Abstract
A critical prerequisite for studying rumen microbial community by high throughput molecular biology methods is good quality community DNA. Current methods of extraction use kits designed for samples from the different origin for rumen. This puts stress on the development of a relevant manual method for DNA extraction. The objective of this study was to modify the existing methods of community DNA extraction and thereby systematic comparison of their efficiency based on DNA yield, purity, 16S rRNA gene sequencing, and identification to determine the optimal DNA extraction methods whose DNA products reflect targeted bacterial communities special to rumen. Enzymatic method, Chemical method, Enzymatic + Chemical method, and Enzymatic + Chemical + Physical method were modified toward evaluation of community DNA extraction from solid, squeezed, and liquid fractions of goat rumen digesta. Each method was assessed critically for nucleic acid yield and its quality. The methods resulting in high nucleic acid yield, optimal purity ratios with intact band on agarose gel electrophoresis were optimized further. Optimized methods were studied using standard polymerase chain reaction (PCR) with universal bacterial primers and 16S rRNA primers ...Continue Reading
References
Dec 1, 2000·Applied and Environmental Microbiology·R I GriffithsM J Bailey
May 26, 2001·Applied and Environmental Microbiology·K TajimaY Benno
Mar 13, 2003·Environmental Science & Technology·J R LeadK J Wilkinson
May 22, 2004·BioTechniques·Zhongtang Yu, Mark Morrison
Sep 3, 2004·BMC Biotechnology·Tae-Jin Kang, Moon-Sik Yang
Nov 30, 2007·Journal of Applied Microbiology·A V KlieveD Ouwerkerk
Jan 6, 2009·Journal of Applied Microbiology·E NettmannM Klocke
Jan 23, 2009·Current Microbiology·Seungha KangChris S McSweeney
Jun 11, 2009·Journal of Applied Microbiology·M LiL L Guan
Aug 4, 2010·Folia Microbiologica·M PopovaD P Morgavi
Aug 9, 2011·International Journal of Microbiology·Jill StiversonZhongtang Yu
Oct 28, 2011·FEMS Microbiology Letters·Konstantinos MinasKaren P Scott
Apr 25, 2012·Folia Microbiologica·Jaime A RoseroJan Kopečný
Jul 4, 2012·BMC Genetics·Elizabeth M RossBen J Hayes
Feb 22, 2013·The ISME Journal·Elie JamiItzhak Mizrahi
Sep 17, 2013·PloS One·Gemma HendersonPeter H Janssen
Oct 16, 2013·Anaerobe·Katerina FliegerovaR John Wallace
Jun 5, 2015·Frontiers in Microbiology·Mark A LeverBo Barker Jørgensen
Oct 10, 2015·Scientific Reports·Gemma HendersonPeter H Janssen
Feb 3, 2016·Microbial Biotechnology·Jun-hua LiuSheng-yong Mao
Jun 3, 2017·Journal of Animal Science and Biotechnology·Wei JinWeiyun Zhu
Feb 16, 2018·Frontiers in Microbiology·Jueeli D VaidyaHauke Smidt