{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T21:40:14Z","timestamp":1789422014343,"version":"build-2803163510"},"reference-count":44,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2023,8,30]],"date-time":"2023-08-30T00:00:00Z","timestamp":1693353600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"China Wool Sheep Industry and Technology System project","award":["CARS-39-14"],"award-info":[{"award-number":["CARS-39-14"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Hu sheep, a locally bred species in China known for its high productivity, is currently suffering from pneumonia. Here, we combine high-throughput 16SrRNA gene sequencing and bacterial culturing to examine the bacterial community in pneumonic Hu Sheep lungs (p &lt; 0.05). The results showed that the abundance and diversity of lung bacteria in healthy sheep were significantly higher than those in pneumonia sheep (p = 0.139), while there was no significant difference between moderate and severe pneumonia. Furthermore, the composition of the lung microbiota community underwent significant alterations between different levels of pneumonia severity. The application of LEfSe analysis revealed a notable enrichment of Mannheimiae within the lungs of sheep afflicted with moderate pneumonia (p &lt; 0.01), surpassing the levels observed in their healthy counterparts. Additionally, Fusobacterium emerged as the prevailing bacterial group within the lungs of sheep suffering from severe pneumonia. Integrating the results of bacterial isolation and identification, we conclusively determined that Mannheimia haemolytica was the primary pathogenic bacterium within the lungs of sheep afflicted with moderate pneumonia. Furthermore, the exacerbation of pneumonia may be attributed to the synergistic interplay between Fusobacterium spp. and other bacterial species. Our results provide new insights for guiding preventive and therapeutic measures for pneumonia of different severities in sheep.<\/jats:p>","DOI":"10.3390\/ani13172763","type":"journal-article","created":{"date-parts":[[2023,8,30]],"date-time":"2023-08-30T09:48:15Z","timestamp":1693388895000},"page":"2763","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Characterization of Lung Microbiomes in Pneumonic Hu Sheep Using Culture Technique and 16S rRNA Gene Sequencing"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8317-6922","authenticated-orcid":false,"given":"Yongqiang","family":"Miao","sequence":"first","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueliang","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianlin","family":"Lei","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingru","family":"Ding","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hang","family":"Feng","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaohu","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyang","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongyang","family":"Ye","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinglong","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2441-0026","authenticated-orcid":false,"given":"Zengqi","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,8,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"636","DOI":"10.14202\/vetworld.2018.636-641","article-title":"Isolation and identification of M. haemolytica by culture and polymerase chain reaction from sheep\u2019s pulmonary samples in Shiraz, Iran","volume":"11","author":"Tabatabaei","year":"2018","journal-title":"Vet. World"},{"key":"ref_2","first-page":"5169040","article-title":"Prevalence of Pneumonia in Sheep and Goats Slaughtered at Elfora Bishoftu Export Abattoir, Ethiopia: A Pathological Investigation","volume":"5","author":"Mekibib","year":"2019","journal-title":"J. Vet. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"101641","DOI":"10.1016\/j.cimid.2021.101641","article-title":"Differential pulmonary immunopathology of domestic sheep (Ovis aries) and bighorn sheep (Ovis canadensis) with Mycoplasma ovipneumoniae infection: A retrospective study","volume":"76","author":"Grossman","year":"2021","journal-title":"Comp. Immunol. Microbiol. Infect. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"866206","DOI":"10.3389\/fvets.2022.866206","article-title":"Serotyping and Seroprevalence of M. haemolytica, Pasteurella multocida, and Bibersteinia trehalosi and Assessment of Determinants of Ovine Pasteurellosis in West Amhara Sub-region, Ethiopia","volume":"9","author":"Getnet","year":"2022","journal-title":"Front. Vet. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Alvarez, J., Calder\u00f3n Bernal, J.M., Torre-Fuentes, L., Hern\u00e1ndez, M., Jimenez, C.E.P., Dom\u00ednguez, L., Fern\u00e1ndez-Garayz\u00e1bal, J.F., Vela, A.I., and Cid, D. (2023). Antimicrobial Susceptibility and Resistance Mechanisms in Mannheimia haemolytica Isolates from Sheep at Slaughter. Animals, 13.","DOI":"10.20944\/preprints202304.0480.v1"},{"key":"ref_6","first-page":"654","article-title":"Isolation, propagation, and characterization studies of an ovine Mycoplasma responsible for proliferative interstitial pneumonia","volume":"62","author":"Carmichael","year":"1972","journal-title":"Cornell Vet."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.prevetmed.2019.04.006","article-title":"Risk factors and productivity losses associated with Mycoplasma ovipneumoniae infection in United States domestic sheep operations","volume":"168","author":"Manlove","year":"2019","journal-title":"Prev. Vet. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1007\/s11259-022-09972-x","article-title":"The first Mycoplasma ovipneumoniae recovered from a sheep with respiratory disease in Brazil\u2014Draft genome and genomic analysis","volume":"46","author":"Gaeta","year":"2022","journal-title":"Vet. Res. Commun."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Windsor, P.A. (2022). Anaemia in Lambs Caused by Mycoplasma ovis: Global and Australian Perspectives. Animals, 12.","DOI":"10.3390\/ani12111372"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1023\/A:1005855318665","article-title":"Bacterial identity and characteristics in healthy and unhealthy respiratory tracts of sheep and calves","volume":"21","author":"Barbour","year":"1997","journal-title":"Vet. Res. Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/j.vetmic.2010.04.011","article-title":"Mycoplasma ovipneumoniae can predispose bighorn sheep to fatal M. haemolytica pneumonia","volume":"145","author":"Dassanayake","year":"2010","journal-title":"Vet. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1038\/s41467-021-22344-4","article-title":"A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation","volume":"12","author":"Das","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S2095-3119(17)61691-5","article-title":"Energy and protein requirements for maintenance of Hu sheep during pregnancy","volume":"17","author":"Zhang","year":"2018","journal-title":"J. Int. Agric."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Miao, Y.Q., Zhao, X.L., Adam, F.E.A., Xie, Q.F., Feng, H., Ding, J.R., Bai, X., Wang, J., and Yang, Z.Q. (2023). Isolation and Identification of Aeromonas veronii in Sheep with Fatal Infection in China: A Case Report. Microorganisms, 11.","DOI":"10.3390\/microorganisms11020333"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1186\/s40168-017-0364-5","article-title":"Comparing microbiotas in the upper aerodigestive and lower respiratory tracts of lambs","volume":"5","author":"Glendinning","year":"2017","journal-title":"Microbiome"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3225","DOI":"10.1128\/AEM.00540-16","article-title":"Variability of the Sheep Lung Microbiota","volume":"82","author":"Glendinning","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.lungcan.2016.10.016","article-title":"Characterization of microbiome in bronchoalveolar lavage fluid of patients with lung cancer comparing with benign mass like lesions","volume":"102","author":"Lee","year":"2016","journal-title":"Lung Cancer"},{"key":"ref_18","first-page":"1775","article-title":"Lung tissue microbial profile in lung cancer is distinct from emphysema","volume":"8","author":"Liu","year":"2018","journal-title":"Am. J. Cancer Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/j.tibtech.2008.02.002","article-title":"Biomedical applications of sheep models: From asthma to vaccines","volume":"26","author":"Scheerlinck","year":"2008","journal-title":"Trends Biotechnol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1016\/j.ajpath.2020.10.017","article-title":"Animal and Cell Culture Models for Cystic Fibrosis: Which Model Is Right for Your Application?","volume":"191","author":"McCarron","year":"2021","journal-title":"Am. J. Pathol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1085079","DOI":"10.3389\/fmicb.2022.1085079","article-title":"LDMD: A database of microbes in human lung disease","volume":"13","author":"Xu","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"E911","DOI":"10.1073\/pnas.1414592112","article-title":"Structure, variation, and assembly of the root-associated microbiomes of rice","volume":"112","author":"Edwards","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"874536","DOI":"10.3389\/fmicb.2022.874536","article-title":"Characteristics of Bacterial Microbiota in Different Intestinal Segments of Aohan Fine-Wool Sheep","volume":"13","author":"Ma","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"16031","DOI":"10.1038\/nmicrobiol.2016.31","article-title":"Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype","volume":"1","author":"Segal","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2223","DOI":"10.1038\/s41396-020-0678-3","article-title":"Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: Prediction of diarrhea","volume":"14","author":"Ma","year":"2020","journal-title":"ISME J."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1165\/rcmb.2019-0273TR","article-title":"Methods in Lung Microbiome Research","volume":"62","author":"Carney","year":"2020","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1186\/s40168-021-01055-4","article-title":"Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota","volume":"9","author":"Baker","year":"2021","journal-title":"Microbiome"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1017\/S1466252312000102","article-title":"The microbiome of the soft palate of swine","volume":"13","author":"Kernaghan","year":"2012","journal-title":"Anim. Health Res. Rev."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1378\/chest.11-0774","article-title":"Advancing respiratory research","volume":"140","author":"Kiley","year":"2011","journal-title":"Chest"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1600746","DOI":"10.1183\/13993003.00746-2016","article-title":"Atopobium and Fusobacterium as novel candidates for sarcoidosis-associated microbiota","volume":"50","author":"Zimmermann","year":"2017","journal-title":"Eur. Respir. J."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3963","DOI":"10.1038\/s41598-021-83524-2","article-title":"Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures","volume":"11","author":"Gupta","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"e0031423","DOI":"10.1128\/spectrum.00314-23","article-title":"Characterization of Lung and Oral Microbiomes in Lung Cancer Patients Using Culturomics and 16S rRNA Gene Sequencing","volume":"11","author":"Sun","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/1751-7915.13353","article-title":"Microbial communities in swine lungs and their association with lung lesions","volume":"12","author":"Huang","year":"2019","journal-title":"Microb. Biotechnol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1186\/s12934-019-1161-6","article-title":"Probiotics isolated from yaks improves the growth performance, antioxidant activity, and cytokines related to immunity and inflammation in mice","volume":"18","author":"Li","year":"2019","journal-title":"Microb. Cell Fact."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Johnston, D., Earley, B., Cormican, P., Murray, G., Kenny, D.A., Waters, S.M., McGee, M., Kelly, A.K., and McCabe, M.S. (2017). Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue. BMC Vet. Res., 13.","DOI":"10.1186\/s12917-017-1035-2"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"616","DOI":"10.7589\/2015-02-039","article-title":"Fusobacterium necrophorum in North American Bighorn Sheep (Ovis canadensis) Pneumonia","volume":"52","author":"Shanthalingam","year":"2016","journal-title":"J. Wildl. Dis."},{"key":"ref_38","first-page":"233","article-title":"Pasteurella haemolytica complicated respiratory infections in sheep and goats","volume":"29","author":"Brogden","year":"1998","journal-title":"Vet. Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"16113","DOI":"10.1038\/nmicrobiol.2016.113","article-title":"Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome","volume":"1","author":"Dickson","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e02284-14","DOI":"10.1128\/mBio.02284-14","article-title":"Application of a neutral community model to assess structuring of the human lung microbiome","volume":"6","author":"Venkataraman","year":"2015","journal-title":"MBio"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1099\/00207713-45-2-297","article-title":"Succiniclasticum ruminis gen. nov., sp. nov., a ruminal bacterium converting succinate to propionate as the sole energy-yielding mechanism","volume":"45","author":"Gylswyk","year":"1995","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.cvfa.2020.03.001","article-title":"Respiratory Bacterial Microbiota in Cattle: From Development to Modulation to Enhance Respiratory Health. The Veterinary clinics of North America","volume":"36","author":"Timsit","year":"2020","journal-title":"Vet. Clin. N. Am. Food Anim. Pract."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"e00629-19","DOI":"10.1128\/mSystems.00629-19","article-title":"Intranasal Bacterial Therapeutics Reduce Colonization by the Respiratory Pathogen M. haemolytica in Dairy Calves","volume":"5","author":"Amat","year":"2020","journal-title":"mSystems"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"108823","DOI":"10.1016\/j.vetmic.2020.108823","article-title":"Strength of association between isolation of Pasteurella multocida and consolidation lesions in ovine pneumonic pasteurellosis","volume":"248","author":"Cid","year":"2020","journal-title":"Vet. Microbiol."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/13\/17\/2763\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T20:43:17Z","timestamp":1760128997000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/13\/17\/2763"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,30]]},"references-count":44,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2023,9]]}},"alternative-id":["ani13172763"],"URL":"https:\/\/doi.org\/10.3390\/ani13172763","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,8,30]]}}}