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https://www.readbyqxmd.com/read/28339832/effects-of-feeding-original-xpc%C3%A2-to-broilers-with-a-live-coccidiosis-vaccine-under-industrial-conditions-part-2-cecal-microbiota-analysis
#1
S H Park, S Roto, H Pavlidis, D McIntyre, K Striplin, L Brammer, S C Ricke
Biological supplements in poultry feed are of continued interest due to the improvements in growth performance, protection from pathogen invasion, and benefits in overall host health. The fermentation metabolites of Diamond V Original XPC™ (XPC) have previously been shown to improve commercial performance and reduce Salmonella in poultry. The current study sought to characterize the cecal microbiota using culture-independent analysis based on 16S rRNA gene in Coccivac-D sprayed broilers supplemented with XPC and/or Salinomycin (SAL)...
March 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/28338218/evaluation-of-targeted-exome-sequencing-for-28-protein-based-blood-group-systems-including-the-homologous-gene-systems-for-blood-group-genotyping
#2
Elizna M Schoeman, Genghis H Lopez, Eunike C McGowan, Glenda M Millard, Helen O'Brien, Eileen V Roulis, Yew-Wah Liew, Jacqueline R Martin, Kelli A McGrath, Tanya Powley, Robert L Flower, Catherine A Hyland
BACKGROUND: Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. STUDY DESIGN AND METHODS: Donor samples (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform...
March 24, 2017: Transfusion
https://www.readbyqxmd.com/read/28337567/novel-16s-rdna-primers-revealed-the-diversity-and-habitats-related-community-structure-of-sphingomonads-in-10-different-niches
#3
Yili Huang, Hao Feng, Hang Lu, Yanhua Zeng
It is believed that sphingomonads are ubiquitously distributed in environments. However detailed information about their community structure and their co-relationship with environmental parameters remain unclear. In this study, novel sphingomonads-specific primers based on the 16S rRNA gene were designed to investigate the distribution of sphingomonads in 10 different niches. Both in silico and in-practice tests on pure cultures and environmental samples showed that Sph384f/Sph701r was an efficient primer set...
March 23, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28337389/development-of-microsatellite-markers-using-illumina-miseq-sequencing-to-characterize-ephedra-gerardiana-ephedraceae
#4
Ji De, Weidong Zhu, Tianmeng Liu, Zhe Wang, Yang Zhong
PREMISE OF THE STUDY: Ephedragerardiana (Ephedraceae), occurring in the Himalayan ranges, is an important plant species used in Tibetan medicine. Due to the lack of molecular markers to characterize genetic diversity, knowledge for conservation and uses of E. gerardiana resources is limited; we therefore developed microsatellite markers for use in this species. METHODS AND RESULTS: Using Illumina MiSeq sequencing technology, we developed 29 polymorphic microsatellite loci suitable for E...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28336973/microbial-community-composition-is-related-to-soil-biological-and-chemical-properties-and-bacterial-wilt-outbreak
#5
Rui Wang, Hongchun Zhang, Liguang Sun, Gaofu Qi, Shu Chen, Xiuyun Zhao
Soil microbes play important roles in plant growth and health. Little is known about the differences of soil microbes between healthy and bacterial wilt infected soils with Ralstonia solanacearum. By Illumina-MiSeq sequencing of 16S rRNA and 18S rRNA gene amplicons, we found the soil microbial composition and diversity were distinct between healthy and bacterial wilt infected soils. Soil microbial community varied at different plant growth stages due to changes of root exudates composition and soil pH. Healthy soils exhibited higher microbial diversity than the bacterial wilt infected soils...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28331217/geographic-distribution-of-cadmium-and-its-interaction-with-the-microbial-community-in-the-longjiang-river-risk-evaluation-after-a-shocking-pollution-accident
#6
MingJiang Zhang, FuKe Huang, GuangYuan Wang, XingYu Liu, JianKang Wen, XiaoSheng Zhang, YaoSi Huang, Yu Xia
A shocking Longjiang River cadmium pollution accident occurred in 2012, the effects of which on microbial communities remain unclear. Alkaline precipitation technology was applied for remediation, but concerns rose about the stability of this technology. To understand the geographic distribution of cadmium and its correlation with microbes, in this study, 39 water samples and 39 sludge samples from this river and 2 soil samples from the nearby farmland were collected for chemical and microbial analyses. The Cd concentrations of all water samples were lower than 0...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28330322/de-novo-transcriptome-sequencing-in-monsonia-burkeana-revealed-putative-genes-for-key-metabolic-pathways-involved-in-tea-quality-and-medicinal-value
#7
Adugna A Woldesemayat, Khayalethu Ntushelo, David M Modise
Monsonia (Monsonia burkeana Planch. ex Harv) is one of the most valuable tea and traditional medicinal plants used in Southern Africa. In spite of this, there is no sequence information regarding this plant in literature. To provide understanding of the naturally occurring tea and drug-specific products and the key pathways for the biosynthesis of these molecules, we sequenced the leaf transcriptome using Illumina MiSeq platform and generated 2,590,652 paired-end reads that were assembled de novo into 45,450 high-quality transcripts...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330225/metagenomics-analysis-of-microbial-communities-associated-with-a-traditional-rice-wine-starter-culture-xaj-pitha-of-assam-india
#8
Sudipta Sankar Bora, Jyotshna Keot, Saurav Das, Kishore Sarma, Madhumita Barooah
This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq(®) System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327631/the-influence-of-environmental-factors-on-communities-of-arbuscular-mycorrhizal-fungi-associated-with-chenopodium-ambrosioides-revealed-by-miseq-sequencing-investigation
#9
Xihui Xu, Chen Chen, Zhou Zhang, Zehua Sun, Yahua Chen, Jiandong Jiang, Zhenguo Shen
Arbuscular mycorrhizal fungi (AMF) affect multiple ecosystem functions and processes, the assemblages of which vary across ecosystems. However, the influences of environmental factors on AMF communities which may shape these communities are still largely unknown. In this study, AMF communities from roots and rhizosphere soils of Chenopodium ambrosioides in different natural soils were investigated. The root habitat showed significantly smaller numbers of OTUs and lower community richness compared to the rhizosphere soil habitat...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28326156/porphyromonas-gingivalis-is-the-most-abundant-species-detected-in-coronary-and-femoral-arteries
#10
J-L C Mougeot, C B Stevens, B J Paster, M T Brennan, P B Lockhart, F K B Mougeot
An association between oral bacteria and atherosclerosis has been postulated. A limited number of studies have used 16S RNA gene sequencing-based metagenomics approaches to identify bacteria at the species level from atherosclerotic plaques in arterial walls. The objective of this study was to establish detailed oral microbiome profiles, at both genus and species level, of clinically healthy coronary and femoral artery tissues from patients with atherosclerosis. Tissue specimens were taken from clinically non-atherosclerotic areas of coronary or femoral arteries used for attachment of bypass grafts in 42 patients with atherosclerotic cardiovascular disease...
2017: Journal of Oral Microbiology
https://www.readbyqxmd.com/read/28326079/differences-in-ureolytic-bacterial-composition-between-the-rumen-digesta-and-rumen-wall-based-on-urec-gene-classification
#11
Di Jin, Shengguo Zhao, Nan Zheng, Dengpan Bu, Yves Beckers, Stuart E Denman, Christopher S McSweeney, Jiaqi Wang
Ureolytic bacteria are key organisms in the rumen producing urease enzymes to catalyze the breakdown of urea to ammonia for the synthesis of microbial protein. However, little is known about the diversity and distribution of rumen ureolytic microorganisms. The urease gene (ureC) has been the target gene of choice for analysis of the urea-degrading microorganisms in various environments. In this study, we investigated the predominant ureC genes of the ureolytic bacteria in the rumen of dairy cows using high-throughput sequencing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28326071/temporal-variations-in-cigarette-tobacco-bacterial-community-composition-and-tobacco-specific-nitrosamine-content-are-influenced-by-brand-and-storage-conditions
#12
Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Eoghan M Smyth, Lauren E Hittle, Joseph N Paulson, Mihai Pop, Stephanie S Buehler, Pamela I Clark, Emmanuel F Mongodin, Amy R Sapkota
Tobacco products, specifically cigarettes, are home to microbial ecosystems that may play an important role in the generation of carcinogenic tobacco-specific nitrosamines (TSNAs), as well as the onset of multiple adverse human health effects associated with the use of these products. Therefore, we conducted time-series experiments with five commercially available brands of cigarettes that were either commercially mentholated, custom-mentholated, user-mentholated, or non-mentholated. To mimic user storage conditions, the cigarettes were incubated for 14 days under three different temperatures and relative humidities (i...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28322295/alterations-in-gastric-microbiota-after-h-pylori-eradication-and-in-different-histological-stages-of-gastric-carcinogenesis
#13
Tung Hiu Li, Youwen Qin, Pak Chung Sham, K S Lau, Kent-Man Chu, Wai K Leung
The role of bacteria other than Helicobacter pylori (HP) in the stomach remains elusive. We characterized the gastric microbiota in individuals with different histological stages of gastric carcinogenesis and after receiving HP eradication therapy. Endoscopic gastric biopsies were obtained from subjects with HP gastritis, gastric intestinal metaplasia (IM), gastric cancer (GC) and HP negative controls. Gastric microbiota was characterized by Illumina MiSeq platform targeting the 16 S rDNA. Apart from dominant H...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28321487/benzene-degradation-in-a-denitrifying-biofilm-reactor-activity-and-microbial-community-composition
#14
Marcelle J van der Waals, Siavash Atashgahi, Ulisses Nunes da Rocha, Bas M van der Zaan, Hauke Smidt, Jan Gerritse
Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions...
March 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28320468/subgingival-microbiota-dysbiosis-in-systemic-lupus-erythematosus-association-with-periodontal-status
#15
Jôice Dias Corrêa, Débora Cerqueira Calderaro, Gilda Aparecida Ferreira, Santuza Maria Souza Mendonça, Gabriel R Fernandes, E Xiao, Antônio Lúcio Teixeira, Eugene J Leys, Dana T Graves, Tarcília Aparecida Silva
BACKGROUND: Periodontitis results from the interaction between a subgingival biofilm and host immune response. Changes in biofilm composition are thought to disrupt homeostasis between the host and subgingival bacteria resulting in periodontal damage. Chronic systemic inflammatory disorders have been shown to affect the subgingival microbiota and clinical periodontal status. However, this relationship has not been examined in subjects with systemic lupus erythematosus (SLE). The objective of our study was to investigate the influence of SLE on the subgingival microbiota and its connection with periodontal disease and SLE activity...
March 20, 2017: Microbiome
https://www.readbyqxmd.com/read/28316574/alterations-of-urinary-microbiota-in-type-2-diabetes-mellitus-with-hypertension-and-or-hyperlipidemia
#16
Fengping Liu, Zongxin Ling, Yonghong Xiao, Qing Yang, Baohong Wang, Li Zheng, Ping Jiang, Lanjuan Li, Wei Wang
Evidence shows urine specimens from different women have different populations of bacteria. The co-occurrence of hypertension and hyperlipidemia in those with diabetes may alter the composition of urine and the microenviroment of the bladder in which bacteria live. The aim of this study was to characterize the urinary microbiota in women with type 2 diabetes mellitus only and those with diabetes plus hypertension and/or hyperlipidemia, and to explore whether the composition of the urinary microbiota is affected by fasting blood glucose, blood pressure, and blood lipids...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28303827/characterisation-of-the-human-oral-microbiome-in-patients-with-coronary-artery-disease-using-next-generation-sequencing-of-16srrna-amplicons
#17
Thangam Menon, Sathya Narayanan Gopalakrishnan, Rayvathy Balasubramanian, Stalin Roy Justin
INTRODUCTION: Oral health is suspected to be linked to heart disease since species of bacteria that cause periodontitis and dental caries have been found in the atherosclerotic plaque in arteries in the heart. OBJECTIVES: The aim of this study was to characterize the oral microbiome in patients with coronary artery disease (CAD) and in a patient with dental caries (DC) without any clinical symptoms of CAD. METHODS: DNA was extracted from the oral swabs collected from the patients and sequencing was performed by next generation sequencing method using Illumina (MiSeq) platform...
January 2017: Indian Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28300212/effect-of-pesticides-on-microbial-communities-in-container-aquatic-habitats
#18
Ephantus J Muturi, Ravi Kiran Donthu, Christopher J Fields, Imelda K Moise, Chang-Hyun Kim
Container aquatic habitats support a specialized community of macroinvertebrates (e.g. mosquitoes) that feed on microbial communities associated with decaying organic matter. These aquatic habitats are often embedded within and around agricultural lands and are frequently exposed to pesticides. We used a microcosm approach to examine the single and combined effects of two herbicides (atrazine, glyphosate), and three insecticides (malathion, carbaryl, permethrin) on microbial communities of container aquatic habitats...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28300176/nanoscale-zero-valent-iron-persulfate-enhanced-upflow-anaerobic-sludge-blanket-reactor-for-dye-removal-insight-into-microbial-metabolism-and-microbial-community
#19
Fei Pan, Xiaohan Zhong, Dongsheng Xia, Xianze Yin, Fan Li, Dongye Zhao, Haodong Ji, Wen Liu
This study investigated the efficiency of nanoscale zero-valent iron combined with persulfate (NZVI/PS) for enhanced degradation of brilliant red X-3B in an upflow anaerobic sludge blanket (UASB) reactor, and examined the effects of NZVI/PS on anaerobic microbial communities during the treatment process. The addition of NZVI (0.5 g/L) greatly enhanced the decolourization rate of X-3B from 63.8% to 98.4%. The Biolog EcoPlate(TM) technique was utilized to examine microbial metabolism in the reactor, and the Illumina MiSeq high-throughput sequencing revealed 22 phyla and 88 genera of the bacteria...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28298449/real-time-sequencing-of-mycobacterium-tuberculosis-are-we-there-yet
#20
Robyn S Lee, Madhukar Pai
Whole genome sequencing has taken a leading role in epidemiologic studies of tuberculosis, but thus far, the real-time, clinical utility has been low, in part due to the requirement for culture. In Votintseva et al (J Clin Microbiol https://doi.org/10.1128/JCM.02483-16), authors present a new method for extracting Mycobacterium tuberculosis DNA directly from smear-positive respiratory samples, generating drug resistance predictions and phylogenetic trees in 44 hours using the Illumina MiSeq. Authors also illustrate the potential for < 24 hour turnaround time from DNA extraction to clinically-relevant results, with Illumina MiniSeq and Oxford Nanopore Technologies' MinION...
March 15, 2017: Journal of Clinical Microbiology
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