Performance comparison of different microbial DNA extraction methods on bird feces

Shengkai Pan,Xiangjiang Zhan,Jiliang Xu,Xian Hou,Zhenzhen Lin

doi:10.1186/s40657-021-00254-9

Shengkai Pan, Xiangjiang Zhan + Show 3 more

Open Access

https://doi.org/10.1186/s40657-021-00254-9

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Abstract

BackgroundAs 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.MethodsIn 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.ResultsBead 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, followed 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.ConclusionsDNA 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 different 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 MoBio when gram-positive bacteria is the research target.

Highlights

As an important player during food digestion, gut microbiota has attracted much attention in diet adaptation studies in birds
It is suggested that only the methods based on physical disruption could yield acceptable amounts of DNA (Eriksson et al 2017) from bird fecal samples. Further performances, such as relative abundance and bacterial diversity, two basic parameters depicting microbiota composition, have not been reported yet. How these DNA extraction methods behave among different avian dietary guilds remains unknown
We evaluated the performance of three methods with different cell lysis strategies on fecal samples from the birds with plant dominant, meat dominant and omnivorous diets, respectively, aiming to explore suitable feces DNA extraction method for birds with specific dietary guilds

Summary

Introduction

As an important player during food digestion, gut microbiota has attracted much attention in diet adaptation studies in birds. It is suggested that only the methods based on physical disruption (e.g., bead beating) could yield acceptable amounts of DNA (Eriksson et al 2017) from bird fecal samples. Further performances, such as relative abundance and bacterial diversity, two basic parameters depicting microbiota composition, have not been reported yet. How these DNA extraction methods behave among different avian dietary guilds remains unknown

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