Recognizing the reagent microbiome

被引:232
作者
de Goffau, Marcus C. [1 ]
Lager, Susanne [2 ,3 ]
Salter, Susannah J. [1 ]
Wagner, Josef [1 ]
Kronbichler, Andreas [4 ,5 ]
Charnock-Jones, D. Stephen [2 ,3 ]
Peacock, Sharon J. [1 ,6 ,7 ]
Smith, Gordon C. S. [2 ,3 ]
Parkhill, Julian [1 ]
机构
[1] Wellcome Sanger Inst, Cambridge, England
[2] Univ Cambridge, NIHR Cambridge Comprehens Biomed Res Ctr, Dept Obstet & Gynaecol, Cambridge, England
[3] Univ Cambridge, Dept Physiol Dev & Neurosci, CTR, Cambridge, England
[4] Med Univ Innsbruck, Dept Internal Med Nephrol & Hypertens 4, Innsbruck, Austria
[5] Addenbrookes Hosp, Vasculitis & Lupus Clin, Cambridge, England
[6] Univ Cambridge, Dept Med, Cambridge, England
[7] London Sch Hyg & Trop Med, London, England
来源
NATURE MICROBIOLOGY | 2018年 / 3卷 / 08期
基金
英国医学研究理事会;
关键词
DIVERSITY; SEQUENCE;
D O I
10.1038/s41564-018-0202-y
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
A noticeable part of the microbiome literature, especially that working with low-biomass samples, is plagued by reagent contamination. Here we describe visual, statistical, methodical and ecological techniques to facilitate recognition of signals that represent contamination.
引用
收藏
页码:851 / 853
页数:3
相关论文
共 19 条
[1]   The Placenta Harbors a Unique Microbiome [J].
Aagaard, Kjersti ;
Ma, Jun ;
Antony, Kathleen M. ;
Ganu, Radhika ;
Petrosino, Joseph ;
Versalovic, James .
SCIENCE TRANSLATIONAL MEDICINE, 2014, 6 (237)
[2]   Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis [J].
Branton, W. G. ;
Lu, J. Q. ;
Surette, M. G. ;
Holt, R. A. ;
Lind, J. ;
Laman, J. D. ;
Power, C. .
SCIENTIFIC REPORTS, 2016, 6
[3]   Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data [J].
Davis, Nicole M. ;
Proctor, Diana M. ;
Holmes, Susan P. ;
Relman, David A. ;
Callahan, Benjamin J. .
MICROBIOME, 2018, 6
[4]   Bacterial pleomorphism and competition in a relative humidity gradient [J].
de Goffau, Marcus C. ;
Yang, Xiaomei ;
van Dijl, Jan Maarten ;
Harmsen, Hermie J. M. .
ENVIRONMENTAL MICROBIOLOGY, 2009, 11 (04) :809-822
[5]   Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data [J].
Eren, A. Murat ;
Maignien, Lois ;
Sul, Woo Jun ;
Murphy, Leslie G. ;
Grim, Sharon L. ;
Morrison, Hilary G. ;
Sogin, Mitchell L. .
METHODS IN ECOLOGY AND EVOLUTION, 2013, 4 (12) :1111-1119
[6]   Topographical and Temporal Diversity of the Human Skin Microbiome [J].
Grice, Elizabeth A. ;
Kong, Heidi H. ;
Conlan, Sean ;
Deming, Clayton B. ;
Davis, Joie ;
Young, Alice C. ;
Bouffard, Gerard G. ;
Blakesley, Robert W. ;
Murray, Patrick R. ;
Green, Eric D. ;
Turner, Maria L. ;
Segre, Julia A. .
SCIENCE, 2009, 324 (5931) :1190-1192
[7]   Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes [J].
Hain, Torsten ;
Steinweg, Christiane ;
Kuenne, Carsten Tobias ;
Billion, Andre ;
Ghai, Rohit ;
Chatterjee, Som Subhra ;
Domann, Eugen ;
Kaerst, Uwe ;
Goesmann, Alexander ;
Bekel, Thomas ;
Bartels, Daniela ;
Kaiser, Olaf ;
Meyer, Folker ;
Puehler, Alfred ;
Weisshaar, Bernd ;
Wehland, Juergen ;
Liang, Chunguang ;
Dandekar, Thomas ;
Lampidis, Robert ;
Kreft, Juergen ;
Goebel, Werner ;
Chakraborty, Trinad .
JOURNAL OF BACTERIOLOGY, 2006, 188 (21) :7405-7415
[8]   A Necrotizing Enterocolitis-Associated Gut Microbiota Is Present in the Meconium: Results of a Prospective Study [J].
Heida, Fardou H. ;
van Zoonen, Anne G. J. F. ;
Hulscher, Jan B. F. ;
te Kiefte, Bastiaan J. C. ;
Wessels, Rianne ;
Kooi, Elisabeth M. W. ;
Bos, Arend F. ;
Harmsen, Hermie J. M. ;
de Goffau, Marcus C. .
CLINICAL INFECTIOUS DISEASES, 2016, 62 (07) :863-870
[9]   Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data [J].
Jervis-Bardy, Jake ;
Leong, Lex E. X. ;
Marri, Shashikanth ;
Smith, Renee J. ;
Choo, Jocelyn M. ;
Smith-Vaughan, Heidi C. ;
Nosworthy, Elizabeth ;
Morris, Peter S. ;
O'Leary, Stephen ;
Rogers, Geraint B. ;
Marsh, Robyn L. .
MICROBIOME, 2015, 3
[10]   Assessment of bacterial diversity in breast milk using culture-dependent and culture-independent approaches [J].
Jost, Ted ;
Lacroix, Christophe ;
Braegger, Christian ;
Chassard, Christophe .
BRITISH JOURNAL OF NUTRITION, 2013, 110 (07) :1253-1262