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- Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis
- Anyeseu Park, Chanhee Lee, Jeong Yoon Lee
- J. Microbiol. 2024;62(5):393-407. Published online March 7, 2024
- DOI: https://doi.org/10.1007/s12275-024-00112-5
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Abstract
- Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.
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Citations
Citations to this article as recorded by
- In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
Journal of Microbiology.2024; 62(5): 409. CrossRef
- In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
Journal Articles
- Prevalence of Indigenous Antibiotic‑Resistant Salmonella Isolates and Their Application to Explore a Lytic Phage vB_SalS_KFSSM with an Intra‑Broad Specificity
- Jaein Choe , Su-Hyeon Kim , Ji Min Han , Jong-Hoon Kim , Mi-Sun Kwak , Do-Won Jeong , Mi-Kyung Park
- J. Microbiol. 2023;61(12):1063-1073. Published online January 2, 2024
- DOI: https://doi.org/10.1007/s12275-023-00098-6
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Abstract
- The consumption of fresh produce has led to increase in antibiotic-resistant (AR) Salmonella outbreaks. In this study, indigenous
Salmonella was isolated from a total of two hundred-two samples including fresh produce and agricultural environmental
samples in Korea. After biochemical confirmation using the Indole, Methyl Red, Voges-Proskauer, Citrate tests, presumable
Salmonella isolates were identified by 16S rRNA sequencing. Identified Salmonella isolates were evaluated for antibiotic
susceptibility against twenty-two antibiotics. The specificity and the efficiency of plating (EOP) of vB_SalS_KFSSM were
evaluated against fifty-three bacterial strains. Twenty-five suspected Salmonella were isolated and confirmed by the positive
result
for methyl red and citrate, of which ten were identified as Salmonella spp. through 16S rRNA gene sequencing. Eight Salmonella isolates (4.0%, n = 8/202) were resistant to at least one antibiotic, among which five were multi-drug resistant. As a lytic phage against Salmonella spp. CMGS-1, vB_SalS_KFSSM was isolated from cow manure. The phage was observed as a tailed phage belonging to the class Caudoviricetes. It exhibited an intra-broad specificity against four indigenous AR Salmonella isolates, two indigenous Salmonella isolates, and five other Salmonella serotypes with great efficiencies (EOP ≥ 0.75). Thus, this study suggested the potential of vB_SalS_KFSSM to combat indigenous AR Salmonella.
- Description of a novel pectin-degrading bacterial species Prevotella pectinovora sp. nov., based on its phenotypic and genomic traits
- Brigita Nograsek , Tomaz Accetto , Lijana Fanedl , Gorazd Avgustin
- J. Microbiol. 2015;53(8):503-510. Published online July 31, 2015
- DOI: https://doi.org/10.1007/s12275-015-5142-0
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- 13 Crossref
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Abstract
- Five strictly anaerobic Gram-negative bacterial strains, P4-65, P4-76T, P5-60, P5-119, and P5-125, presumably belonging to the genus Prevotella were isolated from pig fecal samples. Strains were tested for various phenotypic traits and nearcomplete genome sequences were obtained and analyzed. Phylogenetic analysis based on 16S rRNA gene sequences and multilocus sequence analysis based on five conserved genes confirmed that the strains belong to the genus Prevotella, revealing that they represent a novel and discrete lineage distinct from other known species of this genus. The size of the genome of the isolated strains is 3?.3 Mbp, and the DNA G+C content is 47.5?8.1 mol%. The isolates are strictly anaerobic, rod-shaped with rounded ends, non-motile and non-spore-forming. The main fermentation products are succinate and acetate, with minor concentrations of isovalerate, propionate and isobutyrate. Hydrogen is also produced. Major cellular fatty acids consist of anteiso-C15:0 and iso-C15:0, and a number of additional acids are present in lower concentrations. A substantial portion of genes involved in carbohydrate utilization is devoted to pectin degradation and utilization, while those supporting growth on xylan in ruminal Prevotella could not have been revealed. On the basis of the presented results, a novel species, Prevotella pectinovora sp. nov. is proposed. The type strain is P4-76T (=DSM 29996T =ZIM B1020T).
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Citations
Citations to this article as recorded by- Colonic Microbiota Improves Fiber Digestion Ability and Enhances Absorption of Short-Chain Fatty Acids in Local Pigs of Hainan
Pengxiang Xue, Mingming Xue, Yabiao Luo, Qiguo Tang, Feng Wang, Ruiping Sun, Yanxia Song, Zhe Chao, Meiying Fang
Microorganisms.2024; 12(6): 1033. CrossRef - Contribution of pectin-degrading bacteria to the quality of cigar fermentation: an analysis based on microbial communities and physicochemical components
Youbo Su, Yonghe Cui, Kejian Fu, Lingduo Bu, Yucui Sun, Qi Zhou, Yuming Yin, Yulong Sun, Huating Yang, Lang Wu, Xueru Song
Frontiers in Microbiology.2024;[Epub] CrossRef - Rumen fermentation of meal-fed sheep in response to diets formulated to vary in fiber and protein degradability
Sathya Sujani, Claire B Gleason, Barbara R dos Reis, Robin R White
Journal of Animal Science.2024;[Epub] CrossRef - Effects of supplementation of nonforage fiber source in diets with different starch levels on growth performance, rumen fermentation, nutrient digestion, and microbial flora of Hu lambs
Tongqing Guo, Zhi Lan Wang, Long Guo, Fadi Li, Fei Li
Translational Animal Science.2021;[Epub] CrossRef - Weaning Age and Its Effect on the Development of the Swine Gut Microbiome and Resistome
Devin B. Holman, Katherine E. Gzyl, Kathy T. Mou, Heather K. Allen, Paul D. Cotter
mSystems.2021;[Epub] CrossRef - Comparison of the composition and function of the gut microbiome in herdsmen from two pasture regions, Hongyuan and Xilingol
Chengcong Yang, Chuantao Peng, Hao Jin, Lijun You, Jiao Wang, Haiyan Xu, Zhihong Sun
Food Science & Nutrition.2021; 9(6): 3258. CrossRef - Prevotella in Pigs: The Positive and Negative Associations with Production and Health
Samat Amat, Hannah Lantz, Peris M. Munyaka, Benjamin P. Willing
Microorganisms.2020; 8(10): 1584. CrossRef - Cellulase and Alkaline Treatment Improve Intestinal Microbial Degradation of Recalcitrant Fibers of Rapeseed Meal in Pigs
Cheng Long, Christiane Rösch, Sonja de Vries, Henk Schols, Koen Venema
Journal of Agricultural and Food Chemistry.2020; 68(39): 11011. CrossRef - Dietary Lipids Influence Bioaccessibility of Polyphenols from Black Carrots and Affect Microbial Diversity under Simulated Gastrointestinal Digestion
Chunhe Gu, Hafiz A. R. Suleria, Frank R. Dunshea, Kate Howell
Antioxidants.2020; 9(8): 762. CrossRef - Effect of chemical oxygen demand load on the nitrification and microbial communities in activated sludge from an aerobic nitrifying reactor
Dan Li, Xihong Liang, Zhengwei Li, Yao Jin, Rongqing Zhou, Chongde Wu
Canadian Journal of Microbiology.2020; 66(1): 59. CrossRef - Changes of Microbial Diversity During Swine Manure Treatment Process
Minseok Kim, Jung-Im Yun, Seung-Gun Won, Kyu-Hyun Park
Polish Journal of Microbiology.2018; 67(1): 109. CrossRef - The response of soil bacterial communities to mining subsidence in the west China aeolian sand area
Peili Shi, Yuxiu Zhang, Zhenqi Hu, Kang Ma, Hao Wang, Tuanyao Chai
Applied Soil Ecology.2017; 121: 1. CrossRef - How to Feed the Mammalian Gut Microbiota: Bacterial and Metabolic Modulation by Dietary Fibers
Chiara Ferrario, Rosario Statello, Luca Carnevali, Leonardo Mancabelli, Christian Milani, Marta Mangifesta, Sabrina Duranti, Gabriele A. Lugli, Beatriz Jimenez, Samantha Lodge, Alice Viappiani, Giulia Alessandri, Margerita Dall’Asta, Daniele Del Rio, Andr
Frontiers in Microbiology.2017;[Epub] CrossRef
- Colonic Microbiota Improves Fiber Digestion Ability and Enhances Absorption of Short-Chain Fatty Acids in Local Pigs of Hainan
Research Support, Non-U.S. Gov't
- Phenotypic Characterization and Genomic Analysis of the Shigella sonnei Bacteriophage SP18
- Kyoung-Ho Kim , Ho-Won Chang , Young-Do Nam , Seong Woon Roh , Jin-Woo Bae
- J. Microbiol. 2010;48(2):213-222. Published online May 1, 2010
- DOI: https://doi.org/10.1007/s12275-010-0055-4
- 21 View
- 0 Download
- 12 Scopus
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Abstract
- A novel bacteriophage that infects Shigella sonnei was isolated from the Gap River in Korea, and its phenotypic and genomic characteristics were investigated. The virus, called SP18, showed morphology characteristic of the family Myoviridae, and phylogenetic analysis of major capsid gene (gp23) sequences classified it as a T4-like phage. Based on host spectrum analysis, it is lytic to S. sonnei, but not to Shigella flexneri, Shigella boydii or members of the genera Escherichia and Salmonella. Pyrosequencing of the SP18 bacteriophage genome revealed a 170-kb length sequence. In total, 286 ORFs and 3 tRNA genes were identified, and 259 ORFs showed similarity (BLASTP e-value<0.001) to genes of other bacteriophages. The results from comparative genomic analysis indicated that the enterophage JS98, isolated from human stool, is the closest relative of SP18. Based on phylogenetic analysis of gp23 protein-coding sequences, dot plot comparison and BLASTP analysis of genomes, SP18 and JS98 appear to be closely related to T4-even phages. However, several insertions, deletions, and duplications indicate differences between SP18 and JS98. Comparison of duplicated gp24 genes and the soc gene showed that duplication events are responsible for the differentiation and evolution of T4-like bacteriophages.
Published Erratum
- Erratum to: Physiological roles of catalases Cat1 and Cat2 in Myxococcus xanthus
- Yoshio Kimura , Yuri Yoshioka , Kie Toshikuni
- J. Microbiol. 2023;61(2):271-271.
- DOI: https://doi.org/10.1007/s12275-023-00025-9
- 24 View
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- 1 Web of Science
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