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https://www.readbyqxmd.com/read/28229558/microbial-diversity-of-a-full-scale-uasb-reactor-applied-to-poultry-slaughterhouse-wastewater-treatment-integration-of-16s-rrna-gene-amplicon-and-shotgun-metagenomic-sequencing
#1
Tiago Palladino Delforno, Gileno Vieira Lacerda Júnior, Melline F Noronha, Isabel K Sakamoto, Maria Bernadete A Varesche, Valéria M Oliveira
The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset...
February 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28228091/exploring-the-transcriptome-of-non-model-oleaginous-microalga-dunaliella-tertiolecta-through-high-throughput-sequencing-and-high-performance-computing
#2
Lina Yao, Kenneth Wei Min Tan, Tin Wee Tan, Yuan Kun Lee
BACKGROUND: RNA-Seq technology has received a lot of attention in recent years for microalgal global transcriptomic profiling. It is widely used in transcriptome-wide analysis of gene expression., particularly for microalgal strains with potential as biofuel sources. However, insufficient genomic or transcriptomic information of non-model microalgae has limited the understanding of their regulatory mechanisms and hampered genetic manipulation to enhance biofuel production. As such, an optimal microalgal transcriptomic database construction is a subject of urgent investigation...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28223188/next-generation-sequencing-unravels-homozygous-mutation-in-glucose-6-phosphate-isomerase-gpic-1040g-a-p-arg347his-causing-hemolysis-in-an-indian-infant
#3
Manu Jamwal, Anu Aggarwal, Anirban Das, Arindam Maitra, Prashant Sharma, Shekhar Krishnan, Neeraj Arora, Deepak Bansal, Reena Das
INTRODUCTION: Inherited anemias diagnostic workup requires a step-wise algorithm. Causal genes implicated in congenital hemolytic anemia are numerous, making a gene-by-gene approach by Sanger sequencing time consuming, expensive and labour intensive. Targeted resequencing can be of great use in explaining these cases. METHODOLOGY: Six months female presented with neonatal jaundice and negative family history. Clinical and laboratory evidences were suggestive of hemolytic anemia...
February 20, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28220873/response-of-rhizosphere-soil-microbial-to-deyeuxia-angustifolia-encroaching-in-two-different-vegetation-communities-in-alpine-tundra
#4
Lin Li, Ming Xing, Jiangwei Lv, Xiaolong Wang, Xia Chen
Deyeuxia angustifolia (Komarov) Y. L Chang is an herb species originating from the birch forests in the Changbai Mountain. Recently, this species has been found encroaching into large areas in the western slopes of the alpine tundra in the Changbai Mountain, threatening the tundra ecosystem. In this study, we systematically assessed the response of the rhizosphere soil microbial to D. angustifolia encroaching in alpine tundra by conducting experiments for two vegetation types (shrubs and herbs) by real-time PCR and Illumina Miseq sequencing methods...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28219522/molecular-assessment-of-the-bacterial-community-associated-with-cassava-manihot-esculenta-crantz-cultivation-in-cameroon
#5
Papa Saliou Sarr, Akifumi Sugiyama, Aime Didier Boyogueno Begoude, Kazufumi Yazaki, Shigeru Araki, Eiji Nawata
Bacterial communities play an important role in nutrient cycles and plant development. Their distribution and activity may depend on location and environmental heterogeneity. This study characterized soil bacterial communities in cassava fields of Eastern (Andom) and Southern (Bityili) Cameroon using molecular tools. In both sites, two improved varieties (TMS-96/1414; TMS-92/0326) and a local variety (Local) were grown in a randomized block design. Composite bulk soils were collected at 10months after planting from cassava plots...
April 2017: Microbiological Research
https://www.readbyqxmd.com/read/28212267/effects-of-dietary-yogurt-on-the-healthy-human-gastrointestinal-gi-microbiome
#6
Daniel J Lisko, G Patricia Johnston, Carl G Johnston
The gastrointestinal (GI) tract performs key functions that regulate the relationship between the host and the microbiota. Research has shown numerous benefits of probiotic intake in the modulation of immune responses and human metabolic processes. However, unfavorable attention has been paid to temporal changes of the microbial composition and diversity of the GI tract. This study aimed to investigate the effects of yogurt consumption on the GI microbiome bacteria community composition, structure and diversity during and after a short-term period (42 days)...
February 15, 2017: Microorganisms
https://www.readbyqxmd.com/read/28211884/responses-of-spatial-temporal-dynamics-of-bacterioplankton-community-to-large-scale-reservoir-operation-a-case-study-in-the-three-gorges-reservoir-china
#7
Zhe Li, Lunhui Lu, Jinsong Guo, Jixiang Yang, Jiachao Zhang, Bin He, Linlin Xu
Large rivers are commonly regulated by damming, yet the effects of such disruption on bacterioplankton community structures have not been adequately studied. The aim of this study was to explore the biogeographical patterns present under dam regulation and to uncover the major drivers structuring bacterioplankton communities. Bacterioplankton assemblages in the Three Gorges Reservoir (TGR) were analyzed using Illumina Miseq sequencing by comparing seven sites located within the TGR before and after impoundment...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209832/complete-genome-sequences-of-three-multidrug-resistant-clinical-isolates-of-streptococcus-pneumoniae-serotype-19a-with-different-susceptibilities-to-the-myxobacterial-metabolite-carolacton
#8
Jannik Donner, Boyke Bunk, Isabel Schober, Cathrin Spröer, Simone Bergmann, Michael Jarek, Jörg Overmann, Irene Wagner-Döbler
The full-genome sequences of three drug- and multidrug-resistant Streptococcus pneumoniae clinical isolates of serotype 19A were determined by PacBio single-molecule real-time sequencing, in combination with Illumina MiSeq sequencing. A comparison to the genomes of other pneumococci indicates a high nucleotide sequence identity to strains Hungary19A-6 and TCH8431/19A.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28208114/efficient-degradation-of-chlorimuron-ethyl-by-a-bacterial-consortium-and-shifts-in-the-aboriginal-microorganism-community-during-the-bioremediation-of-contaminated-soil
#9
Chunyan Li, Tongyang Lv, Wanjun Liu, Hailian Zang, Yi Cheng, Dapeng Li
Excessive application of chlorimuron-ethyl has led to soil contamination and limited crop rotation; therefore, tactics to decrease and eliminate residual chlorimuron-ethyl in the environment have attracted increasing attention. In this study, two chlorimuron-ethyl-degrading bacterial strains (Rhodococcus sp. D310-1; Enterobacter sp. D310-5) were used to ferment and prepare a chlorimuron-ethyl-degrading bacterial consortium. To improve the degradation efficiency of the bacterial consortium, the cultivation conditions were optimized using response surface methodology (RSM)...
February 13, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28202080/mentholation-affects-the-cigarette-microbiota-by-selecting-for-bacteria-resistant-to-harsh-environmental-conditions-and-selecting-against-potential-bacterial-pathogens
#10
Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R Babik, Molly C Reid, Eoghan M Smyth, Lauren E Hittle, Joseph N Paulson, Raul Cruz-Cano, Mihai Pop, Stephanie S Buehler, Pamela I Clark, Amy R Sapkota, Emmanuel F Mongodin
BACKGROUND: There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. To address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a commercially-mentholated product...
February 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28196961/bacterial-topography-of-the-healthy-human-lower-respiratory-tract
#11
Robert P Dickson, John R Erb-Downward, Christine M Freeman, Lisa McCloskey, Nicole R Falkowski, Gary B Huffnagle, Jeffrey L Curtis
Although culture-independent techniques have refuted lung sterility in health, controversy about contamination during bronchoscope passage through the upper respiratory tract (URT) has impeded research progress. We sought to establish whether bronchoscopic sampling accurately reflects the lung microbiome in health and to distinguish between two proposed routes of authentic microbial immigration, (i) dispersion along contiguous respiratory mucosa and (ii) subclinical microaspiration. During bronchoscopy of eight adult volunteers without lung disease, we performed seven protected specimen brushings (PSB) and bilateral bronchoalveolar lavages (BALs) per subject...
February 14, 2017: MBio
https://www.readbyqxmd.com/read/28196719/bacterial-community-shift-and-hydrocarbon-transformation-during-bioremediation-of-short-term-petroleum-contaminated-soil
#12
Manli Wu, Xiqiong Ye, Kaili Chen, Wei Li, Jing Yuan, Xin Jiang
A laboratory study was conducted to evaluate the impact of bioaugmentation plus biostimulation (BR, added both nutrients and bacterial consortia), and natural attenuation (NA) on hydrocarbon degradation efficiency and microflora characterization during remediation of a freshly contaminated soil. After 112 days of remediation, the initial level of total petroleum hydrocarbon (TPH) (61,000 mg/kg soil) was reduced by 4.5% and 5.0% in the NA and BR treatments, respectively. Bioremediation did not significantly enhance TPH biodegradation compared to natural attenuation...
February 10, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28196473/2-7-million-samples-genotyped-for-hla-by-next-generation-sequencing-lessons-learned
#13
Gerhard Schöfl, Kathrin Lang, Philipp Quenzel, Irina Böhme, Jürgen Sauter, Jan A Hofmann, Julia Pingel, Alexander H Schmidt, Vinzenz Lange
BACKGROUND: At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-high-volume high-resolution genotyping of HLA loci for the last three and a half years. Here, we report on our experiences in genotyping the HLA, CCR5, ABO, RHD and KIR genes using a direct amplicon sequencing approach on Illumina MiSeq and HiSeq 2500 instruments. RESULTS: Between January 2013 and June 2016, 2,714,110 samples largely from German, Polish and UK-based potential stem cell donors have been processed...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28192086/variant-call-concordance-between-two-laboratory-developed-solid-tumor-targeted-genomic-profiling-assays-using-distinct-workflows-and-sequencing-instruments
#14
Ken J Hampel, Francine B de Abreu, Nikoletta Sidiropoulos, Jason D Peterson, Gregory J Tsongalis
Targeted genomic profiling (TGP) using massively parallel DNA sequencing is becoming the standard methodology in clinical laboratories for detecting somatic variants in solid tumors. The variety of methodologies and sequencing platforms in the marketplace for TGP has resulted in a variety of clinical TGP laboratory developed tests (LDT). The variability of LDTs is a challenge for test-to-test and laboratory-to-laboratory reliability. At the University of Vermont Medical Center (UVMMC), we validated a TGP assay for solid tumors which utilizes DNA hybridization capture and complete exon and selected intron sequencing of 29 clinically actionable genes...
February 10, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28188105/microbial-community-composition-and-function-in-a-pilot-scale-anaerobic-anoxic-aerobic-combined-process-for-the-treatment-of-traditional-chinese-medicine-wastewater
#15
Longyi Lv, Weiguang Li, Chuandong Wu, Liqiang Meng, Wen Qin
Biodegradation of traditional Chinese medicine (TCM) wastewater was investigated in a pilot-scale anaerobic-anoxic-aerobic combined process, which was composed of an expanded granular sludge blanket (EGSB) reactor, a hydrolysis acidification (HA) reactor and a biological contact oxidation (BCO) reactor. In stable stage, the average values of COD and color in the combined process effluent were 45.7mgL(-1) and 13 times, respectively. Excellent linear relations (R(2)>0.915) were achieved between color and UV254 at three color levels...
January 30, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28186189/performance-comparison-of-next-generation-sequencing-platforms-for-determining-hiv-1-coreceptor-use
#16
Stéphanie Raymond, Florence Nicot, Nicolas Jeanne, Olivier Delfour, Romain Carcenac, Caroline Lefebvre, Michelle Cazabat, Karine Sauné, Pierre Delobel, Jacques Izopet
The coreceptor used by HIV-1 must be determined before a CCR5 antagonist, part of the arsenal of antiretroviral drugs, is prescribed because viruses that enter cells using the CXCR4 coreceptor are responsible for treatment failure. HIV-1 tropism is also correlated with disease progression and so must be determined for virological studies. Tropism can be determined by next-generation sequencing (NGS), but not all of these new technologies have been fully validated for use in clinical practice. The Illumina NGS technology is used in many laboratories but its ability to predict HIV-1 tropism has not been evaluated while the 454 GS-Junior (Roche) is used for routine diagnosis...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185542/analysis-of-amplicon-based-ngs-data-from-neurological-disease-gene-panels-a-new-method-for-allele-drop-out-management
#17
Susanna Zucca, Margherita Villaraggia, Stella Gagliardi, Gaetano Salvatore Grieco, Marialuisa Valente, Cristina Cereda, Paolo Magni
BACKGROUND: Amplicon-based targeted resequencing is a commonly adopted solution for next-generation sequencing applications focused on specific genomic regions. The reliability of such approaches rests on the high specificity and deep coverage, although sequencing artifacts attributable to PCR-like amplification can be encountered. Between these artifacts, allele drop-out, which is the preferential amplification of one allele, causes an artificial increase in homozygosity when heterozygous mutations fall on a primer pairing region...
November 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28183752/draft-genome-sequences-of-two-strains-of-salmonella-enterica-serovar-typhimurium-displaying-different-virulence-in-an-experimental-chicken-model
#18
Dele Ogunremi, Burton Blais, Hongsheng Huang, Linru Wang, Mohamed Elmufti, Ray Allain, Jennifer Hazelwood, Chris Grenier, Kingsley Amoako, Mirjana Savic, Nashmil Fattahi Ghazi
Salmonella enterica serovar Typhimurium strains 22495 and 22792, obtained from wild birds, were found to display different virulence attributes in an experimental chicken model. Closed genome sequences were assembled after sequencing with the Roche 454 and Illumina MiSeq platforms. An additional plasmid was present in the more virulent strain 22495.
February 9, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28180085/de-novo-transcriptome-assembly-of-heavy-metal-tolerant-silene-dioica
#19
Radim Cegan, Vojtech Hudzieczek, Roman Hobza
Silene dioica is a dioecious plant of the family Caryophyllaceae. In the present study, we used Illumina sequencing technology (MiSeq) to sequence, de novo assembly and annotate the transcriptomes of male and female copper tolerant S. dioica individuals. We sequenced the normalized mRNA of roots, shoots, flower buds and flowers for each sex. Raw reads of the transcriptome assembly project for S. dioica male and female individual have been deposited in NCBI's Sequence Read Archive (SRA) database with the accession number SRP094611...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28179634/rapid-and-cost-effective-high-throughput-sequencing-for-identification-of-germline-mutations-of-brca1-and-brca2
#20
Somayeh Ahmadloo, Hirofumi Nakaoka, Takahide Hayano, Kazuyoshi Hosomichi, Hua You, Emi Utsuno, Takafumi Sangai, Motoi Nishimura, Kazuyuki Matsushita, Akira Hata, Fumio Nomura, Ituro Inoue
Genetic testing for breast cancer predisposing genes, BRCA1 and BRCA2, can take advantage for early identification of carriers with pathogenic germline mutations. However, conventional approaches based on Sanger sequencing are laborious and expensive. Next-generation sequencing technology has a great impact on investigation of medical genomics and now applied clinical genetics. We provide a protocol based on a pool and capture method followed by high-throughput sequencing, which realizes a rapid, high-quality, high-accuracy and low-cost testing for mutations in BRCA1 and BRCA2 by using small amounts of input DNA...
February 9, 2017: Journal of Human Genetics
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