Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Susannah J. Salter,Michael J. Cox,Elena M. Turek,Szymon T. Calus,William O.C.M. Cookson,Miriam F. Moffatt,Paul Turner,Paul Turner,Julian Parkhill,Nicholas J. Loman,Alan W. Walker,Alan W. Walker +11 more
TLDR
It is demonstrated that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass.Abstract:
The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised.read more
Citations
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A communal catalogue reveals Earth’s multiscale microbial diversity
Luke R. Thompson,Luke R. Thompson,Luke R. Thompson,Jon G. Sanders,Daniel McDonald,Amnon Amir,Joshua Ladau,Kenneth J. Locey,Robert J. Prill,Anupriya Tripathi,Sean M. Gibbons,Sean M. Gibbons,Gail Ackermann,Jose A. Navas-Molina,Stefan Janssen,Evguenia Kopylova,Yoshiki Vázquez-Baeza,Antonio Gonzalez,James T. Morton,Siavash Mirarab,Zhenjiang Zech Xu,Lingjing Jiang,Mohamed F. Haroon,Jad N. Kanbar,Qiyun Zhu,Se Jin Song,Tomasz Kosciolek,Nicholas A. Bokulich,Joshua P Lefler,Colin J. Brislawn,Gregory Humphrey,Sarah M. Owens,Jarrad T. Hampton-Marcell,Jarrad T. Hampton-Marcell,Donna Berg-Lyons,Valerie J. McKenzie,Noah Fierer,Noah Fierer,Jed A. Fuhrman,Aaron Clauset,Rick Stevens,Rick Stevens,Ashley Shade,Katherine S. Pollard,Kelly D. Goodwin,Janet K. Jansson,Jack A. Gilbert,Jack A. Gilbert,Rob Knight +48 more
TL;DR: A meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project is presented, creating both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
Journal ArticleDOI
Interaction between microbiota and immunity in health and disease
TL;DR: In this paper, the authors review features of microbiome-immunity crosstalk and their roles in health and disease, while providing examples of molecular mechanisms orchestrating these interactions in the intestine and extra-intestinal organs.
Journal ArticleDOI
Normalization and microbial differential abundance strategies depend upon data characteristics
Sophie Weiss,Zhenjiang Zech Xu,Shyamal D. Peddada,Amnon Amir,Kyle Bittinger,Antonio Gonzalez,Catherine A. Lozupone,Jesse R. Zaneveld,Yoshiki Vázquez-Baeza,Amanda Birmingham,Embriette R. Hyde,Rob Knight +11 more
TL;DR: These findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study.
Journal ArticleDOI
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.
Nicole M Davis,Diana M. Proctor,Diana M. Proctor,Susan Holmes,David A. Relman,David A. Relman,Benjamin J. Callahan +6 more
TL;DR: The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants.
Journal ArticleDOI
The healthy human microbiome
TL;DR: Several definitions of a ‘healthy microbiome’ that have emerged are reviewed, the current understanding of the ranges of healthy microbial diversity, and gaps such as the characterization of molecular function and the development of ecological therapies to be addressed in the future are reviewed.
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