Shinichi Sunagawa

Last Name

Sunagawa

First Name

Shinichi

ORCID

0000-0003-3065-0314

Organisational unit

09583 - Sunagawa, Shinichi / Sunagawa, Shinichi

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Publications 1 - 10 of 121

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean
Hochart, Corentin; Paoli, Lucas Pierre Antoine; Ruscheweyh, Hans-Joachim; et al. (2023)
Nature Communications
Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.
Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition - a metagenomic analysis
Knoll, Rebecca L.; Forslund, Kristoffer; Kultima, Jens R.; et al. (2017)
American Journal of Physiology. Gastrointestinal and Liver Physiology
Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean
Delmont, Tom O.; Gaia, Morgan; Hinsinger, Damien D.; et al. (2022)
Cell Genomics
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice
Wotzka, Sandra Y.; Kreuzer, Markus; Maier, Lisa; et al. (2019)
Nature Microbiology
The microbiota confers colonization resistance, which blocks Salmonella gut colonization1. As diet affects microbiota composition, we studied whether food composition shifts enhance susceptibility to infection. Shifting mice to diets with reduced fibre or elevated fat content for 24 h boosted Salmonella Typhimurium or Escherichia coli gut colonization and plasmid transfer. Here, we studied the effect of dietary fat. Colonization resistance was restored within 48 h of return to maintenance diet. Salmonella gut colonization was also boosted by two oral doses of oleic acid or bile salts. These pathogen blooms required Salmonella’s AcrAB/TolC-dependent bile resistance. Our data indicate that fat-elicited bile promoted Salmonella gut colonization. Both E. coli and Salmonella show much higher bile resistance than the microbiota. Correspondingly, competitive E. coli can be protective in the fat-challenged gut. Diet shifts and fat-elicited bile promote S. Typhimurium gut infections in mice lacking E. coli in their microbiota. This mouse model may be useful for studying pathogen–microbiota–host interactions, the protective effect of E. coli, to analyse the spread of resistance plasmids and assess the impact of food components on the infection process.
Induced endosymbiosis between a fungus and bacterium reveals a shift from antagonism to commensalism
Gassler, Thomas; Giger, Gabriel H.; Sintsova, Anna; et al. (2025)
Nature Communications
Endosymbioses represent dynamic relationships between organisms that may involve antagonistic phases during their emergence. Here, we induced cell-in-cell interactions between the free-living bacterium Ralstonia pickettii and an endosymbiont-free strain of the fungus Rhizopus microsporus using fluidic force microscopy to investigate the early phase of endosymbiosis formation. Following the implantation of bacteria into the cytosol, the rapid proliferation of R. pickettii compromised host fitness, as evidenced by reduced fungal viability, and triggered immune responses characterized by upregulated expression of stress-related defense genes. Vertical transmission of bacteria across fungal generations enabled repeated rounds of selective passaging, ultimately resulting in transcriptional relaxation of the fungal defense response. High-throughput-imaging revealed that the propagated system accommodated higher bacterial loads within viable spores, with a corresponding reduction in fungal growth. The observed physiological changes and comparative fungal transcriptomic profiles indicated adaptive resilience and a shift from antagonism to commensalism. This transition was characterized by attenuated expression of genes involved in cell wall remodeling and reactive oxygen metabolism. Our experimental system provides insights into the early processes of endosymbiosis, supporting the hypothesis that facultative intracellular pathogens can serve as intermediates toward stable endosymbiotic relationships.
Sublethal systemic LPS in mice enables gut-luminal pathogens to bloom through oxygen species-mediated microbiota inhibition
Kroon, Sanne; Malcic, Dejan; Weidert, Lena; et al. (2025)
Nature Communications
Endotoxin-driven systemic immune activation is a common hallmark across various clinical conditions. During acute critical illness, elevated plasma lipopolysaccharide triggers non-specific systemic immune activation. In addition, a compositional shift in the gut microbiota, including an increase in gut-luminal opportunistic pathogens, is observed. Whether a causal link exists between acute endotoxemia and abundance of gut-luminal opportunistic pathogens is incompletely understood. Here, we model acute, pathophysiological lipopolysaccharide concentrations in mice and show that systemic exposure promotes a 100–10’000-fold expansion of Klebsiella pneumoniae, Escherichia coli, Enterococcus faecium and Salmonella Typhimurium in the gut within one day, without overt enteropathy. Mechanistically, this is driven by a Toll-like receptor 4-dependent increase in gut-luminal oxygen species levels, which transiently halts microbiota fermentation and fuels growth of gut-luminal facultative anaerobic pathogens through oxidative respiration. Thus, systemic immune activation transiently perturbs microbiota homeostasis and favours opportunistic pathogens, potentially increasing the risk of infection in critically ill patients.
Critical Assessment of Metagenome Interpretation: the second round of challenges
Meyer, Fernando; Fritz, Adrian; Deng, Zhi-Luo; et al. (2022)
Nature Methods
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.
Determinants of community structure in the global plankton interactome
Lima-Mendez, Gipsi; Faust, Karoline; Henry, Nicolas; et al. (2015)
Science
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
Salazar Guiral, Guillem; Paoli, Lucas Pierre Antoine; Alberti, Adriana; et al. (2019)
Cell
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms.
The rearing environment persistently modulates mouse phenotypes from the molecular to the behavioural level
Jaric, Ivana; Voelkl, Bernhard; Clerc, Melanie; et al. (2022)
PLoS Biology
The phenotype of an organism results from its genotype and the influence of the environment throughout development. Even when using animals of the same genotype, independent studies may test animals of different phenotypes, resulting in poor replicability due to genotype-by-environment interactions. Thus, genetically defined strains of mice may respond differently to experimental treatments depending on their rearing environment. However, the extent of such phenotypic plasticity and its implications for the replicability of research findings have remained unknown. Here, we examined the extent to which common environmental differences between animal facilities modulate the phenotype of genetically homogeneous (inbred) mice. We conducted a comprehensive multicentre study, whereby inbred C57BL/6J mice from a single breeding cohort were allocated to and reared in 5 different animal facilities throughout early life and adolescence, before being transported to a single test laboratory. We found persistent effects of the rearing facility on the composition and heterogeneity of the gut microbial community. These effects were paralleled by persistent differences in body weight and in the behavioural phenotype of the mice. Furthermore, we show that environmental variation among animal facilities is strong enough to influence epigenetic patterns in neurons at the level of chromatin organisation. We detected changes in chromatin organisation in the regulatory regions of genes involved in nucleosome assembly, neuronal differentiation, synaptic plasticity, and regulation of behaviour. Our findings demonstrate that common environmental differences between animal facilities may produce facility-specific phenotypes, from the molecular to the behavioural level. Furthermore, they highlight an important limitation of inferences from single-laboratory studies and thus argue that study designs should take environmental background into account to increase the robustness and replicability of findings.

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Shinichi Sunagawa

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