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https://www.readbyqxmd.com/read/29330647/absence-of-the-nitrous-oxide-reductase-gene-cluster-in-commercial-alfalfa-inoculants-is-probably-due-to-the-extensive-loss-of-genes-during-rhizobial-domestication
#1
Silvina Brambilla, Romina Frare, Gabriela Soto, Cintia Jozefkowicz, Nicolás Ayub
As other legume crops, alfalfa cultivation increases the emission of the greenhouse gas nitrous oxide (N2O). Since legume-symbiotic nitrogen-fixing bacteria play a crucial role in this emission, it is important to understand the possible impacts of rhizobial domestication on the evolution of denitrification genes. In comparison with the genomes of non-commercial strains, those of commercial alfalfa inoculants exhibit low total genome size, low number of ORFs and high numbers of both frameshifted genes and pseudogenes, suggesting a dramatic loss of genes during bacterial domestication...
January 12, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/29330592/genomic-characterization-of-key-bacteriophages-to-formulate-the-potential-biocontrol-agent-to-combat-enteric-pathogenic-bacteria
#2
Krupa M Parmar, Nishant A Dafale, Hitesh Tikariha, Hemant J Purohit
Combating bacterial pathogens has become a global concern especially when the antibiotics and chemical agents are failing to control the spread due to its resistance. Bacteriophages act as a safe biocontrol agent by selectively lysing the bacterial pathogens without affecting the natural beneficial microflora. The present study describes the screening of prominent enteric pathogens NDK1, NDK2, NDK3, and NDK4 (Escherichia, Klebsiella, Enterobacter, and Serratia) mostly observed in domestic wastewater; against which KNP1, KNP2, KNP3, and KNP4 phages were isolated...
January 12, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29330536/carbon-limitation-drives-gc-content-evolution-of-a-marine-bacterium-in-an-individual-based-genome-scale-model
#3
Ferdi L Hellweger, Yongjie Huang, Haiwei Luo
An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model...
January 12, 2018: ISME Journal
https://www.readbyqxmd.com/read/29330178/development-of-an-efficient-genome-editing-tool-in-bacillus-licheniformis-using-crispr-cas9-nickase
#4
Kaifeng Li, Dongbo Cai, Zhangqian Wang, Zhili He, Shouwen Chen
Bacillus strains are important industrial bacteria that can produce various biochemical products. However, low transformation efficiencies and a lack of effective genome editing tools have hindered its widespread application. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)/cas9 techniques have been utilized in many organisms as genome editing tools because of their high efficiency and easy manipulation. In this study, an efficient genome editing method was developed for Bacillus licheniformis using a CRISPR-Cas9 nickase integrated into the genome of B...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29328062/cyanobacterial-photosynthesis-under-sulfidic-conditions-insights-from-the-isolate-leptolyngbya-sp-strain-hensonii
#5
Trinity L Hamilton, Judith M Klatt, Dirk de Beer, Jennifer L Macalady
We report the isolation of a pinnacle-forming cyanobacterium isolated from a microbial mat covering the sediment surface at Little Salt Spring-a flooded sinkhole in Florida with a perennially microoxic and sulfidic water column. The draft genome of the isolate encodes all of the enzymatic machinery necessary for both oxygenic and anoxygenic photosynthesis, as well as genes for methylating hopanoids at the C-2 position. The physiological response of the isolate to H2S is complex: (i) no induction time is necessary for anoxygenic photosynthesis; (ii) rates of anoxygenic photosynthesis are regulated by both H2S and irradiance; (iii) O2 production is inhibited by H2S concentrations as low as 1 μM and the recovery rate of oxygenic photosynthesis is dependent on irradiance; (iv) under the optimal light conditions for oxygenic photosynthesis, rates of anoxygenic photosynthesis are nearly double those of oxygenic photosynthesis...
January 12, 2018: ISME Journal
https://www.readbyqxmd.com/read/29327679/natural-and-artificial-strategies-to-control-the-conjugative-transmission-of-plasmids
#6
María Getino, Fernando de la Cruz
Conjugative plasmids are the main carriers of transmissible antibiotic resistance (AbR) genes. For that reason, strategies to control plasmid transmission have been proposed as potential solutions to prevent AbR dissemination. Natural mechanisms that bacteria employ as defense barriers against invading genomes, such as restriction-modification or CRISPR-Cas systems, could be exploited to control conjugation. Besides, conjugative plasmids themselves display mechanisms to minimize their associated burden or to compete with related or unrelated plasmids...
January 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29327481/the-genome-and-microbiome-of-a-dikaryotic-fungus-inocybe-terrigena-inocybaceae-revealed-by-metagenomics
#7
Mohammad Bahram, Dan Vanderpool, Mari Pent, Markus Hiltunen, Martin Ryberg
Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr...
January 12, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29327434/a-fast-and-reliable-method-for-monitoring-of-prophage-activating-chemicals
#8
Juan Xu, Bärbel Kiesel, René Kallies, Feng-Lei Jiang, Yi Liu, Thomas Maskow
Bacteriophages, that is viruses that infect bacteria, either lyse bacteria directly or integrate their genome into the bacterial genome as so-called prophages, where they remain at a silent state. Both phages and bacteria are able to survive in this state. However, prophages can be reactivated with the introduction of chemicals, followed by the release of a high number of phage particles, which could infect other bacteria, thus harming ecosystems by a viral bloom. The basics for a fast, automatable analytical method for the detection of prophage-activating chemicals are developed and successfully tested here...
January 12, 2018: Microbial Biotechnology
https://www.readbyqxmd.com/read/29327330/microbiome-analysis-and-omics-studies-of-microbial-denitrification-processes-in-wastewater-treatment-recent-advances
#9
REVIEW
Lili Miao, Zhipei Liu
Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitrogen cycles, is commonly employed for nitrogen removal in engineered wastewater treatment systems. Biological denitrification is performed by denitrifying microbes (bacteria) that use nitrate as terminal electron acceptor. Better understanding the functions of diverse microbial populations in denitrification-based wastewater treatment systems, and the interactions of these populations with operating environments, is essential for improving both treatment performance and system stability...
January 9, 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/29327235/complete-genome-sequence-of-a-phage-hyperparasite-of-candidatus-xenohaliotis-californiensis-rickettsiales-a-pathogen-of-haliotis-spp-gasteropoda
#10
Roberto Flores, Jorge Cáceres-Martínez, Miguel Ángel Del Río-Portilla, Alexei F Licea-Navarro, Ricardo Gonzales-Sánchez, Abraham Guerrero
Bacteriophages are recognized as major mortality agents of microbes, among them intracellular marine rickettsiales-like bacteria. Recently, a phage hyperparasite of Candidatus Xenohaliotis californiensis (CXc) has been described. This bacterium is considered the causal agent of Withering Syndrome (WS) which is a chronic and potentially lethal disease of abalone species from California, USA and the peninsula of Baja California, Mexico. This hyperparasite which infects CXc could be used as a biocontrol agent for WS...
January 11, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29326206/whole-genome-draft-sequences-of-nine-asymptomatic-escherichia-coli-bacteriuria-isolates-from-diabetic-patients
#11
Christoph Stork, Beáta Kovács, Eva Trost, Tamás Kovács, György Schneider, Barnabás Rózsai, Monika Kerényi, Levente Emődy, Ulrich Dobrindt
Escherichia coli can colonize the urinary bladder without causing a disease response in the host. This asymptomatic bacteriuria (ABU) can protect against recurrent symptomatic urinary tract infection by virulent bacteria. Here, we report the whole-genome sequences of nine E. coli ABU isolates from diabetic patients.
January 11, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29324779/filling-gaps-in-bacterial-amino-acid-biosynthesis-pathways-with-high-throughput-genetics
#12
Morgan N Price, Grant M Zane, Jennifer V Kuehl, Ryan A Melnyk, Judy D Wall, Adam M Deutschbauer, Adam P Arkin
For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. We studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge...
January 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29324231/decoding-a-salmonella-typhi-regulatory-network-that-controls-typhoid-toxin-expression-within-human-cells
#13
Casey C Fowler, Jorge E Galán
Salmonella Typhi is the cause of typhoid fever, a major global health concern. An essential virulence factor of this pathogen is typhoid toxin. In contrast to most AB-type toxins, typhoid toxin is exclusively expressed by intracellular bacteria. The regulatory networks that ensure this unique gene expression pattern are unknown. Here, we developed FAST-INSeq, a genome-wide screening approach to identify S. Typhi genes required for typhoid toxin expression within infected cells. We find that typhoid toxin expression is controlled by a silencing and counter-silencing mechanism through the opposing actions of the PhoP/PhoQ two-component regulatory system and the histone-like protein H-NS...
January 10, 2018: Cell Host & Microbe
https://www.readbyqxmd.com/read/29323491/g-quadruplex-identification-in-the-genome-of-protozoan-parasites-points-to-naphthalene-diimide-ligands-as-new-antiparasitic-agents
#14
Efres Belmonte-Reche, Marta Martínez-García, Aurore Guédin, Michela Zuffo, Matilde Arévalo-Ruiz, Filippo Doria, Jenny Campos-Salinas, Marjorie Maynadier, Jose-Juan Lopez-Rubio, Mauro Freccero, Jean-Louis Mergny, Jose María Perez-Victoria, Juan Carlos Morales
G-quadruplexes (G4) are DNA secondary structures which take part in the regulation of gene expression. Putative G4 forming sequences (PQS) have been reported in mammals, yeast, bacteria and viruses. Here, we present PQS searches on the genomes of T. brucei, L. major and P. falciparum. We found telomeric sequences and new PQS motifs. Biophysical experiments showed that EBR1, a 29 nucleotide long highly repeated PQS in T. brucei, forms a stable G4 structure. G4 ligands based on carbohydrate conjugated naphthalene diimides (carb-NDIs) which bind G4's including hTel, could bind EBR1 with selectivity versus dsDNA...
January 11, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29323230/developing-an-in-silico-minimum-inhibitory-concentration-panel-test-for-klebsiella-pneumoniae
#15
Marcus Nguyen, Thomas Brettin, S Wesley Long, James M Musser, Randall J Olsen, Robert Olson, Maulik Shukla, Rick L Stevens, Fangfang Xia, Hyunseung Yoo, James J Davis
Antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes are becoming more feasible and may offer a way to reduce clinical test turnaround times compared to conventional culture-based methods, and in turn, improve patient outcomes. In this study, we use whole genome sequence data from 1668 clinical isolates of Klebsiella pneumoniae to develop a XGBoost-based machine learning model that accurately predicts minimum inhibitory concentrations (MICs) for 20 antibiotics...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29323202/genome-based-classification-of-micromonosporae-with-a-focus-on-their-biotechnological-and-ecological-potential
#16
Lorena Carro, Imen Nouioui, Vartul Sangal, Jan P Meier-Kolthoff, Martha E Trujillo, Maria Del Carmen Montero-Calasanz, Nevzat Sahin, Darren Lee Smith, Kristi E Kim, Paul Peluso, Shweta Deshpande, Tanja Woyke, Nicole Shapiro, Nikos C Kyrpides, Hans-Peter Klenk, Markus Göker, Michael Goodfellow
There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322764/rapid-veterinary-diagnosis-of-bovine-reproductive-infectious-diseases-from-semen-using-paper-origami-dna-microfluidics
#17
Zhugen Yang, Gaolian Xu, Julien Reboud, Syed Atif Ali, Gurpreet Kaur, John McGiven, Nongthombam Boby, Praveen Gupta, Pallab Chaudhuri, Jonathan Mark Cooper
The health and well-being of cattle is a significant concern for global agricultural output. In dairy production within low and middle income countries (LMICs), there is a significant biosensing challenge in detecting sexually transmitted infection (STI) pathogens during animal husbandry, due in part to difficulties associated with the limited infrastructure for veterinary medicine. Here we demonstrate low-cost, multiplexed and sample-to-answer paper-origami tests for the detection of three bovine infectious reproductive diseases in semen samples, collected at a test site in rural India...
January 11, 2018: ACS Sensors
https://www.readbyqxmd.com/read/29322681/gut-microbiome-contributes-to-impairment-of-immunity-in-pulmonary-tuberculosis-patients-by-alteration-of-butyrate-and-propionate-producers
#18
Abhijit Maji, Richa Misra, Darshan B Dhakan, Vipin Gupta, Nitish K Mahato, Rituja Saxena, Parul Mittal, Nitin Thukral, Eshan Sharma, Anoop Singh, Richa Virmani, Mohita Gaur, Harshvardhan Singh, Yasha Hasija, Gunjan Arora, Anurag Agrawal, Anil Chaudhry, Jitendra P Khurana, Vineet K Sharma, Rup Lal, Yogendra Singh
Tuberculosis (TB) is primarily associated with decline in immune health status. As gut microbiome (GM) is implicated in the regulation of host immunity and metabolism, here we investigate GM alteration in TB patients by 16S rRNA gene and whole-genome shotgun sequencing. The study group constituted of patients with pulmonary TB and their healthy household contacts as controls (HCs). Significant alteration of microbial taxonomic and functional capacity was observed in patients with active TB as compared to the HCs...
January 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29322618/genome-enabled-metabolic-reconstruction-of-dominant-chemosynthetic-colonizers-in-deep-sea-massive-sulfide-deposits
#19
Shingo Kato, Takazo Shibuya, Yoshihiro Takaki, Miho Hirai, Takuro Nunoura, Katsuhiko Suzuki
Deep-sea massive sulfide deposits remaining after ceasing of hydrothermal activity potentially provide energy for a chemosynthetic ecosystem in the dark, cold marine environments. Although yet-uncultivated bacteria in the phylum Nitrospirae and the class Deltaproteobacteria are known to dominate the microbial communities of sulfide deposits at and below the seafloor, their metabolic capabilities remain largely elusive. Here, we reveal the metabolic potential of these yet-uncultivated bacteria in hydrothermally inactive sulfide deposits collected at the Southern Mariana Trough by seafloor drilling...
January 10, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29322462/methods-to-determine-mutational-trajectories-after-experimental-evolution-of-antibiotic-resistance
#20
Douglas L Huseby, Diarmaid Hughes
The evolution of bacterial resistance to antibiotics by mutation within the genome (as distinct from horizontal gene transfer of new material into a genome) could occur in a single step but is usually a multistep process. Resistance evolution can be studied in laboratory environments by serial passage of bacteria in liquid culture or on agar, with selection at constant, or varying, concentrations of drug. Whole genome sequencing can be used to make an initial analysis of the evolved mutants. The trajectory of evolution can be determined by sequence analysis of strains from intermediate steps in the evolution, complemented by phenotypic analysis of genetically reconstructed isogenic strains that recapitulate the intermediate steps in the evolution...
2018: Methods in Molecular Biology
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