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https://www.readbyqxmd.com/read/29332216/characteristics-of-arg-carrying-plasmidome-in-the-cultivable-microbial-community-from-wastewater-treatment-system-under-high-oxytetracycline-concentration
#1
Yanhong Shi, Hong Zhang, Zhe Tian, Min Yang, Yu Zhang
Studies on antibiotic production wastewater have shown that even a single antibiotic can select for multidrug resistant bacteria in aquatic environments. It is speculated that plasmids are an important mechanism of multidrug resistance (MDR) under high concentrations of antibiotics. Herein, two metagenomic libraries were constructed with plasmid DNA extracted from cultivable microbial communities in a biological wastewater treatment reactor supplemented with 0 (CONTROL) or 25 mg/L of oxytetracycline (OTC-25)...
January 13, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29330650/a-cold-adapted-endoglucanase-from-camel-rumen-with-high-catalytic-activity-at-moderate-and-low-temperatures-an-anomaly-of-truly-cold-adapted-evolution-in-a-mesophilic-environment
#2
Kamran Khalili Ghadikolaei, Javad Gharechahi, Kamahldin Haghbeen, Kambiz Akbari Noghabi, Ghasem Hosseini Salekdeh, Hossein Shahbani Zahiri
Endoglucanases are important enzymes in plant biomass degradation. They have current and potential applications in various industrial sectors including human and animal food processing, textile, paper, and renewable biofuel production. It is assumed that the cold-active endoglucanases, with high catalytic rates in moderate and cold temperatures, can improve the cost-effectiveness of industrial processes by lowering the need for heating and, thus, energy consumption. In this study, the endoglucanase CelCM3 was procured from a camel rumen metagenome via gene cloning and expression in Escherichia coli BL21 (DE3)...
January 12, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29330494/characterizing-the-bacterial-microbiota-in-different-gastrointestinal-tract-segments-of-the-bactrian-camel
#3
Jing He, Li Yi, Le Hai, Liang Ming, Wanting Gao, Rimutu Ji
The bacterial community plays important roles in the gastrointestinal tracts (GITs) of animals. However, our understanding of the microbial communities in the GIT of Bactrian camels remains limited. Here, we describe the bacterial communities from eight different GIT segments (rumen, reticulum, abomasum, duodenum, ileum, jejunum, caecum, colon) and faeces determined from 11 Bactrian camels using 16S rRNA gene amplicon sequencing. Twenty-seven bacterial phyla were found in the GIT, with Firmicutes, Verrucomicrobia and Bacteroidetes predominating...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330424/metagenomic-and-metabolomic-analyses-unveil-dysbiosis-of-gut-microbiota-in-chronic-heart-failure-patients
#4
Xiao Cui, Lei Ye, Jing Li, Ling Jin, Wenjie Wang, Shuangyue Li, Minghui Bao, Shouling Wu, Lifeng Li, Bin Geng, Xin Zhou, Jian Zhang, Jun Cai
Previous studies suggested a possible gut microbiota dysbiosis in chronic heart failure (CHF). However, direct evidence was lacking. In this study, we investigated the composition and metabolic patterns of gut microbiota in CHF patients to provide direct evidence and comprehensive understanding of gut microbiota dysbiosis in CHF. We enrolled 53 CHF patients and 41 controls. Metagenomic analyses of faecal samples and metabolomic analyses of faecal and plasma samples were then performed. We found that the composition of gut microbiota in CHF was significantly different from controls...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330191/thermophilic-alkaline-fermentation-followed-by-mesophilic-anaerobic-digestion-for-efficient-hydrogen-and-methane-production-from-waste-activated-sludge-focusing-on-dynamics-of-bacterial-pathogens-as-revealed-by-the-combination-of-metagenomic-and-qpcr-analysis
#5
Jingjing Wan, Yuhang Jing, Yue Rao, Shicheng Zhang, Gang Luo
Thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM) for hydrogen and methane production from waste activated sludge (WAS) was investigated. TM process was also compared to mesophilic alkaline fermentation followed by mesophilic anaerobic digestion (MM) process and one-stage mesophilic anaerobic digestion (M) process. The results showed that both hydrogen yield (74.5 mLH2/gVS) and methane yield (150.7 mLCH4/gVS) in TM process were higher than those (6.7 mLH2/gVS and 127.8 mLCH4/gVS) in MM process...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29330189/targeted-synthesis-and-characterization-of-a-gene-cluster-encoding-nad-p-h-dependent-3%C3%AE-3%C3%AE-and-12%C3%AE-hydroxysteroid-dehydrogenases-from-eggerthella-cag-298-a-gut-metagenomic-sequence
#6
Sean M Mythen, Saravanan Devendran, Celia Méndez-García, Isaac Cann, Jason M Ridlon
Gut metagenomic sequences provide a rich source of microbial genes, the majority of which are annotated by homology or unknown. Genes and gene pathways that encode enzymes catalyzing biotransformation of host bile acids are important to identify in gut metagenomic sequences due to the importance of bile acids on gut microbiome structure and host physiology. Hydroxysteroid dehydrogenases (HSDH) are pyridine nucleotide-dependent enzymes with stereo-specificity and regio-specificity for bile acid and steroid hydroxyl groups...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29329522/a-game-improving-the-assembly-of-pooled-functional-metagenomics-sequence-data
#7
Matteo Chiara, Antonio Placido, Ernesto Picardi, Luigi Ruggiero Ceci, David Stephen Horner, Graziano Pesole
BACKGROUND: Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such "functional metagenomics" experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications...
January 12, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29329230/metagenomic-virome-analysis-of-culex-mosquitoes-from-kenya-and-china
#8
Evans Atoni, Yujuan Wang, Samuel Karungu, Cecilia Waruhiu, Ali Zohaib, Vincent Obanda, Bernard Agwanda, Morris Mutua, Han Xia, Zhiming Yuan
Many blood-feeding arthropods are known vectors of viruses that are a source of unprecedented global health concern. Mosquitoes are an integral part of these arthropod vectors. Advancements in next-generation sequencing and bioinformatics has expanded our knowledge on the richness of viruses harbored by arthropods. In the present study, we applied a metagenomic approach to determine the intercontinental virome diversity of Culex quinquefasciatus and Culex tritaeniorhynchus in Kwale, Kenya and provinces of Hubei and Yunnan in China...
January 12, 2018: Viruses
https://www.readbyqxmd.com/read/29327481/the-genome-and-microbiome-of-a-dikaryotic-fungus-inocybe-terrigena-inocybaceae-revealed-by-metagenomics
#9
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/29325543/persistent-mammalian-orthoreovirus-coxsackievirus-and-adenovirus-co-infection-in-a-child-with-a-primary-immunodeficiency-detected-by-metagenomic-sequencing-a-case-report
#10
Dagmara W Lewandowska, Riccarda Capaul, Seraina Prader, Osvaldo Zagordi, Fabienne-Desirée Geissberger, Martin Kügler, Marcus Knorr, Christoph Berger, Tayfun Güngör, Janine Reichenbach, Cyril Shah, Jürg Böni, Andrea Zbinden, Alexandra Trkola, Jana Pachlopnik Schmid, Michael Huber
BACKGROUND: We report a rare case of Mammalian orthoreovirus (MRV) infection in a child with a primary immunodeficiency (PID). Infections with Mammalian orthoreovirus are very rare and probably of zoonotic origin. Only a few cases have been described so far, including one with similar pathogenesis as in our case. CASE PRESENTATION: The patient, age 11, presented with flu-like symptoms and persistent severe diarrhea. Enterovirus has been detected over several months, however, exact typing of a positive cell culture remained inconclusive...
January 11, 2018: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29324778/genetic-diversity-and-recombination-of-enterovirus-g-strains-in-japanese-pigs-high-prevalence-of-strains-carrying-a-papain-like-cysteine-protease-sequence-in-the-enterovirus-g-population
#11
Shinobu Tsuchiaka, Yuki Naoi, Ryo Imai, Tsuneyuki Masuda, Mika Ito, Masataka Akagami, Yoshinao Ouchi, Kazuo Ishii, Shoichi Sakaguchi, Tsutomu Omatsu, Yukie Katayama, Mami Oba, Junsuke Shirai, Yuki Satani, Yasuhiro Takashima, Yuji Taniguchi, Masaki Takasu, Hiroo Madarame, Fujiko Sunaga, Hiroshi Aoki, Shinji Makino, Tetsuya Mizutani, Makoto Nagai
To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain)...
2018: PloS One
https://www.readbyqxmd.com/read/29324047/the-discovery-of-arthropod-specific-viruses-in-hematophagous-arthropods-an-open-door-to-understanding-the-mechanisms-of-arbovirus-and-arthropod-evolution
#12
Charles H Calisher, Stephen Higgs
The discovery of an odd virus from hematophagous arthropods 40 years ago by Stollar and Thomas described cell fusing agent virus in cells derived from Aedes aegypti mosquitoes. Then came the report of Kamiti River virus from Ae. macintoshi in 1999, followed by worldwide reports of the discovery of other viruses of mosquitoes, ticks, and midges that replicate only in arthropods and not in vertebrates or in vertebrate cells. These viruses (now totaling at least 64 published) have genomes analogous to viruses in various families that include arboviruses and nonarboviruses...
January 7, 2018: Annual Review of Entomology
https://www.readbyqxmd.com/read/29322917/identification-of-natural-antimicrobial-peptides-from-bacteria-through-metagenomic-and-metatranscriptomic-analysis-of-high-throughput-transcriptome-data-of-taiwanese-oolong-teas
#13
Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K Robert Lai, Tzong-Yi Lee
BACKGROUND: Anti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12-100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria and viruses. In recent years, the widespread use of antibiotics has resulted in the rapid growth of antibiotic-resistant microorganisms that often induce critical infection and pathogenesis. Recently, the advent of high-throughput technologies has led molecular biology into a data surge in both the amount and scope of data...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322681/gut-microbiome-contributes-to-impairment-of-immunity-in-pulmonary-tuberculosis-patients-by-alteration-of-butyrate-and-propionate-producers
#14
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
#15
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/29322272/a-novel-passerivirus-family-picornaviridae-in-an-outbreak-of-enteritis-with-high-mortality-in-estrildid-finches-uraeginthus-sp
#16
Péter Pankovics, Ákos Boros, Tung Gia Phan, Eric Delwart, Gábor Reuter
An enteric outbreak with high mortality (34/52, 65.4%) was recorded in 2014 in home-reared estrildid finches (Estrildidae) in Hungary. A novel passerivirus was identified in a diseased violet-eared waxbill using viral metagenomics and confirmed by RT-(q)PCR. The complete genome of finch picornavirus strain waxbill/DB01/HUN/2014 (MF977321) showed the highest amino acid sequence identity of 38.9%, 61.6%, 69.6% in P1cap, 2Chel and 3CproDpol, respectively, to passerivirus A1 (GU182406). A high viral load (6.58 × 1010 genomic copies/ml) was measured in a cloacal specimen and in the tissues (spinal cord, lung, and the intestines) of two additional affected finches...
January 10, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29319531/metagenomic-analysis-of-soil-bacterial-community-and-level-of-genes-responsible-for-biodegradation-of-aromatic-hydrocarbons
#17
Jakub Czarny, Justyna Staninska-Pięta, Jolanta Powierska-Czarny, Jacek Nowak, Łukasz Wolko, Agnieszka Piotrowska-Cyplik
The aim of the studies was to compare the composition of soil bacterial metabiomes originating from urbanized areas and areas con¬taminated with hydrocarbons with those from agricultural soil and forest soil obtained from a protected wild-life park area. It should be noted that hydrocarbons are everywhere therefore bacteria capable of their utilization are present in every soil type. In the hydrocarbon-contaminated soil and in the soil of anthropogenic origin, the bacteria belonging to Gammaproteobacteria were dominant (28...
September 27, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/29319528/metagenomic-profiling-of-the-bacterial-community-changes-from-koji-to-mash-stage-in-the-brewing-of-soy-sauce
#18
Hongbin Wang, Quanzeng Wei, Shuqi Gui, Yongrui Feng, Yong Zhang, Yihan Liu, Fuping Lu
The improvement of soy sauce fermentation is restricted by the insufficient information on bacterial community. In this study, bacterial communities in the koji and mash stage were compared based on next-generation sequencing technology. A total of 29 genera were identified in the koji stage, while 34 in the mash stage. After koji stage, 7 genera disappeared and 12 new genera appeared in the mash stage. The dominant bacteria were Kurthia, Weissella and Staphylococcus in the koji stage and Staphylococcus, Kurthia, Enterococcus and Leuconostoc in the mash stage...
December 4, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/29319512/comparison-of-microbial-communities-associated-with-halophyte-salsola-stocksii-and-non-halophyte-triticum-aestivum-using-culture-independent-approaches
#19
Salma Mukhtar, Ayesha Ishaq, Sara Hassan, Samina Mehnaz, Muhammad S Mirza, Kauser A Malik
Halophyte microbiome contributes significantly to plant performance and can provide information regarding complex ecological processes involved in osmoregulation of these plants. The objective of this study is to investigate the microbiomes associated with belowground (rhizosphere), internal (endosphere) and aboveground (phyllosphere) tissues of halophyte (Salsola stocksii) through metagenomics approach. Plant samples were collected from Khewra Salt Mines. The metagenomic DNA from soil, root and shoot samples was isolated with the help of FastDNA spin kit...
September 27, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/29319506/bacterial-communities-from-the-arsenic-mine-in-z%C3%A5-oty-stok-sudety-mountains-poland
#20
Tomasz Cłapa, Dorota Narożna, Rafał Siuda, Andrzej Borkowski, Marek Selwet, Cezary J Mądrzak, Ewa Koźlecka
Investigations of bacterial communities and characterization of mineralogy of the environment in the Złoty Stok As-Au deposit were carried out. PXRD analysis revealed the presence of picropharmacolite as the most common secondary arsenic mineral in the mine. Total DNA was extracted from slime streams or slime biofilms samples to investigate the bacterial communities. PCR amplification of 16S rDNA was performed followed by subcloning of its products. Over 170 clones were analyzed by means of RFLP method. Eight group of clones representing different restriction patterns were identified...
September 27, 2017: Polish Journal of Microbiology
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