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Alexandra M Howat, John Vollmers, Martin Taubert, Carolina Grob, Joanna L Dixon, Jonathan D Todd, Yin Chen, Anne-Kristin Kaster, J C Murrell
The Roseobacter group comprises a significant group of marine bacteria which are involved in global carbon and sulfur cycles. Some members are methylotrophs, using one-carbon compounds as a carbon and energy source. It has recently been shown that methylotrophs generally require a rare earth element when using the methanol dehydrogenase enzyme XoxF for growth on methanol. Addition of lanthanum to methanol enrichments of coastal seawater facilitated the isolation of a novel methylotroph in the Roseobacter group: Marinibacterium anthonyi strain La 6...
2018: Frontiers in Microbiology
Moreno Zolfo, Francesco Asnicar, Paolo Manghi, Edoardo Pasolli, Adrian Tett, Nicola Segata
BACKGROUND: The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context...
May 9, 2018: Biology Direct
Anne Kupczok, Horst Neve, Kun D Huang, Marc P Hoeppner, Knut J Heller, Charles M A P Franz, Tal Dagan
The evolution of asexual organisms is driven not only by the inheritance of genetic modification but also by the acquisition of foreign DNA. The contribution of vertical and horizontal processes to genome evolution depends on their rates per year and is quantified by the ratio of recombination to mutation. These rates have been estimated for bacteria; however, no estimates have been reported for phages. Here, we delineate the contribution of mutation and recombination to dsDNA phage genome evolution. We analyzed 34 isolates of the 936 group of Siphoviridae phages using a Lactococcus lactis strain from a single dairy over 29 years...
May 1, 2018: Molecular Biology and Evolution
Mustafa O Jibrin, Neha Potnis, Sujan Timilsina, Gerald V Minsavage, Gary E Vallad, Pamela D Roberts, Jeffrey B Jones, Erica M Goss
Recombination is a major driver of evolution in bacterial populations because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of plant bacterial pathogens are typically associated with colonization of novel hosts and emergence of new diseases. Here, we show that recombination between evolutionarily and phenotypically distinct plant pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. X. euvesicatoria ( Xe ) and X...
April 20, 2018: Applied and Environmental Microbiology
Valentin Loux, Gwendoline Coeuret, Monique Zagorec, Marie-Christine Champomier Vergès, Stéphane Chaillou
We present here the complete and draft genome sequences of nine Lactobacillus sakei strains, selected from the entire range of clonal complexes from the three known lineages of the species. The strains were chosen to provide a wide view of pangenomic and plasmidic diversity for this important foodborne species.
April 19, 2018: Genome Announcements
Vincent Baby, Jean-Christophe Lachance, Jules Gagnon, Jean-François Lucier, Dominick Matteau, Tom Knight, Sébastien Rodrigue
The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain...
May 2018: MSystems
Eric Bonnet, Marie-Laure Moutet, Céline Baulard, Delphine Bacq-Daian, Florian Sandron, Lilia Mesrob, Bertrand Fin, Marc Delépine, Marie-Ange Palomares, Claire Jubin, Hélène Blanché, Vincent Meyer, Anne Boland, Robert Olaso, Jean-François Deleuze
Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling...
2018: PloS One
Tatiana Murillo, Gabriel Ramírez-Vargas, Thomas Riedel, Jörg Overmann, Joakim M Andersen, Caterina Guzmán-Verri, Esteban Chaves-Olarte, César Rodríguez
Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 = 24; NAP1/ST01 = 19) and SNP densities (NAPCR1/ST54 = 0...
March 1, 2018: Genome Biology and Evolution
Taj Azarian, Lindsay R Grant, Brian J Arnold, Laura L Hammitt, Raymond Reid, Mathuram Santosham, Robert Weatherholtz, Novalene Goklish, Claudette M Thompson, Stephen D Bentley, Katherine L O'Brien, William P Hanage, Marc Lipsitch
In the United States, the introduction of the heptavalent pneumococcal conjugate vaccine (PCV) largely eliminated vaccine serotypes (VT); non-vaccine serotypes (NVT) subsequently increased in carriage and disease. Vaccination also disrupts the composition of the pneumococcal pangenome, which includes mobile genetic elements and polymorphic non-capsular antigens important for virulence, transmission, and pneumococcal ecology. Antigenic proteins are of interest for future vaccines; yet, little is known about how the they are affected by PCV use...
April 4, 2018: PLoS Pathogens
Mikhail A Moldovan, Mikhail S Gelfand
The pangenome is the collection of all groups of orthologous genes (OGGs) from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does not rely on DNA similarity levels and does not require analysis of homologous recombination. Hence this definition is relatively objective and independent of arbitrary thresholds. A systematic analysis of 110 accepted species with the largest numbers of sequenced strains yields results largely consistent with the existing nomenclature...
2018: Frontiers in Microbiology
Marnix H Medema
Microbial and plant specialized metabolites, also known as natural products, are key mediators of microbe-microbe and host-microbe interactions and constitute a rich resource for drug development. In the past decade, genome mining has emerged as a prominent strategy for natural product discovery. Initially, such mining was performed on the basis of individual microbial genome sequences. Now, these efforts are being scaled up to fully genome-sequenced strain collections, pangenomes of bacterial genera, and large sets of metagenome-assembled genomes from microbial communities...
March 2018: MSystems
Cecilia C Cundon, Alejandro Ameal, Elsa Maubecín, Adriana Bentancor
The pangenome of Escherichia coli is composed of a conserved core and variable genomic regions. The constant genetic component allows to determine the phylogeny of the microorganism, while genetic variability promoted the emergence of intestinal pathogenic strains and extraintestinal strains. In this study we characterized 85 extraintestinal pathogenic isolates genetically isolated from canines and felines. We used the Clermont scheme that includes intestinal (A and B1) and extraintestinal (B2 and D) phylogroups, virulence markers (pap1-2, pap3-4, sfa, afa, hlyA, aer and cnf) and hybrid pathogens...
March 15, 2018: Revista Argentina de Microbiología
Hannes Juergens, Javier A Varela, Arthur R Gorter de Vries, Thomas Perli, Veronica J M Gast, Nikola Y Gyurchev, Arun S Rajkumar, Robert Mans, Jack T Pronk, John P Morrissey, Jean-Marc G Daran
While CRISPR-Cas9-mediated genome editing has transformed yeast research, current plasmids and cassettes for Cas9 and guide-RNA expression are species specific. CRISPR tools that function in multiple yeast species could contribute to the intensifying research on non-conventional yeasts. A plasmid carrying a pangenomic origin of replication and two constitutive expression cassettes for Cas9 and ribozyme-flanked gRNAs was constructed. Its functionality was tested by analyzing inactivation of the ADE2 gene in four yeast species...
May 1, 2018: FEMS Yeast Research
Tom O Delmont, A Murat Eren
Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking...
2018: PeerJ
Gretchen L W Heavner, Cresten B Mansfeldt, Garrett E Debs, Sage T Hellerstedt, Annette R Rowe, Ruth E Richardson
Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1TM , including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup...
February 8, 2018: Microorganisms
David A Wilkinson, Andrew J O'Donnell, Rukhshana N Akhter, Ahmed Fayaz, Hamish J Mack, Lynn E Rogers, Patrick J Biggs, Nigel P French, Anne C Midwinter
Campylobacter hyointestinalis is a member of an emerging group of zoonotic Campylobacter spp. that are increasingly identified in both gastric and non-gastric disease in humans. Here, we discovered C. hyointestinalis in three separate classes of New Zealand ruminant livestock; cattle, sheep and deer. To investigate the relevance of these findings we performed a systematic literature review on global C. hyointestinalis epidemiology and used comparative genomics to better understand and classify members of the species...
February 5, 2018: Scientific Reports
Shany Doron, Sarah Melamed, Gal Ofir, Azita Leavitt, Anna Lopatina, Mai Keren, Gil Amitai, Rotem Sorek
The arms race between bacteria and phages led to the development of sophisticated antiphage defense systems, including CRISPR-Cas and restriction-modification systems. Evidence suggests that known and unknown defense systems are located in "defense islands" in microbial genomes. Here, we comprehensively characterized the bacterial defensive arsenal by examining gene families that are clustered next to known defense genes in prokaryotic genomes. Candidate defense systems were systematically engineered and validated in model bacteria for their antiphage activities...
March 2, 2018: Science
Clara López-Hermoso, Rafael R de la Haba, Cristina Sánchez-Porro, Antonio Ventosa
Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T , IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99...
December 21, 2017: Systematic and Applied Microbiology
Clémence Plissonneau, Fanny E Hartmann, Daniel Croll
BACKGROUND: Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence...
January 11, 2018: BMC Biology
Uri Sela, Chad W Euler, Joel Correa da Rosa, Vincent A Fischetti
A fundamental question in human susceptibility to bacterial infections is to what extent variability is a function of differences in the pathogen species or in individual humans. To focus on the pathogen species, we compared in the same individual the human adaptive T and B cell immune response to multiple strains of two major human pathogens, Staphylococcus aureus and Streptococcus pyogenes. We found wide variability in the acute adaptive immune response induced by various strains of a species, with a unique combination of activation within the two arms of the adaptive response...
January 2018: PLoS Pathogens
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