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Microbial genomics

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https://www.readbyqxmd.com/read/28644444/energy-and-carbon-metabolisms-in-a-deep-terrestrial-subsurface-fluid-microbial-community
#1
Lily Momper, Sean P Jungbluth, Michael D Lee, Jan P Amend
The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples were collected from a former gold mine in Lead, South Dakota, USA, now Sanford Underground Research Facility (SURF). We reconstructed 74 genomes from metagenomes (MAGs), enabling the identification of common metabolic pathways...
June 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28644126/extensive-horizontal-gene-transfer-in-cheese-associated-bacteria
#2
Kevin S Bonham, Benjamin E Wolfe, Rachel J Dutton
Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,844 protein coding genes...
June 23, 2017: ELife
https://www.readbyqxmd.com/read/28643787/single-virus-genomics-reveals-hidden-cosmopolitan-and-abundant-viruses
#3
Francisco Martinez-Hernandez, Oscar Fornas, Monica Lluesma Gomez, Benjamin Bolduc, Maria Jose de la Cruz Peña, Joaquín Martínez Martínez, Josefa Anton, Josep M Gasol, Riccardo Rosselli, Francisco Rodriguez-Valera, Matthew B Sullivan, Silvia G Acinas, Manuel Martinez-Garcia
Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28643626/what-defines-the-kingdom-fungi
#4
Thomas A Richards, Guy Leonard, Jeremy G Wideman
The application of environmental DNA techniques and increased genome sequencing of microbial diversity, combined with detailed study of cellular characters, has consistently led to the reexamination of our understanding of the tree of life. This has challenged many of the definitions of taxonomic groups, especially higher taxonomic ranks such as eukaryotic kingdoms. The Fungi is an example of a kingdom which, together with the features that define it and the taxa that are grouped within it, has been in a continual state of flux...
June 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28643623/the-genomic-basis-of-lactobacilli-as-health-promoting-organisms
#5
Elisa Salvetti, Paul W O'Toole
Lactobacilli occupy a unique position in human culture and scientific history. Like brewer's and baker's yeast, lactobacilli have been associated with food production and preservation for thousands of years. Lactobacillus species are used in mixed microbial cultures, such as the classical Lactobacillus bulgaricus/Streptococcus thermophilus inoculum for yogurt fermentation, or combinations of diverse lactobacilli/yeasts in kefir grains. The association of lactobacilli consumption with greater longevity and improved health formed the basis for developing lactobacilli as probiotics, whose market has exploded worldwide in the past 10 years...
June 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28642609/microbial-signatures-associated-with-oropharyngeal-and-oral-squamous-cell-carcinomas
#6
Sagarika Banerjee, Tian Tian, Zhi Wei, Kristen N Peck, Natalie Shih, Ara A Chalian, Bert W O'Malley, Gregory S Weinstein, Michael D Feldman, James Alwine, Erle S Robertson
The microbiome is fundamentally one of the most unique organs in the human body. Dysbiosis can result in critical inflammatory responses and result in pathogenesis contributing to neoplastic events. We used a pan-pathogen array technology (PathoChip) coupled with next-generation sequencing to establish microbial signatures unique to human oral and oropharyngeal squamous cell carcinomas (OCSCC/OPSCC). Signatures for DNA and RNA viruses including oncogenic viruses, gram positive and negative bacteria, fungi and parasites were detected...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28641405/biotransformation-of-ferulic-acid-to-protocatechuic-acid-by-corynebacterium-glutamicum-atcc-21420-engineered-to-express-vanillate-o-demethylase
#7
Naoko Okai, Takaya Masuda, Yasunobu Takeshima, Kosei Tanaka, Ken-Ichi Yoshida, Masanori Miyamoto, Chiaki Ogino, Akihiko Kondo
Ferulic acid (4-hydroxy-3-methoxycinnamic acid, FA) is a lignin-derived phenolic compound abundant in plant biomass. The utilization of FA and its conversion to valuable compounds is desired. Protocatechuic acid (3,4-dihydroxybenzoic acid, PCA) is a precursor of polymers and plastics and a constituent of food. A microbial conversion system to produce PCA from FA was developed in this study using a PCA-producing strain of Corynebacterium glutamicum F (ATCC 21420). C. glutamicum strain F grown at 30 °C for 48 h utilized 2 mM each of FA and vanillic acid (4-hydroxy-3-methoxybenzoic acid, VA) to produce PCA, which was secreted into the medium...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28639622/growth-coupled-overproduction-is-feasible-for-almost-all-metabolites-in-five-major-production-organisms
#8
Axel von Kamp, Steffen Klamt
Computational modelling of metabolic networks has become an established procedure in the metabolic engineering of production strains. One key principle that is frequently used to guide the rational design of microbial cell factories is the stoichiometric coupling of growth and product synthesis, which makes production of the desired compound obligatory for growth. Here we show that the coupling of growth and production is feasible under appropriate conditions for almost all metabolites in genome-scale metabolic models of five major production organisms...
June 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28638372/diversity-and-composition-of-sulfate-reducing-microbial-communities-based-on-genomic-dna-and-rna-transcription-in-production-water-of-high-temperature-and-corrosive-oil-reservoir
#9
Xiao-Xiao Li, Jin-Feng Liu, Lei Zhou, Serge M Mbadinga, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu
Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28637810/mcclintock-an-integrated-pipeline-for-detecting-transposable-element-insertions-in-whole-genome-shotgun-sequencing-data
#10
Michael G Nelson, Raquel S Linheiro, Casey M Bergman
Transposable element (TE) insertions are among the most challenging type of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication. Nevertheless, the recent availability of large resequencing datasets has spurred development of many new methods to detect TE insertions in whole genome shotgun sequences. Here we report an integrated bioinformatics pipeline for the detection of TE insertions in whole genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods...
June 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28637316/incorporating-comparative-genomics-into-the-design-test-learn-cycle-of-microbial-strain-engineering
#11
Maria Sardi, Audrey P Gasch
Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals, and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling, and regulatory rewiring have proven to significantly advance industrial strain engineering...
June 16, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28636321/copper-oxide-nanoparticles-induce-lysogenic-bacteriophage-and-metal-resistance-genes-in-pseudomonas-aeruginosa-pao1
#12
Jianhua Guo, Shu-Hong Gao, Ji Lu, Philip L Bond, Willy Verstraete, Zhiguo Yuan
The intensive use of metal-based nanoparticles results in their continuous release into the environment, leading to potential risks for human health and microbial ecosystems. Although previous studies have indicated that nanoparticles may be toxic to microorganisms, there is a scarcity of data available to assess the underlying molecular mechanisms of inhibitory and biocidal effects of nanoparticles on microorganisms. This study used physiological experiments, microscopy, Live/Dead staining and the genome-wide RNA sequencing to investigate the multiple responses of Pseudomonas aeruginosa to the exposure of copper oxide nanoparticles (CuO NPs)...
June 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28634470/the-dark-side-of-the-mushroom-spring-microbial-mat-life-in-the-shadow-of-chlorophototrophs-ii-metabolic-functions-of-abundant-community-members-predicted-from-metagenomic-analyses
#13
Vera Thiel, Michael Hügler, David M Ward, Donald A Bryant
Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28634080/nong-a-constituent-of-the-nonactin-biosynthetic-gene-cluster-regulates-nocardamine-synthesis-in-streptomyces-albus-j1074
#14
Wanki Park, Jung-Kyun Woo, Jongheon Shin, Ki-Bong Oh
Many factors regulate the expression of specialised secondary metabolite biosynthetic gene clusters, which have been recognised as important for the discovery of novel microbial natural products. A cosmid library based on genomic DNA of the marine-derived Streptomyces puniceus Act1085 was constructed and screened to identify a short gene cluster similar to the nonactin biosynthetic cluster. The ORFs of the gene cluster isolated had high amino acid sequence identity, from 82% to 96%, with corresponding ORFs of the nonactin biosynthetic gene cluster from S...
June 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28633473/experimental-evolution-and-the-adjustment-of-metabolic-strategies-in-lactic-acid-bacteria
#15
Herwig Bachmann, Douwe Molenaar, Filipe Branco Dos Santos, Bas Teusink
Experimental evolution of microbes has gained lots of interest in recent years, mainly due to the ease of strain characterisation through next-generation sequencing. While evolutionary and systems biologists use experimental evolution to address fundamental questions in their respective fields, studies with lactic acid bacteria are often more directed by applied questions. Insight into population and genome dynamics are valuable for experimental design and data interpretation, and it is becoming increasingly apparent how different constraints limit and govern the outcome of microbial adaptation to a selective environment...
June 19, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28632991/uncovering-the-repertoire-of-fungal-secondary-metabolites-from-fleming-s-lab-to-the-international-space-station
#16
Tomasz Boruta
Fungi produce a variety of secondary metabolites (SMs), low-molecular weight compounds associated with many potentially useful biological activities. The examples of biotechnologically relevant fungal metabolites include penicillin, a beta-lactam antibiotic, and lovastatin, a cholesterol-lowering drug. The discovery of pharmaceutical lead compounds within the microbial metabolic pools relies on the selection and biochemical characterization of promising strains. Not all SMs are produced under standard cultivation conditions, hence the uncovering of chemical potential of investigated strains often requires the use of induction strategies to awake the associated biosynthetic genes...
June 20, 2017: Bioengineered
https://www.readbyqxmd.com/read/28632895/genome-mining-reveals-high-incidence-of-putative-lipopeptide-biosynthesis-nrps-pks-clusters-containing-fatty-acyl-amp-ligase-genes-in-biofilm-forming-cyanobacteria
#17
Tomáš Galica, Pavel Hrouzek, Jan Mareš
Cyanobacterial lipopeptides exhibit antimicrobial and antifungal bioactivities with potential for use in pharmaceutical research. However, due to their haemolytic activity and cytotoxic effects against human cells, they may pose a health issue if produced in substantial amounts in the environment. In bacteria, lipopeptides can be synthesized via several well-evidenced mechanisms. In one of them, fatty acyl-AMP ligase (FAAL) initiates the biosynthesis by activation of a fatty acyl residue. We have performed a bioinformatic survey of the cyanobacterial genomic information available in the public databases for the presence of FAAL-containing non-ribosomal peptide synthetase/polyketide synthetase (NRPS/PKS) biosynthetic clusters, as a genetic basis for lipopeptide biosynthesis...
June 20, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28631370/microbial-manganese-iii-reduction-fueled-by-anaerobic-acetate-oxidation
#18
Nadia Szeinbaum, Hui Lin, Jay A Brandes, Martial Taillefert, Jennifer B Glass, Thomas J DiChristina
Soluble manganese in the intermediate +III oxidation state (Mn(3+) ) is a newly identified oxidant in anoxic environments, whereas acetate is a naturally abundant substrate that fuels microbial activity. Microbial populations coupling anaerobic acetate oxidation to Mn(3+) reduction, however, have yet to be identified. We isolated a Shewanella strain capable of oxidizing acetate anaerobically with Mn(3+) as the electron acceptor, and confirmed this phenotype in other strains,. This metabolic connection between acetate and soluble Mn(3+) represents a new biogeochemical link between carbon and manganese cycles...
June 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28628637/survival-bacterial-clearance-and-thrombocytopenia-are-improved-in-polymicrobial-sepsis-by-targeting-nuclear-transport-shuttles
#19
Ruth Ann Veach, Yan Liu, Jozef Zienkiewicz, Lukasz S Wylezinski, Kelli L Boyd, James L Wynn, Jacek Hawiger
The rising tide of sepsis, a leading cause of death in the US and globally, is not adequately controlled by current antimicrobial therapies and supportive measures, thereby requiring new adjunctive treatments. Severe microvascular injury and multiple organ failure in sepsis are attributed to a "genomic storm" resulting from changes in microbial and host genomes encoding virulence factors and endogenous inflammatory mediators, respectively. This storm is mediated by stress-responsive transcription factors that are ferried to the nucleus by nuclear transport shuttles importins/karyopherins...
2017: PloS One
https://www.readbyqxmd.com/read/28626230/engineering-of-obligate-intracellular-bacteria-progress-challenges-and-paradigms
#20
REVIEW
Erin E McClure, Adela S Oliva Chávez, Dana K Shaw, Jason A Carlyon, Roman R Ganta, Susan M Noh, David O Wood, Patrik M Bavoil, Kelly A Brayton, Juan J Martinez, Jere W McBride, Raphael H Valdivia, Ulrike G Munderloh, Joao H F Pedra
It is estimated that approximately one billion people are at risk of infection with obligate intracellular bacteria, but little is known about the underlying mechanisms that govern their life cycles. The difficulty in studying Chlamydia spp., Coxiella spp., Rickettsia spp., Anaplasma spp., Ehrlichia spp. and Orientia spp. is, in part, due to their genetic intractability. Recently, genetic tools have been developed; however, optimizing the genomic manipulation of obligate intracellular bacteria remains challenging...
June 19, 2017: Nature Reviews. Microbiology
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