Agirman G, Hsiao E Y. 2021. SnapShot: The microbiota–gut–brain axis. Cell, 184, 2524.

Baldridge M T, Nice T J, McCune B T, Yokoyama C C, Kambal A, Wheadon M, Diamond M S, Ivanova Y, Artyomov M, Virgin H W. 2015. Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection. Science, 347, 266–269.

Basic M, Keubler L M, Buettner M, Achard M, Breves G, Schröder B, Smoczek A, Jörns A, Wedekind D, Zschemisch N H, Günther C, Neumann D, Lienenklaus S, Weiss S, Hornef M W, Mähler M, Bleich A. 2014. Norovirus triggered microbiota-driven mucosal inflammation in interleukin 10-deficient mice. Inflammatory Bowel Diseases, 20, 431–443.

Baums C G, Schotte U, Amtsberg G, Goethe R. 2004. Diagnostic multiplex PCR for toxin genotyping of Clostridium perfringens isolates. Veterinary Microbiology, 100, 11–16.

Benton H P, Ivanisevic J, Mahieu N G, Kurczy M E, Johnson C H, Franco L, Rinehart D, Valentine E, Gowda H, Ubhi B K, Tautenhahn R, Gieschen A, Fields M W, Patti G J, Siuzdak G. 2015. Autonomous metabolomics for rapid metabolite identification in global profiling. Analytical Chemistry, 87, 884–891.

Berger A K, Yi H, Kearns D B, Mainou B A. 2017. Bacteria and bacterial envelope components enhance mammalian reovirus thermostability. PLoS Pathogens, 13, e1006768.

BIG Data Center Members. 2019. Database resources of the BIG Data Center in 2019. Nucleic Acids Research, 47, D8–D14.

Borgdorff H, Gautam R, Armstrong S D, Xia D, Ndayisaba G F, van Teijlingen N H, Geijtenbeek T B, Wastling J M, van de Wijgert J H. 2016. Cervicovaginal microbiome dysbiosis is associated with proteome changes related to alterations of the cervicovaginal mucosal barrier. Mucosal Immunology, 9, 621–633.

Brian D A, Baric R S. 2005. Coronavirus genome structure and replication. Current Topics in Microbiology and Immunology, 287, 1–30.

Brigidi G S, Bamji S X. 2013. Detection of protein palmitoylation in cultured hippocampal neurons by immunoprecipitation and acyl-biotin exchange (ABE). Journal of Visualized Experiments, 18, 50031.

Callahan B J, McMurdie P J, Rosen M J, Han A W, Johnson A J, Holmes S P. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583.

David S C, Norton T, Tyllis T, Wilson J J, Singleton E V, Laan Z, Davies J, Hirst T R, Comerford I, McColl S R, Paton J C, Alsharifi M. 2019. Direct interaction of whole-inactivated influenza A and pneumococcal vaccines enhances influenza-specific immunity. Nature Microbiology, 4, 1316–1327.

Erickson A K, Jesudhasan P R, Mayer M J, Narbad A, Winter S E, Pfeiffer J K. 2018. Bacteria facilitate enteric virus co-infection of mammalian cells and promote genetic recombination. Cell Host & Microbe, 23, 77–88.e5.

Gelhaus S, Thaa B, Eschke K, Veit M, Schwegmann-Weßels C. 2014. Palmitoylation of the Alphacoronavirus TGEV spike protein S is essential for incorporation into virus-like particles but dispensable for S-M interaction. Virology, 464–465, 397–405.

Hartenian E, Nandakumar D, Lari A, Ly M, Tucker J M, Glaunsinger B A. 2020. The molecular virology of coronaviruses. The Journal of Biological Chemistry, 295, 12910–12934.

Hofmann A F, Hagey L R. 2014. Key discoveries in bile acid chemistry and biology and their clinical applications: History of the last eight decades. Journal of Lipid Research, 55, 1553–1595.

Hosokawa T, Kikuchi Y, Nikoh N, Shimada M, Fukatsu T. 2006. Strict host-symbiont cospeciation and reductive genome evolution in insect gut bacteria. PLoS Biology, 4, e337.

Hou X L, Yu L Y, Liu J. 2007. Development and evaluation of enzyme-linked immunosorbent assay based on recombinant nucleocapsid protein for detection of porcine epidemic diarrhea (PEDV) antibodies. Veterinary Microbiology, 123, 86–92.

Huang J H, Huang X H, Cheng Z Y, Zheng Q S, Sun R Y. 2004. Dose conversion among different animals and healthy volunteers in pharmacological study. Chinese Journal of Clinical Pharmacology and Therapeutics, 9, 1069–1072. (in Chinese)

Jiang H C, Dong H L, Zhang G X, Yu B S, Chapman L R, Fields M W. 2006. Microbial diversity in water and sediment of Lake Chaka, an athalassohaline lake in northwestern China. Applied and Environmental Microbiology, 72, 3832–3845.

Kechin A, Boyarskikh U, Kel A, Filipenko M. 2017. cutPrimers: A new tool for accurate cutting of primers from reads of targeted next generation sequencing. Journal of Computational Biology, 24, 1138–1143.

Kordyukova L V, Serebryakova M V, Khrustalev V V, Veit M. 2019. Differential S-Acylation of enveloped viruses. Protein and Peptide Letters, 26, 588–600.

Lee D, Jang G, Min KC, Lee IH, Won H, Yoon I J, Kang S C, Lee C. 2023. Coinfection with porcine epidemic diarrhea virus and Clostridium perfringens type A enhances disease severity in weaned pigs. Archives of Virology, 168, 166.

Lei S, Samuel H, Twitchell E, Bui T, Ramesh A, Wen K, Weiss M, Li G, Yang X, Jiang X, Yuan L. 2016. Enterobacter cloacae inhibits human norovirus infectivity in gnotobiotic pigs. Scientific Reports, 6, 25017.

Lemonidis K, Werno M W, Greaves J, Diez-Ardanuy C, Sanchez-Perez M C, Salaun C, Thomson D M, Chamberlain L H. 2015. The zDHHC family of S-acyltransferases. Biochemical Society Transactions, 43, 217–221.

Li C, Su M, Yin B, Guo D, Wei S, Kong F, Feng L, Wu R, Sun D. 2019. Integrin αvβ3 enhances replication of porcine epidemic diarrhea virus on Vero E6 and porcine intestinal epithelial cells. Veterinary Microbiology, 237, 108400.

Li Z, Zhang W, Su L, Huang Z, Zhang W, Ma L, Sun J, Guo J, Wen F, Mei K, El-Ashram S, Huang S, Zhao Y. 2022. Difference analysis of intestinal microbiota and metabolites in piglets of different breeds exposed to porcine epidemic diarrhea virus infection. Frontiers in Microbiology, 13, 990642.

Limsuwat N, Boonarkart C, Phakaratsakul S, Suptawiwat O, Auewarakul P. 2020. Influence of cellular lipid content on influenza A virus replication. Archives of Virology, 165, 1151–1161.

Liu H, Yin X, Tian H, Qiu Y, Wang Z, Chen J, Ma D, Zhao B, Du Q, Tong D, Huang Y. 2022. The S protein of a novel recombinant PEDV strain promotes the infectivity and pathogenicity of PEDV in mid-west China. Transboundary and Emerging Diseases, 69, 3704–3723.

Liu S, Zhao L, Zhai Z, Zhao W, Ding J, Dai R, Sun T, Meng H. 2015. Porcine epidemic diarrhea virus infection induced the unbalance of gut microbiota in piglets. Current Microbiology, 71, 643–649.

Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods (San Diego, Calif.), 25, 402–408.

Ma X, Wang Q, Li H, Xu C, Cui N, Zhao X. 2017. 16S rRNA genes Illumina sequencing revealed differential cecal microbiome in specific pathogen free chickens infected with different subgroup of avian leukosis viruses. Veterinary Microbiology, 207, 195–204.

Mehdizadeh Gohari I, A Navarro M, Li J, Shrestha A, Uzal F, A McClane B. 2021. Pathogenicity and virulence of Clostridium perfringens. Virulence, 12, 723–753.

Mertens N, Theuß T, Köchling M, Dohmann K, Lillie-Jaschniski K. 2022. Pathogens detected in 205 German farms with porcine neonatal diarrhea in 2017. Veterinary Sciences, 9, 44.

Monedero V, Collado M C, Rodríguez-Díaz J. 2018. Therapeutic opportunities in intestinal microbiota-virus interactions. Trends in Biotechnology, 36, 645–648.

Nguyen H T, Zhang S, Wang Q, Anang S, Wang J, Ding H, Kappes J C, Sodroski J. 2021. Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Journal of Virology, 95, e02304–20.

Niederwerder M C. 2017. Role of the microbiome in swine respiratory disease. Veterinary Microbiology, 209, 97–106.

Ramadan A A, Mayilsamy K, McGill A R, Ghosh A, Giulianotti M A, Donow H M, Mohapatra S S, Mohapatra S, Chandran B, Deschenes R J, Roy A. 2022. Identification of SARS-CoV-2 spike palmitoylation inhibitors that results in release of attenuated virus with reduced infectivity. Viruses, 14, 531.

Reed L J. 1938. A simple method of estimating fifty percent end points. American Journal of Hygiene, 27, 493–497.

Sanders D W, Jumper C C, Ackerman P J, Bracha D, Donlic A, Kim H, Kenney D, Castello-Serrano I, Suzuki S, Tamura T, Tavares A H, Saeed M, Holehouse A S, Ploss A, Levental I, Douam F, Padera R F, Levy B D, Brangwynne C P. 2021. SARS-CoV-2 requires cholesterol for viral entry and pathological syncytia formation. eLife, 10, e65962.

Song D, Peng Q, Chen Y, Zhou X, Zhang F, Li A, Huang D, Wu Q, Ye Y, He H, Wang L, Tang Y. 2017. Altered gut microbiota profiles in sows and neonatal piglets associated with porcine epidemic diarrhea virus infection. Scientific Reports, 7, 17439.

Sun R Q, Cai R J, Chen Y Q, Liang P S, Chen D K, Song C X. 2012. Outbreak of porcine epidemic diarrhea in suckling piglets, China. Emerging Infectious Diseases, 18, 161–163.

Tabaczar S, Czogalla A, Podkalicka J, Biernatowska A, Sikorski A F. 2017. Protein palmitoylation: Palmitoyltransferases and their specificity. Experimental Biology and Medicine (Maywood, N.J.), 242, 1150–1157.

Tan Z, Dong W, Ding Y, Ding X, Zhang Q, Jiang L. 2019a. Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus. PLoS ONE, 14, e0219868.

Tan Z, Dong W, Ding Y, Ding X, Zhang Q, Jiang L. 2019b. Porcine epidemic diarrhea altered colonic microbiota communities in suckling piglets. Genes, 11, 44.

Thorp E B, Boscarino J A, Logan H L, Goletz J T, Gallagher T M. 2006. Palmitoylations on murine coronavirus spike proteins are essential for virion assembly and infectivity. Journal of Virology, 80, 1280–1289.

Tilg H, Adolph T E, Trauner M. 2022. Gut-liver axis: Pathophysiological concepts and clinical implications. Cell Metabolism, 34, 1700–1718.

Tremaroli V, Bäckhed F. 2012. Functional interactions between the gut microbiota and host metabolism. Nature, 489, 242–249.

Veit M. 2012. Palmitoylation of virus proteins. Biology of the Cell, 104, 493–515.

Wang H, Hui P, Uemoto Y, Ding Y, Yin Z, Bao W. 2023. Metabolomic and proteomic profiling of porcine intestinal epithelial cells infected with porcine epidemic diarrhea virus. International Journal of Molecular Sciences, 24, 5071.

Wang Y, Song F, Zhu J, Zhang S, Yang Y, Chen T, Tang B, Dong L, Ding N, Zhang Q, Bai Z, Dong X, Chen H, Sun M, Zhai S, Sun Y, Yu L, Lan L, Xiao J, Fang X, et al. 2017. GSA: genome sequence archive. Genomics, Proteomics & Bioinformatics, 15, 14–18.

Wypych T P, Wickramasinghe L C, Marsland B J. 2019. The influence of the microbiome on respiratory health. Nature Immunology, 20, 1279–1290.

Yang D, Su M, Li C, Zhang B, Qi S, Sun D, Yin B. 2020. Isolation and characterization of a variant subgroup GII-a porcine epidemic diarrhea virus strain in China. Microbial Pathogenesis, 140, 103922.

Yang M, Yang Y, He Q, Zhu P, Liu M, Xu J, Zhao M. 2021. Intestinal microbiota-a promising target for antiviral therapy? Frontiers in Immunology, 12, 676232.

Yu Y, Li C, Liu J, Zhu F, Wei S, Huang Y, Huang X, Qin Q. 2020. Palmitic acid promotes virus replication in fish cell by modulating autophagy flux and TBK1-IRF3/7 pathway. Frontiers in Immunology, 11, 1764.

Zhang H, Zou C, Peng O, Ashraf U, Xu Q, Gong L, Fan B, Zhang Y, Xu Z, Xue C, Wei X, Zhou Q, Tian X, Shen H, Li B, Zhang X, Cao Y. 2023. Global dynamics of porcine enteric coronavirus PEDV epidemiology, evolution, and transmission. Molecular Biology and Evolution, 40, msad052.

Zhang N, Zhao H, Zhang L. 2019. Fatty acid synthase promotes the palmitoylation of chikungunya virus nsP1. Journal of Virology, 93, e01747–18.

Zhao W, Wang Y, Liu S, Huang J, Zhai Z, He C, Ding J, Wang J, Wang H, Fan W, Zhao J, Meng H. 2015. The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments. PLoS ONE, 10, e0117441.