Zinicola M, Lima F, Lima S, Machado V, Gomez M, Döpfer D, et al. Altered microbiomes in bovine digital dermatitis lesions, and the gut as a pathogen reservoir. PLoS One. 2015;10: e0120504.
Article
Google Scholar
Ariza JM, Döpfer D, Anklam K, Labrut S, Oberle K, Bareille N, et al. Do footbath disinfectants modify the dynamics of the skin microbiota in dairy cattle affected by digital dermatitis? bioRxiv. 2019;soumis:1–33.
Google Scholar
Zinicola M, Higgins H, Lima S, Machado V, Guard C, Bicalho R. Shotgun metagenomic sequencing reveals functional genes and microbiome associated with bovine digital dermatitis. PLoS One. 2015;10: e0133674.
Article
Google Scholar
Hesseling J, Legione AR, Stevenson MA, McCowan CI, Pyman MF, Finochio C, et al. Bovine digital dermatitis in Victoria, Australia. Aust Vet J. 2019; 10:404-13.
Caddey B, Orsel K, Naushad S, Derakhshani H, De Buck J. Identification and quantification of bovine digital dermatitis-associated microbiota across lesion stages in feedlot beef cattle. mSystems. 2021; https://doi.org/10.1128/msystems.00708-21.
Krull AC, Shearer JK, Gorden PJ, Cooper VL, Phillips GJ, Plummer PJ. Deep sequencing analysis reveals the temporal microbiota changes associated with the development of bovine digital dermatitis. Infect Immun. 2014;82:3359–73.
Article
CAS
Google Scholar
Santos TMA, Pereira RV, Caixeta LS, Guard CL, Bicalho RC. Microbial diversity in bovine Papillomatous digital dermatitis in Holstein dairy cows from upstate New York. FEMS Microbiol Ecol. 2012;79:518-29.
Bubier JA, Chesler EJ, Weinstock GM. Host genetic control of gut microbiome composition. Mamm. Genome. 2021.
Srinivas G, Möller S, Wang J, Künzel S, Zillikens D, Baines JF, et al. Genome-wide mapping of gene-microbiota interactions in susceptibility to autoimmune skin blistering. Nat Commun. 2013;4:2462.
Article
Google Scholar
Belheouane M, Gupta Y, Künzel S, Ibrahim S, Baines JF. Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts. Microbiome. 2017;5:59.
Article
Google Scholar
Griffiths BE, Mahen PJ, Hall R, Kakatsidis N, Britten N, Long K, et al. A prospective cohort study on the development of claw horn disruption lesions in dairy cattle; furthering our understanding of the role of the digital cushion. Front Vet Sci. 2020;7:1–9.
Article
CAS
Google Scholar
Blowey RW, Sharp MW. Digital dermatitis in dairy cattle. Vet Rec. 1988;122:505–8.
Article
CAS
Google Scholar
Berry SL, Read DH, Famula TR, Mongini A, Döpfer D. Long-term observations on the dynamics of bovine digital dermatitis lesions on a California dairy after topical treatment with lincomycin HCl. Vet J Elsevier Ltd. 2012;193:654–8.
CAS
Google Scholar
Sánchez-Molano E, Bay V, Smith RF, Oikonomou G, Banos G. Quantitative trait loci mapping for lameness associated phenotypes in holstein-friesian dairy cattle. Front Genet. 2019;10:1–9.
Article
Google Scholar
Bay V, Griffiths B, Carter S, Evans NJ, Lenzi L, Bicalho RC, et al. 16S rRNA amplicon sequencing reveals a polymicrobial nature of complicated claw horn disruption lesions and interdigital phlegmon in dairy cattle. Sci Rep. 2018;8:1–12.
Article
CAS
Google Scholar
Martino C, Morton JT, Marotz CA, Thompson LR, Tripathi A, Knight R, et al. A novel sparse compositional technique reveals microbial perturbations. Msystems. 2019; https://doi.org/10.1128/msystems.00016-19.
Aitchison J, Greenacre M. Biplots of compositional data. J R Stat Soc Ser C Appl Stat. John Wiley & Sons, Ltd; 2002;51:375–92.
Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, et al. Establishing microbial composition measurement standards with reference frames. Nat Commun. Nature Publishing Group; 2019;10:1–11.
Faust K, Raes J. Microbial interactions: from networks to models. Nat Rev Microbiol. 2012;10(8):538–50.
Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015;11(5):e1004226. https://doi.org/10.1371/journal.pcbi.1004226.
Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 2013;10:57–9.
Article
CAS
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. 2011;17:5–7.
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. Nature Publishing Group; 2012;9:357–9.
Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: A fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 2014;30:614–20.
Article
CAS
Google Scholar
Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol BioMed Central Ltd. 2014;15:R46.
Article
Google Scholar
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60.
Article
Google Scholar
Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, et al. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods. 2018;15:962–8.
Article
CAS
Google Scholar
Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2015;44:471–80.
Article
Google Scholar
Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 2012;44:821–4.
Article
CAS
Google Scholar
Amin N, van Duijn CM, Aulchenko YS. A genomic background based method for association analysis in related individuals. PLoS One. 2007;2: e1274.
Article
Google Scholar
Cebamanos L, Gray A, Stewart I, Tenesa A. Regional heritability advanced complex trait analysis for GPU and traditional parallel architectures. Bioinformatics. 2014;30:1177–9.
Article
CAS
Google Scholar
Maruyama Y, Oiki S, Takase R, Mikami B, Murata K, Hashimoto W. Metabolic fate of unsaturated glucuronic/iduronic acids from glycosaminoglycans: Molecular identification and structure determination of streptococcal isomerase and dehydrogenase. J Biol Chem American Society for Biochemistry and Molecular Biology Inc. 2015;290:6281–92.
CAS
Google Scholar
Espiritu HM, Mamuad LL, Kim SH, Jin SJ, Lee SS, Kwon SW, et al. Microbiome shift, diversity, and overabundance of opportunistic pathogens in bovine digital dermatitis revealed by 16s rrna amplicon sequencing. Animals. 2020;10(10):1798. https://doi.org/10.3390/ani10101798.
Hagey JV, Bhatnagar S, Heguy JM, Karle BM, Price PL, Meyer D, et al. Fecal microbial communities in a large representative cohort of California dairy cows. Front Microbiol Front Media SA. 2019;10:1093.
Article
Google Scholar
Petersen C, Round JL. Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol. 2014;6(7):1024-33. https://doi.org/10.1111/cmi.12308.
Calvo-Bado LA, Oakley BB, Dowd SE, Green LE, Medley GF, Ul-Hassan A, et al. Ovine pedomics: the first study of the ovine foot 16S rRNA-based microbiome. ISME J. Nature Publishing Group; 2011;5:1426–37.
Ganda EK, Bisinotto RS, Lima SF, Kronauer K, Decter DH, Oikonomou G, et al. Longitudinal metagenomic profiling of bovine milk to assess the impact of intramammary treatment using a third-generation cephalosporin. Sci Rep. 2016;6:1–13.
Article
Google Scholar
Roberfroid M, Gibson GR, Hoyles L, McCartney AL, Rastall R, Rowland I, et al. Prebiotic effects: metabolic and health benefits. Br J Nutr. 2010;2:S1-63.
Article
Google Scholar
Maguire M, Maguire G. The role of microbiota, and probiotics and prebiotics in skin health. Arch Dermatol Res. Springer Verlag; 2017;309:411–21.
Ellis SR, Nguyen M, Vaughn AR, Notay M, Burney WA, Sandhu S, et al. The skin and gut microbiome and its role in common dermatologic conditions. Microorganisms. MDPI AG; 2019.
Krull AC, Cooper VL, Coatney JW, Shearer JK, Gorden PJ, Plummer PJ. A highly effective protocol for the rapid and consistent induction of digital dermatitis in holstein calves. PLoS One. 2016;11: e0154481.
Article
Google Scholar
Collighan RJ, Woodward MJ. Spirochaetes and other bacterial species associated with bovine digital dermatitis. FEMS Microbiol Lett. 1997;156:37–41.
Article
CAS
Google Scholar
Ulger-Toprak N, Liu C, Summanen PH, Finegold SM. Murdochiella asaccharolytica gen. nov., sp. nov., a Gram-stain-positive, anaerobic coccus isolated from human wound specimens. Int J Syst Evol Microbiol. Microbiology Society; 2010;60:1013–6.
Diop K, Raoult D, Bretelle F, Fenollar F. “Murdochiella vaginalis” sp. nov., a new bacterial species cultivated from the vaginal flora of a woman with bacterial vaginosis. Hum Microbiome J. Elsevier Ltd; 2016;2:15–6.
Xu S. Theoretical basis of the beavis effect. Genetics. 2003;165:2259–68.
Article
Google Scholar
O’Gorman GM, Park SDE, Hill EW, Meade KG, Coussens PM, Agaba M, et al. Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility. BMC Genomics. 2009;10:207.
Article
Google Scholar
Wu J, Sun L, Chen X, Du F, Shi H, Chen C, et al. Cyclic GMP-AMP is an endogenous second messenger in innate immune signaling by cytosolic DNA. Science (80- ). 2013;339:826–30.
Article
CAS
Google Scholar
Lemos MVA, Chiaia HLJ, Berton MP, Feitosa FLB, Aboujaoud C, Camargo GMF, et al. Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure. BMC Genomics. 2016;17:213.
Article
Google Scholar
Lo Vasco VR, Leopizzi M, Chiappetta C, Puggioni C, Della Rocca C, Polonia P, et al. Lypopolysaccharide downregulates the expression of selected phospholipase C genes in cultured endothelial cells. Inflammation. 2013;36:862–8.
Article
CAS
Google Scholar
Heumann D, Roger T. Initial responses to endotoxins and Gram-negative bacteria. Clin Chim Acta. 2002;323(1-2):59–72.
Fink LN, Metzdorff SB, Zeuthen LH, Nellemann C, Kristensen MB, Licht TR, et al. Establishment of tolerance to commensal bacteria requires a complex microbiota and is accompanied by decreased intestinal chemokine expression. AJP Gastrointest Liver Physiol. 2012;302:G55-65.
Article
CAS
Google Scholar
Nerstedt A, Nilsson EC, Ohlson K, Håkansson J, Svensson LT, Löwenadler B, et al. Administration of Lactobacillus evokes coordinated changes in the intestinal expression profile of genes regulating energy homeostasis and immune phenotype in mice. Br J Nutr. 2007;97:1117–27.
Article
CAS
Google Scholar
Wang J-W, Howson J, Haller E, Kerr WG. Identification of a novel Lipopolysaccharide-Inducible gene with key features of both a kinase anchor proteins and chs1/beige Proteins. J Immunol. 2001;166:4586–95.
Article
CAS
Google Scholar
Alangari A, Alsultan A, Adly N, Massaad MJ, Kiani IS, Aljebreen A, et al. LPS-responsive beige-like anchor (LRBA) gene mutation in a family with inflammatory bowel disease and combined immunodeficiency. J Allergy Clin Immunol. 2012;130:481–8.
Article
CAS
Google Scholar
Revel-Vilk S, Fischer U, Keller B, Nabhani S, Gámez-Díaz L, Rensing-Ehl A, et al. Autoimmune lymphoproliferative syndrome-like disease in patients with LRBA mutation. Clin Immunol. 2015;159:84–92.
Article
CAS
Google Scholar
Birnbaum RY, Zvulunov A, Hallel-Halevy D, Cagnano E, Finer G, Ofir R, et al. Seborrhea-like dermatitis with psoriasiform elements caused by a mutation in ZNF750, encoding a putative C2H2 zinc finger protein. Nat Genet. 2006;38:749–51.
Article
CAS
Google Scholar
Yang CF, Hwu WL, Yang LC, Chung WH, Chien YH, Hung CF, et al. A promoter sequence variant of ZNF750 is linked with familial psoriasis. J Invest Dermatol Elsevier Masson SAS. 2008;128:1662–8.
Article
CAS
Google Scholar
Nocek JE, Johnson AB, Socha MT. Digital characteristics in commercial dairy herds fed metal-specific amino acid complexes. J Dairy Sci. 2000;83:1553–72.
Article
CAS
Google Scholar