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https://www.readbyqxmd.com/read/28799297/exploring-the-microbial-diversity-in-jordanian-hot-springs-by-comparative-metagenomic-analysis
#1
Emad I Hussein, Jacob H Jacob, Muhamad Ali K Shakhatreh, Mutaz A Abd Al-Razaq, Abdul-Salam F Juhmani, Christopher T Cornelison
A culture-independent approach was utilized in this study to reveal the microbial diversity in Jordanian hot springs represented by Ma'in and Afra hot springs. Water samples from Ma'in and Afra hot springs were collected in June 2015. The in situ temperature of water samples range was 38-59°C and the pH range was 7.4-8.4. The metagenome was extracted and analyzed using the next generation technology (bTEFAP(®) ). A total of 314,310 sequences were parsed and 288,452 were then clustered. The sequences were predominated by bacteria (>84%) and the relative abundance of archaea in each sample was <1%...
August 10, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28799224/genomic-insights-into-the-pathogenicity-and-environmental-adaptability-of-enterococcus-hirae-r17-isolated-from-pork-offered-for-retail-sale
#2
Zixin Peng, Menghan Li, Wei Wang, Hongtao Liu, Séamus Fanning, Yujie Hu, Jianzhong Zhang, Fengqin Li
Genetic information about Enterococcus hirae is limited, a feature that has compromised our understanding of these clinically challenging bacteria. In this study, comparative analysis was performed of E. hirae R17, a daptomycin-resistant strain isolated from pork purchased from a retail market in Beijing, China, and three other enterococcal genomes (Enterococcus faecium DO, Enterococcus faecalis V583, and E. hirae ATCC(™) 9790). Some 1,412 genes were identified that represented the core genome together with an additional 139 genes that were specific to E...
August 10, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28782284/factors-affecting-the-bacterial-community-composition-and-heterotrophic-production-of-columbia-river-estuarine-turbidity-maxima
#3
Lydie Herfort, Byron C Crump, Caroline S Fortunato, Lee Ann McCue, Victoria Campbell, Holly M Simon, António M Baptista, Peter Zuber
Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production ((3) H-leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs...
August 6, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28782279/biosynthesis-of-the-antimicrobial-cyclic-lipopeptides-nunamycin-and-nunapeptin-by-pseudomonas-fluorescens-strain-in5-is-regulated-by-the-luxr-type-transcriptional-regulator-nunf
#4
Rosanna C Hennessy, Christopher B W Phippen, Kristian F Nielsen, Stefan Olsson, Peter Stougaard
Nunamycin and nunapeptin are two antimicrobial cyclic lipopeptides (CLPs) produced by Pseudomonas fluorescens In5 and synthesized by nonribosomal synthetases (NRPS) located on two gene clusters designated the nun-nup regulon. Organization of the regulon is similar to clusters found in other CLP-producing pseudomonads except for the border regions where putative LuxR-type regulators are located. This study focuses on understanding the regulatory role of the LuxR-type-encoding gene nunF in CLP production of P...
August 6, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28782269/molecular-evolution-of-acetohydroxyacid-synthase-in-bacteria
#5
Yadi Liu, Yanyan Li, Xiaoyuan Wang
Acetohydroxyacid synthase (AHAS) is the key enzyme in the biosynthetic pathways of branched chain amino acids in bacteria. Since it does not exist in animal and plant cells, AHAS is an attractive target for developing antimicrobials and herbicides. In some bacteria, there is a single copy of AHAS, while in others there are multiple copies. Therefore, it is necessary to investigate the origin and evolutionary pathway of various AHASs in bacteria. In this study, all the available protein sequences of AHAS in bacteria were investigated, and an evolutionary model of AHAS in bacteria is proposed, according to gene structure, organization and phylogeny...
August 6, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28766873/analysis-of-nifh-rna-reveals-phylotypes-related-to-geobacter-and-cyanobacteria-as-important-functional-components-of-the%C3%A2-n2-fixing-community-depending-on-depth-and-agricultural%C3%A2-use-of-soil
#6
Priscila A Calderoli, Mónica M Collavino, Filipe Behrends Kraemer, Héctor J M Morrás, O Mario Aguilar
In this survey, a total of 80 787 reads and 28 171 unique NifH protein sequences were retrieved from soil RNA. This dataset extends our knowledge about the structure and diversity of the functional diazotrophic communities in agricultural soils from Argentinean Pampas. Operational taxonomic unit (OTU)-based analyses showed that nifH phylotypes related to Geobacter and Anaeromyxobacter (44.8%), Rhizobiales (29%), Cyanobacteria (16.7%), and Verrucomicrobiales (8%) are key microbial components of N2 fixation in soils associated with no-till management and soil depth...
August 1, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28744982/mcp-aer-cheb-and-chev-contribute-to-the-regulation-of-vibrio-alginolyticus-nd-01-adhesion-under-gradients-of-environmental-factors
#7
Lixing Huang, Lu Wang, Xiangzhi Lin, Yongquan Su, Yingxue Qin, Wendi Kong, Lingmin Zhao, Xiaojin Xu, Qingpi Yan
Adhesion is a key virulence factor of pathogens and can be affected by the environment. Our previously research with RNA-seq indicated that mcp, aer, cheB, and cheV might play roles in the regulation of adhesion in Vibrio alginolyticus (ND-01). In order to determine whether and how environmental factors affect adhesion through these genes, gene silencing was performed followed by quantitative real-time PCR (qRT-PCR), RNAi, transmission electron microscopy, and adhesion, capillary, and motility assays to verify how these genes influence adhesion...
July 25, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28736979/in-vitro-characteristics-of-lactobacillus-spp-strains-isolated-from-the-chicken-digestive-tract-and-their-role-in-the-inhibition-of-campylobacter-colonization
#8
Patrycja A Kobierecka, Agnieszka K Wyszyńska, Tamara Aleksandrzak-Piekarczyk, Maciej Kuczkowski, Anna Tuzimek, Wioletta Piotrowska, Adrian Górecki, Iwona Adamska, Alina Wieliczko, Jacek Bardowski, Elżbieta K Jagusztyn-Krynicka
Campylobacter jejuni/coli infections are the leading cause of bacterial diarrheal illnesses in humans. Many epidemiological studies indicate that improperly prepared meat from chickens that carry a high load of Campylobacter in their intestinal tracts is the key source of human infections. LAB, mainly members of the Lactococcus and Lactobacillus genera, increasingly have been tested as vehicles for the delivery of heterologous bacterial or viral antigens to animal mucosal immune systems. Thus, the objective of this study was to isolate, identify, and characterize Lactobacillus spp...
July 24, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28736905/bacterial-and-fungal-communities-and-contribution-of-physicochemical-factors-during-cattle-farm-waste-composting
#9
Huhe, Chao Jiang, Yanpei Wu, Yunxiang Cheng
During composting, the composition of microbial communities is subject to constant change owing to interactions with fluctuating physicochemical parameters. This study explored the changes in bacterial and fungal communities during cattle farm waste composting and aimed to identify and prioritize the contributing physicochemical factors. Microbial community compositions were determined by high-throughput sequencing. While the predominant phyla in the bacterial and fungal communities were largely consistent during the composting, differences in relative abundances were observed...
July 24, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28714266/potential-biotechnological-capabilities-of-cultivable-mycobiota-from-carwash-effluents
#10
Timothy Sibanda, Ramganesh Selvarajan, Memory Tekere, Hlengilizwe Nyoni, Stephen Meddows-Taylor
Urban life has created man-made extreme environments like carwashes. These environments have, however, not been sufficiently explored for mycobiota that can be sources of biotechnologically useful products, as has been the case with natural extreme environments. Using a combination of culture and molecular techniques, fungi from carwash effluents was characterized for production of lipase and cellulase enzymes, nonpolar and polar biotechnologically relevant secondary metabolites and hydrocarbon utilization...
July 17, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28714263/enhancing-methyl-parathion-degradation-by-the-immobilization-of-burkholderia-sp-isolated-from-agricultural-soils
#11
Maikel Gilberto Fernández-López, Carolina Popoca-Ursino, Enrique Sánchez-Salinas, Raunel Tinoco-Valencia, Jorge Luis Folch-Mallol, Edgar Dantán-González, Ma Laura Ortiz-Hernández
Organophosphate pesticides are of great interest for research because they are currently the most commonly used pesticides. In this study, a bacterial strain capable of completely degrading methyl parathion (MP) was isolated from agricultural soils in central Mexico. This strain was designated strain S5-2 and was identified as Burkholderia cenocepacia. To increase degradation yields, cells were immobilized on three different supports: powdered zeolite and Opuntia sp. and Agave sp. fibers. The results indicated a significant increase in MP hydrolysis and p-nitrophenol (PNP) degradation with immobilized cells compared to free cell cultures...
July 17, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28714256/a1s_2811-a-chea-y-like-hybrid-two-component-regulator-from-acinetobacter%C3%A2-baumannii-atcc17978-is-involved-in-surface-motility-and-biofilm-formation-in-this-bacterium
#12
Rong Chen, Ruichen Lv, Lisheng Xiao, Min Wang, Zongmin Du, Yafang Tan, Yujun Cui, Yanfeng Yan, Yanping Luo, Ruifu Yang, Yajun Song
Two-component systems in Acinetobacter baumannii are associated with its virulence, drug resistance, motility, biofilm formation, and other characteristics. In this study, we used RecAb , a genetic engineering method, to investigate the function of A1S_2811 in A. baumannii strain ATCC17978. A1S_2811, a hypothetical hybrid sensor histidine kinase/response regulator, has four histidine-containing phosphotransfer domains, a CheA-like regulatory domain, and a CheY-like receiver domain at its C terminus. Compared with the ATCC17978 strain, both surface motility and biofilm formation at the gas-liquid interface decreased significantly in the A1S_2811 knock-out strain...
July 17, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28714216/contributions-of-the-oligopeptide-permeases-in-multistep-of-vibrio-alginolyticus-pathogenesis
#13
Wenjia Liu, Lixing Huang, Yongquan Su, Yingxue Qin, Lingmin Zhao, Qingpi Yan
Vibrio alginolyticus has been associated with several diseases of cultivated marine animals, and has led to considerable economic losses. The oligopeptide permease (Opp) has been proven to play a variety of important roles in nutrition and virulence in several bacteria. In our previous research, the opp gene cluster was identified in Vibrio alginolyticus with transcriptome sequence, which also indicated that the Opp system might play roles in the regulation of adhesion. In this study, the relationship between V...
July 17, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28685978/the-viable-but-nonculturable-state-induction-and-genomic-analyses-of-lactobacillus-casei-bm-lc14617-a-beer-spoilage-bacterium
#14
Junyan Liu, Lin Li, Brian M Peters, Bing Li, Lequn Chen, Yang Deng, Zhenbo Xu, Mark E Shirtliff
This study aimed to investigate the viable but nonculturable (VBNC) state and genomic features of a beer-spoilage strain, Lactobacillus caseiBM-LC14617. Induction on the VBNC state of L. casei strain BM-LC14617 was conducted by both low-temperature storage and continuous passage in beer, and formation of VBNC state was detected after 196 ± 3.3 days and 32 ± 1.6 subcultures, respectively. Resuscitation of VBNC cells was successfully induced by addition of catalase, and culturable, VBNC, and resuscitated cells shared similar beer-spoilage capability...
July 6, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28677326/microbial-community-analysis-of-the-hypersaline-water-of-the-dead-sea-using-high-throughput-amplicon-sequencing
#15
Jacob H Jacob, Emad I Hussein, Muhamad Ali K Shakhatreh, Christopher T Cornelison
Amplicon sequencing using next-generation technology (bTEFAP(®) ) has been utilized in describing the diversity of Dead Sea microbiota. The investigated area is a well-known salt lake in the western part of Jordan found in the lowest geographical location in the world (more than 420 m below sea level) and characterized by extreme salinity (approximately, 34%) in addition to other extreme conditions (low pH, unique ionic composition different from sea water). DNA was extracted from Dead Sea water. A total of 314,310 small subunit RNA (SSU rRNA) sequences were parsed, and 288,452 sequences were then clustered...
July 5, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28677248/identification-of-suitable-reference-genes-during-the-formation-of-chlamydospores-in-clonostachys-rosea-67-1
#16
Jun Zhang, Zhanbin Sun, Shidong Li, Manhong Sun
Clonostachys rosea is a potential biocontrol fungus that can produce highly resistant chlamydospores under specific conditions. To investigate the genes related to chlamydospore formation, we identified reliable reference genes for quantification of gene expression in C. rosea 67-1 during sporulation. In this study, nine reference genes, actin (ACT), elongation factor 1 (EF1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone (HIS), RNA polymerase II CTD phosphatase Fcp1 (RPP), succinate-semialdehyde dehydrogenase (SSD), TATA-binding protein (TBP), ubiquitin (UBQ), and ubiquitin-conjugating enzyme (UCE), were selected and cloned from 67-1, and their expression stability during chlamydospore formation was determined using reverse transcription quantitative PCR and assessed using the software geNorm, NormFinder and BestKeeper...
July 5, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28675659/characterization-of-a-deinococcus-radiodurans-mazf-a-uaca-specific-rna-endoribonuclease
#17
Tatsuki Miyamoto, Yuri Ota, Akiko Yokota, Tetsushi Suyama, Satoshi Tsuneda, Naohiro Noda
Microbes are known to withstand environmental stresses by using chromosomal toxin-antitoxin systems. MazEF is one of the most extensively studied toxin-antitoxin systems. In stressful environments, MazF toxins modulate translation by cleaving single-stranded RNAs in a sequence-specific fashion. Previously, a chromosomal gene located at DR0417 in Deinococcus radiodurans was predicted to code for a MazF endoribonuclease (MazFDR0417 ); however, its function remains unclear. In the present study, we characterized the molecular function of MazFDR0417 ...
July 3, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28639414/brachiaria-grasses-brachiaria-spp-harbor-a-diverse-bacterial-community-with-multiple-attributes-beneficial-to-plant-growth-and-development
#18
Collins Mutai, Joyce Njuguna, Sita Ghimire
Endophytic and plant-associated bacteria were isolated from plants and rhizoplane soil of naturally grown Brachiaria grasses at International Livestock Research Institute in Nairobi, Kenya. Eighty-four bacterial strains were isolated from leaf tissues, root tissues, and rhizoplane soil on nutrient agar and 869 media. All bacterial strains were identified to the lowest possible taxonomic unit using 16S rDNA primers and were characterized for the production of Indole-3-acetic acid, hydrogen cyanide, and ACC deaminase; phosphate solubilization; siderophore production; antifungal properties; and plant biomass production...
June 21, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28621084/coregulation-of-the-cyclic-lipopeptides-orfamide-and-sessilin-in-the-biocontrol-strain-pseudomonas-sp-cmr12a
#19
Feyisara E Olorunleke, Nam P Kieu, Evelien De Waele, Marc Timmerman, Marc Ongena, Monica Höfte
Cyclic lipopeptides (CLPs) are synthesized by nonribosomal peptide synthetases (NRPS), which are often flanked by LuxR-type transcriptional regulators. Pseudomonas sp. CMR12a, an effective biocontrol strain, produces two different classes of CLPs namely sessilins and orfamides. The orfamide biosynthesis gene cluster is flanked up- and downstream by LuxR-type regulatory genes designated ofaR1 and ofaR2, respectively, whereas the sessilin biosynthesis gene cluster has one LuxR-type regulatory gene which is situated upstream of the cluster and is designated sesR...
June 15, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28589562/the-complete-genome-sequence-of-exiguobacterium-arabatum-w-01-reveals-potential-probiotic-functions
#20
Meinan Cong, Qingling Jiang, Xiaojin Xu, Lixing Huang, Yongquan Su, Qingpi Yan
Shrimp is extensively cultured worldwide. Shrimp farming is suffering from a variety of diseases. Probiotics are considered to be one of the effective methods to prevent and cure shrimp diseases. Exiguobacterium arabatum W-01, a gram-positive and orange-pigmented bacterium, was isolated from the intestine of a healthy Penaeus vannamei specimen. Whole-genome sequencing revealed a genome of 2,914,854 bp, with 48.02% GC content. In total, 3,083 open reading frames (ORFs) were identified, with an average length of 843...
June 6, 2017: MicrobiologyOpen
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