.S0022-0302(89)79307-3.
-
(1989)
J Dairy Sci
, vol.72
, pp. 1886-1892
-
-
White, D.G.1
Harmon, R.J.2
Matos, J.E.3
Langlois, B.E.4
-
23
-
-
57749099325
-
Food safety: Unpasteurized milk: A continued public health threat
-
Lejeune JT, Rajala-Schultz PJ. 2009. Food safety: unpasteurized milk: a continued public health threat. Clin Infect Dis 48:93–100. http://dx.doi.org/10.1086/595007.
-
(2009)
Clin Infect Dis
, vol.48
, pp. 93-100
-
-
Lejeune, J.T.1
Rajala-Schultz, P.J.2
-
24
-
-
70349153755
-
Investigating the relationship between raw milk bacterial composition, as described by intergenic transcribed spacer-PCR fingerprinting, and pasture altitude
-
Bonizzi I, Buffoni JN, Feligini M, Enne G. 2009. Investigating the relationship between raw milk bacterial composition, as described by intergenic transcribed spacer-PCR fingerprinting, and pasture altitude. J Appl Microbiol 107:1319–1329. http://dx.doi.org/10.1111/j.1365-2672.2009.04311.x.
-
(2009)
J Appl Microbiol
, vol.107
, pp. 1319-1329
-
-
Bonizzi, I.1
Buffoni, J.N.2
Feligini, M.3
Enne, G.4
-
25
-
-
49449093809
-
Eleven-year trends of microbiological quality in bulk tank milk
-
Costello M, Rhee MS, Bates MP, Clark S, Luedecke LO, Kang DH. 2003. Eleven-year trends of microbiological quality in bulk tank milk. Food Protect Trends 23:393–400. http://openagricola.nal.usda.gov/Record/IND44658844.
-
(2003)
Food Protect Trends
, vol.23
, pp. 393-400
-
-
Costello, M.1
Rhee, M.S.2
Bates, M.P.3
Clark, S.4
Luedecke, L.O.5
Kang, D.H.6
-
26
-
-
70349923245
-
Associations among milk quality indicators in raw bulk milk
-
Pantoja JC, Reinemann DJ, Ruegg PL. 2009. Associations among milk quality indicators in raw bulk milk. J Dairy Sci 92:4978–4987. http://dx.doi.org/10.3168/jds.2009-2329.
-
(2009)
J Dairy Sci
, vol.92
, pp. 4978-4987
-
-
Pantoja, J.C.1
Reinemann, D.J.2
Ruegg, P.L.3
-
27
-
-
79956265761
-
Factors associated with coliform count in unpasteurized bulk milk
-
Pantoja JC, Reinemann DJ, Ruegg PL. 2011. Factors associated with coliform count in unpasteurized bulk milk. J Dairy Sci 94:2680–2691. http://dx.doi.org/10.3168/jds.2010-3721.
-
(2011)
J Dairy Sci
, vol.94
, pp. 2680-2691
-
-
Pantoja, J.C.1
Reinemann, D.J.2
Ruegg, P.L.3
-
28
-
-
84986591351
-
Milk cows and production by state and region (Annual)
-
Washington, DC
-
United States Department of Agriculture Economic Research Service (ERS). 2015. Milk cows and production by state and region (annual). USDA ERS, Washington, DC. http://www.ers.usda.gov/data-products/dairy-data.aspx.
-
(2015)
USDA ERS
-
-
-
29
-
-
84986591358
-
Dairy Products Annual Summary. National Agricultural Statistics Service, Agricultural Statistics Board
-
NASS. 2015. Dairy Products Annual Summary. National Agricultural Statistics Service, Agricultural Statistics Board, United States Department of Agriculture. http://usda.mannlib.cornell.edu/MannUsda/viewDocumentInfo.do?documentID_1052.
-
(2015)
United States Department of Agriculture
-
-
-
30
-
-
84888865593
-
Robust methods for differential abundance analysis in marker gene surveys
-
Joseph N, Paulson CS, Corrada Bravo H, Pop M. 2013. Robust methods for differential abundance analysis in marker gene surveys. Nat Methods 10:1200–1202. http://dx.doi.org/10.1038/nmeth.2658.
-
(2013)
Nat Methods
, vol.10
, pp. 1200-1202
-
-
Joseph, N.1
Paulson, C.S.2
Corrada Bravo, H.3
Pop, M.4
-
31
-
-
0035487318
-
Counting the uncountable: Statistical approaches to estimating microbial diversity
-
Hughes JB, Hellman JJ, Ricketts TH, Bohannan BJM. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67:4399–4406. http://dx.doi.org/10.1128/AEM.67.10.4399-4406.2001.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 4399-4406
-
-
Hughes, J.B.1
Hellman, J.J.2
Ricketts, T.H.3
Bohannan, B.J.M.4
-
32
-
-
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. http://dx.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
-
33
-
-
84942550629
-
Effect of commercial hauling practices and tanker cleaning treatments on raw milk microbiological quality
-
Darchuk EM, Waite-Cusic J, Meunier-Goddik L. 2015. Effect of commercial hauling practices and tanker cleaning treatments on raw milk microbiological quality. J Dairy Sci 98:7384–7393. http://dx.doi.org/10.3168/jds.2015-9746.
-
(2015)
J Dairy Sci
, vol.98
, pp. 7384-7393
-
-
Darchuk, E.M.1
Waite-Cusic, J.2
Meunier-Goddik, L.3
-
34
-
-
84924076917
-
Propidium monoazide combined with real-time PCR for selective detection of viable Staphylococcus aureus in milk powder and meat products
-
Zhang Z, Liu W, Xu H, Aguilar ZP, Shah NP, Wei H. 2015. Propidium monoazide combined with real-time PCR for selective detection of viable Staphylococcus aureus in milk powder and meat products. J Dairy Sci 98: 1625–1633. http://dx.doi.org/10.3168/jds.2014-8938.
-
(2015)
J Dairy Sci
, vol.98
, pp. 1625-1633
-
-
Zhang, Z.1
Liu, W.2
Xu, H.3
Aguilar, Z.P.4
Shah, N.P.5
Wei, H.6
-
35
-
-
84862549638
-
Rapid propidium monoazide PCR assay for the exclusive detection of viable Enterobacteriaceae cells in pasteurized milk
-
Soejima T, Minami J, Iwatsuki K. 2012. Rapid propidium monoazide PCR assay for the exclusive detection of viable Enterobacteriaceae cells in pasteurized milk. J Dairy Sci 95:3634–3642. http://dx.doi.org/10.3168/jds.2012-5360.
-
(2012)
J Dairy Sci
, vol.95
, pp. 3634-3642
-
-
Soejima, T.1
Minami, J.2
Iwatsuki, K.3
-
36
-
-
0035344248
-
Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods
-
Smit E, Leeflang P, Gommans S, van den Broek J, van Mil S, Wernars K. 2001. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67:2284–2291. http://dx.doi.org/10.1128/AEM.67.5.2284-2291.2001.
-
(2001)
Appl Environ Microbiol
, vol.67
, pp. 2284-2291
-
-
Smit, E.1
Leeflang, P.2
Gommans, S.3
Van Den Broek, J.4
Van Mil, S.5
Wernars, K.6
-
37
-
-
84954271381
-
Seasonal and growth-dependent dynamics of bacterial community in radish sprouts
-
Asakura H, Tachibana M, Taguchi M, Hiroi T, Kurazono H, Makino S, Kasuga F, Igimi S. 2016. Seasonal and growth-dependent dynamics of bacterial community in radish sprouts. J Food Saf 36:392–401 http://dx.doi.org/10.1111/jfs.12256:10.
-
(2016)
J Food Saf
, vol.36
, pp. 392-401
-
-
Asakura, H.1
Tachibana, M.2
Taguchi, M.3
Hiroi, T.4
Kurazono, H.5
Makino, S.6
Kasuga, F.7
Igimi, S.8
-
38
-
-
84939832873
-
Review of human hand microbiome research
-
Edmonds-Wilson SL, Nurinova NI, Zapka CA, Fierer N, Wilson M. 2015. Review of human hand microbiome research. J Dermatol Sci 80: 3–12. http://dx.doi.org/10.1016/j.jdermsci.2015.07.006.
-
(2015)
J Dermatol Sci
, vol.80
, pp. 3-12
-
-
Edmonds-Wilson, S.L.1
Nurinova, N.I.2
Zapka, C.A.3
Fierer, N.4
Wilson, M.5
-
39
-
-
38349119683
-
Actinobacterial community structure in soils receiving long-term organic and inorganic amendments
-
Piao Z, Yang L, Zhao L, Yin S. 2008. Actinobacterial community structure in soils receiving long-term organic and inorganic amendments. Appl Environ Microbiol 74:526–530. http://dx.doi.org/10.1128/AEM.00843-07.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 526-530
-
-
Piao, Z.1
Yang, L.2
Zhao, L.3
Yin, S.4
-
40
-
-
84874218240
-
Dispersal limitation and the assembly of soil Actinobacteria communities in a long-term chronosequence
-
Eisenlord SD, Zak DR, Upchurch RA. 2012. Dispersal limitation and the assembly of soil Actinobacteria communities in a long-term chronosequence. Ecol Evol 2:538–549. http://dx.doi.org/10.1002/ece3.210.
-
(2012)
Ecol Evol
, vol.2
, pp. 538-549
-
-
Eisenlord, S.D.1
Zak, D.R.2
Upchurch, R.A.3
-
41
-
-
84886729023
-
Responses of soil bacterial and fungal communities to extreme desiccation and rewetting
-
Barnard RL, Osborne CA, Firestone MK. 2013. Responses of soil bacterial and fungal communities to extreme desiccation and rewetting. ISME J 7:2229–2241. http://dx.doi.org/10.1038/ismej.2013.104.
-
(2013)
ISME J
, vol.7
, pp. 2229-2241
-
-
Barnard, R.L.1
Osborne, C.A.2
Firestone, M.K.3
-
42
-
-
33846871043
-
Cultivation-independent assessment of the bacterial diversity of breast milk among healthy women
-
Martín R, Heilig HG, Zoetendal EG, Jiménez E, Fernández L, Smidt H, Rodríguez JM. 2007. Cultivation-independent assessment of the bacterial diversity of breast milk among healthy women. Res Microbiol 158:31–37. http://dx.doi.org/10.1016/j.resmic.2006.11.004.
-
(2007)
Res Microbiol
, vol.158
, pp. 31-37
-
-
Martín, R.1
Heilig, H.G.2
Zoetendal, E.G.3
Jiménez, E.4
Fernández, L.5
Smidt, H.6
Rodríguez, J.M.7
-
43
-
-
0041379456
-
Inhibition of Staphylococcus aureus by the commensal bacteria of human milk
-
Heikkilä MP, Saris PE. 2003. Inhibition of Staphylococcus aureus by the commensal bacteria of human milk. J Appl Microbiol 95:471–478. http://dx.doi.org/10.1046/j.1365-2672.2003.02002.x.
-
(2003)
J Appl Microbiol
, vol.95
, pp. 471-478
-
-
Heikkilä, M.P.1
Saris, P.E.2
-
44
-
-
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. PLoSOne 6: e21313. http://dx.doi.org/10.1371/journal.pone.0021313.
-
(2011)
Plosone
, vol.6
-
-
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
-
45
-
-
35748939361
-
The effect of season on somatic cell count and the incidence of clinical mastitis
-
Olde Riekerink RG, Barkema HW, Stryhn H. 2007. The effect of season on somatic cell count and the incidence of clinical mastitis. J Dairy Sci 90:1704–1715. http://dx.doi.org/10.3168/jds.2006-567.
-
(2007)
J Dairy Sci
, vol.90
, pp. 1704-1715
-
-
Olde Riekerink, R.G.1
Barkema, H.W.2
Stryhn, H.3
-
46
-
-
84986615833
-
-
Reference deleted
-
Reference deleted.
-
-
-
-
47
-
-
84864049306
-
Short communication: Evaluation of bulk tank milk microbiological quality of nine dairy farms in Tennessee
-
Gillespie BE, Lewis MJ, Boonyayatra S, Maxwell ML, Saxton A, Oliver SP, Almeida RA. 2012. Short communication: evaluation of bulk tank milk microbiological quality of nine dairy farms in Tennessee. J Dairy Sci 95:4275–4279. http://dx.doi.org/10.3168/jds.2011-4881.
-
(2012)
J Dairy Sci
, vol.95
, pp. 4275-4279
-
-
Gillespie, B.E.1
Lewis, M.J.2
Boonyayatra, S.3
Maxwell, M.L.4
Saxton, A.5
Oliver, S.P.6
Almeida, R.A.7
-
48
-
-
54949127535
-
Sources of clostridia in raw milk on farms
-
Julien MC, Dion P, Lafrenière C, Antoun H, Drouin P. 2008. Sources of clostridia in raw milk on farms. Appl Environ Microbiol 74:6348–6357. http://dx.doi.org/10.1128/AEM.00913-08.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 6348-6357
-
-
Julien, M.C.1
Dion, P.2
Lafrenière, C.3
Antoun, H.4
Drouin, P.5
-
49
-
-
35748976838
-
Tracking spore-forming bacterial contaminants in fluid milk-processing systems
-
Huck JR, Hammond BH, Murphy SC, Woodcock NH, Boor KJ. 2007. Tracking spore-forming bacterial contaminants in fluid milk-processing systems. J Dairy Sci 90:4872–4883. http://dx.doi.org/10.3168/jds.2007-0196.
-
(2007)
J Dairy Sci
, vol.90
, pp. 4872-4883
-
-
Huck, J.R.1
Hammond, B.H.2
Murphy, S.C.3
Woodcock, N.H.4
Boor, K.J.5
-
50
-
-
0029154174
-
Identification of Clostridium tyrobutyricum as the causative agent of late blowing in cheese by species-specific PCR amplification
-
Klijn N, Nieuwenhof FF, Hoolwerf JD, van der Waals CB, Weerkamp AH. 1995. Identification of Clostridium tyrobutyricum as the causative agent of late blowing in cheese by species-specific PCR amplification. Appl Environ Microbiol 61:2919–2924.
-
(1995)
Appl Environ Microbiol
, vol.61
, pp. 2919-2924
-
-
Klijn, N.1
Nieuwenhof, F.F.2
Hoolwerf, J.D.3
van der Waals, C.B.4
Weerkamp, A.H.5
-
51
-
-
84953883380
-
The prevalence and control of Bacillus and related spore-forming bacteria in the dairy industry
-
Gopal N, Hill C, Ross PR, Beresford TP, Fenelon MA, Cotter PD. 2015. The prevalence and control of Bacillus and related spore-forming bacteria in the dairy industry. Front Microbiol 6:1418. http://dx.doi.org/10.3389/fmicb.2015.01418.
-
(2015)
Front Microbiol
, vol.6
-
-
Gopal, N.1
Hill, C.2
Ross, P.R.3
Beresford, T.P.4
Fenelon, M.A.5
Cotter, P.D.6
-
52
-
-
84959096781
-
Seasonal occurrence and molecular diversity of clos-tridia species spores along cheesemaking streams of 5 commercial dairy plants
-
Bermúdez J, González MJ, Olivera JA, Burgueño JA, Juliano P, Fox EM, Reginensi SM. 2016. Seasonal occurrence and molecular diversity of clos-tridia species spores along cheesemaking streams of 5 commercial dairy plants. J Dairy Sci 99:3358–3366 http://dx.doi.org/10.3168/jds.2015-10079.
-
(2016)
J Dairy Sci
, vol.99
, pp. 3358-3366
-
-
Bermúdez, J.1
González, M.J.2
Olivera, J.A.3
Burgueño, J.A.4
Juliano, P.5
Fox, E.M.6
Reginensi, S.M.7
-
53
-
-
84908324471
-
Prevalence of thermoduric bacteria and spores on 10 Midwest dairy farms
-
Buehner KP, Anand S, Djira GD, Garcia A. 2014. Prevalence of thermoduric bacteria and spores on 10 Midwest dairy farms. J Dairy Sci 97: 6777–6784. http://dx.doi.org/10.3168/jds.2014-8342.
-
(2014)
J Dairy Sci
, vol.97
, pp. 6777-6784
-
-
Buehner, K.P.1
Anand, S.2
Djira, G.D.3
Garcia, A.4
-
54
-
-
35348859178
-
Updated world map of the Koppen-Geiger climate classification
-
Peel MC, Finlayson BL, McMahon TA. 2007. Updated world map of the Koppen-Geiger climate classification. Hydrol Earth Syst Sci 11: 1633–1644. http://dx.doi.org/10.5194/hess-11-1633-2007.
-
(2007)
Hydrol Earth Syst Sci
, vol.11
, pp. 1633-1644
-
-
Peel, M.C.1
Finlayson, B.L.2
McMahon, T.A.3
-
55
-
-
0033073643
-
Bacillus cereus spores in raw milk: Factors affecting the contamination of milk during the grazing period
-
Christiansson A, Bertilsson J, Svensson B. 1999. Bacillus cereus spores in raw milk: factors affecting the contamination of milk during the grazing period. J Dairy Sci 82:305–314. http://dx.doi.org/10.3168/jds.S0022-0302(99)75237-9.
-
(1999)
J Dairy Sci
, vol.82
, pp. 305-314
-
-
Christiansson, A.1
Bertilsson, J.2
Svensson, B.3
-
56
-
-
0006050979
-
Heat-resistant psychrotrophic bacteria isolated from pasteurized milk
-
Washam CJ, Olson HC, Vedamuthu ER. 1977. Heat-resistant psychrotrophic bacteria isolated from pasteurized milk. J Food Protect 40: 101–108.
-
(1977)
J Food Protect
, vol.40
, pp. 101-108
-
-
Washam, C.J.1
Olson, H.C.2
Vedamuthu, E.R.3
-
57
-
-
0035913784
-
Interactions between yeasts and bacteria in the smear surface-ripened cheeses
-
Corsetti A, Rossi J, Gobbetti M. 2001. Interactions between yeasts and bacteria in the smear surface-ripened cheeses. Int J Food Microbiol 69: 1–10. http://dx.doi.org/10.1016/S0168-1605(01)00567-0.
-
(2001)
Int J Food Microbiol
, vol.69
, pp. 1-10
-
-
Corsetti, A.1
Rossi, J.2
Gobbetti, M.3
-
58
-
-
0001766721
-
Presence and activity of psychrotrophic microorganisms in milk and dairy-products—a review
-
Cousin MA. 1982. Presence and activity of psychrotrophic microorganisms in milk and dairy-products—a review. J Food Protect 45:172–207.
-
(1982)
J Food Protect
, vol.45
, pp. 172-207
-
-
Cousin, M.A.1
-
59
-
-
33744789412
-
Pasteurization is effective against multidrug-resistant bacteria
-
Wang CY, Wu HD, Lee LN, Chang HT, Hsu YL, Yu CJ, Yang PC, Hsueh PR. 2006. Pasteurization is effective against multidrug-resistant bacteria. Am J Infect Control 34:320–322. http://dx.doi.org/10.1016/j.ajic.2005.11.006.
-
(2006)
Am J Infect Control
, vol.34
, pp. 320-322
-
-
Wang, C.Y.1
Wu, H.D.2
Lee, L.N.3
Chang, H.T.4
Hsu, Y.L.5
Yu, C.J.6
Yang, P.C.7
Hsueh, P.R.8
-
60
-
-
0037226692
-
Genetic diversity and spoilage potentials among Pseudomonas spp. Isolated from fluid milk products and dairy processing plants
-
Dogan B, Boor KJ. 2003. Genetic diversity and spoilage potentials among Pseudomonas spp. isolated from fluid milk products and dairy processing plants. Appl Environ Microbiol 69:130–138. http://dx.doi.org/10.1128/AEM.69.1.130-138.2003.
-
(2003)
Appl Environ Microbiol
, vol.69
, pp. 130-138
-
-
Dogan, B.1
Boor, K.J.2
-
61
-
-
0036206279
-
Inducible gene expression by nonculturable bacteria in milk after pasteurization
-
Gunasekera TS, Sørensen A, Attfield PV, Sørensen SJ, Veal DA. 2002. Inducible gene expression by nonculturable bacteria in milk after pasteurization. Appl Environ Microbiol 68:1988–1993. http://dx.doi.org/10.1128/AEM.68.4.1988-1993.2002.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 1988-1993
-
-
Gunasekera, T.S.1
Sørensen, A.2
Attfield, P.V.3
Sørensen, S.J.4
Veal, D.A.5
-
62
-
-
84862988254
-
Characterization of contaminants from a sanitized milk processing plant
-
Cleto S, Matos S, Kluskens L, Vieira MJ. 2012. Characterization of contaminants from a sanitized milk processing plant. PLoS One 7:e40189. http://dx.doi.org/10.1371/journal.pone.0040189.
-
(2012)
Plos One
, vol.7
-
-
Cleto, S.1
Matos, S.2
Kluskens, L.3
Vieira, M.J.4
-
63
-
-
0037226692
-
Genetic diversity and spoilage potentials among Pseudomonas spp. Isolated from fluid milk products and dairy processing plants
-
Dogan B, Boor KJ. 2003. Genetic diversity and spoilage potentials among Pseudomonas spp. isolated from fluid milk products and dairy processing plants. Appl Environ Microbiol 69:130–138. http://dx.doi.org/10.1128/AEM.69.1.130-138.2003.
-
(2003)
Appl Environ Microbiol
, vol.69
, pp. 130-138
-
-
Dogan, B.1
Boor, K.J.2
-
64
-
-
84855469896
-
The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (QRT)-PCR
-
Masoud W, Vogensen FK, Lillevang S, Abu Al-Soud W, Sørensen SJ, Jakobsen M. 2012. The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR. Int J Food Microbiol 153:192–202. http://dx.doi.org/10.1016/j.ijfoodmicro.2011.11.014.
-
(2012)
Int J Food Microbiol
, vol.153
, pp. 192-202
-
-
Masoud, W.1
Vogensen, F.K.2
Lillevang, S.3
Abu Al-Soud, W.4
Sørensen, S.J.5
Jakobsen, M.6
-
65
-
-
84951764136
-
Evaluation of bacterial contamination in raw milk, ultra-high temperature milk and infant formula using single molecule, real-time sequencing technology
-
Hou Q, Xu H, Zheng Y, Xi X, Kwok LY, Sun Z, Zhang H, Zhang W. 2015. Evaluation of bacterial contamination in raw milk, ultra-high temperature milk and infant formula using single molecule, real-time sequencing technology. J Dairy Sci 98:8464–8472. http://dx.doi.org/10.3168/jds.2015-9886.
-
(2015)
J Dairy Sci
, vol.98
, pp. 8464-8472
-
-
Hou, Q.1
Xu, H.2
Zheng, Y.3
Xi, X.4
Kwok, L.Y.5
Sun, Z.6
Zhang, H.7
Zhang, W.8
-
66
-
-
84857060110
-
Heat resistance of thermoduric enterococci isolated from milk
-
McAuley CM, Gobius KS, Britz ML, Craven HM. 2012. Heat resistance of thermoduric enterococci isolated from milk. Int J Food Microbiol 154: 162–168. http://dx.doi.org/10.1016/j.ijfoodmicro.2011.12.033.
-
(2012)
Int J Food Microbiol
, vol.154
, pp. 162-168
-
-
McAuley, C.M.1
Gobius, K.S.2
Britz, M.L.3
Craven, H.M.4
-
67
-
-
0036301208
-
Source of enterococci in a farmhouse raw-milk cheese
-
Gelsomino R, Vancanneyt M, Cogan TM, Condon S, Swings J. 2002. Source of enterococci in a farmhouse raw-milk cheese. Appl Environ Microbiol 68:3560–3565. http://dx.doi.org/10.1128/AEM.68.7.3560-3565.2002.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 3560-3565
-
-
Gelsomino, R.1
Vancanneyt, M.2
Cogan, T.M.3
Condon, S.4
Swings, J.5
-
68
-
-
84954086914
-
Microbiological and chemical aspects of Cheddar cheese ripening. A review
-
Marth EH. 1963. Microbiological and chemical aspects of Cheddar cheese ripening. A review. J Dairy Sci 46:869–890. http://dx.doi.org/10.3168/jds.S0022-0302(63)89174-2.
-
(1963)
J Dairy Sci
, vol.46
, pp. 869-890
-
-
Marth, E.H.1
-
69
-
-
77954083280
-
Non-starter lactic acid bacteria used to improve cheese quality and provide health benefits
-
Settanni L, Moschetti G. 2010. Non-starter lactic acid bacteria used to improve cheese quality and provide health benefits. Food Microbiol 27: 691–697. http://dx.doi.org/10.1016/j.fm.2010.05.023.
-
(2010)
Food Microbiol
, vol.27
, pp. 691-697
-
-
Settanni, L.1
Moschetti, G.2
-
70
-
-
54249166516
-
Biodiversity and technological potential of wild lactic acid bacteria from raw cows’ milk
-
Franciosi E, Settanni L, Cavazza A, Poznanski E. 2009. Biodiversity and technological potential of wild lactic acid bacteria from raw cows’ milk. Int Dairy J 19:3–11. http://dx.doi.org/10.1016/j.idairyj.2008.07.008.
-
(2009)
Int Dairy J
, vol.19
, pp. 3-11
-
-
Franciosi, E.1
Settanni, L.2
Cavazza, A.3
Poznanski, E.4
-
71
-
-
79952004315
-
Molecular analysis of bacterial communities in raw cow milk and the impact of refrigeration on its structure and dynamics
-
Raats D, Offek M, Minz D, Halpern M. 2011. Molecular analysis of bacterial communities in raw cow milk and the impact of refrigeration on its structure and dynamics. Food Microbiol 28:465–471. http://dx.doi.org/10.1016/j.fm.2010.10.009.
-
(2011)
Food Microbiol
, vol.28
, pp. 465-471
-
-
Raats, D.1
Offek, M.2
Minz, D.3
Halpern, M.4
-
72
-
-
84907560784
-
Psychrotrophic lactic acid bacteria associated with production batch recalls and sporadic cases of early spoilage in Belgium between 2010 and 2014
-
Pothakos V, Taminiau B, Huys G, Nezer C, Daube G, Devlieghere F. 2014. Psychrotrophic lactic acid bacteria associated with production batch recalls and sporadic cases of early spoilage in Belgium between 2010 and 2014. Int J Food Microbiol 191:157–163. http://dx.doi.org/10.1016/j.ijfoodmicro.2014.09.013.
-
(2014)
Int J Food Microbiol
, vol.191
, pp. 157-163
-
-
Pothakos, V.1
Taminiau, B.2
Huys, G.3
Nezer, C.4
Daube, G.5
Devlieghere, F.6
-
73
-
-
36649016035
-
Culturable psychrotrophic bacterial communities in raw milk and their proteolytic and lipolytic traits
-
Hantsis-Zacharov E, Halpern M. 2007. Culturable psychrotrophic bacterial communities in raw milk and their proteolytic and lipolytic traits. Appl Environ Microbiol 73:7162–7168. http://dx.doi.org/10.1128/AEM.00866-07.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 7162-7168
-
-
Hantsis-Zacharov, E.1
Halpern, M.2
-
74
-
-
33646585117
-
Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut
-
Belenguer A, Duncan SH, Calder AG, Holtrop G, Louis P, Lobley GE, Flint HJ. 2006. Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl Environ Microbiol 72:3593–3599. http://dx.doi.org/10.1128/AEM.72.5.3593-3599.2006.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 3593-3599
-
-
Belenguer, A.1
Duncan, S.H.2
Calder, A.G.3
Holtrop, G.4
Louis, P.5
Lobley, G.E.6
Flint, H.J.7
-
75
-
-
84860483735
-
Nextgeneration sequencing reveals significant bacterial diversity of botrytized wine
-
Bokulich NA, Joseph CM, Allen G, Benson AK, Mills DA. 2012. Nextgeneration sequencing reveals significant bacterial diversity of botrytized wine. PLoS One 7: e36357. http://dx.doi.org/10.1371/journal.pone.0036357.
-
(2012)
Plos One
, vol.7
-
-
Bokulich, N.A.1
Joseph, C.M.2
Allen, G.3
Benson, A.K.4
Mills, D.A.5
-
76
-
-
84906489089
-
Analysis of raw goat milk microbiota: Impact of stage of lactation and lysozyme on microbial diversity
-
McInnis EA, Kalanetra KM, Mills DA, Maga EA. 2015. Analysis of raw goat milk microbiota: impact of stage of lactation and lysozyme on microbial diversity. Food Microbiol 46:121–131. http://dx.doi.org/10.1016/j.fm.2014.07.021.
-
(2015)
Food Microbiol
, vol.46
, pp. 121-131
-
-
McInnis, E.A.1
Kalanetra, K.M.2
Mills, D.A.3
Maga, E.A.4
-
77
-
-
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, Tumbaugh 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
Tumbaugh, P.J.22
Walters, W.A.23
Widmann, J.24
Yatsunenko, T.25
Zaneveld, J.26
Knight, R.27
more..
-
79
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194–2200. http://dx.doi.org/10.1093/bioinformatics/btr381.
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
80
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. http://dx.doi.org/10.1093/bioinformatics/btq461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
81
-
-
33746061683
-
Greengenes, a chimerachecked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. 2006. Greengenes, a chimerachecked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072. http://dx.doi.org/10.1128/AEM.03006-05.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5069-5072
-
-
Desantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Ersen, G.L.10
-
82
-
-
75249107844
-
PyNAST: A flexible tool for aligning sequences to a template alignment
-
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. 2010. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266–267. http://dx.doi.org/10.1093/bioinformatics/btp636.
-
(2010)
Bioinformatics
, vol.26
, pp. 266-267
-
-
Caporaso, J.G.1
Bittinger, K.2
Bushman, F.D.3
Desantis, T.Z.4
Ersen, G.L.5
Knight, R.6
-
83
-
-
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
Ersen, G.L.7
Knight, R.8
Hugenholtz, P.9
-
84
-
-
84355166737
-
Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys
-
Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE. 2012. Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys. ISME J 6:94–103. http://dx.doi.org/10.1038/ismej.2011.82.
-
(2012)
ISME J
, vol.6
, pp. 94-103
-
-
Werner, J.J.1
Koren, O.2
Hugenholtz, P.3
Desantis, T.Z.4
Walters, W.A.5
Caporaso, J.G.6
Angenent, L.T.7
Knight, R.8
Ley, R.E.9
-
85
-
-
84871979584
-
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
-
Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10:57–U11. http://dx.doi.org/10.1038/nmeth.2276.
-
(2013)
Nat Methods
, vol.10
, pp. U11-U57
-
-
Bokulich, N.A.1
Subramanian, S.2
Faith, J.J.3
Gevers, D.4
Gordon, J.I.5
Knight, R.6
Mills, D.A.7
Caporaso, J.G.8
-
86
-
-
84859098571
-
The sva package for removing batch effects and other unwanted variation in highthroughput experiments
-
Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. 2012. The sva package for removing batch effects and other unwanted variation in highthroughput experiments. Bioinformatics 28:882–883. http://dx.doi.org/10.1093/bioinformatics/bts034.
-
(2012)
Bioinformatics
, vol.28
, pp. 882-883
-
-
Leek, J.T.1
Johnson, W.E.2
Parker, H.S.3
Jaffe, A.E.4
Storey, J.D.5
-
87
-
-
33845432928
-
Adjusting batch effects in microarray expression data using empirical Bayes methods
-
Johnson WE, Li C, Rabinovic A. 2007. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8:118–127. http://dx.doi.org/10.1093/biostatistics/kxj037.
-
(2007)
Biostatistics
, vol.8
, pp. 118-127
-
-
Johnson, W.E.1
Li, C.2
Rabinovic, A.3
-
88
-
-
84966910278
-
Vegan: Community ecology package
-
Jari Oksanen FGB, Kindt R, Legendre P, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Henry M, Stevens H, Wagner H. 2015. vegan: community ecology package. R package version 2.3-0. https://cran.rproject.org/web/packages/vegan/index.html.
-
(2015)
R Package Version 2.3-0
-
-
Jari Oksanen, F.1
Kindt, R.2
Legendre, P.3
Minchin, P.R.4
O’Hara, R.B.5
Simpson, G.L.6
Solymos, P.7
Henry, M.8
Stevens, H.9
Wagner, H.10
-
89
-
-
84955281361
-
Estimating diversity via frequency ratios
-
Willis A, Bunge J. 2015. Estimating diversity via frequency ratios. Biometrics 71:1042–1049 http://dx.doi.org/10.1111/biom.12332.
-
(2015)
Biometrics
, vol.71
, pp. 1042-1049
-
-
Willis, A.1
Bunge, J.2
-
90
-
-
84866549438
-
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
-
Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C. 2012. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 13:R79. http://dx.doi.org/10.1186/gb-2012-13-9-r79.
-
(2012)
Genome Biol
, vol.13
, pp. 79
-
-
Morgan, X.C.1
Tickle, T.L.2
Sokol, H.3
Gevers, D.4
Devaney, K.L.5
Ward, D.V.6
Reyes, J.A.7
Shah, S.A.8
Leleiko, N.9
Snapper, S.B.10
Bousvaros, A.11
Korzenik, J.12
Sands, B.E.13
Xavier, R.J.14
Huttenhower, C.15
-
91
-
-
84938612863
-
Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease
-
Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C. 2015. Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol 16:67. http://dx.doi.org/10.1186/s13059-015-0637-x.
-
(2015)
Genome Biol
, vol.16
, pp. 67
-
-
Morgan, X.C.1
Kabakchiev, B.2
Waldron, L.3
Tyler, A.D.4
Tickle, T.L.5
Milgrom, R.6
Stempak, J.M.7
Gevers, D.8
Xavier, R.J.9
Silverberg, M.S.10
Huttenhower, C.11
-
92
-
-
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. http://dx.doi.org/10.1186/gb-2011-12-6-r60.
-
(2011)
Genome Biol
, vol.12
-
-
Segata, N.1
Izard, J.2
Waldron, L.3
Gevers, D.4
Miropolsky, L.5
Garrett, W.S.6
Huttenhower, C.7
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