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Bacterial genomics

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https://www.readbyqxmd.com/read/28231283/rapid-evolution-of-distinct-helicobacter-pylori-subpopulations-in-the-americas
#1
Kaisa Thorell, Koji Yahara, Elvire Berthenet, Daniel J Lawson, Jane Mikhail, Ikuko Kato, Alfonso Mendez, Cosmeri Rizzato, María Mercedes Bravo, Rumiko Suzuki, Yoshio Yamaoka, Javier Torres, Samuel K Sheppard, Daniel Falush
For the last 500 years, the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them. One such organism is the stomach-dwelling bacterium Helicobacter pylori, which is highly prevalent in Latin America where it is a major current public health challenge because of its strong association with gastric cancer. By analyzing the genome sequence of H. pylori isolated in North, Central and South America, we found evidence for admixture between H...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28230768/bioinformatic-analysis-reveals-archaeal-trna-tyr-and-trna-trp-identities-in-bacteria
#2
Takahito Mukai, Noah M Reynolds, Ana Crnković, Dieter Söll
The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNA(Tyr) and tRNA(Trp) genes reveal bacterial or archaeal origins...
February 21, 2017: Life
https://www.readbyqxmd.com/read/28230237/parasitism-drives-host-genome-evolution-insights-from-the-pasteuria-ramosa-daphnia-magna-system
#3
Yann Bourgeois, Anne C Roulin, Kristina Müller, Dieter Ebert
Because parasitism is thought to play a major role in shaping host genomes, it has been predicted that genomic regions associated with resistance to parasites should stand out in genome scans, revealing signals of selection above the genomic background. To test whether parasitism is indeed such a major factor in host evolution and to better understand host-parasite interaction at the molecular level, we studied genome-wide polymorphisms in 97 genotypes of the planktonic crustacean Daphnia magna originating from three localities across Europe...
February 23, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28229213/development-of-a-rapid-identification-method-for-the-differentiation-of-enterococcus-species-using-a-species-specific-multiplex-pcr-based-on-comparative-genomics
#4
Jongbin Park, Gwi-Deuk Jin, Jae In Pak, Jihyun Won, Eun Bae Kim
Enterococci are lactic acid bacteria that are commonly found in food and in animal gut. Since 16 S ribosomal RNA (rRNA) sequences, genetic markers for bacterial identification, are similar among several Enterococcus species, it is very difficult to determine the correct species based on only 16 S rRNA sequences. Therefore, we developed a rapid method for the identification of different Enterococcus species using comparative genomics. We compared 38 genomes of 13 Enterococcus species retrieved from the National Center of Biotechnology Information database and identified 25,623 orthologs...
February 22, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28225085/aidp-a-novel-n-acyl-homoserine-lactonase-gene-from-antarctic-planococcus-sp
#5
Wah Seng See-Too, Robson Ee, Yan-Lue Lim, Peter Convey, David A Pearce, Wai-Fong Yin, Kok-Gan Chan
Planococcus is a Gram-positive halotolerant bacterial genus in the phylum Firmicutes, commonly found in various habitats in Antarctica. Quorum quenching (QQ) is the disruption of bacterial cell-to-cell communication (known as quorum sensing), which has previously been described in mesophilic bacteria. This study demonstrated the QQ activity of a psychrotolerant strain, Planococcus versutus strain L10.15(T), isolated from a soil sample obtained near an elephant seal wallow in Antarctica. Whole genome analysis of this bacterial strain revealed the presence of an N-acyl homoserine lactonase, an enzyme that hydrolyzes the ester bond of the homoserine lactone of N-acyl homoserine lactone (AHLs)...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225058/superstatistical-model-of-bacterial-dna-architecture
#6
Mikhail I Bogachev, Oleg A Markelov, Airat R Kayumov, Armin Bunde
Understanding the physical principles that govern the complex DNA structural organization as well as its mechanical and thermodynamical properties is essential for the advancement in both life sciences and genetic engineering. Recently we have discovered that the complex DNA organization is explicitly reflected in the arrangement of nucleotides depicted by the universal power law tailed internucleotide interval distribution that is valid for complete genomes of various prokaryotic and eukaryotic organisms. Here we suggest a superstatistical model that represents a long DNA molecule by a series of consecutive ~150 bp DNA segments with the alternation of the local nucleotide composition between segments exhibiting long-range correlations...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224054/variant-profiling-of-evolving-prokaryotic-populations
#7
Markus Zojer, Lisa N Schuster, Frederik Schulz, Alexander Pfundner, Matthias Horn, Thomas Rattei
Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes...
2017: PeerJ
https://www.readbyqxmd.com/read/28224040/massilioclostridium-coli-gen-nov-sp-nov-a-new-member-of-the-clostridiaceae-family-isolated-from-the-left-colon-of-a-27-year-old-woman
#8
C I Lo, M Mailhe, D Ricaboni, V Vitton, A Benezech, C Michelle, N Armstrong, F Bittar, P-E Fournier, D Raoult, J-C Lagier
Massilioclostridium coli strain Marseille-P2976(T) (= CSUR P2976 = DSM 103344) is a new bacterial genus isolated from the left colon of a patient who underwent colonoscopy for colorectal cancer screening. Massilioclostridium coli is a Gram-negative bacillus, strict anaerobic, nonsporogenous and nonmotile organism. We describe here the strain Marseille-P2976(T) and provide its complete annotated genome sequence according to taxonogenomics concepts. Its genome is 2 985 330 bp long and contains 2562 predicted genes and 75 RNA genes...
March 2017: New Microbes and New Infections
https://www.readbyqxmd.com/read/28224039/description-of-gorbachella-massiliensis-gen-nov-sp-nov-fenollaria-timonensis-sp-nov-intestinimonas-timonensis-sp-nov-and-collinsella-ihuae-sp-nov-isolated-from-healthy-fresh-stools-with-culturomics
#9
G A Durand, F Cadoret, J C Lagier, P E Fournier, D Raoult
We report here the main characteristics of 'Gorbachella massiliensis' GD7(T) gen. nov., sp. nov., 'Fenollaria timonensis' GD5(T) sp. nov., 'Intestinimonas timonensis' GD4(T) sp. nov., and 'Collinsella ihuae' sp. nov. GD8(T) isolated from one fresh stool of a French volunteer. We used a bacterial culturomics approach combined with taxono-genomics.
March 2017: New Microbes and New Infections
https://www.readbyqxmd.com/read/28223967/secretome-prediction-of-two-m-tuberculosis-clinical-isolates-reveals-their-high-antigenic-density-and-potential-drug-targets
#10
Fernanda Cornejo-Granados, Zyanya L Zatarain-Barrón, Vito A Cantu-Robles, Alfredo Mendoza-Vargas, Camilo Molina-Romero, Filiberto Sánchez, Luis Del Pozo-Yauner, Rogelio Hernández-Pando, Adrián Ochoa-Leyva
The Excreted/Secreted (ES) proteins play important roles during Mycobacterium tuberculosis invasion, virulence, and survival inside the host and they are a major source of immunogenic proteins. However, the molecular complexity of the bacillus cell wall has made difficult the experimental isolation of the total bacterial ES proteins. Here, we reported the genomes of two Beijing genotype M. tuberculosis clinical isolates obtained from patients from Vietnam (isolate 46) and South Africa (isolate 48). We developed a bioinformatics pipeline to predict their secretomes and observed that ~12% of the genome-encoded proteins are ES, being PE, PE-PGRS, and PPE the most abundant protein domains...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28223936/two-pore-channels-catalyzers-of-endolysosomal-transport-and-function
#11
REVIEW
Christian Grimm, Cheng-Chang Chen, Christian Wahl-Schott, Martin Biel
Two-pore channels (TPCs) have recently emerged as a novel class of non-selective cation channels in the endolysosomal system. There are two members in the human genome, TPC1 and TPC2. Studies with TPC knockout and knockdown models have revealed that these channels participate in the regulation of multiple endolysosomal trafficking pathways which when dysregulated can lead to or influence the development of a range of different diseases such as lysosomal storage, metabolic, or infectious diseases. TPCs have been demonstrated to be activated by different endogenous stimuli, PI(3,5)P2 and NAADP, and ATP has been found to block TPC activation via mTOR...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28223462/fallacy-of-the-unique-genome-sequence-diversity-within-single-helicobacter-pylori-strains
#12
Jenny L Draper, Lori M Hansen, David L Bernick, Samar Abedrabbo, Jason G Underwood, Nguyet Kong, Bihua C Huang, Allison M Weis, Bart C Weimer, Arnoud H M van Vliet, Nader Pourmand, Jay V Solnick, Kevin Karplus, Karen M Ottemann
Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223457/the-source-and-evolutionary-history-of-a-microbial-contaminant-identified-through-soil-metagenomic-analysis
#13
Matthew R Olm, Cristina N Butterfield, Alex Copeland, T Christian Boles, Brian C Thomas, Jillian F Banfield
In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223393/novel-bacterial-topoisomerase-inhibitors-with-potent-broad-spectrum-activity-against-drug-resistant-bacteria
#14
Cédric Charrier, Anne-Marie Salisbury, Victoria J Savage, Thomas Duffy, Emmanuel Moyo, Nathan Chaffer-Malam, Nicola Ooi, Rebecca Newman, Jonathan Cheung, Richard Metzger, David McGarry, Mark Pichowicz, Ralph Sigerson, Ian R Cooper, Gary Nelson, Hayley S Butler, Mark Craighead, Andrew J Ratcliffe, Stuart A Best, Neil R Stokes
The Novel Bacterial Topoisomerase Inhibitor class is an investigational type of antibacterial inhibitor of DNA gyrase and topoisomerase IV that do not have cross-resistance with the quinolones. Here, we report the evaluation of the in vitro properties of a new series of this type of small molecules. Exemplar compounds selectively and potently inhibited the catalytic activities of Escherichia coli DNA gyrase and topoisomerase IV but did not block the DNA breakage-reunion step. Compounds showed broad-spectrum inhibitory activity against a wide range of Gram-positive and Gram-negative pathogens, including biodefence microorganisms, and Mycobacterium tuberculosis No cross-resistance with quinolone-resistant Staphylococcus aureus and E...
February 21, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28223255/olegusella-massiliensis-gen-nov-sp-nov-strain-khd7-t-a-new-bacterial-genus-isolated-from-the-female-genital-tract-of-a-patient-with-bacterial-vaginosis
#15
Khoudia Diop, Awa Diop, Florence Bretelle, Frédéric Cadoret, Caroline Michelle, Magali Richez, Jean-François Cocallemen, Didier Raoult, Pierre-Edouard Fournier, Florence Fenollar
Strain KHD7(T), a Gram-stain-positive rod-shaped, non-sporulating, strictly anaerobic bacterium, was isolated from the vaginal swab of a woman with bacterial vaginosis. We studied its phenotypic characteristics and sequenced its complete genome. The major fatty acids were C16:0 (44%), C18:2n6 (22%), and C18:1n9 (14%). The 1,806,744 bp long genome exhibited 49.24% G+C content; 1549 protein-coding and 51 RNA genes. Strain KHD7(T) exhibited a 93.5% 16S rRNA similarity with Olsenella uli, the phylogenetically closest species in the family Coriobacteriaceae...
February 18, 2017: Anaerobe
https://www.readbyqxmd.com/read/28223183/four-distinct-types-of-e-c-1-2-1-30-enzymes-can-catalyze-the-reduction-of-carboxylic-acids-to-aldehydes
#16
Holly Stolterfoht, Daniel Schwendenwein, Christoph W Sensen, Florian Rudroff, Margit Winkler
Increasing demand for chemicals from renewable resources calls for the development of new biotechnological methods for the reduction of oxidized bio-based compounds. Enzymatic carboxylate reduction is highly selective, both in terms of chemo- and product selectivity, but not many carboxylate reductase enzymes (CARs) have been identified on the sequence level to date. Thus far, their phylogeny is unexplored and very little is known about their structure-function-relationship. CARs minimally contain an adenylation domain, a phosphopantetheinylation domain and a reductase domain...
February 18, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28223006/complete-genome-sequence-of-the-drought-resistance-promoting-endophyte-klebsiella-sp-ltgpaf-6f
#17
Lei Zhang, Jun Zhong, Hao Liu, Kaiyun Xin, Chaoqiong Chen, Qiqi Li, Yahong Wei, Yao Wang, Fei Chen, Xihui Shen
Bacterial endophytes with capacity to promote plant growth and improve plant tolerance against biotic and abiotic stresses have importance in agricultural practice and phytoremediation. A plant growth-promoting endophyte named Klebsiella sp. LTGPAF-6F, which was isolated from the roots of the desert plant Alhagi sparsifolia in north-west China, exhibits the ability to enhance the growth of wheat under drought stress. The complete genome sequence of this strain consists of one circular chromosome and two circular plasmids...
February 13, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28222763/the-discovery-of-novel-lpmo-families-with-a-new-hidden-markov-model
#18
Gerben P Voshol, Erik Vijgenboom, Peter J Punt
BACKGROUND: Renewable biopolymers, such as cellulose, starch and chitin are highly resistance to enzymatic degradation. Therefore, there is a need to upgrade current degradation processes by including novel enzymes. Lytic polysaccharide mono-oxygenases (LPMOs) can disrupt recalcitrant biopolymers, thereby enhancing hydrolysis by conventional enzymes. However, novel LPMO families are difficult to identify using existing methods. Therefore, we developed a novel profile Hidden Markov model (HMM) and used it to mine genomes of ascomycetous fungi for novel LPMOs...
February 21, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28222723/rapid-precise-quantification-of-bacterial-cellular-dimensions-across-a-genomic-scale-knockout-library
#19
Tristan Ursell, Timothy K Lee, Daisuke Shiomi, Handuo Shi, Carolina Tropini, Russell D Monds, Alexandre Colavin, Gabriel Billings, Ilina Bhaya-Grossman, Michael Broxton, Bevan Emma Huang, Hironori Niki, Kerwyn Casey Huang
BACKGROUND: The determination and regulation of cell morphology are critical components of cell-cycle control, fitness, and development in both single-cell and multicellular organisms. Understanding how environmental factors, chemical perturbations, and genetic differences affect cell morphology requires precise, unbiased, and validated measurements of cell-shape features. RESULTS: Here we introduce two software packages, Morphometrics and BlurLab, that together enable automated, computationally efficient, unbiased identification of cells and morphological features...
February 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28222186/alpk1-controls-tifa-traf6-dependent-innate-immunity-against-heptose-1-7-bisphosphate-of-gram-negative-bacteria
#20
Milica Milivojevic, Anne-Sophie Dangeard, Christoph Alexander Kasper, Therese Tschon, Mario Emmenlauer, Claudine Pique, Pamela Schnupf, Julie Guignot, Cécile Arrieumerlou
During infection by invasive bacteria, epithelial cells contribute to innate immunity via the local secretion of inflammatory cytokines. These are directly produced by infected cells or by uninfected bystanders via connexin-dependent cell-cell communication. However, the cellular pathways underlying this process remain largely unknown. Here we perform a genome-wide RNA interference screen and identify TIFA and TRAF6 as central players of Shigella flexneri and Salmonella typhimurium-induced interleukin-8 expression...
February 21, 2017: PLoS Pathogens
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