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16S rRNA

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
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
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
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
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
Qing-Yi Xie, Xiao-Dong Bao, Qing-Yu Ma, Fan-Dong Kong, Man-Li Zhou, Bing Yan, You-Xing Zhao
An actinomycete strain, 2603PH03(T), was isolated from a mangrove rhizosphere soil sample collected in Wenchang, China. Phylogenetic analysis of the 16S rRNA gene sequence of strain 2603PH03(T) indicated high similarity to Verrucosispora gifthornensis DSM 44337(T) (99.4%), Verrucosispora andamanensis (99.4%), Verrucosispora fiedleri MG-37(T) (99.4%) and Verrucosispora maris AB18-032(T) (99.4%). The cell wall was found to contain meso-diaminopimelic acid and glycine. The major menaquinones were identified as MK-9(H4), MK-9(H6) and MK-9(H8), with MK-9(H2), MK-10(H2), MK-9(H10) and MK-10(H6) as minor components...
September 22, 2017: Antonie Van Leeuwenhoek
Ji-Hye Han, Kiwoon Baek, Young-Hee Ahn, Wook Jae Lee, Mi-Hwa Lee
A Gram-negative, aerobic, motile by flagella, and light yellow bacterium, designated SS1-76(T), was isolated from sediment of the Nakdong River in Sangju-si, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate SS1-76(T) belongs to the genus Uliginosibacterium of the family Rhodocyclaceae, exhibiting high sequence similarity with the type strains of Uliginosibacterium gangwonense 5YN10-9(T) (96.0%) and Uliginosibacterium paludis KBP-13(T) (94.9%). Strain SS1-76(T) contains ubiquinone-8 as a respiratory quinone and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0, and C14:0 as major fatty acids...
September 22, 2017: Antonie Van Leeuwenhoek
Indrikis A Krams, Sanita Kecko, Priit Jõers, Giedrius Trakimas, Didzis Elferts, Ronalds Krams, Severi Luoto, Markus J Rantala, Inna Inashkina, Dita Gudrā, Dāvids Fridmanis, Jorge Contreras-Garduño, Lelde Grantiņa-Ieviņa, Tatjana Krama
Communities of symbiotic microorganisms that colonize the gastrointestinal tract play an important role in food digestion and protection against opportunistic microbes. Diet diversity increases the number of symbionts in the intestines, a benefit that is considered to impose no cost for the host organism. However, less is known about the possible immunological investments that hosts have to make in order to control the infections caused by symbiont populations that increase due to diet diversity. By using taxonomical composition analysis of the 16S rRNA V3 region, we show that Enterococci are the dominating group of bacteria in the midgut of the larvae of the greater wax moth (Galleria mellonella)...
September 22, 2017: Journal of Experimental Biology
Celine C Lesaulnier, Craig W Herbold, Claus Pelikan, David Berry, Cédric Gérard, Xavier Le Coz, Sophie Gagnot, Jutta Niggemann, Thorsten Dittmar, Gabriel A Singer, Alexander Loy
BACKGROUND: Non-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown. RESULTS: We performed a multifaceted analysis of microbiota and DOM diversity in 12 natural mineral waters from six European countries...
September 22, 2017: Microbiome
Juan Liu, Xiao Liu, Xue-Qin Xiong, Ting Yang, Ting Cui, Na-Li Hou, Xi Lai, Shu Liu, Min Guo, Xiao-Hua Liang, Qian Cheng, Jie Chen, Ting-Yu Li
BACKGROUND: Dysbiosis of gut microbiota are commonly reported in autism spectrum disorder (ASD) and may contribute to behavioral impairment. Vitamin A (VA) plays a role in regulation of gut microbiota. This study was performed to investigate the role of VA in the changes of gut microbiota and changes of autism functions in children with ASD. RESULTS: Sixty four, aged 1 to 8 years old children with ASD completed a 6-month follow-up study with VA intervention. High-performance liquid chromatography was used to assess plasma retinol levels...
September 22, 2017: BMC Microbiology
Sara D'Andreano, Armand Sànchez Bonastre, Olga Francino, Anna Cuscó Martí, Cristina Lecchi, Guido Grilli, Davide Giovanardi, Fabrizio Ceciliani
Hemorrhagic enteritis (HE) is an acute viral disease that affects avian species, particularly turkeys, compromising their commercial production and having a negative effect on animal welfare. Turkey adenovirus 3 (TAdV-3), is the main causal agent of the disease. In this study, we considered 3 groups of turkeys to achieve 2 purposes: 1) A preliminary investigation on the microbiota content in the 4 parts of healthy turkey's intestine (group A), namely duodenum, jejunum, ileum, and ceca was done; 2) an investigation on the relationship between natural infections with TAdV-3 and the intestinal microbiota in the jejunum, where HE mostly develops, comparing group A with animals with molecular positivity for the virus and with clinical signs of HE (group B) and animals with molecular positivity for the virus but without clinical signs (group C)...
October 1, 2017: Poultry Science
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