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Microbial genomics

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https://www.readbyqxmd.com/read/28430102/variable-virulence-phenotype-of-xenorhabdus-bovienii-%C3%AE-proteobacteria-enterobacteriaceae-in-the-absence-of-their-vector-hosts
#1
John G McMullen, Rebecca McQuade, Jean-Claude Ogier, Sylvie Pagès, Sophie Gaudriault, S Patricia Stock
Xenorhabdus bovienii bacteria have a dual lifestyle: they are mutualistic symbionts to many species of Steinernema nematodes and are pathogens to a wide array of insects. Previous studies have shown that virulence of X.bovienii-Steinernema spp. pairs decreases when the nematodes associate with non-cognate bacterial strains. However, the virulence of the X. bovienii strains alone has not been fully investigated. In this study, we characterized the virulence of nine X. bovienii strains in Galleria mellonella and Spodoptera littoralis and performed a comparative genomic analysis to correlate observed phenotypes with strain genotypes...
April 22, 2017: Microbiology
https://www.readbyqxmd.com/read/28429731/the-evolutionary-life-cycle-of-the-polysaccharide-biosynthetic-gene-cluster-based-on-the-sphingomonadaceae
#2
Mengmeng Wu, Haidong Huang, Guoqiang Li, Yi Ren, Zhong Shi, Xiaoyan Li, Xiaohui Dai, Ge Gao, Mengnan Ren, Ting Ma
Although clustering of genes from the same metabolic pathway is a widespread phenomenon, the evolution of the polysaccharide biosynthetic gene cluster remains poorly understood. To determine the evolution of this pathway, we identified a scattered production pathway of the polysaccharide sanxan by Sphingomonas sanxanigenens NX02, and compared the distribution of genes between sphingan-producing and other Sphingomonadaceae strains. This allowed us to determine how the scattered sanxan pathway developed, and how the polysaccharide gene cluster evolved...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28428832/a-meta-analysis-testing-eusocial-co-option-theories-in-termite-gut-physiology-and-symbiosis
#3
Michael E Scharf, Yunpeng Cai, Yijun Sun, Ruchira Sen, Rhitoban Raychoudhury, Drion G Boucias
The termite gut accomplishes key physiologic functions that underlie termite symbiosis and sociality. However, potential candidate functions of the host-symbiont holobiome have not yet been explored across seemingly divergent processes such as digestion, immunity, caste differentiation, and xenobiotic tolerance. This study took a meta-analysis approach for concurrently studying host and symbiont gut metatranscriptome responses of the lower termite Reticulitermes flavipes, which has ancestral characteristics and hosts a diverse mix of eukaryotic and bacterial symbionts...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28428780/genomic-and-transcriptomic-insights-into-calcium-carbonate-biomineralization-by-marine-actinobacterium-brevibacterium-linens-bs258
#4
Yuying Zhu, Ning Ma, Weihua Jin, Shimei Wu, Chaomin Sun
Calcium carbonate (CaCO3) biomineralization has been investigated due to its wide range of scientific and technological implications, however, the molecular mechanisms of this important geomicrobiological process are largely unknown. Here, a urease-positive marine actinobacterium Brevibacterium linens BS258 was demonstrated to effectively form CaCO3 precipitates. Surprisingly, this bacterium could also dissolve the formed CaCO3 with the increase of the Ca(2+) concentration. To disclose the mechanisms of biomineralization, the genome of B...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28428313/draft-genome-sequences-of-two-hydrogenogenic-carboxydotrophic-bacteria-carboxydocella-sp-strains-jdf658-and-ulo1-isolated-from-two-distinct-volcanic-fronts-in-japan
#5
Yuto Fukuyama, Tatsuki Oguro, Kimiho Omae, Yasuko Yoneda, Takashi Yoshida, Yoshihiko Sako
Hydrogenogenic carboxydotrophs may provide hydrogen as primary energy for the microbial community via carbon monoxide oxidation. To investigate the genetics of carbon monoxide metabolism, we report here the draft genome sequences of the hydrogenogenic carboxydotrophs Carboxydocella sp. strains JDF658 (2.60 Mbp; G+C content, 49.2%) and ULO1 (2.70 Mbp; G+C content, 48.8%).
April 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28427280/progress-in-terpene-synthesis-strategies-through-engineering-of-saccharomyces-cerevisiae
#6
Kalaivani Paramasivan, Sarma Mutturi
Terpenes are natural products with a remarkable diversity in their chemical structures and they hold a significant market share commercially owing to their distinct applications. These potential molecules are usually derived from terrestrial plants, marine and microbial sources. In vitro production of terpenes using plant tissue culture and plant metabolic engineering, although receiving some success, the complexity in downstream processing because of the interference of phenolics and product commercialization due to regulations that are significant concerns...
April 20, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28426191/genome-wide-abolishment-of-mobile-genetic-elements-using-genome-shuffling-and-crispr-cas-assisted-mage-allows-the-efficient-stabilization-of-a-bacterial-chassis
#7
Kinga Umenhoffer, Gábor Draskovits, Ákos Nyerges, Ildikó Karcagi, Balázs Bogos, Edit Tímár, Bálint Csörgő, Róbert Herczeg, István Nagy, Tamás Fehér, Csaba Pal, Gyorgy Posfai
The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, non-essential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization...
April 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28420738/sar202-genomes-from-the-dark-ocean-predict-pathways-for-the-oxidation-of-recalcitrant-dissolved-organic-matter
#8
Zachary Landry, Brandon K Swan, Gerhard J Herndl, Ramunas Stepanauskas, Stephen J Giovannoni
Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes...
April 18, 2017: MBio
https://www.readbyqxmd.com/read/28419766/microbial-community-function-in-the-bleaching-disease-of-the-marine-macroalgae-delisea-pulchra
#9
Enrique Zozaya-Valdés, Alexandra J Roth-Schulze, Suhelen Egan, Torsten Thomas
Disease is increasingly viewed as a major factor impacting the health of both natural and cultured populations of marine organisms, including macroalgae. The red macroalga Delisea pulchra suffers from a bleaching disease resulting from host stress and infection by opportunistic bacterial pathogens. However how pathogens cause the disease and how the entire algal-associated community is involved in the process is unclear. Here we perform a metagenomic analysis of microbial communities associated with diseased and healthy D...
April 17, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28419748/the-known-genetic-potential-for-microbial-communities-to-degrade-organic-phosphorus-is-reduced-in-low-ph-soils
#10
Ian D E A Lidbury, Tandra Fraser, Andrew R J Murphy, David J Scanlan, Gary D Bending, Alexandra M E Jones, Jonathan D Moore, Andrew Goodall, Mark Tibbett, John P Hammond, Elizabeth M H Wellington
In soil, bioavailable inorganic orthophosphate is found at low concentrations and thus limits biological growth. To overcome this phosphorus scarcity, plants and bacteria secrete numerous enzymes, namely acid and alkaline phosphatases, which cleave orthophosphate from various organic phosphorus substrates. Using profile hidden Markov modeling approaches, we investigated the abundance of various non specific phosphatases, both acid and alkaline, in metagenomes retrieved from soils with contrasting pH regimes...
April 16, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28419691/the-low-diverse-gastric-microbiome-of-the-jellyfish-cotylorhiza-tuberculata-is-dominated-by-four-novel-taxa
#11
Tomeu Viver, Luis H Orellana, Janet K Hatt, Mercedes Urdiain, Sara Díaz, Michael Richter, Josefa Antón, Massimo Avian, Rudolf Amann, Konstantinos T Konstantinidis, Ramon Rosselló-Móra
Cotylorhiza tuberculata is an important scyphozoan jellyfish producing population blooms in the Mediterranean probably due to pelagic ecosystem's decay. Its gastric cavity can serve as a simple model of microbial - animal digestive associations, yet poorly characterized. Using state-of-the-art metagenomic population binning and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), we show that only four novel clonal phylotypes were consistently associated with multiple jellyfish adults...
April 17, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28418726/u50-a-new-metric-for-measuring-assembly-output-based-on-non-overlapping-target-specific-contigs
#12
Christina J Castro, Terry Fei Fan Ng
Advances in next-generation sequencing technologies enable routine genome sequencing, generating millions of short reads. A crucial step for full genome analysis is the de novo assembly, and currently, performance of different assembly methods is measured by a metric called N50. However, the N50 value can produce skewed, inaccurate results when complex data are analyzed, especially for viral and microbial datasets. To provide a better assessment of assembly output, we developed a new metric called U50. The U50 identifies unique, target-specific contigs by using a reference genome as baseline, aiming at circumventing some limitations that are inherent to the N50 metric...
April 18, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28418111/toward-the-dark-matter-of-natural-products
#13
REVIEW
Toshiyuki Wakimoto
Considering the dynamic features of natural products, our access toward exploring the entire diversity of natural products has been quite limited. It is challenging to assess the diversity of natural products by using conventional analytical methods, even with tandem chromatographic techniques, such as LC-MS and GC-MS. This viewpoint is supported by the sequencing analyses of microbial genomes, which have unveiled the potential of secondary metabolite production far exceeding the number of isolated molecules...
April 18, 2017: Chemical Record: An Official Publication of the Chemical Society of Japan ... [et Al.]
https://www.readbyqxmd.com/read/28411224/concurrent-haloalkanoate-degradation-and-chlorate-reduction-by-pseudomonas-chloritidismutans-aw-1-t
#14
Peng Peng, Ying Zheng, Jasper J Koehorst, Peter J Schaap, Alfons J M Stams, Hauke Smidt, Siavash Atashgahi
Haloalkanoates are environmental pollutants that can be degraded aerobically by microorganisms producing hydrolytic dehalogenases. However, there is lack of information about anaerobic degradation of haloalkanoates. Genome analysis of Pseudomonas chloritidismutans AW-1(T), a facultative anaerobic chlorate-reducing bacterium, showed presence of two putative haloacid dehalogenase genes, l-dex and dehI, encoding an L-2-haloacid dehalogenase (L-DEX) and a halocarboxylic acid dehydrogenase (DehI). Hence, we studied concurrent degradation of haloalkanoates and chlorate as a yet unexplored trait of strain AW-1(T) The deduced amino acid sequences of L-DEX and DehI revealed 33-37% and 26-86% identities with biochemically/structurally characterized L-DEX and D-, DL-2-haloacid dehalogenase enzymes, respectively...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28410545/lps-stimulation-of-cord-blood-reveals-a-newborn-specific-neutrophil-transcriptomic-response-and-cytokine-production
#15
Brittany Mathias, Juan C Mira, Jonathan P Rehfuss, Jaimar C Rincon, Ricardo Ungaro, Dina C Nacionales, M Cecilia Lopez, Henry V Baker, Lyle L Moldawer, Shawn D Larson
BACKGROUND: The neonatal innate immune system differs to microbial infection both quantitatively and qualitatively when compared with adults. Here, we provide the first genome-wide ex-vivo expression profile of umbilical cord blood (UCB) neutrophils from full-term infants prior to and in response to whole-blood lipopolysaccharide (LPS) stimulation. Additionally, we provide cytokine expression prior to and following LPS stimulation. The genomic expression and cytokine profile are compared with LPS-stimulated whole blood from healthy adult subjects (HC)...
May 2017: Shock
https://www.readbyqxmd.com/read/28410234/the-ovarian-cancer-oncobiome
#16
Sagarika Banerjee, Tian Tian, Zhi Wei, Natalie Shih, Michael D Feldman, George Coukos, James C Alwine, Erle S Robertson
Humans and other mammals are colonized by microbial agents across the kingdom which can represent a unique microbiome pattern. Dysbiosis of the microbiome has been associated with pathology including cancer. We have identified a microbiome signature unique to ovarian cancers, one of the most lethal malignancies of the female reproductive system, primarily because of its asymptomatic nature during the early stages in development. We screened ovarian cancer samples along with matched, and non-matched control samples using our pan-pathogen array (PathoChip), combined with capture-next generation sequencing...
March 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28409900/introduction-microbial-local-adaptation-insights-from-natural-populations-genomics-and-experimental-evolution
#17
Tatiana Giraud, Britt Koskella, Anna-Liisa Laine
No abstract text is available yet for this article.
April 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28408979/studying-human-immunodeficiencies-in-humans-advances-in-fundamental-concepts-and-therapeutic-interventions
#18
REVIEW
Helen Su
Immunodeficiencies reveal the crucial role of the immune system in defending the body against microbial pathogens. Given advances in genomics and other technologies, this is currently best studied in humans who have inherited monogenic diseases. Such investigations have provided insights into how gene products normally function in the natural environment and have opened the door to new, exciting treatments for these diseases.
2017: F1000Research
https://www.readbyqxmd.com/read/28407798/utilization-of-defined-microbial-communities-enables-effective-evaluation-of-meta-genomic-assemblies
#19
William W Greenwald, Niels Klitgord, Victor Seguritan, Shibu Yooseph, J Craig Venter, Chad Garner, Karen E Nelson, Weizhong Li
BACKGROUND: Metagenomics is the study of the microbial genomes isolated from communities found on our bodies or in our environment. By correctly determining the relation between human health and the human associated microbial communities, novel mechanisms of health and disease can be found, thus enabling the development of novel diagnostics and therapeutics. Due to the diversity of the microbial communities, strategies developed for aligning human genomes cannot be utilized, and genomes of the microbial species in the community must be assembled de novo...
April 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28405008/targeted-enrichment-and-sequencing-of-recent-endosymbiont-host-lateral-gene-transfers
#20
Julie C Dunning Hotopp, Barton E Slatko, Jeremy M Foster
Lateral gene transfer (LGT) from microbial symbionts to invertebrate animals is described at an increasing rate, particularly between Wolbachia endosymbionts and their diverse invertebrate hosts. We sought to assess the use of a capture system to cost-effectively sequence such LGT from the host genome. The sequencing depth of Illumina paired end data obtained with a Wolbachia capture system correlated well with that for an Illumina paired end data set used to detect LGT in Wolbachia-depleted B. malayi (p-value: <2e-16)...
April 12, 2017: Scientific Reports
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