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Phoompong Boonsaen, Madoka Kinjo, Suriya Sawanon, Yutaka Suzuki, Satoshi Koike, Yasuo Kobayashi
The fibrolytic rumen bacterium Ruminococcus flavefaciensOS14 was isolated from swamp buffalo and its phylogenetic, ecological and digestive properties were partially characterized. Isolates from rumen contents of four swamp buffalo were screened for fibrolytic bacteria; one of the 40 isolates showed a distinctive feature of solubilizing cellulose powder in liquid culture and was identified as R. flavefaciens based on its 16S ribosomal DNA sequence. This isolate, OS14, was employed for detection and digestion studies, for which a quantitative PCR assay was developed and defined cultures were tested with representative forages in Thailand...
October 17, 2017: Animal Science Journal, Nihon Chikusan Gakkaihō
Pierre Pericard, Yoann Dufresne, Loïc Couderc, Samuel Blanquart, Hélène Touzet
Motivation: Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution...
October 11, 2017: Bioinformatics
Caroline C Kim, William J Kelly, Mark L Patchett, Gerald W Tannock, Z Jordens, Halina M Stoklosinski, Jordan W Taylor, Ian M Sims, Tracey J Bell, Douglas I Rosendale
A novel anaerobic pectinolytic bacterium (strain 14(T)) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14(T) belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14(T) was Acetivibrio cellulolyticus (89.7 % sequence similarity). Strain 14(T) shared ~99 % sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut...
October 17, 2017: International Journal of Systematic and Evolutionary Microbiology
Meenakshi Srivastava, Arun Kumar Mishra
Diazotrophy is considered as one of the most crucial and dynamic phenomena in the rice field and also a major source of nitrogen input. The objective of this study was to elucidate possible interactions between diverse and dominant diazotrophic bacterial community and organic carbon composition of the paddy soil. Our results suggest that most abundantly found diazotrophs belong to a proteobacteria group and uncultured bacterial forms. A gene abundance study clearly showed significantly higher diazotrophic abundance (P < 0...
October 17, 2017: Environmental Science and Pollution Research International
Chih-Ping Chen, Chris Tsai, Ming-Huei Lin, Schu-Rern Chern, Shin-Wen Chen, Shih-Ting Lai, Wen-Lin Chen, Chen-Wen Pan, Wayseen Wang
OBJECTIVE: We present the application of non-invasive prenatal testing (NIPT) in late gestation in a pregnancy associated with intrauterine growth restriction (IUGR) and trisomy 22 confined placental mosaicism (CPM). CASE REPORT: A 35-year-old pregnant woman underwent chorionic villus sampling (CVS) at 12 weeks of gestation. The pregnancy was conceived by in vitro fertilization and intracytoplasmic sperm injection. CVS revealed a karyotype of 47,XY,+22 in all of 15 cultured chorionic villi cells...
October 2017: Taiwanese Journal of Obstetrics & Gynecology
Aline Receveur, Sophie Brisset, Jelena Martinovic, Anne Bazin, Laurence Lhomann, Claire Colmant, Dominique Pineau, Valérie Gautier, Lucie Tosca, Gérard Tachdjian
OBJECTIVE: Isochromosome of the long arm of chromosome 20 (i(20q)) is a rare structural abnormality in prenatal diagnosis. Thirty prenatal cases of mosaic i(20q) have been reported, among which only four are associated with fetal malformations. We describe a new prenatal case of i(20q) with fetal malformations. MATERIALS AND METHODS: We also observed a discrepancy between uncultured and cultured amniotic fluid cells by using conventional cytogenetic, fluorescence in situ hybridization and array-SNP analysis...
October 2017: Taiwanese Journal of Obstetrics & Gynecology
Erming Ouyang, Yuan Liu, Jiating Ouyang, Xiaohui Wang
Pharmaceutical wastewater is a typical type of wastewater with high concentrations of organic pollutants, but research on this subject is limited. The microbial community structure of sludge samples collected from the aeration tanks of three different pharmaceutical wastewater treatment systems was investigated using high-throughput sequencing. The three aeration tanks were seeded with the same inocula and stably operated for 40 days. Then, aerobic sludge samples from the three aeration tanks were collected to provide insight into the bacterial community composition of the activated sludges...
October 16, 2017: Environmental Technology
Charlotte Ness, Øystein Garred, Nils A Eide, Theresa Kumar, Ole K Olstad, Thomas P Bærland, Goran Petrovski, Morten C Moe, Agate Noer
PURPOSE: Uveal melanoma (UM) has a high propensity for metastatic spread, and approximately 40-50% of patients die of metastatic disease. Metastases can be found at the time of diagnosis but also several years after the tumor has been removed. The survival of disseminated cancer cells is known to be linked to anchorage independence, anoikis resistance, and an adaptive cellular metabolism. The cultivation of cancer cells as multicellular tumor spheroids (MCTS) by anchorage-independent growth enriches for a more aggressive phenotype...
2017: Molecular Vision
Marie Horká, Karel Šlais, Jiří Šalplachta, Filip Růžička
Pre-separation and pre-concentration of bacteria is an important step especially when they are uncultured and bacterial concentration in the matrix is low. This study describes a preparative method based on isoelectric focusing of colored microorganisms in a cellulose-based separation medium from a high conductivity matrix. The isoelectric points found for the examined cells were 1.8 for Micrococcus luteus, 3.5 for Dietzia sp., and 4.7 for Rhodotorula mucilaginosa using capillary isoelectric focusing. The final positions of the zones of colored microbial cells in the cellulose-bed are indicated by colored pI markers...
October 16, 2017: Analytica Chimica Acta
Francesca Berini, Carmine Casciello, Giorgia Letizia Marcone, Flavia Marinelli
In the transition to the post-petroleum economy, there is a growing demand for novel enzymes with high process performances to replace traditional chemistry with a more 'green' approach. To date, microorganisms encompass the richest source of industrial biocatalysts, but the Earth-living microbiota remains largely untapped by using traditional isolation and cultivation methods. Metagenomics, which is culture-independent, represents a powerful tool for discovering novel enzymes from unculturable microorganisms...
October 4, 2017: FEMS Microbiology Letters
Ksenia Arkhipova, Timofey Skvortsov, John P Quinn, John W McGrath, Christopher Cr Allen, Bas E Dutilh, Yvonne McElarney, Leonid A Kulakov
Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other...
October 13, 2017: ISME Journal
Jürgen F H Strassert, Anna Karnkowska, Elisabeth Hehenberger, Javier Del Campo, Martin Kolisko, Noriko Okamoto, Fabien Burki, Jan Janouškovec, Camille Poirier, Guy Leonard, Steven J Hallam, Thomas A Richards, Alexandra Z Worden, Alyson E Santoro, Patrick J Keeling
Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H(+)-pyrophosphatase...
October 10, 2017: ISME Journal
Qi Zhang
Bacterial resistance to existing drugs is becoming a serious public health issue, urging extensive search for new antibiotics. Teixobactin, a cyclic depsipeptide discovered in a screen of uncultured bacteria, shows potent activity against all the tested Gram-positive bacteria. Remarkably, no teixobactin-resistant bacterial strain has been obtained despite extensive efforts, highlighting the great potential of teixobactin as a lead compound in fighting against antimicrobial resistance (AMR). This review summarizes recent progresses in the understanding of many aspects of teixobactin, including chemical structure, biological activity, biosynthetic pathway, and mode of action...
October 9, 2017: Chemistry: a European Journal
Jason N Woodhouse, A Katharina Makower, Hans-Peter Grossart, Elke Dittmann
Two genome sequences of the phylum Armatimonadetes, derived from terrestrial environments, have been previously described. Here, two additional Armatimonadetes genome sequences were obtained via single-molecule real-time (SMRT) sequencing of an enrichment culture of the bloom-forming cyanobacterium Microcystis sp. isolated from a eutrophic lake (Brandenburg, Germany). The genomes are most closely affiliated with the class Fimbriimonadales, although they are smaller than the 5.6-Mbp type strain genome.
October 5, 2017: Genome Announcements
Madhuree Kumari, Shipra Pandey, Shashank Kumar Mishra, Chandra Shekhar Nautiyal, Aradhana Mishra
In this study, the interaction of biosynthesized silver nanoparticles (BSNP) with native soil via plant transport was assessed in model pathosystem of Arabidopsis thaliana and Alternaria brassicicola. Foliar application of 5 μg/mL of BSNP reduced number of spores of fungi to 2.2 × 10(5) from 7 × 10(5), while numbers of lesions got reduced to 0.9/leaf in treated plants compared to 2.9/leaf in pathogen-infected plant without altering soil pH, electric conductivity, soil organic carbon and soil microbial biomass carbon...
October 2017: 3 Biotech
A S Kol'tsova, A A Pendina, O A Efimova, A N Kaminskaya, A V Tikhonov, N S Osinovskaya, I Yu Sultanov, N Yu Shved, M I Kakhiani, V S Baranov
Using immunofluorescence with specific antibodies, we analyzed DNA hydroxymethylation in uncultured cells from 25 human uterine leiomyomas considering the menstrual cycle phase during surgery and the presence of MED12 gene mutations. It was found that each tumor node had specific DNA hydroxymethylation level that did not depend on the presence of mutations in MED12 gene, but depended on the phase of menstrual cycle. The degree of DNA hydroxymethylation was significantly lower in cells of leiomyomas excised during the luteal phase compared to the follicular phase (p=0...
September 25, 2017: Bulletin of Experimental Biology and Medicine
Mukesh Jain, Alejandra Munoz-Bodnar, Dean W Gabriel
Methylglyoxal (MG) is a cytotoxic, non-enzymatic byproduct of glycolysis that readily glycates proteins and DNA, resulting in carbonyl stress. Glyoxalase I and II (GloA and GloB) sequentially convert MG into D-lactic acid using glutathione (GSH) as a cofactor. The glyoxalase system is essential for the mitigation of MG-induced carbonyl stress, preventing subsequent cell death, and recycling GSH for maintenance of cellular redox poise. All pathogenic Liberibacters identified to date are uncultured, including "Candidatus Liberibacter asiaticus", a psyllid endosymbiont and causal agent of the severely damaging citrus disease 'huanglongbing'...
September 22, 2017: Applied and Environmental Microbiology
Lara M Jochum, Xihan Chen, Mark A Lever, Alexander Loy, Bo Barker Jørgensen, Andreas Schramm, Kasper U Kjeldsen
Most sulfate-reducing microorganisms (SRM) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRM and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRM by amplicon-sequencing and quantifying dsrB, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark...
September 22, 2017: Applied and Environmental Microbiology
Dong-Yan Zhang, Jian Zhao, Shui-Ping Yang, Jing-Jing Mo, Da-Min He, Jun Wang, Jian-Yu Gou, Xue Zhang, Wei Jiang, Ming-Xia Wen
Soil microbes are the important indicator of soil quality. For exploring Chuanminshen violaceum planting to microbial effects in tobacco soil, this paper adopted Illumina MiSeq high-throughput sequencing to research the change of bacteria and fungi at the phylum and genus in the soil. The results showed that the Ch. violaceum planting increased the biodiversity of bacteria and fungi. The influence on fungi was greater than that on bacteria. It greatly increased the sequence of fungi, it obtained 32 978 16S rDNA and 32 229 18S rDNA sequence number...
December 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Jie Deng, Hua Gao, Zhen Gao, Huaxian Zhao, Ying Yang, Qiaofen Wu, Bo Wu, Chengjian Jiang
L-lysine decarboxylase (LDC, EC is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named ldc1E was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs...
2017: PloS One
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