Berlin, K., Koren, S., Chin, C. S., Drake, J. P., Landolin, J. M., & Phillippy, A. M. (2015). Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnology, 33, 623–630.
Article PubMed CAS Google Scholar
Bertelli, C., Laird, M. R., Williams, K. P., Simon Fraser, G., Lau, B. Y., Hoad, G., Winsor, G. L., & Brinkman, F. S. L. (2017). IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Research, 45, W30–W35.
Article PubMed PubMed Central CAS Google Scholar
Chalita, M., Kim, Y. O., Park, S., Oh, H. S., Cho, J. H., Moon, J., Baek, N., Moon, C., Lee, K., Yang, J., et al. (2024). EzBioCloud: A genome-driven database and platform for microbiome identification and discovery. International Journal of Systematic Evolutionary Microbiology, 74, 006421.
Chaudhari, N. M., Gupta, V. K., & Dutta, C. (2016). BPGA—An ultra-fast pan-genome analysis pipeline. Scientific Reports, 6, 24373.
Article PubMed PubMed Central CAS Google Scholar
Eren, A. M., Esen, O. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., & Delmont, T. O. (2015). Anvi’o: An advanced analysis and visualization platform for ‘omics data.’ PeerJ, 3, e1319.
Article PubMed PubMed Central Google Scholar
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17, 368–376.
Article PubMed CAS Google Scholar
Gao, T., Yuan, F., Liu, Z., Liu, W., Zhou, D., Yang, K., Guo, R., Liang, W., Zou, G., Zhou, R., et al. (2020). Proteomic and metabolomic analyses provide insights into the mechanism on arginine metabolism regulated by tRNA modification enzymes GidA and MnmE of Streptococcus suis. Frontiers in Cellular Infection Microbiology, 10, 597408.
Article PubMed PubMed Central Google Scholar
Helmig, R., Uldbjerg, N., Boris, J., & Kilian, M. (1993). Clonal analysis of Streptococcus agalactiae isolated from infants with neonatal sepsis or meningitis and their mothers and from healthy pregnant women. Journal of Infectious Disease, 168, 904–909.
Huson, D. H., & Scornavacca, C. (2012). Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Systematic Biology., 61, 1061–1067.
Ibberson, C. B., Jones, C. L., Singh, S., Wise, M. C., Hart, M. E., Zurawski, D. V., & Horswill, A. R. (2014). Staphylococcus aureus hyaluronidase is a CodY-regulated virulence factor. Infection and Immunity, 82, 4253–4264.
Article PubMed PubMed Central Google Scholar
Jin, D., Chen, C., Li, L., Lu, S., Li, Z., Zhou, Z., Jing, H., Xu, Y., Du, P., Wang, H., et al. (2013). Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis. BMC Microbiology, 13, 141.
Article PubMed PubMed Central CAS Google Scholar
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30, 772–780.
Article PubMed PubMed Central CAS Google Scholar
Kolaczkowski, B., & Thornton, J. W. (2004). Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature, 431, 980–984.
Article PubMed CAS Google Scholar
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35, 1547–1549.
Article PubMed PubMed Central CAS Google Scholar
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947–2948.
Article PubMed CAS Google Scholar
Li, W., & Godzik, A. (2006). Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658–1659.
Article PubMed CAS Google Scholar
Liu, B., Zheng, D., Zhou, S., Chen, L., & Yang, J. (2022). VFDB 2022: A general classification scheme for bacterial virulence factors. Nucleic Acids Research, 50, D912–D917.
Article PubMed CAS Google Scholar
Liu, H., Lei, S., Jia, L., Xia, X., Sun, Y., Jiang, H., Zhu, R., Li, S., Qu, G., Gu, J., et al. (2021). Streptococcus suis serotype 2 enolase interaction with host brain microvascular endothelial cells and RPSA-induced apoptosis lead to loss of BBB integrity. Veterinary Research, 52, 30.
Article PubMed PubMed Central CAS Google Scholar
Liu, Q., Wu, L., Niu, J., & Zhao, X. (2020). Research progress of the composition and function of bacterial phosphotransferase system. Microbiology China, 47, 2266–2277.
Liu, S., Feng, J., Pu, J., Xu, X., Lu, S., Yang, J., Wang, Y., Jin, D., Du, X., Meng, X., et al. (2019). Genomic and molecular characterisation of Escherichia marmotae from wild rodents in Qinghai-Tibet plateau as a potential pathogen. Scientific Reports, 9, 10619.
Article PubMed PubMed Central Google Scholar
Liu, S., Jin, D., Lan, R., Wang, Y., Meng, Q., Dai, H., Lu, S., Hu, S., & Xu, J. (2015). Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana. International Journal of Systematic Evolutionary Microbiology, 65, 2130–2134.
Article PubMed CAS Google Scholar
Man, W. H., de Steenhuijsen Piters, W. A., & Bogaert, D. (2017). The microbiota of the respiratory tract: Gatekeeper to respiratory health. Nature Reviews Microbiology, 15, 259–270.
Article PubMed PubMed Central CAS Google Scholar
Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P., & Goker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics, 14, 60.
Article PubMed PubMed Central Google Scholar
Minnikin, D. E., O’Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., & Parlett, J. H. (1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. Journal of Microbiological Methods, 2, 233–241.
Nobbs, A. H., Lamont, R. J., & Jenkinson, H. F. (2009). Streptococcus Adherence and colonization. Microbiology and Molecular Biology Reviews, 73, 407–450.
Article PubMed PubMed Central CAS Google Scholar
Oggioni, M. R., Memmi, G., Maggi, T., Chiavolini, D., Iannelli, F., & Pozzi, G. (2003). Pneumococcal zinc metalloproteinase ZmpC cleaves human matrix metalloproteinase 9 and is a virulence factor in experimental pneumonia. Molecular Microbiology, 49, 795–805.
Article PubMed CAS Google Scholar
Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., Edwards, R. A., Gerdes, S., Parrello, B., Shukla, M., et al. (2014). The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Research, 42, D206-214.
Article PubMed CAS Google Scholar
Patel, S., & Gupta, R. S. (2018). Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures. Infection, Genetics and Evolution, 66, 130–151.
Article PubMed CAS Google Scholar
Plummer, C., Wu, H., Kerrigan, S. W., Meade, G., Cox, D., & Ian Douglas, C. W. (2005). A serine-rich glycoprotein of Streptococcus sanguis mediates adhesion to platelets via GPIb. British Journal of Haematology, 129, 101–109.
Article PubMed CAS Google Scholar
Pracht, D., Elm, C., Gerber, J., Bergmann, S., Rohde, M., Seiler, M., Kim, K. S., Jenkinson, H. F., Nau, R., & Hammerschmidt, S. (2005). PavA of Streptococcus pneumoniae modulates adherence, invasion, and meningeal inflammation. Infection and Immunity, 73, 2680–2689.
留言 (0)