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Bacteria evolution

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https://www.readbyqxmd.com/read/28748289/genetic-recombinational-events-in-prokaryotes-and-their-viruses-insight-into-the-study-of-evolution-and-biodiversity
#1
REVIEW
Jean-Pierre Gratia
The exact meaning of sexual reproduction and the precise evolutionary period at which recombination first took place remains the subject of intense debates. Despite some unity in biochemical organisation of genetic recombination, a plethora of mechanisms are found to exist in microbes and their viruses. Some routes used by viruses bypass barriers to genetic heterology and provide bacteria with genes conferring a selective advantage, and some contribute to genome enlargement. The present review aims at highlighting the diversity of such mechanisms with a particular focus on spontaneous zygogenesis (or Z-mating)...
July 26, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28744786/genetic-basis-of-exploiting-ecological-opportunity-during-the-long-term-diversification-of-a-bacterial-population
#2
Jessika Consuegra, Jessica Plucain, Joël Gaffé, Thomas Hindré, Dominique Schneider
Adaptive diversification is an essential evolutionary process, one that produces phenotypic innovations including the colonization of available ecological niches. Bacteria can diverge in sympatry when ecological opportunities allow, but the underlying genetic mechanisms are often unknown. Perhaps, the longest-lasting adaptive diversification seen in the laboratory occurred during the long-term evolution experiment, in which 12 populations of Escherichia coli have been evolving independently for more than 65,000 generations from a common ancestor...
July 25, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28744678/variation-of-preserving-organic-matter-bound-in-interlayer-of-montmorillonite-induced-by-microbial-metabolic-process
#3
Yulian Zhao, Faqin Dong, Qunwei Dai, Gang Li, Jie Ma
This paper aimed to investigate the variation of preserving organic matter bound in the interlayer space of montmorillonite (Mt) induced by a microbe metabolic process. We selected Bacillus pumilus as the common soil native bacteria. The alteration of d 001 value, functional group, and C,N organic matter contents caused by bacteria were analyzed by XRD, FTIR, and elementary analyzer, respectively. XRD results showed that the d 001 value of montmorillonite increased with the concentration decreasing and decreased with the culture time increasing after interacting with bacteria indicating the interlayer space of montmorillonite was connected with the organic matter...
July 25, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28743812/horizontal-gene-transfer-of-functional-type-vi-killing-genes-by-natural-transformation
#4
Jacob Thomas, Samit S Watve, William C Ratcliff, Brian K Hammer
Horizontal gene transfer (HGT) can have profound effects on bacterial evolution by allowing individuals to rapidly acquire adaptive traits that shape their strategies for competition. One strategy for intermicrobial antagonism often used by Proteobacteria is the genetically encoded contact-dependent type VI secretion system (T6SS), a weapon used to kill heteroclonal neighbors by direct injection of toxic effectors. Here, we experimentally demonstrate that Vibrio cholerae can acquire new T6SS effector genes via horizontal transfer and utilize them to kill neighboring cells...
July 25, 2017: MBio
https://www.readbyqxmd.com/read/28741105/transmission-fitness-in-co-colonization-and-the-persistence-of-bacterial-pathogens
#5
Maria Gaivão, Francisco Dionisio, Erida Gjini
Humans are often colonized by polymorphic bacteria such as Streptococcus pneumoniae, Bordetella pertussis, Staphylococcus Aureus, and Haemophilus influenzae. Two co-colonizing pathogen clones may interact with each other upon host entry and during within-host dynamics, ranging from competition to facilitation. Here we examine the significance of these exploitation strategies for bacterial spread and persistence in host populations. We model SIS epidemiological dynamics to capture the global behavior of such multi-strain systems, focusing on different parameters of single and dual colonization...
July 24, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28740486/evolution-of-acinetobacter-baumannii-in-vivo-international-clone-ii-more-resistance-to-ceftazidime-mutation-in-ptk
#6
Xiaoting Hua, Zhihui Zhou, Qing Yang, Qiucheng Shi, Qingye Xu, Jianfeng Wang, Keren Shi, Feng Zhao, Long Sun, Zhi Ruan, Yan Jiang, Yunsong Yu
Acinetobacter baumannii is an important nosocomial pathogen worldwide. A more comprehensive understanding of the within-host genomic evolution of A. baumannii would provide a molecule basis for improving treatment of A. baumannii infection. To understand the evolutionary mechanism facilitating A. baumannii survived in human body, we here reported the genomic analysis of A. baumannii isolated sampled from Chinese patients. We used whole-genome sequence of A. baumannii isolates from the same patient to determine single-nucleotide variants, insertion sequence mapping, and gene change...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28738827/bacterial-tail-anchors-can-target-to-the-mitochondrial-outer-membrane
#7
Güleycan Lutfullahoğlu-Bal, Abdurrahman Keskin, Ayşe Bengisu Seferoğlu, Cory D Dunn
BACKGROUND: During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria...
July 24, 2017: Biology Direct
https://www.readbyqxmd.com/read/28737874/-brain-abscess-in-children-ten-years-of-experience-in-a-third-level-pediatric-hospital
#8
Martín Brizuela, Guadalupe Pérez, Soledad Martiren, Ana N Varela Baino, Carola Cedillo, Silvina Ruvinsky, Carolina Epelbaum, Adela Isasmendi, Mirta Litterio, José L Pinheiro, Rosa Bologna
Brain abscess is a focal infection that occurs with a frequency of 0.3-1.3 cases per 100,000 people/year. We describe the epidemiology, clinical and microbiology characteristics of 38 children diagnosed with brain abscess hospitalized between 4/1/2005 and 12/31/2015 at Hospital de Pediatría "Prof. Dr. Juan P. Garrahan" in Buenos Aires City. Twenty-four patients were male. The median age was 132 months. Predisposing factors were detected in 25 children. The median evolution from onset of symptoms to the visit was 7 days...
August 1, 2017: Archivos Argentinos de Pediatría
https://www.readbyqxmd.com/read/28735325/characterization-of-endolithic-culturable-microbial-communities-in-carbonate-rocks-from-a-typical-karst-canyon-in-guizhou-china
#9
Yuan Tang, Jian-Zhong Cheng, Bin Lian
The endolithic environment is a ubiquitous habitat for microorganisms and a critical interface between biology and geology. In this study, a culture-based method and the phylogenetic analysis based on 16S rRNA and internal transcribed spacer (ITS) sequences were used to investigate the diversity of endolithic bacteria and fungi in two main types of carbonate rocks (namely dolomite and limestone) from Nanjiang Canyon in Guizhou karst area, China. The results of bacterial diversity indicated that all bacteria isolated from dolomite and limestone rocks were divided into 4 bacterial groups, including Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes...
January 2, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/28735145/metabolic-gene-targeted-monitoring-of-non-starter-lactic-acid-bacteria-during-cheese-ripening
#10
Alessia Levante, Francesca De Filippis, Antonietta La Storia, Monica Gatti, Erasmo Neviani, Danilo Ercolini, Camilla Lazzi
Long ripened cheeses, such as Grana Padano (GP), a Protected Designation of Origin (PDO) Italian cheese, harbor a viable microbiota mainly composed of non-starter lactic acid bacteria (NSLAB), which contribute to the final characteristics of cheese. The NSLAB species Lactobacillus rhamnosus, Lb. casei and Lb. paracasei are frequently found in GP, and form a closely related taxonomic group (Lb. casei group), making it difficult to distinguish the three species through 16S rRNA sequencing. SpxB, a metabolic gene coding for pyruvate oxidase in Lb...
July 6, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28734362/discrimination-of-bacteria-by-rapid-sensing-their-metabolic-volatiles-using-an-aspiration-type-ion-mobility-spectrometer-a-ims-and-gas-chromatography-mass-spectrometry-gc-ms
#11
Ileana Andreea Ratiu, Victor Bocos-Bintintan, Adrian Patrut, Victor Hugo Moll, Matthew Turner, C L Paul Thomas
The objective of our study was to investigate whether one may quickly and reliably discriminate different microorganism strains by direct monitoring of the headspace atmosphere above their cultures. Headspace samples above a series of in vitro bacterial cultures were directly interrogated using an aspiration type ion mobility spectrometer (a-IMS), which produced distinct profiles ("fingerprints") of ion currents generated simultaneously by the detectors present inside the ion mobility cell. Data processing and analysis using principal component analysis showed net differences in the responses produced by volatiles emitted by various bacterial strains...
August 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28732554/microbial-ecology-and-process-technology-of-sourdough-fermentation
#12
Luc De Vuyst, Simon Van Kerrebroeck, Frédéric Leroy
From a microbiological perspective, sourdough is to be considered as a specific and stressful ecosystem, harboring yeasts and lactic acid bacteria (LAB), that is used for the production of baked goods. With respect to the metabolic impact of the sourdough microbiota, acidification (LAB), flavor formation (LAB and yeasts), and leavening (yeasts and heterofermentative LAB species) are most noticeable. Three distinct types of sourdough fermentation processes can be discerned based on the inocula applied, namely backslopped ones (type 1), those initiated with starter cultures (type 2), and those initiated with a starter culture followed by backslopping (type 3)...
2017: Advances in Applied Microbiology
https://www.readbyqxmd.com/read/28732395/microalgae-bacteria-models-evolution-from-microalgae-steady-state-to-integrated-microalgae-bacteria-wastewater-treatment-models-a-comparative-review
#13
REVIEW
Alessandro Solimeno, Joan García
The search for environmentally neutral alternative fuels had revived the interest for microalgae-bacteria wastewater treatment systems. The potential achieving of bioproducts from microalgae biomass has also greatly contributed. The reactions that occur in these systems are complex, and the degree of scientific knowledge is still scarce compared to that of conventional bacteria wastewater treatments. Mathematical models offer a great opportunity to study the simultaneous effect of the multiple factors affecting microalgae and bacteria, thus allowing for the prediction of final biomass production, and contributing to the system design optimization in terms of operation and control...
July 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28732043/investigation-of-horizontal-gene-transfer-of-pathogenicity-islands-in-escherichia-coli-using-next-generation-sequencing
#14
Maxim Messerer, Wolfgang Fischer, Sören Schubert
Horizontal gene transfer (HGT) contributes to the evolution of bacteria. All extraintestinal pathogenic Escherichia coli (ExPEC) harbour pathogenicity islands (PAIs), however relatively little is known about the acquisition of these PAIs. Due to these islands, ExPEC have properties to colonize and invade its hosts efficiently. Even though these PAIs are known to be acquired by HGT, only very few PAIs do carry mobilization and transfer genes required for the transmission by HGT. In this study, we apply for the first time next-generation sequencing (NGS) and in silico analyses in combination with in vitro experiments to decipher the mechanisms of PAI acquisition in ExPEC...
2017: PloS One
https://www.readbyqxmd.com/read/28729688/improved-genome-recovery-and-integrated-cell-size-analyses-of-individual-uncultured-microbial-cells-and-viral-particles
#15
Ramunas Stepanauskas, Elizabeth A Fergusson, Joseph Brown, Nicole J Poulton, Ben Tupper, Jessica M Labonté, Eric D Becraft, Julia M Brown, Maria G Pachiadaki, Tadas Povilaitis, Brian P Thompson, Corianna J Mascena, Wendy K Bellows, Arvydas Lubys
Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils...
July 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28728121/effect-of-residual-h2o2-from-advanced-oxidation-processes-on-subsequent-biological-water-treatment-a-laboratory-batch-study
#16
Feifei Wang, Doris van Halem, Gang Liu, Karin Lekkerkerker-Teunissen, Jan Peter van der Hoek
H2O2 residuals from advanced oxidation processes (AOPs) may have critical impacts on the microbial ecology and performance of subsequent biological treatment processes, but little is known. The objective of this study was to evaluate how H2O2 residuals influence sand systems with an emphasis on dissolved organic carbon (DOC) removal, microbial activity change and bacterial community evolution. The results from laboratory batch studies showed that 0.25 mg/L H2O2 lowered DOC removal by 10% while higher H2O2 concentrations at 3 and 5 mg/L promoted DOC removal by 8% and 28%...
July 15, 2017: Chemosphere
https://www.readbyqxmd.com/read/28727829/functional-differentiation-and-spatial-temporal-co-expression-networks-of-the-nbs-encoding-gene-family-in-jilin-ginseng-panax-ginseng-c-a-meyer
#17
Rui Yin, Mingzhu Zhao, Kangyu Wang, Yanping Lin, Yanfang Wang, Chunyu Sun, Yi Wang, Meiping Zhang
Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal plants for human health and medicine. It has been documented that over 80% of genes conferring resistance to bacteria, viruses, fungi and nematodes are contributed by the nucleotide binding site (NBS)-encoding gene family. Therefore, identification and characterization of NBS genes expressed in ginseng are paramount to its genetic improvement and breeding. However, little is known about the NBS-encoding genes in ginseng. Here we report genome-wide identification and systems analysis of the NBS genes actively expressed in ginseng (PgNBS genes)...
2017: PloS One
https://www.readbyqxmd.com/read/28727736/persistent-damaged-bases-in-dna-allow-mutagenic-break-repair-in-escherichia-coli
#18
Jessica M Moore, Raul Correa, Susan M Rosenberg, P J Hastings
Bacteria, yeast and human cancer cells possess mechanisms of mutagenesis upregulated by stress responses. Stress-inducible mutagenesis potentially accelerates adaptation, and may provide important models for mutagenesis that drives cancers, host pathogen interactions, antibiotic resistance and possibly much of evolution generally. In Escherichia coli repair of double-strand breaks (DSBs) becomes mutagenic, using low-fidelity DNA polymerases under the control of the SOS DNA-damage response and RpoS general stress response, which upregulate and allow the action of error-prone DNA polymerases IV (DinB), II and V to make mutations during repair...
July 20, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28725416/contrasting-patterns-of-selection-between-mhc-i-and-ii-across-populations-of-humboldt-and-magellanic-penguins
#19
Nicole Sallaberry-Pincheira, Daniel González-Acuña, Pamela Padilla, Gisele P M Dantas, Guillermo Luna-Jorquera, Esteban Frere, Armando Valdés-Velásquez, Juliana A Vianna
The evolutionary and adaptive potential of populations or species facing an emerging infectious disease depends on their genetic diversity in genes, such as the major histocompatibility complex (MHC). In birds, MHC class I deals predominantly with intracellular infections (e.g., viruses) and MHC class II with extracellular infections (e.g., bacteria). Therefore, patterns of MHC I and II diversity may differ between species and across populations of species depending on the relative effect of local and global environmental selective pressures, genetic drift, and gene flow...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28724376/sonication-contribution-to-identifying-prosthetic-joint-infection-with-ralstonia-pickettii-a-case-report-and-review-of-the-literature
#20
Rares Mircea Birlutiu, Mihai Dan Roman, Razvan Silviu Cismasiu, Sorin Radu Fleaca, Crina Maria Popa, Manuela Mihalache, Victoria Birlutiu
BACKGROUND: In the context of an increase number of primary and revision total hip and total knee arthroplasty performed yearly, an increased risk of complication is expected. Prosthetic joint infection (PJI) remains the most common and feared arthroplasty complication. Ralstonia pickettii is a Gram-negative bacterium, that has also been identified in biofilms. It remains an extremely rare cause of PJI. There is no report of an identification of R. pickettii on an extracted spacer loaded with antibiotic...
July 19, 2017: BMC Musculoskeletal Disorders
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