List of works - Shinichi Sunagawa

A community perspective on the concept of marine holobionts: current status, challenges, and future directions

scientific article published on 25 February 2021

A cross-biomes bacterial diversity shed light on ocean-atmosphere microbial transmission

A fair comparison

scientific article published in April 2014

A general non-self response as part of plant immunity

scientific article published in 2021

A global ocean atlas of eukaryotic genes.

scientific article published on 25 January 2018

A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli

scientific article published on 14 April 2020

A roadmap for metagenomic enzyme discovery

publication published on 17 November 2021

Accurate and universal delineation of prokaryotic species ⬇️

scientific article published on July 28, 2013

An integrated catalog of reference genes in the human gut microbiome

scientific article

Antibiotics-induced monodominance of a novel gut bacterial order

scientific article published on 18 January 2019

Assessment of metagenomic assembly using simulated next generation sequencing data

scientific article

Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata

scientific article

Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions

scientific article published on 07 September 2020

Classification and quantification of bacteriophage taxa in human gut metagenomes

scientific article

Computational eco-systems biology in Tara Oceans: translating data into knowledge

scientific article

Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species

scientific article published on 17 October 2019

Coral host transcriptomic states are correlated with Symbiodinium genotypes

scientific article published on 8 February 2010

Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.

scientific article

Country-specific antibiotic use practices impact the human gut resistome

scientific article published on 08 April 2013

Critical Assessment of Metagenome Interpretation: the second round of challenges

scientific article published in April 2022

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton

scientific article

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

scientific article

Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata

scientific article

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

scientific article published on 11 February 2020

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

scientific article published on 2 December 2015

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

scientific article

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

scientific article

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

scientific article published in 2023

Enterotypes in the landscape of gut microbial community composition.

scientific article published on 18 December 2017

Enterotypes of the human gut microbiome

scientific article

Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice

scientific article published on 07 October 2019

Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium).

scientific article

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

scientific article

Extensive Transmission of Microbes along the Gastrointestinal Tract

article

Extensive transmission of microbes along the gastrointestinal tract

article

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

scientific article published on 01 November 2019

Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata

article

Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont

scientific article

Genomic variation landscape of the human gut microbiome

scientific article

Global genetic capacity for mixotrophy in marine picocyanobacteria

scientific article

Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes).

scientific article published on 2 September 2015

Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation

scientific article published on 16 May 2019

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis

scientific article published on 30 December 2016

High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

scientific article published on 29 March 2021

Human gut microbes impact host serum metabolome and insulin sensitivity

scientific article

Hyperthermic stress-induced increase in the expression of glutamate-cysteine ligase and glutathione levels in the symbiotic sea anemone Aiptasia pallida

scientific article

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

scientific article published on 6 July 2014

Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals

scientific article

Individuality and temporal stability of the human gut microbiome.

scientific article published in January 2013

Inter-individual differences in the gene content of human gut bacterial species

scientific article published on 21 April 2015

MOCAT2: a metagenomic assembly, annotation and profiling framework

scientific article

MOCAT: a metagenomics assembly and gene prediction toolkit

scientific article

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Marine microbial diversity

scientific article published on June 2017

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

scientific article published on 01 April 2019

Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities

scientific article published in 2023

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

scientific article published on 18 September 2013

Metagenomic analysis of gut microbial communities from a Central Asian population

article

Metagenomic insights into the human gut resistome and the forces that shape it.

scientific article published on 29 January 2014

Metagenomic species profiling using universal phylogenetic marker genes

scientific article

Microbial abundance, activity and population genomic profiling with mOTUs2

scientific article published on 4 March 2019

Microbiota stability in healthy individuals after single-dose lactulose challenge-A randomized controlled study

scientific article published in PLoS ONE

Minimum Information about an Uncultivated Virus Genome (MIUViG)

scientific article published on 17 December 2018

Natural noncanonical protein splicing yields products with diverse β-amino acid residues

scientific article published in February 2018

Ocean plankton. Determinants of community structure in the global plankton interactome

scientific article published on May 2015

Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport

scientific article

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

scientific article published on May 2015

Ocean plankton. Patterns and ecological drivers of ocean viral communities

scientific article published on May 2015

Ocean plankton. Structure and function of the global ocean microbiome

scientific article published on May 2015

Plankton networks driving carbon export in the oligotrophic ocean

scientific article

Potential of fecal microbiota for early-stage detection of colorectal cancer

scientific article

Publisher Correction: Enterotypes in the landscape of gut microbial community composition

scientific article published on 13 February 2018

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes

scientific article published on 31 October 2017

RNase H As Gene Modifier, Driver of Evolution and Antiviral Defense

scientific article published on 14 September 2017

Rapid evolution of coral proteins responsible for interaction with the environment

scientific article

Richness of human gut microbiome correlates with metabolic markers

scientific article (publication date: 29 August 2013)

Salt-responsive gut commensal modulates TH17 axis and disease

scientific article published on 15 November 2017

Scaling of species distribution explains the vast potential marine prokaryote diversity

scientific article published on 10 December 2019

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

scientific article published on 22 January 2018

Space, time and microdiversity: towards a resolution revolution in microbiomics

scientific article published on 15 October 2020

Structure and function of the global topsoil microbiome

scientific article published in Nature

Subspecies in the global human gut microbiome.

scientific article published on 14 December 2017

Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals

scientific article

Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere

scientific article published on 26 September 2019

Tara Oceans: towards global ocean ecosystems biology

scientific article published on 12 May 2020

Temporal and technical variability of human gut metagenomes

scientific article published on 8 April 2015

Terrestrial and marine influence on atmospheric bacterial diversity over the north Atlantic and Pacific Oceans

scientific article published in 2022

The Ocean Gene Atlas: exploring the biogeography of plankton genes online.

scientific article published in July 2018

The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean

scientific article published on 23 September 2019

The host transcriptome remains unaltered during the establishment of coral-algal symbioses.

scientific article

The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves

scientific article published on 30 June 2021

The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database.

scientific article

Threatened corals provide underexplored microbial habitats

scientific article

Towards standards for human fecal sample processing in metagenomic studies.

scientific article

Towards the biogeography of prokaryotic genes

scientific article published in 2021

Transcriptomic responses to darkness stress point to common coral bleaching mechanisms

article

Transcriptomic responses to heat stress and bleaching in the elkhorn coral Acropora palmata

article

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

scientific article (publication date: 17 November 2015)

metaSNV: A tool for metagenomic strain level analysis

scientific article

miR-802 regulates Paneth cell function and enterocyte differentiation in the mouse small intestine

scientific article published on 07 June 2021

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

scientific article published on 01 January 2020

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

scientific article

List of works by Shinichi Sunagawa

A community perspective on the concept of marine holobionts: current status, challenges, and future directions

A cross-biomes bacterial diversity shed light on ocean-atmosphere microbial transmission

A fair comparison

A general non-self response as part of plant immunity

A global ocean atlas of eukaryotic genes.

A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli

A roadmap for metagenomic enzyme discovery

Accurate and universal delineation of prokaryotic species ⬇️

An integrated catalog of reference genes in the human gut microbiome

Antibiotics-induced monodominance of a novel gut bacterial order

Assessment of metagenomic assembly using simulated next generation sequencing data

Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata

Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions

Classification and quantification of bacteriophage taxa in human gut metagenomes

Computational eco-systems biology in Tara Oceans: translating data into knowledge

Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species

Coral host transcriptomic states are correlated with Symbiodinium genotypes

Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.

Country-specific antibiotic use practices impact the human gut resistome

Critical Assessment of Metagenome Interpretation: the second round of challenges

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Enterotypes in the landscape of gut microbial community composition.

Enterotypes of the human gut microbiome

Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice

Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium).

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Extensive Transmission of Microbes along the Gastrointestinal Tract

Extensive transmission of microbes along the gastrointestinal tract

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata

Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont

Genomic variation landscape of the human gut microbiome

Global genetic capacity for mixotrophy in marine picocyanobacteria

Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes).

Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis

High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

Human gut microbes impact host serum metabolome and insulin sensitivity

Hyperthermic stress-induced increase in the expression of glutamate-cysteine ligase and glutathione levels in the symbiotic sea anemone Aiptasia pallida

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals

Individuality and temporal stability of the human gut microbiome.

Inter-individual differences in the gene content of human gut bacterial species

MOCAT2: a metagenomic assembly, annotation and profiling framework

MOCAT: a metagenomics assembly and gene prediction toolkit

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Marine microbial diversity

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

Metagenomic analysis of gut microbial communities from a Central Asian population

Metagenomic insights into the human gut resistome and the forces that shape it.

Metagenomic species profiling using universal phylogenetic marker genes

Microbial abundance, activity and population genomic profiling with mOTUs2

Microbiota stability in healthy individuals after single-dose lactulose challenge-A randomized controlled study

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Natural noncanonical protein splicing yields products with diverse β-amino acid residues

Ocean plankton. Determinants of community structure in the global plankton interactome

Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

Ocean plankton. Patterns and ecological drivers of ocean viral communities

Ocean plankton. Structure and function of the global ocean microbiome

Plankton networks driving carbon export in the oligotrophic ocean

Potential of fecal microbiota for early-stage detection of colorectal cancer

Publisher Correction: Enterotypes in the landscape of gut microbial community composition

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes

RNase H As Gene Modifier, Driver of Evolution and Antiviral Defense

Rapid evolution of coral proteins responsible for interaction with the environment

Richness of human gut microbiome correlates with metabolic markers

Salt-responsive gut commensal modulates TH17 axis and disease

Scaling of species distribution explains the vast potential marine prokaryote diversity