Kostic AD, Xavier RJ, Gevers D (2014) The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology 146(6):1489–1499. https://doi.org/10.1053/j.gastro.2014.02.009

Article  CAS  PubMed  Google Scholar 

Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI (2011) Human nutrition, the gut microbiome and the immune system. Nature 474(7351):327–336. https://doi.org/10.1038/nature10213

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pitta DW, Indugu N, Kumar S, Vecchiarelli B, Sinha R, Baker LD, Bhukya B, Ferguson JD (2016) Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows. Anaerobe 38:50–60. https://doi.org/10.1016/j.anaerobe.2015.12.003

Article  CAS  PubMed  Google Scholar 

Khan FA, Pandupuspitasari NS, Huang C, Negara W, Ahmed B, Putri EM, Lestari P, Priyatno TP, Prima A, Restitrisnani V, Surachman M, Akhadiarto S, Darmawan IWA, Wahyuni DS, Herdis H (2023) Unlocking gut microbiota potential of dairy cows in varied environmental conditions using shotgun metagenomic approach. BMC Microbiol 23(1):344. https://doi.org/10.1186/s12866-023-03101-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Delgado B, Bach A, Guasch I, Gonzalez C, Elcoso G, Pryce JE, Gonzalez-Recio O (2019) Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle. Sci Rep 9(1):11. https://doi.org/10.1038/s41598-018-36673-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang X, Howe S, Wei X, Deng F, Tsai T, Chai J, Xiao Y, Yang H, Maxwell CV, Li Y, Zhao J (2021) Comprehensive cultivation of the swine gut microbiome reveals high bacterial diversity and guides bacterial isolation in pigs. mSystems 6(4):e0047721. https://doi.org/10.1128/mSystems.00477-21

Article  PubMed  Google Scholar 

Christensen H, Bisgaard M, Bojesen AM, Mutters R, Olsen JE (2003) Genetic relationships among avian isolates classified as Pasteurella haemolytica,‘Actinobacillus salpingitidis’ or Pasteurella anatis with proposal of Gallibacterium anatis gen. nov., comb. nov. and description of additional genomospecies within Gallibacterium gen. nov. Int J Syst Evol Microbiol 53(1):275–287. https://doi.org/10.1099/ijs.0.02330-0

Article  CAS  PubMed  Google Scholar 

Bisgaard M, Korczak BM, Busse HJ, Kuhnert P, Bojesen AM, Christensen H (2009) Classification of the taxon 2 and taxon 3 complex of Bisgaard within Gallibacterium and description of Gallibacterium melopsittaci sp. nov., Gallibacterium trehalosifermentans sp. nov. and Gallibacterium salpingitidis sp. nov. Int J Syst Evol Microbiol 59:735–744. https://doi.org/10.1099/ijs.0.005694-0

Article  CAS  PubMed  Google Scholar 

Gautier AL, Dubois D, Escande F, Avril JL, Trieu-Cuot P, Gaillot O (2005) Rapid and accurate identification of human isolates of Pasteurella and related species by sequencing the sodA gene. J Clin Microbiol 43(5):2307–2314. https://doi.org/10.1128/JCM.43.5.2307-2314.2005

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aubin GG, Haloun A, Treilhaud M, Reynaud A, Corvec S (2013) Gallibacterium anatis bacteremia in a human. J Clin Microbiol 51(11):3897–3899. https://doi.org/10.1128/JCM.01638-13

Article  PubMed  PubMed Central  Google Scholar 

Van Driessche L, Vanneste K, Bogaerts B, De Keersmaecker SCJ, Roosens NH, Haesebrouck F, De Cremer L, Deprez P, Pardon B, Boyen F (2020) Isolation of drug-resistant Gallibacterium anatis from calves with unresponsive bronchopneumonia. Belgium Emerg Infect Dis 26(4):721–730. https://doi.org/10.3201/eid2604.190962

Article  CAS  PubMed  Google Scholar 

Zellner D, Charlton B, Cooper G, Bickford A (2004) Prevalence of Gallibacterium species in California poultry over 10years (1994–2003) from diagnostic specimens. In: Proceedings of the Annual Conference of the American Association of Avian Pathologists Philadelphia, PA, USA. p. 64

Rzewuska M, Karpinska E, Szeleszczuk P, Binek M (2007) Isolation of Gallibacterium spp. from peacocks with respiratory tract infections. Med Weter 63(11):1431–1433

Google Scholar 

Bojesen AM, Christensen JP, Bisgaard M (2007) Gallibacterium infections and other avian Pasteurellaceae. Poultry diseases(sixth edition):160–163

Persson G, Bojesen AM (2015) Bacterial determinants of importance in the virulence of Gallibacterium anatis in poultry. Vet Res 46(1):57. https://doi.org/10.1186/s13567-015-0206-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

Singh SV, Singh B, Sinha D, Vinodh K, Prasanna V, Monika B, Sakshi D (2016) Gallibacterium anatis: an emerging pathogen of poultry birds and domiciled birds. J Veterinar Sci Techno. https://doi.org/10.4172/2157-7579.1000324

Article  Google Scholar 

Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium series. Oxford, pp 95–98

Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67(5):1613–1617. https://doi.org/10.1099/ijsem.0.001755

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876–4882. https://doi.org/10.1093/nar/25.24.4876

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874. https://doi.org/10.1093/molbev/msw054

Article  CAS  PubMed  PubMed Central  Google Scholar 

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

Article  CAS  PubMed  Google Scholar 

Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376. https://doi.org/10.1007/BF01734359

Article  CAS  PubMed  Google Scholar 

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x

Article  PubMed  Google Scholar 

Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120. https://doi.org/10.1007/BF01731581

Article  CAS  PubMed  Google Scholar 

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7):1043–1055. https://doi.org/10.1101/gr.186072.114

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu D, Zhang Y, Fan G, Sun D, Zhang X, Yu Z, Wang J, Wu L, Shi W, Ma J (2022) IPGA: a handy integrated prokaryotes genome and pan-genome analysis web service. iMeta 1(4):e55. https://doi.org/10.1002/imt2.55

Article  PubMed  PubMed Central  Google Scholar 

Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44(14):6614–6624. https://doi.org/10.1093/nar/gkw569

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J (2021) eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 38(12):5825–5829. https://doi.org/10.1093/molbev/msab293

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim J, Na S-I, Kim D, Chun J (2021) UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 59(6):609–615. https://doi.org/10.1007/s12275-021-1231-4

Article  CAS  PubMed