{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T03:41:43Z","timestamp":1793418103054,"version":"4.5.0"},"reference-count":69,"publisher":"Microbiology Society","issue":"12","license":[{"start":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T00:00:00Z","timestamp":1734566400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"crossref","award":["727966"],"award-info":[{"award-number":["727966"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,19]]},"abstract":"<jats:p>\n                  <jats:italic>Streptococcus suis<\/jats:italic> is a Gram-positive opportunistic pathogen causing systemic disease in piglets around weaning age. The factors predisposing to disease are not known. We hypothesized that the tonsillar microbiota might influence disease risk via colonization resistance and\/or co-infections. We conducted a cross-sectional case\u2013control study within outbreak farms complemented by selective longitudinal sampling and comparison with control farms without disease occurrence. We found a small but significant difference in tonsil microbiota composition between case and control piglets (<jats:italic>n<\/jats:italic>=45+45). Variants of putative commensal taxa, including <jats:italic>Rothia nasimurium<\/jats:italic>, were reduced in abundance in case piglets compared to asymptomatic controls. Case piglets had higher relative abundances of <jats:italic>Fusobacterium gastrosuis<\/jats:italic>, <jats:italic>Bacteroides heparinolyticus<\/jats:italic> and uncultured <jats:italic>Prevotella<\/jats:italic> and <jats:italic>Alloprevotella<\/jats:italic> species. Piglets developing disease post-weaning had reduced alpha diversity pre-weaning. Despite case\u2013control pairs receiving equal antimicrobial treatment, case piglets had a higher abundance of antimicrobial resistance genes conferring resistance to antimicrobial classes used to treat <jats:italic>S. suis<\/jats:italic>. This might be an adaption of disease-associated strains to frequent antimicrobial treatment.<\/jats:p>","DOI":"10.1099\/mgen.0.001334","type":"journal-article","created":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T15:17:29Z","timestamp":1734621449000},"source":"Crossref","is-referenced-by-count":8,"title":["Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome"],"prefix":"10.1099","volume":"10","author":[{"given":"Simen","family":"Fredriksen","sequence":"first","affiliation":[{"name":"Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, Wageningen, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos","family":"Neila-Ib\u00e1\u00f1ez","sequence":"additional","affiliation":[{"name":"OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain"},{"name":"IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA),, Campus de la Universitat Autnoma de Barcelona (UAB), Bellaterra, 08193, Catalonia, Spain"},{"name":"Unitat mixta dInvestigaci IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CRSA), Campus de laUniversitat Autnoma de Barcelona (UAB), Bellaterra, 08193, Catalonia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabel","family":"Hennig-Pauka","sequence":"additional","affiliation":[{"name":"Field Station for Epidemiology, University of Veterinary Medicine Hannover, 49456 Bakum, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaonan","family":"Guan","sequence":"additional","affiliation":[{"name":"Schothorst Feed Research B.V., Lelystad, Netherlands"},{"name":"Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, Wageningen, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenelle","family":"Dunkelberger","sequence":"additional","affiliation":[{"name":"Topigs Norsvin USA, Bloomington, MN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabela Fernandes","family":"de Oliveira","sequence":"additional","affiliation":[{"name":"Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, Wageningen, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Laura","family":"Ferrando","sequence":"additional","affiliation":[{"name":"Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, Wageningen, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florencia","family":"Correa-Fiz","sequence":"additional","affiliation":[{"name":"OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain"},{"name":"IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA),, Campus de la Universitat Autnoma de Barcelona (UAB), Bellaterra, 08193, Catalonia, Spain"},{"name":"Unitat mixta dInvestigaci IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CRSA), Campus de laUniversitat Autnoma de Barcelona (UAB), Bellaterra, 08193, Catalonia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Virginia","family":"Aragon","sequence":"additional","affiliation":[{"name":"OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain"},{"name":"IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA),, Campus de la Universitat Autnoma de Barcelona (UAB), Bellaterra, 08193, Catalonia, Spain"},{"name":"Unitat mixta dInvestigaci IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CRSA), Campus de laUniversitat Autnoma de Barcelona (UAB), Bellaterra, 08193, Catalonia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos","family":"Boekhorst","sequence":"additional","affiliation":[{"name":"Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, Wageningen, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"van Baarlen","sequence":"additional","affiliation":[{"name":"Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, Wageningen, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jerry M.","family":"Wells","sequence":"additional","affiliation":[{"name":"Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University, Wageningen, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1016\/s0378-1135(00)00250-9"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(07)70001-4"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2021.676002"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00480"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1016\/s0378-1135(98)00228-4"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1186\/s13567-022-01111-3"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-021-01094-1"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2016.00118"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.20.5.945-947.1984"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1136\/vr.107.2.40"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-12-20"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0215983"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1017\/S1466252312000102"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1080\/21505594.2022.2069390"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-018-1176-x"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2018.00220"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-022-02625-8"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1186\/s42523-022-00162-3"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.21203\/rs.3.rs-126949\/v1"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens7010007"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1186\/s13567-021-00918-w"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1354\/vp.37-2-143"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1002\/1873-3468.12364"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1080\/21505594.2021.1985760"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms7740"},{"key":"R26","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.01712-18","article-title":"Pathotyping the zoonotic pathogen Streptococcus suis: novel genetic markers to differentiate invasive disease-associated isolates from non-disease-associated isolates from England and Wales","volume":"57","author":"Wileman","year":"2019","journal-title":"J Clin Microbiol"},{"key":"R27","first-page":"000992","article-title":"Transcriptomics in serum and culture medium reveal shared and differential gene regulation in pathogenic and commensal Streptococcus suis","volume":"9","author":"Fredriksen","year":"2023","journal-title":"Microb Genom"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2307773120"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.14806\/ej.17.1.200"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3869"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1219"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3988"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061217"},{"key":"R37","first-page":"631","article-title":"The vegan package","volume":"10","author":"Oksanen","year":"2007","journal-title":"Commun Ecol Package"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0541-1"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz848"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkaa345"},{"key":"R42","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-021-02306-1","article-title":"Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox","volume":"22","author":"Wirbel","year":"2021","journal-title":"Genome Biol"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1017\/S1466252311000120"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1186\/s13567-019-0656-9"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1136\/annrheumdis-2017-eular.2874"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-023-01610-1"},{"key":"R47","first-page":"000854","article-title":"Comparative genomics of rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches","volume":"8","author":"de Oliveira","year":"2022","journal-title":"Microb Genom"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-43022-y"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fux010"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2020.00255"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00670-13"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00663-21"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00682-21"},{"key":"R54","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.15791"},{"key":"R55","doi-asserted-by":"publisher","DOI":"10.1016\/j.anaerobe.2017.02.022"},{"key":"R56","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-50187-z"},{"key":"R57","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-018-0192-9"},{"key":"R58","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00941-7"},{"key":"R59","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02590-17"},{"key":"R60","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-49897-1"},{"key":"R61","doi-asserted-by":"publisher","DOI":"10.1007\/s00203-019-01787-w"},{"key":"R62","doi-asserted-by":"publisher","DOI":"10.1111\/mec.16238"},{"key":"R63","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-016-2700-8"},{"key":"R64","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines8030384"},{"key":"R65","first-page":"147","article-title":"Half-lives of immunoglobulins IgG, IgA and IgM in the serum of new-born pigs","volume":"24","author":"Curtis","year":"1973","journal-title":"Immunology"},{"key":"R66","doi-asserted-by":"publisher","DOI":"10.1016\/0167-5877(94)90030-2"},{"key":"R67","doi-asserted-by":"publisher","DOI":"10.1111\/j.1439-0450.1979.tb00826.x"},{"key":"R68","doi-asserted-by":"publisher","DOI":"10.2460\/ajvr.2001.62.1805"},{"key":"R69","doi-asserted-by":"publisher","DOI":"10.1046\/j.0931-1793.2003.00700.x"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001334?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T15:17:32Z","timestamp":1734621452000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001334"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,19]]},"references-count":69,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2024,12,19]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001334","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,19]]}}}