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  1. Article ; Online: Studying the gut virome in the metagenomic era

    Sanzhima Garmaeva / Trishla Sinha / Alexander Kurilshikov / Jingyuan Fu / Cisca Wijmenga / Alexandra Zhernakova

    BMC Biology, Vol 17, Iss 1, Pp 1-

    challenges and perspectives

    2019  Volume 14

    Abstract: Abstract The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses ... ...

    Abstract Abstract The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2019-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Genetic, parental and lifestyle factors influence telomere length

    Sergio Andreu-Sánchez / Geraldine Aubert / Aida Ripoll-Cladellas / Sandra Henkelman / Daria V. Zhernakova / Trishla Sinha / Alexander Kurilshikov / Maria Carmen Cenit / Marc Jan Bonder / Lude Franke / Cisca Wijmenga / Jingyuan Fu / Monique G. P. van der Wijst / Marta Melé / Peter Lansdorp / Alexandra Zhernakova

    Communications Biology, Vol 5, Iss 1, Pp 1-

    2022  Volume 14

    Abstract: Deep molecular and phenotypic data highlights the links of human telomere lengths from six different blood cells with genetics, parental phenotypes mediated by epigenetic signals and expression changes at the single cell level. ...

    Abstract Deep molecular and phenotypic data highlights the links of human telomere lengths from six different blood cells with genetics, parental phenotypes mediated by epigenetic signals and expression changes at the single cell level.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Stability of the human gut virome and effect of gluten-free diet

    Sanzhima Garmaeva / Anastasia Gulyaeva / Trishla Sinha / Andrey N. Shkoporov / Adam G. Clooney / Stephen R. Stockdale / Johanne E. Spreckels / Thomas D.S. Sutton / Lorraine A. Draper / Bas E. Dutilh / Cisca Wijmenga / Alexander Kurilshikov / Jingyuan Fu / Colin Hill / Alexandra Zhernakova

    Cell Reports, Vol 35, Iss 7, Pp 109132- (2021)

    2021  

    Abstract: Summary: The human gut microbiome consists of bacteria, archaea, eukaryotes, and viruses. The gut viruses are relatively underexplored. Here, we longitudinally analyzed the gut virome composition in 11 healthy adults: its stability, variation, and the ... ...

    Abstract Summary: The human gut microbiome consists of bacteria, archaea, eukaryotes, and viruses. The gut viruses are relatively underexplored. Here, we longitudinally analyzed the gut virome composition in 11 healthy adults: its stability, variation, and the effect of a gluten-free diet. Using viral enrichment and a de novo assembly-based approach, we demonstrate the quantitative dynamics of the gut virome, including dsDNA, ssDNA, dsRNA, and ssRNA viruses. We observe highly divergent individual viral communities, carrying on an average 2,143 viral genomes, 13.1% of which were present at all 3 time points. In contrast to previous reports, the Siphoviridae family dominates over Microviridae in studied individual viromes. We also show individual viromes to be stable at the family level but to vary substantially at the genera and species levels. Finally, we demonstrate that lower initial diversity of the human gut virome leads to a more pronounced effect of the dietary intervention on its composition.
    Keywords gut ; virome ; bacteriophage ; microbiome ; gluten ; viral-like particles ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Relationship between gut microbiota and circulating metabolites in population-based cohorts

    Dina Vojinovic / Djawad Radjabzadeh / Alexander Kurilshikov / Najaf Amin / Cisca Wijmenga / Lude Franke / M. Arfan Ikram / Andre G. Uitterlinden / Alexandra Zhernakova / Jingyuan Fu / Robert Kraaij / Cornelia M. van Duijn

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 7

    Abstract: Here, the authors provide an in-depth study of the metabolome in two large population-based prospective cohorts and identify 32 microbial traits associated with various metabolic biomarkers and specific lipoprotein subfractions, providing insights into ... ...

    Abstract Here, the authors provide an in-depth study of the metabolome in two large population-based prospective cohorts and identify 32 microbial traits associated with various metabolic biomarkers and specific lipoprotein subfractions, providing insights into the role of microbiota in influencing host lipid levels.
    Keywords Science ; Q
    Language English
    Publishing date 2019-12-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Relationship between gut microbiota and circulating metabolites in population-based cohorts

    Dina Vojinovic / Djawad Radjabzadeh / Alexander Kurilshikov / Najaf Amin / Cisca Wijmenga / Lude Franke / M. Arfan Ikram / Andre G. Uitterlinden / Alexandra Zhernakova / Jingyuan Fu / Robert Kraaij / Cornelia M. van Duijn

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 7

    Abstract: Here, the authors provide an in-depth study of the metabolome in two large population-based prospective cohorts and identify 32 microbial traits associated with various metabolic biomarkers and specific lipoprotein subfractions, providing insights into ... ...

    Abstract Here, the authors provide an in-depth study of the metabolome in two large population-based prospective cohorts and identify 32 microbial traits associated with various metabolic biomarkers and specific lipoprotein subfractions, providing insights into the role of microbiota in influencing host lipid levels.
    Keywords Science ; Q
    Language English
    Publishing date 2019-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Impact of commonly used drugs on the composition and metabolic function of the gut microbiota

    Arnau Vich Vila / Valerie Collij / Serena Sanna / Trishla Sinha / Floris Imhann / Arno R. Bourgonje / Zlatan Mujagic / Daisy M. A. E. Jonkers / Ad A. M. Masclee / Jingyuan Fu / Alexander Kurilshikov / Cisca Wijmenga / Alexandra Zhernakova / Rinse K. Weersma

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 11

    Abstract: Here, via a metagenomics analysis of population-based and disease cohorts, Vich Vila et al. study the impact of 41 commonly used medications on the taxonomic structures, metabolic potential and resistome of the gut microbiome, underscoring the importance ...

    Abstract Here, via a metagenomics analysis of population-based and disease cohorts, Vich Vila et al. study the impact of 41 commonly used medications on the taxonomic structures, metabolic potential and resistome of the gut microbiome, underscoring the importance of correcting for multiple drug use in microbiome studies.
    Keywords Science ; Q
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Impact of commonly used drugs on the composition and metabolic function of the gut microbiota

    Arnau Vich Vila / Valerie Collij / Serena Sanna / Trishla Sinha / Floris Imhann / Arno R. Bourgonje / Zlatan Mujagic / Daisy M. A. E. Jonkers / Ad A. M. Masclee / Jingyuan Fu / Alexander Kurilshikov / Cisca Wijmenga / Alexandra Zhernakova / Rinse K. Weersma

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 11

    Abstract: Here, via a metagenomics analysis of population-based and disease cohorts, Vich Vila et al. study the impact of 41 commonly used medications on the taxonomic structures, metabolic potential and resistome of the gut microbiome, underscoring the importance ...

    Abstract Here, via a metagenomics analysis of population-based and disease cohorts, Vich Vila et al. study the impact of 41 commonly used medications on the taxonomic structures, metabolic potential and resistome of the gut microbiome, underscoring the importance of correcting for multiple drug use in microbiome studies.
    Keywords Science ; Q
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: MicroRNA drop in the bloodstream and microRNA boost in the tumour caused by treatment with ribonuclease A leads to an attenuation of tumour malignancy.

    Nadezhda Mironova / Olga Patutina / Evgenyi Brenner / Alexander Kurilshikov / Valentin Vlassov / Marina Zenkova

    PLoS ONE, Vol 8, Iss 12, p e

    2013  Volume 83482

    Abstract: Novel data showing an important role of microRNAs in mediating tumour progression opened a new field of possible molecular targets for cytotoxic ribonucleases. Recently, antitumour and antimetastatic activities of pancreatic ribonuclease A were ... ...

    Abstract Novel data showing an important role of microRNAs in mediating tumour progression opened a new field of possible molecular targets for cytotoxic ribonucleases. Recently, antitumour and antimetastatic activities of pancreatic ribonuclease A were demonstrated and here genome-wide profiles of microRNAs in the tumour and blood of mice bearing Lewis lung carcinoma after treatment with RNase A were analysed by high-throughput Sequencing by Oligonucleotide Ligation and Detection (SOLiD™) sequencing technology. Sequencing data showed that RNase A therapy resulted in the boost of 116 microRNAs in tumour tissue and a significant drop of 137 microRNAs in the bloodstream that were confirmed by qPCR. The microRNA boost in the tumour was accompanied by the overexpression of microRNA processing genes: RNASEN (Drosha), xpo5, dicer1, and eif2c2 (Ago2). Ribonuclease activity of RNase A was shown to be crucial for the activation of both microRNA synthesis and expression of the microRNA processing genes. In the tumour tissue, RNase A caused the upregulation of both oncomirs and tumour-suppressor microRNAs, including microRNAs of the let-7 family, known to negatively regulate tumour progression. Our results suggest that the alteration of microRNA signature caused by RNase A treatment leads to the attenuation of tumour malignancy.
    Keywords Medicine ; R ; Science ; Q
    Subject code 616
    Language English
    Publishing date 2013-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Detection of stable community structures within gut microbiota co-occurrence networks from different human populations

    Matthew A. Jackson / Marc Jan Bonder / Zhana Kuncheva / Jonas Zierer / Jingyuan Fu / Alexander Kurilshikov / Cisca Wijmenga / Alexandra Zhernakova / Jordana T. Bell / Tim D. Spector / Claire J. Steves

    PeerJ, Vol 6, p e

    2018  Volume 4303

    Abstract: Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa ... ...

    Abstract Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.
    Keywords Microbiome ; Gut ; Human ; Population ; Networks ; Co-occurrence ; Medicine ; R ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2018-02-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Intestinal microbiome composition and its relation to joint pain and inflammation

    Cindy G. Boer / Djawad Radjabzadeh / Carolina Medina-Gomez / Sanzhima Garmaeva / Dieuwke Schiphof / Pascal Arp / Thomas Koet / Alexander Kurilshikov / Jingyuan Fu / M. Arfan Ikram / Sita Bierma-Zeinstra / André G. Uitterlinden / Robert Kraaij / Alexandra Zhernakova / Joyce B. J. van Meurs

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 9

    Abstract: Alterations to the microbiome are now associated with various diseases. Here the authors analyze microbiomes from a large population based cohort and show positive correlations between abundance of Streptococcus spp. and osteoarthritis-related knee pain. ...

    Abstract Alterations to the microbiome are now associated with various diseases. Here the authors analyze microbiomes from a large population based cohort and show positive correlations between abundance of Streptococcus spp. and osteoarthritis-related knee pain.
    Keywords Science ; Q
    Language English
    Publishing date 2019-10-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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