Comparison of rumen bacteria distribution in original rumen digesta, rumen liquid and solid fractions in lactating Holstein cows
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摘要
Background: Original rumen digesta, rumen liquid and solid fractions have been frequently used to assess the rumen bacterial community. However, bacterial profiles in rumen original digesta, liquid and solid fractions vary from each other and need to be better established.Methods: To compare bacterial profiles in each fraction, samples of rumen digesta from six cows fed either a high fiber diet(HFD) or a high energy diet(HED) were collected via rumen fistulas. Rumen digesta was then squeezed through four layers of cheesecloth to separate liquid and solid fractions. The bacterial profiles of rumen original digesta, liquid and solid fractions were analyzed with High-throughput sequencing technique.Results: Rumen bacterial diversity was mainly affected by diet and individual cow(P > 0.05) rather than rumen fraction. Bias distributed bacteria were observed in solid and liquid fractions of rumen content using Venn diagram and LEf Se analysis. Fifteen out of 16 detected biomarkers(using LEf Se analysis) were found in liquid fraction, and these 15 biomarkers contributed the most to the bacterial differences among rumen content fractions.Conclusions: Similar results were found when using samples of original rumen digesta, rumen liquid or solid fractions to assess diversity of rumen bacteria; however, more attention should be draw onto bias distributed bacteria in different ruminal fractions, especially when liquid fraction has been used as a representative sample for rumen bacterial study.
Background: Original rumen digesta, rumen liquid and solid fractions have been frequently used to assess the rumen bacterial community. However, bacterial profiles in rumen original digesta, liquid and solid fractions vary from each other and need to be better established.Methods: To compare bacterial profiles in each fraction, samples of rumen digesta from six cows fed either a high fiber diet(HFD) or a high energy diet(HED) were collected via rumen fistulas. Rumen digesta was then squeezed through four layers of cheesecloth to separate liquid and solid fractions. The bacterial profiles of rumen original digesta, liquid and solid fractions were analyzed with High-throughput sequencing technique.Results: Rumen bacterial diversity was mainly affected by diet and individual cow(P > 0.05) rather than rumen fraction. Bias distributed bacteria were observed in solid and liquid fractions of rumen content using Venn diagram and LEf Se analysis. Fifteen out of 16 detected biomarkers(using LEf Se analysis) were found in liquid fraction, and these 15 biomarkers contributed the most to the bacterial differences among rumen content fractions.Conclusions: Similar results were found when using samples of original rumen digesta, rumen liquid or solid fractions to assess diversity of rumen bacteria; however, more attention should be draw onto bias distributed bacteria in different ruminal fractions, especially when liquid fraction has been used as a representative sample for rumen bacterial study.
Background: Original rumen digesta, rumen liquid and solid fractions have been frequently used to assess the rumen bacterial community. However, bacterial profiles in rumen original digesta, liquid and solid fractions vary from each other and need to be better established.Methods: To compare bacterial profiles in each fraction, samples of rumen digesta from six cows fed either a high fiber diet(HFD) or a high energy diet(HED) were collected via rumen fistulas. Rumen digesta was then squeezed through four layers of cheesecloth to separate liquid and solid fractions. The bacterial profiles of rumen original digesta, liquid and solid fractions were analyzed with High-throughput sequencing technique.Results: Rumen bacterial diversity was mainly affected by diet and individual cow(P > 0.05) rather than rumen fraction. Bias distributed bacteria were observed in solid and liquid fractions of rumen content using Venn diagram and LEf Se analysis. Fifteen out of 16 detected biomarkers(using LEf Se analysis) were found in liquid fraction, and these 15 biomarkers contributed the most to the bacterial differences among rumen content fractions.Conclusions: Similar results were found when using samples of original rumen digesta, rumen liquid or solid fractions to assess diversity of rumen bacteria; however, more attention should be draw onto bias distributed bacteria in different ruminal fractions, especially when liquid fraction has been used as a representative sample for rumen bacterial study.
引文
1.Henderson G,Cox F,Kittelmann S,Miri VH,Zethof M,Noel SJ,et al.Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.PLo S One.2013;8:e74787.
2.Shen JS,Chai Z,Song LJ,Liu JX,Wu YM.Insertion depth of oral stomach tubes may affect the fermentation parameters of ruminal fluid collected in dairy cows1.J Dairy Sci.2012;95:5978-84.
3.Golder HM,Denman SE,Mc Sweeney C,Celi P,Lean IJ.Ruminal bacterial community shifts in grain-,sugar-,and histidine-challenged dairy heifers.J Dairy Sci.2014;97:5131-50.
4.Jami E,Israel A,Kotser A,Mizrahi I.Exploring the bovine rumen bacterial community from birth to adulthood.ISME J.2013;7:1069-79.
5.Li RW,Connor EE,Li C,Baldwin RL,Sparks ME.Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools.Environ Microbiol.2012;14:129-39.
6.Lima FS,Oikonomou G,Lima SF,Bicalho MLS,Ganda EK,de Oliveira Filho JC,et al.Prepartum and postpartum rumen fluid microbiomes:characterization and correlation with production traits in dairy cows.Appl Environ Microbiol.2015;81:1327-37.
7.Nieman CC,Steensma KM,Rowntree JE,Beede DK,Utsumi SA.Differential response to stocking rates and feeding by two genotypes of HolsteinFriesian cows in a pasture-based automatic milking system.Animal.2015;9:2039-49.
8.Sandri M,Manfrin C,Pallavicini A,Stefanon B.Microbial biodiversity of the liquid fraction of rumen content from lactating cows.Animal.2014;8:572-9.
9.Fliegerova K,Tapio I,Bonin A,Mrazek J,Callegari ML,Bani P,et al.Effect of DNA extraction and sample preservation method on rumen bacterial population.Anaerobe.2014;29:80-4.
10.McKain N,Genc B,Snelling TJ,Wallace RJ.Differential recovery of bacterial and archaeal 16S r RNA genes from ruminal digesta in response to glycerol as cryoprotectant.J Microbiol Methods.2013;95:381-3.
11.Petri RM,Schwaiger T,Penner GB,Beauchemin KA,Forster RJ,Mc Kinnon JJ,et al.Changes in the rumen epimural bacterial diversity of beef cattle as affected by diet and induced ruminal acidosis.Appl Environ Microbiol.2013;79:3744-55.
12.Singh KM,Jisha TK,Reddy B,Parmar N,Patel A,Patel AK,et al.Microbial profiles of liquid and solid fraction associated biomaterial in buffalo rumen fed green and dry roughage diets by tagged 16S r RNA gene pyrosequencing.Mol Biol Rep.2015;42:95-103.
13.Magoc T,Salzberg SL.FLASH:fast length adjustment of short reads to improve genome assemblies.Bioinformatics.2011;27:2957-63.
14.Caporaso JG,Lauber CL,Walters WA,Berg-Lyons D,Lozupone CA,Turnbaugh PJ,et al.Global patterns of 16S r RNA diversity at a depth of millions of sequences per sample.Proc Natl Acad Sci.2011;108:4516-22.
15.Edgar RC.Search and clustering orders of magnitude faster than BLAST.Bioinformatics.2010;26:2460-1.
16.Wang Q,Garrity GM,Tiedje JM,Cole JR.Naive bayesian classifier for rapid assignment of r RNA sequences into the new bacterial taxonomy.Appl Environ Microbiol.2007;73:5261-7.
17.De Santis TZ,Hugenholtz P,Larsen N,Rojas M,Brodie EL,Keller K,et al.Greengenes,a chimera-checked 16S r RNA gene database and workbench compatible with arb.Appl Environ Microbiol.2006;72:5069-72.
18.Russell JB.Factors that alter rumen microbial ecology.Science.2001;292:1119-22.
19.Henderson G,Cox F,Ganesh S,Jonker A,Young W,Abecia L,et al.Rumen microbial community composition varies with diet and host,but a core microbiome is found across a wide geographical range.Sci Rep.2015;5:14567.
20.Brulc JM,Antonopoulos DA,Miller ME,Wilson MK,Yannarell AC,Dinsdale EA,et al.Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases.Proc Natl Acad Sci U S A.2009;106:1948-53.
21.de Menezes AB,Lewis E,O’Donovan M,O’Neill BF,Clipson N,Doyle EM.Microbiome analysis of dairy cows fed pasture or total mixed ration diets.FEMS Microbiol Ecol.2011;78:256-65.
22.Thoetkiattikul H,Mhuantong W,Laothanachareon T,Tangphatsornruang S,Pattarajinda V,Eurwilaichitr L,et al.Comparative analysis of microbial profiles in cow rumen fed with different dietary fiber by tagged 16S r RNAgene pyrosequencing.Curr Microbiol.2013;67:130-7.
23.Tajima K,Aminov RI,Nagamine T,Matsui H,Nakamura M,Benno Y.Dietdependent shifts in the bacterial population of the rumen revealed with real-time PCR.Appl Environ Microbiol.2001;67:2766-74.
24.Hook SE,Steele MA,Northwood KS,Dijkstra J,France J,Wright AG,et al.Impact of subacute ruminal acidosis(SARA)adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows.FEMS Microbiol Ecol.2011;78:275-84.
25.Fernando SC,Purvis HT,Najar FZ,Sukharnikov LO,Krehbiel CR,Nagaraja TG,et al.Rumen microbial population dynamics during adaptation to a highgrain diet.Appl Environ Microbiol.2010;76:7482-90.
26.Zebeli Q,Tafaj M,Weber I,Steingass H,Drochner W.Effects of dietary forage particle size and concentrate level on fermentation profile,in vitro degradation characteristics and concentration of liquid-or solid-associated bacterial mass in the rumen of dairy cows.Anim Feed Sci Technol.2008;140:307-25.
27.Castro-Carrera T,Toral PG,Frutos P,Mc Ewan NR,Hervás G,Abecia L,et al.Rumen bacterial community evaluated by 454 pyrosequencing and terminal restriction fragment length polymorphism analyses in dairy sheep fed marine algae.J Dairy Sci.2014;97:1661-9.
28.Ramos-Morales E,Arco-Pérez A,Martín-García AI,Yá?ez-Ruiz DR,Frutos P,Hervás G.Use of stomach tubing as an alternative to rumen cannulation to study ruminal fermentation and microbiota in sheep and goats.Anim Feed Sci Technol.2014;198:57-66.
29.Lodge-Ivey SL,Browne-Silva J,Horvath MB.Technical note:Bacterial diversity and fermentation end products in rumen fluid samples collected via oral lavage or rumen cannula.2009.87:2333-7.
2.Shen JS,Chai Z,Song LJ,Liu JX,Wu YM.Insertion depth of oral stomach tubes may affect the fermentation parameters of ruminal fluid collected in dairy cows1.J Dairy Sci.2012;95:5978-84.
3.Golder HM,Denman SE,Mc Sweeney C,Celi P,Lean IJ.Ruminal bacterial community shifts in grain-,sugar-,and histidine-challenged dairy heifers.J Dairy Sci.2014;97:5131-50.
4.Jami E,Israel A,Kotser A,Mizrahi I.Exploring the bovine rumen bacterial community from birth to adulthood.ISME J.2013;7:1069-79.
5.Li RW,Connor EE,Li C,Baldwin RL,Sparks ME.Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools.Environ Microbiol.2012;14:129-39.
6.Lima FS,Oikonomou G,Lima SF,Bicalho MLS,Ganda EK,de Oliveira Filho JC,et al.Prepartum and postpartum rumen fluid microbiomes:characterization and correlation with production traits in dairy cows.Appl Environ Microbiol.2015;81:1327-37.
7.Nieman CC,Steensma KM,Rowntree JE,Beede DK,Utsumi SA.Differential response to stocking rates and feeding by two genotypes of HolsteinFriesian cows in a pasture-based automatic milking system.Animal.2015;9:2039-49.
8.Sandri M,Manfrin C,Pallavicini A,Stefanon B.Microbial biodiversity of the liquid fraction of rumen content from lactating cows.Animal.2014;8:572-9.
9.Fliegerova K,Tapio I,Bonin A,Mrazek J,Callegari ML,Bani P,et al.Effect of DNA extraction and sample preservation method on rumen bacterial population.Anaerobe.2014;29:80-4.
10.McKain N,Genc B,Snelling TJ,Wallace RJ.Differential recovery of bacterial and archaeal 16S r RNA genes from ruminal digesta in response to glycerol as cryoprotectant.J Microbiol Methods.2013;95:381-3.
11.Petri RM,Schwaiger T,Penner GB,Beauchemin KA,Forster RJ,Mc Kinnon JJ,et al.Changes in the rumen epimural bacterial diversity of beef cattle as affected by diet and induced ruminal acidosis.Appl Environ Microbiol.2013;79:3744-55.
12.Singh KM,Jisha TK,Reddy B,Parmar N,Patel A,Patel AK,et al.Microbial profiles of liquid and solid fraction associated biomaterial in buffalo rumen fed green and dry roughage diets by tagged 16S r RNA gene pyrosequencing.Mol Biol Rep.2015;42:95-103.
13.Magoc T,Salzberg SL.FLASH:fast length adjustment of short reads to improve genome assemblies.Bioinformatics.2011;27:2957-63.
14.Caporaso JG,Lauber CL,Walters WA,Berg-Lyons D,Lozupone CA,Turnbaugh PJ,et al.Global patterns of 16S r RNA diversity at a depth of millions of sequences per sample.Proc Natl Acad Sci.2011;108:4516-22.
15.Edgar RC.Search and clustering orders of magnitude faster than BLAST.Bioinformatics.2010;26:2460-1.
16.Wang Q,Garrity GM,Tiedje JM,Cole JR.Naive bayesian classifier for rapid assignment of r RNA sequences into the new bacterial taxonomy.Appl Environ Microbiol.2007;73:5261-7.
17.De Santis TZ,Hugenholtz P,Larsen N,Rojas M,Brodie EL,Keller K,et al.Greengenes,a chimera-checked 16S r RNA gene database and workbench compatible with arb.Appl Environ Microbiol.2006;72:5069-72.
18.Russell JB.Factors that alter rumen microbial ecology.Science.2001;292:1119-22.
19.Henderson G,Cox F,Ganesh S,Jonker A,Young W,Abecia L,et al.Rumen microbial community composition varies with diet and host,but a core microbiome is found across a wide geographical range.Sci Rep.2015;5:14567.
20.Brulc JM,Antonopoulos DA,Miller ME,Wilson MK,Yannarell AC,Dinsdale EA,et al.Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases.Proc Natl Acad Sci U S A.2009;106:1948-53.
21.de Menezes AB,Lewis E,O’Donovan M,O’Neill BF,Clipson N,Doyle EM.Microbiome analysis of dairy cows fed pasture or total mixed ration diets.FEMS Microbiol Ecol.2011;78:256-65.
22.Thoetkiattikul H,Mhuantong W,Laothanachareon T,Tangphatsornruang S,Pattarajinda V,Eurwilaichitr L,et al.Comparative analysis of microbial profiles in cow rumen fed with different dietary fiber by tagged 16S r RNAgene pyrosequencing.Curr Microbiol.2013;67:130-7.
23.Tajima K,Aminov RI,Nagamine T,Matsui H,Nakamura M,Benno Y.Dietdependent shifts in the bacterial population of the rumen revealed with real-time PCR.Appl Environ Microbiol.2001;67:2766-74.
24.Hook SE,Steele MA,Northwood KS,Dijkstra J,France J,Wright AG,et al.Impact of subacute ruminal acidosis(SARA)adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows.FEMS Microbiol Ecol.2011;78:275-84.
25.Fernando SC,Purvis HT,Najar FZ,Sukharnikov LO,Krehbiel CR,Nagaraja TG,et al.Rumen microbial population dynamics during adaptation to a highgrain diet.Appl Environ Microbiol.2010;76:7482-90.
26.Zebeli Q,Tafaj M,Weber I,Steingass H,Drochner W.Effects of dietary forage particle size and concentrate level on fermentation profile,in vitro degradation characteristics and concentration of liquid-or solid-associated bacterial mass in the rumen of dairy cows.Anim Feed Sci Technol.2008;140:307-25.
27.Castro-Carrera T,Toral PG,Frutos P,Mc Ewan NR,Hervás G,Abecia L,et al.Rumen bacterial community evaluated by 454 pyrosequencing and terminal restriction fragment length polymorphism analyses in dairy sheep fed marine algae.J Dairy Sci.2014;97:1661-9.
28.Ramos-Morales E,Arco-Pérez A,Martín-García AI,Yá?ez-Ruiz DR,Frutos P,Hervás G.Use of stomach tubing as an alternative to rumen cannulation to study ruminal fermentation and microbiota in sheep and goats.Anim Feed Sci Technol.2014;198:57-66.
29.Lodge-Ivey SL,Browne-Silva J,Horvath MB.Technical note:Bacterial diversity and fermentation end products in rumen fluid samples collected via oral lavage or rumen cannula.2009.87:2333-7.