ArticleThe ISME journal2022
Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates.
Article in The ISME journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 102 citations in OpenAlex.
- Animal gut microbes and microbiomes in the 21st century and beyond.Science China. Life sciences · 2026Review
- Nutritional Strategies for Methane, Nitrogen, and Phosphorus Mitigation in Ruminants: Mechanisms, Applications, and Regional Adaptations.Microorganisms · 2026Review
- The price of survival: comparative adaptation to high altitudes between yaks and cattle.Animal microbiome · 2026Article
- Yeast culture promotes butyrate produced fibrolytic bacteria as intracellular hydrogen sink in the rumen.Microbiome · 2026Article
- Microbial landscapes in dairy cow diseases: from localized dysbiosis to inter-organ axes.NPJ biofilms and microbiomes · 2026Review
- A curated database of rumen ciliate protozoal 18S rRNA gene sequences for metataxonomic applications.BMC genomic data · 2026Article
- Article
- Mining expansin-like proteins from rumen microbiota and functional characterization of two anaerobic fungal expansin-like proteins.Journal of animal science and biotechnology · 2025Article
- Evolution and ecology of commensal gut protists: recent advances.Current opinion in genetics & development · 2025Review
- The crosstalk between host and rumen microbiome in cattle: insights from multi-omics approaches and genome-wide association studies.World journal of microbiology & biotechnology · 2025Review
- Strain-resolved comparison of beef and draft cattle rumen microbiomes using single-microbe genomics.Animal microbiome · 2025Article
- Protozoal populations drive system-wide variation in the rumen microbiome.Nature communications · 2025Article
- Dietary selection of distinct gastrointestinal microorganisms drives fiber utilization dynamics in goats.Microbiome · 2025Article
- Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.Genome research · 2025Article
- Effective Gene Expression Prediction and Optimization from Protein Sequences.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Internal transcribed spacers enable species-level Metataxonomic analysis of ciliated protozoa.ISME communications · 2025Article
- Studies on the concerted interaction of microbes in the gastrointestinal tract of ruminants on lignocellulose and its degradation mechanism.Frontiers in microbiology · 2025Review
- Multiomics of yaks reveals significant contribution of microbiome into host metabolism.NPJ biofilms and microbiomes · 2024Article
- Review
- Giants' cooperation: a draft genome of the giant ciliateMicrobial genomics · 2024Article
Corrections and comments
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Authors and funding
21 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the biodiversity and genetics of gut microbiomes has important implications for host physiology and industrial enzymes, whereas most studies have been focused on bacteria and archaea, and to a lesser extent on fungi and viruses. One group, still underexplored and elusive, is ciliated protozoa, despite its importance in shaping microbiota populations. Integrating single-cell sequencing and an assembly-and-identification pipeline, we acquired 52 high-quality ciliate genomes of 22 rumen morphospecies from 11 abundant morphogenera. With these genomes, we resolved the taxonomic and phylogenetic framework that revised the 22 morphospecies into 19 species spanning 13 genera and reassigned the genus Dasytricha from Isotrichidae to a new family Dasytrichidae. Comparative genomic analyses revealed that extensive horizontal gene transfers and gene family expansion provided rumen ciliate species with a broad array of carbohydrate-active enzymes (CAZymes) to degrade all major kinds of plant and microbial carbohydrates. In particular, the genomes of Diplodiniinae and Ophryoscolecinae species encode as many CAZymes as gut fungi, and ~80% of their degradative CAZymes act on plant cell-wall. The activities of horizontally transferred cellulase and xylanase of ciliates were experimentally verified and were 2-9 folds higher than those of the inferred corresponding bacterial donors. Additionally, the new ciliate dataset greatly facilitated rumen metagenomic analyses by allowing ~12% of the metagenomic sequencing reads to be classified as ciliate sequences.
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