keyword
MENU ▼
Read by QxMD icon Read
search

16s

keyword
https://www.readbyqxmd.com/read/28438014/characterization-of-a-glutamate-decarboxylase-gad-from-enterococcus-avium-m5-isolated-from-jeotgal-a-fermented-korean-sea-food
#1
Kang Wook Lee, Jae Min Shim, Zhuang Yao, Jeong A Kim, Hyun-Jin Kim, Jeong Hwan Kim
To develop starters for the production of functional foods or materials, lactic acid bacteria producing γ-aminobutyric acid (GABA) were screened from jeotgals, Korean fermented sea foods. One isolate producing high amount of GABA from monosodium L-glutamate (MSG) was identified as Enterococcus avium by 16S rRNA gene sequencing. E. avium M5 produced 18.47 ± 1.26 mg/ml GABA when incubated for 48 h at 37°C in MRS broth with MSG (3%, w/v). A gadB gene encoding glutamate decarboxylase (GAD) was cloned and overexpressed in E...
April 25, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28437776/large-scale-seaweed-cultivation-diverges-water-and-sediment-microbial-communities-in-the-coast-of-nan-ao-island-south-china-sea
#2
Xinfei Xie, Zhili He, Xiaojuan Hu, Huaqun Yin, Xueduan Liu, Yufeng Yang
Seaweed cultivation not only provides economy benefits, but also remediates the environment contaminated by mariculture of animals (e.g., fish, shrimps). However, the response of microbial communities to seaweed cultivation is poorly understood. In this study, we analyzed the diversity, composition, and structure of water and sediment microbial communities at a seaweed, Gracilaria lemaneiformis, cultivation zone and a control zone near Nan'ao Island, South China Sea by MiSeq sequencing of 16S rRNA gene amplicons...
April 21, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28437572/nearly-a-decade-long-repeatable-seasonal-diversity-patterns-of-bacterioplankton-communities-in-the-eutrophic-lake-donghu-wuhan-china
#3
Qingyun Yan, James C Stegen, Yuhe Yu, Ye Deng, Xinghao Li, Shu Wu, LilI Dai, Xiang Zhang, Jinjin Li, Chun Wang, Jiajia Ni, Xuemei Li, Hongjuan Hu, Fanshu Xiao, Weisong Feng, Daliang Ning, Zhili H E, Joy D Van Nostrand, Liyou Wu, Jizhong Zhou
Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long-term variations of bacterioplankton communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28437450/esprit-forest-parallel-clustering-of-massive-amplicon-sequence-data-in-subquadratic-time
#4
Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun
The rapid development of sequencing technology has led to an explosive accumulation of genomic sequence data. Clustering is often the first step to perform in sequence analy- sis, and hierarchical clustering is one of the most commonly used approaches for this purpose. However, it is currently computationally expensive to perform hierarchical clustering of extremely large sequence datasets due to its quadratic time and space complexities. In this paper we developed a new algorithm called ESPRIT-Forest for parallel hierarchical clustering of sequences...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28437181/isolation-of-brucella-inopinata-like-bacteria-from-white-s-and-denny-s-tree-frogs
#5
Masanobu Kimura, Yumi Une, Michio Suzuki, Eun-Sil Park, Koichi Imaoka, Shigeru Morikawa
Brucella inopinata strain BO1 and B. sp. strain BO2 isolated from human patients, respectively, are genetically different from classical Brucella species. We isolated bacteria of the genus Brucella from two species of wild-caught tropical frogs kept in the facilities in Japan: White's tree frog, which inhabits Oceania, and Denny's tree frog, which inhabits Southeast Asia. Phylogenetic analyses based on 16S rRNA and recA gene sequences and multilocus sequence analysis showed that two isolates of Brucella spp...
February 16, 2017: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/28435379/shifts-of-subgingival-bacterial-population-after-nonsurgical-and-pharmacological-therapy-of-localized-aggressive-periodontitis-followed-for-1-year-by-ion-torrent-pgm-platform
#6
Giuseppina Campisciano, Annamaria Toschetti, Manola Comar, Rosanna Di Taranto, Federico Berton, Claudio Stacchi
The possibility of targeting the hypervariable region V3 of the 16S rRNA gene using Ion Torrent Personal Genome Machine (PGM) could provide a complete analysis of subgingival plaque samples, potentially able to identify microbiological species missed by culture-based methods. A 16-year-old female smoker patient, affected by localized aggressive periodontitis, underwent a full-mouth disinfection protocol and was inserted in a 3-month recall program. Microbiological samples were collected at baseline and at 30, 100, 365 days follow-up and analyzed by Ion Torrent PGM...
January 2017: European Journal of Dentistry
https://www.readbyqxmd.com/read/28434745/hot-topic-16s-rrna-gene-sequencing-reveals-the-microbiome-of-the-virgin-and-pregnant-bovine-uterus
#7
S G Moore, A C Ericsson, S E Poock, P Melendez, M C Lucy
We tested the hypothesis that the uterus of virgin heifers and pregnant cows possessed a resident microbiome by 16S rRNA gene sequencing of the virgin and pregnant bovine uterus. The endometrium of 10 virgin heifers in estrus and the amniotic fluid, placentome, intercotyledonary placenta, cervical lumen, and external cervix surface (control) of 5 pregnant cows were sampled using aseptic techniques. The DNA was extracted, the V4 hypervariable region of the 16S rRNA gene was amplified, and amplicons were sequenced using Illumina MiSeq technology (Illumina Inc...
April 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28434214/chitinimonas-naiadis-sp-nov-isolated-from-a-freshwater-river
#8
Shalem Raj Padakandla, Jong-Chan Chae
A rod shaped, aerobic, Gram-stain-negative, and motile bacterium, strain AR2(T), was isolated from a water sample of Yeongsan river, Republic of Korea. Strain AR2(T) clustered closely with the members of the genus Chitinimonas and showed the highest 16S rRNA gene sequence similarity with Chitinimonas prasina LY03(T) (96.4%), Chitinimonas viridis HMD2169(T) (96.4%), Chitinimonas taiwanensis cf(T) (96.2%), and Chitinimonas koreensis R2A43-10(T) (94.2%). The predominant fatty acids of strain AR2(T) were identified to be summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c), C16:0, and C10:03-OH...
April 21, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28434178/massilia-chloroacetimidivorans-sp-nov-a-chloroacetamide-herbicide-degrading-bacterium-isolated-from-soil
#9
Hyosun Lee, Dong-Uk Kim, Sooyeon Park, Jung-Hoon Yoon, Jong-Ok Ka
A Gram-stain negative, rod-shaped, aerobic bacterial strain, designated TA-C7e(T), was isolated from an agricultural soil obtained from Taean region, Korea. Phylogenetically, the strain was grouped with the genus Massilia and shared 95.33-97.97% 16S rRNA sequence similarity with the type strains of other species of the genus Massilia. The DNA-DNA hybridisation between TA-C7e(T) and Massilia haematophila KACC 13771(T), Massilia suwonesis KACC 12635(T), and Massilia yuzhufengensis KACC 16569(T) revealed a low level of relatedness (<40%)...
April 22, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28434085/exploring-the-oral-microflora-of-preschool-children
#10
Wen Ren, Qun Zhang, Xuenan Liu, Shuguo Zheng, Lili Ma, Feng Chen, Tao Xu, Baohua Xu
The oral cavity is one of the most important and complicated habitats in our body and supports diverse microbial communities. In this study, we aimed to determine the bacterial diversity and composition of various oral micro-niches. Samples were collected from supragingival plaque, saliva, and tongue coating from 10 preschool children (30 samples total). 16S rRNA gene pyrosequencing dataset generated 314,639 clean reads with an average of 10,488 ± 2,787 reads per sample. The phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria were predominant, accounting for more than 90% of the total sequences...
April 22, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28433694/bacteroidales-markers-for-microbial-source-tracking-in-southeast-asia
#11
Jean Pierre Nshimyimana, Mercedes C Cruz, R Janelle Thompson, Stefan Wuertz
The island city country of Singapore served as a model to validate the use of host-associated Bacteroidales 16S rRNA gene marker assays for identifying sources of fecal pollution in the urban tropical environment of Southeast Asia. A total of 295 samples were collected from sewage, humans, domesticated animals (cats, dogs, rabbits and chicken), and wild animals (birds, monkeys and wild boars). Samples were analyzed by real time PCR using five human-associated assays (HF183-SYBR Green, HF183, BacHum, BacH and B...
April 10, 2017: Water Research
https://www.readbyqxmd.com/read/28433493/a-rare-and-emerging-pathogen-raoultella-planticola-identification-based-on-16s-rrna-in-an-infant
#12
Serkan Atıcı, Zeynep Alp Ünkar, Sevliya Öcal Demir, Gülşen Akkoç, Nurhayat Yakut, Şerife Yılmaz, Kübra Erdem, Aslı Çınar Memişoğlu, Nurver Ülger, Ahmet Soysal, Eren Özek, Mustafa Bakır
Raoultella planticola is rarely associated with clinical infection, and a limited number of pediatric cases have been reported. Herein we report a case of bacteremia presumptively secondary to bilateral conjunctivitis in an infant caused by R. planticola which was successfully treated with piperacillin-tazobactam. It should be kept in mind that R. planticola can be a pathogen in pediatric age groups.
April 19, 2017: Journal of Infection and Public Health
https://www.readbyqxmd.com/read/28432951/microbial-communities-in-the-functional-areas-of-a-biofilm-reactor-with-anaerobic-aerobic-process-for-oily-wastewater-treatment
#13
Jianhua Li, Shanshan Sun, Ping Yan, Li Fang, Yang Yu, Yangdong Xiang, Di Wang, Yejing Gong, Yanjun Gong, Zhongzhi Zhang
Microbial communities in the functional areas of biofilm reactors with large height-diameter ratio using the anaerobic-aerobic (A/O) reflux process was investigated to treat heavy oil refinery wastewater without pretreatment. In the process, chemical oxygen demand (COD) and total nitrogen (TN) removal reached 93.2% and 82.8%, and the anaerobic biofilm reactor was responsible for 95% and 99%, respectively. Areas for hydrolysis acidification and acetic acid production, methane production, and COD recovery were obvious in the anaerobic reactor...
April 10, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28432442/smokeless-tobacco-products-harbor-diverse-bacterial-microbiota-that-differ-across-products-and-brands
#14
Eoghan M Smyth, Prachi Kulkarni, Emma Claye, Stephen Stanfill, Robert Tyx, Cynthia Maddox, Emmanuel F Mongodin, Amy R Sapkota
Smokeless tobacco products contain numerous chemical compounds, including known human carcinogens. Other smokeless tobacco constituents, including bacteria, may also contribute to adverse health effects among smokeless tobacco users. However, there is a lack of data regarding the microbial constituents of smokeless tobacco. Our goal was to characterize the bacterial microbiota of different smokeless tobacco products and evaluate differences across product types and brands. DNA was extracted from 15 brands of smokeless tobacco products (including dry snuff, moist snuff, snus, and Swedish snus) and 6 handmade products (e...
April 22, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28432098/inhibitory-effect-of-coumarin-on-syntrophic-fatty-acid-oxidizing-and-methanogenic-cultures-and-biogas-reactor-microbiomes
#15
Denny Popp, Caroline M Plugge, Sabine Kleinsteuber, Hauke Harms, Heike Sträuber
Coumarins are widely found in plants as natural constituents having antimicrobial activity. When considering plants rich in coumarins for biogas production, adverse effects on microorganisms driving the anaerobic digestion process are expected. Furthermore, coumarin derivatives like warfarin, which are used as anti-coagulating medicine, are found in wastewater affecting its treatment. Coumarin as the structure common to all coumarins inhibits the anaerobic digestion process. However, details of this inhibition are still elusive...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431945/in-vitro-fermentation-behaviors-of-fucosylated-chondroitin-sulfate-from-pearsonothuria-graeffei-by-human-gut-microflora
#16
Chao-Yang Wei, Ning-Bo Liao, Yu Zhang, Xing-Qian Ye, Shan Li, Ya-Qin Hu, Dong-Hong Liu, Robert J Linhardt, Xin Wang, Shi-Guo Chen
A fucosylated chondroitin sulfate (FCS-pg) with highly repeated structure from Pearsonothuria graeffei was subjected to a in vitro fermentation model to investigate its fermentability and effects on human gut microflora. High performance liquid chromatography (HPLC) measurement found FCS-pg can be fermented to short chain fatty acids (SCFAs) by gut microflora from partial human fecal samples. 16S rRNA gene-based polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE) profiling and real-time quantitative PCR analysis showed that FCS-pg mainly increased the proportions of Clostridium cluster XI, Bacteriodes prevotella group, Bifidobacterium genus, Clostridium cluster I and Clostridium cluster XIVab, whereas the numbers of the Enterobacteriaceae and Lactobacillus decreased...
April 18, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28431935/diversity-changes-of-microbial-communities-into-hospital-surface-environments
#17
Rika Yano, Tomoko Shimoda, Reina Watanabe, Yasutoshi Kuroki, Torahiko Okubo, Shinji Nakamura, Junji Matsuo, Sadako Yoshimura, Hiroyuki Yamaguchi
Previous works have demonstrated considerable variability in hospital cleanliness in Japan, suggesting that contamination is driven by factors that are currently poorly controlled. We undertook 16S rRNA sequence analysis to study population structures of hospital environmental microbiomes to see which factor(s) impacted contamination. One hundred forty-four samples were collected from surfaces of three hospitals with distinct sizes ("A": >500 beds, "B": 100-500 beds, "C": <100 beds). Sample locations of two ward types (Surgical and Internal) included patient room bed table (multiple) (4BT), patient overbed table (multiple) (4OT), patient room sink (multiple) (4S), patient room bed table (single) (SBT), patient overbed table (single) (SOT), patient room sink (single) (SS), nurse desk (ND), and nurse wagon (NW)...
April 18, 2017: Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy
https://www.readbyqxmd.com/read/28431497/effect-of-ensiled-mulberry-leaves-and-sun-dried-mulberry-fruit-pomace-on-the-fecal-bacterial-community-composition-in-finishing-steers
#18
Yan Li, Qingxiang Meng, Bo Zhou, Zhenming Zhou
BACKGROUND: Here, we aimed to investigate the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on fecal bacterial communities in Simmental crossbred finishing steers. To this end, the steers were reared on a standard TMR diet, standard diet containing EML, and standard diet containing SMFP. The protein and energy levels of all the diets were similar. Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene and quantitative real-time PCR were used to analyze and detect the fecal bacterial community...
April 21, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28431082/compositional-differences-among-female-associated-and-embryo-associated-microbiota-of-the-viviparous-pacific-beetle-cockroach-diploptera-punctata
#19
Paul A Ayayee, George Keeney, Zakee L Sabree, Agustí Muñoz-Garcia
All cockroach species, except one, harbor the endosymbiont Blattabacterium, transmitted from females to embryos. Adult cockroaches acquire non-Blattabacterium bacteria as part of their gut microbiota over time, but our knowledge of the possible transmission of these non-Blattabacterium bacteria from females to embryos is rudimentary. We characterized the gut microbiota of gravid viviparous Diploptera punctata females and the non-Blattabacterium microbiota of associated developing embryos, as well as the gut microbiota of non-gravid females, and the microbiota of orphan embryos (females not included), following high-throughput sequencing of the 16S rRNA gene to assess bacterial transference...
April 18, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28430048/a-spinal-epidural-abscess-due-to-streptobacillus-moniliformis-infection-following-a-rat-bite-case-report
#20
Alexander Hammer, Dorit Wolff, Walter Geißdörfer, Michael Schrey, Renate Ziegler, Hans-Herbert Steiner, Christian Bogdan
The authors describe the case of a 40-year-old man suffering from an epidural abscess in the thoracic spine due to a rarely isolated pathogen, Streptobacillus moniliformis, the causative agent of rat bite fever. Besides diffuse abdominal pain, ataxia, paresthesia, hypesthesia, and enhanced reflexes of the lower extremities, the patient suffered from a decreased sensation of bladder filling. His history was also positive for a rat bite 6 weeks earlier. Magnetic resonance imaging showed an epidural, space-occupying lesion compressing the spinal cord at the vertebral levels of T6-8...
April 21, 2017: Journal of Neurosurgery. Spine
keyword
keyword
32595
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"