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https://www.readbyqxmd.com/read/28588563/insight-into-potential-probiotic-markers-predicted-in-lactobacillus-pentosus-mp-10-genome-sequence
#1
Hikmate Abriouel, Beatriz Pérez Montoro, Carlos S Casimiro-Soriguer, Antonio J Pérez Pulido, Charles W Knapp, Natacha Caballero Gómez, Sonia Castillo-Gutiérrez, María D Estudillo-Martínez, Antonio Gálvez, Nabil Benomar
Lactobacillus pentosus MP-10 is a potential probiotic lactic acid bacterium originally isolated from naturally fermented Aloreña green table olives. The entire genome sequence was annotated to in silico analyze the molecular mechanisms involved in the adaptation of L. pentosus MP-10 to the human gastrointestinal tract (GIT), such as carbohydrate metabolism (related with prebiotic utilization) and the proteins involved in bacteria-host interactions. We predicted an arsenal of genes coding for carbohydrate-modifying enzymes to modify oligo- and polysaccharides, such as glycoside hydrolases, glycoside transferases, and isomerases, and other enzymes involved in complex carbohydrate metabolism especially starch, raffinose, and levan...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28540258/horizontally-acquired-biosynthesis-genes-boost-coxiella-burnetii-s-physiology
#2
Abraham S Moses, Jess A Millar, Matteo Bonazzi, Paul A Beare, Rahul Raghavan
Coxiella burnetii, the etiologic agent of acute Q fever and chronic endocarditis, has a unique biphasic life cycle, which includes a metabolically active intracellular form that occupies a large lysosome-derived acidic vacuole. C. burnetii is the only bacterium known to thrive within such an hostile intracellular niche, and this ability is fundamental to its pathogenicity; however, very little is known about genes that facilitate Coxiella's intracellular growth. Recent studies indicate that C. burnetii evolved from a tick-associated ancestor and that the metabolic capabilities of C...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28534089/comparison-of-microbiomes-between-red-poultry-mite-populations-dermanyssus-gallinae-predominance-of-bartonella-like-bacteria
#3
Jan Hubert, Tomas Erban, Jan Kopecky, Bruno Sopko, Marta Nesvorna, Martina Lichovnikova, Sabine Schicht, Christina Strube, Olivier Sparagano
Blood feeding red poultry mites (RPM) serve as vectors of pathogenic bacteria and viruses among vertebrate hosts including wild birds, poultry hens, mammals, and humans. The microbiome of RPM has not yet been studied by high-throughput sequencing. RPM eggs, larvae, and engorged adult/nymph samples obtained in four poultry houses in Czechia were used for microbiome analyses by Illumina amplicon sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. A laboratory RPM population was used as positive control for transcriptome analysis by pyrosequencing with identification of sequences originating from bacteria...
May 22, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28526791/pseudomonas-chlororaphis-produces-two-distinct-r-tailocins-that-contribute-to-bacterial-competition-in-biofilms-and-on-roots
#4
Robert J Dorosky, Jun Myoung Yu, Leland S Pierson, Elizabeth A Pierson
R-type tailocins are high molecular weight bacteriocins that resemble bacteriophage tails and are encoded within the genomes of many Pseudomonas species. In this study, analysis of the P. chlororaphis 30-84 R-tailocin gene cluster revealed that it encodes the structural components to produce two R-tailocins of different ancestral origin. Two distinct R-tailocin populations differing in length were observed in UV induced lysates of P. chlororaphis 30-84 via transmission electron microscopy. Mutants defective in the production of one or both R-tailocins demonstrated that the killing spectrum of each tailocin is limited to Pseudomonas species...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28487432/deciphering-mcr-2-colistin-resistance
#5
Jian Sun, Yongchang Xu, Rongsui Gao, Jingxia Lin, Wenhui Wei, Swaminath Srinivas, Defeng Li, Run-Shi Yang, Xing-Ping Li, Xiao-Ping Liao, Ya-Hong Liu, Youjun Feng
Antibiotic resistance is a prevalent problem in public health worldwide. In general, the carbapenem β-lactam antibiotics are considered a final resort against lethal infections by multidrug-resistant bacteria. Colistin is a cationic polypeptide antibiotic and acts as the last line of defense for treatment of carbapenem-resistant bacteria. Very recently, a new plasmid-borne colistin resistance gene, mcr-2, was revealed soon after the discovery of the paradigm gene mcr-1, which has disseminated globally. However, the molecular mechanisms for MCR-2 colistin resistance are poorly understood...
May 9, 2017: MBio
https://www.readbyqxmd.com/read/28460038/antismash-4-0-improvements-in-chemistry-prediction-and-gene-cluster-boundary-identification
#6
Kai Blin, Thomas Wolf, Marc G Chevrette, Xiaowen Lu, Christopher J Schwalen, Satria A Kautsar, Hernando G Suarez Duran, Emmanuel L C de Los Santos, Hyun Uk Kim, Mariana Nave, Jeroen S Dickschat, Douglas A Mitchell, Ekaterina Shelest, Rainer Breitling, Eriko Takano, Sang Yup Lee, Tilmann Weber, Marnix H Medema
Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures...
April 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449650/structure-genetics-and-worldwide-spread-of-new-delhi-metallo-%C3%AE-lactamase-ndm-a-threat-to-public-health
#7
REVIEW
Asad U Khan, Lubna Maryam, Raffaele Zarrilli
BACKGROUND: The emergence of carbapenemase producing bacteria, especially New Delhi metallo-β-lactamase (NDM-1) and its variants, worldwide, has raised amajor public health concern. NDM-1 hydrolyzes a wide range of β-lactam antibiotics, including carbapenems, which are the last resort of antibiotics for the treatment of infections caused by resistant strain of bacteria. MAIN BODY: In this review, we have discussed bla NDM-1variants, its genetic analysis including type of specific mutation, origin of country and spread among several type of bacterial species...
April 27, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28405712/emergence-of-new-srnas-in-enteric-bacteria-is-associated-with-low-expression-and-rapid-evolution
#8
Fenil R Kacharia, Jess A Millar, Rahul Raghavan
Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks...
April 12, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28353400/evolutionary-history-of-subtilases-in-land-plants-and-their-involvement-in-symbiotic-interactions
#9
Alexander Taylor, Yin-Long Qiu
Subtilases, a family of proteases involved in a variety of developmental processes in land plants, are also involved in both mutualistic symbiosis and host-pathogen interactions in different angiosperm lineages. We examined the evolutionary history of subtilase genes across land plants through a phylogenetic analysis integrating amino acid sequence data from full genomes, transcriptomes, and characterized subtilases of 341 species of diverse green algae and land plants along with subtilases from 12 species of other eukaryotes, archaea, and bacteria...
June 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28344994/a-new-broad-range-plasmid-for-dna-delivery-in-eukaryotic-cells-using-lactic-acid-bacteria-in%C3%A2-vitro-and-in%C3%A2-vivo-assays
#10
Pamela Mancha-Agresti, Mariana Martins Drumond, Fillipe Luiz Rosa do Carmo, Monica Morais Santos, Janete Soares Coelho Dos Santos, Franco Venanzi, Jean-Marc Chatel, Sophie Yvette Leclercq, Vasco Azevedo
Lactococcus lactis is well documented as a promising candidate for development of novel oral live vaccines. It has been broadly engineered for heterologous expression, as well as for plasmid expression vector delivery, directly inside eukaryotic cells, for DNA vaccine, or as therapeutic vehicle. This work describes the characteristics of a new plasmid, pExu (extra chromosomal unit), for DNA delivery using L. lactis and evaluates its functionality both by in vitro and in vivo assays. This plasmid exhibits the following features: (1) a theta origin of replication and (2) an expression cassette containing a multiple cloning site and a eukaryotic promoter, the cytomegalovirus (pCMV)...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28337182/new-insights-into-the-anti-pathogenic-potential-of-lactococcus-garvieae-against-staphylococcus-aureus-based-on-rna-sequencing-profiling
#11
Pierre Delpech, Etienne Rifa, Graham Ball, Sabine Nidelet, Emeric Dubois, Geneviève Gagne, Marie-Christine Montel, Céline Delbès, Stéphanie Bornes
The bio-preservation potential of Lactococcus garvieae lies in its capacity to inhibit the growth of staphylococci, especially Staphylococcus aureus, in dairy products and in vitro. In vitro, inhibition is modulated by the level of aeration, owing to hydrogen peroxide (H2O2) production by L. garvieae under aeration. The S. aureus response to this inhibition has already been studied. However, the molecular mechanisms of L. garvieae underlying the antagonism against S. aureus have never been explored. This study provides evidence of the presence of another extracellular inhibition effector in vitro...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28275945/enrichment-culture-and-identification-of-endophytic-methanotrophs-isolated-from-peatland-plants
#12
Zofia Stępniewska, Weronika Goraj, Agnieszka Kuźniar, Natalia Łopacka, Magdalena Małysza
Aerobic methane-oxidizing bacteria (MOB) are an environmentally significant group of microorganisms due to their role in the global carbon cycle. Research conducted over the past few decades has increased the interest in discovering novel genera of methane-degrading bacteria, which efficiently utilize methane and decrease the global warming effect. Moreover, methanotrophs have more promising applications in environmental bioengineering, biotechnology, and pharmacy. The investigations were undertaken to recognize the variety of endophytic methanotrophic bacteria associated with Carex nigra, Vaccinium oxycoccus, and Eriophorum vaginatum originating from Moszne peatland (East Poland)...
March 9, 2017: Folia Microbiologica
https://www.readbyqxmd.com/read/28242668/plasmid-mediated-novel-blandm-17-gene-encoding-a-carbapenemase-with-enhanced-activity-in-a-sequence-type-48-escherichia-coli-strain
#13
Zhihai Liu, Yang Wang, Timothy R Walsh, Dejun Liu, Zhangqi Shen, Rongmin Zhang, Wenjuan Yin, Hong Yao, Jiyun Li, Jianzhong Shen
Carbapenem-resistant Enterobacteriaceae (CRE) have spread worldwide, leaving very few treatment options available. New Delhi metallo-beta-lactamase (NDM) is the main carbapenemase mediating CRE resistance and is of increasing concern. NDM-positive Enterobacteriaceae of human origin are frequently identified; however, the emergence of NDM, and particularly novel variants, in bacteria of food animal origin has never been reported. Here, we characterize a novel NDM variant (assigned NDM-17) identified in a β-lactam-resistant sequence type 48 (ST48) Escherichia coli strain that was isolated from a chicken in China...
May 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28236853/in-pursuit-of-cancer-metastasis-therapy-by-bacteria-and-its-biofilms-history-or-future
#14
Mohd Adnan, Saif Khan, Eyad Al-Shammari, Mitesh Patel, Mohd Saeed, Sibte Hadi
The 20th century observation of increasing comprehensive load of cancer, advanced cancer prevention strategies, creative hypotheses and control procedures by research communities are being traversed and stimulated in multiple facets. Inference of genetically modified non-pathogenic and natural bacterial species as potential anti-tumor agents is one such original perspective. Live, genetically modified non-pathogenic or attenuated bacterial species are able to form biofilms by multiplying selectively or non-selectively on cancer cells, which will lead to metastasis disruption...
March 2017: Medical Hypotheses
https://www.readbyqxmd.com/read/28231283/rapid-evolution-of-distinct-helicobacter-pylori-subpopulations-in-the-americas
#15
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
#16
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/28174306/a-mobile-element-in-muts-drives-hypermutation-in-a-marine-vibrio
#17
Nathaniel D Chu, Sean A Clarke, Sonia Timberlake, Martin F Polz, Alan D Grossman, Eric J Alm
Bacteria face a trade-off between genetic fidelity, which reduces deleterious mistakes in the genome, and genetic innovation, which allows organisms to adapt. Evidence suggests that many bacteria balance this trade-off by modulating their mutation rates, but few mechanisms have been described for such modulation. Following experimental evolution and whole-genome resequencing of the marine bacterium Vibrio splendidus 12B01, we discovered one such mechanism, which allows this bacterium to switch to an elevated mutation rate...
February 7, 2017: MBio
https://www.readbyqxmd.com/read/28164795/comparative-genomic-analysis-of-the-genus-enterococcus
#18
Zhi Zhong, Wenyi Zhang, Yuqin Song, Wenjun Liu, Haiyan Xu, Xiaoxia Xi, Bilige Menghe, Heping Zhang, Zhihong Sun
As important lactic acid bacteria, Enterococcus species are widely used in the production of fermented food. However, as some strains of Enterococcus are opportunistic pathogens, their safety has not been generally accepted. In recent years, a large number of new species have been described and classified within the genus Enterococcus, so a better understanding of the genetic relationships and evolution of Enterococcus species is needed. In this study, the genomes of 29 type strains of Enterococcus species were sequenced...
March 2017: Microbiological Research
https://www.readbyqxmd.com/read/28127420/permanent-draft-genome-of-thiobacillus-thioparus-dsm-505-t-an-obligately-chemolithoautotrophic-member-of-the-betaproteobacteria
#19
Lee P Hutt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, Tatiparthi Reddy, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Rich Boden
Thiobacillus thioparus DSM 505(T) is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture C(T) (=DSM 505(T) = ATCC 8158(T)) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28088165/genomic-characterization-of-ensifer-aridi-a-proposed-new-species-of-nitrogen-fixing-rhizobium-recovered-from-asian-african-and-american-deserts
#20
Antoine Le Quéré, Nisha Tak, Hukam Singh Gehlot, Celine Lavire, Thibault Meyer, David Chapulliot, Sonam Rathi, Ilham Sakrouhi, Guadalupe Rocha, Marine Rohmer, Dany Severac, Abdelkarim Filali-Maltouf, Jose-Antonio Munive
BACKGROUND: Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. RESULTS: Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced...
January 14, 2017: BMC Genomics
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