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https://www.readbyqxmd.com/read/28808878/role-of-intestinal-microbiome-in-american-ginseng-mediated-colon-cancer-protection-in-high-fat-diet-fed-aom-dss-mice
#1
C-Z Wang, W-H Huang, C-F Zhang, J-Y Wan, Y Wang, C Yu, S Williams, T-C He, W Du, M W Musch, E B Chang, C-S Yuan
OBJECTIVE: Chronic intestinal inflammation is a risk factor for colorectal cancer (CRC) initiation and development. Diets that are rich in Western style fats have been shown to promote CRC. This study was conducted to investigate the role of intestinal microbiome in American ginseng-mediated CRC chemoprevention in a mouse model. The population and diversity of enteric microbiome were evaluated after the ginseng treatment. METHODS: Using an azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced gut inflammation and tumorigenesis mouse model, the effects of oral American ginseng on high fat diet-associated enteric pathology were determined...
August 14, 2017: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/28808698/subgingival-microbiome-of-gingivitis-in-chinese-undergraduates
#2
Ke Deng, Xiang Ying Ouyang, Yi Chu, Qian Zhang
OBJECTIVE: To analyse the microbiome composition of health and gingivitis in Chinese undergraduates with high-throughput sequencing. METHODS: Sequencing of 16S rRNA gene amplicons was performed with the MiSeq system to compare subgingival bacterial communities from 54 subjects with gingivitis and 12 periodontally healthy controls. RESULTS: A total of 1,967,372 sequences representing 14 phyla, 104 genera, and 96 species were detected. Analysis of similarities (Anosim) test and Principal Component Analysis (PCA) showed significantly different community profiles between the health control and the subjects with gingivitis...
2017: Chinese Journal of Dental Research
https://www.readbyqxmd.com/read/28805891/increasing-corn-distillers-solubles-alters-the-liquid-fraction-of-the-ruminal-microbiome
#3
J C McCann, J R Segers, H Derakhshani, T L Felix, E Khafipour, D W Shike
Five ruminally fistulated steers were used in a 5 × 5 Latin square design to determine the effects of increasing dietary fat and sulfur from condensed distiller's solubles (CDS) on the ruminal microbiome. Treatments included a corn-based control (CON) and 4 levels of CDS (0, 10, 19, and 27%) in a coproduct-based (corn gluten feed and soybean hulls) diet. Fat concentrations were 1.79, 4.43, 6.80, and 8.91% for diets containing 0, 10, 19, and 27% CDS, respectively. Steers were fed for ad libitum intake once daily...
August 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28803260/microbial-volatile-compounds-alter-the-soil-microbial-community
#4
Jun Yuan, Mengli Zhao, Rong Li, Qiwei Huang, Waseem Raza, Christopher Rensing, Qirong Shen
Volatile organic compounds (VOCs) from soil bacteria are likely to have an important role in the interactions among soil microorganisms. However, their effects on the soil microbial community have not been extensively studied. In this study, the effect of bacterial VOCs generated by growing Bacillus amyloliquefaciens NJN-6 on modified MS medium on soil microbial community was evaluated. B. amyloliquefaciens NJN-6 was able to produce 48 volatile compounds as determined by solid-phase microextraction-GC/MS. MiSeq sequencing data showed that bacterial VOCs could alter the composition of both soil bacterial and soil fungal communities and could decrease the alpha-diversity of the soil microbial community...
August 12, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28800828/culture-dependent-and-culture-independent-assessment-of-spoilage-community-growth-on-vp-lamb-meat-from-packaging-to-past-end-of-shelf-life
#5
Mandeep Kaur, Hongshan Shang, Mark Tamplin, Tom Ross, John P Bowman
Packaging and storage temperature are important factors that influence the shelf-life of vacuum packed (VP) meat. In this study the shelf-life of VP bone-in lamb hind shanks stored at 8 °C and -1.2 °C was determined in parallel to analyses of starting and eventual spoilage bacterial communities via Illumina MiSeq based 16S rRNA amplicon sequencing. The mean total viable counts (TVC) and lactic acid bacterial viable counts (LAB) were observed to increase to log 7.5 CFU/cm(2) and 7 CFU/cm(2) after 6 and 42 days at 8 °C and -1...
December 2017: Food Microbiology
https://www.readbyqxmd.com/read/28799325/comparison-between-next-generation-and-sanger-based-sequencing-for-the-detection-of-transmitted-drug-resistance-mutations-among-recently-infected-hiv-1-patients-in-israel-2000-2014
#6
Roy Moscona, Daniela Ram, Marina Wax, Efrat Bucris, Itzchak Levy, Ella Mendelson, Orna Mor
INTRODUCTION: Transmitted drug-resistance mutations (TDRM) may hamper successful anti-HIV-1 therapy and impact future control of the HIV-1 epidemic. Recently infected, therapy-naïve individuals are best suited for surveillance of such TDRM. In this study, TDRM, detected by next-generation sequencing (NGS) were compared to those identified by Sanger-based population sequencing (SBS) in recently infected HIV-1 patients. METHODS: Historical samples from 80 recently infected HIV-1 patients, diagnosed between 2000 and 2014, were analysed by MiSeq (NGS) and ABI (SBS)...
August 11, 2017: Journal of the International AIDS Society
https://www.readbyqxmd.com/read/28798730/characterization-of-the-culturable-subpopulations-of-lactobacillus-in-the-chicken-intestinal-tract-as-a-resource-for-probiotic-development
#7
Bishnu Adhikari, Young M Kwon
To gain better understanding of the distributions of the culturable Lactobacillus species in the chicken intestinal tract, we collected ceca, and distal ileum from 10 3-weeks-old broiler chickens. Lactobacillus strains from cecal lumen contents (M-CL), and those associated with mucosa of ceca (M-CM) and ileum (M-IM) were recovered on de Man, Rogosa and Sharpe (MRS) agar plates, and used for microbiota analysis. The total cecal content (T-CL) was also used directly for microbiota analysis. We purposefully focused on MRS-recovered populations to gain understanding of the culturable subpopulations of Lactobacillus, since the culturability is an important phenotype in order to exploit the chicken gut microbiota as a resource for development of probiotics...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28797931/changes-in-the-gut-microbial-communities-following-addition-of-walnuts-to-the-diet
#8
Lauri O Byerley, Derrick Samuelson, Eugene Blanchard, Meng Luo, Brittany N Lorenzen, Shelia Banks, Monica A Ponder, David A Welsh, Christopher M Taylor
Walnuts are rich in omega-3 fatty acids, phytochemicals and antioxidants making them unique compared to other foods. Consuming walnuts has been associated with health benefits including a reduced risk of heart disease and cancer. Dysbiosis of the gut microbiome has been linked to several chronic diseases. One potential mechanism by which walnuts may exert their health benefit is through modifying the gut microbiome. This study identified the changes in the gut microbial communities that occur following the inclusion of walnuts in the diet...
July 9, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28796833/bile-microbiota-in-primary-sclerosing-cholangitis-impact-on-disease-progression-and-development-of-biliary-dysplasia
#9
Pedro Pereira, Velma Aho, Johanna Arola, Sonja Boyd, Kalle Jokelainen, Lars Paulin, Petri Auvinen, Martti Färkkilä
OBJECTIVE: The etiopathogenesis and risk for development of biliary neoplasia in primary sclerosing cholangitis (PSC) are largely unknown. Microbes or their metabolites have been suggested to play a role. To explore this potential microbial involvement, we evaluated the differences in biliary microbiota in PSC patients at an early disease stage without previous endoscopic retrograde cholangiography (ERC) examinations, advanced disease stage, and with biliary dysplasia or cholangiocarcinoma...
2017: PloS One
https://www.readbyqxmd.com/read/28796800/the-temporal-dynamics-of-the-tracheal-microbiome-in-tracheostomised-patients-with-and-without-lower-respiratory-infections
#10
Marcos Pérez-Losada, Robert J Graham, Madeline Coquillette, Amenah Jafarey, Eduardo Castro-Nallar, Manuel Aira, Robert J Freishtat, Jonathan M Mansbach
BACKGROUND: Airway microbiota dynamics during lower respiratory infection (LRI) are still poorly understood due, in part, to insufficient longitudinal studies and lack of uncontaminated lower airways samples. Furthermore, the similarity between upper and lower airway microbiomes is still under debate. Here we compare the diversity and temporal dynamics of microbiotas directly sampled from the trachea via tracheostomy in patients with (YLRI) and without (NLRI) lower respiratory infections...
2017: PloS One
https://www.readbyqxmd.com/read/28793919/prevention-of-diabetes-in-overweight-obese-children-through-a-family-based-intervention-program-including-supervised-exercise-predikid-project-study-protocol-for-a-randomized-controlled-trial
#11
Lide Arenaza, María Medrano, María Amasene, Beatriz Rodríguez-Vigil, Ignacio Díez, Manuel Graña, Ignacio Tobalina, Edurne Maiz, Edurne Arteche, Eider Larrarte, Inge Huybrechts, Catherine L Davis, Jonatan R Ruiz, Francisco B Ortega, Javier Margareto, Idoia Labayen
BACKGROUND: The global pandemic of obesity has led to an increased risk for prediabetes and type-2 diabetes (T2D). The aims of the current project are: (1) to evaluate the effect of a 22-week family based intervention program, including supervised exercise, on insulin resistance syndrome (IRS) risk in children with a high risk of developing T2D and (2) to identify the profile of microRNA in circulating exosomes and in peripheral blood mononuclear cells in children with a high risk of developing T2D and its response to a multidisciplinary intervention program including exercise...
August 10, 2017: Trials
https://www.readbyqxmd.com/read/28791467/banana-fusarium-wilt-disease-incidence-is-influenced-by-shifts-of-soil-microbial-communities-under-different-monoculture-spans
#12
Zongzhuan Shen, C Ryan Penton, Nana Lv, Chao Xue, Xianfu Yuan, Yunze Ruan, Rong Li, Qirong Shen
The continuous cropping of banana in the same field may result in a serious soil-borne Fusarium wilt disease and a severe yield decline, a phenomenon known as soil sickness. Although soil microorganisms play key roles in maintaining soil health, the alternations of soil microbial community and relationship between these changes and soil sickness under banana monoculture are still unclear. Bacterial and fungal communities in the soil samples collected from banana fields with different monoculture spans were profiled by sequencing of the 16S rRNA genes and internal transcribed spacer using the MiSeq platform to explore the relationship between banana monoculture and Fusarium wilt disease in the present study...
August 8, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28783566/autoclaved-sludge-as-the-ideal-seed-to-culture-anammox-bacteria-reactor-performance-and-microbial-community-diversity
#13
Yu Wang, Cui-Na Bu, Qi Kang, Hafiz Adeel Ahmad, Jian Zhang, Baoyu Gao, Shou-Qing Ni
Reducing activity of commensal bacteria in inocula may enhance anammox bacteria proliferation and realization of anammox process. Fast start-up of anammox process in an UASB reactor was successfully achieved by using autoclaved sludge (anaerobic granular sludge pretreated by autoclaving) and 0.3% active anammox sludge as inoculum. Continuous experiments indicated that R2 (autoclaved sludge addition) could shorten the start-up period from 72days to 63days. The first 50days anammox population specific growth rates (μ) of R1 (the control) and R2 were determined to be 0...
July 29, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28780383/microbiome-of-peri-implantitis-affected-and-healthy-dental-sites-in-patients-with-a-history-of-chronic-periodontitis
#14
Danae Apatzidou, David F Lappin, Graham Hamilton, Christos A Papadopoulos, Antonis Konstantinidis, Marcello P Riggio
OBJECTIVE: To determine the composition of the microbiome of peri-implantitis sites and corresponding dental sites in subjects with a history of chronic periodontitis. DESIGN: Clinical and radiographic examination assessed the periodontal/peri-implant disease status. Plaque samples were collected from one diseased implant with peri-implantitis, functional for at least two years and healthy sites in ten non-smokers who had received periodontal treatment prior to implant placement...
July 13, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28776936/a-from-benchtop-to-desktop-workflow-for-validating-hts-data-and-for-taxonomic-identification-in-diet-metabarcoding-studies
#15
Emmanuel Corse, Emese Meglécz, Gaït Archambaud, Morgane Ardisson, Jean-François Martin, Christelle Tougard, Rémi Chappaz, Vincent Dubut
The main objective of this work was to develop and validate a robust and reliable 'from benchtop-to-desktop' metabarcoding workflow to investigate the diet of invertebrate-eaters. We applied our workflow to fecal DNA samples of an invertebrate-eating fish species. A fragment of the COI gene was amplified by combining two minibarcoding primer sets to maximize the taxonomic coverage. Amplicons were sequenced by an Illumina MiSeq platform. We developed a filtering approach based on a series of non-arbitrary thresholds established from control samples and from molecular replicates in order to address the elimination of cross-contamination, PCR/sequencing errors and mistagging artifacts...
August 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28774990/complete-genome-sequence-of-achromobacter-denitrificans-pr1
#16
Ana C Reis, Kevin Kroll, Margarita Gomila, Boris A Kolvenbach, Philippe F X Corvini, Olga C Nunes
Achromobacter denitrificans strain PR1 was isolated from an enrichment culture able to use sulfamethoxazole as an energy source. Here, we describe the complete genome of this strain sequenced by Illumina MiSeq and Oxford Nanopore MinION.
August 3, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28774263/evaluation-of-high-throughput-isomir-identification-tools-illuminating-the-early-isomirome-of-tribolium-castaneum
#17
Daniel Amsel, Andreas Vilcinskas, André Billion
BACKGROUND: MicroRNAs carry out post-transcriptional gene regulation in animals by binding to the 3' untranslated regions of mRNAs, causing their degradation or translational repression. MicroRNAs influence many biological functions, and dysregulation can therefore disrupt development or even cause death. High-throughput sequencing and the mining of animal small RNA data has shown that microRNA genes can yield differentially expressed isoforms, known as isomiRs. Such isoforms are particularly relevant during early development, and the extension or truncation of the 5' end can change the profile of mRNA targets compared to the original mature sequence...
August 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28771569/disruption-in-the-cecal-microbiota-of-chickens-challenged-with-clostridium-perfringens-and-other-factors-was-alleviated-by-bacillus-licheniformis-supplementation
#18
Yicen Lin, Shuai Xu, Dong Zeng, Xueqin Ni, Mengjia Zhou, Yan Zeng, Hesong Wang, Yi Zhou, Hui Zhu, Kangcheng Pan, Guangyao Li
Clostridium perfringens can induce necrotic enteritis of chickens, which causes large economic losses every year. Bacillus licheniformis, a probiotic, can inhibit the growth of pathogenic bacteria such as Clostridium perfringens, thereby improving the health status of chickens. However, from a microbial ecology perspective, the mechanisms by which alterations to the gut microbiota improve health remain unknown. In this study, we used Illumina MiSeq sequencing to investigate the cecal microbiota of a negative control group (NC), a C...
2017: PloS One
https://www.readbyqxmd.com/read/28768482/comparative-genomic-analysis-and-characterization-of-incompatibility-group-fib-plasmid-encoded-virulence-factors-of-salmonella-enterica-isolated-from-food-sources
#19
Bijay K Khajanchi, Nur A Hasan, Seon Young Choi, Jing Han, Shaohua Zhao, Rita R Colwell, Carl E Cerniglia, Steven L Foley
BACKGROUND: The degree to which the chromosomal mediated iron acquisition system contributes to virulence of many bacterial pathogens is well defined. However, the functional roles of plasmid encoded iron acquisition systems, specifically Sit and aerobactin, have yet to be determined for Salmonella spp. In a recent study, Salmonella enterica strains isolated from different food sources were sequenced on the Illumina MiSeq platform and found to harbor the incompatibility group (Inc) FIB plasmid...
August 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28766745/exploring-the-microbiome-of-healthy-and-diseased-peri-implant-sites-using-illumina-sequencing
#20
I Sanz-Martin, J Doolittle-Hall, R P Teles, M Patel, G N Belibasakis, C H Hämmerle, R E Jung, F R F Teles
AIM: To compare the microbiome of healthy (H) and diseased (P) peri-implant sites and determine the core peri-implant microbiome. MATERIALS AND METHODS: Submucosal biofilms from 32 H and 35 P sites were analyzed using 16S rRNA sequencing (MiSeq, Illumina), QIIME and HOMINGS. Differences between groups were determined using Principal Coordinate Analysis (PCoA), t-tests and Wilcoxon rank sum test and FDR-adjusted. The peri-implant core microbiome was determined. RESULTS: PCoA showed partitioning between H and P at all taxonomic levels...
August 2, 2017: Journal of Clinical Periodontology
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