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https://www.readbyqxmd.com/read/28918154/hot-topic-geographical-distribution-and-strain-diversity-of-lactobacillus-wasatchensis-isolated-from-cheese-with-unwanted-gas-formation
#1
Michele Culumber, Donald J McMahon, Fatih Ortakci, Lauren Montierth, Beatriz Villalba, Jeffery R Broadbent, Craig J Oberg
Lactobacillus wasatchensis, an obligate heterofermentative nonstarter lactic acid bacteria (NSLAB) implicated in causing gas defects in aged cheeses, was originally isolated from an aged Cheddar produced in Logan, Utah. To determine the geographical distribution of this organism, we isolated slow-growing NSLAB from cheeses collected in different regions of the United States, Australia, New Zealand, and Ireland. Seven of the cheeses showed significant gas defects and 12 did not. Nonstarter lactic acid bacteria were isolated from these cheeses on de Man, Rogosa, and Sharpe medium supplemented with ribose, a preferred substrate for Lb...
September 13, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28871340/phza-the-shunt-switch-of-phenazine-1-6-dicarboxylic-acid-biosynthesis-in-pseudomonas-chlororaphis-ht66
#2
Shuqi Guo, Yining Wang, Bona Dai, Wei Wang, Hongbo Hu, Xianqing Huang, Xuehong Zhang
Natural phenazines are versatile secondary metabolites that are mainly produced by Pseudomonas and Streptomyces. All phenazine-type metabolites originate from two precursors: phenazine-1-carboxylic acid (PCA) in Pseudomonas or phenazine-1,6-dicarboxylic acid (PDC) in Streptomyces and other bacteria. Although the biosynthesis of PCA in Pseudomonas has been extensively studied, the origin of PDC still remains unclear. Comparing the phenazine biosynthesis operons of different species, we found that the phzA gene was restricted to Pseudomonas in which PCA is produced...
September 5, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28863779/optimization-of-a-metatranscriptomic-approach-to-study-the-lignocellulolytic-potential-of-the-higher-termite-gut-microbiome
#3
Martyna Marynowska, Xavier Goux, David Sillam-Dussès, Corinne Rouland-Lefèvre, Yves Roisin, Philippe Delfosse, Magdalena Calusinska
BACKGROUND: Thanks to specific adaptations developed over millions of years, the efficiency of lignin, cellulose and hemicellulose decomposition of higher termite symbiotic system exceeds that of many other lignocellulose utilizing environments. Especially, the examination of its symbiotic microbes should reveal interesting carbohydrate-active enzymes, which are of primary interest for the industry. Previous metatranscriptomic reports (high-throughput mRNA sequencing) highlight the high representation and overexpression of cellulose and hemicelluloses degrading genes in the termite hindgut digestomes, indicating the potential of this technology in search for new enzymes...
September 1, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28854628/genomic-epidemiology-of-ndm-1-encoding-plasmids-in-latin-american-clinical-isolates-reveals-insights-into-the-evolution-of-multidrug-resistance
#4
Ricaurte Alejandro Marquez-Ortiz, Leanne Haggerty, Narda Olarte, Carolina Duarte, Ulises Garza-Ramos, Jesus Silva-Sanchez, Betsy E Castro, Eby M Sim, Mauricio Beltran, María V Moncada, Alberto Valderrama, Jaime E Castellanos, Ian G Charles, Natasha Vanegas, Javier Escobar-Perez, Nicola K Petty
Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28839126/ancestor-of-land-plants-acquired-the-dna-3-methyladenine-glycosylase-mag-gene-from-bacteria-through-horizontal-gene-transfer
#5
Huimin Fang, Liexiang Huangfu, Rujia Chen, Pengcheng Li, Shuhui Xu, Enying Zhang, Wei Cao, Li Liu, Youli Yao, Guohua Liang, Chenwu Xu, Yong Zhou, Zefeng Yang
The origin and evolution of land plants was an important event in the history of life and initiated the establishment of modern terrestrial ecosystems. From water to terrestrial environments, plants needed to overcome the enhanced ultraviolet (UV) radiation and many other DNA-damaging agents. Evolving new genes with the function of DNA repair is critical for the origin and radiation of land plants. In bacteria, the DNA-3-methyladenine glycosylase (MAG) recognizes of a variety of base lesions and initiates the process of the base excision repair for damaged DNA...
August 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28790994/insight-into-the-origin-and-evolution-of-the-vibrio-parahaemolyticus-pandemic-strain
#6
REVIEW
Romilio T Espejo, Katherine García, Nicolas Plaza
A strain of Vibrio parahaemolyticus that emerged in 1995 caused the first known pandemic involving this species. This strain comprises clonal autochthonous ocean-dwelling bacteria whose evolution has occurred in the ocean environment. The low sequence diversity in this population enabled the discovery of information on its origin and evolution that has been hidden in bacterial clones that have evolved over a long period. Multilocus sequencing and microarray analysis, together with phylogenetic analysis, of pandemic and pre-pandemic isolates has suggested that the founder clone was an O3:K6 non-pathogenic strain that initially acquired a toxRS/new region and subsequently acquired at least seven novel genomic islands...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28789673/gene-and-transcript-abundances-of-bacterial-type-iii-secretion-systems-from-the-rumen-microbiome-are-correlated-with-methane-yield-in-sheep
#7
Janine Kamke, Priya Soni, Yang Li, Siva Ganesh, William J Kelly, Sinead C Leahy, Weibing Shi, Jeff Froula, Edward M Rubin, Graeme T Attwood
BACKGROUND: Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH4/kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. METHODS: Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep...
August 8, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28765217/rip-seq-suggests-translational-regulation-by-l7ae-in-archaea
#8
Michael Daume, Michael Uhl, Rolf Backofen, Lennart Randau
L7Ae is a universal archaeal protein that recognizes and stabilizes kink-turn (k-turn) motifs in RNA substrates. These structural motifs are widespread in nature and are found in many functional RNA species, including ribosomal RNAs. Synthetic biology approaches utilize L7Ae/k-turn interactions to control gene expression in eukaryotes. Here, we present results of comprehensive RNA immunoprecipitation sequencing (RIP-Seq) analysis of genomically tagged L7Ae from the hyperthermophilic archaeon Sulfolobus acidocaldarius A large set of interacting noncoding RNAs was identified...
August 1, 2017: MBio
https://www.readbyqxmd.com/read/28742812/broad-range-lytic-bacteriophages-that-kill-staphylococcus-aureus-local-field-strains
#9
Virginia Abatángelo, Natalia Peressutti Bacci, Carina A Boncompain, Ariel A Amadio, Soledad Carrasco, Cristian A Suárez, Héctor R Morbidoni
Staphylococcus aureus is a very successful opportunistic pathogen capable of causing a variety of diseases ranging from mild skin infections to life-threatening sepsis, meningitis and pneumonia. Its ability to display numerous virulence mechanisms matches its skill to display resistance to several antibiotics, including β-lactams, underscoring the fact that new anti-S. aureus drugs are urgently required. In this scenario, the utilization of lytic bacteriophages that kill bacteria in a genus -or even species- specific way, has become an attractive field of study...
2017: PloS One
https://www.readbyqxmd.com/read/28697368/gene-evolution-getting-something-from-nothing
#10
Caroline M Weisman, Sean R Eddy
New genes arise from pre-existing genes, but some de novo origin from non-genic sequence also seems plausible. A new study has surprisingly concluded that 25% of random DNA sequences yield beneficial products when expressed in bacteria.
July 10, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28658542/the-nutrition-gut-microbiome-physiology-axis-and-allergic-diseases
#11
REVIEW
Craig McKenzie, Jian Tan, Laurence Macia, Charles R Mackay
Dietary and bacterial metabolites influence immune responses. This raises the question whether the increased incidence of allergies, asthma, some autoimmune diseases, cardiovascular disease, and others might relate to intake of unhealthy foods, and the decreased intake of dietary fiber. In recent years, new knowledge on the molecular mechanisms underpinning a 'diet-gut microbiota-physiology axis' has emerged to substantiate this idea. Fiber is fermented to short chain fatty acids (SCFAs), particularly acetate, butyrate, and propionate...
July 2017: Immunological Reviews
https://www.readbyqxmd.com/read/28588563/insight-into-potential-probiotic-markers-predicted-in-lactobacillus-pentosus-mp-10-genome-sequence
#12
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
#13
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
#14
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
#15
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 contains the structural components to produce two R-tailocins of different ancestral origins. 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...
August 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28487432/deciphering-mcr-2-colistin-resistance
#16
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
#17
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
#18
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
#19
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
#20
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
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