Extraction and Amplification

What are the microbiome biases created by using different nucleic acid extraction or amplification methods? How do technical parameters such as beadbeating, choice of primers, PCR cycle number etc change the ratio of microbial taxa in the analyzed community?  Also see my pages on Sample Storage and Contamination Issues.

Created August 2016, updated September 2016.

Inspired by this post: The unbearable madness of microbiome – Mick Watson – Opiniomics

General papers (addressing multiple technical issues)

Considerations for optimizing microbiome analysis using a marker gene –  Jacobo de la Cuesta-Zuluaga – Frontiers in Nutrition – August 2016

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies – Daryl M Gohl – Nature Biotechnology – July 2016

DNA extraction methods 

A method for assessing efficiency of bacterial cell disruption and DNA release – Olle M. de Bruin – BMC Microbiology – August 2016

Bead-beating artefacts in the Bacteroidetes to Firmicutes ratio of the human stool metagenome – Heidi C. Vebø – Journal of Microbiological Methods – August 2016

The effect of DNA extraction methodology on gut microbiota research applications – Konstantinos Gerasimidis – BMC Research Notes – July 2016

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition – Berith E Knudsen – bioRxiv – July 2016

High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy – Yuichiro Nishimoto – Gut – June 2016

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice – Alan W. Walker – Microbiome – June 2016

16S rRNA gene primer pairs

Choice of molecular barcode will affect species prevalence but not bacterial community composition – Karen Lebret – Marine Genomics – September 2016

Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs – Martin A. Fischer – Frontiers in Microbiology – August 2016

Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys – William Walters – mSystems – December 2015

18S / ITS primer pairs (fungi and other eukaryotes)

Fungal identification biases in microbiome projects – Leho Tedersoo – Environmental Microbiology Reports – July 2016

New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA – Asma Asemaninejad – PLOS ONE – July 2016

Microbial community assembly and metabolic function during mammalian corpse decomposition – Jessica L. Metcalf – Science – January 2016

Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys – William Walters – mSystems – December 2015

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide – Suzanne M. Prober – Ecology Letters – November 2014

Meeting Report: Fungal ITS Workshop (October 2012) – Scott T. Bates – Standards in Genomic Sciences – April 2013

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi – Conrad L. Schoch – PNAS – March 2012

 

Sequencing platform

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates – Victor Kunin – Environmental Microbiology  – August 2009