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https://www.readbyqxmd.com/read/28730541/increased-sequencing-depth-does-not-increase-captured-diversity-of-arbuscular-mycorrhizal-fungi
#1
Martti Vasar, Reidar Andreson, John Davison, Teele Jairus, Mari Moora, Maido Remm, J P W Young, Martin Zobel, Maarja Öpik
The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing...
July 20, 2017: Mycorrhiza
https://www.readbyqxmd.com/read/28730144/molecular-characterization-of-the-human-stomach-microbiota-in-gastric-cancer-patients
#2
Guoqin Yu, Javier Torres, Nan Hu, Rafael Medrano-Guzman, Roberto Herrera-Goepfert, Michael S Humphrys, Lemin Wang, Chaoyu Wang, Ti Ding, Jacques Ravel, Philip R Taylor, Christian C Abnet, Alisa M Goldstein
Helicobacter pylori (Hp) is the primary cause of gastric cancer but we know little of its relative abundance and other microbes in the stomach, especially at the time of gastric cancer diagnosis. Here we characterized the taxonomic and derived functional profiles of gastric microbiota in two different sets of gastric cancer patients, and compared them with microbial profiles in other body sites. Paired non-malignant and tumor tissues were sampled from 160 gastric cancer patients with 80 from China and 80 from Mexico...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28729279/complete-genome-sequence-of-an-avian-metapneumovirus-subtype-a-strain-isolated-from-chicken-gallus-gallus-in-brazil
#3
Laís S Rizotto, Guilherme P Scagion, Tereza C Cardoso, Raphael M Simão, Leonardo C Caserta, Julia C Benassi, Lara B Keid, Trícia M F de S Oliveira, Rodrigo M Soares, Clarice W Arns, Steven Van Borm, Helena L Ferreira
We report here the complete genome sequence of an avian metapneumovirus (aMPV) isolated from a tracheal tissue sample of a commercial layer flock. The complete genome sequence of aMPV-A/chicken/Brazil-SP/669/2003 was obtained using MiSeq (Illumina, Inc.) sequencing. Phylogenetic analysis of the complete genome classified the isolate as avian metapneumovirus subtype A.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28728056/sequence-based-diversity-of-23-autosomal-str-loci-in-koreans-investigated-using-an-in-house-massively-parallel-sequencing-panel
#4
Eun Hye Kim, Hwan Young Lee, So Yeun Kwon, Eun Young Lee, Woo Ick Yang, Kyoung-Jin Shin
As DNA databases continue to grow and international cooperation increases, forensic STR loci have expanded to increase the discriminatory power and inter-database compatibility. Current capillary electrophoresis (CE) and/or massively parallel sequencing (MPS)-based commercial STR analysis systems reflect such changing trends of expanding STR loci. Due to the general gains of larger multiplexing and the detection of sequence variation, the application of MPS technology to STR analysis has further improved discrimination and is expected to aid in mixture interpretation by increasing the effective number of alleles...
July 9, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28725665/data-on-haplotype-supported-immunoglobulin-germline-gene-inference
#5
Ufuk Kirik, Lennart Greiff, Fredrik Levander, Mats Ohlin
Data that defines IGHV (immunoglobulin heavy chain variable) germline gene inference using sequences of IgM-encoding transcriptomes obtained by Illumina MiSeq sequencing technology are described. Such inference is used to establish personalized germline gene sets for in-depth antibody repertoire studies and to detect new antibody germline genes from widely available immunoglobulin-encoding transcriptome data sets. Specifically, the data has been used to validate (Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery (DOI: 10...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28725009/the-salivary-microbiome-as-an-indicator-of-carcinogenesis-in-patients-with-oropharyngeal-squamous-cell-carcinoma-a-pilot-study
#6
Axel Wolf, Christine Moissl-Eichinger, Alexandra Perras, Kaisa Koskinen, Peter V Tomazic, Dietmar Thurnher
This study aimed to undertake an initial, comparative analysis of the oral salivary microbiome of patients with oral and oropharyngeal squamous cell carcinoma versus healthy controls. This project, conceived as a pilot study, included 11 patients (1 female, 10 male, mean age 61.6 yrs., SD = 8.2 yrs.) and 11 healthy controls (1 female, 10 male, mean age 46.7 yrs., SD = 15.1 yrs.). Samples of saliva were analysed by high-throughput sequencing of the 16S rRNA gene using the MiSeq platform. Sequence data revealed microbial changes that may mirror disease progression and reflect clinical preconditions such as age, alcohol consumption, tumour size, lymph node status, smoking habit, and tumour HPV-positivity...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724921/saliva-and-tooth-biofilm-bacterial-microbiota-in-adolescents-in-a-low-caries-community
#7
Linda Eriksson, Pernilla Lif Holgerson, Ingegerd Johansson
The oral cavity harbours a complex microbiome that is linked to dental diseases and serves as a route to other parts of the body. Here, the aims were to characterize the oral microbiota by deep sequencing in a low-caries population with regular dental care since childhood and search for association with caries prevalence and incidence. Saliva and tooth biofilm from 17-year-olds and mock bacteria communities were analysed using 16S rDNA Illumina MiSeq (v3-v4) and PacBio SMRT (v1-v8) sequencing including validity and reliability estimates...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724229/microbial-association-with-the-dynamics-of-particulate-organic-carbon-in-response-to-the-amendment-of-elevated-co2-derived-wheat-residue-into-a-mollisol
#8
Yanhong Wang, Zhenhua Yu, Yansheng Li, Guanghua Wang, Junjie Liu, Judong Liu, Xiaobing Liu, Jian Jin
As the chemical quality of crop residue is likely to be affected by elevated CO2 (eCO2), residue amendments may influence soil organic carbon (SOC) sequestration. However, in Mollisols, the dynamics of the SOC fractions in response to amendment with wheat residue produced under eCO2 and the corresponding microbial community composition remain unknown. Such investigation is essential to residue management, which affects the soil quality and productivity of future farming systems. To narrow this knowledge gap, (13)C-labeled shoot and root residue derived from ambient CO2 (aCO2) or eCO2 were amended into Mollisols and incubated for 200days...
July 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28723942/comparative-analysis-of-vaginal-microbiota-sampling-using-16s-rrna-gene-analysis
#9
Seppo Virtanen, Ilkka Kalliala, Pekka Nieminen, Anne Salonen
BACKGROUND: Molecular methods such as next-generation sequencing are actively being employed to characterize the vaginal microbiota in health and disease. Previous studies have focused on characterizing the biological variation in the microbiota, and less is known about how factors related to sampling contribute to the results. Our aim was to investigate the impact of a sampling device and anatomical sampling site on the quantitative and qualitative outcomes relevant for vaginal microbiota research...
2017: PloS One
https://www.readbyqxmd.com/read/28723901/2b-rad-genotyping-for-population-genomic-studies-of-chagas-disease-vectors-rhodnius-ecuadoriensis-in-ecuador
#10
Luis E Hernandez-Castro, Marta Paterno, Anita G Villacís, Björn Andersson, Jaime A Costales, Michele De Noia, Sofía Ocaña-Mayorga, Cesar A Yumiseva, Mario J Grijalva, Martin S Llewellyn
BACKGROUND: Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses...
July 19, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28716079/the-human-jejunum-has-an-endogenous-microbiota-that-differs-from-those-in-the-oral-cavity-and-colon
#11
Olof H Sundin, Antonio Mendoza-Ladd, Mingtao Zeng, Diana Diaz-Arévalo, Elisa Morales, B Matthew Fagan, Javier Ordoñez, Philip Velez, Nishaal Antony, Richard W McCallum
BACKGROUND: The upper half of the human small intestine, known as the jejunum, is the primary site for absorption of nutrient-derived carbohydrates, amino acids, small peptides, and vitamins. In contrast to the colon, which contains 10(11)-10(12) colony forming units of bacteria per ml (CFU/ml), the normal jejunum generally ranges from 10(3) to 10(5) CFU per ml. Because invasive procedures are required to access the jejunum, much less is known about its bacterial microbiota. Bacteria inhabiting the jejunal lumen have been investigated by classical culture techniques, but not by culture-independent metagenomics...
July 17, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28715471/habitat-and-indigenous-gut-microbes-contribute-to-the-plasticity-of-gut-microbiome-in-oriental-river-prawn-during-rapid-environmental-change
#12
Cheng-Yu Chen, Po-Cheng Chen, Francis Cheng-Hsuan Weng, Grace Tzun-Wen Shaw, Daryi Wang
Growing evidence points out that the capacity of organisms to acclimate or adapt to new habitat conditions basically depends on their phenomic plasticity attributes, of which their gut commensal microbiota might be an essential impact factor. Especially in aquatic organisms, which are in direct and continual contact with the aquatic environment, the complex and dynamic microbiota have significant effects on health and development. However, an understanding of the relative contribution of internal sorting (host genetic) and colonization (environmental) processes is still unclear...
2017: PloS One
https://www.readbyqxmd.com/read/28715458/evaluation-of-metagenetic-community-analysis-of-planktonic-copepods-using-illumina-miseq-comparisons-with-morphological-classification-and-metagenetic-analysis-using-roche-454
#13
Junya Hirai, Satoshi Nagai, Kiyotaka Hidaka
Metagenetics is a rapid and taxonomically comprehensive method for revealing community structures within environmental samples, based on large amounts of sequence data produced by high-throughput sequencers. Because community structures of planktonic copepods are important in the ocean owing to their high diversity and abundance, a metagenetic analysis of the 28S D2 region using Roche 454 was previously developed. However, the Illumina MiSeq platform with a high sequence output is being used more frequently in metagenetics, and non-calanoid copepods have not previously been fully evaluated...
2017: PloS One
https://www.readbyqxmd.com/read/28715041/diagnostic-single-gene-analyses-beyond-sanger-economic-high-throughput-sequencing-of-small-genes-involved-in-congenital-coagulation-and-platelet-disorders
#14
Juliane Najm, Matthias Rath, Winnie Schröder, Ute Felbor
Molecular testing of congenital coagulation and platelet disorders offers confirmation of clinical diagnoses, supports genetic counselling, and enables predictive and prenatal diagnosis. In some cases, genotype-phenotype correlations are important for predicting the clinical course of the disease and adaptation of individualized therapy. Until recently, genotyping has been mainly performed by Sanger sequencing. While next generation sequencing (NGS) enables the parallel analysis of multiple genes, the cost-value ratio of custom-made panels can be unfavorable for analyses of specific small genes...
July 17, 2017: Hämostaseologie
https://www.readbyqxmd.com/read/28713847/next-generation-sequencing-of-the-dna-virome-from-fecal-samples
#15
Cynthia L Monaco, Douglas S Kwon
Herein we describe a detailed protocol for DNA virome analysis of low input human stool samples (Monaco et al., 2016). This protocol is divided into four main steps: 1) stool samples are pulverized to evenly distribute microbial matter; 2) stool is enriched for virus-like particles and DNA is extracted by phenol-chloroform; 3) purified DNA is multiple-strand displacement amplified (MDA) and fragmented; and 4) libraries are constructed and sequenced using Illumina Miseq. Subsequent sequence analysis for viral sequence identification should be sensitive but stringent...
March 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28713349/the-gut-microbiota-of-healthy-chilean-subjects-reveals-a-high-abundance-of-the-phylum-verrucomicrobia
#16
Sayaka Fujio-Vejar, Yessenia Vasquez, Pamela Morales, Fabien Magne, Patricia Vera-Wolf, Juan A Ugalde, Paola Navarrete, Martin Gotteland
The gut microbiota is currently recognized as an important factor regulating the homeostasis of the gastrointestinal tract and influencing the energetic metabolism of the host as well as its immune and central nervous systems. Determining the gut microbiota composition of healthy subjects is therefore necessary to establish a baseline allowing the detection of microbiota alterations in pathologic conditions. Accordingly, the aim of this study was to characterize the gut microbiota of healthy Chilean subjects using 16S rRNA gene sequencing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28713339/concurrent-methane-production-and-oxidation-in-surface-sediment-from-aarhus-bay-denmark
#17
Ke-Qing Xiao, Felix Beulig, Kasper U Kjeldsen, Bo B Jørgensen, Nils Risgaard-Petersen
Marine surface sediments, which are replete with sulfate, are typically considered to be devoid of endogenous methanogenesis. Yet, methanogenic archaea are present in those sediments, suggesting a potential for methanogenesis. We used an isotope dilution method based on sediment bag incubation and spiking with (13)C-CH4 to quantify CH4 turnover rates in sediment from Aarhus Bay, Denmark. In two independent experiments, highest CH4 production and oxidation rates (>200 pmol cm(-3) d(-1)) were found in the top 0-2 cm, below which rates dropped below 100 pmol cm(-3) d(-1) in all other segments down to 16 cm...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28711820/integrated-metagenomics-and-molecular-ecological-network-analysis-of-bacterial-community-composition-during-the-phytoremediation-of-cadmium-contaminated-soils-by-bioenergy-crops
#18
Zhaojin Chen, Yuan Zheng, Chuanyu Ding, Xuemin Ren, Jian Yuan, Feng Sun, Yuying Li
Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24μg pot(-1), respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla...
July 13, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28710619/genome-sequencing-of-steroid-producing-bacteria-with-illumina-technology
#19
Victoria Y Shtratnikova, Mikhail I Schelkunov, Marina V Donova
Illumina technology is widely used for bacterial whole-genome sequencing due to its simplicity, cheapness, reliability, and abundant software for manipulation with raw data. Illumina technology belongs to a second generation of whole genome sequencing that yields great amount of short reads for genome regions. Genomic DNA is fragmented to short pieces. DNA fragments are amplified for signal increasing, and are read using sequencing-by-synthesis. Millions of short reads up to 100-300 bp in length are assembled in continuous sequences...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28708872/nasopharyngeal-microbiota-in-infants-and-changes-during-viral-upper-respiratory-tract-infection-and-acute-otitis-media
#20
Tasnee Chonmaitree, Kristofer Jennings, Georgiy Golovko, Kamil Khanipov, Maria Pimenova, Janak A Patel, David P McCormick, Michael J Loeffelholz, Yuriy Fofanov
BACKGROUND: Interferences between pathogenic bacteria and specific commensals are known. We determined the interactions between nasopharyngeal microbial pathogens and commensals during viral upper respiratory tract infection (URI) and acute otitis media (AOM) in infants. METHODS: We analyzed 971 specimens collected monthly and during URI and AOM episodes from 139 infants. The 16S rRNA V4 gene regions were sequenced on the Illumina MiSeq platform. RESULTS: Among the high abundant genus-level nasopharyngeal microbiota were Moraxella, Haemophilus, and Streptococcus (3 otopathogen genera), Corynebacterium, Dolosigranulum, Staphylococcus, Acinetobacter, Pseudomonas, and Bifidobacterium...
2017: PloS One
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