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Bacterial genomics

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https://www.readbyqxmd.com/read/29356451/gene-encoding-the-ctp-synthetase-as-an-appropriate-molecular-tool-for-identification-and-phylogenetic-study-of-the-family-bifidobacteriaceae
#1
Jiří Killer, Chahrazed Mekadim, Radko Pechar, Věra Bunešová, Jakub Mrázek, Eva Vlková
An alternative molecular marker with respect to the 16S rRNA gene demonstrating better identification and phylogenetic parameters has not been designed for the whole Bifidobacteriaceae family, which includes the genus Bifidobacterium and scardovial genera. Therefore, the aim of the study was to find such a gene in available genomic sequences, suggest appropriate means and conditions for asmplification and sequencing of the desired region of the selected gene in various strains of the bacterial family and verify the importance in classification and phylogeny...
January 22, 2018: MicrobiologyOpen
https://www.readbyqxmd.com/read/29355427/stannous-fluoride-effects-on-gene-expression-of-streptococcus-mutans-and-actinomyces-viscosus
#2
Y Shi, R Li, D J White, A R Biesbrock
A genome-wide transcriptional analysis was performed to elucidate the bacterial cellular response of Streptococcus mutans and Actinomyces viscosus to NaF and SnF2. The minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) of SnF2 were predetermined before microarray study. Gene expression profiling microarray experiments were carried out in the absence (control) and presence (experimental) of 10 ppm and 100 ppm Sn2+ (in the form of SnF2) and fluoride controls for 10-min exposures (4 biological replicates/treatment)...
February 2018: Advances in Dental Research
https://www.readbyqxmd.com/read/29354650/the-logics-of-metabolic-regulation-in-bacteria-challenges-biosensor-based-metabolic-engineering
#3
COMMENT
Matthieu Jules
Synthetic Biology (SB) aims at the rational design and engineering of novel biological functions and systems. By facilitating the engineering of living organisms, SB promises to facilitate the development of many new applications for health, biomanufacturing, and the environment. Over the last decade, SB promoted the construction of libraries of components enabling the fine-tuning of genetic circuits expression and the development of novel genome engineering methodologies for many organisms of interest. SB thus opened new perspectives in the field of metabolic engineering, which was until then mainly limited to (over)producing naturally synthesized metabolic compounds...
December 11, 2017: Microbial Cell
https://www.readbyqxmd.com/read/29353387/inter-individual-variation-in-health-and-disease-associated-with-pulmonary-infectious-agents
#4
Kirsten C Verhein, Heather L Vellers, Steven R Kleeberger
Respiratory infectious diseases resulting from bacterial or viral pathogens such as Mycobacterium tuberculosis, Streptococcus pneumoniae, respiratory syncytial virus (RSV), or influenza, are major global public health concerns. Lower respiratory tract infections are leading causes of morbidity and mortality, only behind ischemic heart disease and stroke (GBD 2015 LRI Collaborators in Lancet Infect Dis 17(11):1133-1161, 2017). Developing countries are particularly impacted by these diseases. However, while many are infected with viruses such as RSV (> 90% of all individuals are infected by age 2), only sub-populations develop severe disease...
January 20, 2018: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29352323/identification-of-a-molecular-marker-tightly-linked-to-bacterial-wilt-resistance-in-tomato-by-genome-wide-snp-analysis
#5
Boyoung Kim, In Sun Hwang, Hyung Jin Lee, Je Min Lee, Eunyoung Seo, Doil Choi, Chang-Sik Oh
Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar 'Hawaii7996'. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29352198/orid-structure-controls-repd-initiation-during-rolling-circle-replication
#6
Algirdas Toleikis, Martin R Webb, Justin E Molloy
Bacterial antibiotic resistance is often carried by circular DNA plasmids that are copied separately from the genomic DNA and can be passed to other bacteria, spreading the resistance. The chloramphenicol-resistance plasmid pC221 from Staphylococcus aureus is duplicated by a process called asymmetric rolling circle replication. It is not fully understood how the replication process is regulated but its initiation requires a plasmid-encoded protein called RepD that nicks one strand of the parent plasmid at the double-stranded origin of replication (oriD)...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29351892/identification-and-functional-analysis-of-cassava-della-proteins-in-plant-disease-resistance-against-cassava-bacterial-blight
#7
Xiaolin Li, Wen Liu, Bing Li, Guoyin Liu, Yunxie Wei, Chaozu He, Haitao Shi
Gibberellin (GA) is an essential plant hormone in plant growth and development as well as various stress responses. DELLA proteins are important repressors of GA signal pathway. GA and DELLA have been extensively investigated in several model plants. However, the in vivo roles of GA and DELLA in cassava, one of the most important crops and energy crops in the tropical area, are unknown. In this study, systematic genome-wide analysis identified 4 MeDELLAs in cassava, as evidenced by the evolutionary tree, gene structures and motifs analyses...
December 26, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29351633/evolutionary-genetics-of-cytoplasmic-incompatibility-genes-cifa-and-cifb-in-prophage-wo-of-wolbachia
#8
Amelia R I Lindsey, Danny W Rice, Sarah R Bordenstein, Andrew W Brooks, Seth R Bordenstein, Irene L G Newton
The bacterial endosymbiont Wolbachia manipulates arthropod reproduction to facilitate its maternal spread through host populations. The most common manipulation is cytoplasmic incompatibility (CI): Wolbachia-infected males produce modified sperm that cause embryonic mortality, unless rescued by embryos harboring the same Wolbachia. The genes underlying CI, cifA and cifB, were recently identified in the eukaryotic association module of Wolbachia's prophage WO. Here, we use transcriptomic and genomic approaches to address three important evolutionary facets of the cif genes...
January 17, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29351563/a-consensus-linkage-map-of-lentil-based-on-dart-markers-from-three-ril-mapping-populations
#9
Duygu Ates, Secil Aldemir, Ahmad Alsaleh, Semih Erdogmus, Seda Nemli, Abdullah Kahriman, Hakan Ozkan, Albert Vandenberg, Bahattin Tanyolac
BACKGROUND: Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. MATERIALS AND METHODS: A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39)...
2018: PloS One
https://www.readbyqxmd.com/read/29351318/invasive-bacterial-disease-trends-and-characterization-of-group-b-streptococcal-isolates-among-young-infants-in-southern-mozambique-2001-2015
#10
Betuel Sigaúque, Miwako Kobayashi, Delfino Vubil, Ariel Nhacolo, Alberto Chaúque, Benild Moaine, Sérgio Massora, Inácio Mandomando, Tacilta Nhampossa, Quique Bassat, Fabiana Pimenta, Clara Menéndez, Maria da Gloria Carvalho, Eusebio Macete, Stephanie J Schrag
BACKGROUND: Maternal group B streptococcal (GBS) vaccines under development hold promise to prevent GBS disease in young infants. Sub-Saharan Africa has the highest estimated disease burden, although data on incidence and circulating strains are limited. We described invasive bacterial disease (IBD) trends among infants <90 days in rural Mozambique during 2001-2015, with a focus on GBS epidemiology and strain characteristics. METHODS: Community-level birth and mortality data were obtained from Manhiça's demographic surveillance system...
2018: PloS One
https://www.readbyqxmd.com/read/29350130/ecology-and-evolution-of-chromosomal-gene-transfer-between-environmental-microorganisms-and-pathogens
#11
José Luis Martínez
Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been acquired by horizontal gene transfer from other (usually unknown) microorganisms. Similarly, in the case of resistance to antibiotics, besides mutation-driven resistance, the incorporation of novel resistance genes is a widespread evolutionary procedure for the acquisition of this phenotype. Current information in the field supports the idea that most (if not all) genes acquired by horizontal gene transfer by bacterial pathogens and contributing to their virulence potential or to antibiotic resistance originate in environmental, not human-pathogenic, microorganisms...
January 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29350065/molecular-typing-of-lactobacillus-brevis-isolates-from-korean-food-using-repetitive-element-polymerase-chain-reaction
#12
Jasmine Kaur, Anshul Sharma, Sulhee Lee, Young-Seo Park
Lactobacillus brevis is a part of a large family of lactic acid bacteria that are present in cheese, sauerkraut, sourdough, silage, cow manure, feces, and the intestinal tract of humans and rats. It finds its use in food fermentation, and so is considered a "generally regarded as safe" organism. L. brevis strains are extensively used as probiotics and hence, there is a need for identifying and characterizing these strains. For identification and discrimination of the bacterial species at the subspecific level, repetitive element-polymerase chain reaction method is a reliable genomic fingerprinting tool...
January 1, 2018: Food Science and Technology International, Ciencia y Tecnología de Los Alimentos Internacional
https://www.readbyqxmd.com/read/29349599/evolution-of-eukaryal-and-archaeal-pseudouridine-synthase-pus10
#13
Elisabeth Fitzek, Archi Joardar, Ramesh Gupta, Matt Geisler
In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to m5U54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB. Although eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not clear for the two reasons...
January 18, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29348333/draft-genome-sequence-and-annotation-of-the-obligate-bacterial-endosymbiont-caedibacter-taeniospiralis-causative-agent-of-the-killer-phenotype-in-paramecium-tetraurelia
#14
Nestor Zaburannyi, Katrin Grosser, Gilles Gasparoni, Rolf Müller, Martina Schrallhammer, Martin Simon
Caedibacter taeniospiralis is an obligate endosymbiont living in the cytoplasm of Paramecium tetraureliaC. taeniospiralis causes the so-called killer trait, eliminating intraspecific competitors of its host when released into the medium by the concerted action of the unusual protein structure R-body (refractile body) in addition to an as-yet-unknown toxin.
January 18, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29348236/a-global-atlas-of-the-dominant-bacteria-found-in-soil
#15
Manuel Delgado-Baquerizo, Angela M Oliverio, Tess E Brewer, Alberto Benavent-González, David J Eldridge, Richard D Bardgett, Fernando T Maestre, Brajesh K Singh, Noah Fierer
The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six continents and found that only 2% of bacterial phylotypes (~500 phylotypes) consistently accounted for almost half of the soil bacterial communities worldwide. Despite the overwhelming diversity of bacterial communities, relatively few bacterial taxa are abundant in soils globally. We clustered these dominant taxa into ecological groups to build the first global atlas of soil bacterial taxa...
January 19, 2018: Science
https://www.readbyqxmd.com/read/29346641/uncovering-behavioural-diversity-amongst-high-strength-pseudomonas-spp-surfactants-at-the-limit-of-liquid-surface-tension-reduction
#16
Kamaluddeen Kabir, Yusuf Y Deeni, Simona M Hapca, Luke Moore, Andrew J Spiers
Bacterial bio-surfactants have a wide range of biological functions and biotechnological applications. Previous analyses had suggested a limit to their reduction of aqueous liquid surface tensions (γMin), and here we confirm this in an analysis of 25 Pseudomonas spp. strains isolated from soil which produce high-strength surfactants that reduce surface tensions to 25.2 ± 0.1-26.5 ± 0.2 mN.m-1 (the surface tension of sterile growth medium and pure water was 52.9 ± 0.4 mN.m-1 and 72.1 ± 1.2 mN.m-1, respectively)...
January 16, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#17
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346530/bacterioplankton-composition-in-tropical-high-elevation-lakes-of-the-andean-plateau
#18
Pablo Aguilar, Cristina Dorador, Irma Vila, Ruben Sommaruga
High-elevation lakes in the tropics are subject to extreme environmental fluctuations and microbes may harbour a unique genomic repertoire, but their composition and diversity are largely unknown. Here we compared the planktonic bacterial community composition (BCC) and diversity of three tropical lakes located in the high Andean plateau (???4400 m above sea level) during the dry and wet season. Diversity in these lakes was higher in the cool and wet season than in the warm and dry one. OTUs composition was significantly different among lakes and between seasons...
January 16, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29346449/within-host-selection-for-faster-replicating-bacterial-symbionts
#19
Ewa Chrostek, Luis Teixeira
Wolbachia is a widespread, intracellular symbiont of arthropods, able to induce reproductive distortions and antiviral protection in insects. Wolbachia can also be pathogenic, as is the case with wMelPop, a virulent variant of the endosymbiont of Drosophila melanogaster. An extensive genomic amplification of the 20kb region encompassing eight Wolbachia genes, called Octomom, is responsible for wMelPop virulence. The Octomom copy number in wMelPop can be highly variable between individual D. melanogaster flies, even when comparing siblings arising from a single female...
2018: PloS One
https://www.readbyqxmd.com/read/29346438/colonization-of-the-cervicovaginal-space-with-gardnerella-vaginalis-leads-to-local-inflammation-and-cervical-remodeling-in-pregnant-mice
#20
Luz-Jeannette Sierra, Amy G Brown, Guillermo O Barilá, Lauren Anton, Carrie E Barnum, Snehal S Shetye, Louis J Soslowsky, Michal A Elovitz
The role of the cervicovaginal (CV) microbiome in regulating cervical function during pregnancy is poorly understood. Gardnerella vaginalis (G. vaginalis) is the most common bacteria associated with the diagnosis of bacterial vaginosis (BV). While BV has been associated with preterm birth (PTB), clinical trials targeting BV do not decrease PTB rates. It remains unknown if G. vaginalis is capable of triggering molecular, biomechanical and cellular events that could lead to PTB. The objective of this study was to determine if cervicovaginal colonization with G...
2018: PloS One
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