{"entity": "researcher", "timestamp": "2026-08-14T13:29:09.635Z", "family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "affiliations": ["Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5"}}, "publications": [{"entity": "publication", "iuid": "8ed54f29f33f4ce39d346fdb35295c92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ed54f29f33f4ce39d346fdb35295c92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ed54f29f33f4ce39d346fdb35295c92"}}, "title": "Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.", "authors": [{"family": "Prast-Nielsen", "given": "Stefanie", "initials": "S", "orcid": "0000-0001-5877-7988", "researcher": {"href": "https://publications.scilifelab.se/researcher/baea894b3ac14408a7492df2fc6c796e.json"}}, {"family": "Granstr\u00f6m", "given": "Anna L\u00f6f", "initials": "AL", "orcid": "0000-0003-2169-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c08d2119eca4e67936cd5b5d2dc47d3.json"}}, {"family": "Kiasat", "given": "Ali", "initials": "A", "orcid": "0000-0001-5568-3265", "researcher": {"href": "https://publications.scilifelab.se/researcher/f92cb577648943a2a09efe76787545c4.json"}}, {"family": "Ahlstr\u00f6m", "given": "Gustav", "initials": "G"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/6538b950bbd440e3aa32435d23c98074.json"}}, {"family": "Rautiainen", "given": "Susanne", "initials": "S", "orcid": "0000-0001-7193-6082", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb22af02cdd04e80b1a0809b163ad56e.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Andersson", "given": "Fredrik O", "initials": "FO"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications.scilifelab.se/researcher/17bed8be7a9c46b5a94147b80fd58e82.json"}}, {"family": "Gustafsson", "given": "Ulf O", "initials": "UO", "orcid": "0000-0001-9549-061X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4302890c32a24317aa1d0f6807c4458e.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "35039", "issn-l": "2045-2322"}, "abstract": "Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.", "doi": "10.1038/s41598-025-18106-7", "pmid": "41062543", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12508173"}, {"db": "pii", "key": "10.1038/s41598-025-18106-7"}], "notes": [], "created": "2025-11-07T15:05:48.239Z", "modified": "2025-11-07T15:05:53.602Z"}, {"entity": "publication", "iuid": "e20232eba3084478a0d4cb3b52b4a953", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e20232eba3084478a0d4cb3b52b4a953.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e20232eba3084478a0d4cb3b52b4a953"}}, "title": "Transient colonizing microbes promote gut dysbiosis and functional impairment.", "authors": [{"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Meslier", "given": "Victoria", "initials": "V", "orcid": "0000-0003-2699-0092", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cd1d7bc18954f988d1e3f5200e124eb.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Garcia-Guevara", "given": "Fernando", "initials": "F"}, {"family": "Etienne-Mesmin", "given": "Lucie", "initials": "L", "orcid": "0000-0001-6104-6043", "researcher": {"href": "https://publications.scilifelab.se/researcher/51e9e5819e4e43b08593df4c66c1f0b3.json"}}, {"family": "Clasen", "given": "Frederick", "initials": "F"}, {"family": "Park", "given": "Junseok", "initials": "J", "orcid": "0000-0003-2312-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5b77f5a5b98479db82a0790affe0a46.json"}}, {"family": "Plaza O\u00f1ate", "given": "Florian", "initials": "F", "orcid": "0000-0001-6036-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a2a015ed8dd47f29f37ef700ccf65d0.json"}}, {"family": "Cai", "given": "Haizhuang", "initials": "H"}, {"family": "Le Chatelier", "given": "Emmanuelle", "initials": "E", "orcid": "0000-0002-2724-0536", "researcher": {"href": "https://publications.scilifelab.se/researcher/99c1ea4535d24ffca619adc5e54b5e80.json"}}, {"family": "Pons", "given": "Nicolas", "initials": "N"}, {"family": "Pereira", "given": "Marcela", "initials": "M"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Lee", "given": "Doheon", "initials": "D", "orcid": "0000-0001-9070-4316", "researcher": {"href": "https://publications.scilifelab.se/researcher/766833afa7534fb68e04525078040b65.json"}}, {"family": "Proctor", "given": "Gordon", "initials": "G", "orcid": "0000-0002-5684-841X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d55a1e72dd9444239c5054ccf7876be3.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Blanquet-Diot", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0003-0692-8726", "researcher": {"href": "https://publications.scilifelab.se/researcher/0689cb23d6fa472aab4623c4c8e611db.json"}}, {"family": "Moyes", "given": "David", "initials": "D", "orcid": "0000-0002-1657-918X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6f9404ad0b420bb54962af7f9ff2f5.json"}}, {"family": "Almeida", "given": "Mathieu", "initials": "M", "orcid": "0000-0003-4971-0049", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cbbdb8b00b84a33a862ef1f8f030555.json"}}, {"family": "Ehrlich", "given": "S Dusko", "initials": "SD"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S", "orcid": "0000-0001-5834-4533", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fcd41a9a3645c3b733564c99a97aea.json"}}], "type": "journal article", "published": "2024-09-08", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "10", "issue": "1", "pages": "80", "issn-l": "2055-5008"}, "abstract": "Species composition of the healthy adult gut microbiota tends to be stable over time. Destabilization of the gut microbiome under the influence of different factors is the main driver of the microbial dysbiosis and subsequent impacts on host physiology. Here, we used metagenomics data from a Swedish longitudinal cohort, to determine the stability of the gut microbiome and uncovered two distinct microbial species groups; persistent colonizing species (PCS) and transient colonizing species (TCS). We validated the continuation of this grouping, generating gut metagenomics data for additional time points from the same Swedish cohort. We evaluated the existence of PCS/TCS across different geographical regions and observed they are globally conserved features. To characterize PCS/TCS phenotypes, we performed bioreactor fermentation with faecal samples and metabolic modeling. Finally, using chronic disease gut metagenome and other multi-omics data, we identified roles of TCS in microbial dysbiosis and link with abnormal changes to host physiology.", "doi": "10.1038/s41522-024-00561-1", "pmid": "39245657", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11381545"}, {"db": "pii", "key": "10.1038/s41522-024-00561-1"}], "notes": [], "created": "2024-11-25T10:18:41.173Z", "modified": "2025-02-28T14:15:02.782Z"}, {"entity": "publication", "iuid": "043ab27fa61944e99a7e279442373b57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/043ab27fa61944e99a7e279442373b57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/043ab27fa61944e99a7e279442373b57"}}, "title": "Integration of molecular profiles in a longitudinal wellness profiling cohort.", "authors": [{"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Koistinen", "given": "Ina Schuppe", "initials": "IS"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Olsson", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-9730-1915", "researcher": {"href": "https://publications.scilifelab.se/researcher/2460963d77ee4eee9409fbd8c257d910.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Stenlund", "given": "Hans", "initials": "H"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Olin", "given": "Axel", "initials": "A", "orcid": "0000-0002-1161-4476", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dfb8efde80a4a508c93714729259aba.json"}}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Jansson", "given": "Per-Anders", "initials": "PA"}, {"family": "Anger\u00e5s", "given": "Oskar", "initials": "O"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Kjellqvist", "given": "Sanela", "initials": "S"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-4871-8818", "researcher": {"href": "https://publications.scilifelab.se/researcher/1689878e0c5542d08d3e2d5043a6ce5c.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}], "type": "journal article", "published": "2020-09-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "4487"}, "abstract": "An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.", "doi": "10.1038/s41467-020-18148-7", "pmid": "32900998", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative", "Cellular Immunomonitoring": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18148-7"}, {"db": "pmc", "key": "PMC7479148"}], "notes": [], "created": "2020-09-10T05:17:29.818Z", "modified": "2025-10-17T13:03:16.662Z"}]}