Relation between metabolic state, microbial community structure and methane production in dairy cows

Die Methan (CH4) Produktion der Milchkühe wird durch eine Vielzahl von umwelt- und wirtsspezifischen Faktoren beeinflusst, wobei Trockensubstanzaufnahme und Rationszusammensetzung die größte Auswirkung haben. Der größte Teil des CH4 wird von Archaeen im Pansen produziert. Auch die kurzkettige Fettsäure (SCFA) Acetat wird im Pansen durch mikrobielle Fermentation gebildet und kann vom Wirtstier zur Milchfettsynthese im Euter verwendet werden. Die Acetatbildung im Pansen korreliert mit der CH4 Produktion. Allerdings kann Milchfett auch aus nicht veresterten Fettsäuren (NEFA) und Triacylgylcerolen endogenen Ursprungs synthetisiert werden, insbesondere aus mobilisiertem Körperfett. In dieser Studie wurde die Hypothese überprüft, dass eine Verdrängung des zur Milchfettbildung genutzten Acetats durch eine höhere Körperfettmobilisation in der Frühlaktation die ruminale Acetatproduktion senkt und damit die Bildung von CH4 verringert. Ein weiteres Ziel war zu untersuchen, ob der Anstieg der CH4 Produktion im Laktationsverlauf mit einer Veränderung des Mikrobioms assoziiert ist, und ob sich Kühe mit hoher oder niedriger CH4 Emission in ihrer Bakterien- und Archaeen-Zusammensetzung unterscheiden. 20 Holstein Kühe wurden in ihrer ersten Laktation untersucht; ihre Futteraufnahme und Rationszusammensetzung wurde analysiert. Im Verlauf des Versuchs wurden mehrfach Blut- und Pansensaftproben gewonnen. Die Plasma-NEFA-Konzentrationen wurden photometrisch, die Pansen-SCFA-Konzentrationen mittels Gaschromatographie analysiert. Während des Beobachtungszeitraums wurde an 4 Zeitpunkten die individuelle CH4 Produktion in Respirationskammern erfasst. In einer Untergruppe von 9 Kühen wurden Pansensaftproben von 3 Zeitpunkten während der Laktation einer DNA-Extraktion unterzogen und bakterielle und archaeale 16S rRNA Amplicons wurden sequenziert. Die Bakterien- und Archaeenpopulation im Pansensaft wurden beschrieben und Pansenmikrobiom der CH4 Ausbeute gegenübergestellt. Statistische Auswertungen wurden mit repeated measurements ANOVA und Tukey Tests, sowie mit der Pearsons‘ Korrelation für ausgewählte Parameter durchgeführt. Mikrobielle Daten wurden mit multivariaten Analysen (PERMANOVA) weiterverarbeitet und Bray-Curtis-Unähnlichkeiten ermittelt. Die gesamte CH4 Produktion stieg signifikant von durchschnittlich 208 l/Tag in der Trockenperiode auf 516 l/Tag in der Spätlaktation an. Der Grad der Körperfettmobilisation, ausgedrückt als Plasma NEFA Konzentration, und die CH4 Ausbeute waren in der Frühlaktation negativ korreliert (p = 0,002). Kühe mit hoher Fettmobilisation (NEFA > 580 μmol/l) neigten nur vor der Geburt, aber nicht während der Laktation zu höheren Pansenacetat Konzentrationen als Tiere mit niedriger Mobilisation (NEFA < 580 μmol/l). Trotz einer möglichst gleichbleibenden Rationszusammensetzung während der Laktation änderte sich das Mikrobiom mit der Zeit signifikant, was sich in einer Abnahme des Artenreichtums und der Biodiversität zeigte. In der Spätlaktation, als die CH4 Ausbeute am höchsten war, gab es keinen Unterschied in der bakteriellen oder archealen Populationsstruktur zwischen den drei Kühen mit der schwächsten und den dreien mit der stärksten CH4 Ausbeute. Parallel zum Anstieg der CH4 Produktion von 434,3 l/Tag auf 540,5 l/Tag veränderte sich das Verhältnis von (Acetat + Butyrat) / Propionat im Pansensaft mit dem Fortschreiten der Laktation von 3,5 auf 4,4. Dennoch war kein Zusammenhang zwischen der Konzentration der ruminalen SCFA und der CH4 Ausbeute festzustellen. Der Stoffwechselzustand des Tieres, insbesondere der Grad der Körperfettmobilisierung bei negativer Energiebilanz, nahm Einfluss auf die CH4-Ausbeute. Die Zusammensetzung des Mikrobioms im Pansen und dessen Stoffwechselnetzwerk veränderte sich mit der Zeit. Es war jedoch in dieser Studie nicht möglich, einzelne Mikroorganismen als Prädiktor für die CH4-Emission von Milchkühen zu identifizieren. Vielmehr scheinen Verschiebungen der mikrobiellen Gemeinschaften insgesamt für die Veränderung der CH4 Ausbeute verantwortlich zu sein.:1 Introduction 1 2 Background 2 2.1 Greenhouse Gases 2 2.2 Dairy cows and their importance to food production 3 2.3 Rumen functions 5 2.3.1 Anatomy and Physiology 5 2.3.2 Rumen microbes 7 2.3.2.1 Bacteria 8 2.3.2.2 Archaea 11 2.3.3 Short-chain fatty acids 12 2.3.4 Methane formation 15 2.4 Interrelationship between methane and host animal physiology 15 2.4.1 Physiologic aspects affecting methane formation 15 2.5 Effects of feed composition and feed contents on methane production 16 2.5.1 Relationship of ruminal short-chain fatty acids and methane production 17 2.5.2 Milk fatty acids to estimate methane emission 19 2.6 Description of methods 20 2.6.1 Methane Measurement 20 2.6.2 Sampling of rumen contents 21 2.6.3 Methods to identify microbes 22 2.7 Objective and realization of the studies 23 3 Publications 26 3.1 First Publication 26 3.1.1 Supplement first Publication 40 3.2 Second Publication 42 3.2.1 Supplement second Publication 56 4 Discussion 60 4.1 Assessment of experimental design 60 4.1.1 Animals 60 4.1.2 Feed 61 4.1.3 Rumen fluid 61 4.1.4 Blood and milk metabolites 62 4.2 Assessment of results 62 4.2.1 Variance of methane emissions 62 4.2.2 Rumen short-chain fatty acids and methane 65 4.2.3 Acetate in the cows’ metabolism and methane production 66 4.2.4 Fat mobilization in early lactation 67 4.2.5 NEFA in the context of metabolism 68 4.2.6 Rumen microbes 69 4.2.6.1 Microbial community change over time 70 4.2.6.2 Community differences between individuals 71 4.2.6.3 Relationship between microbes and methane production levels 72 4.2.7 Further considerations 74 5 Conclusions 75 6 Summary 77 7 Zusammenfassung 79 8 References 81Methane (CH4) production in dairy cows is influenced by a variety of environmental and host-specific factors, among which dry matter intake and ration composition have the greatest impact. The major part of CH4 is produced in the rumen by Archaea. The short-chain fatty acid (SCFA) acetate is also produced in the rumen by microbial fermentation and can be used by the host to synthesize milk fat in the mammary gland. The production of acetate is correlated with ruminal CH4 production. Milk fat can also be synthesized from non-esterified fatty acids (NEFA) and triacylglycerol that originate from endogenous fat stores of dairy cows, especially during times of fat mobilization. This study checked the hypothesis that a higher fat mobilization during early lactation decreases ruminal acetate production by replacing acetate for milk fat synthesis and, thus, decreases synthesis of CH4. Another aim of this study was to test the hypothesis that increases in CH4 yield over the course of lactation are associated with changes in rumen microbial community profile, and that high and low CH4 emitting cows differ in their bacterial and archaeal community structure. A herd of 20 Holstein cows was studied during the course of their first lactation; feed intake and diet composition was monitored. Blood and rumen fluid were repeatedly sampled throughout the trial. Plasma NEFA concentrations were analyzed by photometrical analysis, and rumen SCFA concentrations by gas chromatography. Individual CH4 production was measured in respiration chambers at four times during the observation period. In a subgroup of 9 cows, rumen fluid samples from 3 timepoints during lactation were subjected to DNA extraction and bacterial and archaeal 16S rRNA amplicons were sequenced. The bacterial and archaeal community structures in the rumen fluid were described, and the rumen microbiome composition linked to CH4 yield. Statistical analysis was conducted using repeated measurement ANOVA and Tukey tests, as well as Pearsons’ correlation for selected parameters. Microbial data was further treated with multivariate analyses (PERMANOVA) and Bray-Curtis dissimilarities were determined. Total CH4 production increased significantly over time from an average 208 L/day during the dry period to 516 L/day in late lactation. The level of fat mobilization, expressed as blood plasma NEFA concentrations, and CH4 yield showed an inverse relationship in early lactation (p = 0.002). High mobilizing cows (NEFA > 580 μmol/L) tended to show higher ruminal acetate concentrations than low mobilizing cows (NEFA < 580 μmol/L) only before parturition and not during lactation. Despite a diet composition that was kept as constant as possible throughout the lactation, the microbial community changed significantly over time as indicated by a decrease in species richness and species evenness. However, in late lactation when CH4 yield was highest, no difference in bacterial or archaeal community structure could be detected between the three highest CH4 yielding cows and the three lowest CH4 yielding cows. The ratio of (acetate + butyrate) / propionate in rumen fluid changed significantly with progressing lactation from 3.5 to 4.4, accompanied by an increase in CH4 production from 434.3 L/d to 540.5 L/d. However, no correlation between the concentration of ruminal SCFA and CH4 yield was found. The metabolic state of the animal, especially the degree of fat mobilization during times of negative energy balance, had an impact on CH4 yield. Also, the microbial community composition in the rumen and its metabolic network is adaptable and changes over time. However, in this study individual microorganisms could not be identified to serve as predictor for CH4 emission from dairy cows at the moment. Rather, shifts in the microbial communities as a whole appear to be responsible for the changes in CH4 yield.:1 Introduction 1 2 Background 2 2.1 Greenhouse Gases 2 2.2 Dairy cows and their importance to food production 3 2.3 Rumen functions 5 2.3.1 Anatomy and Physiology 5 2.3.2 Rumen microbes 7 2.3.2.1 Bacteria 8 2.3.2.2 Archaea 11 2.3.3 Short-chain fatty acids 12 2.3.4 Methane formation 15 2.4 Interrelationship between methane and host animal physiology 15 2.4.1 Physiologic aspects affecting methane formation 15 2.5 Effects of feed composition and feed contents on methane production 16 2.5.1 Relationship of ruminal short-chain fatty acids and methane production 17 2.5.2 Milk fatty acids to estimate methane emission 19 2.6 Description of methods 20 2.6.1 Methane Measurement 20 2.6.2 Sampling of rumen contents 21 2.6.3 Methods to identify microbes 22 2.7 Objective and realization of the studies 23 3 Publications 26 3.1 First Publication 26 3.1.1 Supplement first Publication 40 3.2 Second Publication 42 3.2.1 Supplement second Publication 56 4 Discussion 60 4.1 Assessment of experimental design 60 4.1.1 Animals 60 4.1.2 Feed 61 4.1.3 Rumen fluid 61 4.1.4 Blood and milk metabolites 62 4.2 Assessment of results 62 4.2.1 Variance of methane emissions 62 4.2.2 Rumen short-chain fatty acids and methane 65 4.2.3 Acetate in the cows’ metabolism and methane production 66 4.2.4 Fat mobilization in early lactation 67 4.2.5 NEFA in the context of metabolism 68 4.2.6 Rumen microbes 69 4.2.6.1 Microbial community change over time 70 4.2.6.2 Community differences between individuals 71 4.2.6.3 Relationship between microbes and methane production levels 72 4.2.7 Further considerations 74 5 Conclusions 75 6 Summary 77 7 Zusammenfassung 79 8 References 8

Genetic diversity fuels gene discovery for tobacco and alcohol use

Tobacco and alcohol use are heritable behaviours associated with 15% and 5.3% of worldwide deaths, respectively, due largely to broad increased risk for disease and injury(1-4). These substances are used across the globe, yet genome-wide association studies have focused largely on individuals of European ancestries(5). Here we leveraged global genetic diversity across 3.4 million individuals from four major clines of global ancestry (approximately 21% non-European) to power the discovery and fine-mapping of genomic loci associated with tobacco and alcohol use, to inform function of these loci via ancestry-aware transcriptome-wide association studies, and to evaluate the genetic architecture and predictive power of polygenic risk within and across populations. We found that increases in sample size and genetic diversity improved locus identification and fine-mapping resolution, and that a large majority of the 3,823 associated variants (from 2,143 loci) showed consistent effect sizes across ancestry dimensions. However, polygenic risk scores developed in one ancestry performed poorly in others, highlighting the continued need to increase sample sizes of diverse ancestries to realize any potential benefit of polygenic prediction.Peer reviewe

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Funding GMP, PN, and CW are supported by NHLBI R01HL127564. GMP and PN are supported by R01HL142711. AG acknowledge support from the Wellcome Trust (201543/B/16/Z), European Union Seventh Framework Programme FP7/2007–2013 under grant agreement no. HEALTH-F2-2013–601456 (CVGenes@Target) & the TriPartite Immunometabolism Consortium [TrIC]-Novo Nordisk Foundation’s Grant number NNF15CC0018486. JMM is supported by American Diabetes Association Innovative and Clinical Translational Award 1–19-ICTS-068. SR was supported by the Academy of Finland Center of Excellence in Complex Disease Genetics (Grant No 312062), the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, and University of Helsinki HiLIFE Fellow and Grand Challenge grants. EW was supported by the Finnish innovation fund Sitra (EW) and Finska Läkaresällskapet. CNS was supported by American Heart Association Postdoctoral Fellowships 15POST24470131 and 17POST33650016. Charles N Rotimi is supported by Z01HG200362. Zhe Wang, Michael H Preuss, and Ruth JF Loos are supported by R01HL142302. NJT is a Wellcome Trust Investigator (202802/Z/16/Z), is the PI of the Avon Longitudinal Study of Parents and Children (MRC & WT 217065/Z/19/Z), is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215–2001) and the MRC Integrative Epidemiology Unit (MC_UU_00011), and works within the CRUK Integrative Cancer Epidemiology Programme (C18281/A19169). Ruth E Mitchell is a member of the MRC Integrative Epidemiology Unit at the University of Bristol funded by the MRC (MC_UU_00011/1). Simon Haworth is supported by the UK National Institute for Health Research Academic Clinical Fellowship. Paul S. de Vries was supported by American Heart Association grant number 18CDA34110116. Julia Ramierz acknowledges support by the People Programme of the European Union’s Seventh Framework Programme grant n° 608765 and Marie Sklodowska-Curie grant n° 786833. Maria Sabater-Lleal is supported by a Miguel Servet contract from the ISCIII Spanish Health Institute (CP17/00142) and co-financed by the European Social Fund. Jian Yang is funded by the Westlake Education Foundation. Olga Giannakopoulou has received funding from the British Heart Foundation (BHF) (FS/14/66/3129). CHARGE Consortium cohorts were supported by R01HL105756. Study-specific acknowledgements are available in the Additional file 32: Supplementary Note. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services.Peer reviewedPublisher PD

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Abstract Background Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Funding Information: GMP, PN, and CW are supported by NHLBI R01HL127564. GMP and PN are supported by R01HL142711. AG acknowledge support from the Wellcome Trust (201543/B/16/Z), European Union Seventh Framework Programme FP7/2007–2013 under grant agreement no. HEALTH-F2-2013–601456 (CVGenes@Target) & the TriPartite Immunometabolism Consortium [TrIC]-Novo Nordisk Foundation’s Grant number NNF15CC0018486. JMM is supported by American Diabetes Association Innovative and Clinical Translational Award 1–19-ICTS-068. SR was supported by the Academy of Finland Center of Excellence in Complex Disease Genetics (Grant No 312062), the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, and University of Helsinki HiLIFE Fellow and Grand Challenge grants. EW was supported by the Finnish innovation fund Sitra (EW) and Finska Läkaresällskapet. CNS was supported by American Heart Association Postdoctoral Fellowships 15POST24470131 and 17POST33650016. Charles N Rotimi is supported by Z01HG200362. Zhe Wang, Michael H Preuss, and Ruth JF Loos are supported by R01HL142302. NJT is a Wellcome Trust Investigator (202802/Z/16/Z), is the PI of the Avon Longitudinal Study of Parents and Children (MRC & WT 217065/Z/19/Z), is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215–2001) and the MRC Integrative Epidemiology Unit (MC_UU_00011), and works within the CRUK Integrative Cancer Epidemiology Programme (C18281/A19169). Ruth E Mitchell is a member of the MRC Integrative Epidemiology Unit at the University of Bristol funded by the MRC (MC_UU_00011/1). Simon Haworth is supported by the UK National Institute for Health Research Academic Clinical Fellowship. Paul S. de Vries was supported by American Heart Association grant number 18CDA34110116. Julia Ramierz acknowledges support by the People Programme of the European Union’s Seventh Framework Programme grant n° 608765 and Marie Sklodowska-Curie grant n° 786833. Maria Sabater-Lleal is supported by a Miguel Servet contract from the ISCIII Spanish Health Institute (CP17/00142) and co-financed by the European Social Fund. Jian Yang is funded by the Westlake Education Foundation. Olga Giannakopoulou has received funding from the British Heart Foundation (BHF) (FS/14/66/3129). CHARGE Consortium cohorts were supported by R01HL105756. Study-specific acknowledgements are available in the Additional file : Supplementary Note. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services. Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe

Relation between metabolic state, microbial community structure and methane production in dairy cows

Die Methan (CH4) Produktion der Milchkühe wird durch eine Vielzahl von umwelt- und wirtsspezifischen Faktoren beeinflusst, wobei Trockensubstanzaufnahme und Rationszusammensetzung die größte Auswirkung haben. Der größte Teil des CH4 wird von Archaeen im Pansen produziert. Auch die kurzkettige Fettsäure (SCFA) Acetat wird im Pansen durch mikrobielle Fermentation gebildet und kann vom Wirtstier zur Milchfettsynthese im Euter verwendet werden. Die Acetatbildung im Pansen korreliert mit der CH4 Produktion. Allerdings kann Milchfett auch aus nicht veresterten Fettsäuren (NEFA) und Triacylgylcerolen endogenen Ursprungs synthetisiert werden, insbesondere aus mobilisiertem Körperfett. In dieser Studie wurde die Hypothese überprüft, dass eine Verdrängung des zur Milchfettbildung genutzten Acetats durch eine höhere Körperfettmobilisation in der Frühlaktation die ruminale Acetatproduktion senkt und damit die Bildung von CH4 verringert. Ein weiteres Ziel war zu untersuchen, ob der Anstieg der CH4 Produktion im Laktationsverlauf mit einer Veränderung des Mikrobioms assoziiert ist, und ob sich Kühe mit hoher oder niedriger CH4 Emission in ihrer Bakterien- und Archaeen-Zusammensetzung unterscheiden. 20 Holstein Kühe wurden in ihrer ersten Laktation untersucht; ihre Futteraufnahme und Rationszusammensetzung wurde analysiert. Im Verlauf des Versuchs wurden mehrfach Blut- und Pansensaftproben gewonnen. Die Plasma-NEFA-Konzentrationen wurden photometrisch, die Pansen-SCFA-Konzentrationen mittels Gaschromatographie analysiert. Während des Beobachtungszeitraums wurde an 4 Zeitpunkten die individuelle CH4 Produktion in Respirationskammern erfasst. In einer Untergruppe von 9 Kühen wurden Pansensaftproben von 3 Zeitpunkten während der Laktation einer DNA-Extraktion unterzogen und bakterielle und archaeale 16S rRNA Amplicons wurden sequenziert. Die Bakterien- und Archaeenpopulation im Pansensaft wurden beschrieben und Pansenmikrobiom der CH4 Ausbeute gegenübergestellt. Statistische Auswertungen wurden mit repeated measurements ANOVA und Tukey Tests, sowie mit der Pearsons‘ Korrelation für ausgewählte Parameter durchgeführt. Mikrobielle Daten wurden mit multivariaten Analysen (PERMANOVA) weiterverarbeitet und Bray-Curtis-Unähnlichkeiten ermittelt. Die gesamte CH4 Produktion stieg signifikant von durchschnittlich 208 l/Tag in der Trockenperiode auf 516 l/Tag in der Spätlaktation an. Der Grad der Körperfettmobilisation, ausgedrückt als Plasma NEFA Konzentration, und die CH4 Ausbeute waren in der Frühlaktation negativ korreliert (p = 0,002). Kühe mit hoher Fettmobilisation (NEFA > 580 μmol/l) neigten nur vor der Geburt, aber nicht während der Laktation zu höheren Pansenacetat Konzentrationen als Tiere mit niedriger Mobilisation (NEFA < 580 μmol/l). Trotz einer möglichst gleichbleibenden Rationszusammensetzung während der Laktation änderte sich das Mikrobiom mit der Zeit signifikant, was sich in einer Abnahme des Artenreichtums und der Biodiversität zeigte. In der Spätlaktation, als die CH4 Ausbeute am höchsten war, gab es keinen Unterschied in der bakteriellen oder archealen Populationsstruktur zwischen den drei Kühen mit der schwächsten und den dreien mit der stärksten CH4 Ausbeute. Parallel zum Anstieg der CH4 Produktion von 434,3 l/Tag auf 540,5 l/Tag veränderte sich das Verhältnis von (Acetat + Butyrat) / Propionat im Pansensaft mit dem Fortschreiten der Laktation von 3,5 auf 4,4. Dennoch war kein Zusammenhang zwischen der Konzentration der ruminalen SCFA und der CH4 Ausbeute festzustellen. Der Stoffwechselzustand des Tieres, insbesondere der Grad der Körperfettmobilisierung bei negativer Energiebilanz, nahm Einfluss auf die CH4-Ausbeute. Die Zusammensetzung des Mikrobioms im Pansen und dessen Stoffwechselnetzwerk veränderte sich mit der Zeit. Es war jedoch in dieser Studie nicht möglich, einzelne Mikroorganismen als Prädiktor für die CH4-Emission von Milchkühen zu identifizieren. Vielmehr scheinen Verschiebungen der mikrobiellen Gemeinschaften insgesamt für die Veränderung der CH4 Ausbeute verantwortlich zu sein.:1 Introduction 1 2 Background 2 2.1 Greenhouse Gases 2 2.2 Dairy cows and their importance to food production 3 2.3 Rumen functions 5 2.3.1 Anatomy and Physiology 5 2.3.2 Rumen microbes 7 2.3.2.1 Bacteria 8 2.3.2.2 Archaea 11 2.3.3 Short-chain fatty acids 12 2.3.4 Methane formation 15 2.4 Interrelationship between methane and host animal physiology 15 2.4.1 Physiologic aspects affecting methane formation 15 2.5 Effects of feed composition and feed contents on methane production 16 2.5.1 Relationship of ruminal short-chain fatty acids and methane production 17 2.5.2 Milk fatty acids to estimate methane emission 19 2.6 Description of methods 20 2.6.1 Methane Measurement 20 2.6.2 Sampling of rumen contents 21 2.6.3 Methods to identify microbes 22 2.7 Objective and realization of the studies 23 3 Publications 26 3.1 First Publication 26 3.1.1 Supplement first Publication 40 3.2 Second Publication 42 3.2.1 Supplement second Publication 56 4 Discussion 60 4.1 Assessment of experimental design 60 4.1.1 Animals 60 4.1.2 Feed 61 4.1.3 Rumen fluid 61 4.1.4 Blood and milk metabolites 62 4.2 Assessment of results 62 4.2.1 Variance of methane emissions 62 4.2.2 Rumen short-chain fatty acids and methane 65 4.2.3 Acetate in the cows’ metabolism and methane production 66 4.2.4 Fat mobilization in early lactation 67 4.2.5 NEFA in the context of metabolism 68 4.2.6 Rumen microbes 69 4.2.6.1 Microbial community change over time 70 4.2.6.2 Community differences between individuals 71 4.2.6.3 Relationship between microbes and methane production levels 72 4.2.7 Further considerations 74 5 Conclusions 75 6 Summary 77 7 Zusammenfassung 79 8 References 81Methane (CH4) production in dairy cows is influenced by a variety of environmental and host-specific factors, among which dry matter intake and ration composition have the greatest impact. The major part of CH4 is produced in the rumen by Archaea. The short-chain fatty acid (SCFA) acetate is also produced in the rumen by microbial fermentation and can be used by the host to synthesize milk fat in the mammary gland. The production of acetate is correlated with ruminal CH4 production. Milk fat can also be synthesized from non-esterified fatty acids (NEFA) and triacylglycerol that originate from endogenous fat stores of dairy cows, especially during times of fat mobilization. This study checked the hypothesis that a higher fat mobilization during early lactation decreases ruminal acetate production by replacing acetate for milk fat synthesis and, thus, decreases synthesis of CH4. Another aim of this study was to test the hypothesis that increases in CH4 yield over the course of lactation are associated with changes in rumen microbial community profile, and that high and low CH4 emitting cows differ in their bacterial and archaeal community structure. A herd of 20 Holstein cows was studied during the course of their first lactation; feed intake and diet composition was monitored. Blood and rumen fluid were repeatedly sampled throughout the trial. Plasma NEFA concentrations were analyzed by photometrical analysis, and rumen SCFA concentrations by gas chromatography. Individual CH4 production was measured in respiration chambers at four times during the observation period. In a subgroup of 9 cows, rumen fluid samples from 3 timepoints during lactation were subjected to DNA extraction and bacterial and archaeal 16S rRNA amplicons were sequenced. The bacterial and archaeal community structures in the rumen fluid were described, and the rumen microbiome composition linked to CH4 yield. Statistical analysis was conducted using repeated measurement ANOVA and Tukey tests, as well as Pearsons’ correlation for selected parameters. Microbial data was further treated with multivariate analyses (PERMANOVA) and Bray-Curtis dissimilarities were determined. Total CH4 production increased significantly over time from an average 208 L/day during the dry period to 516 L/day in late lactation. The level of fat mobilization, expressed as blood plasma NEFA concentrations, and CH4 yield showed an inverse relationship in early lactation (p = 0.002). High mobilizing cows (NEFA > 580 μmol/L) tended to show higher ruminal acetate concentrations than low mobilizing cows (NEFA < 580 μmol/L) only before parturition and not during lactation. Despite a diet composition that was kept as constant as possible throughout the lactation, the microbial community changed significantly over time as indicated by a decrease in species richness and species evenness. However, in late lactation when CH4 yield was highest, no difference in bacterial or archaeal community structure could be detected between the three highest CH4 yielding cows and the three lowest CH4 yielding cows. The ratio of (acetate + butyrate) / propionate in rumen fluid changed significantly with progressing lactation from 3.5 to 4.4, accompanied by an increase in CH4 production from 434.3 L/d to 540.5 L/d. However, no correlation between the concentration of ruminal SCFA and CH4 yield was found. The metabolic state of the animal, especially the degree of fat mobilization during times of negative energy balance, had an impact on CH4 yield. Also, the microbial community composition in the rumen and its metabolic network is adaptable and changes over time. However, in this study individual microorganisms could not be identified to serve as predictor for CH4 emission from dairy cows at the moment. Rather, shifts in the microbial communities as a whole appear to be responsible for the changes in CH4 yield.:1 Introduction 1 2 Background 2 2.1 Greenhouse Gases 2 2.2 Dairy cows and their importance to food production 3 2.3 Rumen functions 5 2.3.1 Anatomy and Physiology 5 2.3.2 Rumen microbes 7 2.3.2.1 Bacteria 8 2.3.2.2 Archaea 11 2.3.3 Short-chain fatty acids 12 2.3.4 Methane formation 15 2.4 Interrelationship between methane and host animal physiology 15 2.4.1 Physiologic aspects affecting methane formation 15 2.5 Effects of feed composition and feed contents on methane production 16 2.5.1 Relationship of ruminal short-chain fatty acids and methane production 17 2.5.2 Milk fatty acids to estimate methane emission 19 2.6 Description of methods 20 2.6.1 Methane Measurement 20 2.6.2 Sampling of rumen contents 21 2.6.3 Methods to identify microbes 22 2.7 Objective and realization of the studies 23 3 Publications 26 3.1 First Publication 26 3.1.1 Supplement first Publication 40 3.2 Second Publication 42 3.2.1 Supplement second Publication 56 4 Discussion 60 4.1 Assessment of experimental design 60 4.1.1 Animals 60 4.1.2 Feed 61 4.1.3 Rumen fluid 61 4.1.4 Blood and milk metabolites 62 4.2 Assessment of results 62 4.2.1 Variance of methane emissions 62 4.2.2 Rumen short-chain fatty acids and methane 65 4.2.3 Acetate in the cows’ metabolism and methane production 66 4.2.4 Fat mobilization in early lactation 67 4.2.5 NEFA in the context of metabolism 68 4.2.6 Rumen microbes 69 4.2.6.1 Microbial community change over time 70 4.2.6.2 Community differences between individuals 71 4.2.6.3 Relationship between microbes and methane production levels 72 4.2.7 Further considerations 74 5 Conclusions 75 6 Summary 77 7 Zusammenfassung 79 8 References 8

Relation between metabolic state, microbial community structure and methane production in dairy cows

Die Methan (CH4) Produktion der Milchkühe wird durch eine Vielzahl von umwelt- und wirtsspezifischen Faktoren beeinflusst, wobei Trockensubstanzaufnahme und Rationszusammensetzung die größte Auswirkung haben. Der größte Teil des CH4 wird von Archaeen im Pansen produziert. Auch die kurzkettige Fettsäure (SCFA) Acetat wird im Pansen durch mikrobielle Fermentation gebildet und kann vom Wirtstier zur Milchfettsynthese im Euter verwendet werden. Die Acetatbildung im Pansen korreliert mit der CH4 Produktion. Allerdings kann Milchfett auch aus nicht veresterten Fettsäuren (NEFA) und Triacylgylcerolen endogenen Ursprungs synthetisiert werden, insbesondere aus mobilisiertem Körperfett. In dieser Studie wurde die Hypothese überprüft, dass eine Verdrängung des zur Milchfettbildung genutzten Acetats durch eine höhere Körperfettmobilisation in der Frühlaktation die ruminale Acetatproduktion senkt und damit die Bildung von CH4 verringert. Ein weiteres Ziel war zu untersuchen, ob der Anstieg der CH4 Produktion im Laktationsverlauf mit einer Veränderung des Mikrobioms assoziiert ist, und ob sich Kühe mit hoher oder niedriger CH4 Emission in ihrer Bakterien- und Archaeen-Zusammensetzung unterscheiden. 20 Holstein Kühe wurden in ihrer ersten Laktation untersucht; ihre Futteraufnahme und Rationszusammensetzung wurde analysiert. Im Verlauf des Versuchs wurden mehrfach Blut- und Pansensaftproben gewonnen. Die Plasma-NEFA-Konzentrationen wurden photometrisch, die Pansen-SCFA-Konzentrationen mittels Gaschromatographie analysiert. Während des Beobachtungszeitraums wurde an 4 Zeitpunkten die individuelle CH4 Produktion in Respirationskammern erfasst. In einer Untergruppe von 9 Kühen wurden Pansensaftproben von 3 Zeitpunkten während der Laktation einer DNA-Extraktion unterzogen und bakterielle und archaeale 16S rRNA Amplicons wurden sequenziert. Die Bakterien- und Archaeenpopulation im Pansensaft wurden beschrieben und Pansenmikrobiom der CH4 Ausbeute gegenübergestellt. Statistische Auswertungen wurden mit repeated measurements ANOVA und Tukey Tests, sowie mit der Pearsons‘ Korrelation für ausgewählte Parameter durchgeführt. Mikrobielle Daten wurden mit multivariaten Analysen (PERMANOVA) weiterverarbeitet und Bray-Curtis-Unähnlichkeiten ermittelt. Die gesamte CH4 Produktion stieg signifikant von durchschnittlich 208 l/Tag in der Trockenperiode auf 516 l/Tag in der Spätlaktation an. Der Grad der Körperfettmobilisation, ausgedrückt als Plasma NEFA Konzentration, und die CH4 Ausbeute waren in der Frühlaktation negativ korreliert (p = 0,002). Kühe mit hoher Fettmobilisation (NEFA > 580 μmol/l) neigten nur vor der Geburt, aber nicht während der Laktation zu höheren Pansenacetat Konzentrationen als Tiere mit niedriger Mobilisation (NEFA < 580 μmol/l). Trotz einer möglichst gleichbleibenden Rationszusammensetzung während der Laktation änderte sich das Mikrobiom mit der Zeit signifikant, was sich in einer Abnahme des Artenreichtums und der Biodiversität zeigte. In der Spätlaktation, als die CH4 Ausbeute am höchsten war, gab es keinen Unterschied in der bakteriellen oder archealen Populationsstruktur zwischen den drei Kühen mit der schwächsten und den dreien mit der stärksten CH4 Ausbeute. Parallel zum Anstieg der CH4 Produktion von 434,3 l/Tag auf 540,5 l/Tag veränderte sich das Verhältnis von (Acetat + Butyrat) / Propionat im Pansensaft mit dem Fortschreiten der Laktation von 3,5 auf 4,4. Dennoch war kein Zusammenhang zwischen der Konzentration der ruminalen SCFA und der CH4 Ausbeute festzustellen. Der Stoffwechselzustand des Tieres, insbesondere der Grad der Körperfettmobilisierung bei negativer Energiebilanz, nahm Einfluss auf die CH4-Ausbeute. Die Zusammensetzung des Mikrobioms im Pansen und dessen Stoffwechselnetzwerk veränderte sich mit der Zeit. Es war jedoch in dieser Studie nicht möglich, einzelne Mikroorganismen als Prädiktor für die CH4-Emission von Milchkühen zu identifizieren. Vielmehr scheinen Verschiebungen der mikrobiellen Gemeinschaften insgesamt für die Veränderung der CH4 Ausbeute verantwortlich zu sein.:1 Introduction 1 2 Background 2 2.1 Greenhouse Gases 2 2.2 Dairy cows and their importance to food production 3 2.3 Rumen functions 5 2.3.1 Anatomy and Physiology 5 2.3.2 Rumen microbes 7 2.3.2.1 Bacteria 8 2.3.2.2 Archaea 11 2.3.3 Short-chain fatty acids 12 2.3.4 Methane formation 15 2.4 Interrelationship between methane and host animal physiology 15 2.4.1 Physiologic aspects affecting methane formation 15 2.5 Effects of feed composition and feed contents on methane production 16 2.5.1 Relationship of ruminal short-chain fatty acids and methane production 17 2.5.2 Milk fatty acids to estimate methane emission 19 2.6 Description of methods 20 2.6.1 Methane Measurement 20 2.6.2 Sampling of rumen contents 21 2.6.3 Methods to identify microbes 22 2.7 Objective and realization of the studies 23 3 Publications 26 3.1 First Publication 26 3.1.1 Supplement first Publication 40 3.2 Second Publication 42 3.2.1 Supplement second Publication 56 4 Discussion 60 4.1 Assessment of experimental design 60 4.1.1 Animals 60 4.1.2 Feed 61 4.1.3 Rumen fluid 61 4.1.4 Blood and milk metabolites 62 4.2 Assessment of results 62 4.2.1 Variance of methane emissions 62 4.2.2 Rumen short-chain fatty acids and methane 65 4.2.3 Acetate in the cows’ metabolism and methane production 66 4.2.4 Fat mobilization in early lactation 67 4.2.5 NEFA in the context of metabolism 68 4.2.6 Rumen microbes 69 4.2.6.1 Microbial community change over time 70 4.2.6.2 Community differences between individuals 71 4.2.6.3 Relationship between microbes and methane production levels 72 4.2.7 Further considerations 74 5 Conclusions 75 6 Summary 77 7 Zusammenfassung 79 8 References 81Methane (CH4) production in dairy cows is influenced by a variety of environmental and host-specific factors, among which dry matter intake and ration composition have the greatest impact. The major part of CH4 is produced in the rumen by Archaea. The short-chain fatty acid (SCFA) acetate is also produced in the rumen by microbial fermentation and can be used by the host to synthesize milk fat in the mammary gland. The production of acetate is correlated with ruminal CH4 production. Milk fat can also be synthesized from non-esterified fatty acids (NEFA) and triacylglycerol that originate from endogenous fat stores of dairy cows, especially during times of fat mobilization. This study checked the hypothesis that a higher fat mobilization during early lactation decreases ruminal acetate production by replacing acetate for milk fat synthesis and, thus, decreases synthesis of CH4. Another aim of this study was to test the hypothesis that increases in CH4 yield over the course of lactation are associated with changes in rumen microbial community profile, and that high and low CH4 emitting cows differ in their bacterial and archaeal community structure. A herd of 20 Holstein cows was studied during the course of their first lactation; feed intake and diet composition was monitored. Blood and rumen fluid were repeatedly sampled throughout the trial. Plasma NEFA concentrations were analyzed by photometrical analysis, and rumen SCFA concentrations by gas chromatography. Individual CH4 production was measured in respiration chambers at four times during the observation period. In a subgroup of 9 cows, rumen fluid samples from 3 timepoints during lactation were subjected to DNA extraction and bacterial and archaeal 16S rRNA amplicons were sequenced. The bacterial and archaeal community structures in the rumen fluid were described, and the rumen microbiome composition linked to CH4 yield. Statistical analysis was conducted using repeated measurement ANOVA and Tukey tests, as well as Pearsons’ correlation for selected parameters. Microbial data was further treated with multivariate analyses (PERMANOVA) and Bray-Curtis dissimilarities were determined. Total CH4 production increased significantly over time from an average 208 L/day during the dry period to 516 L/day in late lactation. The level of fat mobilization, expressed as blood plasma NEFA concentrations, and CH4 yield showed an inverse relationship in early lactation (p = 0.002). High mobilizing cows (NEFA > 580 μmol/L) tended to show higher ruminal acetate concentrations than low mobilizing cows (NEFA < 580 μmol/L) only before parturition and not during lactation. Despite a diet composition that was kept as constant as possible throughout the lactation, the microbial community changed significantly over time as indicated by a decrease in species richness and species evenness. However, in late lactation when CH4 yield was highest, no difference in bacterial or archaeal community structure could be detected between the three highest CH4 yielding cows and the three lowest CH4 yielding cows. The ratio of (acetate + butyrate) / propionate in rumen fluid changed significantly with progressing lactation from 3.5 to 4.4, accompanied by an increase in CH4 production from 434.3 L/d to 540.5 L/d. However, no correlation between the concentration of ruminal SCFA and CH4 yield was found. The metabolic state of the animal, especially the degree of fat mobilization during times of negative energy balance, had an impact on CH4 yield. Also, the microbial community composition in the rumen and its metabolic network is adaptable and changes over time. However, in this study individual microorganisms could not be identified to serve as predictor for CH4 emission from dairy cows at the moment. Rather, shifts in the microbial communities as a whole appear to be responsible for the changes in CH4 yield.:1 Introduction 1 2 Background 2 2.1 Greenhouse Gases 2 2.2 Dairy cows and their importance to food production 3 2.3 Rumen functions 5 2.3.1 Anatomy and Physiology 5 2.3.2 Rumen microbes 7 2.3.2.1 Bacteria 8 2.3.2.2 Archaea 11 2.3.3 Short-chain fatty acids 12 2.3.4 Methane formation 15 2.4 Interrelationship between methane and host animal physiology 15 2.4.1 Physiologic aspects affecting methane formation 15 2.5 Effects of feed composition and feed contents on methane production 16 2.5.1 Relationship of ruminal short-chain fatty acids and methane production 17 2.5.2 Milk fatty acids to estimate methane emission 19 2.6 Description of methods 20 2.6.1 Methane Measurement 20 2.6.2 Sampling of rumen contents 21 2.6.3 Methods to identify microbes 22 2.7 Objective and realization of the studies 23 3 Publications 26 3.1 First Publication 26 3.1.1 Supplement first Publication 40 3.2 Second Publication 42 3.2.1 Supplement second Publication 56 4 Discussion 60 4.1 Assessment of experimental design 60 4.1.1 Animals 60 4.1.2 Feed 61 4.1.3 Rumen fluid 61 4.1.4 Blood and milk metabolites 62 4.2 Assessment of results 62 4.2.1 Variance of methane emissions 62 4.2.2 Rumen short-chain fatty acids and methane 65 4.2.3 Acetate in the cows’ metabolism and methane production 66 4.2.4 Fat mobilization in early lactation 67 4.2.5 NEFA in the context of metabolism 68 4.2.6 Rumen microbes 69 4.2.6.1 Microbial community change over time 70 4.2.6.2 Community differences between individuals 71 4.2.6.3 Relationship between microbes and methane production levels 72 4.2.7 Further considerations 74 5 Conclusions 75 6 Summary 77 7 Zusammenfassung 79 8 References 8

Body fat mobilization in early lactation influences methane production of dairy cows

Long-chain fatty acids mobilized during early lactation of dairy cows are increasingly used as energy substrate at the expense of acetate. As the synthesis of acetate in the rumen is closely linked to methane (CH4) production, we hypothesized that decreased acetate utilization would result in lower ruminal acetate levels and thus CH4 production. Twenty heifers were sampled for blood, rumen fluid and milk, and CH4 production was measured in respiration chambers in week −4, +5, +13 and +42 relative to first parturition. Based on plasma non-esterified fatty acid (NEFA) concentration determined in week +5, animals were grouped to the ten highest (HM; NEFA &gt; 580 μmol) and ten lowest (LM; NEFA &lt; 580 μmol) mobilizing cows. Dry matter intake (DMI), milk yield and ruminal short-chain fatty acids did not differ between groups, but CH4/DMI was lower in HM cows in week +5. There was a negative regression between plasma NEFA and plasma acetate, between plasma NEFA and CH4/DMI and between plasma cholecystokinin and CH4/DMI in week +5. Our data show for the first time that fat mobilization of the host in early lactation is inversely related with ruminal CH4 production and that this effect is not attributed to different DMI

Loss-of-function genomic variants highlight potential therapeutic targets for cardiovascular disease.

Pharmaceutical drugs targeting dyslipidemia and cardiovascular disease (CVD) may increase the risk of fatty liver disease and other metabolic disorders. To identify potential novel CVD drug targets without these adverse effects, we perform genome-wide analyses of participants in the HUNT Study in Norway (n = 69,479) to search for protein-altering variants with beneficial impact on quantitative blood traits related to cardiovascular disease, but without detrimental impact on liver function. We identify 76 (11 previously unreported) presumed causal protein-altering variants associated with one or more CVD- or liver-related blood traits. Nine of the variants are predicted to result in loss-of-function of the protein. This includes ZNF529:p.K405X, which is associated with decreased low-density-lipoprotein (LDL) cholesterol (P = 1.3 × 10-8) without being associated with liver enzymes or non-fasting blood glucose. Silencing of ZNF529 in human hepatoma cells results in upregulation of LDL receptor and increased LDL uptake in the cells. This suggests that inhibition of ZNF529 or its gene product should be prioritized as a novel candidate drug target for treating dyslipidemia and associated CVD