— Invited Review — Metagenomic investigation of gastrointestinal microbiome in cattle
2
조회
0
다운로드
9
인용
0
참고문헌
키워드
초록
The gastrointestinal (GI) tract, including the rumen and the other intestinal segments of cattle, harbors a diverse, complex, and dynamic microbiome that drives feed digestion and fermentation in cattle, determining feed efficiency and output of pollutants. This microbiome also plays an important role in affecting host health. Research has been conducted for more than a century to understand the microbiome and its relationship to feed efficiency and host health. The traditional cultivation-based research elucidated some of the major metabolism, but studies using molecular biology techniques conducted from late 1980’s to the late early 2000’s greatly expanded our view of the diversity of the rumen and intestinal microbiome of cattle. Recently, metagenomics has been the primary technology to characterize the GI microbiome and its relationship with host nutrition and health. This review addresses the main methods/techniques in current use, the knowledge gained, and some of the challenges that remain. Most of the primers used in quantitative real-time polymerase chain reaction quantification and diversity analysis using metagenomics of ruminal bacteria, archaea, fungi, and protozoa were also compiled.
Abstract
The gastrointestinal (GI) tract, including the rumen and the other intestinal segments of cattle, harbors a diverse, complex, and dynamic microbiome that drives feed digestion and fermentation in cattle, determining feed efficiency and output of pollutants. This microbiome also plays an important role in affecting host health. Research has been conducted for more than a century to understand the microbiome and its relationship to feed efficiency and host health. The traditional cultivation-based research elucidated some of the major metabolism, but studies using molecular biology techniques conducted from late 1980’s to the late early 2000’s greatly expanded our view of the diversity of the rumen and intestinal microbiome of cattle. Recently, metagenomics has been the primary technology to characterize the GI microbiome and its relationship with host nutrition and health. This review addresses the main methods/techniques in current use, the knowledge gained, and some of the challenges that remain. Most of the primers used in quantitative real-time polymerase chain reaction quantification and diversity analysis using metagenomics of ruminal bacteria, archaea, fungi, and protozoa were also compiled.
참고문헌 (148)
- Deng W, "The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review", Mol Biol Rep, 35, pp.265~274 (2008)
- Kobayashi Y, "Application of molecular biology to rumen microbes - review", Asian-Australas J Anim Sci, 12, pp.77~83 (1999)
- White BA, "Molecular analysis of Archaea, Bacteria and Eucarya communities in the rumen - review", Asian-Australas J Anim Sci, 12, pp.129~138 (1999)
- McSweeney CS, "Development of an oligonucleotide probe targeting 16S rRNA and its application for detection and quantitation of the ruminal bacterium Synergistes jonesii in a mixed-population chemostat", Appl Environ Microbiol, 59, pp.1607~1612 (1993)
- Yanagita K, "Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization", Biosci Biotechnol Biochem, 64, pp.1737~1742 (2000)
- Larue R, "Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing", Environ Microbiol, 7, pp.530~543 (2005)
- Wei G, "The microbial community in the feces of the giant panda (Ailuropoda melanoleuca) as determined by PCR-TGGE profiling and clone library analysis", Microb Ecol, 54, pp.194~202 (2007)
- Welkie DG, "ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle", Anaerobe, 16, pp.94~100 (2010)
- Yu Z, "Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis", Appl Environ Microbiol, 70, pp.4800~4806 (2004)
- Rattray RM, "Molecular characterization of sheep ruminal enrichments that detoxify pyrrolizidine alkaloids by denaturing gradient gel electrophoresis and cloning", Microb Ecol, 54, pp.264~275 (2007)
- Tajima K, "Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries", FEMS Microbiol Ecol, 29, pp.159~169 (1999)
- Kim M, "Status of the phylogenetic diversity census of ruminal microbiomes", FEMS Microbiol Ecol, 76, pp.49~63 (2011)
- Brulc JM, "Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases", Proc Natl Acad Sci USA, 106, pp.1948~1953 (2009)
- Callaway TR, "Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing", J Anim Sci, 88, pp.3977~3983 (2010)
- Paz HA, "Rumen bacterial community composition in Holstein and Jersey cows is different under same dietary condition and is not affected by sampling method", Front Microbiol, 7, pp.1206~ (2016)
- Wells JE, "Prevalence and level of Escherichia coli O157:H7 in feces and on hides of feedlot steers fed diets with or without wet distillers grains with solubles", J Food Prot, 72, pp.1624~1633 (2009)
- Myer PR, "Cecum microbial communities from steers differing in feed efficiency", J Anim Sci, 93, pp.5327~5340 (2015)
- Myer PR, "Microbial community profiles of the jejunum from steers differing in feed efficiency", J Anim Sci, 94, pp.327~338 (2016)
- Yu Z, "Improved extraction of PCR-quality community DNA from digesta and fecal samples", Biotechniques, 36, pp.808~812 (2004)
- Kim M, "Investigation of ruminal bacterial diversity in dairy cattle fed supplementary monensin alone and in combination with fat, using pyrosequencing analysis", Can J Microbiol, 60, pp.65~71 (2014)
- Kim M, "Effect of haylage and monensin supplementation on ruminal bacterial communities of feedlot cattle", Curr Microbiol, 69, pp.169~175 (2014)
- Kim M, "Investigation of bacterial diversity in the feces of cattle fed different diets", J Anim Sci, 92, pp.683~694 (2014)
- Myer PR, "Rumen microbiome from steers differing in feed efficiency", PLoS ONE, 10, pp.e0129174~ (2015)
- Myer PR, "Microbial community profiles of the colon from steers differing in feed efficiency", SpringerPlus, 4, pp.454~ (2015)
- Woese CR, "Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids", Microbiol Rev, 47, pp.621~669 (1983)
- Yu Z, "Evaluations of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens by Archaea-specific PCR and denaturing gradient gel electrophoresis", Appl Environ Microbiol, 74, pp.889~893 (2008)
- Lueders T, "Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage", Environ Microbiol, 3, pp.194~204 (2001)
- Luton PE, "The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill", Microbiology, 148, pp.3521~3530 (2002)
- Daquiado AR, "Methanogenic archaea diversity in Hanwoo (Bos taurus coreanae) rumen fluid, rectal dung, and barn floor manure using a culture-independent method based on mcrA gene sequences", Anaerobe, 27, pp.77~81 (2014)
- Denman SE, "Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane", FEMS Microbiol Ecol, 62, pp.313~322 (2007)
- Lwin KO, "Comparative analysis of methanogen diversity in the rumen of crossbred buffalo and cattle in the Philippines by using the functional gene mcrA", Mol Biol Rep, 39, pp.10769~10774 (2012)
- Ozutsumi Y, "McrA gene and 16S rRNA gene in the phylogenetic analysis of methanogens in the rumen of faunated and unfaunated cattle", Anim Sci J, 83, pp.727~734 (2012)
- Ozutsumi Y, "The effect of protozoa on the composition of rumen bacteria in cattle using 16S rRNA gene clone libraries", Biosci Biotechnol Biochem, 69, pp.499~506 (2005)
- Tajima K, "Rumen bacterial community transition during adaptation to high-grain diet", Anaerobe, 6, pp.273~284 (2000)
- Tajima K, "Influence of high temperature and humidity on rumen bacterial diversity in Holstein heifers", Anaerobe, 13, pp.57~64 (2007)
- Zhou M, "Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies", Appl Environ Microbiol, 75, pp.6524~6533 (2009)
- Lukas F, "PCR-DGGE analysis of bacterial population attached to the bovine rumen wall", Folia Microbiol, 55, pp.345~348 (2010)
- 조수정, "16S rDNA Analysis of Bacterial Diversity in Three Fractions of Cow Rumen", Journal of Microbiology and Biotechnology, 16(1), pp.92~101 (2006), 한국미생물·생명공학회
- Kim M, "Phylogenetic diversity of bacterial communities in bovine rumen as affected by diets and microenvironments", Folia Microbiol, 56, pp.453~458 (2011)
- Bekele AZ, "Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis", FEMS Microbiol Lett, 305, pp.49~57 (2010)
- Bekele AZ, "Phylogenetic diversity and dietary association of rumen Treponema revealed using group-specific 16S rRNA gene-based analysis", FEMS Microbiol Lett, 316, pp.51~60 (2011)
- Patra A, "Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances", J Anim Sci Biotechnol, 8, pp.13~ (2017)
- Kim M, "A meta-analysis of bacterial diversity in the feces of cattle", Curr Microbiol, 72, pp.145~151 (2016)
- C.S. McSweeney, "Application of Recent DNA", RNA-based Techniques in Rumen Ecology, 2007, pp.20(2), 283~294[DOI]
- Kim M, "Quantitative comparisons of select cultured and uncultured microbial populations in the rumen of cattle fed different diets", J Anim Sci Biotechnol, 3, pp.28~ (2012)
- Stevenson DM, "Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR", Appl Microbiol Biotechnol, 75, pp.165~174 (2007)
- Weimer PJ, "Effect of monen sin feeding and withdrawal on populations of individual bacterial species in the rumen of lactating dairy cows fed high-starch rations", Appl Microbiol Biotechnol, 80, pp.135~145 (2008)
- Tajima K, "Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR", Appl Environ Microbiol, 67, pp.2766~2774 (2001)
- Khafipour E, "Rumen microbiome composition determined using two nutritional models of subacute ruminal acidosis", Appl Environ Microbiol, 75, pp.7115~7124 (2009)
- Klieve AV, "Establishing populations of Megasphaera elsdenii YE 34 and Butyrivibrio fibrisolvens YE 44 in the rumen of cattle fed high grain diets", J Appl Microbiol, 95, pp.621~630 (2003)
- Stiverson J, "Populations of select cultured and uncultured bacteria in the rumen of sheep and the effect of diets and ruminal fractions", Int J Microbiol, 2011, pp.750613~ (2011)
- Poulsen M, "Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen", Nat Commun, 4, pp.1428~ (2013)
- Sylvester JT, "Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR", J Nutr, 134, pp.3378~3384 (2004)
- Abrar A, "Diversity and fluctuation in ciliate protozoan population in the rumen of cattle", Anim Sci J, 87, pp.1188~1192 (2016)
- Hook SE, "Impact of high-concentrate feeding and low ruminal pH on methanogens and protozoa in the rumen of dairy cows", Microb Ecol, 62, pp.94~105 (2011)
- Kittelmann S, "Characterization of rumen ciliate community composition in domestic sheep, deer, and cattle, feeding on varying diets, by means of PCR-DGGE and clone libraries", FEMS Microbiol Ecol, 75, pp.468~481 (2011)
- Skillman LC, "Development and validation of a real-time PCR method to quantify rumen protozoa and examination of variability between Entodinium populations in sheep offered a hay-based diet", Appl Environ Microbiol, 72, pp.200~206 (2006)
- Orpin CG, "Studies on the rumen flagellate Neocallimastix frontalis", J Gen Microbiol, 91, pp.249~262 (1975)
- Denman SE, "Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen", FEMS Microbiol Ecol, 58, pp.572~582 (2006)
- Bowman BH, "Molecular evolution of the fungi: relationship of the Basidiomycetes, Ascomycetes, and Chytridiomycetes", Mol Biol Evol, 9, pp.285~296 (1992)
- Edwards JE, "Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen", FEMS Microbiol Ecol, 66, pp.537~545 (2008)
- Mao S, "Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function", Sci Rep, 5, pp.16116~ (2015)
- de Oliveira MN, "Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer", Vet Microbiol, 164, pp.307~314 (2013)
- Zhou M, "Methanogen prevalence throughout the gastrointestinal tract of pre-weaned dairy calves", Gut Microbes, 5, pp.628~638 (2014)
- Frey JC, "Comparative studies of microbial populations in the rumen, duodenum, ileum and faeces of lactating dairy cows", J Appl Microbiol, 108, pp.1982~1993 (2010)
- Kang S, "Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray", Inflamm Bowel Dis, 16, pp.2034~2042 (2010)
- Palmer C, "Rapid quantitative profiling of complex microbial populations", Nucleic Acids Res, 34, pp.e5~ (2006)
- Kim M, "Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities", J Appl Microbiol, 117, pp.949~960 (2014)
- Patra AK, "Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray) analysis", Front Microbiol, 6, pp.297~ (2015)
- Suzuki S, "Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays", BMC Genomics, 8, pp.373~ (2007)
- Rimour S, "GoArrays: highly dynamic and efficient microarray probe design", Bioinformatics, 21, pp.1094~1103 (2005)
- Pitta DW, "Rumen bacterial diversity dynamics associated with changing from bermudagrass hay to grazed winter wheat diets", Microb Ecol, 59, pp.511~522 (2010)
- Cersosimo LM, "Influence of periparturient and postpartum diets on rumen methanogen communities in three breeds of primiparous dairy cows", BMC Microbiol, 16, pp.78~ (2016)
- Fouts DE, "Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen", PLoS One, 7, pp.e48289~ (2012)
- Henderson G, "Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range", Sci Rep, 5, pp.14567~ (2015)
- Caporaso JG, "Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample", Proc Natl Acad Sci USA, 108(Suppl 1), pp.4516~4522 (2011)
- Nelson MC, "Analysis, optimization and verification of illumina-generated 16S rRNA gene amplicon surveys", PLoS ONE, 9, pp.e94249~ (2014)
- Myer PR, "Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers", J Microbiol Methods, 127, pp.132~140 (2016)
- Caporaso JG, "QIIME allows analysis of high-throughput community sequencing data", Nat Methods, 7, pp.335~336 (2010)
- Schloss PD, "Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities", Appl Environ Microbiol, 75, pp.7537~7541 (2009)
- Haas BJ, "Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons", Genome Res, 21, pp.494~504 (2011)
- Edgar RC, "UCHIME improves sensitivity and speed of chimera detection", Bioinformatics, 27, pp.2194~2200 (2011)
- Edgar RC, "Search and clustering orders of magnitude faster than BLAST", Bioinformatics, 26, pp.2460~2461 (2010)
- McDonald D, "An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea", ISME J, 6, pp.610~618 (2012)
- Werner JJ, "Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys", ISME J, 6, pp.94~103 (2012)
- Pruesse E, "SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB", Nucleic Acids Res, 35, pp.7188~7196 (2007)
- Quast C, "The SILVA ribosomal RNA gene database project: improved data processing and web-based tools", Nucleic Acids Res, 41, pp.D590~D596 (2013)
- Yilmaz P, "The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks", Nucleic Acids Res, 42, pp.D643~D648 (2014)
- Wang Q, "Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy", Appl Environ Microbiol, 73, pp.5261~5267 (2007)
- Lozupone C, "UniFrac: an effective distance metric for microbial community comparison", ISME J, 5, pp.169~172 (2011)
- Ter Braak CJF, "Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis", Ecology, 67, pp.1167~1179 (1986)
- Clarke KR, "Non-parametric multivariate analyses of changes in community structure", Aust J Ecol, 18, pp.117~143 (1993)
- Anderson MJ, "A new method for non-parametric multivariate analysis of variance", Austral Ecol, 26, pp.32~46 (2001)
- Weimer PJ, "Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations", Front Microbiol, 6, pp.296~ (2015)
- Turnbaugh PJ, "A core gut microbiome in obese and lean twins", Nature, 457, pp.480~484 (2009)
- Langille MG, "Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences", Nat Biotechnol, 31, pp.814~821 (2013)
- Liu J, "Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants", J Dairy Sci, 99, pp.9668~9681 (2016)
- Firkins JL, "Ruminant Nutrition Symposium: How to use data on the rumen microbiome to improve our understanding of ruminant nutrition", J Anim Sci, 93, pp.1450~1470 (2015)
- Poretsky R, "Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics", PLoS One, 9, pp.e93827~ (2014)
- von Wintzingerode F, "Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis", FEMS Microbiol Rev, 21, pp.213~229 (1997)
- Nayfach S, "Toward accurate and quantitative comparative metagenomics", Cell, 166, pp.1103~1116 (2016)
- Ross EM, "Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing", J Dairy Sci, 96, pp.6030~6046 (2013)
- Patel V, "Characterization of the rumen microbiome of Indian Kankrej cattle (Bos indicus) adapted to different forage diet", Appl Microbiol Biotechnol, 98, pp.9749~9761 (2014)
- Pitta DW, "Metagenomic analysis of the rumen microbiome of steers with wheat-induced frothy bloat", Front Microbiol, 7, pp.689~ (2016)
- Zhang J, "Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle", Sci Rep, 7, pp.42189~ (2017)
- Dai X, "Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen", Appl Environ Microbiol, 81, pp.1375~1386 (2015)
- Shinkai T, "Comprehensive detection of bacterial carbohydrate-active enzyme coding genes expressed in cow rumen", Anim Sci J, 87, pp.1363~1370 (2016)
- Ka JO, "Monitoring the size and metabolic activity of the bacterial community during biostimulation of fuel-contaminated soil using competitive PCR and RT-PCR", Microb Ecol, 42, pp.267~273 (2001)
- Jami E, "Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency", PLoS One, 9, pp.e85423~ (2014)
- Walter J, "Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers", Appl Environ Microbiol, 66, pp.297~303 (2000)
- Maeda H, "Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria", FEMS Immunol Med Microbiol, 39, pp.81~86 (2003)
- Yu Y, "Group‐specific primer and probe sets to detect methanogenic communities using quantitative real‐time polymerase chain reaction", Biotechnol Bioeng, 89, pp.670~679 (2005)
- Muyzer G, "Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA", Appl Environ Microbiol, 59, pp.695~700 (1993)
- Fierer N, "Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays", Appl Environ Microbiol, 71, pp.4117~4120 (2005)
- Lee DH, "Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism", Appl Environ Microbiol, 62, pp.3112~3120 (1996)
- Guo X, "Development of a real-time PCR method for Firmicutes and Bacteroidetes in faeces and its application to quantify intestinal population of obese and lean pigs", Lett Appl Microbiol, 47, pp.367~373 (2008)
- Schwieger F, "A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis", Appl Environ Microbiol, 64, pp.4870~4876 (1998)
- Muhling M, "Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities", ISME J, 2, pp.379~392 (2008)
- Larsen N, "Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults", PLoS One, 5, pp.e9085~ (2010)
- Matsuki T, "Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces", Appl Environ Microbiol, 68, pp.5445~5451 (2002)
- Layton A, "Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water", Appl Environ Microbiol, 72, pp.4214~4224 (2006)
- Bartosch S, "Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota", Appl Environ Microbiol, 70, pp.3575~3581 (2004)
- Lane DJ, "Nucleic acid techniques in bacterial systematic", pp.115~175 (1991), John Wiley and Sons
- Ramirez-Farias C, "Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii", Br J Nutr, 101, pp.541~550 (2009)
- Delroisse JM, "Quantification of Bifidobacterium spp. and Lactobacillus spp. in rat fecal samples by real-time PCR", Microbiol Res, 163, pp.663~670 (2008)
- Chaucheyras-Durand F, "Live yeasts enhance fibre degradation in the cow rumen through an increase in plant substrate colonization by fibrolytic bacteria and fungi", J Appl Microbiol, 120, pp.560~570 (2016)
- Paillard D, "Relation between phylogenetic position, lipid metabolism and butyrate production by different Butyrivibrio-like bacteria from the rumen", Antonie Van Leeuwenhoek, 91, pp.417~422 (2007)
- Li M, "Effects of sampling location and time, and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen", J Appl Microbiol, 107, pp.1924~1934 (2009)
- Koike S, "Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococus albus and Ruminococcus flavefaciens", FEMS Microbiol Lett, 204, pp.361~366 (2001)
- Petri RM, "Changes in the rumen epimural bacterial diversity of beef cattle as affected by diet and induced ruminal acidosis", Appl Environ Microbiol, 79, pp.3744~3755 (2013)
- Belanche A, "Shifts in the rumen microbiota due to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation", J Nutr, 142, pp.1684~1692 (2012)
- Ouwerkerk D, "Enumeration of Megasphaera elsdenii in rumen contents by real-time Taq nuclease assay", J Appl Microbiol, 92, pp.753~758 (2002)
- Hernandez-Sanabria E, "Impact of feed efficiency and diet on adaptive variations in the bacterial community in the rumen fluid of cattle", Appl Environ Microbiol, 78, pp.1203~1214 (2012)
- Rinttila T, "Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR", J Appl Microbiol, 97, pp.1166~1177 (2004)
- Wetzels SU, "Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle", Front Microbiol, 7, pp.274~ (2016)
- Angel R, "Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen", PLoS One, 6, pp.e20453~ (2011)
- Steinberg LM, "mcrA-targeted real-time quantitative PCR method to examine methanogen communities", Appl Environ Microbiol, 75, pp.4435~4442 (2009)
- Hook SE, "Long-term monensin supplementation does not significantly affect the quantity or diversity of methanogens in the rumen of the lactating dairy cow", Appl Environ Microbiol, 75, pp.374~380 (2009)
- Tymensen LD, "Structures of free-living and protozoa-associated methanogen communities in the bovine rumen differ according to comparative analysis of 16S rRNA and mcrA genes", Microbiology, 158, pp.1808~1817 (2012)
- Mihajlovski A, "Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity", Environ Microbiol Rep, 2, pp.272~280 (2010)
- Tymensen LD, "Community structure analysis of methanogens associated with rumen protozoa reveals bias in universal archaeal primers", Appl Environ Microbiol, 78, pp.4051~4056 (2012)
- DeLong EF., "Archaea in coastal marine environments", Proc Natl Acad Sci USA, 89, pp.5685~5689 (1992)
- Whitford MF, "Phylogenetic analysis of methanogens from the bovine rumen", BMC Microbiol, 1, pp.5~ (2001)
- Kozich JJ, "Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform", Appl Environ Microbiol, 79, pp.5112~5120 (2013)
- Mosher JJ, "Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples", J Microbiol Methods, 95, pp.175~181 (2013)
- Cersosimo LM, "Examination of the rumen bacteria and methanogenic archaea of wild impalas (Aepyceros melampus melampus) from Pongola, South Africa", Microb Ecol, 69, pp.577~585 (2015)
- Wright AD, "Improved strategy for presumptive identification of methanogens using 16S riboprinting", J Microbiol Methods, 55, pp.337~349 (2003)
- Penton CR, "Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing", PLoS One, 9, pp.e93893~ (2014)
