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16S rRNA

Renwen Zhang, Xiaoxue Han, Zhanfeng Xia, Xiaoxia Luo, Chuanxing Wan, Lili Zhang
A novel actinomycete strain, designated TRM 49605(T), was isolated from a desert soil sample from Lop Nur, Xinjiang, north-west China, and characterised using a polyphasic taxonomic approach. The strain exhibited antifungal activity against the following strains: Saccharomyces cerevisiae, Curvularia lunata, Aspergillus flavus, Aspergillus niger, Fusarium oxysporum, Penicillium citrinum, Candida albicans and Candida tropicalis; Antibacterial activity against Bacillus subtilis, Staphylococcus epidermidis and Micrococcus luteus; and no antibacterial activity against Escherichia coli...
October 17, 2016: Antonie Van Leeuwenhoek
Emilie Cauchie, Mathieu Gand, Gilles Kergourlay, Bernard Taminiau, Laurent Delhalle, Nicolas Korsak, Georges Daube
In order to control food losses and wastage, monitoring the microbial diversity of food products, during processing and storage is important, as studies have highlighted the metabolic activities of some microorganisms which can lead to spoilage. Knowledge of this diversity can be greatly improved by using a metagenetic approach based on high throughput 16S rRNA gene sequencing, which enables a much higher resolution than culture-based methods. Moreover, the Jameson effect, a phenomenon described by Jameson in 1962, is often used to classify bacterial strains within an ecosystem...
October 12, 2016: International Journal of Food Microbiology
S A Sarker, B Berger, Y Deng, S Kieser, F Foata, D Moine, P Descombes, S Sultana, S Huq, P K Bardhan, V Vuillet, F Praplan, H Brüssow
A T4-like coliphage cocktail was given with different oral doses to healthy Bangladeshi children in a placebo-controlled randomized phase I safety trial. Fecal phage detection was oral dose dependent suggesting passive gut transit of coliphages through the gut. No adverse effects of phage application were seen clinically and by clinical chemistry. Similar results were obtained for a commercial phage preparation (Coliproteus from Microgen/Russia). By 16S rRNA gene sequencing only a low degree of fecal microbiota conservation was seen in healthy children from Bangladesh who were sampled over a time interval of 7 days suggesting a substantial temporal fluctuation of the fecal microbiota composition...
October 17, 2016: Environmental Microbiology
Juan Chen, Chao Wang, Zhi-Jun Shen, Gui-Feng Gao, Hai-Lei Zheng
Polybrominated diphenyl ethers (PBDEs) have become ubiquitous environmental contaminants, particularly in mangrove wetlands. However, little is known about the long-term effect of mangrove plants on PBDE removal from contaminated sediments. A 12-month microcosm experiment was conducted to understand the effect of two mangrove species, namely Avicennia marina (Am) and Aegiceras corniculatum (Ac), on PBDE removal from the sediments spiked with 2000ngg(-1) dry weight of BDE-47, and to explore the microbial mechanism responsible for the planting-induced effects on BDE-47 removal...
October 14, 2016: Science of the Total Environment
Habteab Habtom, Sandrine Demanèche, Lorna Dawson, Chen Azulay, Ofra Matan, Patrick Robe, Ron Gafny, Pascal Simonet, Edouard Jurkevitch, Zohar Pasternak
The ubiquity and transferability of soil makes it a resource for the forensic investigator, as it can provide a link between agents and scenes. However, the information contained in soils, such as chemical compounds, physical particles or biological entities, is seldom used in forensic investigations; due mainly to the associated costs, lack of available expertise, and the lack of soil databases. The microbial DNA in soil is relatively easy to access and analyse, having thus the potential to provide a powerful means for discriminating soil samples or linking them to a common origin...
October 6, 2016: Forensic Science International. Genetics
Shradha Subedi, Fanrong Kong, Peter Jelfs, Timothy J Gray, Meng Xiao, Vitali Sintchenko, Sharon C-A Chen
Accurate identification of slowly growing nontuberculous mycobacteria (SG-NTM) of clinical significance remains problematic. This study evaluated a novel method of SG-NTM identification by amplification of the mycobacterial 16S-23S rRNA internal transcribed spacer (ITS) region followed by resolution of amplified fragments by sequencer-based capillary gel electrophoresis (SCGE). Fourteen American Type Culture Collection (ATCC) strains and 103 clinical/environmental isolates (total n = 24 species) of SG-NTM were included...
2016: PloS One
Rafael Laso-Pérez, Gunter Wegener, Katrin Knittel, Friedrich Widdel, Katie J Harding, Viola Krukenberg, Dimitri V Meier, Michael Richter, Halina E Tegetmeyer, Dietmar Riedel, Hans-Hermann Richnow, Lorenz Adrian, Thorsten Reemtsma, Oliver Lechtenfeld, Florin Musat
The anaerobic formation and oxidation of methane involve unique enzymatic mechanisms and cofactors that are believed to be all specific for C1-compounds. Here we found that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4-hydrocarbon butane. The archaea, proposed genus Candidatus Syntrophoarchaeum, showed the characteristic autofluorescence of methanogens, and contained highly expressed genes encoding enzymes similar to methyl-coenzyme M reductase (MCR)...
October 17, 2016: Nature
Michael P Palmer, Rachael Melton-Kreft, Laura Nistico, N Louisa Hiller, Leon H J Kim, Gregory T Altman, Daniel T Altman, Nicholas G Sotereanos, Fen Z Hu, Patrick J De Meo, Garth D Ehrlich
BACKGROUND: Preliminary studies have identified known bacterial pathogens in the knees of patients with osteoarthritis (OA) before arthroplasty. AIMS: The current study was designed to determine the incidence and types of bacteria present in the synovial fluid of native knee joints from adult patients with diagnoses of septic arthritis and OA. PATIENTS AND METHODS: Patients were enrolled between October 2010 and January 2013. Synovial fluid samples from the affected knee were collected and evaluated with both traditional microbial culture and polymerase chain reaction-electrospray ionization-time-of-flight mass spectrometry (molecular diagnostics [MDx]) to prospectively characterize the microbial content...
October 17, 2016: Genetic Testing and Molecular Biomarkers
T N Hustoft, T Hausken, S O Ystad, J Valeur, K Brokstad, J G Hatlebakk, G A Lied
BACKGROUND: A diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) is increasingly recommended for patients with irritable bowel syndrome (IBS). We aimed to investigate the effects of a blinded low-FODMAP vs high-fructo-oligosaccharides (FOS) diet on symptoms, immune activation, gut microbiota composition, and short-chain fatty acids (SCFAs). METHODS: Twenty patients with diarrhea-predominant or mixed IBS were instructed to follow a low-FODMAP diet (LFD) throughout a 9-week study period...
October 16, 2016: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
Yangyang Ge, Junli Zhu, Xiaofeng Ye
Ten strains were isolated from a spoiled large yellow croaker (Pseudosciaena crocea). All of them were able to grow aerobically from 4 °C to 30 °C, and reduce trimethylamine N-oxide (TMAO) to trimethylamine (TMA) and produce H2 S except the SB01, PF05 and PF07. Biochemical characterization and phylogenetic analysis of 16S rRNA gene showed that eight H2 S producing isolates were closely related to Shewanella baltica, and two isolates PF05 and PF07 were identified as P. fluorescens and P. fragi, respectively...
October 16, 2016: Letters in Applied Microbiology
D Kušar, U Zajc, V Jenčič, M Ocepek, J Higgins, M Žolnir-Dovč, M Pate
Fish are commonly infected with non-tuberculous mycobacteria (NTM), which should be regarded as potential pathogens when handling aquarium fish and equipment. This study examined 107 aquarium fish from pet shops. Cultivation of the fish samples using different selective media was conducted for identification of NTM. Isolates were identified using the GenoType Mycobacterium common mycobacteria and additional species assays, sequencing of the 16S rRNA and rpoB genes, and real-time PCR assay for identification of Mycobacterium (M...
October 17, 2016: Journal of Fish Diseases
Lianshuo Li, Zicheng Wang, Peng He, Shining Ma, Jie Du, Rui Jiang
Although networks of microbial species have been widely used in the analysis of 16S rRNA sequencing data of a microbiome, the construction and analysis of a complete microbial gene network is in general problematic because of the large number of microbial genes in metagenomics studies. To overcome this limitation, we propose to map microbial genes to functional units, including KEGG orthologous groups and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) orthologous groups, to enable the construction and analysis of a microbial functional network...
October 13, 2016: Genomics, Proteomics & Bioinformatics
Joanne E Sordillo, Yanjiao Zhou, Michael J McGeachie, John Ziniti, Nancy Lange, Nancy Laranjo, Jessica R Savage, Vincent Carey, George O'Connor, Megan Sandel, Robert Strunk, Leonard Bacharier, Robert Zeiger, Scott T Weiss, George Weinstock, Diane R Gold, Augusto A Litonjua
BACKGROUND: The gut microbiome in infancy influences immune system maturation, and may have an important impact allergic disease risk. OBJECTIVE: To determine how prenatal and early life factors impact the gut microbiome in a relatively large, ethnically diverse study population of infants at 3-6 months of age, who were enrolled in VDAART, a clinical trial of vitamin D supplementation in pregnancy to prevent asthma and allergies in offspring. METHODS: We performed 16S rRNA gene sequencing on 333 infants' stool samples...
October 13, 2016: Journal of Allergy and Clinical Immunology
Isabella Gandolfi, Claudia Canedoli, Valeria Imperato, Ilario Tagliaferri, Panagiotis Gkorezis, Jaco Vangronsveld, Emilio Padoa Schioppa, Maddalena Papacchini, Giuseppina Bestetti, Andrea Franzetti
Plants and their associated bacteria have been suggested to play a role in air pollution mitigation, especially in urban areas. Particularly, epiphytic bacteria might be able to degrade atmospheric hydrocarbons. However, phyllospheric bacterial communities are highly variable depending on several factors, e.g. tree species, leaf age and physiology, environmental conditions. In this work, bacterial communities hosted by urban Platanus x acerifolia leaves were taxonomically characterized using high throughput sequencing of 16S rRNA gene, and their temporal and spatial variability was assessed by comparing samples collected from different locations in the city of Milan (Italy) and in different months...
October 13, 2016: Environmental Pollution
Stefanie P Glaeser, Swapnil Doijad, Muaz Hijazin, Trinad Chakraborty, Enevold Falsen, Val Hall, Peter Kämpfer
During the years 1994-2011 five strictly anaerobic, Gram-stain-positive, diphtheroid bacteria (strains CCUG 31793(T), CCUG 44221, CCUG 61255, CCUG 45114, and CCUG 44993) were isolated from different clinical samples in Sweden and the United Kingdom. Comparative analysis of 16S rRNA gene sequences showed that the five strains shared 99-100% 16S rRNA gene sequence similarity among each other and 98.3-98.6% sequence similarity to Varibaculum cambriense DSM 15806(T). Genomic fingerprint patterns generated with ERIC-, BOX-, and RAPD-PCR, and whole genome sequence (WGS) based comparison by in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI) analysis and six housekeeping gene (atpA, rpoB, pgi, metG, gltA and gyrA) based multilocus sequence analysis (MLSA) showed that the strains could be differentiated from V...
September 20, 2016: Systematic and Applied Microbiology
Long Jin, So-Ra Ko, Yingshun Cui, Chang Soo Lee, Hee-Mock Oh, Chi-Yong Ahn, Hyung-Gwan Lee
A polyphasic taxonomic study was carried out on strain EBR-8-1(T) isolated from a biofilm reactor in Korea. The cells of the strain were Gram-stain negative, non-spore-forming, non-motile, and short rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of this strain with Betaproteobacteria, which showed high pairwise sequence similarities with Pusillimonas noertemannii BN9(T) (99.1 %), Pusillimonas soli MJ07(T) (97.3 %), Pusillimonas ginsengisoli DCY25(T) (97.2 %), and Pusillimonas harenae B201(T) (96...
October 15, 2016: Antonie Van Leeuwenhoek
M Mulet, M Gomila, A Ramírez, S Cardew, E R B Moore, J Lalucat, E García-Valdés
Fifty-two Pseudomonas strains that were difficult to identify at the species level in the phenotypic routine characterizations employed by clinical microbiology laboratories were selected for genotypic-based analysis. Species level identifications were done initially by partial sequencing of the DNA dependent RNA polymerase sub-unit D gene (rpoD). Two other gene sequences, for the small sub-unit ribosonal RNA (16S rRNA) and for DNA gyrase sub-unit B (gyrB) were added in a multilocus sequence analysis (MLSA) study to confirm the species identifications...
October 15, 2016: European Journal of Clinical Microbiology & Infectious Diseases
Xihui Xu, Zhou Zhang, Shunli Hu, Zhepu Ruan, Jiandong Jiang, Chen Chen, Zhenguo Shen
Soil provides a critical environment for microbial community development. However, microorganisms may be sensitive to substances such as heavy metals (HMs), which are common soil contaminants. This study investigated bacterial communities using 16S ribosomal RNA (rRNA) gene fragment sequencing in geographic regions with and without HM pollution to elucidate the effects of soil properties and HMs on bacterial communities. No obvious changes in the richness or diversity of bacterial communities were observed between samples from mining and control areas...
October 15, 2016: Environmental Science and Pollution Research International
Martina I Gocke, Arnaud Huguet, Sylvie Derenne, Steffen Kolb, Michaela A Dippold, Guido L B Wiesenberg
Soils, paleosols and terrestrial sediments serve as archives for studying climate change, and represent important terrestrial carbon pools. Archive functioning relies on the chronological integrity of the respective units. Incorporation of younger organic matter (OM) e.g. by plant roots and associated microorganisms into deep subsoil and underlying soil parent material may reduce reliability of paleoenvironmental records and stability of buried OM. Long-term effects of sedimentary characteristics and deep rooting on deep subsoil microbial communities remain largely unknown...
October 13, 2016: Science of the Total Environment
Else Marie Fykse, Tone Aarskaug, Elisabeth H Madslien, Marius Dybwad
High-throughput amplicon sequencing of six biomass samples from a full-scale anaerobic reactor at a Norwegian wood and pulp factory using Biothane Biobed Expanded Granular Sludge Bed (EGSB) technology during start-up and first year of operation was performed. A total of 106,166 16S rRNA gene sequences (V3-V5 region) were obtained. The number of operational taxonomic units (OTUs) ranged from 595 to 2472, and a total of 38 different phyla and 143 families were observed. The predominant phyla were Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, and Spirochaetes...
September 30, 2016: Bioresource Technology
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