{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:51:26Z","timestamp":1792785086387,"version":"4.5.0"},"reference-count":62,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T00:00:00Z","timestamp":1787011200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T00:00:00Z","timestamp":1790380800000},"content-version":"vor","delay-in-days":39,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100007620","name":"Department of Education of Liaoning Province","doi-asserted-by":"publisher","award":["LJ212410161048"],"award-info":[{"award-number":["LJ212410161048"]}],"id":[{"id":"10.13039\/501100007620","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007620","name":"Department of Education of Liaoning Province","doi-asserted-by":"publisher","award":["JYTMS20230566"],"award-info":[{"award-number":["JYTMS20230566"]}],"id":[{"id":"10.13039\/501100007620","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010086","name":"Foundation of Liaoning Province Education Administration","doi-asserted-by":"publisher","award":["Non"],"award-info":[{"award-number":["Non"]}],"id":[{"id":"10.13039\/501100010086","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Youth Talent Cultivation Fund Project of Dalian Medical University.","id":[{"id":"https:\/\/ror.org\/04c8eg608","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"DOI":"10.1038\/s42003-026-10793-w","type":"journal-article","created":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T09:25:30Z","timestamp":1787045130000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Gut microbiota-derived acetate mitigates Escherichia fergusonii-induced gut dysbiosis exacerbating Klebsiella pneumoniae pulmonary infection in mice"],"prefix":"10.1038","volume":"9","author":[{"given":"Yuyuan","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shibo","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yicheng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunming","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2970-1663","authenticated-orcid":false,"given":"Dong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingda","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengfei","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2874-5691","authenticated-orcid":false,"given":"Encheng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9023-1010","authenticated-orcid":false,"given":"Yang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,18]]},"reference":[{"key":"10793_CR1","doi-asserted-by":"publisher","first-page":"e131","DOI":"10.1016\/S2666-5247(23)00290-2","volume":"5","author":"JR Verani","year":"2024","unstructured":"Verani, J. R. et al. Child deaths caused by Klebsiella pneumoniae in sub-Saharan Africa and South Asia: a secondary analysis of Child Health and Mortality Prevention Surveillance (CHAMPS) data. Lancet Microbe 5, e131\u2013e141 (2024).","journal-title":"Lancet Microbe"},{"key":"10793_CR2","doi-asserted-by":"crossref","unstructured":"Pina-Iturbe, A., Hoppe-Elsholz, G., Suazo, I. D., Kalergis, A. M. & Bueno, S. M. Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258. Microb. Genom. 9, 001138 (2023).","DOI":"10.1099\/mgen.0.001138"},{"key":"10793_CR3","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1111\/imr.12563","volume":"279","author":"S Kim","year":"2017","unstructured":"Kim, S., Covington, A. & Pamer, E. G. The intestinal microbiota: antibiotics, colonization resistance, and enteric pathogens. Immunol. Rev. 279, 90\u2013105 (2017).","journal-title":"Immunol. Rev."},{"key":"10793_CR4","doi-asserted-by":"crossref","unstructured":"Aktas, A., Ekren, B. Y., Yasa, B., Sezerman, O. U. & Nakipoglu, Y. Investigation of the impact of antibiotic administration on the preterm infants\u2019 gut microbiome using next-generation sequencing-based 16S rRNA gene analysis. Antibiotics 13, 977 (2024).","DOI":"10.3390\/antibiotics13100977"},{"key":"10793_CR5","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1136\/gutjnl-2015-309728","volume":"65","author":"TJ Schuijt","year":"2016","unstructured":"Schuijt, T. J. et al. The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia. Gut 65, 575\u2013583 (2016).","journal-title":"Gut"},{"key":"10793_CR6","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.856633","volume":"12","author":"L Wen","year":"2022","unstructured":"Wen, L. et al. Gut microbiota protected against Pseudomonas aeruginosa pneumonia via restoring Treg\/Th17 balance and metabolism. Front. Cell Infect. Microbiol 12, 856633 (2022).","journal-title":"Front. Cell Infect. Microbiol"},{"key":"10793_CR7","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1097\/SHK.0b013e3182184ee7","volume":"36","author":"LW Chen","year":"2011","unstructured":"Chen, L. W., Chen, P. H. & Hsu, C. M. Commensal microflora contribute to host defense against Escherichia coli pneumonia through Toll-like receptors. Shock 36, 67\u201375 (2011).","journal-title":"Shock"},{"key":"10793_CR8","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.954339","volume":"13","author":"S Rastogi","year":"2022","unstructured":"Rastogi, S., Mohanty, S., Sharma, S. & Tripathi, P. Possible role of gut microbes and host\u2019s immune response in gut-lung homeostasis. Front. Immunol. 13, 954339 (2022).","journal-title":"Front. Immunol."},{"key":"10793_CR9","doi-asserted-by":"publisher","DOI":"10.1016\/j.intimp.2023.110971","volume":"124","author":"X Zeng","year":"2023","unstructured":"Zeng, X. et al. Gut microbiota-derived autoinducer-2 regulates lung inflammation through the gut-lung axis. Int Immunopharmacol. 124, 110971 (2023).","journal-title":"Int Immunopharmacol."},{"key":"10793_CR10","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1053\/j.gastro.2022.09.024","volume":"164","author":"N Nagata","year":"2023","unstructured":"Nagata, N. et al. Human gut microbiota and its metabolites impact immune responses in COVID-19 and its complications. Gastroenterology 164, 272\u2013288 (2023).","journal-title":"Gastroenterology"},{"key":"10793_CR11","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1237998","volume":"14","author":"N Alvarado-Pena","year":"2023","unstructured":"Alvarado-Pena, N., Galeana-Cadena, D., Gomez-Garcia, I. A., Mainero, X. S. & Silva-Herzog, E. The microbiome and the gut-lung axis in tuberculosis: interplay in the course of disease and treatment. Front. Microbiol. 14, 1237998 (2023).","journal-title":"Front. Microbiol."},{"key":"10793_CR12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35767-4","volume":"14","author":"R Le Guern","year":"2023","unstructured":"Le Guern, R. et al. Gut colonisation with multidrug-resistant Klebsiella pneumoniae worsens Pseudomonas aeruginosa lung infection. Nat. Commun. 14, 78 (2023).","journal-title":"Nat. Commun."},{"key":"10793_CR13","doi-asserted-by":"crossref","unstructured":"Wang, Y. et al. Intestinal Klebsiella pneumoniae contributes to pneumonia by synthesizing glutamine in multiple myeloma. Cancers 14, 4188 (2022).","DOI":"10.3390\/cancers14174188"},{"key":"10793_CR14","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1392376","volume":"14","author":"Y Tang","year":"2024","unstructured":"Tang, Y. et al. Gut microbes improve prognosis of Klebsiella pneumoniae pulmonary infection through the lung-gut axis. Front. Cell Infect. Microbiol. 14, 1392376 (2024).","journal-title":"Front. Cell Infect. Microbiol."},{"key":"10793_CR15","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1139436","volume":"13","author":"Y Wan","year":"2023","unstructured":"Wan, Y. et al. Effect of metformin on sepsis-associated acute lung injury and gut microbiota in aged rats with sepsis. Front. Cell Infect. Microbiol. 13, 1139436 (2023).","journal-title":"Front. Cell Infect. Microbiol."},{"key":"10793_CR16","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.vetmic.2014.04.016","volume":"172","author":"W Gaastra","year":"2014","unstructured":"Gaastra, W., Kusters, J. G., van Duijkeren, E. & Lipman, L. J. Escherichia fergusonii. Vet. Microbiol. 172, 7\u201312 (2014).","journal-title":"Vet. Microbiol."},{"key":"10793_CR17","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/s12866-024-03728-0","volume":"25","author":"S Khataee","year":"2025","unstructured":"Khataee, S. et al. Optimized extraction and kinetic study of cholesterol oxidase from a newly isolated Escherichia fergusonii strain from local whey samples: insights through a combined experimental study and artificial neural network modeling. BMC Microbiol. 25, 32 (2025).","journal-title":"BMC Microbiol."},{"key":"10793_CR18","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01617-21","volume":"10","author":"B Tang","year":"2022","unstructured":"Tang, B. et al. Escherichia fergusonii, an underrated repository for antimicrobial resistance in food animals. Microbiol. Spectr. 10, e0161721 (2022).","journal-title":"Microbiol. Spectr."},{"key":"10793_CR19","doi-asserted-by":"publisher","DOI":"10.1016\/j.virusres.2023.199219","volume":"336","author":"K Jung","year":"2023","unstructured":"Jung, K., Wang, Q., Chang, K. O. & Saif, L. J. Intestinal colonization with Escherichia fergusonii enhances infectivity of GII.12 human norovirus in gnotobiotic pigs. Virus Res. 336, 199219 (2023).","journal-title":"Virus Res."},{"key":"10793_CR20","doi-asserted-by":"crossref","unstructured":"Le Guern, R. et al. Impact of the timing of antibiotic administration on digestive colonization with carbapenemase-producing Enterobacteriaceae in a murine model. Antimicrob. Agents Chemother. 63, e00360-19 (2019).","DOI":"10.1128\/AAC.00360-19"},{"key":"10793_CR21","doi-asserted-by":"publisher","first-page":"L480","DOI":"10.1152\/ajplung.00296.2022","volume":"324","author":"CB Hildebrand","year":"2023","unstructured":"Hildebrand, C. B. et al. Short-chain fatty acids improve inflamm-aging and acute lung injury in old mice. Am. J. Physiol. Lung Cell Mol. Physiol. 324, L480\u2013L492 (2023).","journal-title":"Am. J. Physiol. Lung Cell Mol. Physiol."},{"key":"10793_CR22","doi-asserted-by":"crossref","unstructured":"Karampatakis, T., Tsergouli, K. & Behzadi, P. Carbapenem-resistant Klebsiella pneumoniae: virulence factors, molecular epidemiology and latest updates in treatment options. Antibiotics 12, 234 (2023).","DOI":"10.3390\/antibiotics12020234"},{"key":"10793_CR23","doi-asserted-by":"publisher","first-page":"4332","DOI":"10.1172\/JCI43918","volume":"120","author":"C Ubeda","year":"2010","unstructured":"Ubeda, C. et al. Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J. Clin. Invest. 120, 4332\u20134341 (2010).","journal-title":"J. Clin. Invest."},{"key":"10793_CR24","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1128\/jcm.21.1.77-81.1985","volume":"21","author":"JJ Farmer 3rd","year":"1985","unstructured":"Farmer, J. J. 3rd et al. Escherichia fergusonii and Enterobacter taylorae, two new species of Enterobacteriaceae isolated from clinical specimens. J. Clin. Microbiol. 21, 77\u201381 (1985).","journal-title":"J. Clin. Microbiol."},{"key":"10793_CR25","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/829532","volume":"2013","author":"GM Rimoldi","year":"2013","unstructured":"Rimoldi, G. M. & Moeller, R. B. Jr Escherichia fergusonii associated with pneumonia in a beef cow. J. Vet. Med. 2013, 829532 (2013).","journal-title":"J. Vet. Med."},{"key":"10793_CR26","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1017\/S002202991200074X","volume":"80","author":"M Maifreni","year":"2013","unstructured":"Maifreni, M. et al. Identification of the Enterobacteriaceae in Montasio cheese and assessment of their amino acid decarboxylase activity. J. Dairy Res. 80, 122\u2013127 (2013).","journal-title":"J. Dairy Res."},{"key":"10793_CR27","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1016\/j.vetmic.2012.05.020","volume":"160","author":"JY Oh","year":"2012","unstructured":"Oh, J. Y. et al. Isolation and epidemiological characterization of heat-labile enterotoxin-producing Escherichia fergusonii from healthy chickens. Vet. Microbiol. 160, 170\u2013175 (2012).","journal-title":"Vet. Microbiol."},{"key":"10793_CR28","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1016\/j.jcmgh.2021.12.003","volume":"13","author":"FZ Xin","year":"2022","unstructured":"Xin, F. Z. et al. Escherichia fergusonii promotes nonobese nonalcoholic fatty liver disease by interfering with host hepatic lipid metabolism through its own msRNA 23487. Cell Mol. Gastroenterol. Hepatol. 13, 827\u2013841 (2022).","journal-title":"Cell Mol. Gastroenterol. Hepatol."},{"key":"10793_CR29","doi-asserted-by":"publisher","DOI":"10.1016\/j.taap.2022.116066","volume":"447","author":"SS Bhattacharya","year":"2022","unstructured":"Bhattacharya, S. S. et al. Crosstalk between gut microbiota and lung inflammation in murine toxicity models of respiratory exposure or co-exposure to carbon nanotube particles and cigarette smoke extract. Toxicol. Appl. Pharm. 447, 116066 (2022).","journal-title":"Toxicol. Appl. Pharm."},{"key":"10793_CR30","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1137369","volume":"14","author":"X Wu","year":"2023","unstructured":"Wu, X. et al. Coinfection with influenza virus and non-typeable Haemophilus influenzae aggregates inflammatory lung injury and alters gut microbiota in COPD mice. Front. Microbiol 14, 1137369 (2023).","journal-title":"Front. Microbiol"},{"key":"10793_CR31","doi-asserted-by":"publisher","DOI":"10.1016\/j.ecoenv.2022.114329","volume":"248","author":"L Deng","year":"2022","unstructured":"Deng, L. et al. Protective effect and mechanism of baicalin on lung inflammatory injury in BALB\/cJ mice induced by PM2.5. Ecotoxicol. Environ. Saf. 248, 114329 (2022).","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"10793_CR32","doi-asserted-by":"publisher","DOI":"10.1016\/j.psj.2023.102598","volume":"102","author":"J Ye","year":"2023","unstructured":"Ye, J. et al. Changed cecal microbiota involved in growth depression of broiler chickens induced by immune stress. Poult. Sci. 102, 102598 (2023).","journal-title":"Poult. Sci."},{"key":"10793_CR33","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1002\/JLB.3MA0322-458RR","volume":"112","author":"H Liu","year":"2022","unstructured":"Liu, H. et al. A high-calorie diet aggravates LPS-induced pneumonia by disturbing the gut microbiota and Th17\/Treg balance. J. Leukoc. Biol. 112, 127\u2013141 (2022).","journal-title":"J. Leukoc. Biol."},{"key":"10793_CR34","doi-asserted-by":"crossref","unstructured":"Vareille-Delarbre, M. et al. Immunomodulatory effects of Lactobacillus plantarum on inflammatory response induced by Klebsiella pneumoniae. Infect. Immun. 87, e00570-19 (2019).","DOI":"10.1128\/IAI.00570-19"},{"key":"10793_CR35","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1136\/gutjnl-2021-325010","volume":"71","author":"J Bilinski","year":"2022","unstructured":"Bilinski, J. et al. Rapid resolution of COVID-19 after faecal microbiota transplantation. Gut 71, 230\u2013232 (2022).","journal-title":"Gut"},{"key":"10793_CR36","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1180336","volume":"14","author":"M Wang","year":"2023","unstructured":"Wang, M., Zhang, Y., Li, C., Chang, W. & Zhang, L. The relationship between gut microbiota and COVID-19 progression: new insights into immunopathogenesis and treatment. Front. Immunol. 14, 1180336 (2023).","journal-title":"Front. Immunol."},{"key":"10793_CR37","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2023.e13801","volume":"9","author":"T Ralli","year":"2023","unstructured":"Ralli, T., Saifi, Z., Rathee, A., Aeri, V. & Kohli, K. Decoding the bidirectional relationship between gut microbiota and COVID-19. Heliyon 9, e13801 (2023).","journal-title":"Heliyon"},{"key":"10793_CR38","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-024-01306-7","volume":"16","author":"S Nooij","year":"2024","unstructured":"Nooij, S. et al. Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection. Genome Med. 16, 37 (2024).","journal-title":"Genome Med."},{"key":"10793_CR39","doi-asserted-by":"crossref","unstructured":"Maruyama, D. et al. Regulation of lung immune tone by the gut-lung axis via dietary fiber, gut microbiota, and short-chain fatty acids. Preprint at bioRxiv https:\/\/pubmed.ncbi.nlm.nih.gov\/37662303\/ (2023).","DOI":"10.1101\/2023.08.24.552964"},{"key":"10793_CR40","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1038\/s41385-019-0160-6","volume":"12","author":"AT Dang","year":"2019","unstructured":"Dang, A. T. & Marsland, B. J. Microbes, metabolites, and the gut-lung axis. Mucosal Immunol. 12, 843\u2013850 (2019).","journal-title":"Mucosal Immunol."},{"key":"10793_CR41","doi-asserted-by":"publisher","DOI":"10.1186\/s12967-024-05376-4","volume":"22","author":"L Hu","year":"2024","unstructured":"Hu, L. et al. Gut microbiota-derived acetate attenuates lung injury induced by influenza infection via protecting airway tight junctions. J. Transl. Med. 22, 570 (2024).","journal-title":"J. Transl. Med."},{"key":"10793_CR42","doi-asserted-by":"crossref","unstructured":"Merenstein, D. et al. Bifidobacterium animalis subsp. lactis BB-12 protects against antibiotic-induced functional and compositional changes in human fecal microbiome. Nutrients 13, 2814 (2021).","DOI":"10.3390\/nu13082814"},{"key":"10793_CR43","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36323-4","volume":"14","author":"J Niu","year":"2023","unstructured":"Niu, J. et al. Microbiota-derived acetate enhances host antiviral response via NLRP3. Nat. Commun. 14, 642 (2023).","journal-title":"Nat. Commun."},{"key":"10793_CR44","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1038\/nature09646","volume":"469","author":"S Fukuda","year":"2011","unstructured":"Fukuda, S. et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469, 543\u2013547 (2011).","journal-title":"Nature"},{"key":"10793_CR45","doi-asserted-by":"publisher","DOI":"10.3389\/fped.2020.595157","volume":"8","author":"Q Zhang","year":"2020","unstructured":"Zhang, Q., Ran, X., He, Y., Ai, Q. & Shi, Y. Acetate downregulates the activation of NLRP3 inflammasomes and attenuates lung injury in neonatal mice with bronchopulmonary dysplasia. Front. Pediatr. 8, 595157 (2020).","journal-title":"Front. Pediatr."},{"key":"10793_CR46","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1038\/nature12726","volume":"504","author":"N Arpaia","year":"2013","unstructured":"Arpaia, N. et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504, 451\u2013455 (2013).","journal-title":"Nature"},{"key":"10793_CR47","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10703-1","volume":"10","author":"M Hu","year":"2019","unstructured":"Hu, M. et al. Decreased maternal serum acetate and impaired fetal thymic and regulatory T cell development in preeclampsia. Nat. Commun. 10, 3031 (2019).","journal-title":"Nat. Commun."},{"key":"10793_CR48","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1084\/jem.20181639","volume":"216","author":"MT Sorbara","year":"2019","unstructured":"Sorbara, M. T. et al. Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification. J. Exp. Med. 216, 84\u201398 (2019).","journal-title":"J. Exp. Med."},{"key":"10793_CR49","doi-asserted-by":"publisher","first-page":"e065871","DOI":"10.1136\/bmj-2021-065871","volume":"375","author":"C Cilloniz","year":"2021","unstructured":"Cilloniz, C., Torres, A. & Niederman, M. S. Management of pneumonia in critically ill patients. BMJ 375, e065871 (2021).","journal-title":"BMJ"},{"key":"10793_CR50","doi-asserted-by":"publisher","first-page":"4165","DOI":"10.1128\/AEM.70.7.4165-4169.2004","volume":"70","author":"M Gueimonde","year":"2004","unstructured":"Gueimonde, M., Tolkko, S., Korpimaki, T. & Salminen, S. New real-time quantitative PCR procedure for quantification of bifidobacteria in human fecal samples. Appl. Environ. Microbiol. 70, 4165\u20134169 (2004).","journal-title":"Appl. Environ. Microbiol."},{"key":"10793_CR51","first-page":"621","volume":"16","author":"M Berizi","year":"2021","unstructured":"Berizi, M. et al. Development of a quantitative real-time PCR assay for detection of Toxoplasma gondii in brain samples. Iran. J. Parasitol. 16, 621\u2013630 (2021).","journal-title":"Iran. J. Parasitol."},{"key":"10793_CR52","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1099\/00221287-148-1-257","volume":"148","author":"MA Nadkarni","year":"2002","unstructured":"Nadkarni, M. A., Martin, F. E., Jacques, N. A. & Hunter, N. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148, 257\u2013266 (2002).","journal-title":"Microbiology"},{"key":"10793_CR53","doi-asserted-by":"publisher","DOI":"10.1016\/j.micres.2024.127794","volume":"286","author":"RG Uttarwar","year":"2024","unstructured":"Uttarwar, R. G. et al. Effects of Bifidobacterium animalis subsp. lactis BB-12 and yogurt on mice during oral antibiotic administration. Microbiol. Res. 286, 127794 (2024).","journal-title":"Microbiol. Res."},{"key":"10793_CR54","doi-asserted-by":"crossref","unstructured":"de Paula, T. P. et al. Treatment with atorvastatin provides additional benefits to imipenem in a model of gram-negative Pneumonia induced by Klebsiella pneumoniae in mice. Antimicrob. Agents Chemother. 62, e00764-17 (2018).","DOI":"10.1128\/AAC.00764-17"},{"key":"10793_CR55","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1038\/nm.2087","volume":"16","author":"TB Clarke","year":"2010","unstructured":"Clarke, T. B. et al. Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity. Nat. Med. 16, 228\u2013231 (2010).","journal-title":"Nat. Med"},{"key":"10793_CR56","doi-asserted-by":"publisher","first-page":"4596","DOI":"10.1128\/IAI.02212-14","volume":"82","author":"TB Clarke","year":"2014","unstructured":"Clarke, T. B. Early innate immunity to bacterial infection in the lung is regulated systemically by the commensal microbiota via nod-like receptor ligands. Infect. Immun. 82, 4596\u20134606 (2014).","journal-title":"Infect. Immun."},{"key":"10793_CR57","doi-asserted-by":"publisher","first-page":"3132","DOI":"10.4049\/jimmunol.172.5.3132","volume":"172","author":"S Knapp","year":"2004","unstructured":"Knapp, S. et al. Toll-like receptor 2 plays a role in the early inflammatory response to murine pneumococcal pneumonia but does not contribute to antibacterial defense. J. Immunol. 172, 3132\u20133138 (2004).","journal-title":"J. Immunol."},{"key":"10793_CR58","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1126\/science.1241165","volume":"341","author":"PM Smith","year":"2013","unstructured":"Smith, P. M. et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341, 569\u2013573 (2013).","journal-title":"Science"},{"key":"10793_CR59","doi-asserted-by":"publisher","DOI":"10.1186\/s40635-018-0184-3","volume":"6","author":"SHC Mai","year":"2018","unstructured":"Mai, S. H. C. et al. Body temperature and mouse scoring systems as surrogate markers of death in cecal ligation and puncture sepsis. Intens. Care Med Exp. 6, 20 (2018).","journal-title":"Intens. Care Med Exp."},{"key":"10793_CR60","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2021.111909","volume":"141","author":"Y Li","year":"2021","unstructured":"Li, Y. et al. Probiotic fermentation of Ganoderma lucidum fruiting body extracts promoted its immunostimulatory activity in mice with dexamethasone-induced immunosuppression. Biomed. Pharmacother. 141, 111909 (2021).","journal-title":"Biomed. Pharmacother."},{"key":"10793_CR61","doi-asserted-by":"publisher","first-page":"1678","DOI":"10.3389\/fmicb.2020.01678","volume":"11","author":"N Pauly","year":"2020","unstructured":"Pauly, N. et al. ChromID((R)) CARBA Agar fails to detect Carbapenem-resistant Enterobacteriaceae with slightly reduced susceptibility to carbapenems. Front. Microbiol. 11, 1678 (2020).","journal-title":"Front. Microbiol."},{"key":"10793_CR62","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1016\/j.vetmic.2010.01.014","volume":"144","author":"G Foster","year":"2010","unstructured":"Foster, G. et al. Use of citrate adonitol agar as a selective medium for the isolation of Escherichia fergusonii from a captive reindeer herd. Vet. Microbiol. 144, 484\u2013486 (2010).","journal-title":"Vet. Microbiol."}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-10793-w","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-10793-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-10793-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T01:02:14Z","timestamp":1790470934000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-10793-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,18]]},"references-count":62,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["10793"],"URL":"https:\/\/doi.org\/10.1038\/s42003-026-10793-w","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,18]]},"assertion":[{"value":"23 September 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"1258"}}