Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates

Identifying rumen protozoa in microscopic images of ruminant with improved YOLACT instance segmentation

(2022) Zhenni Shang et al.   BIOSYSTEMS ENGINEERING

Comparative genomics reveals new functional insights in uncultured MAST species

(2021) Aurelie Labarre et al.   ISME Journal

The macronuclear genome of anaerobic ciliate Entodinium caudatum reveals its biological features adapted to the distinct rumen environment

(2021) Tansol Park et al.   GENOMICS

Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets

(2021) Daniele De Luca et al.   ISME Journal

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

(2021) Mosè Manni et al.   MOLECULAR BIOLOGY AND EVOLUTION

Niche partitioning facilitates coexistence of closely related honey bee gut bacteria

(2021) Silvia Brochet et al.   eLife

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

(2021) Fei Xie et al.   Microbiome

Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem

(2021) Ronnie Solomon et al.   ISME Journal

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extending Burk Dehority’s Perspectives on the Role of Ciliate Protozoa in the Rumen

(2020) Jeffrey L. Firkins et al.   Frontiers in Microbiology

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

Metagenomic Analyses of Microbial and Carbohydrate-Active Enzymes in the Rumen of Dairy Goats Fed Different Rumen Degradable Starch

(2020) Jing Shen et al.   Frontiers in Microbiology

A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

(2020) Junhua Li et al.   GigaScience

A Combinational Strategy for Effective Heterologous Production of Functional Human Lysozyme in Pichia pastoris

(2020) Huahua He et al.   Frontiers in Bioengineering and Biotechnology

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

CAFE 5 models variation in evolutionary rates among gene families

(2020) Fábio K Mendes et al.   BIOINFORMATICS

Fibre digestion by rumen microbiota – a review of recent metagenomic and metatranscriptomic studies

(2019) Stephanie A Terry et al.   CANADIAN JOURNAL OF ANIMAL SCIENCE

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

(2019) Lei Chen et al.   SCIENCE

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

(2019) Robert D. Stewart et al.   NATURE BIOTECHNOLOGY

Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment

(2019) Jin-Mei Feng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inhibition of Rumen Protozoa by Specific Inhibitors of Lysozyme and Peptidases in vitro

(2019) Tansol Park et al.   Frontiers in Microbiology

Insight into the functional roles of Glu175 in the hyperthermostable xylanase XYL10C-ΔN through structural analysis and site-saturation mutagenesis

(2018) Shuai You et al.   Biotechnology for Biofuels

“Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘omics”

(2018) Xyrus X Maurer-Alcalá et al.   Genome Biology and Evolution

Evolutionary Associations of Endosymbiotic Ciliates Shed Light on the Timing of the Marsupial–Placental Split

(2018) Peter Vďačný   MOLECULAR BIOLOGY AND EVOLUTION

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

(2018) Rekha Seshadri et al.   NATURE BIOTECHNOLOGY

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

(2018) Robert D. Stewart et al.   Nature Communications

Impact of disulfide bonds on the folding and refolding capability of a novel thermostable GH45 cellulase

(2018) Hong Yang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation

(2018) Andrea Söllinger et al.   mSystems

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

(2018) Evgenia V Kriventseva et al.   NUCLEIC ACIDS RESEARCH

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Dynamics of methanogenesis, ruminal fermentation and fiber digestibility in ruminants following elimination of protozoa: a meta-analysis

(2018) Zongjun Li et al.   Journal of Animal Science and Biotechnology

Leveraging single-cell genomics to expand the fungal tree of life

(2018) Steven R. Ahrendt et al.   Nature Microbiology

Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

(2017) Francesco Rubino et al.   ISME Journal

Inhibition of the Rumen Ciliate Entodinium caudatum by Antibiotics

(2017) Tansol Park et al.   Frontiers in Microbiology

A parts list for fungal cellulosomes revealed by comparative genomics

(2017) Charles H. Haitjema et al.   Nature Microbiology

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants

(2016) Sheerli Kruger Ben Shabat et al.   ISME Journal

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists

(2016) Yan Zhao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq

(2016) Iain C Macaulay et al.   Nature Protocols

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

(2016) Kevin V. Solomon et al.   SCIENCE

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

(2016) Eileen P Hamilton et al.   eLife

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

The Role of Ciliate Protozoa in the Rumen

(2015) Charles J. Newbold et al.   Frontiers in Microbiology

Design and Validation of Four New Primers for Next-Generation Sequencing To Target the 18S rRNA Genes of Gastrointestinal Ciliate Protozoa

(2014) Suzanne L. Ishaq et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The symbiotic intestinal ciliates and the evolution of their hosts

(2014) Seung Yeo Moon-van der Staay et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Diet Alters Both the Structure and Taxonomy of the Ovine Gut Microbial Ecosystem

(2013) M. J. Ellison et al.   DNA RESEARCH

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

(2013) Sandra Kittelmann et al.   PLoS One

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes

(2013) Estienne C. Swart et al.   PLOS BIOLOGY

Activity-Based Metagenomic Screening and Biochemical Characterization of Bovine Ruminal Protozoan Glycoside Hydrolases

(2011) Seth D. Findley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Relative diversity and community structure analysis of rumen protozoa according to T-RFLP and microscopic methods

(2011) Lisa Tymensen et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Impact of High-Concentrate Feeding and Low Ruminal pH on Methanogens and Protozoa in the Rumen of Dairy Cows

(2011) Sarah E. Hook et al.   MICROBIAL ECOLOGY

Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach

(2011) Meng Qi et al.   PLoS One

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH