Article
Agriculture, Dairy & Animal Science
Hae-In Jung, Sungkwon Park, Kai-Min Niu, Sang-Won Lee, Damini Kothari, Kwon Jung Yi, Soo-Ki Kim
Summary: SK3146, a novel strain isolated from pig feed, possesses an immense probiotic potential with a diverse range of hydrolases and bacteriocin encoding gene in its genome sequence.
JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY
(2021)
Article
Environmental Sciences
Mengyuan Qi, Xiaodan Ma, Bin Liang, Liying Zhang, Deyong Kong, Zhiling Li, Aijie Wang
Summary: The study focused on two important degraders of sulfonamide antibiotics, investigating their complete genomes and verifying complete degradation and bacterial growth. Results showed that one of the strains, P27, not only degraded sulfonamide antibiotics but also transformed them into nitrogen-containing heterocyclic products, indicating a broad substrate spectrum and significant bioremediation potential.
ENVIRONMENTAL RESEARCH
(2022)
Article
Environmental Sciences
Duantao Cao, Shuhong He, Xin Li, Lihong Shi, Feiyan Wang, Sumei Yu, Shiji Xu, Chao Ju, Hua Fang, Yunlong Yu
Summary: The bacterial strain Arthrobacter sp. C2 was isolated for atrazine degradation, showing degradation rates of 0.34, 1.94, and 18.64 mg/L/d at different concentrations. The optimal conditions for degradation were at 30°C and pH 7.0-9.0, and a metabolic pathway for atrazine degradation was proposed. The introduction of strain C2 into soil can enhance atrazine degradation and eliminate its toxic effects on wheat growth.
Article
Virology
Weizhong Chang, Xiaoli Jiao, Hongyan Sui, Suranjana Goswami, Brad T. Sherman, Caroline Fromont, Juan Manuel Caravaca, Bao Tran, Tomozumi Imamichi
Summary: This study assembled and annotated the complete genome of HSV-2 strain G using PacBio long sequencing reads. It analyzed the 'alpha' sequence and identified packaging signals homologous to HSV-1, as well as determined the termini and cleavage site of the linear genome. The study also visualized four HSV-2 genome isomers using Oxford Nanopore Technology sequencing reads. Additionally, the coding sequences of strain G were compared with other HSV-2 strains and a phylogenetic analysis was conducted.
Article
Virology
Konstantina Katsarou, Christos Andronis, Anthony James, Kostas Euthymiou, Nikoleta Kryovrysanaki, Polykseni G. Pappi, Kriton Kalantidis
Summary: Using high-throughput sequencing, a new carlavirus sequence was identified in a 28-year-old 'Kotsifali' grapevine sample collected in Heraklion, Greece. The complete genome sequence of 8299 nt was confirmed using RT-PCR and 5'/3' RACE with Sanger sequencing, revealing five open reading frames (ORFs) but lacking ORF6 which is present in some Carlavirus members. Based on its similarity to carlaviruses infecting caper, it is proposed to name this new virus as Grapevine Carlavirus 1 according to the ICTV nomenclature.
ARCHIVES OF VIROLOGY
(2023)
Article
Agricultural Engineering
Abhishek Singh, Anand Kumar Pandey, Suresh Kumar Dubey
Summary: The study showed that Arthrobacter sp. BHU FT2 strain has a high potential for efficient degradation of isoprene, which could be utilized in large-scale bio-filtration units for isoprene degradation.
BIORESOURCE TECHNOLOGY
(2021)
Article
Chemistry, Physical
Gillian Li Yin Lee, Nur Nadhirah Zakaria, Hiroyuki Futamata, Kenshi Suzuki, Azham Zulkharnain, Noor Azmi Shaharuddin, Peter Convey, Khadijah Nabilah Mohd Zahri, Siti Aqlima Ahmad
Summary: This study revealed that the indigenous Antarctic bacteria Arthrobacter sp. strains AQ5-05 and AQ5-06 degrade phenol through the ortho-cleavage pathway, with an optimum degradation temperature of 10 to 15 degrees Celsius. The research suggests the potential use of cold-adapted bacteria in the bioremediation of phenol pollution in cold environments.
Article
Biotechnology & Applied Microbiology
Zhipeng Li, Zeping Du, Hebin Li, Yanhong Chen, Mingjing Zheng, Zedong Jiang, Xiping Du, Hui Ni, Yanbing Zhu
Summary: Marine bacterium Microbulbifer sp. ALW1 can effectively degrade Laminaria japonica thallus fragments and produce various enzymes. ALW1 has unique cell morphology, physiological, and biochemical characteristics compared to other related species. The complete genome of ALW1 has been sequenced and can be utilized in potential industrial applications.
Article
Immunology
Hongyan Liu, Zhengyi Fu, Shengjie Zhou, Jing Hu, Rui Yang, Gang Yu, Zhenhua Ma
Summary: In this study, the parasite from yellowfin tuna was examined and identified as a species similar to Pennella sp. Morphological observations and molecular analysis confirmed the similarity, and the mitochondrial genome of the parasite was characterized. This study provided important information for the identification and further research of Pennella genus parasites.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Cheng Jiang, Haohao Yan, Xiaohui Shen, Yuting Zhang, Yue Wang, Shanshan Sun, Hanyi Jiang, Hailian Zang, Xinyue Zhao, Ning Hou, Ziwei Li, Liwen Wang, Hanjun Wang, Chunyan Li
Summary: In this study, the whole genome of a psychrotrophic lignin-degrading bacterium was sequenced, revealing unique genes related to lignin degradation and low-temperature adaptability. The DyP enzyme was found to participate in the first-step reaction of lignin degradation and the bacterium showed genetic compensation mechanism to degrade lignin in the absence of the DyP gene. This research improves our understanding of the metabolic mechanism of psychrotrophic lignin-degrading bacteria and provides potential applications for energy-saving production using cold-adapted lignin-degrading enzymes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Zhengying Cao, Linyi Yang, Yaxuan Xin, Wenbin Xu, Qishao Li, Haorong Zhang, Yuxiang Tu, Yu Song, Peiyao Xin
Summary: This study conducted comparative genomic and phylogenetic analyses on seven Neocinnamomum taxa, revealing the genetic structure and evolutionary characteristics of these species. The chloroplast genome of Neocinnamomum has a size range of 150,753-150,956 bp and contains 128 annotated genes. The study identified 31 preferred codons and three highly variable regions. The results of this study will serve as a reference for molecular marker development and phylogenetic research in Neocinnamomum.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Sadia Mehmood Satti, Edgar Castro-Aguirre, Aamer Ali Shah, Terence L. Marsh, Rafael Auras
Summary: The genomes of Pseudomonas aeruginosa S3, Sphingobacterium S2, and Geobacillus EC-3, isolated from compost, were annotated to understand their ability to degrade poly(lactic acid) (PLA). The draft genomes revealed catabolic genes for biodegradation of xenobiotics, aromatic compounds, and lactic acid, as well as genes related to biofilm formation and regulation. These isolates possess essential genetic elements for PLA metabolism at both mesophilic and thermophilic temperatures.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Agricultural Engineering
Jia Cao, Weijun Wang, Zixi Zhao, Xiaolu Liu, Qing X. Li
Summary: The study showed a direct association between rhamnolipids biosynthesis and DBT biodegradation induced by different carbon sources in a Paraburkholderia specie. Glycerol can induce the strain C3 to produce at least four rhamnolipids, suggesting a viable approach of using the biodiesel byproduct to remediate contaminated environments.
BIORESOURCE TECHNOLOGY
(2021)
Article
Microbiology
Masahiro Ito, Tetsu Shimizu, Akira Nakamura
Summary: Kaistia sp. strain 32K is an aerobic Gram-negative bacterium isolated from soil in Japan. The complete genome sequence of this bacterium is 5.4 Mbp in size and contains 4,919 protein-coding sequences.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Shan Shan Qi, Margo Cnockaert, Aurelien Carlier, Peter Vandamme
Summary: Three novel Pedobacter species were isolated from the phyllosphere of Arabidopsis thaliana seedlings, named as Pedobacter gandavensis, Pedobacter foliorum, and Pedobacter planticolens. Genomic and phenotypic analyses confirmed the distinct characteristics of each strain, supporting their classification as new species within the Pedobacter genus.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Infectious Diseases
Theresa J. Smith, Karen K. Hill, Gary Xie, Brian T. Foley, Charles H. D. Williamson, Jeffrey T. Foster, Shannon L. Johnson, Olga Chertkov, Hazuki Teshima, Henry S. Gibbons, Lauren A. Johnsky, Mark A. Karavis, Leonard A. Smith
INFECTION GENETICS AND EVOLUTION
(2015)
Article
Pharmacology & Pharmacy
K. K. Hill, G. Xie, B. T. Foley, T. J. Smith
Article
Biotechnology & Applied Microbiology
Charles H. D. Williamson, Jason W. Sahl, Theresa J. Smith, Gary Xie, Brian T. Foley, Leonard A. Smith, Rafael A. Fernandez, Miia Lindstrom, Hannu Korkeala, Paul Keim, Jeffrey Foster, Karen Hill
Article
Evolutionary Biology
Maria Soledad Ramirez, Gang Xie, German M. Traglia, Shannon L. Johnson, Karen W. Davenport, David van Duin, Azam Ramazani, Federico Perez, Michael R. Jacobs, David J. Sherratt, Robert A. Bonomo, Patrick S. G. Chain, Marcelo E. Tolmasky
GENOME BIOLOGY AND EVOLUTION
(2016)
Article
Medicine, Research & Experimental
Cliff Shunsheng Han
MEDICAL HYPOTHESES
(2016)
Article
Genetics & Heredity
Ulrike Kappler, Karen Davenport, Scott Beatson, Alla Lapidus, Chongle Pan, Cliff Han, Maria del Carmen Montero-Calasanz, Miriam Land, Loren Hauser, Manfred Rohde, Markus Goeker, Natalia Ivanova, Tanja Woyke, Hans-Peter Klenk, Nikos C. Kyrpides
STANDARDS IN GENOMIC SCIENCES
(2016)
Article
Multidisciplinary Sciences
Cliff S. Han, Melanie Ann Martin, Armand E. K. Dichosa, Ashlynn R. Daughton, Seth Frietze, Hillard Kaplan, Michael D. Gurven, Joe Alcock
Article
Infectious Diseases
Jessica Z. Kubicek-Sutherland, Gary Xie, Migun Shakya, Priya K. Dighe, Lindsey L. Jacobs, Hajnalka Daligault, Karen Davenport, Loreen R. Stromberg, Zachary R. Stromberg, Qiuying Cheng, Prakasha Kempaiah, John Michael Ong'echa, Vincent Otieno, Evans Raballah, Samuel Anyona, Collins Ouma, Patrick S. G. Chain, Douglas J. Perkins, Harshini Mukundan, Benjamin H. McMahon, Norman A. Doggett
Summary: Non-typhoidal Salmonella (NTS) is a major global health concern, particularly in areas affected by malnutrition and comorbidities like HIV and malaria. This study identified a unique NTS isolate named UGA14 that displayed novel plasmid, pseudogene and resistance features, as well as the ability to ferment both lactose and sucrose, highlighting the co-evolution of plasmid-mediated metabolic traits and cephalosporin resistance in NTS strains. The findings emphasize the importance of combined genomic and phenotypic approaches in detecting and characterizing atypical NTS isolates to inform efforts in controlling invasive and antimicrobial resistant NTS.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Biology
Gary Xie, Jeanne M. Fair
Summary: This study introduced a Shortest Unique Representative Hidden Markov Model (HMM) approach for identifying bacterial toxin, virulence factor (VF), and antimicrobial resistance (AR) in short sequence reads. Unique representative domain sequences of toxin genes, VFs, and ARs were constructed to avoid potential false positives, and HMM models were used for accurate identification. The approach showed relatively high specificity and sensitivity when the appropriate cutoff value was applied, allowing for recognition of protein sequences of known toxins and pathogens.
BMC RESEARCH NOTES
(2021)
Article
Microbiology
Hannah L. Woo, Kristen M. DeAngelis, Hazuki Teshima, Karen Davenport, Hajnalka Daligault, Tracy Erkkila, Lynne Goodwin, Wei Gu, Chien-Chi Lo, Christine Munk, Matthew Scholz, Yan Xu, Patrick Chain, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Blake A. Simmons, Terry C. Hazen
GENOME ANNOUNCEMENTS
(2017)
Article
Microbiology
Gary Xie, Ryan P. Chastain-Gross, Myriam Belanger, Dibyendu Kumar, Joan A. Whitlock, Li Liu, William G. Farmerie, Collin L. Zeng, Hajnalka E. Daligault, Cliff S. Han, Thomas S. Brettin, Ann Progulske-Fox
GENOME ANNOUNCEMENTS
(2017)
Article
Microbiology
Ryan P. Chastain-Gross, Gary Xie, Myriam Belanger, Dibyendu Kumar, Joan A. Whitlock, Li Liu, Sarah M. Raines, William G. Farmerie, Hajnalka E. Daligault, Cliff S. Han, Thomas S. Brettin, Ann Progulske-Fox
GENOME ANNOUNCEMENTS
(2017)
Article
Microbiology
Gary Xie, Ryan P. Chastain-Gross, Myriam Belanger, Dibyendu Kumar, Joan A. Whitlock, Li Liu, William G. Farmerie, Hajnalka E. Daligault, Cliff S. Han, Thomas S. Brettin, Ann Progulske-Fox
GENOME ANNOUNCEMENTS
(2015)
Article
Microbiology
Ryan P. Chastain-Gross, Gary Xie, Myriam Belanger, Dibyendu Kumar, Joan A. Whitlock, Li Liu, William G. Farmerie, Hajnalka E. Daligault, Cliff S. Han, Thomas S. Brettin, Ann Progulske-Fox
GENOME ANNOUNCEMENTS
(2015)
Article
Microbiology
Hong Lin, Gerhard Pietersen, Cliff Han, David Alan Read, Binghai Lou, Goutam Gupta, Edwin L. Civerolo
GENOME ANNOUNCEMENTS
(2015)
