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https://www.readbyqxmd.com/read/28205101/microbial-community-compositions-in-different-functional-zones-of-carrousel-oxidation-ditch-system-for-domestic-wastewater-treatment
#1
Dong Xu, Sitong Liu, Qian Chen, Jinren Ni
The microbial community diversity in anaerobic-, anoxic- and oxic-biological zones of a conventional Carrousel oxidation ditch system for domestic wastewater treatment was systematically investigated. The monitored results of the activated sludge sampled from six full-scale WWTPs indicated that Proteobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Verrucomicrobia, Acidobacteria and Nitrospirae were dominant phyla, and Nitrospira was the most abundant and ubiquitous genus across the three biological zones...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28198609/an-unusual-flavin-dependent-halogenase-from-the-metagenome-of-the-marine-sponge-theonella-swinhoei-wa
#2
Duncan R M Smith, Agustinus R Robert Uria, Eric J N Helfrich, Daniela Milbredt, Karl-Heinz van-Pee, Joern Piel, Rebecca J M Goss
Uncultured bacteria from sponges have been demonstrated to be responsible for the generation of many potent, bioactive natural products including halogenated metabolites.1 The identification of gene clusters from the metagenomes of such bacterial communities enables the discovery of enzymes that mediate new and useful chemistries and allows insight to be gained into the biogenesis of potentially pharmacologically important natural products. Here we report a new pathway to the keramamides (krm); the first functional evidence for the existence of a distinct producer in the Theonella swinhoei WA chemotype is revealed, and a key enzyme on the pathway, a unique flavin dependent halogenase with a broad substrate specificity, and with potential as a useful new biocatalytic tool is described...
February 15, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28174314/a-ferredoxin-and-f420h2-dependent-electron-bifurcating-heterodisulfide-reductase-with-homologs-in-the-domains-bacteria-and-archaea
#3
Zhen Yan, Mingyu Wang, James G Ferry
: Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO2-reducing methanogenic anaerobes (methanogens) from the domain Archaea Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized...
February 7, 2017: MBio
https://www.readbyqxmd.com/read/28166249/approach-to-determine-the-diversity-of-legionella-species-by-nested-pcr-dgge-in-aquatic-environments
#4
Wen-Chien Huang, Hsin-Chi Tsai, Chi-Wei Tao, Jung-Sheng Chen, Yi-Jia Shih, Po-Min Kao, Tung-Yi Huang, Bing-Mu Hsu
In this study, we describe a nested PCR-DGGE strategy to detect Legionella communities from river water samples. The nearly full-length 16S rRNA gene was amplified using bacterial primer in the first step. After, the amplicons were employed as DNA templates in the second PCR using Legionella specific primer. The third round of gene amplification was conducted to gain PCR fragments apposite for DGGE analysis. Then the total numbers of amplified genes were observed in DGGE bands of products gained with primers specific for the diversity of Legionella species...
2017: PloS One
https://www.readbyqxmd.com/read/28161182/differential-effects-of-monensin-and-a-blend-of-essential-oils-on-rumen-microbiota-composition-of-transition-dairy-cows
#5
M Schären, C Drong, K Kiri, S Riede, M Gardener, U Meyer, J Hummel, T Urich, G Breves, S Dänicke
In response to oral application, monensin alters the rumen microbiota, increasing ruminal propionate production and energy availability in the animal. Data from different studies indicate that the susceptibility of rumen bacteria to monensin is mainly cell-wall dependent but tracing its activity to specific microbial groups has been challenging. Several studies have shown a similar effect for essential oils but results are inconsistent. To investigate the influence of monensin and a blend of essential oils (BEO, containing thymol, guaiacol, eugenol, vanillin, salicylaldehyde, and limonene) on the rumen microbiome, rumen liquid samples were collected orally on d 56 postpartum from cows that had either received a monensin controlled-release capsule 3 wk antepartum, a diet containing a BEO from 3 wk antepartum onward, or a control diet (n = 12)...
February 1, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28158295/genomic-sequence-of-candidatus-liberibacter-solanacearum-haplotype-c-and-its-comparison-with-haplotype-a-and-b-genomes
#6
Jinhui Wang, Minna Haapalainen, Thomas Schott, Sarah M Thompson, Grant R Smith, Anne I Nissinen, Minna Pirhonen
Haplotypes A and B of 'Candidatus Liberibacter solanacearum' (CLso) are associated with diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, D and E are associated with symptoms on apiaceous plants. To date, one complete genome of haplotype B and two high quality draft genomes of haplotype A have been obtained for these unculturable bacteria using metagenomics from the psyllid vector Bactericera cockerelli. Here, we present the first genomic sequences obtained for the carrot-associated CLso...
2017: PloS One
https://www.readbyqxmd.com/read/28148982/bio-prospecting-laccases-in-the-bacterial-diversity-of-activated-sludge-from-pulp-and-paper-industry
#7
Vijaya Gupta, Neena Capalash, Naveen Gupta, Prince Sharma
Activated sludge is an artificial ecosystem known to harbor complex microbial communities. Bacterial diversity in activated sludge from pulp and paper industry was studied to bioprospect for laccase, the multicopper oxidase applicable in a large number of industries due to its ability to utilize a wide range of substrates. Bacterial diversity using 454 pyrosequencing and laccase diversity using degenerate primers specific to conserved copper binding domain of laccase like multicopper oxidase (LMCO) genes were investigated...
March 2017: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/28128359/accessing-the-genomic-information-of-unculturable-oceanic-picoeukaryotes-by-combining-multiple-single-cells
#8
Jean-François Mangot, Ramiro Logares, Pablo Sánchez, Fran Latorre, Yoann Seeleuthner, Samuel Mondy, Michael E Sieracki, Olivier Jaillon, Patrick Wincker, Colomban de Vargas, Ramon Massana
Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell...
January 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28125031/phylogenetic-heatmaps-highlight-composition-biases-in-sequenced-reads
#9
Sulbha Choudhari, Andrey Grigoriev
Due to advancements in sequencing technology, sequence data production is no longer a constraint in the field of microbiology and has made it possible to study uncultured microbes or whole environments using metagenomics. However, these new technologies introduce different biases in metagenomic sequencing, affecting the nucleotide distribution of resulting sequence reads. Here, we illustrate such biases using two methods. One is based on phylogenetic heatmaps (PGHMs), a novel approach for compact visualization of sequence composition differences between two groups of sequences containing the same phylogenetic groups...
January 24, 2017: Microorganisms
https://www.readbyqxmd.com/read/28117431/culture-adaptation-of-malaria-parasites-selects-for-convergent-loss-of-function-mutants
#10
Antoine Claessens, Muna Affara, Samuel A Assefa, Dominic P Kwiatkowski, David J Conway
Cultured human pathogens may differ significantly from source populations. To investigate the genetic basis of laboratory adaptation in malaria parasites, clinical Plasmodium falciparum isolates were sampled from patients and cultured in vitro for up to three months. Genome sequence analysis was performed on multiple culture time point samples from six monoclonal isolates, and single nucleotide polymorphism (SNP) variants emerging over time were detected. Out of a total of five positively selected SNPs, four represented nonsense mutations resulting in stop codons, three of these in a single ApiAP2 transcription factor gene, and one in SRPK1...
January 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28114970/culture-supernatant-of-adipose-stem-cells-can-ameliorate-allergic-airway-inflammation-via-recruitment-of-cd4-cd25-foxp3-t-cells
#11
Hak Sun Yu, Mi-Kyung Park, Shin Ae Kang, Kyu-Sup Cho, Sue Jean Mun, Hwan-Jung Roh
BACKGROUND: In a previous study, we demonstrated that intravenous administration of adipose tissue stem cells (ASCs) could significantly reduce allergic symptoms and suppress eosinophilic inflammation. METHODS: To evaluate the secretome of ASCs, we administrated culture supernatant of ASCs (ASC sup, which contains the ASC secretome) and uncultured fresh medium (con sup) into a mouse model of allergic airway inflammation. Subsequently we observed the mice for signs of inflammation and investigated Th1-, Th2-, and Treg-related cytokine levels as well as recruitment of Treg cells into the airway...
January 23, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/28106880/discovery-of-anaerobic-lithoheterotrophic-haloarchaea-ubiquitous-in-hypersaline-habitats
#12
Dimitry Y Sorokin, Enzo Messina, Francesco Smedile, Pawel Roman, Jaap S Sinninghe Damsté, Sergio Ciordia, Maria Carmen Mena, Manuel Ferrer, Peter N Golyshin, Ilya V Kublanov, Nazar I Samarov, Stepan V Toshchakov, Violetta La Cono, Michail M Yakimov
Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum...
January 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/28097050/microbial-communities-mediating-algal-detritus-turnover-under-anaerobic-conditions
#13
Jessica M Morrison, Chelsea L Murphy, Kristina Baker, Richard M Zamor, Steve J Nikolai, Shawn Wilder, Mostafa S Elshahed, Noha H Youssef
BACKGROUND: Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored...
2017: PeerJ
https://www.readbyqxmd.com/read/28087803/epiphytic-planctomycetes-communities-associated-with-three-main-groups-of-macroalgae
#14
Joana Bondoso, Filipa Godoy-Vitorino, Vanessa Balagué, Josep M Gasol, Jens Harder, Olga Maria Lage
Planctomycetes, a unique group of widespread and understudied bacteria, are known to be associated with macroalgae. The temporal dynamics and the host-specific association of planctomycetal communities on Fucus spiralis, Ulva sp. and Chondrus crispus from two locations in the North Coast of Portugal were assessed both by denaturing gradient gel electrophoresis (DGGE) with group-specific primers and 16S rDNA amplicon libraries. The epiphytic planctomycetal communities showed a significant association with the host macroalgal species independently of the geographical location and the season...
January 12, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28087277/identification-of-ubact-a-ubiquitin-like-protein-along-with-other-homologous-components-of-a-conjugation-system-and-the-proteasome-in-different-gram-negative-bacteria
#15
Gilad Lehmann, Ronald G Udasin, Ido Livneh, Aaron Ciechanover
Systems analogous to the eukaryotic ubiquitin-proteasome system have been previously identified in Archaea, and Actinobacteria (gram-positive), but not in gram-negative bacteria. Here, we report the bioinformatic identification of a novel prokaryotic ubiquitin-like protein, which we name UBact. The phyletic distribution of UBact covers at least five gram-negative bacterial phyla, including Nitrospirae, Armatimonadetes, Verrucomicroba, Nitrospinae, and Planctomycetes. Additionally, it was identified in seven candidate (uncultured) phyla and one Archaeon...
January 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28081358/microbial-diversity-during-fermentation-of-sweet-paste-a-chinese-traditional-seasoning-using-pcr-denaturing-gradient-gel-electrophoresis
#16
Ping Mao, Yuanliang Hu, Tingting Liao, Zhaoting Wang, Shumiao Zhao, Yunxiang Liang, Yongmei Hu
The aim of this study was to elucidate the changes in the microbial community and biochemical properties of a traditional sweet paste during fermentation. PCR-denaturing gradient gel electrophoresis (DGGE) analysis showed that Aspergillus oryzae was the predominant species in the koji and the majority of the fungi isolated belonged to 2 Zygosaccharomyces species in the mash. The bacterial DGGE profiles revealed the presence of Bacillus subtilis during fermentation, and Lactobacillus acidipiscis, Lactobacillus pubuzihii, Lactobacillus sp, Staphylococcus kloosi and several uncultured bacteria were also detected in the mash after 14 days of main fermentation...
January 12, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28049922/comparison-of-fecal-microbiota-of-three-captive-carnivore-species-inhabiting-korea
#17
Choa An, Yumiko Okamoto, Siyu Xu, Kyung Yeon Eo, Junpei Kimura, Naomichi Yamamoto
This study aimed at characterizing fecal microbiota of three captive carnivore species of leopard cats Prionailurus bengalensis, Eurasian otters Lutra lutra and raccoon dogs Nyctereutes procyonoides. We used DNA barcoding sequencing to analyze 16S rRNA genes of uncultured bacteria in the feces collected in the Seoul Zoo. The sequencing analyses revealed that: 1) Firmicutes was the most dominant phylum for all three animals; 2) bacterial genus-rank compositions were distinct across species of the animals; and 3) bacterial community memberships were different across species of the studied animals...
December 30, 2016: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28049838/insights-into-the-lifestyle-of-uncultured-bacterial-natural-product-factories-associated-with-marine-sponges
#18
Gerald Lackner, Eike Edzard Peters, Eric J N Helfrich, Jörn Piel
The as-yet uncultured filamentous bacteria "Candidatus Entotheonella factor" and "Candidatus Entotheonella gemina" live associated with the marine sponge Theonella swinhoei Y, the source of numerous unusual bioactive natural products. Belonging to the proposed candidate phylum "Tectomicrobia," Candidatus Entotheonella members are only distantly related to any cultivated organism. The Ca E. factor has been identified as the source of almost all polyketide and modified peptides families reported from the sponge host, and both Ca Entotheonella phylotypes contain numerous additional genes for as-yet unknown metabolites...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28040137/prenatal-diagnosis-of-familial-transmission-of-17q12-microduplication-associated-with-no-apparent-phenotypic-abnormality
#19
Chih-Ping Chen, Chung-Hu Fu, Yi-Hui Lin, Schu-Rern Chern, Peih-Shan Wu, Yen-Ni Chen, Shin-Wen Chen, Wayseen Wang
OBJECTIVE: We present prenatal diagnosis of familial transmission of 17q12 duplication associated with no apparent phenotypic abnormality. CASE REPORT: A 36-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Cytogenetic analysis revealed a karyotype of 46,XY. Array comparative genomic hybridization of uncultured amniocytes revealed a 1.42-Mb duplication of 17q12 or arr 17q12 (34,822,465-36,243,365) × 3 encompassing 12 Online Mendelian Inheritance in Man (OMIM) genes including LHX1, ACACA, and HNF1B...
December 2016: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28032398/cultivation-and-characterisation-of-the-surface-markers-and-carbohydrate-profile-of-human-corneal-endothelial-cells
#20
Richárd Nagymihály, Zoltán Veréb, Réka Albert, Laura Sidney, Harminder Dua, Andrew Hopkinson, Goran Petrovski
BACKGROUND: To characterise human corneal endothelial cell (HCEnC) cultures generated by the peel-and-digest method based on their surface protein/carbohydrate expression pattern. METHODS: QPCR was used to compare expression of Vimentin, CD90, Cytokeratin-19, ZO-1, Claudin 14 in cultured HCEnC and cell line B4G12 versus stromal cells. Fluorescence-activated cell sorting (FACS) was used to assess surface protein distribution of cultured and uncultured HCEnC. Distribution of surface proteins/ carbohydrates was visualised by immunofluorescent and lectin staining...
December 29, 2016: Clinical & Experimental Ophthalmology
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