ArticleJournal of advanced research2025
New insights into the enteric methane production based on the archaeal genome atlas of ruminant gastrointestinal tract.
Article in Journal of advanced research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Age-related shifts of dissolved hydrogen and its impact on rumen fermentation dynamics and microbial communities in goats (Capra hircus).BMC microbiology · 2026Article
- Microbial landscapes in dairy cow diseases: from localized dysbiosis to inter-organ axes.NPJ biofilms and microbiomes · 2026Review
- Phytosterols improve feed efficiency in yaks by enriching rumen Succiniclasticum.Animal microbiome · 2026Article
- A comprehensive ruminant microbial catalog (CRMC) reveals convergent selection for key vitamin-synthesizing pathways and genes across ruminants and human.GigaScience · 2026Article
- Intracellular accumulation of hydrophobic 1,3-PDN inhibits methanogenesis in rumen methanogens.The ISME journal · 2026Article
- Mechanisms and Applications of Gastrointestinal Microbiota-Metabolite Interactions in Ruminants: A Review.Microorganisms · 2025Review
- Dietary Protein-Induced Changes in Archaeal Compositional Dynamics, Methanogenic Pathways, and Antimicrobial Resistance Profiles in Lactating Sheep.Microorganisms · 2025Article
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Authors and funding
6 authors.
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Abstract
introductionAs one of the important components of ruminant gastrointestinal tract (GIT) microbiome, archaea are involved in many biological processes, especially methanogenesis. In spite of being a well-recognised member of the mammalian gut microbiome, it remains poorly characterized, partly due to the lack of a unified reference genome catalog.
objectivesThis study aimed to construct a unified genome atlas that captures the wider diversity in archaea and is thus more appropriate for functional and taxonomic exploration of ruminant GIT archaea.
methodsWe collected archaeal genomes from public sources and new data of this study. We performed phylogenetic and functional genomics analysis, prophage identification based on the genomes. Using collected genomes as a reference, we conducted metagenomic and metatranscriptomic analysis on rumen fluid samples from 18 dairy cows, and investigated the correlation between rumen archaeal communities and methane (CH
resultsWe constructed the ruminant GIT archaeal genomes (RGAG) by compiling 405 strain-level (160 species) non-redundant archaeal genomes from more than 10 ruminant species. Investigating the functional heterogeneity and methanogenic structure within RGAG revealed that it possessed 1,124 (99.5%) unknown microbial biosynthetic gene clusters. A survey of RGAG-borne prophages identified 63 prophages with 122 host-beneficial genes and 18 auxiliary metabolic genes. The pipeline for both metagenomics and metatranscriptomics generated in the study revealed the roles of archaeal genomes under-assessed in general multi-omics analysis. The highly expressed genus Methanosphaera was negatively correlated with CH
conclusionA unified genome atlas of ruminant GIT archaea is constructed in the study. Our analyses revealed the advantages of metatranscriptomics over metagenomics in studying rumen archaeal communities and further demonstrated that the multifaceted functions of ruminant archaea remain undiscovered. Differences in rumen archaeal community structure among cattle with different CH
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