{"entity": "researcher", "timestamp": "2026-07-14T00:48:05.761Z", "family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "affiliations": ["Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden. anders.andersson@scilifelab.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2"}}, "publications": [{"entity": "publication", "iuid": "9bafa70241894ebcab4e2bf9d0640d40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bafa70241894ebcab4e2bf9d0640d40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bafa70241894ebcab4e2bf9d0640d40"}}, "title": "Comparing DNA metabarcoding with light microscopy to identify eukaryotic phytoplankton in the Baltic Sea, Kattegat and Skagerrak", "authors": [{"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Brugel", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1298-3839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Hedblom", "given": "Mikael", "initials": "M"}, {"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT", "orcid": "0000-0001-9544-5755", "researcher": {"href": "https://publications.scilifelab.se/researcher/896a2f678e3143a2b855c1afa8e93499.json"}}, {"family": "Karlson", "given": "Bengt", "initials": "B", "orcid": "0000-0002-7524-3504", "researcher": {"href": "https://publications.scilifelab.se/researcher/44722b5ece5b420bb59fdb749833f443.json"}}, {"family": "Latz", "given": "Meike A C", "initials": "MAC", "orcid": "0000-0002-6583-9291", "researcher": {"href": "https://publications.scilifelab.se/researcher/664c30300eab4888a2e5562e077aab01.json"}}, {"family": "Lindh", "given": "Markus", "initials": "M"}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}], "type": "journal-article", "published": "2026-05-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Marine phytoplankton monitoring has long relied on microscopy, but DNA metabarcoding has recently emerged as a complementary approach. This study assessed the applicability of DNA metabarcoding of the 18S ribosomal RNA gene in marine monitoring and compared its results with conventional microscopy. We analyzed data from 232 surface water samples from 17 monitoring stations in the Baltic Sea, Kattegat, and Skagerrak. Metabarcoding detected more orders, genera, and species than microscopy, with a 43% overlap in the most common genera identified by both methods. Despite attempts to normalize sequence reads to spike-in DNA or DNA concentrations, the correlations between abundances derived from the two methods were weak, though varied considerably between taxonomic groups and geographical areas. Correlations were consistently stronger when using carbon and biovolume concentrations than cell abundances. Our results highlight the potential of metabarcoding to expand biodiversity assessments and advance our understanding of microbial biodiversity in marine ecosystems. As a complement to microscopy, it can enhance existing monitoring efforts. Future improvements in reference database completeness, adoption of long-read sequencing technologies, and better characterization of gene copy number variability per cell are needed to further extend the applicability of metabarcoding for quantitative analyses.", "doi": "10.1038/s41598-026-48838-z", "pmid": "42156811", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13190673"}, {"db": "pii", "key": "10.1038/s41598-026-48838-z"}], "notes": [], "created": "2026-06-08T17:17:40.513Z", "modified": "2026-07-04T18:59:51.656Z"}, {"entity": "publication", "iuid": "16a8d45180854dfdb468144fa9775e34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16a8d45180854dfdb468144fa9775e34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16a8d45180854dfdb468144fa9775e34"}}, "title": "Generalist phyllosphere taxa dominate microbial communities on macrophytes across a natural salinity gradient", "authors": [{"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Fen\u00e1ndez-Ju\u00e1rez", "given": "Victor", "initials": "V"}, {"family": "Delgado", "given": "Luis F", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Bengtsson", "given": "Mia M", "initials": "MM"}, {"family": "Gyraite", "given": "Greta", "initials": "G", "orcid": "0000-0002-7079-7997", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9fa8139fbc64e7e990587ca8e5f6d52.json"}}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH", "orcid": "0000-0002-8961-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b27965acd74a7a95e97b77abee769d.json"}}, {"family": "Katarzyte", "given": "Marija", "initials": "M"}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Martin", "given": "Georg", "initials": "G", "orcid": "0000-0002-5289-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa7c61072034af188ed3685ce83ca3c.json"}}, {"family": "Rakowski", "given": "Marcin", "initials": "M"}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}], "type": "journal-article", "published": "2026-04-04", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "21", "issue": "1", "issn-l": null}, "abstract": "Shallow coastal habitats are characterized by diverse macrophytes and often feature steep abiotic gradients, including salinity variations, which can shape the leaf- surface epi-microbiome (phyllosphere). To elucidate the effect of salinity and host identity on the phyllosphere of aquatic macrophytes in shallow water, we sampled the leaf surface microbiota across a salinity range of 6-15. Samples included the eelgrass Zostera marina, as well as the Eurasian water milfoil (Myriophyllum spicatum), muskgrass (Chara spp.), and sago pondweed (Stuckenia pectinata) in the brackish Baltic Sea during the summer of 2022. Microbial communities were characterized using 16S and 18S rRNA gene amplicon sequencing.\n\nAs hypothesized, the phyllosphere bacterial and protist community composition was distinct from the surrounding seawater microbiome. Typically associated taxa included the genera Loktanella, Pseudorhodobacter, the methylotrophic genus Methylotenera, unclassified Synechococcales, and Rhodobacteriaceae. Protist genera such as Picochlorum were consistently detected across all macrophyte hosts, while Cocconeis, Cyclotella, Mondous and unclassified Bacillariophyceae were present in all phyllospheres except Chara spp. Both, salinity and host species significantly influenced the composition and prevalence of the microbiota, primarily through shifts in the abundance of typical phyllosphere taxa. However, only 4-11% of phyllosphere taxa were uniquely associated with a specific salinity or macrophyte host.\n\nOur results demonstrate that aquatic macrophytes harbor a distinct and characteristic phyllosphere microbiome. The low proportion of host- or salinity specific taxa suggests that the most abundant members of this community are generalists, broadly adapted to the phyllosphere niche rather than being narrowly specialized. This implies that the presence of the macrophyte itself, providing a stable, nutrient-rich surface, exerts a stronger deterministic influence on the microbial community than the host identity or salinity fluctuations. Consequently, the phyllosphere appears relatively resilient to environmental variability, particularly salinity fluctuations. This highlights the robust nature of host-microbiome interactions and their importance for conservation of aquatic macrophyte ecosystems.", "doi": "10.1186/s40793-026-00881-z", "pmid": "41935342", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13067490"}, {"db": "pii", "key": "10.1186/s40793-026-00881-z"}], "notes": [], "created": "2026-04-10T12:05:26.160Z", "modified": "2026-04-16T09:42:39.411Z"}, {"entity": "publication", "iuid": "a4925370cf2840a29d01394990c7cb68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4925370cf2840a29d01394990c7cb68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4925370cf2840a29d01394990c7cb68"}}, "title": "Spatial overlap and temporal synchrony between guilds of insect hosts and parasitoids", "authors": [{"family": "van Dijk", "given": "Laura J A", "initials": "LJA", "orcid": "0000-0003-1015-8496", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c9432c19234fd5bc5dfc0a037dae0f.json"}}, {"family": "Goodsell", "given": "Robert M", "initials": "RM", "orcid": "0000-0002-3349-1876", "researcher": {"href": "https://publications.scilifelab.se/researcher/84f42755a394403b95486707bf4a83bd.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Fisher", "given": "Brian L", "initials": "BL", "orcid": "0000-0002-4653-3270", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e4747cc54254e8181f595e6fe21b953.json"}}, {"family": "Iwaszkiewicz\u2010Eggebrecht", "given": "Elzbieta", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Lukasik", "given": "Piotr", "initials": "P"}, {"family": "Miraldo", "given": "Andreia", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Pe\u00f1a\u2010Aguilera", "given": "Pablo", "initials": "P"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}], "type": "journal-article", "published": "2026-02-10", "journal": {"title": "Journal of Animal Ecology", "issn": "0021-8790", "issn-l": null}, "abstract": "How communities are structured into functional groups and trophic layers is key to understanding ecosystem functioning. Nonetheless, we lack insights about spatiotemporal variation in guild composition of communities and its causes. To investigate spatial and temporal patterns and drivers of variation in insect feeding guilds, we combined data from a nationwide survey of Swedish insects using Malaise traps and DNA metabarcoding with a comprehensive trait database. We assigned species into one of three feeding guilds (phytophages, saprophages, predators) or into one of three associated parasitoid guilds. We then analysed patterns in species richness for each guild. Species richness declined with latitude in all guilds. Beyond this gradient, local variation in species richness matched between hosts and their parasitoids. Yet, hosts and their parasitoids responded differently to habitat. The phenological peak of parasitoid species richness appeared later than the peak of their hosts, but the length of time lags varied among guilds. Spatiotemporal patterns were driven by guild-specific responses to temperature, though much variation remained between seasons and locations even when controlling for temperature. Overall, these patterns suggest that shifts in both climate and land use may alter the synchrony of insect trophic layers, with unknown consequences.", "doi": "10.1111/1365-2656.70228", "pmid": "41665095", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2026-02-27T13:20:10.573Z", "modified": "2026-03-24T09:07:39.535Z"}, {"entity": "publication", "iuid": "394d345f587e4a8fa382227d3718c80e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/394d345f587e4a8fa382227d3718c80e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/394d345f587e4a8fa382227d3718c80e"}}, "title": "HAPP: High-accuracy pipeline for processing deep metabarcoding data.", "authors": [{"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Granqvist", "given": "Emma", "initials": "E", "orcid": "0000-0002-1513-1674", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b07f15f8724fdbbcdf34e6d6837147.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "van Dijk", "given": "Laura J A", "initials": "LJA"}, {"family": "Goodsell", "given": "Robert", "initials": "R"}, {"family": "Godeiro", "given": "Nerivania N", "initials": "NN", "orcid": "0000-0002-1669-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/990e5c3362f94d76af29742ab5876a8a.json"}}, {"family": "Bellini", "given": "Bruno C", "initials": "BC"}, {"family": "Orsholm", "given": "Johanna", "initials": "J"}, {"family": "\u0141ukasik", "given": "Piotr", "initials": "P"}, {"family": "Miraldo", "given": "Andreia", "initials": "A"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "PLoS Comput. Biol.", "issn": "1553-7358", "issn-l": "1553-734X", "volume": "21", "issue": "11", "pages": "e1013558"}, "abstract": "Deep metabarcoding offers an efficient and reproducible approach to biodiversity monitoring, but noisy data and incomplete reference databases challenge accurate diversity estimation and taxonomic annotation. Here, we introduce a novel algorithm, NEEAT, for removing spurious operational taxonomic units (OTUs) originating from nuclear-embedded mitochondrial DNA sequences (NUMTs) or sequencing errors. It integrates 'echo' signals across samples with the identification of unusual evolutionary patterns among similar DNA sequences. We also extensively benchmark current tools for chimera removal, taxonomic annotation and OTU clustering of deep metabarcoding data. The best performing tools/parameter settings are integrated into HAPP, a high-accuracy pipeline for processing deep metabarcoding data. Tests using CO1 data from BOLD and large-scale metabarcoding data on insects demonstrate that HAPP significantly outperforms existing methods, while enabling efficient analysis of extensive datasets by parallelizing computations across taxonomic groups.", "doi": "10.1371/journal.pcbi.1013558", "pmid": "41202092", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12622834"}, {"db": "pii", "key": "PCOMPBIOL-D-25-00687"}], "notes": [], "created": "2025-11-21T11:45:11.315Z", "modified": "2025-11-21T12:27:09.804Z"}, {"entity": "publication", "iuid": "14a490b69be949de8cbbefbdfbe5d0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14a490b69be949de8cbbefbdfbe5d0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14a490b69be949de8cbbefbdfbe5d0e5"}}, "title": "Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar.", "authors": [{"family": "Miraldo", "given": "A", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Sundh", "given": "J", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "E", "initials": "E"}, {"family": "Buczek", "given": "M", "initials": "M"}, {"family": "Goodsell", "given": "R", "initials": "R"}, {"family": "Johansson", "given": "H", "initials": "H"}, {"family": "Fisher", "given": "B L", "initials": "BL", "orcid": "0000-0002-4653-3270", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e4747cc54254e8181f595e6fe21b953.json"}}, {"family": "Raharinjanahary", "given": "D", "initials": "D"}, {"family": "Rajoelison", "given": "E T", "initials": "ET"}, {"family": "Ranaivo", "given": "C", "initials": "C"}, {"family": "Randrianandrasana", "given": "C", "initials": "C"}, {"family": "Rafanomezantsoa", "given": "J-J", "initials": "J"}, {"family": "Manoharan", "given": "L", "initials": "L"}, {"family": "Granqvist", "given": "E", "initials": "E", "orcid": "0000-0002-1513-1674", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b07f15f8724fdbbcdf34e6d6837147.json"}}, {"family": "van Dijk", "given": "L J A", "initials": "LJA"}, {"family": "Alberg", "given": "L", "initials": "L"}, {"family": "\u00c5hl\u00e9n", "given": "D", "initials": "D"}, {"family": "Aspebo", "given": "M", "initials": "M"}, {"family": "\u00c5str\u00f6m", "given": "S", "initials": "S"}, {"family": "Bellviken", "given": "A", "initials": "A"}, {"family": "Bergman", "given": "P-E", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "S", "initials": "S"}, {"family": "Bj\u00f6rkman", "given": "M P", "initials": "MP", "orcid": "0000-0001-5768-1976", "researcher": {"href": "https://publications.scilifelab.se/researcher/9821ee4a87c74dde82d9a6a4ebc2b1fc.json"}}, {"family": "Deng", "given": "J", "initials": "J"}, {"family": "Desborough", "given": "L", "initials": "L"}, {"family": "Dolff", "given": "E", "initials": "E"}, {"family": "Eliasson", "given": "A", "initials": "A"}, {"family": "Elmquist", "given": "H", "initials": "H"}, {"family": "Emanuelsson", "given": "H", "initials": "H"}, {"family": "Erixon", "given": "R", "initials": "R"}, {"family": "Fahlen", "given": "L", "initials": "L"}, {"family": "Frogner", "given": "C", "initials": "C"}, {"family": "F\u00fcrst", "given": "P", "initials": "P"}, {"family": "Grabs", "given": "A", "initials": "A"}, {"family": "Grudd", "given": "H", "initials": "H", "orcid": "0000-0002-9033-2505", "researcher": {"href": "https://publications.scilifelab.se/researcher/97348870e86e4c75ae6ce0be4cc99699.json"}}, {"family": "Guasconi", "given": "D", "initials": "D"}, {"family": "Gunnarsson", "given": "M", "initials": "M"}, {"family": "H\u00e4ggqvist", "given": "S", "initials": "S"}, {"family": "Hed", "given": "A", "initials": "A"}, {"family": "H\u00f6rnstr\u00f6m", "given": "E", "initials": "E"}, {"family": "J\u00f6nsson", "given": "A", "initials": "A"}, {"family": "Kanerot", "given": "S", "initials": "S"}, {"family": "Karlsson", "given": "A", "initials": "A"}, {"family": "Karlsson", "given": "D", "initials": "D", "orcid": "0000-0003-4639-823X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ecfa3c78df4076bce64c7eeb36ee4f.json"}}, {"family": "Klinth", "given": "M", "initials": "M"}, {"family": "Kraft", "given": "T", "initials": "T", "orcid": "0000-0002-1143-5494", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd6da126be9d48658afb96aac9532ead.json"}}, {"family": "Lahti", "given": "R", "initials": "R"}, {"family": "Larsson", "given": "M", "initials": "M"}, {"family": "Lernefalk", "given": "H", "initials": "H"}, {"family": "Lestander", "given": "Y", "initials": "Y"}, {"family": "Lindholm", "given": "L-T", "initials": "L"}, {"family": "Lindholm", "given": "M", "initials": "M"}, {"family": "Ljung", "given": "U", "initials": "U"}, {"family": "Ljung", "given": "K", "initials": "K"}, {"family": "Lundberg", "given": "J", "initials": "J", "orcid": "0000-0003-4316-9183", "researcher": {"href": "https://publications.scilifelab.se/researcher/86b74c200f2b402cad6b82cdf63259c9.json"}}, {"family": "Lundin", "given": "E", "initials": "E", "orcid": "0000-0002-3785-8305", "researcher": {"href": "https://publications.scilifelab.se/researcher/842e65aa96ef4dcaa8af13bf9e3f73f8.json"}}, {"family": "Malmenius", "given": "M", "initials": "M"}, {"family": "Marquina", "given": "D", "initials": "D"}, {"family": "Martinelli", "given": "J", "initials": "J"}, {"family": "Mertz", "given": "L", "initials": "L"}, {"family": "Nilsson", "given": "J", "initials": "J"}, {"family": "Patchett", "given": "A", "initials": "A"}, {"family": "Persson", "given": "N", "initials": "N"}, {"family": "Persson", "given": "J", "initials": "J"}, {"family": "Prus-Frankowska", "given": "M", "initials": "M"}, {"family": "Regazzoni", "given": "E", "initials": "E"}, {"family": "Rosander", "given": "K-G", "initials": "K"}, {"family": "Rydg\u00e5rd", "given": "M", "initials": "M"}, {"family": "Sandblom", "given": "C", "initials": "C"}, {"family": "Skord", "given": "J", "initials": "J"}, {"family": "St\u00e5lhandske", "given": "T", "initials": "T"}, {"family": "Svensson", "given": "F", "initials": "F"}, {"family": "Szpryngiel", "given": "S", "initials": "S", "orcid": "0000-0003-2965-2873", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec77cb9136184887b68a4ae8c4360927.json"}}, {"family": "Tajani", "given": "K", "initials": "K"}, {"family": "Tyboni", "given": "M", "initials": "M"}, {"family": "Ugarph", "given": "C", "initials": "C"}, {"family": "Vestermark", "given": "L", "initials": "L"}, {"family": "Vilhelmsson", "given": "J", "initials": "J"}, {"family": "Wahlgren", "given": "N", "initials": "N"}, {"family": "Wass", "given": "A", "initials": "A"}, {"family": "Wetterstrand", "given": "P", "initials": "P"}, {"family": "\u0141ukasik", "given": "P", "initials": "P", "orcid": "0000-0002-4164-6487", "researcher": {"href": "https://publications.scilifelab.se/researcher/71d69a579a304425b70249e7db42ad67.json"}}, {"family": "Tack", "given": "A J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}, {"family": "Andersson", "given": "A F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Roslin", "given": "T", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Ronquist", "given": "F", "initials": "F"}], "type": "journal article", "published": "2025-05-21", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "12", "issue": "1", "pages": "835"}, "abstract": "We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, Malaise trap samples were collected weekly (biweekly or monthly in the winter, when feasible) at 203 locations within 100 sites in Sweden and weekly at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of CO1 (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.", "doi": "10.1038/s41597-025-05151-0", "pmid": "40399316", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12095508"}, {"db": "pii", "key": "10.1038/s41597-025-05151-0"}], "notes": [], "created": "2025-11-19T08:51:31.233Z", "modified": "2025-11-21T12:26:09.639Z"}, {"entity": "publication", "iuid": "7ce72a774ad944e293841aa4dca43010", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7ce72a774ad944e293841aa4dca43010.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7ce72a774ad944e293841aa4dca43010"}}, "title": "Temperature, sediment resuspension, and salinity drive the prevalence of Vibrio vulnificus in the coastal Baltic Sea.", "authors": [{"family": "Fern\u00e1ndez-Ju\u00e1rez", "given": "V\u00edctor", "initials": "V", "orcid": "0000-0002-8090-5154", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29935a6fb20407c803cbb6b555573b6.json"}}, {"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Gusmao", "given": "Joao Bosco", "initials": "JB"}, {"family": "Delgado-Zambrano", "given": "Luis Fernando", "initials": "LF"}, {"family": "Coll-Garc\u00eda", "given": "Guillem", "initials": "G", "orcid": "0000-0003-2123-4108", "researcher": {"href": "https://publications.scilifelab.se/researcher/5960bdad0e9d4fe2b5b45610cd047c62.json"}}, {"family": "Papazachariou", "given": "Vasiliki", "initials": "V"}, {"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}], "type": "journal article", "published": "2024-10-16", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "15", "issue": "10", "pages": "e0156924", "issn-l": null}, "abstract": "The number of Vibrio-related infections in humans, e.g., by Vibrio vulnificus, has increased along the coasts of the Baltic Sea. Due to climate change, vibriosis risk is expected to increase. It is, therefore, pertinent to design a strategy for mitigation of the vibriosis threat in the Baltic Sea area, but a prerequisite is to identify the environmental conditions promoting the occurrence of pathogenic Vibrio spp., like V. vulnificus. To address this, we sampled three coastal Baltic sites in Finland, Germany, and Denmark with salinities between 6 and 21 from May to October 2022. The absolute and relative abundances of Vibrio spp. and V. vulnificus in water were compared to environmental conditions, including the presence of the eelgrass Zostera marina, which has been suggested to reduce pathogenic Vibrio species abundance. In the water column, V. vulnificus only occurred at the German station between July and August at salinity 8.1-11.2. Temperature and phosphate (PO43-) were identified as the most influencing factors for Vibrio spp. and V. vulnificus. The accumulation of Vibrio spp. in the sediment and the co-occurrence with sediment bacteria in the water column indicate that sediment resuspension contributed to V. vulnificus abundance. Interestingly, V. vulnificus co-occurred with specific cyanobacteria taxa, as well as specific bacteria associated with cyanobacteria. Although we found no reduction in Vibrio spp. or V. vulnificus associated with eelgrass beds, our study underscores the importance of extended heatwaves and sediment resuspension, which may elevate the availability of PO43-, for Vibrio species levels at intermediate salinities in the Baltic Sea.\n\nElevated sea surface temperatures are increasing the prevalence of pathogenic Vibrio at higher latitudes. The recent increase in Vibrio-related wound infections and deaths along the Baltic coasts is, therefore, of serious health concern. We used culture-independent data generated from three Baltic coastal sites in Denmark, Germany, and Finland from May to October (2022), with a special focus on Vibrio vulnificus, and combined it with environmental data. Our temporal model shows that temperature, combined with sediment resuspension, drives the prevalence of V. vulnificus at intermediate salinities in the coastal Baltic Sea.", "doi": "10.1128/mbio.01569-24", "pmid": "39297655", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11481517"}], "notes": [], "created": "2024-11-25T10:28:33.004Z", "modified": "2025-02-28T14:21:03.290Z"}, {"entity": "publication", "iuid": "81ad9ffc2ee842da9ab47f23725f0cd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81ad9ffc2ee842da9ab47f23725f0cd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81ad9ffc2ee842da9ab47f23725f0cd9"}}, "title": "Control of Vibrio vulnificus proliferation in the Baltic Sea through eutrophication and algal bloom management", "authors": [{"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Fern\u00e1ndez-Ju\u00e1rez", "given": "Victor", "initials": "V"}, {"family": "Delgado", "given": "Luis F", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Sperlea", "given": "Theodor", "initials": "T", "orcid": "0000-0003-4307-2963", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e0963de222d42eb915c9d5b47c7a1f7.json"}}, {"family": "Hassenr\u00fcck", "given": "Christiane", "initials": "C", "orcid": "0000-0003-1909-1726", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d2e4404c3844df588509a3efa92a7fa.json"}}, {"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Pansch", "given": "Christian", "initials": "C"}, {"family": "Katar\u017eyt\u0117", "given": "Marija", "initials": "M"}, {"family": "Bruck", "given": "Florian", "initials": "F"}, {"family": "Ahrens", "given": "Alwin", "initials": "A"}, {"family": "Rakowski", "given": "Marcin", "initials": "M"}, {"family": "Piwosz", "given": "Kasia", "initials": "K", "orcid": "0000-0002-3248-3364", "researcher": {"href": "https://publications.scilifelab.se/researcher/69c75bc4dc65411b9afe81b06a9398fa.json"}}, {"family": "Stevenson", "given": "Angela", "initials": "A", "orcid": "0000-0001-9487-0047", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4b1330bf98345e8b8f1e63f643929d1.json"}}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH", "orcid": "0000-0002-8961-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b27965acd74a7a95e97b77abee769d.json"}}, {"family": "Gyrait\u0117", "given": "Greta", "initials": "G", "orcid": "0000-0002-7079-7997", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9fa8139fbc64e7e990587ca8e5f6d52.json"}}, {"family": "Schulz-Bull", "given": "Detlef", "initials": "D"}, {"family": "Benterbusch-Brockm\u00f6ller", "given": "Heike", "initials": "H"}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Dupke", "given": "Susann", "initials": "S"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}], "type": "journal-article", "published": "2024-05-09", "journal": {"title": "Commun Earth Environ", "issn": "2662-4435", "volume": "5", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1038/s43247-024-01410-x", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-02-28T14:16:21.117Z", "modified": "2025-12-04T19:40:44.806Z"}, {"entity": "publication", "iuid": "9362d0a9e2424b878878c0da9a3d7c67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9362d0a9e2424b878878c0da9a3d7c67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9362d0a9e2424b878878c0da9a3d7c67"}}, "title": "A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea.", "authors": [{"family": "Latz", "given": "Meike A C", "initials": "MAC", "orcid": "0000-0002-6583-9291", "researcher": {"href": "https://publications.scilifelab.se/researcher/664c30300eab4888a2e5562e077aab01.json"}}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Brugel", "given": "Sonia", "initials": "S"}, {"family": "Hedblom", "given": "Mikael", "initials": "M"}, {"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT", "orcid": "0000-0001-9544-5755", "researcher": {"href": "https://publications.scilifelab.se/researcher/896a2f678e3143a2b855c1afa8e93499.json"}}, {"family": "Karlson", "given": "Bengt", "initials": "B"}, {"family": "Lindh", "given": "Markus", "initials": "M"}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "dataset", "published": "2024-01-02", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "11", "issue": "1", "pages": "18", "issn-l": "2052-4463"}, "abstract": "The Baltic Sea is one of the largest brackish water environments on earth and is characterised by pronounced physicochemical gradients and seasonal dynamics. Although the Baltic Sea has a long history of microscopy-based plankton monitoring, DNA-based metabarcoding has so far mainly been limited to individual transect cruises or time-series of single stations. Here we report a dataset covering spatiotemporal variation in prokaryotic and eukaryotic microbial communities and physicochemical parameters. Within 13-months between January 2019 and February 2020, 341 water samples were collected at 22 stations during monthly cruises along the salinity gradient. Both salinity and seasonality are strongly reflected in the data. Since the dataset was generated with both metabarcoding and microscopy-based methods, it provides unique opportunities for both technical and ecological analyses, and is a valuable biodiversity reference for future studies, in the prospect of climate change.", "doi": "10.1038/s41597-023-02825-5", "pmid": "38168085", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10761891"}, {"db": "pii", "key": "10.1038/s41597-023-02825-5"}], "notes": [], "created": "2024-01-10T09:46:47.061Z", "modified": "2024-11-25T10:20:00.758Z"}, {"entity": "publication", "iuid": "c7dc193c604c4e5fa865e49344129528", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7dc193c604c4e5fa865e49344129528.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7dc193c604c4e5fa865e49344129528"}}, "title": "New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system.", "authors": [{"family": "Bittner", "given": "Meriel J", "initials": "MJ", "orcid": "0000-0002-3798-6315", "researcher": {"href": "https://publications.scilifelab.se/researcher/5abcc332fec3408f996fff6e2470f304.json"}}, {"family": "Bannon", "given": "Catherine C", "initials": "CC", "orcid": "0000-0002-8581-1069", "researcher": {"href": "https://publications.scilifelab.se/researcher/176684868401463e8e36980a8f297ab8.json"}}, {"family": "Rowland", "given": "Elden", "initials": "E", "orcid": "0000-0003-4756-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c1d771d5585492681b9c2a296a78914.json"}}, {"family": "Sundh", "given": "John", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Bertrand", "given": "Erin M", "initials": "EM", "orcid": "0000-0002-5950-6810", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc79515185fc4304bb690324be48adf2.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Paerl", "given": "Ryan W", "initials": "RW", "orcid": "0000-0003-3980-8181", "researcher": {"href": "https://publications.scilifelab.se/researcher/1267dafcedd84e77aa550169e4340998.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "issn-l": null, "volume": "4", "issue": "1", "pages": "ycad016"}, "abstract": "Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74-117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 (Burkholderiales), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.", "doi": "10.1093/ismeco/ycad016", "pmid": "38390520", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10881298"}, {"db": "pii", "key": "ycad016"}, {"db": "figshare", "key": "10.6084/m9.figshare.23634429"}], "notes": [], "created": "2024-03-14T11:11:47.095Z", "modified": "2025-02-28T14:18:29.377Z"}, {"entity": "publication", "iuid": "b4a18704cfbc4ac4a6d0e4d56abbcea3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4a18704cfbc4ac4a6d0e4d56abbcea3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4a18704cfbc4ac4a6d0e4d56abbcea3"}}, "title": "Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity.", "authors": [{"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT", "orcid": "0000-0001-9544-5755", "researcher": {"href": "https://publications.scilifelab.se/researcher/896a2f678e3143a2b855c1afa8e93499.json"}}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Delgado", "given": "Luis Fernando", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Deng", "given": "Ziling", "initials": "Z", "orcid": "0000-0002-6970-6453", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0e06ceb2acf478598cc7080e732cd2b.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2023-05-26", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "21", "pages": "eadg2059", "issn-l": "2375-2548"}, "abstract": "The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.", "doi": "10.1126/sciadv.adg2059", "pmid": "37235649", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10219603"}], "notes": [], "created": "2023-11-27T21:57:15.016Z", "modified": "2024-01-16T13:48:33.355Z"}, {"entity": "publication", "iuid": "ee01bdbaa4114eec92a4d6c0407a11d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee01bdbaa4114eec92a4d6c0407a11d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee01bdbaa4114eec92a4d6c0407a11d8"}}, "title": "Linking prokaryotic genome size variation to metabolic potential and environment.", "authors": [{"family": "Rodr\u00edguez-Gij\u00f3n", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-1649-6894", "researcher": {"href": "https://publications.scilifelab.se/researcher/d25dfecc53e94af0b79799621f131631.json"}}, {"family": "Buck", "given": "Moritz", "initials": "M", "orcid": "0000-0001-6632-5324", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba68bf651630488dab4d146b11cf612a.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Izabel-Shen", "given": "Dandan", "initials": "D", "orcid": "0000-0002-3280-1166", "researcher": {"href": "https://publications.scilifelab.se/researcher/21fcbf89ed644524852f2e12217f5371.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}], "type": "journal article", "published": "2023-03-27", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "3", "issue": "1", "pages": "25", "issn-l": null}, "abstract": "While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.", "doi": "10.1038/s43705-023-00231-x", "pmid": "36973336", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10042847"}, {"db": "pii", "key": "10.1038/s43705-023-00231-x"}], "notes": [], "created": "2023-10-04T12:20:23.424Z", "modified": "2024-01-16T13:48:33.810Z"}, {"entity": "publication", "iuid": "61e6bc05d92f4403aba21ee521531b70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61e6bc05d92f4403aba21ee521531b70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61e6bc05d92f4403aba21ee521531b70"}}, "title": "ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.", "authors": [{"family": "Prager", "given": "Maria", "initials": "M", "orcid": "0000-0003-4897-8422", "researcher": {"href": "https://publications.scilifelab.se/researcher/4edcc39683ae4adb9f8000321271ae44.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2023-01-05", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "24", "issue": "1", "pages": "6", "issn-l": "1471-2105"}, "abstract": "The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.\n\nThe ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure.\n\nThe ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.", "doi": "10.1186/s12859-022-05120-z", "pmid": "36604610", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9817246"}, {"db": "pii", "key": "10.1186/s12859-022-05120-z"}], "notes": [], "created": "2023-11-23T14:14:28.588Z", "modified": "2023-11-23T14:14:28.644Z"}, {"entity": "publication", "iuid": "ff4664ca9052497caeef1c1bccdbfa76", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff4664ca9052497caeef1c1bccdbfa76.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff4664ca9052497caeef1c1bccdbfa76"}}, "title": "\ufeffIntroducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms", "authors": [{"family": "Nilsson", "given": "R Henrik", "initials": "RH", "orcid": "0000-0002-8052-0107", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f74b9c6c3d4e749adacffa0efb80b2.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Bissett", "given": "Andrew", "initials": "A"}, {"family": "Finstad", "given": "Anders G", "initials": "AG", "orcid": "0000-0003-4529-6266", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5f25bcb9fcf48048e4ed9b5377b848a.json"}}, {"family": "Foss\u00f8y", "given": "Frode", "initials": "F"}, {"family": "Grosjean", "given": "Marie", "initials": "M"}, {"family": "Hope", "given": "Michael", "initials": "M"}, {"family": "Jeppesen", "given": "Thomas S", "initials": "TS", "orcid": "0000-0003-1691-239X", "researcher": {"href": "https://publications.scilifelab.se/researcher/50c1a9d451504813a5160db621356cd9.json"}}, {"family": "K\u00f5ljalg", "given": "Urmas", "initials": "U"}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Prager", "given": "Maria", "initials": "M", "orcid": "0000-0003-4897-8422", "researcher": {"href": "https://publications.scilifelab.se/researcher/4edcc39683ae4adb9f8000321271ae44.json"}}, {"family": "Suominen", "given": "Saara", "initials": "S", "orcid": "0000-0001-9401-8460", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc0b8fbef068422c91a108b6fa297521.json"}}, {"family": "Svenningsen", "given": "Cecilie S", "initials": "CS", "orcid": "0000-0002-9216-2917", "researcher": {"href": "https://publications.scilifelab.se/researcher/91e23da698614b6496183fe5f16a7c6c.json"}}, {"family": "Schigel", "given": "Dmitry", "initials": "D", "orcid": "0000-0002-2919-1168", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4b1cd30c0404d9b8c2caf5d5c2fed1d.json"}}], "type": "journal-article", "published": "2022-08-02", "journal": {"title": "MBMG", "issn": "2534-9708", "volume": "6", "issn-l": null}, "abstract": null, "doi": "10.3897/mbmg.6.84960", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-27T22:02:38.982Z", "modified": "2025-12-04T19:28:41.646Z"}, {"entity": "publication", "iuid": "c3b67c44bad84085803c8a248a084eca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3b67c44bad84085803c8a248a084eca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3b67c44bad84085803c8a248a084eca"}}, "title": "Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing.", "authors": [{"family": "Latz", "given": "Meike A C", "initials": "MAC", "orcid": "0000-0002-6583-9291", "researcher": {"href": "https://publications.scilifelab.se/researcher/664c30300eab4888a2e5562e077aab01.json"}}, {"family": "Grujcic", "given": "Vesna", "initials": "V", "orcid": "0000-0002-3322-599X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cd1ed7a2d7e477d8f8c5a340152b36c.json"}}, {"family": "Brugel", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1298-3839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879.json"}}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "John", "given": "Uwe", "initials": "U", "orcid": "0000-0002-1297-4086", "researcher": {"href": "https://publications.scilifelab.se/researcher/76918fd58a374cdcacfe02298e7d29a3.json"}}, {"family": "Karlson", "given": "Bengt", "initials": "B", "orcid": "0000-0002-7524-3504", "researcher": {"href": "https://publications.scilifelab.se/researcher/44722b5ece5b420bb59fdb749833f443.json"}}, {"family": "Andersson", "given": "Agneta", "initials": "A", "orcid": "0000-0001-7819-9038", "researcher": {"href": "https://publications.scilifelab.se/researcher/812b8d6654af4482a308367f052f64c7.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": "22", "issue": "6", "pages": "2304-2318"}, "abstract": "High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last decade. Currently, the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics data sets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.", "doi": "10.1111/1755-0998.13623", "pmid": "35437888", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2022-08-19T08:37:10.426Z", "modified": "2024-01-16T13:48:35.514Z"}, {"entity": "publication", "iuid": "551c288a5ec247cc99cca4008efbf761", "links": {"self": {"href": "https://publications.scilifelab.se/publication/551c288a5ec247cc99cca4008efbf761.json"}, "display": {"href": "https://publications.scilifelab.se/publication/551c288a5ec247cc99cca4008efbf761"}}, "title": "Evaluating metagenomic assembly approaches for biome-specific gene catalogues.", "authors": [{"family": "Delgado", "given": "Luis Fernando", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2022-05-06", "journal": {"title": "Microbiome", "issn": "2049-2618", "issn-l": "2049-2618", "volume": "10", "issue": "1", "pages": "72"}, "abstract": "For many environments, biome-specific microbial gene catalogues are being recovered using shotgun metagenomics followed by assembly and gene calling on the assembled contigs. The assembly is typically conducted either by individually assembling each sample or by co-assembling reads from all the samples. The co-assembly approach can potentially recover genes that display too low abundance to be assembled from individual samples. On the other hand, combining samples increases the risk of mixing data from closely related strains, which can hamper the assembly process. In this respect, assembly on individual samples followed by clustering of (near) identical genes is preferable. Thus, both approaches have potential pros and cons, but it remains to be evaluated which assembly strategy is most effective. Here, we have evaluated three assembly strategies for generating gene catalogues from metagenomes using a dataset of 124 samples from the Baltic Sea: (1) assembly on individual samples followed by clustering of the resulting genes, (2) co-assembly on all samples, and (3) mix assembly, combining individual and co-assembly.\n\nThe mix-assembly approach resulted in a more extensive nonredundant gene set than the other approaches and with more genes predicted to be complete and that could be functionally annotated. The mix assembly consists of 67 million genes (Baltic Sea gene set, BAGS) that have been functionally and taxonomically annotated. The majority of the BAGS genes are dissimilar (< 95% amino acid identity) to the Tara Oceans gene dataset, and hence, BAGS represents a valuable resource for brackish water research.\n\nThe mix-assembly approach represents a feasible approach to increase the information obtained from metagenomic samples. Video abstract.", "doi": "10.1186/s40168-022-01259-2", "pmid": "35524337", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9074274"}, {"db": "pii", "key": "10.1186/s40168-022-01259-2"}], "notes": [], "created": "2022-08-19T08:37:40.525Z", "modified": "2024-01-16T13:48:36.706Z"}, {"entity": "publication", "iuid": "a01c0f9e1e8e43ee84cc57054dbeba25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a01c0f9e1e8e43ee84cc57054dbeba25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a01c0f9e1e8e43ee84cc57054dbeba25"}}, "title": "Ecologically coherent population structure of uncultivated bacterioplankton.", "authors": [{"family": "Sj\u00f6qvist", "given": "Conny", "initials": "C"}, {"family": "Delgado", "given": "Luis Fernando", "initials": "LF"}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362", "volume": "15", "issue": "10", "pages": "3034-3049"}, "abstract": "Bacterioplankton are main drivers of biogeochemical cycles and important components of aquatic food webs. While sequencing-based studies have revealed how bacterioplankton communities are structured in time and space, relatively little is known about intraspecies diversity patterns and their ecological relevance. Here, we use the newly developed software POGENOM (POpulation GENomics from Metagenomes) to investigate genomic diversity and differentiation in metagenome-assembled genomes from the Baltic Sea, and investigate their genomic variation using metagenome data spanning a 1700 km transect and covering seasonal variation at one station. The majority of the investigated species, representing several major bacterioplankton clades, displayed population structures correlating significantly with environmental factors such as salinity and temperature. Population differentiation was more pronounced over spatial than temporal scales. We discovered genes that have undergone adaptation to different salinity regimes, potentially responsible for the populations' existence along with the salinity range. This in turn implies the broad existence of ecotypes that may remain undetected by rRNA gene sequencing. Our findings emphasize the importance of physiological barriers, and highlight the role of adaptive divergence as a structuring mechanism of bacterioplankton species.", "doi": "10.1038/s41396-021-00985-z", "pmid": "33953362", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-021-00985-z"}, {"db": "pmc", "key": "PMC8443644"}], "notes": [], "created": "2021-10-01T09:00:18.178Z", "modified": "2024-01-16T13:48:38.415Z"}, {"entity": "publication", "iuid": "598bd6b5445f44679e26ebb6cb896fe5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/598bd6b5445f44679e26ebb6cb896fe5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/598bd6b5445f44679e26ebb6cb896fe5"}}, "title": "The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.", "authors": [{"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Simone", "given": "Domenico", "initials": "D"}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "de Bruijn", "given": "Ino", "initials": "I", "orcid": "0000-0001-5427-4750", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c71c59a5f064f4c84150c7b5cd366ac.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2021-03-08", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "307", "issn-l": "2399-3642"}, "abstract": "The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in 'metabolic standby'. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of 'kill-the-winner' oscillations creating slow motion 'boom and burst' cycles.", "doi": "10.1038/s42003-021-01810-1", "pmid": "33686191", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-01810-1"}, {"db": "pmc", "key": "PMC7940616"}], "notes": [], "created": "2021-06-09T12:14:33.814Z", "modified": "2024-01-16T13:48:40.474Z"}, {"entity": "publication", "iuid": "f0dc43b7323e459ca55148bf15d20642", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0dc43b7323e459ca55148bf15d20642.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0dc43b7323e459ca55148bf15d20642"}}, "title": "Genome sequence of segmented filamentous bacteria present in the human intestine.", "authors": [{"family": "Jonsson", "given": "Hans", "initials": "H"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dfdcf0109a942228d35d8dbfdede585.json"}}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Lundin", "given": "Eva", "initials": "E"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2020-09-04", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "485", "issn-l": "2399-3642"}, "abstract": "Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host's intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome has been reported. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65-71% average amino acid identity to the others. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB genome. We thus conclude that a unique SFB variant exists in humans and foresee a renewed interest in the elucidation of SFB functionality in this environment.", "doi": "10.1038/s42003-020-01214-7", "pmid": "32887924", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-01214-7"}, {"db": "pmc", "key": "PMC7474095"}], "notes": [], "created": "2020-11-16T08:52:13.095Z", "modified": "2024-01-16T13:48:41.758Z"}, {"entity": "publication", "iuid": "b666d402dd5343929e0fbb695aca0efe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b666d402dd5343929e0fbb695aca0efe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b666d402dd5343929e0fbb695aca0efe"}}, "title": "Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J", "orcid": "0000-0002-2467-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4d517d4f20046c08405f8aeecf4ad2a.json"}}, {"family": "Bennke", "given": "Christin", "initials": "C"}, {"family": "Beier", "given": "Sara", "initials": "S", "orcid": "0000-0003-3707-4487", "researcher": {"href": "https://publications.scilifelab.se/researcher/5358a1e162474073a69b08c32e7c5420.json"}}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Quince", "given": "Christopher", "initials": "C"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2020-03-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "119", "issn-l": "2399-3642"}, "abstract": "The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.", "doi": "10.1038/s42003-020-0856-x", "pmid": "32170201", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-0856-x"}, {"db": "pmc", "key": "PMC7070063"}], "notes": [], "created": "2020-07-08T13:04:08.349Z", "modified": "2024-01-16T13:48:42.773Z"}, {"entity": "publication", "iuid": "68c53403732e496f9fd2f1e5affc34d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68c53403732e496f9fd2f1e5affc34d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68c53403732e496f9fd2f1e5affc34d3"}}, "title": "Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.", "authors": [{"family": "Hu", "given": "Yue O O", "initials": "YOO", "orcid": "0000-0002-2025-2198", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8675dd0fbc44f892614c848dbade8f.json"}}, {"family": "Ndegwa", "given": "Nelson", "initials": "N", "orcid": "0000-0002-5853-879X", "researcher": {"href": "https://publications.scilifelab.se/researcher/69494d497aca4285a950e335c2978135.json"}}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Johansson", "given": "Sebastian", "initials": "S"}, {"family": "Logue", "given": "J\u00fcrg Brendan", "initials": "JB"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Fagerberg", "given": "Jens", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2018-08-09", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "11907", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.", "doi": "10.1038/s41598-018-29920-7", "pmid": "30093614", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-29920-7"}, {"db": "pmc", "key": "PMC6085348"}], "notes": [], "created": "2018-10-31T19:44:54.553Z", "modified": "2024-01-16T13:48:45.757Z"}, {"entity": "publication", "iuid": "b616130aa5e24ecab64baeba6c16c0a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b616130aa5e24ecab64baeba6c16c0a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b616130aa5e24ecab64baeba6c16c0a8"}}, "title": "Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.", "authors": [{"family": "Svartstr\u00f6m", "given": "Olov", "initials": "O"}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Terrapon", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3693-6017", "researcher": {"href": "https://publications.scilifelab.se/researcher/08f47757224649faa4a6e81854b8578f.json"}}, {"family": "Lombard", "given": "Vincent", "initials": "V"}, {"family": "de Bruijn", "given": "Ino", "initials": "I"}, {"family": "Malmsten", "given": "Jonas", "initials": "J", "orcid": "0000-0003-1868-3746", "researcher": {"href": "https://publications.scilifelab.se/researcher/31afb191067641c9b2190aa36db6d225.json"}}, {"family": "Dalin", "given": "Ann-Marie", "initials": "AM"}, {"family": "El Muller", "given": "Emilie", "initials": "E"}, {"family": "Shah", "given": "Pranjul", "initials": "P"}, {"family": "Wilmes", "given": "Paul", "initials": "P"}, {"family": "Henrissat", "given": "Bernard", "initials": "B"}, {"family": "Aspeborg", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8576-4370", "researcher": {"href": "https://publications.scilifelab.se/researcher/973b41980bd34391aa3be4e54b19ff2f.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "11", "issn": "1751-7370", "issue": "11", "pages": "2538-2551", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.", "doi": "10.1038/ismej.2017.108", "pmid": "28731473", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "EMS73237"}, {"db": "pmc", "key": "PMC5648042"}, {"db": "pii", "key": "ismej2017108"}], "notes": [], "created": "2017-11-03T16:11:39.460Z", "modified": "2024-01-16T13:48:47.346Z"}]}