Performance comparison of different microbial DNA extraction methods on bird feces  

作　　者：Xian Hou Shengkai Pan Zhenzhen Lin Jiliang Xu Xiangjiang Zhan 

机构地区：[1]School of Ecology and Nature Conservation,Beijing Forestry University,Beijing 100083,China [2]Key Lab of Animal Ecology and Conservation Biology,Institute of Zoology,Chinese Academy of Sciences,Beijing 100101,China [3]Cardiff University-Institute of Zoology Joint Laboratory for Biocomplex-ity Research,Chinese Academy of Sciences,Beijing 100101,China [4]Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sci-ences,Kunming 650223,China

出　　处：《Avian Research》2021年第2期247-254,共8页鸟类学研究（英文版）

基　　金：This study was supported by National Natural Science Foundation of China(No.31930013,31872240);the National Key Program of Research and Development,Ministry of Science and Technology(2016YFC0503200);Youth Innovation Promotion Association of Chinese Academy of Sciences(2020086)to SP.

摘　　要：Background:As an important player during food digestion,gut microbiota has attracted much attention in diet adaptation studies in birds.Microbiota extracted from feces has been widely used as a proxy for gut microbiota.Although several methods have been developed for microbial DNA extraction,their performances in the bird feces have not been systematacially evaluated yet.Methods:In this study,we applied three DNA extraction methods(Qiagen,MoBio and Bead)to extract DNA from feces of three avian dietary guilds(granivore,omnivore and carnivore),sequenced V4 region of 16S rRNA gene for each extract and evaluated the performances of DNA yield,DNA integrity,microbial composition,cell lysis capacity and alpha diversity for the three methods on each dietary guild.Results:Bead method was the best on the performance of both DNA yield and DNA integrity regardless of dietary guild.In granivore,microbial relative abundance at both species and phylum levels,alpha diversity and cell lysis capacity were comparable among all methods.In omnivore,Qiagen had the best performance on alpha diversity,fol-lowed by Bead and MoBio.There were small variations on microbial relative abundance at both species and phylum levels among different extraction methods.MoBio exhibited the best performance on cell lysis capacity.In carnivore,considerable variations were found on microbial relative abundance at both species and phylum levels.Qiagen had the best performance on alpha diversity,followed by MoBio and Bead.MoBio had the highest cell lysis capacity.Conclusions:DNA yield and integrity have no obvious impact on microbial composition,alpha diversity or cell lysis capacity.The microbiota results(e.g.,microbial composition,cell lysis capacity,alpha diversity)obtained from differ-ent methods are comparable in granivorous avian species but not in omnivorous or carnivorous birds.Either method could be used in granivore microbiota studies.For omnivores and carnivores,we recommend Qiagen method when the research purpose is microbial diversity and MoBi

关 键 词：16S rRNA Alpha diversity AVIAN Dietary guild FECES DNA extraction method Microbial relative abundance 

分 类 号：Q958[生物学—动物学]