Publications

185 Publikationen filtern

Die Publikationen filtern

Highlighted authors are members of the University of Jena.

  1. Examining the healthy human microbiome concept

    Year of publicationPublished in:Nature Reviews Microbiology R. Joos, K. Boucher, A. Lavelle, M. Arumugam, M. Blaser, M. Claesson, G. Clarke, P. Cotter, L. De Sordi, M. Dominguez-Bello, B. Dutilh, S. Ehrlich, T. Ghosh, C. Hill, C. Junot, L. Lahti, T. Lawley, T. Licht, E. Maguin, T. Makhalanyane, J. Marchesi, J. Matthijnssens, J. Raes, J. Ravel, A. Salonen, P. Scanlan, A. Shkoporov, C. Stanton, I. Thiele, I. Tolstoy, J. Walter, B. Yang, N. Yutin, A. Zhernakova, H. Zwart, L. Derosa, L. Zitvogel, P. Veiga, C. Vecchi, J. Trebicka, D. Serra, N. Segata, R. Schierwagen, A. Sarati, J. Rodriquez, M. Rhimi, P. Ravaud, P. Prost, N. Pons, F. Pinto, V. Morozova, A. Metwaly, A. Kriaa, A. Krag, S. Kampshoff, A. Jarde, A. Iyappan, M. Israelsen, D. Hazenbrink, Z. Hassani, D. Haller, Y. Godoy, A. Fasano, C. Druart, M. Cordaillat-Simmons, M. Claesson, F. Carraturo, I. Boutron, P. Bork, H. Blottière, F. Betsou, A. Typas, F. Asnicar, J. Doré, R. Ross
    University Bibliography Jena:
    fsu_mods_00017943External link

  3. SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks

    Year of publicationPublished in:ISME Communications A. Van Eijnatten, L. Van Zon, E. Manousou, M. Bikineeva, E. Wubs, W. Van der Putten, E. Morriën, B. Dutilh, L. Snoek
    Correlation networks are commonly used to explore microbiome data. In these networks, nodes are microbial taxa and edges represent correlations between their abundances. As clusters of correlating taxa (co-abundance clusters) often indicate a shared response to environmental drivers, network visualization contributes to the system understanding. Currently,most tools for creating and visualizing co-abundance networks from microbiome data either require the researcher to have coding skills or are not user-friendly, with high time expenditure and limited customizability. Furthermore, existing tools lack a focus on the association between environmental drivers and the structure of the microbiome, even though many edges in correlation networks can be understood through a shared association of two taxa with the environment. For these reasons, we developed SpeSpeNet (Species-Species Network, https://tbb.bio.uu.nl/SpeSpeNet), a practical and user-friendly R-shiny tool to construct and visualize correlation networks from taxonomic abundance tables. The details of data preprocessing, network construction, and visualization are automated, require no programming ability for the web version, and are highly customizable, including associations with user-provided environmental data. Here, we present the details of SpeSpeNet and demonstrate its utility using three case studies.
    University Bibliography Jena:
    fsu_mods_00026957External link

  4. Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025

    Year of publicationPublished in:The Journal of general virology D. Turner, E. Adriaenssens, R. Amann, P. Bardy, N. Bartlau, J. Barylski, S. Błażejak, M. Bouzari, A. Briegel, Y. Briers, D. Carrillo, X. Chen, D. Claessen, R. Cook, M. Crisci, A. Dechesne, P. Deptula, B. Dutilh, B. Ely, L. Fieseler, P. Fogg, A. Fukudome, M. Ganjoor, I. Gientka, K. Holmfeldt, P. Kalatzis, K. Kauffman, A. Kempff, P. Knezevic, E. Koonin, A. Kropinski, M. Krupovic, I. Kurtböke, K. Lambon, R. Lavigne, S. Lehman, H. Liu, C. Lood, R. Lurz, S. Mäntynen, C. Matrishin, M. Middelboe, A. Millard, C. Moraru, D. Nielsen, F. Nobrega, T. Nunoura, H. Oksanen, V. Ongenae, B. Parra, C. Pas, J. Pogliano, M. Poranen, S. Potipimpanon, A. Prichard, H. Pye, D. Rothschild-Rodriguez, D. Rozen, J. Santini, Y. Sha, D. Shymialevich, B. Sokołowska, A. Soleimani-Delfan, P. Średnicka, P. Tavares, A. Telatin, I. Tolstoy, S. Urayama, V. van Neer, F. Vogensen, Q. Wen, A. Wichels, M. Wójcicki, . Ictv Taxonomy Summary Consortium
    This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.
    University Bibliography Jena:
    fsu_mods_00028013External link

  5. Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

    Year of publicationPublished in:Microbiome T. Demina, H. Marttila, I. Pessi, M. Männistö, B. Dutilh, S. Roux, J. Hultman
    Background: Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils. Results: Five virus isolates, Tunturi 1–5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63–98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils. Conclusions: This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic. ¹dEr⁵zbⁿHYtsQKⁱgHwMEJhVⁱdeo Abstract
    University Bibliography Jena:
    fsu_mods_00023295External link

  6. Ultrafast and accurate sequence alignment and clustering of viral genomes

    Year of publicationPublished in:Nature methods: techniques for life scientists and chemists A. Zielezinski, A. Gudyś, J. Barylski, K. Siminski, P. Rozwalak, B. Dutilh, S. Deorowicz
    University Bibliography Jena:
    fsu_mods_00025017External link

  7. Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity

    Year of publicationPublished in:Microbiology Research A. Nair, S. Doijad, M. Suryavanshi, A. Dey, S. Singh Malik, B. Dutilh, S. Barbuddhe
    The early growth phase is a critical period for the development of the chicken gut microbiome. In this study, the spatiotemporal diversity of the gastrointestinal microbiota, shifts in taxonomic composition, and relative abundances of the main bacterial taxa were characterized in Kadaknath, a high-value indigenous Indian chicken breed, using sequencing of the V3–V4 region 16S rRNA gene. To assess microbiome composition and bacterial abundance shifts, three chickens per growth phase (3, 28, and 35 days) were sampled, with microbiota analyzed from three gut regions (crop, small intestine, and ceca) per bird. The results revealed Firmicutes as the most abundant phylum and Lactobacillus as the dominant genus across all stages. Lactobacillus was particularly abundant in the crop at early stages (3 and 28 days), while the ceca exhibited a transition towards the dominance of genus Phocaeicola by day 35. Microbial richness and evenness increased with age, reflecting microbiome maturation, and the analyses of the microbial community composition revealed distinct spatiotemporal differences, with the ceca on day 35 showing the highest differentiation. Pathogen analysis highlighted a peak in poultry-associated taxa Campylobacter, Staphylococcus, and Clostridium paraputrificum in 3-day-old Kadaknath, particularly in the small intestine, underscoring the vulnerability of early growth stages. These findings provide critical insights into age-specific microbiome development and early life-stage susceptibility to pathogens, emphasizing the need for targeted interventions to optimize poultry health management and growth performance.
    University Bibliography Jena:
    fsu_mods_00023419External link

  8. Exogenous carbon-to-nitrogen imbalance drives soil viral roles in microbial carbon mineralization and necromass accrual

    Year of publicationPublished in:Soil Biology and Biochemistry: SBB S. Wang, J. López Arcondo, N. Xie, Y. Wang, Y. Zhang, M. Radosevich, B. Dutilh, X. Liang
    University Bibliography Jena:
    fsu_mods_00027037External link

  9. Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data

    Year of publicationPublished in:Journal of Cheminformatics P. Peets, A. Litos, K. Dührkop, D. Garza, J. van der Hooft, S. Böcker, B. Dutilh
    University Bibliography Jena:
    fsu_mods_00025218External link

  11. Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage

    Year of publicationPublished in:Nature Communications P. de Jonge, B. van den Born, A. Zwinderman, M. Nieuwdorp, B. Dutilh, H. Herrema
    Viruses are core components of the human microbiome, impacting health through interactions with gut bacteria and the immune system. Most human microbiome viruses are bacteriophages, which exclusively infect bacteria. Until recently, most gut virome studies focused on low taxonomic resolution (e.g., viral operational taxonomic units), hampering population-level analyses. We previously identified an expansive and widespread bacteriophage lineage in inhabitants of Amsterdam, the Netherlands. Here, we study their biodiversity and evolution in various human populations. Based on a phylogeny using sequences from six viral genome databases, we propose the Candidatus order Heliusvirales. We identify heliusviruses in 82% of 5441 individuals across 39 studies, and in nine metagenomes from humans that lived in Europe and North America between 1000 and 5000 years ago. We show that a large lineage started to diversify when Homo sapiens first appeared some 300,000 years ago. Ancient peoples and modern hunter-gatherers have distinct Ca. Heliusvirales populations with lower richness than modern urbanized people. Urbanized people suffering from type 1 and type 2 diabetes, as well as inflammatory bowel disease, have higher Ca. Heliusvirales richness than healthy controls. We thus conclude that these ancient core members of the human gut virome have thrived with increasingly westernized lifestyles.
    University Bibliography Jena:
    fsu_mods_00015685External link

  12. Structural color in the bacterial domain: the ecogenomics of a 2-dimensional optical phenotype

    Year of publicationPublished in:Proceedings of the National Academy of Sciences of the United States of America : PNAS A. Zomer, C. Ingham, F. Meijenfeldt, Á. Doncel, G. van de Kerkhof, R. Hamidjaja, S. Schouten, L. Schertel, K. Müller, L. Catón, R. Hahnke, H. Bolhuis, S. Vignolini, B. Dutilh, F. von Meijenfeldt, Á. Escobar Doncel
    Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here, we collected and sequenced a set of 87 structurally colored bacterial isolates and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two-dimensional packing of cells capable of producing SC. A pan-genome-wide association approach was used to identify genes associated with SC. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilization and metabolism, was found to be involved. Using this information, we constructed a classifier to predict SC directly from bacterial genome sequences and validated it by cultivating and scoring 100 strains that were not part of the training set. We predicted that SCr is widely distributed within gram-negative bacteria. Analysis of over 13,000 assembled metagenomes suggested that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides a large-scale ecogenomics view of SC in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon.
    University Bibliography Jena:
    fsu_mods_00015350External link
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