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Bacterial genomics

Jiawei Wang, Bingjiao Yang, André Leier, Tatiana T Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Zhang Yanju, Tatsuya Akutsu, Kuo-Chen Chou, Richard A Strugnell, Jiangning Song, Trevor Lithgow
Motivation: Many Gram-negative bacteria use type VI secretion systems (T6SS) to export effector proteins into adjacent target cells. These secreted effectors (T6SEs) play vital roles in the competitive survival in bacterial populations, as well as pathogenesis of bacteria. Although various computational analyses have been previously applied to identify effectors secreted by certain bacterial species, there is no universal method available to accurately predict T6SS effector proteins from the growing tide of bacterial genome sequence data...
March 14, 2018: Bioinformatics
Rosa Margesin, De-Chao Zhang, Luciana Albuquerque, Hugo J C Froufe, Conceição Egas, Milton S da Costa
A Gram-stain-negative, rod-shaped, motile, catalase-positive and cytochrome c oxidase-positive bacterial strain, designated AM20-91T , was isolated from alpine forest soil. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain AM20-91T was related to the genus Lysobacter and had highest 16S rRNA gene sequence similarities to the type strains of Lysobacter novalis THG-PC7T (97.8 %), Luteimonas tolerans UM1T (97.7 %) and Lysobacter ximonensis XM415T (97.0 %). The strain contained ubiquinone 8 as the predominant respiratory quinone; its polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminophospholipids...
March 16, 2018: International Journal of Systematic and Evolutionary Microbiology
Angela Contreras, Magdalena Ribbeck, Guillermo D Gutiérrez, Pablo M Cañon, Sebastián N Mendoza, Eduardo Agosin
The effect of ethanol on the metabolism of Oenococcus oeni , the bacterium responsible for the malolactic fermentation (MLF) of wine, is still scarcely understood. Here, we characterized the global metabolic response in O. oeni PSU-1 to increasing ethanol contents, ranging from 0 to 12% (v/v). We first optimized a wine-like, defined culture medium, MaxOeno, to allow sufficient bacterial growth to be able to quantitate different metabolites in batch cultures of O. oeni . Then, taking advantage of the recently reconstructed genome-scale metabolic model iSM454 for O...
2018: Frontiers in Microbiology
Satoshi Kawato, Reiko Nozaki, Hidehiro Kondo, Ikuo Hirono
Vibrio penaeicida is a bacterial pathogen of cultured shrimp. The draft genome sequence of V. penaeicida strain TUMSAT-NU1 consists of 100 scaffolds with a total of 6.41 Mbp. We identified possible virulence factors, and we found that V. penaeicida and Vibrio nigripulchritudo are closely related.
March 15, 2018: Genome Announcements
Konstantinos C Tsolis, Evridiki-Pandora Tsare, Georgia Orfanoudaki, Tobias Busche, Katerina Kanaki, Reshmi Ramakrishnan, Frederic Rousseau, Joost Schymkowitz, Christian Rückert, Jörn Kalinowski, Jozef Anné, Spyridoula Karamanou, Maria I Klapa, Anastassios Economou
BACKGROUND: Members of the genus Streptomyces are Gram-positive bacteria that are used as important cell factories to produce secondary metabolites and secrete heterologous proteins. They possess some of the largest bacterial genomes and thus proteomes. Understanding their complex proteomes and metabolic regulation will improve any genetic engineering approach. RESULTS: Here, we performed a comprehensive annotation of the subcellular localization of the proteome of Streptomyces lividans TK24 and developed the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb) to make this information widely accessible...
March 15, 2018: Microbial Cell Factories
Urmi Bajpai, Abhishek Kumar Mehta, Kandasamy Eniyan, Avni Sinha, Ankita Ray, Simran Virdi, Shazeb Ahmad, Aridni Shah, Deepanksha Arora, Devyani Marwaha, Gunjan Chauhan, Prarthna Saraswat, Punita Bathla, Ruchi Singh
Bacteriophages are being considered as a promising natural resource for the development of alternative strategies against mycobacterial diseases, especially in the context of the wide spread occurrence of drug-resistance amongst the clinical isolates of M. tuberculosis. However, there isn't much information documented on mycobacteriophages from India. Here, we report the isolation of 17 mycobacteriophages using M. smegmatis as the bacterial host where 9 phages also lyse M. tuberculosis H37Rv. We present detailed analysis of one of these mycobacteriophage (PDRPv)...
March 15, 2018: Canadian Journal of Microbiology
Suhyung Cho, Donghui Choe, Eunju Lee, Sun Chang Kim, Bernhard Ø Palsson, Byung-Kwan Cho
Along with functional advances in the use of CRISPR/Cas9 for genome editing, endonuclease-deficient Cas9 (dCas9) has provided a versatile molecular tool for exploring gene functions. In principle, differences in cell phenotypes that result from the RNA-guided modulation of transcription levels by dCas9 are critical for inferring with gene function; however, the effect of intracellular dCas9 expression on bacterial morphology has not been systematically elucidated. Here, we observed unexpected morphological changes in Escherichia coli mediated by dCas9, which were then characterized using RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq)...
March 15, 2018: ACS Synthetic Biology
Tomoko Kubori, Tomoe Kitao, Hiroki Ando, Hiroki Nagai
The intracellular bacterial pathogen Legionella pneumophila establishes the replicative niche as a result of the actions of a large array of effector proteins delivered via the Legionella type IV secretion system (T4SS). Many effector proteins are expected to be involved in biogenesis and regulation of the Legionella-containing vacuole (LCV) that is highly decorated with ubiquitin. Here, we identified a Legionella deubiquitinase (DUB), designated LotA, by carrying out a genome analysis to find proteins resembling the eukaryotic ovarian tumor (OTU) superfamily of cysteine proteases...
March 15, 2018: Cellular Microbiology
Mickael Silva, Miguel P Machado, Diogo N Silva, Mirko Rossi, Jacob Moran-Gilad, Sergio Santos, Mario Ramirez, João André Carriço
Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers...
March 15, 2018: Microbial Genomics
Sujuan Yuan, Tiankui Qiao, Xuan Li, Xibing Zhuang, Wei Chen, Xue Chen, Qi Zhang
Unmethylated cytosine-phosphorothioate-guanine (CpG)-containing oligodeoxynucleotides (ODNs) are synthetic DNA sequences that mimic bacterial DNA, and are known to serve as ligands for Toll-like receptor 9 (TLR9). The interaction between a CpG ODNs with TLR9 activates the complex downstream cascade that contributes to exerting its function. In the present study, the results of clonogenic assays demonstrated that the activation of TLR9 by CpG ODNs significantly increased the radiosensitivity of A549 lung cancer cells, with a sensitivity enhancement ratio (SER) of 1...
April 2018: Oncology Letters
Dilruba Sharmin, Yong Guo, Tomoyasu Nishizawa, Shoko Ohshima, Yoshinori Sato, Yusuke Takashima, Kazuhiko Narisawa, Hiroyuki Ohta
Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the growth and metabolic potential of their hosts. To date, two EHB belonging to the family Burkholderiaceae have been isolated and characterized as new taxa, Burkholderia rhizoxinica (HKI 454T ) and Mycoavidus cysteinexigens (B1-EBT ), in Japan. Metagenome sequencing was recently reported for Mortierella elongata AG77 together with its endosymbiont M. cysteinexigens (Mc-AG77) from a soil/litter sample in the USA. In the present study, we elucidated the complete genome sequence of B1-EBT and compared it with those of Mc-AG77 and HKI 454T ...
March 14, 2018: Microbes and Environments
Hwa Young Kim, Sang-Mi Yu, Sang Chul Jeong, Sang Sun Yoon, Young Taek Oh
The stringent response (SR), which is activated by accumulation of (p)ppGpp under conditions of growth-inhibiting stresses, plays an important role ongrowth and virulence in Vibrio cholerae . Herein, we carried out a genome-wide screen using transposon random mutagenesis to identify genes controlled by SR in (p)ppGpp-overproducing mutant strain. One of the identified SR target genes was the flaC encoding flagellin. Genetic studies using flaC and SR mutants demonstrated that FlaC involved in bacterial growth, toxin production, and normal flagellum function under conditions of high (p)ppGpp levels, suggesting FlaC plays an important role in SR-induced pathogenicityin V...
March 15, 2018: Journal of Microbiology and Biotechnology
Linkun Wu, Jun Chen, Zhigang Xiao, Xiaocheng Zhu, Juanying Wang, Hongmiao Wu, Yanhong Wu, Zhongyi Zhang, Wenxiong Lin
The production and quality of Rehmannia glutinosa can be dramatically reduced by replant disease under consecutive monoculture. The root-associated microbiome, also known as the second genome of the plant, was investigated to understand its impact on plant health. Culture-dependent and culture-independent pyrosequencing analysis was applied to assess the shifts in soil bacterial communities in the rhizosphere and rhizoplane under consecutive monoculture. The results show that the root-associated microbiome (including rhizosphere and rhizoplane microbiomes) was significantly impacted by rhizocompartments and consecutive monoculture...
March 14, 2018: International Journal of Molecular Sciences
Satyendra Kumar Singh, Ajit Kumar, Gopal Nath, Tej Bali Singh, Mukti Nath Mishra
BACKGROUND: WHO MDT is the main drug regimen for treating leprosy and has been used for more than three decades. Many cases of relapse of leprosy have been reported, which points towards the emergence of drug resistance with the antileprotic drugs. OBJECTIVES: To find the resistance with the antileprotic drugs by detecting the mutations in drug resistance determining region of the rpoB, folP1 and gyrA genes of Mycobacterium leprae. METHODS: Leprosy patients with bacterial index ≥2 were included in the study...
March 14, 2018: Indian Journal of Dermatology, Venereology and Leprology
Inam Ullah Khan, Neeli Habib, Min Xiao, Xing Huang, Nasr Ullah Khan, Wan-Taek Im, Iftikhar Ahmed, Xiao-Yang Zhi, Wen-Jun Li
A Gram-stain negative, aerobic, motile, non-spore-forming and rod-shaped bacterial strain, designated YIM 730227T , was isolated from a soil sample, collected from Karak district, Khyber-Pakhtun-Khwa, Pakistan. The bacterium was characterized using a polyphasic taxonomic approach. Pairwise comparison of the 16S rRNA gene sequences showed that strain YIM 730227T is closely related to Phenylobacterium lituiforme FaiI3T (97.5% sequence similarity), Phenylobacterium muchangponense A8T (97.4%), Phenylobacterium panacis DCY109T (97...
March 14, 2018: Antonie Van Leeuwenhoek
Kris Niño G Valdehuesa, Kristine Rose M Ramos, Llewelyn S Moron, Imchang Lee, Grace M Nisola, Won-Keun Lee, Wook-Jin Chung
The continued research in the isolation of novel bacterial strains is inspired by the fact that native microorganisms possess certain desired phenotypes necessary for recombinant microorganisms in the biotech industry. Most studies have focused on the isolation and characterization of strains from marine ecosystems as they present a higher microbial diversity than other sources. In this study, a marine bacterium, W5C, was isolated from red seaweed collected from Yeosu, South Korea. The isolate can utilize several natural polysaccharides such as agar, alginate, carrageenan, and chitin...
March 13, 2018: Current Microbiology
Scot P Ouellette
Chlamydia is an obligate intracellular bacterium and, as such, has significantly reduced its genome size and content. Although recent advances have allowed for transformation of C. trachomatis with an exogenous plasmid, genetic manipulation of Chlamydia remains challenging. In particular, the ability to create conditional knockouts has not been developed. This is particularly important given the likelihood that most genes within the small genome of Chlamydia may be essential. Here, I describe the feasibility of using CRISPR interference (CRISPRi) based on the catalytically inactive Cas9 variant (dCas9) of Staphylococcus aureus to inducibly, and reversibly, repress gene expression in C...
2018: Frontiers in Cellular and Infection Microbiology
Guangrui Dong, Jiao Shen, Qing Zhang, Jianping Wang, Qingyi Yu, Ray Ming, Kai Wang, Jisen Zhang
Saccharum spontaneum is a major Saccharum species that contributed to the origin of modern sugarcane cultivars, and due to a high degree of polyploidy is considered to be a plant species with one of the most complex genetics. Fluorescence in situ hybridization (FISH) is a powerful and widely used tool in genome studies. Here, we demonstrated that FISH based on bacterial artificial chromosome (BAC) clones can be used as a specific cytological marker to identify S. spontaneum individual chromosomes and study the relationship between S...
2018: Frontiers in Plant Science
Xiang Zhang, Adil Mardinoglu, Leo A B Joosten, Jan A Kuivenhoven, Yang Li, Mihai G Netea, Albert K Groen
Immunity and cellular metabolism are tightly interconnected but it is not clear whether different pathogens elicit specific metabolic responses. To address this issue, we studied differential metabolic regulation in peripheral blood mononuclear cells (PBMCs) of healthy volunteers challenged by Candida albicans, Borrelia burgdorferi , lipopolysaccharide, and Mycobacterium tuberculosis in vitro . By integrating gene expression data of stimulated PBMCs of healthy individuals with the KEGG pathways, we identified both common and pathogen-specific regulated pathways depending on the time of incubation...
2018: Frontiers in Physiology
Karissa L Cross, Payal Chirania, Weili Xiong, Clifford J Beall, James G Elkins, Richard J Giannone, Ann L Griffen, Adam M Guss, Robert L Hettich, Snehal S Joshi, Elaine M Mokrzan, Roman K Martin, Igor B Zhulin, Eugene J Leys, Mircea Podar
The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously uncultured Desulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives, D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities...
March 13, 2018: MBio
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