Leveraging Gastrointestinal Microbiota‒Host Co-oscillation Patterns for Improving Nitrogen Utilization Efficiency in Ruminants: A Review

Journal of Nutrition, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Язык: Английский

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Egoviruses: distant relatives of poxviruses abundant in the gut microbiome of humans and animals worldwide

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 23, 2024

Abstract Large and giant double-stranded DNA viruses within the phylum Nucleocytoviricota are diverse prevalent in environment where they substantially affect ecology evolution of eukaryotes 1–4 . Until now, these were only sporadically found digestive system vertebrates 5–7 Here, we present identification genomic characterization a proposed third order class Pokkesviricetes that currently consists poxviruse s asfuviruses 8 Members this newly identified provisionally named “ Egovirales ” commonly worldwide abundant >10% livestock animals, >2% humans, wild animals. Egoviruses have linear genomes up to 467 kbp length likely form multilayered icosahedral capsids, similar those asfuviruses. However, phylogenetic analysis conserved viral genes indicates egoviruses sister group poxviruses, with implications for capsid evolution. The diversity already far exceeds all known poxviruses animal-associated Phylogenetic analyses patterns virus distribution across suggest can be either specialists or generalists associated single multiple vertebrate species, respectively. Notably, one egovirus clade is human-specific, evolutionarily constrained, spread continents, demonstrating long-term association between human population on global scale. not expand ecological evolutionary scope , but also represent diverse, widespread, infecting eukaryotic cells vertebrates.

Язык: Английский

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Ruminal microbiome changes across lactation in primiparous Holstein cows with varying methane intensity: Heritability assessment

Journal of Dairy Science, Год журнала: 2024, Номер 107(9), С. 7064 - 7078

Опубликована: Май 23, 2024

Methane is a potent greenhouse gas produced during the ruminal fermentation and associated with loss of feed energy. Therefore, efforts to reduce methane emissions have been ongoing in last decades. production highly influenced by factors such as microbiome host genetics. Previous studies proposed use long-term emissions, composition moderately heritable trait genetic improvement accumulates over time. Lactation stage another important factor that might influence but potential associations not evaluated previously. This study sought examine changes lactation period primiparous Holstein cows differing intensity estimate heritability abundance relevant microorganisms. Ruminal content samples from 349 14 - 378 d milk were collected May 2018 June 2019. (MI) each cow was calculated concentration/milk yield. Up 64 taxonomic features (TF) 20 phyla had significant differential between low high MI early lactation, 16 TF mid none late lactation. Taxonomical within Firmicutes, Proteobacteria, Melainabacteria, Cyanobacteria, Bacteroidetes Actinobacteria MI, whereas eukaryotic those Euryarchaeota, Verrucomicrobia, Kiritimatiellaeota, Lentisphaerae MI. Out 60 found be differentially abundant 56 also when compared first third In general, microbes more (e.g., Acidaminococcus, Aeromonas Weimeria genera) showed moderate heritabilities (0.03 0.33). These results suggest some modulate rumen through selective breeding for lower Differences extreme levels likely result variations physiology these noticeable probably due interactions phenotype environmental period. Our may precise difference, hence, this should considered optimize sampling periods establish reference population genomic selection scenarios.

Язык: Английский

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Phylogenomics corroborates morphology: New discussions on the systematics of Trichostomatia (Ciliophora, Litostomatea)

European Journal of Protistology, Год журнала: 2024, Номер 95, С. 126093 - 126093

Опубликована: Май 24, 2024

Язык: Английский

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Interaction between methanotrophy and gastrointestinal nematodes infection on the rumen microbiome of lambs

FEMS Microbiology Ecology, Год журнала: 2024, Номер 100(6)

Опубликована: Май 14, 2024

Abstract Complex cross-talk occurs between gastrointestinal nematodes and gut symbiotic microbiota, with consequences for animal metabolism. To investigate the connection methane production endoparasites, this study evaluated effect of mixed infection Haemonchus contortus Trichostrongylus colubriformis on methanogenic methanotrophic community in rumen microbiota lambs using shotgun metagenomic real-time quantitative PCR (qPCR). The content was collected from six Santa Inês lambs, (7 months old) before after 42 days by esophageal tube. analysis showed that affected microbial structure leading to decreased abundance methanotrophs bacteria, i.e. α-proteobacteria β-proteobacteria, anaerobic archaea (ANME), protozoa, sulfate-reducing syntrophic bacteria methanogens, geobacter, genes related pyruvate, fatty acid, nitrogen, sulfur metabolisms, ribulose monophosphate cycle, Entner–Doudoroff Pathway. Additionally, mcrA gene did not change. co-occurrence networks enabled us identify interactions each taxon communities determine reshaping microbiome associations nematode infection. Besides, correlation ANMEs lower animal’s postinfection. Our findings suggest parasites potentially lead metabolism-related microorganisms genes.

Язык: Английский

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CompareM2 is a genomes-to-report pipeline for comparing microbial genomes

Опубликована: Июль 16, 2024

Abstract Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and archaeal genomes derived from isolates metagenomic assemblies. CompareM2 is easy to install operate, integrates community-adopted tools perform genome quality control annotation, taxonomic functional predictions, as well analyses core- pan-genome partitions phylogenetic relations. The central results generated via the workflow are emphasized in portable dynamic report document. free software welcomes modifications pull requests community on its Git repository at https://github.com/cmkobel/comparem2 .

Язык: Английский

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Effects of yeast culture supplementation on milk yield, rumen fermentation, metabolism, and bacterial composition in dairy goats

Frontiers in Veterinary Science, Год журнала: 2024, Номер 11

Опубликована: Авг. 7, 2024

The effects of yeast culture (YC) on dairy goat milk yield and potential rumen microbial population changes fermentation are poorly understood. This study aimed to evaluate the YC in goats explore mechanisms. Forty Laoshan with a weight 51.23 ± 2.23 kg daily 1.41 0.26 were randomly divided into 4 groups: control (no YC), YC1 (10 g/day per goat), YC2 (25 YC3 (40 goat). pre-feeding period was 15 days, official 60 days. milked twice daily, individual recorded. On last day period, fluid collected measure fermentation, perform quantitative polymerase chain reaction (PCR), detect metabolites. Compared group, group had greater yield; higher acetic acid, butyric total volatile fatty acid contents; lower ammonia-N (NH

Язык: Английский

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Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 15, 2024

Abstract Rumen microbiota enable ruminants to grow on fibrous plant materials but also produce methane, driving 5% of global greenhouse gas emissions and leading a loss gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane in when supplemented feed. Yet we lack system-wide, species-resolved understanding how the rumen remodels following inhibition this influences animal production. Here, conducted large-scale trial with 51 dairy calves analyse responses 3-NOP, pairing host performance, emissions, nutritional profiles genome-resolved metagenomic metatranscriptomic data. 3-NOP supplementation decreased by an average 62%, modulated short-chain fatty acid H 2 levels, did not affect dietary intake or performance. We created microbial genome catalogue unprecedented mapping rate. observed strong reduction methanogens stimulation reductive acetogens, primarily novel uncultivated lineages Candidatus Faecousia. However, there was shift major fermentative communities away from acetate production response hydrogen accumulation. Thus, divergent hydrogenotrophic limit potential productivity gains reduction. Reporting one largest reductions field date, study links ruminant specific species. These findings emphasise importance microbiota-wide analysis for optimising mitigation strategies identify promising simultaneously reduce while increasing Significance Statement One strategy increase sustainability livestock is modulate absorbable nutrients rather than potent methane. Previous studies show supplementing feed methanogenesis reduces leads inconsistent gains. Here report definitive trial, combining data, meta-omics, structural modelling, resolve key microbes pathways controlling nutrient ruminants. that shifts composition gene expression hydrogen-cycling offer insights at resolution, data analytical framework provide valuable resources develop solutions enhance sustainability.

Язык: Английский

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Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade

The ISME Journal, Год журнала: 2023, Номер 17(11), С. 1895 - 1906

Опубликована: Авг. 31, 2023

Abstract The Clostridia is a dominant bacterial class in the guts of various animals and are considered to nutritionally contribute animal host. Here, we discovered clostridial endosymbionts cellulolytic protists termite guts, which have never been reported with evidence. We obtained (near-)complete genome sequences three endosymbiotic Clostridia, each associated different parabasalid protist species infection rates: Trichonympha agilis, Pseudotrichonympha grassii, Devescovina sp. All these previously known harbor permanently-associated, mutualistic Endomicrobia or Bacteroidales that supplement nitrogenous compounds. genomes were small size (1.0–1.3 Mbp) exhibited signatures an obligately-intracellular parasite, such as extremely limited capability synthesize amino acids, cofactors, nucleotides disrupted glycolytic pathway no net ATP-generating system. Instead, encoded ATP/ADP translocase and, interestingly, regulatory proteins unique eukaryotes general possibly used interfere host cellular processes. These formed clade metagenome-assembled (MAGs) derived from other animals, including human ruminants, MAGs shared characteristics parasites. Gene flux analysis suggested acquisition gene common ancestor was probably key emergence this parasitic clade. Taken together, provide novel insights into multilayered symbiotic system gut by adding presence parasitism present example putative energy parasites

Язык: Английский

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Enhancing rumen microbial diversity and its impact on energy and protein metabolism in forage-fed goats

Frontiers in Veterinary Science, Год журнала: 2023, Номер 10

Опубликована: Дек. 21, 2023

Introduction This study explores if promoting a complex rumen microbiota represents an advantage or handicap in the current dairy production systems which ruminants are artificially reared absence of contact with adult animals and fed preserved monophyte forage. Methods In order to promote different microbial diversity, total 36 newborn goat kids were reared, divided 4 groups daily inoculated during 10 weeks autoclaved fluid (AUT), fresh from goats adapted forage (RFF) concentrate (RFC) diets, inoculation (CTL). At 6 months age all shifted oats hay diet determine their ability digest low quality Results discussion Early life promoted increase overall diversity was detected later life. As result, at RFF RFC had higher bacterial (+50 OTUs) methanogens (+4 presence protozoal community (+32 OTUs), whereas CTL remained protozoa-free. superior protozoa beneficial effects on energy metabolism allowing faster adaptation diet, digestion (+21% NDF digestibility) energetically favourable shift fermentation pattern acetate butyrate (+92%) propionate (+19%) production. These associated certain taxa diverse community. On contrary, (mostly Entodinium ) negative impact N leading protein breakdown lower flow host based purine derivatives urinary excretion (-17% -54%). The fluid, as source products but not viable microbes, smaller than using inoculum. findings suggest that enhancing desirable attribute when forages supply does represent limiting factor for microbiota.

Язык: Английский

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