{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T22:52:14Z","timestamp":1781650334495,"version":"3.54.5"},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T00:00:00Z","timestamp":1781568000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T00:00:00Z","timestamp":1781568000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100004909","name":"Universidade Federal Do Rio Grande Do Sul","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004909","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Braz J Microbiol"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The swine lower respiratory tract (LRT) microbiota has increasingly been investigated, but important knowledge gaps remain, limiting our understanding of microbial communities involved in respiratory health and disease. This longitudinal study evaluated the LRT bacterial composition of pigs with pulmonary lesions (PL+) compatible with\n                    <jats:italic>Mycoplasma hyopneumoniae<\/jats:italic>\n                    infection and without pulmonary lesions (PL-) across production phases from nursery to slaughter. Using\n                    <jats:italic>16\u00a0S-rRNA<\/jats:italic>\n                    gene sequencing of intratracheal mucus and lung fragments, we observed longitudinal shifts in bacterial community composition. PL- animals showed higher observed richness and Shannon diversity during the finishing phases, whereas PL+ animals showed reduced alpha-diversity values and less pronounced temporal variation in relative composition. A total of 18 ASVs were detected across all sampled phases in both groups, suggesting a small set of persistent taxa; however, their prevalence, abundance, and ecological relevance remain unclear in the present analysis. Furthermore, LEfSe identified ASVs classified as\n                    <jats:italic>Tetragenococcus halophilus<\/jats:italic>\n                    and\n                    <jats:italic>Bdellovibrio bacteriovorus<\/jats:italic>\n                    as candidate discriminant taxa associated with PL\u2009+\u2009and PL- groups, respectively; these associations should be treated as preliminary and dataset-specific. Together, these findings suggest that pulmonary lesion status is associated with altered respiratory bacterial community patterns and support longitudinal approaches for investigating swine respiratory health.\n                  <\/jats:p>","DOI":"10.1007\/s42770-026-01981-1","type":"journal-article","created":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T21:56:59Z","timestamp":1781647019000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Pulmonary lesions reshape swine respiratory microbiota: evidence of bacterial dysbiosis and reduced diversity"],"prefix":"10.1007","volume":"57","author":[{"given":"Kendra","family":"Rodeghiero","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela Merker","family":"Breyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karine Ludwig","family":"Takeuti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7282-6117","authenticated-orcid":false,"given":"Franciele Maboni","family":"Siqueira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,16]]},"reference":[{"key":"1981_CR1","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.vetmic.2017.02.017","volume":"209","author":"MC Niederwerder","year":"2017","unstructured":"Niederwerder MC (2017) Role of the microbiome in swine respiratory disease. Vet Microbiol 209:97\u2013106","journal-title":"Vet Microbiol"},{"key":"1981_CR2","first-page":"410","volume":"15","author":"P Tadee","year":"2025","unstructured":"Tadee P, Khaodang P, Patchanee P, Buddhasiri S, Eiamsam-ang T, Kittiwan N et al (2025) Characterization of lung microbiome in subclinical pneumonic Thai pigs using 16S rRNA gene sequencing. Anim (Basel) 15:410","journal-title":"Anim (Basel)"},{"key":"1981_CR3","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/s42523-020-00070-4","volume":"3","author":"M Pirolo","year":"2021","unstructured":"Pirolo M, Espinosa-Gongora C, Bogaert D, Guardabassi L (2021) The porcine respiratory microbiome: recent insights and future challenges. Anim Microbiome 3:9","journal-title":"Anim Microbiome"},{"key":"1981_CR4","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s42523-023-00226-y","volume":"5","author":"M Pirolo","year":"2023","unstructured":"Pirolo M, Espinosa-Gongora C, Alberdi A, Eisenhofer R, Soverini M, Eriksen EO et al (2023) Bacterial topography of the upper and lower respiratory tract in pigs. Anim Microbiome 5:5","journal-title":"Anim Microbiome"},{"key":"1981_CR5","doi-asserted-by":"publisher","first-page":"e0181503","DOI":"10.1371\/journal.pone.0181503","volume":"12","author":"FM Siqueira","year":"2017","unstructured":"Siqueira FM, Perez-Wohlfeil E, Carvalho FM, Trelles O, Schrank IS, Vasconcelos ATR et al (2017) Microbiome overview in swine lungs. PLoS ONE 12:e0181503. https:\/\/doi.org\/10.1371\/journal.pone.0181503","journal-title":"PLoS ONE"},{"key":"1981_CR6","doi-asserted-by":"publisher","first-page":"674","DOI":"10.3390\/vetsci9120674","volume":"9","author":"HMS Almeida","year":"2022","unstructured":"Almeida HMS, Sonalio K, Mechler-Dreibi ML, Petri FAM, Storino GY, Maes D et al (2022) Experimental infection with Mycoplasma hyopneumoniae strain 232 in swine influences the lower respiratory microbiota. Vet Sci 9:674. https:\/\/doi.org\/10.3390\/vetsci9120674","journal-title":"Vet Sci"},{"key":"1981_CR7","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1111\/j.1439-0442.2007.00920.x","volume":"54","author":"F Ostanello","year":"2007","unstructured":"Ostanello F, Dottori M, Gusmara C, Leotti G, Sala V (2007) Pneumonia disease assessment using a slaughterhouse lung-scoring method. J Vet Med Physiol Pathol Clin Med 54:70\u201375. https:\/\/doi.org\/10.1111\/j.1439-0442.2007.00920.x","journal-title":"J Vet Med Physiol Pathol Clin Med"},{"key":"1981_CR8","first-page":"231","volume":"13","author":"F Madec","year":"1981","unstructured":"Madec F, Derrien H, Fr\u00e9quence (1981) intensit\u00e9 et localisation des l\u00e9sions pulmonaires chez le porc charcutier: r\u00e9sultats d\u2019une premi\u00e8re s\u00e9rie d\u2019observations en abattoir. J Rech Porc Fr 13:231\u2013236","journal-title":"J Rech Porc Fr"},{"key":"1981_CR9","doi-asserted-by":"publisher","first-page":"2178797","DOI":"10.1080\/19490976.2023.2178797","volume":"15","author":"L Grieneisen","year":"2023","unstructured":"Grieneisen L, Blekhman R, Archie E (2023) How longitudinal data can contribute to our understanding of host genetic effects on the gut microbiome. Gut Microbes 15:2178797. https:\/\/doi.org\/10.1080\/19490976.2023.2178797","journal-title":"Gut Microbes"},{"key":"1981_CR10","doi-asserted-by":"publisher","first-page":"1068","DOI":"10.1186\/s12864-025-12282-6","volume":"26","author":"L Wang","year":"2025","unstructured":"Wang L, Qi G, Shi Y et al (2025) A systematic longitudinal study of microbiome: integrating temporal-spatial dimensions with causal and deep learning models. BMC Genomics 26:1068. https:\/\/doi.org\/10.1186\/s12864-025-12282-6","journal-title":"BMC Genomics"},{"key":"1981_CR11","unstructured":"World Organisation for Animal Health (WOAH) (2026) WOAH: World Organisation for Animal Health [Internet]. WOAH, Paris. Available from: https:\/\/www.woah.org\/"},{"key":"1981_CR12","doi-asserted-by":"publisher","first-page":"106475","DOI":"10.1016\/j.mimet.2022.106475","volume":"197","author":"KL Takeuti","year":"2022","unstructured":"Takeuti KL, Michaelsen TR, Sabedot C, Nagae RY, Forner RAN, Mazzarollo A et al (2022) Mycoplasma hyopneumoniae detection by PCR in naturally infected finishing pigs. J Microbiol Methods 197:106475. https:\/\/doi.org\/10.1016\/j.mimet.2022.106475","journal-title":"J Microbiol Methods"},{"key":"1981_CR13","doi-asserted-by":"publisher","first-page":"115449","DOI":"10.1016\/j.ab.2023.115449","volume":"687","author":"GM Breyer","year":"2024","unstructured":"Breyer GM, De Carli S, Jacques da Silva MER, Dias ME, Varela APM, Mann MB et al (2024) Alternative amplicon-PCR protocol for maximizing bacterial and fungal sequencing in low-biomass samples. Anal Biochem 687:115449. https:\/\/doi.org\/10.1016\/j.ab.2023.115449","journal-title":"Anal Biochem"},{"key":"1981_CR14","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1128\/AEM.01043-13","volume":"79","author":"JJ Kozich","year":"2013","unstructured":"Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analysing amplicon sequence data on the Illumina MiSeq platform. Appl Environ Microbiol 79:5112\u20135120. https:\/\/doi.org\/10.1128\/AEM.01043-13","journal-title":"Appl Environ Microbiol"},{"key":"1981_CR15","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114\u20132120","journal-title":"Bioinformatics"},{"key":"1981_CR16","doi-asserted-by":"publisher","first-page":"e100","DOI":"10.1002\/cpbi.100","volume":"70","author":"M Estaki","year":"2020","unstructured":"Estaki M, Jiang L, Bokulich NA et al (2020) QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data. Curr Protoc Bioinf 70:e100","journal-title":"Curr Protoc Bioinf"},{"key":"1981_CR17","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581\u2013583","journal-title":"Nat Methods"},{"key":"1981_CR18","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast C, Pruesse E, Yilmaz P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590\u2013D596","journal-title":"Nucleic Acids Res"},{"key":"1981_CR19","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie PJ, Holmes S (2013) phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8:e61217","journal-title":"PLoS ONE"},{"key":"1981_CR20","volume-title":"R: A language and environment for statistical computing","author":"R Core Team","year":"2024","unstructured":"R Core Team (2024) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna"},{"key":"1981_CR21","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.21105\/joss.01686","volume":"4","author":"H Wickham","year":"2019","unstructured":"Wickham H, Averick M, Bryan J, Chang W, McGowan L, Fran\u00e7ois R et al (2019) Welcome to the Tidyverse. J Open Source Softw 4:1686","journal-title":"J Open Source Softw"},{"key":"1981_CR22","unstructured":"Sjoberg D ggsankey: Sankey, alluvial and sankey bump plots for ggplot2. Available from: https:\/\/github.com\/davidsjoberg\/ggsankey"},{"key":"1981_CR23","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-98141-3","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"H Wickham","year":"2009","unstructured":"Wickham H (2009) ggplot2: Elegant Graphics for Data Analysis. Springer, New York. https:\/\/doi.org\/10.1007\/978-0-387-98141-3"},{"key":"1981_CR24","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1017\/S1466252311000120","volume":"12","author":"T Opriessnig","year":"2011","unstructured":"Opriessnig T, Gim\u00e9nez-Lirola LG, Halbur PG (2011) Polymicrobial respiratory disease in pigs. Anim Health Res Rev 12:133\u2013148","journal-title":"Anim Health Res Rev"},{"key":"1981_CR25","doi-asserted-by":"publisher","first-page":"1329073","DOI":"10.3389\/fvets.2023.1329073","volume":"10","author":"N Ramos","year":"2023","unstructured":"Ramos N, Sibila M, Neira V, Editorial (2023) Porcine respiratory disease complex: dynamics of polymicrobial infections, synergistic effects and management strategies. Front Vet Sci 10:1329073","journal-title":"Front Vet Sci"},{"key":"1981_CR26","doi-asserted-by":"publisher","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","volume":"12","author":"N Segata","year":"2011","unstructured":"Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS et al (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60. https:\/\/doi.org\/10.1186\/gb-2011-12-6-r60","journal-title":"Genome Biol"},{"key":"1981_CR27","unstructured":"Cao Y (2022) microbiomeMarker: microbiome biomarker analysis toolkit. Version 1.2.2; Available from: https:\/\/github.com\/yiluheihei\/microbiomeMarker"},{"key":"1981_CR28","unstructured":"Oksanen J, Simpson G, Blanchet F, Kindt R, Legendre P, Minchin P et al (2025) vegan: Community ecology package. R package version 2.8-0"},{"key":"1981_CR29","doi-asserted-by":"publisher","first-page":"3218","DOI":"10.3389\/fmicb.2018.03218","volume":"9","author":"Q Wang","year":"2018","unstructured":"Wang Q, Cai R, Huang A, Wang X, Qu W, Shi L et al (2018) Comparison of oropharyngeal microbiota in healthy piglets and piglets with respiratory disease. Front Microbiol 9:3218. https:\/\/doi.org\/10.3389\/fmicb.2018.03218","journal-title":"Front Microbiol"},{"key":"1981_CR30","doi-asserted-by":"publisher","first-page":"1069","DOI":"10.3390\/ani14071069","volume":"14","author":"X Tang","year":"2024","unstructured":"Tang X (2024) Probiotic roles of Clostridium butyricum in piglets: considering aspects of intestinal barrier function. Anim (Basel) 14:1069. https:\/\/doi.org\/10.3390\/ani14071069","journal-title":"Anim (Basel)"},{"key":"1981_CR31","doi-asserted-by":"publisher","first-page":"2926","DOI":"10.1039\/c8fo02370k","volume":"10","author":"G Cao","year":"2019","unstructured":"Cao G, Tao F, Hu Y, Li Z, Zhang Y, Deng B et al (2019) Positive effects of a Clostridium butyricum-based compound probiotic on growth performance and immune responses in weaned piglets. Food Funct 10:2926\u20132934. https:\/\/doi.org\/10.1039\/c8fo02370k","journal-title":"Food Funct"},{"key":"1981_CR32","doi-asserted-by":"publisher","first-page":"573","DOI":"10.3390\/microorganisms8040573","volume":"8","author":"M Vacca","year":"2020","unstructured":"Vacca M, Celano G, Calabrese FM, Portincasa P, Gobbetti M, De Angelis M (2020) The controversial role of human gut Lachnospiraceae. Microorganisms 8:573","journal-title":"Microorganisms"},{"key":"1981_CR33","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/s41579-021-00559-y","volume":"19","author":"A Tett","year":"2021","unstructured":"Tett A, Pasolli E, Masetti G, Ercolini D, Segata N (2021) Prevotella diversity, niches and interactions with the human host. Nat Rev Microbiol 19:585\u2013599","journal-title":"Nat Rev Microbiol"},{"key":"1981_CR34","doi-asserted-by":"publisher","first-page":"640253","DOI":"10.3389\/fmicb.2021.640253","volume":"12","author":"J Teichmann","year":"2021","unstructured":"Teichmann J, Cockburn DW (2021) In vitro fermentation reveals changes in butyrate production dependent on resistant starch source and microbiome composition. Front Microbiol 12:640253","journal-title":"Front Microbiol"},{"key":"1981_CR35","doi-asserted-by":"publisher","first-page":"e16","DOI":"10.1017\/gmb.2023.14","volume":"4","author":"F Notting","year":"2023","unstructured":"Notting F, Pirovano W, Sybesma W, Kort R (2023) The butyrate-producing and spore-forming bacterial genus Coprococcus as a potential biomarker for neurological disorders. Gut Microbiome 4:e16","journal-title":"Gut Microbiome"},{"key":"1981_CR36","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/s13213-025-01794-x","volume":"75","author":"SM Al-Maaqar","year":"2025","unstructured":"Al-Maaqar SM, Al Johni ARS, Al-Tayyar NA, Alhamad JA, Ghyathuddin AAK, Alsubhi WA et al (2025) Bdellovibrio bacteriovorus: a magic weapon against bacterial pathogens. Ann Microbiol 75:11. https:\/\/doi.org\/10.1186\/s13213-025-01794-x","journal-title":"Ann Microbiol"},{"key":"1981_CR37","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1080\/09593330.2024.2348675","volume":"46","author":"X Dong","year":"2025","unstructured":"Dong X, Duan L, Zhan M, Xu Y, Yu R (2025) Predatory Bdellovibrio-and-like organism mixtures on efficient MBR in-situ membrane fouling diminishment and mechanisms. Environ Technol 46:179\u2013193","journal-title":"Environ Technol"},{"key":"1981_CR38","doi-asserted-by":"publisher","first-page":"630","DOI":"10.1080\/21505594.2021.1912424","volume":"12","author":"FM Cavallo","year":"2021","unstructured":"Cavallo FM, Jordana L, Friedrich AW, Glasner C, van Dijl JM (2021) Bdellovibrio bacteriovorus: a potential living antibiotic to control bacterial pathogens. Virulence 12:630\u2013646. https:\/\/doi.org\/10.1080\/21505594.2021.1912424","journal-title":"Virulence"},{"key":"1981_CR39","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1186\/s12866-022-02561-7","volume":"22","author":"DH Kim","year":"2022","unstructured":"Kim DH, Kim SA, Jo YM et al (2022) Probiotic potential of Tetragenococcus halophilus EFEL7002 isolated from Korean soy Meju. BMC Microbiol 22:149. https:\/\/doi.org\/10.1186\/s12866-022-02561-7","journal-title":"BMC Microbiol"},{"key":"1981_CR40","doi-asserted-by":"publisher","first-page":"2515","DOI":"10.1099\/ijs.0.63869-0","volume":"55","author":"TR Whitehead","year":"2005","unstructured":"Whitehead TR, Cotta MA, Collins MD, Falsen E, Lawson PA (2005) Bacteroides coprosuis sp. nov., isolated from swine-manure storage pits. Int J Syst Evol Microbiol 55:2515\u20132518. https:\/\/doi.org\/10.1099\/ijs.0.63869-0","journal-title":"Int J Syst Evol Microbiol"}],"container-title":["Brazilian Journal of Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s42770-026-01981-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s42770-026-01981-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s42770-026-01981-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T21:57:02Z","timestamp":1781647022000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s42770-026-01981-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,16]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["1981"],"URL":"https:\/\/doi.org\/10.1007\/s42770-026-01981-1","relation":{},"ISSN":["1517-8382","1678-4405"],"issn-type":[{"value":"1517-8382","type":"print"},{"value":"1678-4405","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,16]]},"assertion":[{"value":"17 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 May 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 June 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All experimental procedures conducted in this study followed the ethical guidelines for the use of animals in scientific research with experimental protocol approved by the Animal Ethics Committee of the Federal University of Rio Grande do Sul, under number 36730.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}},{"value":"The authors declare no competing interests. Author Franciele Maboni Siqueira is one of the guest editors of the Collection Microbial Diversity, and this article was independently handled by another member of the journal editorial board.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"174"}}