{"entity": "researcher", "timestamp": "2026-10-12T21:08:29.149Z", "family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "affiliations": ["European Molecular Biology Laboratory, Heidelberg, Germany."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f"}}, "publications": [{"entity": "publication", "iuid": "636ade3645a445628ee42ef4730d546a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/636ade3645a445628ee42ef4730d546a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/636ade3645a445628ee42ef4730d546a"}}, "title": "Fast, flexible gene cluster family delineation with IGUA", "authors": [{"family": "Larralde", "given": "Martin", "initials": "M", "orcid": "0000-0002-3947-4444", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e048b839197434d8af8ab34bd50cf5e.json"}}, {"family": "Blom", "given": "Josefin", "initials": "J", "orcid": "0009-0000-9910-7374", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/361785c07fb04b5497ce209141d2c337.json"}}, {"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H", "orcid": "0000-0001-9807-1082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5485a48dfde4e53b14d39c54f2b2483.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}}], "type": "posted-content", "published": "2025-05-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.05.15.654203", "pmid": null, "labels": {"DDLS Fellow": "", "Laura Carroll": ""}, "xrefs": [], "notes": [], "created": "2026-10-01T08:31:02.314Z", "modified": "2026-10-01T08:31:02.379Z"}, {"entity": "publication", "iuid": "e608034f8699475b897a7ea9a05b34d3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e608034f8699475b897a7ea9a05b34d3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e608034f8699475b897a7ea9a05b34d3"}}, "title": "PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity", "authors": [{"family": "Larralde", "given": "Martin", "initials": "M", "orcid": "0000-0002-3947-4444", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e048b839197434d8af8ab34bd50cf5e.json"}}, {"family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}], "type": "posted-content", "published": "2025-02-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.02.13.638148", "pmid": null, "labels": {"Laura Carroll": "", "DDLS Fellow": ""}, "xrefs": [], "notes": [], "created": "2025-03-18T17:33:38.582Z", "modified": "2026-10-01T08:31:39.104Z"}, {"entity": "publication", "iuid": "0032013e4e1a4d598d2e1c183adb5f66", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0032013e4e1a4d598d2e1c183adb5f66.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0032013e4e1a4d598d2e1c183adb5f66"}}, "title": "Bacillamide D produced by Bacillus cereus from the mouse intestinal bacterial collection (miBC) is a potent cytotoxin in vitro.", "authors": [{"family": "Hohmann", "given": "Maximilian", "initials": "M"}, {"family": "Brunner", "given": "Valentina", "initials": "V"}, {"family": "Johannes", "given": "Widya", "initials": "W"}, {"family": "Schum", "given": "Dominik", "initials": "D", "orcid": "0009-0001-2706-6208", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ed4ed5f3f264263a9c3e0b16895c5f4.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Liu", "given": "Tianzhe", "initials": "T"}, {"family": "Sasaki", "given": "Daisuke", "initials": "D"}, {"family": "Bosch", "given": "Johanna", "initials": "J", "orcid": "0000-0003-3982-849X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9219b59c825f4c6d95b753db69fcc604.json"}}, {"family": "Clavel", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7229-5595", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e2197de37974b5c91d68b955f9ee3ec.json"}}, {"family": "Sieber", "given": "Stephan A", "initials": "SA", "orcid": "0000-0002-9400-906X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed221037cc8f4af18984505bc69cd193.json"}}, {"family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}}, {"family": "Tschurtschenthaler", "given": "Markus", "initials": "M", "orcid": "0000-0002-0060-4790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88ddb86362d1430791cbf916b8091d50.json"}}, {"family": "Jan\u00dfen", "given": "Klaus-Peter", "initials": "KP", "orcid": "0000-0002-4707-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b6efb5e10ce471780a443fbbcba2615.json"}}, {"family": "Gulder", "given": "Tobias A M", "initials": "TAM", "orcid": "0000-0001-6013-3161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/649b2a17f6964525acada09aa3a652eb.json"}}], "type": "journal article", "published": "2024-05-28", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "655", "issn-l": "2399-3642"}, "abstract": "The gut microbiota influences human health and the development of chronic diseases. However, our understanding of potentially protective or harmful microbe-host interactions at the molecular level is still in its infancy. To gain further insights into the hidden gut metabolome and its impact, we identified a cryptic non-ribosomal peptide BGC in the genome of Bacillus cereus DSM 28590 from the mouse intestine ( www.dsmz.de/miBC ), which was predicted to encode a thiazol(in)e substructure. Cloning and heterologous expression of this BGC revealed that it produces bacillamide D. In-depth functional evaluation showed potent cytotoxicity and inhibition of cell migration using the human cell lines HCT116 and HEK293, which was validated using primary mouse organoids. This work establishes the bacillamides as selective cytotoxins from a bacterial gut isolate that affect mammalian cells. Our targeted structure-function-predictive approach is demonstrated to be a streamlined method to discover deleterious gut microbial metabolites with potential effects on human health.", "doi": "10.1038/s42003-024-06208-3", "pmid": "38806706", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11133360"}, {"db": "pii", "key": "10.1038/s42003-024-06208-3"}], "notes": [], "created": "2025-03-18T17:31:56.201Z", "modified": "2025-04-08T06:10:47.544Z"}, {"entity": "publication", "iuid": "47a145341f044ab38d42b8c60fe13b3d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/47a145341f044ab38d42b8c60fe13b3d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/47a145341f044ab38d42b8c60fe13b3d"}}, "title": "Biosynthetic potential of the global ocean microbiome.", "authors": [{"family": "Paoli", "given": "Lucas", "initials": "L", "orcid": "0000-0003-0771-8309", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/116b5518d78f4cdfa7c7d6c7cdc7aeff.json"}}, {"family": "Ruscheweyh", "given": "Hans-Joachim", "initials": "HJ", "orcid": "0000-0001-7473-6086", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5c268ed49844847a079447ecfe4e88e.json"}}, {"family": "Forneris", "given": "Clarissa C", "initials": "CC"}, {"family": "Hubrich", "given": "Florian", "initials": "F"}, {"family": "Kautsar", "given": "Satria", "initials": "S"}, {"family": "Bhushan", "given": "Agneya", "initials": "A"}, {"family": "Lotti", "given": "Alessandro", "initials": "A"}, {"family": "Clayssen", "given": "Quentin", "initials": "Q"}, {"family": "Salazar", "given": "Guillem", "initials": "G", "orcid": "0000-0002-9786-1493", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e8355f28c644d7ab8085e6b16b2e6d2.json"}}, {"family": "Milanese", "given": "Alessio", "initials": "A", "orcid": "0000-0002-7050-2239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/45e9fe0111144358960531b419f2e1a7.json"}}, {"family": "Carlstr\u00f6m", "given": "Charlotte I", "initials": "CI"}, {"family": "Papadopoulou", "given": "Chrysa", "initials": "C", "orcid": "0000-0002-3909-7378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ad57234e149441d1b0b41cc5ad56cc38.json"}}, {"family": "Gehrig", "given": "Daniel", "initials": "D"}, {"family": "Karasikov", "given": "Mikhail", "initials": "M", "orcid": "0000-0001-6200-5972", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62afc29351cf45229987fc8c46a5058b.json"}}, {"family": "Mustafa", "given": "Harun", "initials": "H"}, {"family": "Larralde", "given": "Martin", "initials": "M", "orcid": "0000-0002-3947-4444", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e048b839197434d8af8ab34bd50cf5e.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "S\u00e1nchez", "given": "Pablo", "initials": "P", "orcid": "0000-0003-2787-822X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/485a43fed85b44d59992684545810243.json"}}, {"family": "Zayed", "given": "Ahmed A", "initials": "AA", "orcid": "0000-0003-2793-2679", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9ce1b7d6c164081bfd089054bbfbbfe.json"}}, {"family": "Cronin", "given": "Dylan R", "initials": "DR"}, {"family": "Acinas", "given": "Silvia G", "initials": "SG", "orcid": "0000-0002-3439-0428", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3d2775837da4504bc2d078a3ecbd3fe.json"}}, {"family": "Bork", "given": "Peer", "initials": "P", "orcid": "0000-0002-2627-833X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b2c7fb225454cb592da4b2af6d6b645.json"}}, {"family": "Bowler", "given": "Chris", "initials": "C", "orcid": "0000-0003-3835-6187", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f9da2e44f754892887a817f5ce71838.json"}}, {"family": "Delmont", "given": "Tom O", "initials": "TO", "orcid": "0000-0001-7053-7848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/878c9b5ebce5497182da1843d94fc821.json"}}, {"family": "Gasol", "given": "Josep M", "initials": "JM", "orcid": "0000-0001-5238-2387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbc878eda2704738b6f85fe4190bbb7f.json"}}, {"family": "Gossert", "given": "Alvar D", "initials": "AD", "orcid": "0000-0001-7732-495X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a574c3c72f9487b964deb86619874bb.json"}}, {"family": "Kahles", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0002-3411-0692", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07956568aa6041ea8e0cc27848f9e039.json"}}, {"family": "Sullivan", "given": "Matthew B", "initials": "MB", "orcid": "0000-0001-8398-8234", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e95585b7d0724fe4b1f95da9953e630e.json"}}, {"family": "Wincker", "given": "Patrick", "initials": "P"}, {"family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}}, {"family": "Robinson", "given": "Serina L", "initials": "SL", "orcid": "0000-0001-6947-7913", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/258518282d5f43268420a8bf71ddccd8.json"}}, {"family": "Piel", "given": "J\u00f6rn", "initials": "J", "orcid": "0000-0002-2282-8154", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2ec40bb2c076459885dbe76ca9657099.json"}}, {"family": "Sunagawa", "given": "Shinichi", "initials": "S", "orcid": "0000-0003-3065-0314", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a02fe8bae87447c914b3fe1cba5a21e.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "607", "issue": "7917", "pages": "111-118", "issn-l": "0028-0836"}, "abstract": "Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.", "doi": "10.1038/s41586-022-04862-3", "pmid": "35732736", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pmc", "key": "PMC9259500"}, {"db": "pii", "key": "10.1038/s41586-022-04862-3"}], "notes": [], "created": "2023-05-13T11:52:35.405Z", "modified": "2025-03-18T17:29:17.445Z"}, {"entity": "publication", "iuid": "8218cfa66e574583b9d300b455ba81ce", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8218cfa66e574583b9d300b455ba81ce.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8218cfa66e574583b9d300b455ba81ce"}}, "title": "Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.", "authors": [{"family": "Tramontano", "given": "Melanie", "initials": "M", "orcid": "0000-0001-6407-527X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7eb22c8f8f17483ca714daa532e877c9.json"}}, {"family": "Andrejev", "given": "Sergej", "initials": "S", "orcid": "0000-0002-7875-0261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fbe1b5aed7d4931896ef1c99dafcfc4.json"}}, {"family": "Pruteanu", "given": "Mihaela", "initials": "M", "orcid": "0000-0003-0484-8503", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b7d7b54ba2149289249a07339f63993.json"}}, {"family": "Kl\u00fcnemann", "given": "Martina", "initials": "M"}, {"family": "Kuhn", "given": "Michael", "initials": "M", "orcid": "0000-0002-2841-872X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e248cde011f94e6b9dd2de922062d0d6.json"}}, {"family": "Galardini", "given": "Marco", "initials": "M", "orcid": "0000-0003-2018-8242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bade63af21bc49e59c5687ea303157de.json"}}, {"family": "Jouhten", "given": "Paula", "initials": "P"}, {"family": "Zelezniak", "given": "Aleksej", "initials": "A"}, {"family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}}, {"family": "Bork", "given": "Peer", "initials": "P", "orcid": "0000-0002-2627-833X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b2c7fb225454cb592da4b2af6d6b645.json"}}, {"family": "Typas", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-0797-9018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d38ea7a531ad47cfa26df998f0e54dbe.json"}}, {"family": "Patil", "given": "Kiran Raosaheb", "initials": "KR", "orcid": "0000-0002-6166-8640", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/093a0e7ad5e0464a993d8e00861eea15.json"}}], "type": "journal article", "published": "2018-04-00", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "issn-l": "2058-5276", "volume": "3", "issue": "4", "pages": "514-522"}, "abstract": "Bacterial metabolism plays a fundamental role in gut microbiota ecology and host-microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth characteristics of 96 phylogenetically diverse gut bacterial strains across 4 rich and 15 defined media. The vast majority of strains (76) grow in at least one defined medium, enabling accurate assessment of their biosynthetic capabilities. These do not necessarily match phylogenetic similarity, thus indicating a complex evolution of nutritional preferences. We identify mucin utilizers and species inhibited by amino acids and short-chain fatty acids. Our analysis also uncovers media for in vitro studies wherein growth capacity correlates well with in vivo abundance. Further value of the underlying resource is demonstrated by correcting pathway gaps in available genome-scale metabolic models of gut microorganisms. Together, the media resource and the extracted knowledge on growth abilities widen experimental and computational access to the gut microbiota.", "doi": "10.1038/s41564-018-0123-9", "pmid": "29556107", "labels": {"Aleksej Zelezniak": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41564-018-0123-9"}], "notes": [], "created": "2018-12-03T14:45:45.267Z", "modified": "2022-11-04T11:51:57.019Z"}]}