Improving Rumen Function

Tools to understand the ruminal microbiomeColonization and establishment of the rumen microbiota – opportunities to influence productivity and methane emissionsIntroductionEstablishment of the rumen microbiotaColonization: from birth (pre-ruminant) to a fully functional rumenInteraction host-microbiotaWeaning and stabilization of the rumen microbiotaMicrobial activities and functionsModes of transmissionImpact of management practicesModulating the gastrointestinal microbiota in young ruminants for health and productionCase studies: early-life strategies for improving health and productionCase studies: early-life strategies for reducing enteric methane emissionsConclusion and future trendsWhere to look for further informationReferencesA question of culture: bringing the gut microbiome to life in the -omics eraIntroductionCulturing methods and nutrient effects on microbial growth: an overviewNitrogen sourcesCarbon sourcesMicronutrientsReductantsGenome-directed isolation of gut microbesMolecular-based isolation of gut microbesAntibody-based isolation of gut microbesConclusion and future trendsReferencesRumen metabolomics – a powerful tool for discovery and understanding of rumen functionality and healthIntroductionThe rumen metabolome: technologies for analysis and extraction techniquesTools for the interpretation of metabolomic dataFactors impacting the rumen metabolomeFuture trends in researchConclusionReferencesA conceptual approach to the mathematical modelling of microbial functionality in the rumenIntroductionConceptual approaches in modelling whole rumen functionInteractions between ruminant host and rumen contentIntra-ruminal conditionsTypes of microbial functionalityMicrobial interactionsConcepts of microbial community dynamicsQuantifying rumen microbial functionalityUnits and sampling techniquesConclusion and future trendsWhere to look for further informationReferencesThe rumen microbiotaGenome sequencing and the rumen microbiomeIntroductionThe first rumen microbial genomeThe power of sequencing a single genomeCuration of a reference genome catalogue for the rumen microbiomeApplication of metagenomic data for novel genome constructionComparative genomics and key functions in the rumenThe genome as a blueprint of the proteomeGenome sequencing and interactions across the microbiomeViral sequences in the genome and prophage infectionsUsing CRISPR sequences to reveal phage:host interactionsCompetition resources in a microbiomeThe effect of antimicrobials in the rumenConclusionFuture trendsWhere to look for further informationReferencesThe Rumen ArchaeaIntroductionArchaea in the rumenCultivation of methanogenic Archaea from the rumenThe use of molecular techniques to identify and quantify rumen methanogensHydrogenotrophic methanogens: Methanobrevibacter ruminantium M1Other hydrogenotrophic methanogensMethanobrevibacter olleyae YLM1Methanobrevibacter sp. AbM4Mathanobrevibacter millerae SM9Methanobacterium formicicum BRM9Methylotrophic methanogensMethanogens belonging to the order MethanomassiliicoccalesMethanosphaera sp. BMSAcetoclastic methanogens: Methanosarcina sp. CM1ConclusionsReferencesRuminal-ciliated protozoaIntroductionDiscovery of rumen protozoaRumen protozoal taxonomy and population ‘types’Rumen protozoal genomicsEcological fluctuations in protozoa populationsProtozoa interactions in the rumenRumen bacteria-protozoa interactionsRumen fungi-protozoa interactionsRumen methanogen-protozoa interactionsRumen plant-protozoal interactionsChallenges of working with rumen protozoaThe effects of protozoal function on ruminant nutrition, health and emissionsRumen protozoa and Nitrogen-use efficiencyRumen protozoa and fibre digestionRumen protozoa and healthiness of ruminant productsRumen protozoa and methane emissionsCase study: manipulating the rumen ciliatesFuture trends and conclusionsWhere to look for further informationReferencesThe anaerobic rumen fungiIntroductionThe life cycle of anaerobic fungiTaxonomy and morphological features of anaerobic fungiGenera and species of anaerobic fungiMonocentric generaPolycentric generaBulbous generaGenomics of anaerobic fungiSingle-cell genomicsTranscriptomicsMeta-omics of anaerobic fungiMetagenomicsMetatranscriptomicsInteractions between rumen fungi and other components of the rumen ecosystemInteraction between anaerobic fungi and methanogensEffect of feed composition on fungal rumen populationEffect of anaerobic rumen fungi on metabolic intermediates for host utilizationManipulation of rumen fungal population for increased lignocelluloses degradationConclusionWhere to look for further informationReferencesRuminal viruses and extrachromosomal genetic elementsIntroductionExtrachromosomal elementsViral genomesPlasmidsOther extrachromosomal elements and membrane vesiclesRumen virusesRole and impact of the mobilome on rumen functionCell lysisHorizontal gene transferModulation of microbial populationsInfluence development of phenotypic traits and growth habitsInfluence on the ruminant hostConclusion and future trendsAcknowledgementsWhere to look for further informationReferencesThe rumen wall microbiota communityIntroductionThe rumen wall microbial communityComposition and function of rumen wall bacteriaComposition and function of rumen wall archaeaThe development of the rumen wall microbiomeFactors affecting the epimural microbiotaThe impact of the epimural microbiota on ruminant productionMilk compositionFeed efficiencyMethane emissionsChallenges and future trendsBetter illustration of microbial functionsBetter understanding of host-microbial interactionMore effective manipulation strategiesImproved sample collection and data handlingConclusionsAcknowledgmentReferencesNutrient processing in the rumen and host interactionsRuminal fibre digestionIntroductionLignocellulosic biomassCelluloseHemicelluloseCarbohydrate-active enzymesGlycoside hydrolasesCarbohydrate-binding modules (CBMs)Other CAZyme familiesProkaryotic strategies for fibre digestion in the rumenCellulosomesSecreted enzymesPolysaccharide utilization lociPULs are in the gram positives as wellFibrobacter succinogenes and outer-membrane vesicles (OMVs)Bacteroidetes, the type IX secretion system and multi-modular CAZymesCurrent gaps in knowledgeThe eukaryotesHow much CAZyme and glycan diversity is there in the rumen?What do functional omic studies tell us?Improving the fibre digestion processSummary and future trendsWhere to look for further informationReferencesRuminal protein breakdown and ammonia assimilationIntroductionMicrobial nitrogen metabolismRuminal proteolysis and deaminationAmmonia assimilationAmmonium transportEnzymatic pathways of ammonium assimilationMechanisms of regulationAmmonium assimilation in rumen bacteriaArchael nitrogen metabolismAnaerobic rumen fungiCiliate protozoaMicrobial protein synthesisIntra-ruminal recycling of microbial proteinCase study to advance understanding of protozoa-mediated proteolysis and intra-ruminal recycling of microbial proteinCase study using sequencing approaches with protozoal in vitro or ex vivo culturesOpportunities to improve efficiency of ruminal nitrogen (N) metabolismMeasurement of rumen-degraded proteinRuminal proteolysis as affected by diet or additivesConclusionFuture trendsWhere to look for further informationReferencesFactors influencing the efficiency of rumen energy metabolismIntroductionMain pathways of rumen fermentationProduction of volatile fatty acidsGeneration of adenosine triphosphate (ATP)Disposal of metabolic hydrogenMethaneSignificanceMethane production and the VFA profileThe methanogenesis-inhibited rumen fermentationFactors influencing the efficiency of microbial growthEnergy sinksOther factors influencing growth efficiencyFuture work on strategies for increasing the efficiency of microbial growthInteractions between rumen energy and nitrogen metabolismConsequences of inhibiting rumen methanogenesis on microbial synthesis of amino acidsEffect of nitrogen on energy spillingSynchronyConclusion and future trendsWhere to look for further informationReferencesUnderstanding rumen lipid metabolism to optimize dairy products for enhanced human health and to monitor animal healthIntroductionRuminal metabolism of dietary lipids and de novo fatty acid synthesisLipolysis and biohydroganation of dietary lipidsDe novo fatty acid synthesis by rumen bacteriaDigestion and transfer of dietary and rumen fatty acids to the mammary gland and fatty acid metabolism in the mammary glandIntestinal digestion of fatty acidsFatty acid transport in blood and transfer to the mammary glandEndogenous fatty acid metabolism in the mammary glandEndogenous mammary metabolism of odd and branched-chain fatty acidsEndogenous mammary metabolism of saturated and mono-unsaturated fatty acidsImpact of ruminant fatty acids on human healthImpact of ruminant trans fatty acids on human healthImpact of conjugated linoleic acids and n-3 fatty acids on human healthRumen bypass polyunsaturated fatty acid (PUFA) products to improve the milk fatty acid profileRumen lipid protection technologiesMilk fatty acids originating from the rumen as biomarkers to monitor animal healthRumen bacteria related to the accumulation of trans-70 intermediatesRumen bacteria and their odd- and branched-chain fatty acidsRumen bacteria associated with the accumulation of tra ns- 7 0 intermediates, rich in odd-chain fatty acids and poor in iso-fatty acids linked to inflammation?Trans and odd- and branched-chain fatty acids in milk fat to identify subacute ruminal acidosis (risk)ConclusionWhere to look for further informationReferencesNutritional factors affecting greenhouse gas production from ruminants: implications for enteric and manure emissionsIntroductionGreenhouse gas productionBalancing enteric methane production and manure emissionsDiet digestibility and fermentable carbohydratesNitrogen contentDietary fatCase study: Dried distillers’ grains plus solubles (DDGS)Nitro-based compoundsNitrate-nitrooxypropanol (3-NOP)Plant secondary compoundsTanninsCarbon-derived materialsHumic substancesBiocharMicrobial hydrogen utilisationFuture trends and conclusionWhere to look for further informationReferencesHost-rumen microbiome interactions and influences on feed conversion efficiency (FCE), methane production and other productivity traitsIntroductionCore community, resilience and natural variation in rumen microbiome compositionMicrobiome-dependent traitsMethane productionNitrogen compounds: utilization and emissionMicrobiome and host geneticsReferencesThe rumen as a modulator of immune function in cattleIntroductionPrevalence of subacute ruminal acidosis (SARA) in dairy herdsRumen health, metabolic activity and disordersRumen health and the mammary immune systemConclusionsAcknowledgementsWhere to look for further informationReferencesNutritional strategies to optimise ruminal functionRole of the rumen microbiome in pasture-fed ruminant production systemsIntroductionDiet and rumen microbiomeCellulose degradation in the rumenBacterial degradation of celluloseFungi and celluloseProtozoa and cellulose degradationThe rumen microbiome and feed efficiencyAssociation of volatile fatty acids (VFAs) profile and feed efficiencyAssociation of digestibility and feed efficiencyThe rumen microbiome and methane productionMethane production and residual feed intakeThe impact of forage plants on animal performanceGrassland management and animal performanceLegumes and animal performanceGrasses and animal performanceConclusionWhere to look for further informationReferencesOptimising ruminal function: the role of silage and concentrate in dairy cow nutrition to improve feed efficiency and reduce methane and nitrogen emissionsIntroductionRole of silage: grass, forage legumes and maizeSilage plant speciesGrass silagesForage legume silagesMaize silagesMaize silage versus grass and forage legume silagesRole of concentrates: lipids, carbohydrates and proteinLipidsCarbohydratesProteinCase study: Effects of milled rapeseed on milk production, milk fat composition and ruminal CH4 emissions of dairy cows in practical farm conditionsSummary and future trendsWhere to look for further informationReferencesThe use of feedlot/cereal grains in improving feed efficiency and reducing by-products such as methane in ruminantsIntroductionTypes of cereal grains fed to cattleCereal grain productionDietary factors affecting methane production by ruminantsThe role of starch and forage in methane formationH2 sinks in the rumen and methane productionUsing cereal grains to improve feed efficiency and reduce methane productionMicrobiology of cereal grain fermentationBacteria and archaea involved in fermentationFeed retention timeAcidosis and other negative feed effectsSummaryWhere to look for further informationReferencesPlant secondary compounds: beneficial roles in sustainable ruminant nutrition and productivityIntroductionEssential oils (EO)TanninsSaponinsFuture trends and conclusionReferencesThe use of probiotics as supplements for ruminantsIntroductionCritical periods in the ruminant lifecycle as targets for probioticsDefinitions, delivery mechanisms and regulationDefinitionsDelivery mechanismsRegulationBenefits and modes of action of probiotics: young ruminantsBenefits and modes of action of probiotics: feed efficiency in adult ruminantsBenefits and modes of action of probiotics: methane productionBenefits and modes of action of probiotics: pathogen controlBenefits and modes of action of probiotics: effects on the immune systemConclusions and future trendsAcknowledgmentsWhere to look for further information sectionReferences
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