{"entity": "researcher", "timestamp": "2026-09-26T00:13:28.330Z", "family": "Park", "given": "Junseok", "initials": "J", "orcid": "0000-0003-2312-9440", "affiliations": ["Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Republic of Korea."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b504f733bc9496d819482f62c785653.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b504f733bc9496d819482f62c785653"}}, "publications": [{"entity": "publication", "iuid": "6a9a97b75ea54a1a8a60f2167d4f7e4c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6a9a97b75ea54a1a8a60f2167d4f7e4c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6a9a97b75ea54a1a8a60f2167d4f7e4c"}}, "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-affiliated.scilifelab.se/researcher/c28bda7f74d642e3a5cfac62dfacf872.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-affiliated.scilifelab.se/researcher/709370b652de470087b950366e245b35.json"}}, {"family": "Clasen", "given": "Frederick", "initials": "F"}, {"family": "Park", "given": "Junseok", "initials": "J", "orcid": "0000-0003-2312-9440", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b504f733bc9496d819482f62c785653.json"}}, {"family": "Plaza O\u00f1ate", "given": "Florian", "initials": "F", "orcid": "0000-0001-6036-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c22c1408f9ab406e8d5491808d49bac1.json"}}, {"family": "Cai", "given": "Haizhuang", "initials": "H"}, {"family": "Le Chatelier", "given": "Emmanuelle", "initials": "E", "orcid": "0000-0002-2724-0536", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53d36db65048483ab2d3ab2af6dd2907.json"}}, {"family": "Pons", "given": "Nicolas", "initials": "N", "orcid": "0000-0003-1926-8077", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae4838eaffb44fe49098db611baaa8a7.json"}}, {"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-affiliated.scilifelab.se/researcher/a5c6814a31e644b9bc544d4da759a438.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Lee", "given": "Doheon", "initials": "D", "orcid": "0000-0001-9070-4316", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e1e5a53040c49d0a8c1c4ae6a380da8.json"}}, {"family": "Proctor", "given": "Gordon", "initials": "G", "orcid": "0000-0002-5684-841X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/379255ab5c1d433ea3c7600dbde5afea.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca58bf2d214047e0ae5e38a42a0f2808.json"}}, {"family": "Blanquet-Diot", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0003-0692-8726", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22b6341651f749b789f069a37197af1b.json"}}, {"family": "Moyes", "given": "David", "initials": "D", "orcid": "0000-0002-1657-918X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a069e8663b0846b6a0007e09631df3ed.json"}}, {"family": "Almeida", "given": "Mathieu", "initials": "M", "orcid": "0000-0003-4971-0049", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f61223c6a54344d0b6d262d7704c938b.json"}}, {"family": "Ehrlich", "given": "S Dusko", "initials": "SD"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S", "orcid": "0000-0001-5834-4533", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77b9e28bdf3843599bb44a920179cd0e.json"}}], "type": "journal article", "published": "2024-09-08", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "10", "issue": "1", "pages": "80", "issn-l": null}, "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": {"SciLifeLab Fellow": "", "Saeed Shoaie": "", "Adil Mardinoglu": ""}, "xrefs": [{"db": "pmc", "key": "PMC11381545"}, {"db": "pii", "key": "10.1038/s41522-024-00561-1"}], "notes": [], "created": "2026-09-23T09:02:27.578Z", "modified": "2026-09-24T14:19:28.756Z"}, {"entity": "publication", "iuid": "bc1f72d5b6d141ca8a4c64c4aa406d55", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bc1f72d5b6d141ca8a4c64c4aa406d55.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bc1f72d5b6d141ca8a4c64c4aa406d55"}}, "title": "Global compositional and functional states of the human gut microbiome in health and disease.", "authors": [{"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Portlock", "given": "Theo", "initials": "T"}, {"family": "Le Chatelier", "given": "Emmanuelle", "initials": "E"}, {"family": "Garcia-Guevara", "given": "Fernando", "initials": "F"}, {"family": "Clasen", "given": "Frederick", "initials": "F"}, {"family": "O\u00f1ate", "given": "Florian Plaza", "initials": "FP"}, {"family": "Pons", "given": "Nicolas", "initials": "N"}, {"family": "Begum", "given": "Neelu", "initials": "N"}, {"family": "Harzandi", "given": "Azadeh", "initials": "A"}, {"family": "Proffitt", "given": "Ceri", "initials": "C"}, {"family": "Rosario", "given": "Dorines", "initials": "D"}, {"family": "Vaga", "given": "Stefania", "initials": "S"}, {"family": "Park", "given": "Junseok", "initials": "J", "orcid": "0000-0003-2312-9440", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b504f733bc9496d819482f62c785653.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Johansson", "given": "Fredric", "initials": "F"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Edwards", "given": "Lindsey A", "initials": "LA"}, {"family": "Lombard", "given": "Vincent", "initials": "V"}, {"family": "Gauthier", "given": "Franck", "initials": "F"}, {"family": "Steves", "given": "Claire J", "initials": "CJ"}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D", "orcid": "0000-0003-4186-3788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2f7905f6b864d3286b28b99dbb59627.json"}}, {"family": "Henrissat", "given": "Bernard", "initials": "B"}, {"family": "Lee", "given": "Doheon", "initials": "D"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Shawcross", "given": "Debbie L", "initials": "DL"}, {"family": "Proctor", "given": "Gordon", "initials": "G"}, {"family": "Almeida", "given": "Mathieu", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Moyes", "given": "David L", "initials": "DL"}, {"family": "Ehrlich", "given": "Stanislav Dusko", "initials": "SD"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}], "type": "journal article", "published": "2024-07-23", "journal": {"title": "Genome Res", "issn": "1549-5469", "volume": "34", "issue": "6", "pages": "967-978", "issn-l": "1088-9051"}, "abstract": "The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.", "doi": "10.1101/gr.278637.123", "pmid": "39038849", "labels": {"SciLifeLab Fellow": "", "Saeed Shoaie": "", "Adil Mardinoglu": ""}, "xrefs": [{"db": "pmc", "key": "PMC11293553"}, {"db": "pii", "key": "gr.278637.123"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2026-09-23T13:43:41.641Z", "modified": "2026-09-23T13:43:41.705Z"}]}