The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases

References

• Aggeletopoulou I, Mouzaki A, Thomopoulos K, Triantos C. 2023. miRNA molecules—late breaking treatment for inflammatory bowel diseases? Int J Mol Sci. 24(3):2233. https://doi.org/10.3390/ijms24032233.
   PubMed Web of Science ®Google Scholar
• Agrawal P, Kurcon T, Pilobello KT, Rakus JF, Koppolu S, Liu Z, Batista BS, Eng WS, Hsu K-L, Liang Y, et al. 2014. Mapping posttranscriptional regulation of the human glycome uncovers microRNA defining the glycocode. Proc Natl Acad Sci USA. 111(11):4338–4343. https://doi.org/10.1073/pnas.1321524111.
   PubMed Web of Science ®Google Scholar
• Alexander TW, Timsit E, Amat S. 2020. The role of the bovine respiratory bacterial microbiota in health and disease. Anim Health Res Rev. 21(2):168–171. https://doi.org/10.1017/S1466252320000316.
   PubMed Web of Science ®Google Scholar
• Almagro-Moreno S, Boyd EF. 2009. Insights into the evolution of sialic acid catabolism among bacteria. BMC Evol Biol. 9(1):118. https://doi.org/10.1186/1471-2148-9-118.
   PubMedGoogle Scholar
• Amat S, Subramanian S, Timsit E, Alexander TW. 2017. Probiotic bacteria inhibit the bovine respiratory pathogen Mannheimia haemolytica serotype 1 in vitro. Lett Appl Microbiol. 64(5):343–349. https://doi.org/10.1111/lam.12723.
   PubMed Web of Science ®Google Scholar
• Arcangioli M-A, Duet A, Meyer G, Dernburg A, Bézille P, Poumarat F, Le Grand D. 2008. The role of Mycoplasma bovis in bovine respiratory disease outbreaks in veal calf feedlots. Vet J. 177(1):89–93. https://doi.org/10.1016/j.tvjl.2007.03.008.
   PubMed Web of Science ®Google Scholar
• Arike L, Holmén-Larsson J, Hansson GC. 2017. Intestinal Muc2 mucin O-glycosylation is affected by microbiota and regulated by differential expression of glycosyltranferases. Glycobiology. 27(4):318–328. https://doi.org/10.1093/glycob/cww134.
   PubMed Web of Science ®Google Scholar
• Atanasova KR, Reznikov LR. 2019. Strategies for measuring airway mucus and mucins. Respir Res. 20(1):261. https://doi.org/10.1186/s12931-019-1239-z.
   PubMed Web of Science ®Google Scholar
• Awad F, Chhabra R, Baylis M, Ganapathy K. 2014. An overview of infectious bronchitis virus in chickens. Worlds Poult Sci J. 70(2):375–384. https://doi.org/10.1017/S0043933914000385.
   Web of Science ®Google Scholar
• Bansil R, Turner BS. 2018. The biology of mucus: composition, synthesis and organization. Adv Drug Deliv Rev. 124:3–15. https://doi.org/10.1016/j.addr.2017.09.023.
   PubMed Web of Science ®Google Scholar
• Belkasmi SFZ, Fellahi S, Touzani CD, Faraji FZ, Maaroufi I, Delverdier M, Guérin J-L, Fihri OF, El Houadfi M, Ducatez MF, et al. 2020. Co-infections of chickens with avian influenza virus H9N2 and Moroccan Italy 02 infectious bronchitis virus: effect on pathogenesis and protection conferred by different vaccination programmes. Avian Pathol. 49(1):21–28. https://doi.org/10.1080/03079457.2019.1656328.
   PubMed Web of Science ®Google Scholar
• Belzer C, Chia LW, Aalvink S, Chamlagain B, Piironen V, Knol J, de Vos WM. 2017. Microbial metabolic networks at the mucus layer lead to diet-independent butyrate and vitamin B12 production by intestinal symbionts. mBio. 8(5):e00770-17. https://doi.org/10.1128/mBio.00770-17.
   PubMed Web of Science ®Google Scholar
• Belzer C. 2022. Nutritional strategies for mucosal health: the interplay between microbes and mucin glycans. Trends Microbiol. 30(1):13–21. https://doi.org/10.1016/j.tim.2021.06.003.
   PubMed Web of Science ®Google Scholar
• Bergstrom K, Fu J, Johansson MEV, Liu X, Gao N, Wu Q, Song J, McDaniel JM, McGee S, Chen W, et al. 2017. Core 1– and 3–derived O-glycans collectively maintain the colonic mucus barrier and protect against spontaneous colitis in mice. Mucosal Immunol. 10(1):91–103. https://doi.org/10.1038/mi.2016.45.
   PubMed Web of Science ®Google Scholar
• Bergstrom K, Xia L. 2022. The barrier and beyond: roles of intestinal mucus and mucin-type O-glycosylation in resistance and tolerance defense strategies guiding host-microbe symbiosis. Gut Microbes. 14(1):2052699. https://doi.org/10.1080/19490976.2022.2052699.
   PubMed Web of Science ®Google Scholar
• Blakebrough-Hall C, McMeniman JP, González LA. 2020. An evaluation of the economic effects of bovine respiratory disease on animal performance, carcass traits, and economic outcomes in feedlot cattle defined using four BRD diagnosis methods. J Anim Sci. 98(2):skaa005. https://doi.org/10.1093/jas/skaa005.
   PubMed Web of Science ®Google Scholar
• Bond SL, Timsit E, Workentine M, Alexander T, Léguillette R. 2017. Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone. BMC Microbiol. 17(1):184. https://doi.org/10.1186/s12866-017-1092-5.
   PubMedGoogle Scholar
• Bond SL, Workentine M, Hundt J, Gilkerson JR, Léguillette R, UCVM Class of 2019. 2020. Effects of nebulized dexamethasone on the respiratory microbiota and mycobiota and relative equine herpesvirus-1, 2, 4, 5 in an equine model of asthma. J Vet Intern Med. 34(1):307–321. https://doi.org/10.1111/jvim.15671.
   PubMed Web of Science ®Google Scholar
• Brazil JC, Parkos CA. 2022. Finding the sweet spot: glycosylation mediated regulation of intestinal inflammation. Mucosal Immunol. 15(2):211–222. https://doi.org/10.1038/s41385-021-00466-8.
   PubMed Web of Science ®Google Scholar
• Brogaard L, Larsen LE, Heegaard PMH, Anthon C, Gorodkin J, Dürrwald R, Skovgaard K. 2018. IFN-λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs. PLoS One. 13(4):e0194765. https://doi.org/10.1371/journal.pone.0194765.
   PubMed Web of Science ®Google Scholar
• Budden KF, Gellatly SL, Wood DLA, Cooper MA, Morrison M, Hugenholtz P, Hansbro PM. 2017. Emerging pathogenic links between microbiota and the gut–lung axis. Nat Rev Microbiol. 15(1):55–63. https://doi.org/10.1038/nrmicro.2016.142.
   PubMed Web of Science ®Google Scholar
• Burger-van Paassen N, Vincent A, Puiman PJ, van der Sluis M, Bouma J, Boehm G, van Goudoever JB, van Seuningen I, Renes IB. 2009. The regulation of intestinal mucin MUC2 expression by short-chain fatty acids: implications for epithelial protection. Biochem J. 420(2):211–219. https://doi.org/10.1042/BJ20082222.
   PubMed Web of Science ®Google Scholar
• Button B, Cai L-H, Ehre C, Kesimer M, Hill DB, Sheehan JK, Boucher RC, Rubinstein M. 2012. A periciliary brush promotes the lung health by separating the mucus layer from airway epithelia. Science. 337(6097):937–941. https://doi.org/10.1126/science.1223012.
   PubMed Web of Science ®Google Scholar
• Byrd-Leotis L, Liu R, Bradley KC, Lasanajak Y, Cummings SF, Song X, Heimburg-Molinaro J, Galloway SE, Culhane MR, Smith DF, et al. 2014. Shotgun glycomics of pig lung identifies natural endogenous receptors for influenza viruses. Proc Natl Acad Sci USA. 111(22):E2241–50. https://doi.org/10.1073/pnas.1323162111.
   PubMed Web of Science ®Google Scholar
• Caballero I, Ringot-Destrez B, Si-Tahar M, Barbry P, Guillon A, Lantier I, Berri M, Chevaleyre C, Fleurot I, Barc C, et al. 2021. Evidence of early increased sialylation of airway mucins and defective mucociliary clearance in CFTR-deficient piglets. J Cyst Fibros. 20(1):173–182. https://doi.org/10.1016/j.jcf.2020.09.009.
   PubMed Web of Science ®Google Scholar
• Capaldo CT, Powell DN, Kalman D. 2017. Layered defense: how mucus and tight junctions seal the intestinal barrier. J Mol Med (Berl). 95(9):927–934. https://doi.org/10.1007/s00109-017-1557-x.
   PubMed Web of Science ®Google Scholar
• Carnoy C, Scharfman A, Van Brussel E, Lamblin G, Ramphal R, Roussel P. 1994. Pseudomonas aeruginosa outer membrane adhesins for human respiratory mucus glycoproteins. Infect Immun. 62(5):1896–1900. https://doi.org/10.1128/iai.62.5.1896-1900.1994.
   PubMed Web of Science ®Google Scholar
• Chai J, Capik SF, Kegley B, Richeson JT, Powell JG, Zhao J. 2022. Bovine respiratory microbiota of feedlot cattle and its association with disease. Vet Res. 53(1):4. https://doi.org/10.1186/s13567-021-01020-x.
   PubMed Web of Science ®Google Scholar
• Chang Y-C, Olson J, Beasley FC, Tung C, Zhang J, Crocker PR, Varki A, Nizet V. 2014. Group B streptococcus engages an inhibitory siglec through sialic acid mimicry to blunt innate immune and inflammatory responses in vivo. PLoS Pathog. 10(1):e1003846. https://doi.org/10.1371/journal.ppat.1003846.
   PubMed Web of Science ®Google Scholar
• Chatterjee M, van Putten JPM, Strijbis K. 2020. Defensive properties of mucin glycoproteins during respiratory infections—relevance for SARS-CoV-2. mBio. 11(6):e02374-20. https://doi.org/10.1128/mBio.02374-20.
   Web of Science ®Google Scholar
• Chen X, Yang H, Jia J, Chen Y, Wang J, Chen H, Jiang C. 2021. Mulberry leaf polysaccharide supplementation contributes to enhancing the respiratory mucosal barrier immune response in Newcastle disease virus–vaccinated chicks. Poult Sci. 100(2):592–602. https://doi.org/10.1016/j.psj.2020.11.039.
   PubMed Web of Science ®Google Scholar
• Chowdhury IH, Narra HP, Sahni A, Khanipov K, Schroeder CLC, Patel J, Fofanov Y, Sahni SK. 2017. Expression profiling of long noncoding RNA splice variants in human microvascular endothelial cells: lipopolysaccharide effects in vitro. Mediators Inflamm. 2017:3427461–3427418. https://doi.org/10.1155/2017/3427461.
   PubMed Web of Science ®Google Scholar
• Clark A, Mach N. 2023. The gut mucin-microbiota interactions: a missing key to optimizing endurance performance. Front Physiol. 14:1284423. https://doi.org/10.3389/fphys.2023.1284423.
   PubMed Web of Science ®Google Scholar
• Clausen TM, Sandoval DR, Spliid CB, Pihl J, Perrett HR, Painter CD, Narayanan A, Majowicz SA, Kwong EM, McVicar RN, et al. 2020. SARS-CoV-2 infection depends on cellular heparan sulfate and ACE2. Cell. 183(4):1043–1057.e15. https://doi.org/10.1016/j.cell.2020.09.033.
   PubMed Web of Science ®Google Scholar
• Correa-Fiz F, dos Santos JMG, Illas F, Aragon V. 2019. Antimicrobial removal on piglets promotes health and higher bacterial diversity in the nasal microbiota. Sci Rep. 9(1):6545. https://doi.org/10.1038/s41598-019-43022-y.
   PubMedGoogle Scholar
• Correa-Fiz F, Fraile L, Aragon V. 2016. Piglet nasal microbiota at weaning may influence the development of Glässer’s disease during the rearing period. BMC Genomics. 17(1):404. https://doi.org/10.1186/s12864-016-2700-8.
   PubMedGoogle Scholar
• Critcher M, Hassan AA, Huang ML. 2022. Seeing the forest through the trees: characterizing the glycoproteome. Trends Biochem Sci. 47(6):492–505. https://doi.org/10.1016/j.tibs.2022.02.007.
   PubMed Web of Science ®Google Scholar
• Dang AT, Marsland BJ. 2019. Microbes, metabolites, and the gut–lung axis. Mucosal Immunol. 12(4):843–850. https://doi.org/10.1038/s41385-019-0160-6.
   PubMed Web of Science ®Google Scholar
• de Jong H, Wösten MMSM, Wennekes T. 2022. Sweet impersonators: molecular mimicry of host glycans by bacteria. Glycobiology. 32(1):11–22. https://doi.org/10.1093/glycob/cwab104.
   PubMed Web of Science ®Google Scholar
• Dempsey J, Zhang A, Cui JY. 2018. Coordinate regulation of long non-coding RNAs and protein-coding genes in germ-free mice. BMC Genomics. 19(1):834. https://doi.org/10.1186/s12864-018-5235-3.
   PubMedGoogle Scholar
• Diao H, Jiao AR, Yu B, Mao XB, Chen DW. 2019. Gastric infusion of short-chain fatty acids can improve intestinal barrier function in weaned piglets. Genes Nutr. 14(1):4. https://doi.org/10.1186/s12263-019-0626-x.
   PubMedGoogle Scholar
• Do DN, Dudemaine P-L, Mathur M, Suravajhala P, Zhao X, Ibeagha-Awemu EM. 2021. miRNA regulatory functions in farm animal diseases, and biomarker potentials for effective therapies. Int J Mol Sci. 22(6):3080. https://doi.org/10.3390/ijms22063080.
   PubMed Web of Science ®Google Scholar
• Enaud R, Prevel R, Ciarlo E, Beaufils F, Wieërs G, Guery B, Delhaes L. 2020. The gut-lung axis in health and respiratory diseases: a place for inter-organ and inter-kingdom crosstalks. Front Cell Infect Microbiol. 10:9. https://doi.org/10.3389/fcimb.2020.00009.
   PubMed Web of Science ®Google Scholar
• Ericsson AC, Personett AR, Grobman ME, Rindt H, Reinero CR. 2016. Composition and predicted metabolic capacity of upper and lower airway microbiota of healthy dogs in relation to the fecal microbiota. PLoS One. 11(5):e0154646. https://doi.org/10.1371/journal.pone.0154646.
   PubMed Web of Science ®Google Scholar
• Ericsson AC, Personett AR, Rindt H, Grobman ME, Reinero CR. 2020. Respiratory dysbiosis and population-wide temporal dynamics in canine chronic bronchitis and non-inflammatory respiratory disease. PLoS One. 15(1):e0228085. https://doi.org/10.1371/journal.pone.0228085.
   PubMed Web of Science ®Google Scholar
• Ermund A, Meiss LN, Rodriguez-Pineiro AM, Bähr A, Nilsson HE, Trillo-Muyo S, Ridley C, Thornton DJ, Wine JJ, Hebert H, et al. 2017. The normal trachea is cleaned by MUC5B mucin bundles from the submucosal glands coated with the MUC5AC mucin. Biochem Biophys Res Commun. 492(3):331–337. https://doi.org/10.1016/j.bbrc.2017.08.113.
   PubMed Web of Science ®Google Scholar
• Espinosa-Gongora C, Larsen N, Schønning K, Fredholm M, Guardabassi L. 2016. Differential analysis of the nasal microbiome of pig carriers or non-carriers of staphylococcus aureus. PLoS One. 11(8):e0160331. https://doi.org/10.1371/journal.pone.0160331.
   PubMed Web of Science ®Google Scholar
• Fahy JV, Dickey BF. 2010. Airway mucus function and dysfunction. N Engl J Med. 363(23):2233–2247. https://doi.org/10.1056/NEJMra0910061.
   PubMed Web of Science ®Google Scholar
• Fan L, Lu Y, Wang Y, Zhang X, Wu Y, Sun H, Zhang J. 2022. Respiratory MUC5B disproportion is involved in severe community-acquired pneumonia. BMC Pulm Med. 22(1):90. https://doi.org/10.1186/s12890-022-01870-x.
   Web of Science ®Google Scholar
• Filaire F, Lebre L, Foret-Lucas C, Vergne T, Daniel P, Lelièvre A, de Barros A, Jbenyeni A, Bolon P, Paul M, et al. 2022. Highly pathogenic avian influenza A(H5N8) clade 2.3.4.4b virus in dust samples from poultry farms, France, 2021. Emerg Infect Dis. 28(7):1446–1450. https://doi.org/10.3201/eid2807.212247.
   PubMed Web of Science ®Google Scholar
• Fleming DS, Miller LC. 2019. Differentially expressed MiRNAs and tRNA genes affect host homeostasis during highly pathogenic porcine reproductive and respiratory syndrome virus infections in young pigs. Front Genet. 10:691. https://doi.org/10.3389/fgene.2019.00691.
   PubMed Web of Science ®Google Scholar
• Foissac S, Djebali S, Munyard K, Vialaneix N, Rau A, Muret K, Esquerré D, Zytnicki M, Derrien T, Bardou P, et al. 2019. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol. 17(1):108. https://doi.org/10.1186/s12915-019-0726-5.
   PubMed Web of Science ®Google Scholar
• Gaeta NC, Lima SF, Teixeira AG, Ganda EK, Oikonomou G, Gregory L, Bicalho RC. 2017. Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics. J Dairy Sci. 100(2):1445–1458. https://doi.org/10.3168/jds.2016-11522.
   PubMed Web of Science ®Google Scholar
• Gao Y, Zhou J, Qi H, Wei J, Yang Y, Yue J, Liu X, Zhang Y, Yang R. 2020. LncRNA lncLy6C induced by microbiota metabolite butyrate promotes differentiation of Ly6Chigh to Ly6Cint/neg macrophages through lncLy6C/C/EBPβ/Nr4A1 axis. Cell Discov. 6(1):87. https://doi.org/10.1038/s41421-020-00211-8.
   PubMed Web of Science ®Google Scholar
• Gaudino M, Lion A, Sagné E, Nagamine B, Oliva J, Terrier O, Errazuriz-Cerda E, Scribe A, Sikht F-Z, Simon E, et al. 2023. The activation of the RIG-I/MDA5 signaling pathway upon influenza D virus infection impairs the pulmonary proinflammatory response triggered by mycoplasma bovis superinfection. J Virol. 97(2):e0142322. https://doi.org/10.1128/jvi.01423-22.
   PubMed Web of Science ®Google Scholar
• Gaudino M, Valarcher J-F, Hägglund S, Näslund K, Zohari S, Ducatez MF, Meyer G. 2023. Molecular and genetic characterization of bovine parainfluenza type 3 European field and vaccine strains. Infect Genet Evol. 113:105483. https://doi.org/10.1016/j.meegid.2023.105483.
   PubMed Web of Science ®Google Scholar
• Giromini C, Baldi A, Rebucci R, Lanzoni D, Policardi M, Sundaram TS, Purup S. 2022. Role of short chain fatty acids to counteract inflammatory stress and mucus production in human intestinal HT29-MTX-E12 cells. Foods. 11(13):1983. https://doi.org/10.3390/foods11131983.
   PubMed Web of Science ®Google Scholar
• Gollwitzer ES, Saglani S, Trompette A, Yadava K, Sherburn R, McCoy KD, Nicod LP, Lloyd CM, Marsland BJ. 2014. Lung microbiota promotes tolerance to allergens in neonates via PD-L1. Nat Med. 20(6):642–647. https://doi.org/10.1038/nm.3568.
   PubMed Web of Science ®Google Scholar
• Goto Y, Uematsu S, Kiyono H. 2016. Epithelial glycosylation in gut homeostasis and inflammation. Nat Immunol. 17(11):1244–1251. https://doi.org/10.1038/ni.3587.
   PubMed Web of Science ®Google Scholar
• Guabiraba R, Schouler C. 2015. Avian colibacillosis: still many black holes. FEMS Microbiol Lett. 362(15):fnv118. https://doi.org/10.1093/femsle/fnv118.
   PubMed Web of Science ®Google Scholar
• Guinat C, Nicolas G, Vergne T, Bronner A, Durand B, Courcoul A, Gilbert M, Guérin J-L, Paul MC. 2018. Spatio-temporal patterns of highly pathogenic avian influenza virus subtype H5N8 spread, France, 2016 to 2017. Eurosurveillance. 23(26):1700791. https://doi.org/10.2807/1560-7917.ES.2018.23.26.1700791.
   Web of Science ®Google Scholar
• Gum JR. 1992. Mucin genes and the proteins they encode: structure, diversity, and regulation. Am J Respir Cell Mol Biol. 7(6):557–564. https://doi.org/10.1165/ajrcmb/7.6.557.
   PubMed Web of Science ®Google Scholar
• Guo Y, McMullen C, Timsit E, Hallewell J, Orsel K, van der Meer F, Yan S, Alexander TW. 2020. Genetic relatedness and antimicrobial resistance in respiratory bacteria from beef calves sampled from spring processing to 40 days after feedlot entry. Vet Microbiol. 240:108478. https://doi.org/10.1016/j.vetmic.2019.108478.
   PubMed Web of Science ®Google Scholar
• Gupta SK, Parlane N, Bridgeman B, Lynch AT, Dangerfield EM, Timmer MSM, Stocker BL, Wedlock DN. 2023. The trehalose glycolipid C18Brar promotes antibody and T-cell immune responses to Mannheimia haemolytica and Mycoplasma ovipneumoniae whole cell antigens in sheep. PLoS One. 18(1):e0278853. https://doi.org/10.1371/journal.pone.0278853.
   PubMed Web of Science ®Google Scholar
• Hansen MS, Pors SE, Jensen HE, Bille-Hansen V, Bisgaard M, Flachs EM, Nielsen OL. 2010. An investigation of the pathology and pathogens associated with porcine respiratory disease complex in Denmark. J Comp Pathol. 143(2–3):120–131. https://doi.org/10.1016/j.jcpa.2010.01.012.
   PubMed Web of Science ®Google Scholar
• Hansson GC. 2019. Mucus and mucins in diseases of the intestinal and respiratory tracts. J Intern Med. 285(5):479–490. https://doi.org/10.1111/joim.12910.
   PubMed Web of Science ®Google Scholar
• Harms PA, Halbur PG, Sorden SD. 2002. Three cases of porcine respiratory disease complex associated with porcine circovirus type 2 infection. J Swine Health Prod. 10:27–30.
   Web of Science ®Google Scholar
• Hauber H-P, Schulz M, Pforte A, Mack D, Zabel P, Schumacher U. 2008. Inhalation with fucose and galactose for treatment of Pseudomonas aeruginosa in cystic fibrosis patients. Int J Med Sci. 5(6):371–376. https://doi.org/10.7150/ijms.5.371.
   PubMedGoogle Scholar
• Hilton WM. 2014. BRD in 2014: where have we been, where are we now, and where do we want to go? Anim Health Res Rev. 15(2):120–122. https://doi.org/10.1017/S1466252314000115.
   PubMed Web of Science ®Google Scholar
• Hoegger MJ, Fischer AJ, McMenimen JD, Ostedgaard LS, Tucker AJ, Awadalla MA, Moninger TO, Michalski AS, Hoffman EA, Zabner J, et al. 2014. Impaired mucus detachment disrupts mucociliary transport in a piglet model of cystic fibrosis. Science. 345(6198):818–822. https://doi.org/10.1126/science.1255825.
   PubMed Web of Science ®Google Scholar
• Hoffman CL, Lalsiamthara J, Aballay A. 2020. Host mucin is exploited by Pseudomonas aeruginosa to provide monosaccharides required for a successful infection. mBio. 11(2):e00060-20. https://doi.org/10.1128/mBio.00060-20.
   PubMed Web of Science ®Google Scholar
• Holman DB, McAllister TA, Topp E, Wright ADG, Alexander TW. 2015. The nasopharyngeal microbiota of feedlot cattle that develop bovine respiratory disease. Vet Microbiol. 180(1–2):90–95. https://doi.org/10.1016/j.vetmic.2015.07.031.
   PubMed Web of Science ®Google Scholar
• Holt HR, Alarcon P, Velasova M, Pfeiffer DU, Wieland B. 2011. BPEX Pig Health Scheme: a useful monitoring system for respiratory disease control in pig farms? BMC Vet Res. 7(1):82. https://doi.org/10.1186/1746-6148-7-82.
   PubMedGoogle Scholar
• Huang ML, Fisher CJ, Godula K. 2016. Glycomaterials for probing host–pathogen interactions and the immune response. Exp Biol Med (Maywood). 241(10):1042–1053. https://doi.org/10.1177/1535370216647811.
   PubMed Web of Science ®Google Scholar
• Jame-Chenarboo F, Ng HH, Macdonald D, Mahal LK. 2022. High-throughput analysis reveals miRNA upregulating α-2,6-sialic acid through direct miRNA-mRNA interactions. ACS Cent Sci. 8(11):1527–1536. https://doi.org/10.1021/acscentsci.2c00748.
   PubMed Web of Science ®Google Scholar
• Jia N, Byrd-Leotis L, Matsumoto Y, Gao C, Wein AN, Lobby JL, Kohlmeier JE, Steinhauer DA, Cummings RD. 2020. The human lung glycome reveals novel glycan ligands for influenza A virus. Sci Rep. 10(1):5320. https://doi.org/10.1038/s41598-020-62074-z.
   PubMed Web of Science ®Google Scholar
• Jiang N, Liu H, Wang P, Huang J, Han H, Wang Q. 2019. Illumina MiSeq Sequencing investigation of microbiota in bronchoalveolar lavage fluid and cecum of the swine infected with PRRSV. Curr Microbiol. 76(2):222–230. https://doi.org/10.1007/s00284-018-1613-y.
   PubMed Web of Science ®Google Scholar
• Jin C, Kenny DT, Skoog EC, Padra M, Adamczyk B, Vitizeva V, Thorell A, Venkatakrishnan V, Lindén SK, Karlsson NG, et al. 2017. Structural diversity of human gastric mucin glycans. Mol Cell Proteomics. 16(5):743–758. https://doi.org/10.1074/mcp.M116.067983.
   PubMed Web of Science ®Google Scholar
• Kavanaugh NL, Zhang AQ, Nobile CJ, Johnson AD, Ribbeck K. 2014. Mucins suppress virulence traits of Candida albicans. mBio. 5(6):e01911. https://doi.org/10.1128/mBio.01911-14.
   PubMed Web of Science ®Google Scholar
• Kim S, Shin Y-C, Kim T-Y, Kim Y, Lee Y-S, Lee S-H, Kim M-N, O E, Kim KS, Kweon M-N. 2021. Mucin degrader Akkermansia muciniphila accelerates intestinal stem cell-mediated epithelial development. Gut Microbes. 13(1):1–20. https://doi.org/10.1080/19490976.2021.1892441.
   PubMed Web of Science ®Google Scholar
• Klima CL, Holman DB, Ralston BJ, Stanford K, Zaheer R, Alexander TW, McAllister TA. 2019. Lower respiratory tract microbiome and resistome of bovine respiratory disease mortalities. Microb Ecol. 78(2):446–456. https://doi.org/10.1007/s00248-019-01361-3.
   PubMed Web of Science ®Google Scholar
• Klima CL, Zaheer R, Cook SR, Booker CW, Hendrick S, Alexander TW, McAllister TA. 2014. Pathogens of bovine respiratory disease in North American feedlots conferring multidrug resistance via integrative conjugative elements. J Clin Microbiol. 52(2):438–448. https://doi.org/10.1128/JCM.02485-13.
   PubMed Web of Science ®Google Scholar
• Kosinska-Selbi B, Mielczarek M, Szyda J. 2020. Review: long non-coding RNA in livestock. Animal. 14(10):2003–2013. https://doi.org/10.1017/S1751731120000841.
   PubMed Web of Science ®Google Scholar
• Kuiken T, Leighton FA, Fouchier RAM, LeDuc JW, Peiris JSM, Schudel A, Stöhr K, Osterhaus ADME. 2005. Pathogen surveillance in animals. Science. 309(5741):1680–1681. https://doi.org/10.1126/science.1113310.
   PubMed Web of Science ®Google Scholar
• Kunej T. 2019. Rise of systems glycobiology and personalized glycomedicine: why and how to integrate glycomics with multiomics science? OMICS. 23(12):615–622. https://doi.org/10.1089/omi.2019.0149.
   PubMed Web of Science ®Google Scholar
• Lacasta D. 2019. Preface: special issue on sheep respiratory diseases. Small Ruminant Res. 181:85–86. https://doi.org/10.1016/j.smallrumres.2019.10.011.
   Web of Science ®Google Scholar
• Li JD, Feng W, Gallup M, Kim JH, Gum J, Kim Y, Basbaum C. 1998. Activation of NF-κB via a Src-dependent Ras-MAPK-pp90rsk pathway is required for Pseudomonas aeruginosa-induced mucin overproduction in epithelial cells. Proc Natl Acad Sci USA. 95(10):5718–5723. https://doi.org/10.1073/pnas.95.10.5718.
   PubMed Web of Science ®Google Scholar
• Li N, Ma WT, Pang M, Fan QL, Hua JL. 2019. The commensal microbiota and viral infection: a comprehensive review. Front Immunol. 10:1551. https://doi.org/10.3389/fimmu.2019.01551.
   PubMed Web of Science ®Google Scholar
• Li W, Du X, Yang Y, Yuan L, Yang M, Qin L, Wang L, Zhou K, Xiang Y, Qu X, et al. 2021. miRNA‐34b/c regulates mucus secretion in RSV‐infected airway epithelial cells by targeting FGFR1. J Cell Mol Med. 25(22):10565–10574. https://doi.org/10.1111/jcmm.16988.
   PubMed Web of Science ®Google Scholar
• Lion A, Secula A, Rançon C, Boulesteix O, Pinard A, Deslis A, Hägglund S, Salem E, Cassard H, Näslund K, et al. 2021. Enhanced Pathogenesis Caused by Influenza D Virus and Mycoplasma bovis Coinfection in Calves: a Disease Severity Linked with Overexpression of IFN-γ as a Key Player of the Enhanced Innate Immune Response in Lungs. Kibenge FSB, editor. Microbiol Spectr. 9(3):e01690-21. https://doi.org/10.1128/spectrum.01690-21.
   PubMed Web of Science ®Google Scholar
• Luan SJ, Sun YB, Wang Y, Sa RN, Zhang HF. 2019. Bacillus amyloliquefaciens spray improves the growth performance, immune status, and respiratory mucosal barrier in broiler chickens. Poult Sci. 98(3):1403–1409. https://doi.org/10.3382/ps/pey478.
   PubMed Web of Science ®Google Scholar
• Macauley MS, Kawasaki N, Peng W, Wang S-H, He Y, Arlian BM, McBride R, Kannagi R, Khoo K-H, Paulson JC, et al. 2015. Unmasking of CD22 co-receptor on germinal center B-cells Z. J Biol Chem. 290(50):30066–30077. https://doi.org/10.1074/jbc.M115.691337.
   PubMed Web of Science ®Google Scholar
• Mach N, Baranowski E, Nouvel LX, Citti C. 2021. The airway pathobiome in complex respiratory diseases: a perspective in domestic animals. Front Cell Infect Microbiol. 11:583600. https://doi.org/10.3389/fcimb.2021.583600.
   PubMed Web of Science ®Google Scholar
• Mach N, Clark A. 2017. Micronutrient deficiencies and the human gut microbiota. Trends Microbiol. 25(8):607–610. https://doi.org/10.1016/j.tim.2017.06.004.
   PubMed Web of Science ®Google Scholar
• Mach N, Plancade S, Pacholewska A, Lecardonnel J, Rivière J, Moroldo M, Vaiman A, Morgenthaler C, Beinat M, Nevot A, et al. 2016. Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in the horse. Sci Rep. 6(1):22932. https://doi.org/10.1038/srep22932.
   PubMedGoogle Scholar
• Mahmmod YS, Correa-Fiz F, Aragon V. 2020. Variations in association of nasal microbiota with virulent and non-virulent strains of Glaesserella (Haemophilus) parasuis in weaning piglets. Vet Res. 51(1):7. https://doi.org/10.1186/s13567-020-0738-8.
   PubMed Web of Science ®Google Scholar
• Malaker SA, Riley NM, Shon DJ, Pedram K, Krishnan V, Dorigo O, Bertozzi CR. 2022. Revealing the human mucinome. Nat Commun. 13(1):3542. https://doi.org/10.1038/s41467-022-31062-4.
   PubMedGoogle Scholar
• Malmuthuge N, Guan LL. 2021. Noncoding RNAs: regulatory molecules of host–microbiome crosstalk. Trends Microbiol. 29(8):713–724. https://doi.org/10.1016/j.tim.2020.12.003.
   PubMed Web of Science ®Google Scholar
• Malmuthuge N, Liang G, Guan LL. 2019. Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes. Genome Biol. 20(1):172. https://doi.org/10.1186/s13059-019-1786-0.
   PubMed Web of Science ®Google Scholar
• Man WH, De Steenhuijsen Piters WAA, Bogaert D. 2017. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol. 15(5):259–270. https://doi.org/10.1038/nrmicro.2017.14.
   PubMed Web of Science ®Google Scholar
• Mariadassou M, Nouvel LX, Constant F, Morgavi DP, Rault L, Barbey S, Helloin E, Rué O, Schbath S, Launay F, et al. 2023. Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd. Anim Microbiome. 5(1):32. https://doi.org/10.1186/s42523-023-00252-w.
   PubMedGoogle Scholar
• Martínez-Moliner V, Soler-Llorens P, Moleres J, Garmendia J, Aragon V. 2012. Distribution of genes involved in sialic acid utilization in strains of Haemophilus parasuis. Microbiology (Reading). 158(Pt 8):2117–2124. https://doi.org/10.1099/mic.0.056994-0.
   PubMedGoogle Scholar
• May M, Brown DR. 2009. Secreted sialidase activity of canine mycoplasmas. Vet Microbiol. 137(3–4):380–383. https://doi.org/10.1016/j.vetmic.2009.01.009.
   PubMed Web of Science ®Google Scholar
• Mazel-Sanchez B, Yildiz S, Schmolke M. 2019. Ménage à trois: virus, host, and microbiota in experimental infection models. Trends Microbiol. 27(5):440–452. https://doi.org/10.1016/j.tim.2018.12.004.
   PubMed Web of Science ®Google Scholar
• McMullen C, Alexander TW, Léguillette R, Workentine M, Timsit E. 2020. Topography of the respiratory tract bacterial microbiota in cattle. Microbiome. 8(1):91. https://doi.org/10.1186/s40168-020-00869-y.
   PubMed Web of Science ®Google Scholar
• McMullen C, Orsel K, Alexander TW, van der Meer F, Plastow G, Timsit E. 2019. Comparison of the nasopharyngeal bacterial microbiota of beef calves raised without the use of antimicrobials between healthy calves and those diagnosed with bovine respiratory disease. Vet Microbiol. 231:56–62. https://doi.org/10.1016/j.vetmic.2019.02.030.
   PubMed Web of Science ®Google Scholar
• Meldrum OW, Chotirmall SH. 2021. Mucus, microbiomes and pulmonary disease. Biomedicines. 9(6):675. https://doi.org/10.3390/biomedicines9060675.
   PubMed Web of Science ®Google Scholar
• Meng F, Wu NH, Seitz M, Herrler G, Valentin-Weigand P. 2016. Efficient suilysin-mediated invasion and apoptosis in porcine respiratory epithelial cells after streptococcal infection under air-liquid interface conditions. Sci Rep. 6(1):26748. https://doi.org/10.1038/srep26748.
   PubMedGoogle Scholar
• Miao Y, Niu D, Wang Z, Wang J, Wu Z, Bao J, Hu W, Guo Y, Li R, Ishfaq M, et al. 2022. Mycoplasma gallisepticum induced inflammation-mediated Th1/Th2 immune imbalance via JAK/STAT signaling pathway in chicken trachea: involvement of respiratory microbiota. Vet Microbiol. 265:109330. https://doi.org/10.1016/j.vetmic.2021.109330.
   PubMed Web of Science ®Google Scholar
• Much P, Winner F, Stipkovits L, Rosengarten R, Citti C. 2002. Mycoplasma gallisepticum: influence of cell invasiveness on the outcome of experimental infection in chickens. FEMS Immunol Med Microbiol. 34(3):181–186. (02)00378-4. https://doi.org/10.1016/S0928-8244.
   PubMedGoogle Scholar
• Muranaka M, Yamanaka T, Katayama Y, Hidari K, Kanazawa H, Suzuki T, Oku K, Oyamada T. 2011. Distribution of influenza virus sialoreceptors on upper and lower respiratory tract in horses and dogs. J Vet Med Sci. 73(1):125–127. https://doi.org/10.1292/jvms.10-0276.
   PubMed Web of Science ®Google Scholar
• Nason R, Büll C, Konstantinidi A, Sun L, Ye Z, Halim A, Du W, Sørensen DM, Durbesson F, Furukawa S, et al. 2021. Display of the human mucinome with defined O-glycans by gene engineered cells. Nat Commun. 12(1):4070. https://doi.org/10.1038/s41467-021-24366-4.
   PubMed Web of Science ®Google Scholar
• Ngunjiri JM, Taylor KJM, Abundo MC, Jang H, Elaish M, Kc M, Ghorbani A, Wijeratne S, Weber BP, Johnson TJ, et al. 2019. Farm stage, bird age, and body site dominantly affect the quantity, taxonomic composition, and dynamics of respiratory and gut microbiota of commercial layer chickens. Appl Environ Microbiol. 85(9):1–17. https://doi.org/10.1128/AEM.03137-18.
   Web of Science ®Google Scholar
• Nicola I, Cerutti F, Grego E, Bertone I, Gianella P, D’Angelo A, Peletto S, Bellino C. 2017. Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves. Microbiome. 5(1):152. https://doi.org/10.1186/s40168-017-0372-5.
   PubMedGoogle Scholar
• Oladunni FS, Horohov DW, Chambers TM. 2019. EHV-1: a constant threat to the horse industry. Front Microbiol. 10:2668. https://doi.org/10.3389/fmicb.2019.02668.
   PubMed Web of Science ®Google Scholar
• Oliva J, Eichenbaum A, Belin J, Gaudino M, Guillotin J, Alzieu J-P, Nicollet P, Brugidou R, Gueneau E, Michel E, et al. 2019. Serological evidence of influenza D virus circulation among cattle and small ruminants in France. Viruses. 11(6):516. https://doi.org/10.3390/v11060516.
   PubMed Web of Science ®Google Scholar
• Oliveira ED, Quaglio AEV, Magro DO, Di Stasi LC, Sassaki LY. 2023. Intestinal microbiota and miRNA in IBD: a narrative review about discoveries and perspectives for the future. Int J Mol Sci. 24(8):7176. https://doi.org/10.3390/ijms24087176.
   PubMed Web of Science ®Google Scholar
• Ottman N, Reunanen J, Meijerink M, Pietilä TE, Kainulainen V, Klievink J, Huuskonen L, Aalvink S, Skurnik M, Boeren S, et al. 2017. Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function. PLoS One. 12(3):e0173004. https://doi.org/10.1371/journal.pone.0173004.
   PubMed Web of Science ®Google Scholar
• Pacholewska A, Mach N, Mata X, Vaiman A, Schibler L, Barrey E, Gerber V. 2016. Novel equine tissue miRNAs and breed-related miRNA expressed in serum. BMC Genomics. 17(1):831. https://doi.org/10.1186/s12864-016-3168-2.
   PubMedGoogle Scholar
• Pajic P, Shen S, Qu J, May AJ, Knox S, Ruhl S, Gokcumen O. 2022. A mechanism of gene evolution generating mucin function. Sci Adv. 8(34):eabm8757. https://doi.org/10.1126/sciadv.abm8757.
   PubMed Web of Science ®Google Scholar
• Pant K, Yadav AK, Gupta P, Islam R, Saraya A, Venugopal SK. 2017. Butyrate induces ROS-mediated apoptosis by modulating miR-22/SIRT-1 pathway in hepatic cancer cells. Redox Biol. 12:340–349. https://doi.org/10.1016/j.redox.2017.03.006.
   PubMed Web of Science ®Google Scholar
• Paone P, Cani PD. 2020. Mucus barrier, mucins and gut microbiota: the expected slimy partners? Gut. 69(12):2232–2243. https://doi.org/10.1136/gutjnl-2020-322260.
   PubMed Web of Science ®Google Scholar
• Park GY, Yu HJ, Son JS, Park SJ, Cha H-J, Song KS. 2020. Specific bacteriophage of Bordetella bronchiseptica regulates B. bronchiseptica-induced microRNA expression profiles to decrease inflammation in swine nasal turbinate cells. Genes Genomics. 42(4):441–447. https://doi.org/10.1007/s13258-019-00906-7.
   PubMed Web of Science ®Google Scholar
• Patel JG, Patel BJ, Patel SS, Raval SH, Parmar RS, Joshi DV, Chauhan HC, Chandel BS, Patel BK. 2018. Metagenomic of clinically diseased and healthy broiler affected with respiratory disease complex. Data Brief. 19:82–85. https://doi.org/10.1016/j.dib.2018.05.010.
   PubMedGoogle Scholar
• Pearce SC, Weber GJ, van Sambeek DM, Soares JW, Racicot K, Breault DT. 2020. Intestinal enteroids recapitulate the effects of short-chain fatty acids on the intestinal epithelium. PLoS One. 15(4):e0230231. https://doi.org/10.1371/journal.pone.0230231.
   PubMed Web of Science ®Google Scholar
• Peng L, Li Z-R, Green RS, Holzman IR, Lin J. 2009. Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in caco-2 cell monolayers. J Nutr. 139(9):1619–1625. https://doi.org/10.3945/jn.109.104638.
   PubMed Web of Science ®Google Scholar
• Pereira FC, Wasmund K, Cobankovic I, Jehmlich N, Herbold CW, Lee KS, Sziranyi B, Vesely C, Decker T, Stocker R, et al. 2020. Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization. Nat Commun. 11(1):41467. https://doi.org/10.1038/s41467-020-18928-1.
   Web of Science ®Google Scholar
• Pérez-Cobas AE, Rodríguez-Beltrán J, Baquero F, Coque TM. 2023. Ecology of the respiratory tract microbiome. Trends Microbiol. 31(9):972–984. https://doi.org/10.1016/j.tim.2023.04.006.
   PubMed Web of Science ®Google Scholar
• Pirolo M, Espinosa-Gongora C, Bogaert D, Guardabassi L. 2021. The porcine respiratory microbiome: recent insights and future challenges. Anim Microbiome. 3(1):9. https://doi.org/10.1186/s42523-020-00070-4.
   PubMedGoogle Scholar
• Qin R, Mahal LK. 2021. The host glycomic response to pathogens. Curr Opin Struct Biol. 68:149–156. https://doi.org/10.1016/j.sbi.2020.12.011.
   PubMed Web of Science ®Google Scholar
• Qin S, Ruan W, Yue H, Tang C, Zhou K, Zhang B. 2018. Viral communities associated with porcine respiratory disease complex in intensive commercial farms in Sichuan province, China. Sci Rep. 8(1):13341. https://doi.org/10.1038/s41598-018-31554-8.
   PubMedGoogle Scholar
• Rasaei D, Hosseinian SA, Asasi K, Shekarforoush SS, Khodakaram-Tafti A. 2023. The beneficial effects of spraying of probiotic Bacillus and Lactobacillus bacteria on broiler chickens experimentally infected with avian influenza virus H9N2. Poult Sci. 102(7):102669. https://doi.org/10.1016/j.psj.2023.102669.
   PubMed Web of Science ®Google Scholar
• Reddy VRAP, Trus I, Nauwynck HJ. 2017. Presence of DNA extracellular traps but not MUC5AC and MUC5B mucin in mucoid plugs/casts of infectious laryngotracheitis virus (ILTV) infected tracheas of chickens. Virus Res. 227:135–142. https://doi.org/10.1016/j.virusres.2016.09.025.
   PubMed Web of Science ®Google Scholar
• Reily C, Stewart TJ, Renfrow MB, Novak J. 2019. Glycosylation in health and disease. Nat Rev Nephrol. 15(6):346–366. https://doi.org/10.1038/s41581-019-0129-4.
   PubMed Web of Science ®Google Scholar
• Ricci S, Petri RM, Pacífico C, Castillo-Lopez E, Rivera-Chacon R, Sener-Aydemir A, Reisinger N, Zebeli Q, Kreuzer-Redmer S. 2022. Characterization of presence and activity of microRNAs in the rumen of cattle hints at possible host-microbiota cross-talk mechanism. Sci Rep. 12(1):13812. https://doi.org/10.1038/s41598-022-17445-z.
   PubMed Web of Science ®Google Scholar
• Ridley C, Thornton DJ. 2018. Mucins: the frontline defence of the lung. Biochem Soc Trans. 46(5):1099–1106. https://doi.org/10.1042/BST20170402.
   PubMedGoogle Scholar
• Rose MC, Voynow JA. 2006. Respiratory tract mucin genes and mucin glycoproteins in health and disease. Physiol Rev. 86(1):245–278. https://doi.org/10.1152/physrev.00010.2005.
   PubMed Web of Science ®Google Scholar
• Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, et al. 2014. Muc5b is required for airway defence. Nature. 505(7483):412–416. https://doi.org/10.1038/nature12807.
   PubMed Web of Science ®Google Scholar
• Salem E, Dhanasekaran V, Cassard H, Hause B, Maman S, Meyer G, Ducatez MF. 2020. Global transmission, spatial segregation, and recombination determine the long-term evolution and epidemiology of bovine coronaviruses. Viruses. 12(5):534. https://doi.org/10.3390/v12050534.
   PubMed Web of Science ®Google Scholar
• Samy A, Naguib MM. 2018. Avian respiratory coinfection and impact on avian influenza pathogenicity in domestic poultry: field and experimental findings. Vet Sci. 5(1):23. https://doi.org/10.3390/vetsci5010023.
   PubMedGoogle Scholar
• Schaefer A, Lai SK. 2022. The biophysical principles underpinning muco-trapping functions of antibodies. Hum Vaccin Immunother. 18(2):1939605. https://doi.org/10.1080/21645515.2021.1939605.
   PubMed Web of Science ®Google Scholar
• Scher JU, Joshua V, Artacho A, Abdollahi-Roodsaz S, Öckinger J, Kullberg S, Sköld M, Eklund A, Grunewald J, Clemente JC, et al. 2016. The lung microbiota in early rheumatoid arthritis and autoimmunity. Microbiome. 4(1):60. https://doi.org/10.1186/s40168-016-0206-x.
   PubMedGoogle Scholar
• Schnaar RL. 2015. Glycans and glycan-binding proteins in immune regulation: a concise introduction to glycobiology for the allergist. J Allergy Clin Immunol. 135(3):609–615. https://doi.org/10.1016/j.jaci.2014.10.057.
   PubMed Web of Science ®Google Scholar
• Schulz BL, Sloane AJ, Robinson LJ, Prasad SS, Lindner RA, Robinson M, Bye PT, Nielson DW, Harry JL, Packer NH, et al. 2007. Glycosylation of sputum mucins is altered in cystic fibrosis patients. Glycobiology. 17(7):698–712. https://doi.org/10.1093/glycob/cwm036.
   PubMed Web of Science ®Google Scholar
• Severi E, Hood DW, Thomas GH. 2007. Sialic acid utilization by bacterial pathogens. Microbiology (Reading). 153(Pt 9):2817–2822. https://doi.org/10.1099/mic.0.2007/009480-0.
   PubMedGoogle Scholar
• Shamseer L, Moher D, Clarke M, Ghersi D, Liberati A, Petticrew M, Shekelle P, Stewart LA, the PRISMA-P Group. 2015. PRISMA-P (preferred reporting items for systematic review and meta-analysis protocols) 2015 checklist : recommended items to address in a systematic review protocol *. BMJ. 349(jan02 1):g7647–g7647. https://doi.org/10.1111/j.1532-950X.2010.00691.x.
   PubMed Web of Science ®Google Scholar
• Sharp JM, Gilmour NJL, Rushton B. 1978. Ovine pneumonia. N Z Vet J. 26(6):165–165. https://doi.org/10.1080/00480169.1978.34527.
   PubMed Web of Science ®Google Scholar
• Shipunov I, Kupaev V. 2022. Glycome assessment in patients with respiratory diseases. Trans Meta Syndrome Res. 5:10–15. https://doi.org/10.1016/j.tmsr.2022.02.001.
   Google Scholar
• Siddiqui S, Johansson K, Joo A, Bonser LR, Koh KD, Le Tonqueze O, Bolourchi S, Bautista RA, Zlock L, Roth TL, et al. 2021. Epithelial miR-141 regulates IL-13–induced airway mucus production. JCI Insight. 6(5):e139019. https://doi.org/10.1172/jci.insight.139019.
   Web of Science ®Google Scholar
• Simon JC, Marchesi JR, Mougel C, Selosse MA. 2019. Host-microbiota interactions: from holobiont theory to analysis. Microbiome. 7(1):5. https://doi.org/10.1186/s40168-019-0619-4.
   PubMedGoogle Scholar
• Skovgaard K, Cirera S, Vasby D, Podolska A, Breum SØ, Dürrwald R, Schlegel M, Heegaard PMH. 2013. Expression of innate immune genes, proteins and microRNAs in lung tissue of pigs infected experimentally with influenza virus (H1N2). Innate Immun. 19(5):531–544. https://doi.org/10.1177/1753425912473668.
   PubMed Web of Science ®Google Scholar
• Skrzypek K, Tertil M, Golda S, Ciesla M, Weglarczyk K, Collet G, Guichard A, Kozakowska M, Boczkowski J, Was H, et al. 2013. Interplay between heme oxygenase-1 and miR-378 affects non-small cell lung carcinoma growth, vascularization, and metastasis. Antioxid Redox Signal. 19(7):644–660. https://doi.org/10.1089/ars.2013.5184.
   PubMed Web of Science ®Google Scholar
• Smirnova MG, Guo L, Birchall JP, Pearson JP. 2003. LPS up-regulates mucin and cytokine mRNA expression and stimulates mucin and cytokine secretion in goblet cells. Cell Immunol. 221(1):42–49. https://doi.org/10.1016/S0008-8749.(03)00059-5.
   PubMed Web of Science ®Google Scholar
• Sommer F, Nookaew I, Sommer N, Fogelstrand P, Bäckhed F. 2015. Site-specific programming of the host epithelial transcriptome by the gut microbiota. Genome Biol. 16(1):62. https://doi.org/10.1186/s13059-015-0614-4.
   PubMedGoogle Scholar
• Song D, Iverson E, Kaler L, Boboltz A, Scull MA, Duncan GA. 2022. MUC5B mobilizes and MUC5AC spatially aligns mucociliary transport on human airway epithelium. Sci Adv. 8(47):eabq5049. https://doi.org/10.1126/sciadv.abq5049.
   PubMed Web of Science ®Google Scholar
• Stencel-Baerenwald JE, Reiss K, Reiter DM, Stehle T, Dermody TS. 2014. The sweet spot: defining virus–sialic acid interactions. Nat Rev Microbiol. 12(11):739–749. https://doi.org/10.1038/nrmicro3346.
   PubMed Web of Science ®Google Scholar
• Su S, Fu X, Li G, Kerlin F, Veit M. 2017. Novel influenza D virus: epidemiology, pathology, evolution and biological characteristics. Virulence. 8(8):1580–1591. https://doi.org/10.1080/21505594.2017.1365216.
   PubMed Web of Science ®Google Scholar
• Suzuki N, Abe T, Natsuka S. 2022. Structural analysis of N-glycans in chicken trachea and lung reveals potential receptors of chicken influenza viruses. Sci Rep. 12(1):2081. https://doi.org/10.1038/s41598-022-05961-x.
   PubMed Web of Science ®Google Scholar
• Thai P, Loukoianov A, Wachi S, Wu R. 2008. Regulation of airway mucin gene expression. Annu Rev Physiol. 70(1):405–429. https://doi.org/10.1146/annurev.physiol.70.113006.100441.
   PubMedGoogle Scholar
• Thornton DJ, Rousseau K, McGuckin MA. 2008. Structure and function of the polymeric mucins in airways mucus. Annu Rev Physiol. 70(1):459–486. https://doi.org/10.1146/annurev.physiol.70.113006.100702.
   PubMed Web of Science ®Google Scholar
• Thu CT, Mahal LK. 2020. Sweet control: microRNA regulation of the glycome. Biochemistry. 59(34):3098–3110. https://doi.org/10.1021/acs.biochem.9b00784.
   PubMed Web of Science ®Google Scholar
• Timoneda O, Núñez-Hernández F, Balcells I, Muñoz M, Castelló A, Vera G, Pérez LJ, Egea R, Mir G, Córdoba S, et al. 2014. The role of viral and host MicroRNAs in the Aujeszky’s disease virus during the infection process. PLoS One. 9(1):e86965. https://doi.org/10.1371/journal.pone.0086965.
   PubMed Web of Science ®Google Scholar
• Timsit E, Workentine M, Crepieux T, Miller C, Regev-Shoshani G, Schaefer A, Alexander T. 2017. Effects of nasal instillation of a nitric oxide-releasing solution or ­parenteral administration of tilmicosin on the nasopharyngeal microbiota of beef feedlot cattle at high-risk of developing respiratory tract disease. Res Vet Sci. 115:117–124. https://doi.org/10.1016/j.rvsc.2017.02.001.
   PubMed Web of Science ®Google Scholar
• Umar S, Guerin JL, Ducatez MF. 2016. Low pathogenic avian influenza and coinfecting pathogens: a review of experimental infections in avian models. Avian Dis. 61(1):3–15. https://doi.org/10.1637/11514-101316-review.
   Web of Science ®Google Scholar
• van Leenen K, Van Driessche L, De Cremer L, Masmeijer C, Boyen F, Deprez P, Pardon B. 2020. Comparison of bronchoalveolar lavage fluid bacteriology and cytology in calves classified based on combined clinical scoring and lung ultrasonography. Prev Vet Med. 176:104901. https://doi.org/10.1016/j.prevetmed.2020.104901.
   PubMed Web of Science ®Google Scholar
• Varki A. 2007. Glycan-based interactions involving vertebrate sialic-acid-recognizing proteins. Nature. 446(7139):1023–1029. https://doi.org/10.1038/nature05816.
   PubMed Web of Science ®Google Scholar
• Varki A. 2008. Sialic acids in human health and disease. Trends Mol Med. 14(8):351–360. https://doi.org/10.1016/j.molmed.2008.06.002.
   PubMed Web of Science ®Google Scholar
• Vayssier-Taussat M, Kazimirova M, Hubalek Z, Hornok S, Farkas R, Cosson J-F, Bonnet S, Vourch G, Gasqui P, Mihalca AD, et al. 2015. Emerging horizons for tick-borne pathogens: from the “one pathogen-one disease” vision to the pathobiome paradigm. Future Microbiol. 10(12):2033–2043. https://doi.org/10.2217/fmb.15.114.
   PubMed Web of Science ®Google Scholar
• Vlasak R, Luytjes W, Spaan W, Palese P. 1988. Human and bovine coronaviruses recognize sialic acid-containing receptors similar to those of influenza C viruses. Proc Natl Acad Sci USA. 85(12):4526–4529. https://doi.org/10.1073/pnas.85.12.4526.
   PubMed Web of Science ®Google Scholar
• Wallace LE, Liu M, van Kuppeveld FJM, de Vries E, de Haan CAM. 2021. Respiratory mucus as a virus-host range determinant. Trends Microbiol. 29(11):983–992. https://doi.org/10.1016/j.tim.2021.03.014.
   PubMed Web of Science ®Google Scholar
• Walther T, Karamanska R, Chan RWY, Chan MCW, Jia N, Air G, Hopton C, Wong MP, Dell A, Malik Peiris JS, et al. 2013. Glycomic analysis of human respiratory tract tissues and correlation with influenza virus infection. PLoS Pathog. 9(3):e1003223. https://doi.org/10.1371/journal.ppat.1003223.
   PubMed Web of Science ®Google Scholar
• Wang J, Ishfaq M, Li J. 2021. Lactobacillus salivarius ameliorated Mycoplasma gallisepticum-induced inflammatory injury and secondary Escherichia coli infection in chickens: involvement of intestinal microbiota. Vet Immunol Immunopathol. 233:110192. https://doi.org/10.1016/j.vetimm.2021.110192.
   PubMed Web of Science ®Google Scholar
• Wang Q, Cai R, Huang A, Wang X, Qu W, Shi L, Li C, Yan H. 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.
   PubMed Web of Science ®Google Scholar
• Wang T, He Q, Yao W, Shao Y, Li J, Huang F. 2019. The variation of nasal microbiota caused by low levels of gaseous ammonia exposure in growing pigs. Front Microbiol. 10:1083. https://doi.org/10.3389/fmicb.2019.01083.
   PubMed Web of Science ®Google Scholar
• Wang X, Chen H, Liu J, Gai L, Yan X, Guo Z, Liu F. 2021. Emerging advances of non-coding RNAs and competitive endogenous RNA regulatory networks in asthma. Bioengineered. 12(1):7820–7836. https://doi.org/10.1080/21655979.2021.1981796.
   PubMed Web of Science ®Google Scholar
• Wasik BR, Barnard KN, Parrish CR. 2016. Effects of sialic acid modifications on virus binding and infection. Trends Microbiol. 24(12):991–1001. https://doi.org/10.1016/j.tim.2016.07.005.
   PubMed Web of Science ®Google Scholar
• Wheeler KM, Cárcamo-Oyarce G, Turner BS, Dellos-Nolan S, Co JY, Lehoux S, Cummings RD, Wozniak DJ, Ribbeck K. 2019. Mucin glycans attenuate the virulence of Pseudomonas aeruginosa in infection. Nat Microbiol. 4(12):2146–2154. https://doi.org/10.1038/s41564-019-0581-8.
   PubMed Web of Science ®Google Scholar
• Wypych TP, Wickramasinghe LC, Marsland BJ. 2019. The influence of the microbiome on respiratory health. Nat Immunol. 20(10):1279–1290. https://doi.org/10.1038/s41590-019-0451-9.
   PubMed Web of Science ®Google Scholar
• Xia B, Royall JA, Damera G, Sachdev GP, Cummings RD. 2005. Altered O-glycosylation and sulfation of airway mucins associated with cystic fibrosis. Glycobiology. 15(8):747–775. https://doi.org/10.1093/glycob/cwi061.
   PubMed Web of Science ®Google Scholar
• Yitbarek A, Astill J, Hodgins DC, Parkinson J, Nagy É, Sharif S. 2019. Commensal gut microbiota can modulate adaptive immune responses in chickens vaccinated with whole inactivated avian influenza virus subtype H9N2. Vaccine. 37(44):6640–6647. https://doi.org/10.1016/j.vaccine.2019.09.046.
   PubMed Web of Science ®Google Scholar
• Yitbarek A, Taha-Abdelaziz K, Hodgins DC, Read L, Nagy É, Weese JS, Caswell JL, Parkinson J, Sharif S. 2018. Gut microbiota-mediated protection against influenza virus subtype H9N2 in chickens is associated with modulation of the innate responses. Sci Rep. 8(1):13189. https://doi.org/10.1038/s41598-018-31613-0.
   PubMedGoogle Scholar
• Yu X, Dang VT, Fleming FE, von Itzstein M, Coulson BS, Blanchard H. 2012. Structural basis of rotavirus strain preference toward N-acetyl- or N-glycolylneuraminic acid-containing receptors. J Virol. 86(24):13456–13466. https://doi.org/10.1128/JVI.06975-11.
   PubMed Web of Science ®Google Scholar
• Zeineldin M, Elolimy AA, Barakat R. 2020. Meta-analysis of bovine respiratory microbiota: link between respiratory microbiota and bovine respiratory health. FEMS Microbiol Ecol. 96(8):fiaa127. https://doi.org/10.1093/femsec/fiaa127.
   PubMed Web of Science ®Google Scholar
• Zeineldin M, Lowe J, Aldridge B. 2019. Contribution of the mucosal microbiota to bovine respiratory health. Trends Microbiol. 27(9):753–770. https://doi.org/10.1016/j.tim.2019.04.005.
   PubMed Web of Science ®Google Scholar
• Zeineldin M, Lowe J, de Godoy M, Maradiaga N, Ramirez C, Ghanem M, Abd El-Raof Y, Aldridge B. 2017. Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease. Vet Microbiol. 208:30–37. https://doi.org/10.1016/j.vetmic.2017.07.006.
   PubMed Web of Science ®Google Scholar
• Zhang M, Hill JE, Fernando C, Alexander TW, Timsit E, van der Meer F, Huang Y. 2019. Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease. Transbound Emerg Dis. 66(3):1379–1386. https://doi.org/10.1111/tbed.13172.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Wang L, Qiu L, Pan R, Bai H, Jiang Y, Wang Z, Bi Y, Chen G, Chang G, et al. 2019. Expression patterns of novel circular RNAs in chicken cells after avian leukosis virus subgroup J infection. Gene. 701:72–81. https://doi.org/10.1016/j.gene.2019.03.030.
   PubMed Web of Science ®Google Scholar
• Zhong T, Perelman JM, Kolosov VP, Zhou X. 2011. MiR-146a negatively regulates neutrophil elastase-induced MUC5AC secretion from 16HBE human bronchial epithelial cells. Mol Cell Biochem. 358(1–2):249–255. https://doi.org/10.1007/s11010-011-0975-2.
   PubMed Web of Science ®Google Scholar