Comparison of DNA extraction methods for human gut microbial community profiling.

The human gut harbors a vast range of microbes that have significant impact on health and disease. Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development. Accurate profiling of the highly complex gut microbiome requires DNA extraction methods that provide sufficient coverage of the original community as well as adequate quality and quantity. We tested nine different DNA extraction methods using three commercial kits (TianLong Stool DNA/RNA Extraction Kit (TS), QIAamp DNA Stool Mini Kit (QS), and QIAamp PowerFecal DNA Kit (QP)) with or without additional bead-beating step using manual or automated methods and compared them in terms of DNA extraction ability from human fecal sample. All methods produced DNA in sufficient concentration and quality for use in sequencing, and the samples were clustered according to the DNA extraction method. Inclusion of bead-beating step especially resulted in higher degrees of microbial diversity and had the greatest effect on gut microbiome composition. Among the samples subjected to bead-beating method, TS kit samples were more similar to QP kit samples than QS kit samples. Our results emphasize the importance of mechanical disruption step for a more comprehensive profiling of the human gut microbiome.

[1]  Qiang Feng,et al.  A metagenome-wide association study of gut microbiota in type 2 diabetes , 2012, Nature.

[2]  Timothy L. Tickle,et al.  Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment , 2012, Genome Biology.

[3]  Hong-Wei Zhou,et al.  Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags. , 2013, Journal of microbiological methods.

[4]  J. Raes,et al.  Population-level analysis of gut microbiome variation , 2016, Science.

[5]  C. Manichanh,et al.  Processing faecal samples: a step forward for standards in microbial community analysis , 2014, BMC Microbiology.

[6]  A. Clooney,et al.  16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform , 2016, BMC Microbiology.

[7]  L. Lebrun,et al.  Method optimization for fecal sample collection and fecal DNA extraction. , 2015, Biopreservation and biobanking.

[8]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[9]  Morris A. Swertz,et al.  Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity , 2016, Science.

[10]  M. W. Taylor,et al.  Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences , 2015, Front. Microbiol..

[11]  Frank Møller Aarestrup,et al.  Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition , 2016 .

[12]  J. Raes.  Microbiome-based companion diagnostics: no longer science fiction? , 2016, Gut.

[13]  W. D. de Vos,et al.  Semi-automated extraction of microbial DNA from feces for qPCR and phylogenetic microarray analysis. , 2010, Journal of microbiological methods.

[14]  A. Klindworth,et al.  Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies , 2012, Nucleic acids research.

[15]  B. Roe,et al.  A core gut microbiome in obese and lean twins , 2008, Nature.

[16]  C. Lees,et al.  Explorer The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16 S rRNA Gene Sequencing , 2017 .

[17]  Angela C. Poole,et al.  Human Genetics Shape the Gut Microbiome , 2014, Cell.

[18]  T. Vatanen,et al.  The effect of host genetics on the gut microbiome , 2016, Nature Genetics.

[19]  Joshua N. Daly,et al.  Comparison of DNA Extraction Methods for Microbial Community Profiling with an Application to Pediatric Bronchoalveolar Lavage Samples , 2012, PloS one.

[20]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[21]  Janne Nikkilä,et al.  Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. , 2010, Journal of microbiological methods.

[22]  Jiajie Zhang,et al.  PEAR: a fast and accurate Illumina Paired-End reAd mergeR , 2013, Bioinform..

[23]  J. Ravel,et al.  Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome , 2012, PloS one.

[24]  Philip Abraham,et al.  An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples , 2016, Scientific Reports.

[25]  C. Huttenhower,et al.  Metagenomic biomarker discovery and explanation , 2011, Genome Biology.

[26]  Yun-Mi Song,et al.  The effect of heritability and host genetics on the gut microbiota and metabolic syndrome , 2016, Gut.

[27]  Mirjam Kooistra-Smid,et al.  Improved detection of microbial DNA after bead-beating before DNA isolation. , 2010, Journal of microbiological methods.

[28]  A. Paterson,et al.  Association of host genome with intestinal microbial composition in a large healthy cohort , 2016, Nature Genetics.

[29]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.