Co-diversification of an intestinal Mycoplasma and its salmonid host

Integrative analyses of probiotics, pathogenic infections and host immune response highlight the importance of gut microbiota in understanding disease recovery in rainbow trout ( Oncorhynchus mykiss )

(2022) Jacob Agerbo Rasmussen et al.   JOURNAL OF APPLIED MICROBIOLOGY

A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

(2022) Jacob Agerbo Rasmussen et al.   Microbiome

How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample

(2021) Alexandra Meziti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Intestinal microbial communities of rainbow trout (Oncorhynchus mykiss) may be improved by feeding a Hermetia illucens meal/low-fishmeal diet

(2021) Simona Rimoldi et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

Gnotobiotic rainbow trout (Oncorhynchus mykiss) model reveals endogenous bacteria that protect against Flavobacterium columnare infection

(2021) David Pérez-Pascual et al.   PLoS Pathogens

Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts

(2021) Jacob A. Rasmussen et al.   Communications Biology

Genome erosion and evidence for an intracellular niche – exploring the biology of mycoplasmas in Atlantic salmon

(2021) B. Cheaib et al.   AQUACULTURE

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

(2021) Fei Xie et al.   Microbiome

AdImpute: An Imputation Method for Single-Cell RNA-Seq Data Based on Semi-Supervised Autoencoders

(2021) Li Xu et al.   Frontiers in Genetics

A full factorial design to investigate interactions of variable essential amino acids, trace minerals and vitamins on Atlantic salmon smoltification and post transfer performance

(2021) Katerina Kousoulaki et al.   Aquaculture Reports

Effects of feed ration and temperature on Chinook salmon (Oncorhynchus tshawytscha) microbiota in freshwater recirculating aquaculture systems

(2021) Ruixiang Zhao et al.   AQUACULTURE

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

(2021) Tom O. Delmont et al.   ISME Journal

Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr

(2021) Vesta Skrodenytė-Arbačiauskienė et al.   MICROBIAL ECOLOGY

Disentangling host–microbiota complexity through hologenomics

(2021) Antton Alberdi et al.   NATURE REVIEWS GENETICS

Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar

(2020) C Heys et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Salinity and fish age affect the gut microbiota of farmed Chinook salmon (Oncorhynchus tshawytscha)

(2020) Ruixiang Zhao et al.   AQUACULTURE

Co-evolution and Co-speciation of Host-Gut Bacteria Systems

(2020) Mathieu Groussin et al.   Cell Host & Microbe

Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research

(2020) Lasse Nyholm et al.   iScience

Diversity of gut microbiomes in marine fishes is shaped by host‐related factors

(2020) Qi Huang et al.   MOLECULAR ECOLOGY

The structural variation landscape in 492 Atlantic salmon genomes

(2020) Alicia C. Bertolotti et al.   Nature Communications

Community-led, integrated, reproducible multi-omics with anvi’o

(2020) A. Murat Eren et al.   Nature Microbiology

Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle

(2019) Beatriz Delgado et al.   Scientific Reports

GToTree: a user-friendly workflow for phylogenomics

(2019) Michael D Lee   BIOINFORMATICS

Adaptive Evolution within Gut Microbiomes of Healthy People

(2019) Shijie Zhao et al.   Cell Host & Microbe

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

(2019) Even Sannes Riiser et al.   ENVIRONMENTAL MICROBIOLOGY

Population genetic analysis reveals a geographically limited transition zone between two genetically distinct Atlantic salmon lineages in Norway

(2019) Vidar Wennevik et al.   Ecology and Evolution

Prevalence and genotypes of infectious salmon anaemia virus (ISAV) in returning wild Atlantic salmon ( Salmo salar L.) in northern Norway

(2019) Abdullah Sami Madhun et al.   JOURNAL OF FISH DISEASES

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

(2019) Nicholas D. Youngblut et al.   Nature Communications

Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade

(2019) Tom O Delmont et al.   eLife

Prevalence of piscine orthoreovirus and salmonid alphavirus in sea-caught returning adult Atlantic salmon (Salmo salar L.) in northern Norway

(2018) A S Madhun et al.   JOURNAL OF FISH DISEASES

Applied Hologenomics: Feasibility and Potential in Aquaculture

(2018) Morten T. Limborg et al.   TRENDS IN BIOTECHNOLOGY

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

(2018) Tom O. Delmont et al.   PeerJ

Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs

(2018) Maelle Sevellec et al.   Microbiome

Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species

(2018) Katharina Fietz et al.   Microbiome

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

(2018) M. Lisandra Zepeda Mendoza et al.   Nature Ecology & Evolution

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)

(2018) Ryan M. Brown et al.   FISH & SHELLFISH IMMUNOLOGY

Lower levels of Persistent Organic Pollutants, metals and the marine omega 3-fatty acid DHA in farmed compared to wild Atlantic salmon ( Salmo salar )

(2017) Anne-Katrine Lundebye et al.   ENVIRONMENTAL RESEARCH

Comprehensive microsatellite baseline for genetic stock identification of Atlantic salmon (Salmo salar L.) in northernmost Europe

(2017) Mikhail Ozerov et al.   ICES JOURNAL OF MARINE SCIENCE

The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders

(2017) C Karlsen et al.   JOURNAL OF FISH DISEASES

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

(2017) Mathieu Groussin et al.   Nature Communications

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

(2017) Thomas Nordahl Petersen et al.   PLoS One

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

(2016) Leighton Pritchard et al.   Analytical Methods

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation?

(2016) Antton Alberdi et al.   TRENDS IN ECOLOGY & EVOLUTION

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

boral - Bayesian Ordination and Regression Analysis of Multivariate Abundance Data in r

(2016) Francis K.C. Hui   Methods in Ecology and Evolution

The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos

(2016) Felix Sommer et al.   Cell Reports

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

Widespread episodic thiamine deficiency in Northern Hemisphere wildlife

(2016) Lennart Balk et al.   Scientific Reports

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

(2015) Chris CR Smith et al.   ISME Journal

The biogeography of the atlantic salmon (Salmo salar) gut microbiome

(2015) Martin S Llewellyn et al.   ISME Journal

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

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

(2015) A. Murat Eren et al.   PeerJ

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

ITEP: An integrated toolkit for exploration of microbial pan-genomes

(2014) Matthew N Benedict et al.   BMC GENOMICS

Gut microbes of mammalian herbivores facilitate intake of plant toxins

(2014) Kevin D. Kohl et al.   ECOLOGY LETTERS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

The thiamine deficiency syndrome M74, a reproductive disorder of Atlantic salmon (Salmo salar) feeding in the Baltic Sea, is related to the fat and thiamine content of prey fish

(2012) M. Keinanen et al.   ICES JOURNAL OF MARINE SCIENCE

THE ROLES OF HOST EVOLUTIONARY RELATIONSHIPS (GENUS: NASONIA) AND DEVELOPMENT IN STRUCTURING MICROBIAL COMMUNITIES

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ggplot2: Elegant Graphics for Data Analysis

(2011) Cedric Ginestet   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS