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 microbiot...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 MoBio when gram-positive bacteria is the research target.展开更多
Following publication of the original article(Hou et al.2021),the authors identified an error in Fig.1.The cor-rect figure is given below.The original article(Hou et al.2021)has been updated.
Accurate individual identification is required to estimate survival rates in avian populations.For endangered species,non-invasive methods of obtaining individual identification,such as using molted feathers as a sour...Accurate individual identification is required to estimate survival rates in avian populations.For endangered species,non-invasive methods of obtaining individual identification,such as using molted feathers as a source of DNA for microsatellite markers,are preferred because of less disturbance,easy sample preparation and high efficiency.With the availability of many avian genomes,a few pipelines isolating genome-wide microsatellites have been published,but it is still a challenge to isolate microsatellites from the reference genome efficiently.Here,we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome.We have identified over 95000 microsatellite loci and established a system comprising 10 highly polymorphic markers(PIC value:0.49–0.93,mean:0.79)for an endangered species,saker falcon(Falco cherrug).These markers(except 1)were successfully amplified in 126 molted feathers,exhibiting high amplification success rates(83.9–99.7%),high quality index(0.90–0.97)and low allelic dropout rates(1–9.5%).To further assess the efficiency of this marker system in a population study,we identified individual sakers using these molted feathers(adult)and 146 plucked feathers(offspring).The use of parent and offspring samples enabled us to infer the genotype of missing samples(N=28),and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers.Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.展开更多
In line with the"ecosystem approach"of the Convention on Biological Diversity(CBD)(Secretariat of the Convention on Biological Diversity,2004)toward recognizing the service value in maintaining the essential...In line with the"ecosystem approach"of the Convention on Biological Diversity(CBD)(Secretariat of the Convention on Biological Diversity,2004)toward recognizing the service value in maintaining the essential balance of biodiversity,there has been a conceptual shift toward conservation frameworks that integrate a wider range of dedicated conservationists(Pearson,2016).In this paper,we explore the saker falcon Falco cherrug(hereafter saker)to illustrate how intrinsic service and cultural values within this conceptual paradigm enhance its conservation.展开更多
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.
文摘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 MoBio when gram-positive bacteria is the research target.
文摘Following publication of the original article(Hou et al.2021),the authors identified an error in Fig.1.The cor-rect figure is given below.The original article(Hou et al.2021)has been updated.
基金Stipend and research expenses of Xian Hou were provided by the National Key Program of Research and Development,Ministry of Science and Technology,China(2016YFC0503200)the National Natural Science Foundation of China(Nos.31522052 and 31471993)+1 种基金This project was funded by the Environment Agency of Abu DhabiThe fieldwork was partially supported by the Science and Technology Service Network Initiative of Chinese Academy of Sciences(KFJ_STSZDTP-013-1).
文摘Accurate individual identification is required to estimate survival rates in avian populations.For endangered species,non-invasive methods of obtaining individual identification,such as using molted feathers as a source of DNA for microsatellite markers,are preferred because of less disturbance,easy sample preparation and high efficiency.With the availability of many avian genomes,a few pipelines isolating genome-wide microsatellites have been published,but it is still a challenge to isolate microsatellites from the reference genome efficiently.Here,we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome.We have identified over 95000 microsatellite loci and established a system comprising 10 highly polymorphic markers(PIC value:0.49–0.93,mean:0.79)for an endangered species,saker falcon(Falco cherrug).These markers(except 1)were successfully amplified in 126 molted feathers,exhibiting high amplification success rates(83.9–99.7%),high quality index(0.90–0.97)and low allelic dropout rates(1–9.5%).To further assess the efficiency of this marker system in a population study,we identified individual sakers using these molted feathers(adult)and 146 plucked feathers(offspring).The use of parent and offspring samples enabled us to infer the genotype of missing samples(N=28),and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers.Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.
基金the National Key Program of Research and Development,Ministry of Science and Technology(2016YFC0503200)the National Natural Science Foundation of China(31930013,31900340)+1 种基金Biodiversity Survey,Monitoring and Assessment Project(2019-2023)of Ministry of Ecology and Environment,Chinathe Second Tibetan Plateau Scientific Expedition and Research Program(STEP)(2019QZKK0501)。
文摘In line with the"ecosystem approach"of the Convention on Biological Diversity(CBD)(Secretariat of the Convention on Biological Diversity,2004)toward recognizing the service value in maintaining the essential balance of biodiversity,there has been a conceptual shift toward conservation frameworks that integrate a wider range of dedicated conservationists(Pearson,2016).In this paper,we explore the saker falcon Falco cherrug(hereafter saker)to illustrate how intrinsic service and cultural values within this conceptual paradigm enhance its conservation.
