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Items: 1 to 20 of 211

1.

Ironing out the wrinkles in the rare biosphere through improved OTU clustering.

Huse SM, Welch DM, Morrison HG, Sogin ML.

Environ Microbiol. 2010 Jul;12(7):1889-98. doi: 10.1111/j.1462-2920.2010.02193.x. Epub 2010 Mar 11.

2.

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.

Kunin V, Engelbrektson A, Ochman H, Hugenholtz P.

Environ Microbiol. 2010 Jan;12(1):118-23. doi: 10.1111/j.1462-2920.2009.02051.x. Epub 2009 Aug 27.

PMID:
19725865
3.

Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis.

Schloss PD, Westcott SL.

Appl Environ Microbiol. 2011 May;77(10):3219-26. doi: 10.1128/AEM.02810-10. Epub 2011 Mar 18.

4.
5.

A new methodology combining PCR, cloning, and sequencing of clones discriminated by RFLP for the study of microbial populations: application to an UASB reactor sample.

Ramos CG, Grilo AM, Sousa SA, Barbosa ML, Nadais H, Leitão JH.

Appl Microbiol Biotechnol. 2010 Jan;85(3):801-6. doi: 10.1007/s00253-009-2268-1.

PMID:
19844706
6.

Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation.

Leloup J, Fossing H, Kohls K, Holmkvist L, Borowski C, Jørgensen BB.

Environ Microbiol. 2009 May;11(5):1278-91. doi: 10.1111/j.1462-2920.2008.01855.x. Epub 2009 Feb 10.

PMID:
19220398
7.

Acinetobacter diversity in environmental samples assessed by 16S rRNA gene PCR-DGGE fingerprinting.

Vanbroekhoven K, Ryngaert A, Wattiau P, Mot R, Springael D.

FEMS Microbiol Ecol. 2004 Oct 1;50(1):37-50. doi: 10.1016/j.femsec.2004.05.007.

8.

Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere.

Jumpponen A, Jones KL.

New Phytol. 2009 Oct;184(2):438-48. doi: 10.1111/j.1469-8137.2009.02990.x. Epub 2009 Aug 11.

9.

Monitoring the impact of hydrocarbon contamination and nutrient addition on microbial density, activity, and diversity in soil.

Taok M, Mundo J, Sarde CO, Schoefs O, Cochet N.

Can J Microbiol. 2010 Feb;56(2):145-55. doi: 10.1139/w09-119.

PMID:
20237576
10.

Bacterial diversity at different depths in lead-zinc mine tailings as revealed by 16S rRNA gene libraries.

Zhang HB, Shi W, Yang MX, Sha T, Zhao ZW.

J Microbiol. 2007 Dec;45(6):479-84.

11.

Diversity analysis of magnetotactic bacteria in Lake Miyun, northern China, by restriction fragment length polymorphism.

Lin W, Li J, Schüler D, Jogler C, Pan Y.

Syst Appl Microbiol. 2009 Aug;32(5):342-50. doi: 10.1016/j.syapm.2008.10.005. Epub 2009 Jan 24.

PMID:
19168303
12.

A comparison of methods for clustering 16S rRNA sequences into OTUs.

Chen W, Zhang CK, Cheng Y, Zhang S, Zhao H.

PLoS One. 2013 Aug 13;8(8):e70837. doi: 10.1371/journal.pone.0070837. eCollection 2013.

13.

Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data.

Koskinen K, Auvinen P, Björkroth KJ, Hultman J.

J Comput Biol. 2015 Aug;22(8):743-51. doi: 10.1089/cmb.2014.0268. Epub 2014 Dec 19.

PMID:
25525895
14.

bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences.

Chen SY, Deng F, Huang Y, Jia X, Liu YP, Lai SJ.

J Comput Biol. 2016 Apr;23(4):229-38. doi: 10.1089/cmb.2015.0214. Epub 2016 Mar 7.

PMID:
26950196
15.

Bacteriophage predation regulates microbial abundance and diversity in a full-scale bioreactor treating industrial wastewater.

Shapiro OH, Kushmaro A, Brenner A.

ISME J. 2010 Mar;4(3):327-36. doi: 10.1038/ismej.2009.118. Epub 2009 Nov 19.

PMID:
19924159
17.

Prokaryotic diversity in continuous cropping and rotational cropping soybean soil.

Tang H, Xiao C, Ma J, Yu M, Li Y, Wang G, Zhang L.

FEMS Microbiol Lett. 2009 Sep;298(2):267-73. doi: 10.1111/j.1574-6968.2009.01730.x. Epub 2009 Jul 16.

18.

Assessment of microbial communities by graph partitioning in a study of soil fungi in two Alpine meadows.

Zinger L, Coissac E, Choler P, Geremia RA.

Appl Environ Microbiol. 2009 Sep;75(18):5863-70. doi: 10.1128/AEM.00748-09. Epub 2009 Jul 17.

19.

Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes.

Eiler A, Bertilsson S.

Environ Microbiol. 2004 Dec;6(12):1228-43. Erratum in: Environ Microbiol. 2007 Mar;9(3):838.

PMID:
15560821
20.

Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR.

Lazarevic V, Gaïa N, Girard M, Schrenzel J.

BMC Microbiol. 2016 Apr 23;16:73. doi: 10.1186/s12866-016-0689-4.

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