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Mihir Rabha, Shaswati Sharma, Sumita Acharjee, Bidyut Kumar Sarmah
We have identified both crystalliferous and acrystalliferous Bt isolates from the Assam soil of North East India for the first time. A total of 301 Bacillus type colonies were selected based on their appearance and colony morphology. Out of these colonies, 42 isolates had characteristics similar to Bt isolates on MYP (Mannitol Egg Yolk Polymyxin) agar base medium. The ERIC-PCR and 16S rDNA analyses confirmed that 42 isolates are Bacillus thuringiensis. Phase contrast microscopy showed that 37 isolates produced crystal endospore during the sporulation phase and 5 acrystalliferous isolates were also found...
October 2017: 3 Biotech
Ashley A Hibberd, Anna Lyra, Arthur C Ouwehand, Peter Rolny, Helena Lindegren, Lennart Cedgård, Yvonne Wettergren
OBJECTIVE: The colonic microbiota is altered in patients with colorectal cancer (CRC). We investigated the microbiota composition of patients with colon cancer compared with controls devoid of neoplastic or inflammatory disease and the potential to modify the colonic microbiota with probiotics. DESIGN: Biopsy samples were obtained from the normal mucosa and tumour during colonoscopy from 15 patients with colon cancer. Subsequent patient-matched samples were taken at surgery from the tumour and nearby mucosa from the patients with cancer, eight of whom had received two daily tablets totalling 1...
2017: BMJ Open Gastroenterology
Zongxin Ling, Fengping Liu, Li Shao, Yiwen Cheng, Lanjuan Li
Evidence has shown that dysbiosis of the urinary microbiota existed in female type 2 diabetes mellitus (T2DM) patients. Perturbations of intestinal microbiota are linked to proinflammatory chemokine interleukin-8 (IL-8); however, the correlations between urinary microbiota and IL-8 are not well studied. Here, we investigated the associations between the altered urinary microbiota and urinary IL-8 in female T2DM patients. A modified four-tube midstream urine technique was used to collect urine specimens from 70 female T2DM patients and 70 matched healthy controls (HCs)...
2017: Frontiers in Immunology
Jun Li, Haihong Hao, Guyue Cheng, Chunbei Liu, Saeed Ahmed, Muhammad A B Shabbir, Hafiz I Hussain, Menghong Dai, Zonghui Yuan
Fluoroquinolones (FQs) are important antibiotics used for treatment of Salmonella infection in poultry in many countries. However, oral administration of fluoroquinolones may affect the composition and abundance of a number of bacterial taxa in the chicken intestine. Using 16S rRNA gene sequencing, the microbial shifts in the gut of Salmonella infected chickens in response to enrofloxacin treatments at different dosages (0, 0.1, 4, and 100 mg/kg b.w.) were quantitatively evaluated. The results showed that the shedding levels of Salmonella were significantly reduced in the high dosage group as demonstrated by both the culturing method and 16S rRNA sequencing method...
2017: Frontiers in Microbiology
Markus V Lindh, Brianne M Maillot, Christine N Shulse, Andrew J Gooday, Diva J Amon, Craig R Smith, Matthew J Church
Marine bacteria regulate fluxes of matter and energy essential for pelagic and benthic organisms and may also be involved in the formation and maintenance of commercially valuable abyssal polymetallic nodules. Future mining of these nodule fields is predicted to have substantial effects on biodiversity and physicochemical conditions in mined areas. Yet, the identity and distributions of bacterial populations in deep-sea sediments and associated polymetallic nodules has received relatively little attention. We examined bacterial communities using high-throughput sequencing of bacterial 16S rRNA gene fragments from samples collected in the water column, sediment, and polymetallic nodules in the Pacific Ocean (bottom depth ≥4,000 m) in the eastern Clarion-Clipperton Zone...
2017: Frontiers in Microbiology
Hee Soo Lee, Mirae Kwon, Sunhak Heo, Min Gon Kim, Geun-Bae Kim
This study investigated the psychrotrophic bacteria isolated from chicken meat to characterize their microbial composition during refrigerated storage. The bacterial community was identified by the Illumina MiSeq method based on bacterial DNA extracted from spoiled chicken meat. Molecular identification of the isolated psychrotrophic bacteria was carried out using 16S rDNA sequencing and their putrefactive potential was investigated by the growth at low temperature as well as their proteolytic activities in chicken meat...
2017: Korean Journal for Food Science of Animal Resources
Hiroyuki Fujikura, Kei Kasahara, Yoshihiko Ogawa, Nobuyasu Hirai, Seiya Yoshii, Shingo Yoshihara, Taku Ogawa, Shinsuke Yonekawa, Natsuko Imakita, Yuichi Nishioka, Tatsuo Yoneda, Katsunori Yoshida, Ken-Ichi Samejima, Kaori Tanabe, Yoshihiko Saito, Hisakazu Yano, Keiichi Mikasa
Mycobacterium wolinskyi belongs to the Mycobacterium smegmatis group, which comprises rapidly growing non-tuberculous mycobacteria. The number of case reports on M. wolinskyi infections associated with postoperative wounds has increased in recent years. We herein report a case of peritonitis due to M. wolinskyi after peritoneal catheter embedment surgery. Identification was achieved based on 16S ribosomal RNA and rpoB gene sequencing of the isolate. The patient recovered following catheter removal and treatment with levofloxacin and minocycline for one month...
September 25, 2017: Internal Medicine
Naoya Maekawa, Satoru Konnai, Michelle M Balbin, Claro N Mingala, Karlo R B Gicana, Francis A E M Bernando, Shiro Murata, Kazuhiko Ohashi
Canine monocytic ehrlichiosis (CME), caused by a rickettsial bacterium, Ehrlichia canis, is distributed worldwide, particularly in tropical and subtropical regions. Transmission of E. canis is primarily mediated by the vector tick, Rhipicephalus sanguineus sensu lato and the bacteria then infect and replicate in monocytes and macrophages. Many cases are seen in veterinary hospitals and treated routinely; however, the genetic variation of E. canis strains found in the Philippines has been poorly investigated to date...
September 20, 2017: Ticks and Tick-borne Diseases
Christa Strasser, Walter Spindelböck, Josef Oswald, Bernhard Haid
The intestinal microbiome is an ecosystem of bacterial microorganisms that is linked to metabolic and immune-related diseases. Our trial is analyzing 16S RNA sequencing data for the intestinal microbiome in children with urogenital malformations who do or do not receive antibiotic prophylaxis as part of their treatment.
September 21, 2017: European Urology Focus
Haizhu Zhou, Wei Guo, Bo Xu, Zhanwei Teng, Dapeng Tao, Yujie Lou, Yunhang Gao
Lignin, a common natural polymers, is abundant and complex, and termites can break down and utilize the lignin in their food. In this study an attempt was made to isolate and characterize the lignolytic bacteria from termite (Reticulitermes chinensis Snyder) gut. Two strains (PY12 and MX5) with high lignin peroxidase (LiP) activity were screened using the azure B method. By analyzing their 16S rRNA, the strain PY12 was classified as Enterobacter hormaechei; MX5, as Bacillus licheniformis. We then optimized the different conditions of liquid fermentation medium, and obtained LiP activities of 278 U/L and 256 U/L for PY12 and MX5, respectively...
September 21, 2017: Microbial Pathogenesis
Sankalp Misra, Vijay Kant Dixit, Mohammad Haneef Khan, Shashank Kumar Mishra, Gyanendra Dviwedi, Sumit Yadav, Alok Lehri, Puneet Singh Chauhan
A comprehensive survey for 09 agro-climatic zones of Uttar Pradesh, India was conducted to isolate and characterize salt tolerant 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase possessing plant growth promoting (PGP) rhizobacteria for salt stress amelioration in rice. Here, we have isolated 1125 bacteria having the ability to tolerate 1M NaCl and out of those, 560 were screened for utilizing ACC as sole nitrogen source. 560 isolates were subjected for bacteria coated seed germination assay under 100mM salt (NaCl) stress resulting to 77 isolates which were further evaluated for seed germination assay, PGP and abiotic stress tolerance ability in vitro...
December 2017: Microbiological Research
Jinguang Liu, Xingxiang Wang, Taolin Zhang, Xiaogang Li
Phenolic acids can enhance the mycotoxin production and activities of hydrolytic enzymes related to pathogenicity of soilborne fungus Fusarium oxysporum. However, characteristics of phenolic acid-degrading bacteria have not been investigated. The objectives of this study were to isolate and characterize bacteria capable of growth on benzoic and vanillic acids as the sole carbon source in the peanut rhizosphere. Twenty-four bacteria were isolated, and the identification based on 16S rRNA gene sequencing revealed that pre-exposure to phenolic acids before sowing shifted the dominant culturable bacterial degraders from Arthrobacter to Burkholderia stabilis-like isolates...
December 2017: Microbiological Research
Ningxi Yu, Peter A Lobue, Xiaoyu Cao, Patrick A Limbach
Liquid chromatography tandem mass spectrometry (LC-MS/MS) has proven to be a powerful analytical tool for the characterization of modified ribonucleic acids (RNAs). The typical approach for analyzing modified nucleosides within RNA sequences by mass spectrometry involves ribonuclease digestion followed by LC-MS/MS analysis and data interpretation. Here we describe a new software tool, RNAModMapper (RAMM), to assist in the interpretation of LC-MS/MS data. RAMM is a stand-alone package that requires user-submitted DNA or RNA sequences to create a local database against which collision-induced dissociation (CID) data of modified oligonucleotides can be compared...
September 24, 2017: Analytical Chemistry
Lan-Jia Pan, Jie Li, Chun-Xing Li, Xiao-da Tang, Guang-Wei Yu, Yin Wang
Ciprofloxacin (CIP) is an antibiotic drug frequently detected in manure compost and is difficult to decompose at high temperatures, resulting in a potential threat to the environment. Microbial degradation is an effective and environmentally friendly method to degrade CIP. In this study, a thermophilic bacterium that can degrade CIP was isolated from sludge sampled from an antibiotics pharmaceutical factory. This strain is closely related to Thermus thermophilus based on 16S rRNA gene sequence analysis and is designated C419...
September 7, 2017: Journal of Hazardous Materials
Nikos Pinotsis, Gabriel Waksman
The methylationlation of U1498 located in the 16S ribosomal RNA of Escherichia coli is an important modification affecting ribosomal activity. RsmE methyltransferases methylate specifically this position in a mechanism that requires an S-adenosyl-L-methionine (AdoMet) molecule as cofactor. Here we report the structure of Apo and AdoMet-bound Lpg2936 from Legionella pneumophila at 1.5 Å and 2.3 Å, respectively. The protein comprises an N-terminal PUA domain and a C-terminal SPOUT domain. The latter is responsible for protein dimerization and cofactor binding...
September 22, 2017: Protein Science: a Publication of the Protein Society
B C Roland, D Lee, L S Miller, A Vegesna, R Yolken, E Severance, E Prandovszky, X E Zheng, G E Mullin
BACKGROUND: Small intestinal bacterial overgrowth (SIBO) has been associated with anatomical and motility-related abnormalities. Specifically, obesity has been postulated to alter small bowel motility, leading to SIBO. AIMS: (i) Assess the prevalence of SIBO in obesity; (ii) determine the relationship of obesity and SIBO, using small bowel transit time (SBTT) and pH; (iii) profile the gut microbiome in obese and non-obese patients with SIBO. METHODS: Thirty consecutive participants referred for SIBO underwent lactulose breath tests (LBTs) and wireless motility capsule (WMC) studies...
September 21, 2017: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
N Sood, P K Pradhan, D K Verma, M K Yadav, Ravindra, A K Dev, T R Swaminathan, N K Sood
Chlamydial infections are recognised as causative agent of epitheliocystis, reported from over 90 fish species. In the present study, the farmed striped catfish Pangasianodon hypophthalmus (14-15 cm, 70-90 g) with a history of cumulative mortality of about 23% during June and July 2015, were brought to the laboratory. The histopathological examination of gills from the affected fish revealed presence of granular basophilic intracellular inclusions, mostly at the base of the interlamellar region and in gill filaments...
September 22, 2017: Journal of Fish Diseases
George S Watts, Ken Youens-Clark, Marvin J Slepian, Donna M Wolk, Marc M Oshiro, Gregory S Metzger, Dalia Dhingra, Lee D Cranmer, Bonnie L Hurwitz
AIMS: Test the choice of 16S rRNA gene amplicon and data analysis method on the accuracy of identification of clinically important bacteria utilizing a benchtop sequencer. METHODS AND RESULTS: Nine 16S rRNA amplicons were tested on an Ion Torrent PGM to identify 41 strains of clinical importance. The V1-V2 region identified 40 of 41 isolates to the species level. Three data analysis methods were tested, finding that the Ribosomal Database Project's SequenceMatch outperformed BLAST and the Ion Reporter Metagenomics analysis pipeline...
September 20, 2017: Journal of Applied Microbiology
Purnima Singh, Shiv M Singh, Ram N Singh, Simantini Naik, Utpal Roy, Alok Srivastava, Manfred Bölter
Permafrost soils are unique habitats in polar environment and are of great ecological relevance. The present study focuses on the characterization of bacterial communities from permafrost profiles of Svalbard, Arctic. Counts of culturable bacteria range from 1.50 × 10(3) to 2.22 × 10(5) CFU g(-1) , total bacterial numbers range from 1.14 × 10(5) to 5.52 × 10(5) cells g(-1) soil. Bacterial isolates are identified through 16S rRNA gene sequencing. Arthrobacter and Pseudomonas are the most dominant genera, and A...
September 21, 2017: Journal of Basic Microbiology
Xing Huang, Hao Zhang, Feng Chen, Man Song
Strain QCT6, capable of degrading metribuzin, was isolated from metribuzin-contaminated soil. The isolate was identified as Paracoccus sp. according to its physiological characteristics, biochemical tests, and 16S rRNA gene phylogenetic analysis. In liquid culture, 86.4% of 50 mg/L metribuzin was removed by strain QCT6 after incubation for 7 days. The product of metribuzin degradation by QCT6 was identified as deamino-metribuzin, which has reduced phytotoxicity on the growth of maize. After being marked with the gfp gene, the colonization and distribution of gfp-tagged QCT6 were directly observed with a confocal laser scanning microscope...
September 22, 2017: Current Microbiology
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