SCOPUS 정보 검색 플랫폼

Volumn 1, Issue 3, 2016, Pages

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

(7) Song, Se Jin a,b Amir, Amnon a Metcalf, Jessica L a,b Amato, Katherine R c Xu, Zhenjiang Zech a Humphrey, Greg a Knight, Rob a,d

a UNIVERSITY OF CALIFORNIA SAN DIEGO (United States)

b UNIVERSITY OF COLORADO (United States)

c NORTHWESTERN UNIVERSITY (United States)

d UNIVERSITY OF CALIFORNIA (United States)

Author keywords

DNA stability; Fecal microbiome; Sample storage

Indexed keywords

EID: 84982224114 PISSN: None EISSN: 23795077 Source Type: Journal
DOI: 10.1128/mSystems.00021-16 Document Type: Article

Times cited : (349)

References (22)

1
- 46249085739
- Evolution of mammals and their gut microbes
- Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI. 2008. Evolution of mammals and their gut microbes. Science 320:1647-1651. http://dx.doi.org/10.1126/science.1155725.
- (2008) Science , vol.320 , pp. 1647-1651
- Ley, R.E.¹ Hamady, M.² Lozupone, C.³ Turnbaugh, P.J.⁴ Ramey, R.R.⁵ Bircher, J.S.⁶ Schlegel, M.L.⁷ Tucker, T.A.⁸ Schrenzel, M.D.⁹ Knight, R.¹⁰ Gordon, J.I.¹¹

2
- 79956301905
- Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans
- Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI. 2011. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332:970-974. http://dx.doi.org/10.1126/science.1198719.
- (2011) Science , vol.332 , pp. 970-974
- Muegge, B.D.¹ Kuczynski, J.² Knights, D.³ Clemente, J.C.⁴ González, A.⁵ Fontana, L.⁶ Henrissat, B.⁷ Knight, R.⁸ Gordon, J.I.⁹

3
- 84896339094
- Convergence of gut microbiomes in myrmecophagous mammals
- Delsuc F, Metcalf JL, Wegener Parfrey L, Song SJ, González A, Knight R. 2014. Convergence of gut microbiomes in myrmecophagous mammals. Mol Ecol 23:1301-1317. http://dx.doi.org/10.1111/mec.12501.
- (2014) Mol Ecol , vol.23 , pp. 1301-1317
- Delsuc, F.¹ Metcalf, J.L.² Wegener Parfrey, L.³ Song, S.J.⁴ González, A.⁵ Knight, R.⁶

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. http:// dx.doi.org/10.1038/nature11234.
- (2012) Nature , vol.486 , pp. 207-214

5
- 84996584385
- The microbiome of uncontacted Amerindians
- Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcon O, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG. 2015. The microbiome of uncontacted Amerindians. Sci Adv 1:e1500183. http://dx.doi.org/10.1126/sciadv.1500183.
- (2015) Sci Adv , vol.1 , pp. e1500183
- Clemente, J.C.¹ Pehrsson, E.C.² Blaser, M.J.³ Sandhu, K.⁴ Gao, Z.⁵ Wang, B.⁶ Magris, M.⁷ Hidalgo, G.⁸ Contreras, M.⁹ Noya-Alarcon, O.¹⁰ Lander, O.¹¹ McDonald, J.¹² Cox, M.¹³ Walter, J.¹⁴ Oh, P.L.¹⁵ Ruiz, J.F.¹⁶ Rodriguez, S.¹⁷ Shen, N.¹⁸ Song, S.J.¹⁹ Metcalf, J.²⁰ more..

6
- 84941805672
- Shifts in the gut microbiome observed in wildlife faecal samples exposed to natural weather conditions: Lessons from time-series analyses using next-generation sequencing for application in field studies
- Menke S, Meier M, Sommer S. 2015. Shifts in the gut microbiome observed in wildlife faecal samples exposed to natural weather conditions: lessons from time-series analyses using next-generation sequencing for application in field studies. Methods Ecol Evol 6:1080-1087. http://dx.doi.org/10.1111/2041-210X.12394.
- (2015) Methods Ecol Evol , vol.6 , pp. 1080-1087
- Menke, S.¹ Meier, M.² Sommer, S.³

7
- 77951941062
- Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples
- Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N. 2010. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett 307:80-86. http://dx.doi.org/10.1111/j.1574-6968.2010.01965.x.
- (2010) FEMS Microbiol Lett , vol.307 , pp. 80-86
- Lauber, C.L.¹ Zhou, N.² Gordon, J.I.³ Knight, R.⁴ Fierer, N.⁵

8
- 84940374269
- Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota
- Hammer TJ, Dickerson JC, Fierer N. 2015. Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota. PeerJ 3:e1190. http://dx.doi.org/10.7717/peerj.1190.
- (2015) PeerJ , vol.3 , pp. e1190
- Hammer, T.J.¹ Dickerson, J.C.² Fierer, N.³

9
- 84899898655
- Comparison of methods for fecal microbiome biospecimen collection
- Dominianni C, Wu J, Hayes RB, Ahn J. 2014. Comparison of methods for fecal microbiome biospecimen collection. BMC Microbiol 14:103. http://dx.doi.org/10.1186/1471-2180-14-103.
- (2014) BMC Microbiol , vol.14 , pp. 103
- Dominianni, C.¹ Wu, J.² Hayes, R.B.³ Ahn, J.⁴

10
- 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. http://dx.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

11
- 84957831145
- Collecting fecal samples for microbiome analyses in epidemiology studies
- Sinha R, Chen J, Amir A, Vogtmann E, Shi J, Inman KS, Flores-Munguia R, Sampson J, Knight R, Chia N. 2016. Collecting fecal samples for microbiome analyses in epidemiology studies. Cancer Epi-demiol Biomarkers Prev 25:407-416. http://dx.doi.org/10.1158/1055-9965.EPI-15-0951.
- (2016) Cancer Epi-Demiol Biomarkers Prev , vol.25 , pp. 407-416
- Sinha, R.¹ Chen, J.² Amir, A.³ Vogtmann, E.⁴ Shi, J.⁵ Inman, K.S.⁶ Flores-Munguia, R.⁷ Sampson, J.⁸ Knight, R.⁹ Chia, N.¹⁰

12
- 84936951148
- Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks
- Hale VL, Tan CL, Knight R, Amato KR. 2015. Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks. J Microbiol Methods 113:16-26. http://dx.doi.org/10.1016/j.mimet.2015.03.021.
- (2015) J Microbiol Methods , vol.113 , pp. 16-26
- Hale, V.L.¹ Tan, C.L.² Knight, R.³ Amato, K.R.⁴

13
- 2642551732
- Recommendations on the use of alcohols for preservation of ant specimens (Hymenoptera, Formicidae)
- King JR, Porter SD. 2004. Recommendations on the use of alcohols for preservation of ant specimens (Hymenoptera, Formicidae). Insectes Soc 51:197-202. http://dx.doi.org/10.1007/s00040-003-0709-x.
- (2004) Insectes Soc , vol.51 , pp. 197-202
- King, J.R.¹ Porter, S.D.²

14
- 84864828841
- Evaluation of different storage methods to characterize the fecal bacterial communities of captive western lowland gorillas (Gorilla gorilla gorilla)
- Vlcková K, Mrázek J, Kopecný J, Petrželková KJ. 2012. Evaluation of different storage methods to characterize the fecal bacterial communities of captive western lowland gorillas (Gorilla gorilla gorilla). J Microbiol Methods 91:45-51. http://dx.doi.org/10.1016/j.mimet.2012.07.015.
- (2012) J Microbiol Methods , vol.91 , pp. 45-51
- Vlcková, K.¹ Mrázek, J.² Kopecný, J.³ Petrželková, K.J.⁴

15
- 84858709310
- Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis
- Bahl MI, Bergström A, Licht TR. 2012. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett 329: 193-197. http://dx.doi.org/10.1111/j.1574-6968.2012.02523.x.
- (2012) FEMS Microbiol Lett , vol.329 , pp. 193-197
- Bahl, M.I.¹ Bergström, A.² Licht, T.R.³

16
- 84929119983
- The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations
- Fouhy F, Deane J, Rea MC, O’Sullivan Ó, Ross RP, O’Callaghan G, Plant BJ, Stanton C. 2015. The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations. PLoS One 10:e0119355. http://dx.doi.org/10.1371/journal.pone.0119355.
- (2015) PLoS One , vol.10 , pp. e0119355
- Fouhy, F.¹ Deane, J.² Rea, M.C.³ O’Sullivan, Ó.⁴ Ross, R.P.⁵ O’Callaghan, G.⁶ Plant, B.J.⁷ Stanton, C.⁸

17
- 84947460747
- Sample storage conditions significantly influence faecal microbiome profiles
- Choo JM, Leong LE, Rogers GB. 2015. Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep 5:16350. http://dx.doi.org/10.1038/srep16350.
- (2015) Sci Rep , vol.5 , pp. 16350
- Choo, J.M.¹ Leong, L.E.² Rogers, G.B.³

18
- 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 more..

19
- 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

20
- 33947269742
- Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities
- Lozupone CA, Hamady M, Kelley ST, Knight R. 2007. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-1585. http://dx.doi.org/10.1128/AEM.01996-06.
- (2007) Appl Environ Microbiol , vol.73 , pp. 1576-1585
- Lozupone, C.A.¹ Hamady, M.² Kelley, S.T.³ Knight, R.⁴

21
- 85041895226
- Okansen J, Blanchet FG, Kindt R, Legendre P, Minchen PR, O’Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H. 2015. vegan: community ecology package version 2.3-2. R Project for Statistical Computing. https://www.r-project.org/.
- (2015) Vegan: Community Ecology Package Version 2.3-2. R Project for Statistical Computing
- Okansen, J.¹ Blanchet, F.G.² Kindt, R.³ Legendre, P.⁴ Minchen, P.R.⁵ O’Hara, R.B.⁶ Simpson, G.L.⁷ Solymos, P.⁸ Stevens, M.H.H.⁹ Wagner, H.¹⁰

22
- 56249113343
- Building predictive models in R using the caret package
- Kuhn M. 2008. Building predictive models in R using the caret package. J Stat Softw 28:1-26.
- (2008) J Stat Softw , vol.28 , pp. 1-26
- Kuhn, M.¹

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.