Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

(2021) Caitlin M. Singleton et al.   Nature Communications

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

(2020) Eli L. Moss et al.   NATURE BIOTECHNOLOGY

The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease

(2020) Rachel Pilla et al.   Frontiers in Veterinary Science

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

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

Interplay between Neuroendocrine Biomarkers and Gut Microbiota in Dogs Supplemented with Grape Proanthocyanidins: Results of Dietary Intervention Study

(2020) Elisa Scarsella et al.   Animals

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

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

metaFlye: scalable long-read metagenome assembly using repeat graphs

(2020) Mikhail Kolmogorov et al.   NATURE METHODS

Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome

(2020) Dylan G. Maghini et al.   Nature Protocols

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing

(2019) You Che et al.   Microbiome

Linking the resistome and plasmidome to the microbiome

(2019) Thibault Stalder et al.   ISME Journal

Fecal short‐chain fatty acid concentrations and dysbiosis in dogs with chronic enteropathy

(2019) Yasushi Minamoto et al.   JOURNAL OF VETERINARY INTERNAL MEDICINE

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

(2019) Samuel M Nicholls et al.   GigaScience

Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data

(2019) Krithika Arumugam et al.   Microbiome

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system

(2019) Vincent Somerville et al.   BMC MICROBIOLOGY

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

(2019) Denis Bertrand et al.   NATURE BIOTECHNOLOGY

Oral Administration of Compound Probiotics Improved Canine Feed Intake, Weight Gain, Immunity and Intestinal Microbiota

(2019) Haiyan Xu et al.   Frontiers in Immunology

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification

(2019) Florian P Breitwieser et al.   BIOINFORMATICS

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

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

Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs

(2019) Jessica K. Jarett et al.   PeerJ

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

(2018) Daniel H. Huson et al.   Biology Direct

oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements

(2018) Xiaobin Li et al.   NUCLEIC ACIDS RESEARCH

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

(2018) Tom O. Delmont et al.   PeerJ

Similarity of the dog and human gut microbiomes in gene content and response to diet

(2018) Luis Pedro Coelho et al.   Microbiome

Effect of dietary fat to starch content on fecal microbiota composition and activity in dogs1

(2018) Sofia Schauf et al.   JOURNAL OF ANIMAL SCIENCE

Effect of probiotic treatment on the clinical course, intestinal microbiome, and toxigenic Clostridium perfringens in dogs with acute hemorrhagic diarrhea

(2018) Anna-Lena Ziese et al.   PLoS One

Blautia argi sp. nov., a new anaerobic bacterium isolated from dog faeces

(2018) Jayoung Paek et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2018) Chirag Jain et al.   Nature Communications

Safety assessment of commensal enterococci from dogs

(2017) Ivana Kubašová et al.   FOLIA MICROBIOLOGICA

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Rapid resistome mapping using nanopore sequencing

(2017) Eric van der Helm et al.   NUCLEIC ACIDS RESEARCH

Role of the gastrointestinal microbiota in small animal health and disease

(2017) Alana Redfern et al.   VETERINARY RECORD

Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions

(2017) Qinghong Li et al.   mBio

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

(2016) Ravi Ranjan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs

(2016) Misa Sandri et al.   BMC Veterinary Research

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks

(2016) Yoshiki Vázquez-Baeza et al.   Nature Microbiology

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Microbiota alterations in acute and chronic gastrointestinal inflammation of cats and dogs

(2014) Julia B Honneffer   WORLD JOURNAL OF GASTROENTEROLOGY

Prevalence and Antimicrobial Resistance of Enterococcus Species: A Hospital-Based Study in China

(2014) Wei Jia et al.   International Journal of Environmental Research and Public Health

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inflammatory Bowel Diseases Phenotype, C. difficile and NOD2 Genotype Are Associated with Shifts in Human Ileum Associated Microbial Composition

(2012) Ellen Li et al.   PLoS One

The Fecal Microbiome in Dogs with Acute Diarrhea and Idiopathic Inflammatory Bowel Disease

(2012) Jan S. Suchodolski et al.   PLoS One

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice

(2010) Kelly S Swanson et al.   ISME Journal

Phylogenetic analysis of 16S rRNA gene sequences reveals distal gut bacterial diversity in wild wolves (Canis lupus)

(2010) Honghai Zhang et al.   MOLECULAR BIOLOGY REPORTS

Analysis of bacterial diversity in the canine duodenum, jejunum, ileum, and colon by comparative 16S rRNA gene analysis

(2008) Jan S. Suchodolski et al.   FEMS MICROBIOLOGY ECOLOGY