Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle

The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induce...
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Autor*in:	Stefanie Urimare Wetzels [verfasserIn] Evelyne eMann [verfasserIn] Barbara U Metzler-Zebeli [verfasserIn] Poulad ePourazad [verfasserIn] Muhammad eQumar [verfasserIn] Fenja eKlevenhusen [verfasserIn] Beate ePinior [verfasserIn] Martin eWagner [verfasserIn] Qendrim eZebeli [verfasserIn] Stephan eSchmitz-Esser [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2016

Schlagwörter:	Campylobacter Cattle Kingella microbiota feeding Rumen epithelium

Übergeordnetes Werk:	In: Frontiers in Microbiology - Frontiers Media S.A., 2011, 7(2016)
Übergeordnetes Werk:	volume:7 ; year:2016

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fmicb.2016.00274

Katalog-ID:	DOAJ073384968

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allfields	10.3389/fmicb.2016.00274 doi (DE-627)DOAJ073384968 (DE-599)DOAJd2a5fdaabbeb43e89f375a1862eb807f DE-627 ger DE-627 rakwb eng QR1-502 Stefanie Urimare Wetzels verfasserin aut Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a one-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6,833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5% and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P<0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P<0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host. Campylobacter Cattle Kingella microbiota feeding Rumen epithelium Microbiology Evelyne eMann verfasserin aut Barbara U Metzler-Zebeli verfasserin aut Poulad ePourazad verfasserin aut Muhammad eQumar verfasserin aut Fenja eKlevenhusen verfasserin aut Beate ePinior verfasserin aut Martin eWagner verfasserin aut Qendrim eZebeli verfasserin aut Stephan eSchmitz-Esser verfasserin aut Stephan eSchmitz-Esser verfasserin aut In Frontiers in Microbiology Frontiers Media S.A., 2011 7(2016) (DE-627)642889384 (DE-600)2587354-4 1664302X nnns volume:7 year:2016 https://doi.org/10.3389/fmicb.2016.00274 kostenfrei https://doaj.org/article/d2a5fdaabbeb43e89f375a1862eb807f kostenfrei http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00274/full kostenfrei https://doaj.org/toc/1664-302X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2016
spelling	10.3389/fmicb.2016.00274 doi (DE-627)DOAJ073384968 (DE-599)DOAJd2a5fdaabbeb43e89f375a1862eb807f DE-627 ger DE-627 rakwb eng QR1-502 Stefanie Urimare Wetzels verfasserin aut Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a one-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6,833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5% and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P<0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P<0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host. Campylobacter Cattle Kingella microbiota feeding Rumen epithelium Microbiology Evelyne eMann verfasserin aut Barbara U Metzler-Zebeli verfasserin aut Poulad ePourazad verfasserin aut Muhammad eQumar verfasserin aut Fenja eKlevenhusen verfasserin aut Beate ePinior verfasserin aut Martin eWagner verfasserin aut Qendrim eZebeli verfasserin aut Stephan eSchmitz-Esser verfasserin aut Stephan eSchmitz-Esser verfasserin aut In Frontiers in Microbiology Frontiers Media S.A., 2011 7(2016) (DE-627)642889384 (DE-600)2587354-4 1664302X nnns volume:7 year:2016 https://doi.org/10.3389/fmicb.2016.00274 kostenfrei https://doaj.org/article/d2a5fdaabbeb43e89f375a1862eb807f kostenfrei http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00274/full kostenfrei https://doaj.org/toc/1664-302X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2016
allfields_unstemmed	10.3389/fmicb.2016.00274 doi (DE-627)DOAJ073384968 (DE-599)DOAJd2a5fdaabbeb43e89f375a1862eb807f DE-627 ger DE-627 rakwb eng QR1-502 Stefanie Urimare Wetzels verfasserin aut Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a one-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6,833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5% and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P<0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P<0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host. Campylobacter Cattle Kingella microbiota feeding Rumen epithelium Microbiology Evelyne eMann verfasserin aut Barbara U Metzler-Zebeli verfasserin aut Poulad ePourazad verfasserin aut Muhammad eQumar verfasserin aut Fenja eKlevenhusen verfasserin aut Beate ePinior verfasserin aut Martin eWagner verfasserin aut Qendrim eZebeli verfasserin aut Stephan eSchmitz-Esser verfasserin aut Stephan eSchmitz-Esser verfasserin aut In Frontiers in Microbiology Frontiers Media S.A., 2011 7(2016) (DE-627)642889384 (DE-600)2587354-4 1664302X nnns volume:7 year:2016 https://doi.org/10.3389/fmicb.2016.00274 kostenfrei https://doaj.org/article/d2a5fdaabbeb43e89f375a1862eb807f kostenfrei http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00274/full kostenfrei https://doaj.org/toc/1664-302X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2016
allfieldsGer	10.3389/fmicb.2016.00274 doi (DE-627)DOAJ073384968 (DE-599)DOAJd2a5fdaabbeb43e89f375a1862eb807f DE-627 ger DE-627 rakwb eng QR1-502 Stefanie Urimare Wetzels verfasserin aut Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a one-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6,833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5% and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P<0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P<0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host. Campylobacter Cattle Kingella microbiota feeding Rumen epithelium Microbiology Evelyne eMann verfasserin aut Barbara U Metzler-Zebeli verfasserin aut Poulad ePourazad verfasserin aut Muhammad eQumar verfasserin aut Fenja eKlevenhusen verfasserin aut Beate ePinior verfasserin aut Martin eWagner verfasserin aut Qendrim eZebeli verfasserin aut Stephan eSchmitz-Esser verfasserin aut Stephan eSchmitz-Esser verfasserin aut In Frontiers in Microbiology Frontiers Media S.A., 2011 7(2016) (DE-627)642889384 (DE-600)2587354-4 1664302X nnns volume:7 year:2016 https://doi.org/10.3389/fmicb.2016.00274 kostenfrei https://doaj.org/article/d2a5fdaabbeb43e89f375a1862eb807f kostenfrei http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00274/full kostenfrei https://doaj.org/toc/1664-302X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2016
allfieldsSound	10.3389/fmicb.2016.00274 doi (DE-627)DOAJ073384968 (DE-599)DOAJd2a5fdaabbeb43e89f375a1862eb807f DE-627 ger DE-627 rakwb eng QR1-502 Stefanie Urimare Wetzels verfasserin aut Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a one-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6,833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5% and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P<0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P<0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host. Campylobacter Cattle Kingella microbiota feeding Rumen epithelium Microbiology Evelyne eMann verfasserin aut Barbara U Metzler-Zebeli verfasserin aut Poulad ePourazad verfasserin aut Muhammad eQumar verfasserin aut Fenja eKlevenhusen verfasserin aut Beate ePinior verfasserin aut Martin eWagner verfasserin aut Qendrim eZebeli verfasserin aut Stephan eSchmitz-Esser verfasserin aut Stephan eSchmitz-Esser verfasserin aut In Frontiers in Microbiology Frontiers Media S.A., 2011 7(2016) (DE-627)642889384 (DE-600)2587354-4 1664302X nnns volume:7 year:2016 https://doi.org/10.3389/fmicb.2016.00274 kostenfrei https://doaj.org/article/d2a5fdaabbeb43e89f375a1862eb807f kostenfrei http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00274/full kostenfrei https://doaj.org/toc/1664-302X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2016
language	English
source	In Frontiers in Microbiology 7(2016) volume:7 year:2016
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topic_facet	Campylobacter Cattle Kingella microbiota feeding Rumen epithelium Microbiology
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container_title	Frontiers in Microbiology
authorswithroles_txt_mv	Stefanie Urimare Wetzels @@aut@@ Evelyne eMann @@aut@@ Barbara U Metzler-Zebeli @@aut@@ Poulad ePourazad @@aut@@ Muhammad eQumar @@aut@@ Fenja eKlevenhusen @@aut@@ Beate ePinior @@aut@@ Martin eWagner @@aut@@ Qendrim eZebeli @@aut@@ Stephan eSchmitz-Esser @@aut@@
publishDateDaySort_date	2016-01-01T00:00:00Z
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topic_title	QR1-502 Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle Campylobacter Cattle Kingella microbiota feeding Rumen epithelium
topic	misc QR1-502 misc Campylobacter misc Cattle misc Kingella misc microbiota misc feeding misc Rumen epithelium misc Microbiology
topic_unstemmed	misc QR1-502 misc Campylobacter misc Cattle misc Kingella misc microbiota misc feeding misc Rumen epithelium misc Microbiology
topic_browse	misc QR1-502 misc Campylobacter misc Cattle misc Kingella misc microbiota misc feeding misc Rumen epithelium misc Microbiology
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title	Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle
ctrlnum	(DE-627)DOAJ073384968 (DE-599)DOAJd2a5fdaabbeb43e89f375a1862eb807f
title_full	Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle
author_sort	Stefanie Urimare Wetzels
journal	Frontiers in Microbiology
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author_browse	Stefanie Urimare Wetzels Evelyne eMann Barbara U Metzler-Zebeli Poulad ePourazad Muhammad eQumar Fenja eKlevenhusen Beate ePinior Martin eWagner Qendrim eZebeli Stephan eSchmitz-Esser
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title_sort	epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle
callnumber	QR1-502
title_auth	Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle
abstract	The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a one-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6,833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5% and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P<0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P<0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host.
abstractGer	The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a one-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6,833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5% and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P<0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P<0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host.
abstract_unstemmed	The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a one-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6,833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5% and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P<0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P<0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host.
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title_short	Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle
url	https://doi.org/10.3389/fmicb.2016.00274 https://doaj.org/article/d2a5fdaabbeb43e89f375a1862eb807f http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00274/full https://doaj.org/toc/1664-302X
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author2	Evelyne eMann Barbara U Metzler-Zebeli Poulad ePourazad Muhammad eQumar Fenja eKlevenhusen Beate ePinior Martin eWagner Qendrim eZebeli Stephan eSchmitz-Esser
author2Str	Evelyne eMann Barbara U Metzler-Zebeli Poulad ePourazad Muhammad eQumar Fenja eKlevenhusen Beate ePinior Martin eWagner Qendrim eZebeli Stephan eSchmitz-Esser
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