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  1. Article ; Online: Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut

    Hiroki Nishiyama / Hisashi Endo / Romain Blanc-Mathieu / Hiroyuki Ogata

    Microorganisms, Vol 8, Iss 1663, p

    2020  Volume 1663

    Abstract: The aim of this study was to elucidate the ecological structure of the human gut temperate bacteriophage community and its role in inflammatory bowel disease (IBD). Temperate bacteriophages make up a large proportion of the human gut microbiota and are ... ...

    Abstract The aim of this study was to elucidate the ecological structure of the human gut temperate bacteriophage community and its role in inflammatory bowel disease (IBD). Temperate bacteriophages make up a large proportion of the human gut microbiota and are likely to play a role in IBD pathogenesis. However, many of these bacteriophages await characterization in reference databases. Therefore, we conducted a large-scale reconstruction of temperate bacteriophage and bacterial genomes from the whole-metagenome sequence data generated by the IBD Multi’omics Database project. By associating phages with their hosts via genome comparisons, we found that temperate bacteriophages infect a phylogenetically wide range of bacteria. The majority of variance in bacteriophage community composition was explained by variation among individuals, but differences in the abundance of temperate bacteriophages were identified between IBD and non-IBD patients. Of note, in active ulcerative colitis patients, temperate bacteriophages infecting Bacteroides uniformis and Bacteroides thetaiotaomicron —two species experimentally proven to be beneficial to gut homeostasis—were over-represented, whereas their hosts were under-represented in comparison with non-IBD patients. Supporting the mounting evidence that gut viral community plays a vital role in IBD, our results show potential association between temperate bacteriophages and IBD pathogenesis.
    Keywords temperate bacteriophage ; inflammatory bowel disease ; ulcerative colitis ; Crohn’s disease ; gut microbiota ; Biology (General) ; QH301-705.5
    Subject code 610
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean

    Hisashi Endo / Hiroyuki Ogata / Koji Suzuki

    Scientific Reports, Vol 8, Iss 1, Pp 1-

    2018  Volume 13

    Abstract: Abstract Diatoms and haptophytes are two major phytoplankton groups, playing pivotal roles in global biogeochemical cycles and marine ecosystems. In general, diatoms have higher growth rates than haptophytes, whereas haptophytes tend to have higher ... ...

    Abstract Abstract Diatoms and haptophytes are two major phytoplankton groups, playing pivotal roles in global biogeochemical cycles and marine ecosystems. In general, diatoms have higher growth rates than haptophytes, whereas haptophytes tend to have higher nutrient uptake affinity. However, precise linkages between their ecological traits and geographical distributions remain poorly understood. Herein, we examined the basin-scale variability of the abundance and taxonomic composition of these two phytoplankton groups across 35 sites in the Pacific Ocean using DNA metabarcoding. The diatom community was generally dominated by a few genera at each sample site, whereas the haptophyte community consisted of a large number of genera in most of the sites. The coexistence of various haptophyte genera might be achieved by diversification of their ecophysiological traits such as mixotrophy. On the other hand, the diatom community might experience greater inter-genus competition due to the rapid uptake of nutrients. Our data further supports the notion that their distinct ecological strategies underlie the emergence of contrasting diversity patterns of these phytoplankton groups in the central Pacific at a basin scale.
    Keywords Medicine ; R ; Science ; Q
    Subject code 551
    Language English
    Publishing date 2018-07-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Genomic adaptation of giant viruses in polar oceans

    Lingjie Meng / Tom O. Delmont / Morgan Gaïa / Eric Pelletier / Antonio Fernàndez-Guerra / Samuel Chaffron / Russell Y. Neches / Junyi Wu / Hiroto Kaneko / Hisashi Endo / Hiroyuki Ogata

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 12

    Abstract: Abstract Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of ...

    Abstract Abstract Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus–host network at the polar–nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.
    Keywords Science ; Q
    Subject code 551
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

    Hiroki Ban / Shinya Sato / Shinya Yoshikawa / Kazumasa Yamada / Yoji Nakamura / Mutsuo Ichinomiya / Naoki Sato / Romain Blanc-Mathieu / Hisashi Endo / Akira Kuwata / Hiroyuki Ogata

    Communications Biology, Vol 6, Iss 1, Pp 1-

    2023  Volume 14

    Abstract: Abstract The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister ... ...

    Abstract Abstract The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Response of Spring Diatoms to CO2 Availability in the Western North Pacific as Determined by Next-Generation Sequencing.

    Hisashi Endo / Koji Sugie / Takeshi Yoshimura / Koji Suzuki

    PLoS ONE, Vol 11, Iss 4, p e

    2016  Volume 0154291

    Abstract: Next-generation sequencing (NGS) technologies have enabled us to determine phytoplankton community compositions at high resolution. However, few studies have adopted this approach to assess the responses of natural phytoplankton communities to ... ...

    Abstract Next-generation sequencing (NGS) technologies have enabled us to determine phytoplankton community compositions at high resolution. However, few studies have adopted this approach to assess the responses of natural phytoplankton communities to environmental change. Here, we report the impact of different CO2 levels on spring diatoms in the Oyashio region of the western North Pacific as estimated by NGS of the diatom-specific rbcL gene (DNA), which encodes the large subunit of RubisCO. We also examined the abundance and composition of rbcL transcripts (cDNA) in diatoms to assess their physiological responses to changing CO2 levels. A short-term (3-day) incubation experiment was carried out on-deck using surface Oyashio waters under different pCO2 levels (180, 350, 750, and 1000 μatm) in May 2011. During the incubation, the transcript abundance of the diatom-specific rbcL gene decreased with an increase in seawater pCO2 levels. These results suggest that CO2 fixation capacity of diatoms decreased rapidly under elevated CO2 levels. In the high CO2 treatments (750 and 1000 μatm), diversity of diatom-specific rbcL gene and its transcripts decreased relative to the control treatment (350 μatm), as well as contributions of Chaetocerataceae, Thalassiosiraceae, and Fragilariaceae to the total population, but the contributions of Bacillariaceae increased. In the low CO2 treatment, contributions of Bacillariaceae also increased together with other eukaryotes. These suggest that changes in CO2 levels can alter the community composition of spring diatoms in the Oyashio region. Overall, the NGS technology provided us a deeper understanding of the response of diatoms to changes in CO2 levels in terms of their community composition, diversity, and photosynthetic physiology.
    Keywords Medicine ; R ; Science ; Q
    Subject code 333
    Language English
    Publishing date 2016-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: An intubated 7‐month‐old infant with a retropharyngeal abscess and multidrug‐resistant Streptococcus mitis

    Yoshihisa Watanabe / Yoshiro Nagao / Hisashi Endo / Ichiro Yamane / Masaaki Hirata / Kuniya Hatakeyama

    Clinical Case Reports, Vol 7, Iss 12, Pp 2443-

    2019  Volume 2448

    Abstract: Abstract The profile of antimicrobial resistance (ie, antibiogram) may be disparate between children and adults. An infant developed severe deep neck infection with a multidrug‐resistant microbe. The microbe was more drug‐resistant in children than in ... ...

    Abstract Abstract The profile of antimicrobial resistance (ie, antibiogram) may be disparate between children and adults. An infant developed severe deep neck infection with a multidrug‐resistant microbe. The microbe was more drug‐resistant in children than in adults, in our hospital. Treatment of a child should be guided by the antibiogram obtained from children.
    Keywords age ; antibiogram ; antimicrobial resistance ; antimicrobial susceptibility ; deep neck infection ; pediatrics ; Medicine ; R ; Medicine (General) ; R5-920
    Language English
    Publishing date 2019-12-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: An Optimized Metabarcoding Method for Mimiviridae

    Florian Prodinger / Hisashi Endo / Yasuhiro Gotoh / Yanze Li / Daichi Morimoto / Kimiho Omae / Kento Tominaga / Romain Blanc-Mathieu / Yoshihito Takano / Tetsuya Hayashi / Keizo Nagasaki / Takashi Yoshida / Hiroyuki Ogata

    Microorganisms, Vol 8, Iss 506, p

    2020  Volume 506

    Abstract: Mimiviridae is a group of viruses with large genomes and virions. Ecological relevance of Mimiviridae in marine environments has been increasingly recognized through the discoveries of novel isolates and metagenomic studies. To facilitate ecological ... ...

    Abstract Mimiviridae is a group of viruses with large genomes and virions. Ecological relevance of Mimiviridae in marine environments has been increasingly recognized through the discoveries of novel isolates and metagenomic studies. To facilitate ecological profiling of Mimiviridae , we previously proposed a meta-barcoding approach based on 82 degenerate primer pairs (i.e., MEGAPRIMER) targeting the DNA polymerase gene of Mimiviridae . The method detected a larger number of operational taxonomic units (OTUs) in environmental samples than previous methods. However, it required large quantities of DNA and was laborious due to the use of individual primer pairs. Here, we examined coastal seawater samples using varying PCR conditions and purification protocols to streamline the MEGAPRIMER method. Mixing primer pairs in “cocktails” reduced the required amount of environmental DNA by 90%, while reproducing the results obtained by the original protocol. We compared the results obtained by the meta-barcoding approach with quantifications using qPCR for selected OTUs. This revealed possible amplification biases among different OTUs, but the frequency profiles for individual OTUs across multiple samples were similar to those obtained by qPCR. We anticipate that the newly developed MEGAPRIMER protocols will be useful for ecological investigation of Mimiviridae in a larger set of environmental samples.
    Keywords ‘Megaviridae’ ; Mimiviridae ; DNA polymerase ; MEGAPRIMER ; primer cocktail ; Biology (General) ; QH301-705.5
    Subject code 500
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

    Hiroto Kaneko / Romain Blanc-Mathieu / Hisashi Endo / Samuel Chaffron / Tom O. Delmont / Morgan Gaia / Nicolas Henry / Rodrigo Hernández-Velázquez / Canh Hao Nguyen / Hiroshi Mamitsuka / Patrick Forterre / Olivier Jaillon / Colomban de Vargas / Matthew B. Sullivan / Curtis A. Suttle / Lionel Guidi / Hiroyuki Ogata

    iScience, Vol 24, Iss 1, Pp 102002- (2021)

    2021  

    Abstract: Summary: The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export ... ...

    Abstract Summary: The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral “shunt” and “shuttle”). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.
    Keywords Oceanography ; Biogeoscience ; Global Carbon Cycle ; Virology ; Viral Microbiology ; Carbon Cycle ; Science ; Q
    Subject code 550
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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