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https://www.readbyqxmd.com/read/28549288/ecological-effects-of-soil-properties-and-metal-concentrations-on-the-composition-and-diversity-of-microbial-communities-associated-with-land-use-patterns-in-an-electronic-waste-recycling-region
#1
Wencheng Wu, Changxun Dong, Jiahui Wu, Xiaowen Liu, Yingxin Wu, Xianbin Chen, Shixiao Yu
Soil microbes play vital roles in ecosystem functions, and soil microbial communities may be strongly structured by land use patterns associated with electronic waste (e-waste) recycling activities, which can increase the heavy metal concentration in soils. In this study, a suite of soils from five land use types (paddy field, vegetable field, dry field, forest field, and e-waste recycling site) were collected in Longtang Town, Guangdong Province, South China. Soil physicochemical properties and heavy metal concentrations were measured, and the indigenous microbial assemblages were profiled using 16S rRNA high-throughput sequencing and clone library analyses...
May 23, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28549260/identification-of-oral-cavity-biofilm-forming-bacteria-and-determination-of-their-growth-inhibition-by-acacia-arabica-tamarix-aphylla-l-and-melia-azedarach-l-medicinal-plants
#2
Muhammad Khalid, Danial Hassani, Muhammad Bilal, Zahid Ali Butt, Muhammad Hamayun, Ayaz Ahmad, Danfeng Huang, Anwar Hussain
OBJECTIVE: Biofilms are complex, multi-species bacterial communities that colonize the oral cavity in the form of plaque and are known to cause dental caries and periodontal disease. Present study demonstrated the potential of three selected medicinal plants against isolated and identified dental biofilm forming strains. METHODS: Pathogenic bacteria from dental biofilms were isolated, cultured, identified by phylogenetic analysis using PCR-based 16S ribosomal RNA (or 16S rRNA) nucleotide sequences and were analyzed for their biofilm forming capability...
May 18, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28546547/bioturbation-as-a-key-driver-behind-the-dominance-of-bacteria-over-archaea-in-near-surface-sediment
#3
Xihan Chen, Thorbjørn Joest Andersen, Yuki Morono, Fumio Inagaki, Bo Barker Jørgensen, Mark Alexander Lever
The factors controlling the relative abundances of Archaea and Bacteria in marine sediments are poorly understood. We determined depth distributions of archaeal and bacterial 16S rRNA genes by quantitative PCR at eight stations in Aarhus Bay, Denmark. Bacterial outnumber archaeal genes 10-60-fold in uppermost sediments that are irrigated and mixed by macrofauna. This bioturbation is indicated by visual observations of sediment color and faunal tracks, by porewater profiles of dissolved inorganic carbon and sulfate, and by distributions of unsupported (210)Pb and (137)Cs...
May 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28546480/draft-genome-sequence-of-streptomyces-phaeoluteigriseus-dsm41896
#4
Jana K Schniete, Talal S Salih, Lis Algora-Gallardo, Tiago Santos, Sara Filgueira-Martinez, Paul R Herron
The draft genome for the type strain Streptomyces phaeoluteigriseus DSM41896 (ISP 5182) is reported. It was classified as a member of the Streptomyces violaceusniger clade; however, a polyphasic study showed it was a separate species based on its distinct spore morphology and 16S rRNA sequence. The genome sequence confirms it as a separate species.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546029/gardnerella-vaginalis-bacteremia-associated-with-severe-acute-encephalopathy-in-a-young-female-patient
#5
Jacques Tankovic, Albertas Timinskas, Migle Janulaitiene, Milda Zilnyte, Jean-Luc Baudel, Eric Maury, Aurelija Zvirbliene, Milda Pleckaityte
Gardnerella vaginalis is a facultative anaerobic bacterium that inhabits the genitourinary tract of both healthy women and those with bacterial vaginosis. We report a case of G. vaginalis bacteremia associated with severe toxic encephalopathy in a young woman. Anaerobic blood cultures yielded pure growth of small gram-variable rods later identified as G. vaginalis by both rapid biochemical tests and 16S rRNA gene sequencing. The patient recovered after treatment with amoxicillin-clavulanate according to the in vitro susceptibility testing...
May 22, 2017: Anaerobe
https://www.readbyqxmd.com/read/28545131/major-changes-in-microbial-diversity-and-community-composition-across-gut-sections-of-a-juvenile-panchlora-cockroach
#6
Erin A Gontang, Frank O Aylward, Camila Carlos, Tijana Glavina Del Rio, Mansi Chovatia, Alison Fern, Chien-Chi Lo, Stephanie A Malfatti, Susannah G Tringe, Cameron R Currie, Roberto Kolter
Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica...
2017: PloS One
https://www.readbyqxmd.com/read/28545071/characterization-of-the-urinary-microbiome-in-healthy-dogs
#7
Erin N Burton, Leah A Cohn, Carol N Reinero, Hans Rindt, Stephen G Moore, Aaron C Ericsson
The urinary bladder in healthy dogs has dogmatically been considered free of bacteria. This study used culture independent techniques to characterize the healthy canine urinary microbiota. Urine samples collected by antepubic cystocentesis from dogs without urinary infection were used for DNA extraction. Genital tract and rectal samples were collected simultaneously from the same dogs. The V4 hypervariable region of the 16S rRNA bacterial gene was amplified and compared against Greengenes database for OTU assignment and relative abundance for urine, genital, and rectal samples...
2017: PloS One
https://www.readbyqxmd.com/read/28544522/metagenomic-potential-for-and-diversity-of-n-cycle-driving-microorganisms-in-the-bothnian-sea-sediment
#8
Olivia Rasigraf, Julia Schmitt, Mike S M Jetten, Claudia Lüke
The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases...
May 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28544080/the-skin-microbiome-of-cow-nose-rays-rhinoptera-bonasus-in-an-aquarium-touch-tank-exhibit
#9
Patrick J Kearns, Jennifer L Bowen, Michael F Tlusty
Public aquaria offer numerous educational opportunities for visitors while touch-tank exhibits offer guests the ability to directly interact with marine life via physical contact. Despite the popularity of touch-tanks, there is a paucity of research about animal health in these exhibits and, in particular, there is little research on the microbial communities in these highly interactive exhibits. Microbial community structure can have implications for both host health and habitat function. To better understand the microbiome of a touch-tank we used high-throughput sequencing of the 16S rRNA gene to analyze the microbial community on the dorsal and ventral surfaces of cow-nose rays (Rhinoptera bonasus) as well as their environment in a frequently visited touch-tank exhibit at the New England Aquarium...
May 23, 2017: Zoo Biology
https://www.readbyqxmd.com/read/28543707/viable-bacteria-persist-on-antibiotic-spacers-following-two-stage-revision-for-periprosthetic-joint-infection
#10
Dongzhu Ma, Robert M Q Shanks, Charles M Davis, David W Craft, Thomas K Wood, Brian R Hamlin, Kenneth L Urish
Treatment in periprosthetic joint infection (PJI) remains challenging. The failure rate of two-stage revision and irrigation and debridement with component retention in PJI suggests that biofilm cells have a high tolerance to antibiotic chemotherapy. Previous work has demonstrated that biofilm cells have high antibiotic tolerance in vitro, but there is little clinical evidence to support these observations. The aim of this study was to determine if retrieved antibiotic spacers from two-stage revision total knee arthroplasty for PJI have evidence of remaining viable bacteria...
May 19, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28543439/metagenomic-profiling-of-the-microbial-freshwater-communities-in-two-bulgarian-reservoirs
#11
Ivan Iliev, Galina Yahubyan, Mariana Marhova, Elena Apostolova, Mariyana Gozmanova, Gana Gecheva, Sonya Kostadinova, Angelina Ivanova, Vesselin Baev
Microorganisms inhabiting freshwater environments are an integral part of the aquatic ecosystems. Very few data are available regarding the profiles of the microbial communities in the reservoirs in Bulgaria, despite their key role in the biogeochemical processes. In the present study, we provide the first comprehensive metagenomic analysis on the planktonic bacterial diversity of two large and economically important Bulgarian reservoirs (Batak and Tsankov Kamak) using next-generation sequencing of 16S ribosomal RNA gene (16S rRNA)...
May 22, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28543188/cd44-deletion-leading-to-attenuation-of-experimental-autoimmune-encephalomyelitis-results-from-alterations-in-gut-microbiome-in-mice
#12
Kumaraswamy Naidu Chitrala, Hongbing Guan, Narendra P Singh, Brandon Busbee, Alexa Gandy, Pegah Mehrpouya-Bahrami, Mitra S Ganewatta, Chuanbing Tang, Saurabh Chatterjee, Prakash Nagarkatti, Mitzi Nagarkatti
Dysbiosis in gut microbiome has been shown to be associated with inflammatory and autoimmune diseases. Previous studies from our laboratory demonstrated the pivotal role played by CD44 in the regulation of experimental autoimmune encephalomyelitis (EAE), a murine model of multiple sclerosis. In the current study, we determined whether these effects resulted from an alteration in gut microbiota and the short-chain fatty acid (SCFA) production in CD44KO mice. Fecal transfer from naïve CD44KO but not CD44WT mice, into EAE-induced CD44WT mice, led to significant amelioration of EAE...
May 23, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/28542573/development-of-real-time-pcr-and-loop-mediated-isothermal-amplification-lamp-assays-for-the-differential-detection-of-digital-dermatitis-associated-treponemes
#13
Kelly Anklam, Megan Kulow, Wataru Yamazaki, Dörte Döpfer
Bovine digital dermatitis (DD) is a severe infectious cause of lameness in cattle worldwide, with important economic and welfare consequences. There are three treponeme phylogroups (T. pedis, T. phagedenis, and T. medium) that are implicated in playing an important causative role in DD. This study was conducted to develop real-time PCR and loop-mediated isothermal amplification (LAMP) assays for the detection and differentiation of the three treponeme phylogroups associated with DD. The real-time PCR treponeme phylogroup assays targeted the 16S-23S rDNA intergenic space (ITS) for T...
2017: PloS One
https://www.readbyqxmd.com/read/28542542/comparative-analysis-of-bacterial-community-structure-in-the-rhizosphere-of-maize-by-high-throughput-pyrosequencing
#14
Yi Yang, Na Wang, Xinyan Guo, Yi Zhang, Boping Ye
In this study, we designed a microcosm experiment to explore the composition of the bacterial community in the rhizosphere of maize and bulk soil by sequencing the V3-V4 region of the 16S rRNA gene on the Illumina system. 978-1239 OTUs (cut off level of 3%) were found in rhizosphere and bulk soil samples. Rhizosphere shared features with the bulk soil, such as predominance of Acidobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes and TM7. At genus level, many of the dominant rhizosphere genera (Chitinophaga, Nitrospira, Flavobacterium, etc...
2017: PloS One
https://www.readbyqxmd.com/read/28541458/microbiome-analysis-of-a-disease-affecting-the-deep-sea-sponge-geodia-barretti
#15
Heidi M Luter, Raymond J Bannister, Steve Whalan, Tina Kutti, Mari-Carmen Pineda, Nicole S Webster
Reports of sponge disease are becoming increasingly frequent, although almost all instances involve shallow-water, tropical species. Here, we describe the first disease affecting the deep-water sponge, Geodia barretti. The disease is characterised by brown/black discolouration of the sponge tissue, extensive levels of tissue disintegration and increased levels of fouling. Disease prevalence was quantified using video survey transects conducted between 100 and 220 meters in Korsfjorden, Norway and the microbial communities of healthy and diseased sponges were compared using 16S rRNA gene sequencing...
May 24, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28539917/diversity-of-extremely-halophilic-archaeal-and-bacterial-communities-from-commercial-salts
#16
Ashagrie Gibtan, Kyounghee Park, Mingyeong Woo, Jung-Kue Shin, Dong-Woo Lee, Jae Hak Sohn, Minjung Song, Seong Woon Roh, Sang-Jae Lee, Han-Seung Lee
Salting is one of the oldest food preservation techniques. However, salt is also the source of living halophilic microorganisms that may affect human health. In order to determine the microbial communities of commercial salts, an investigation were done using amplicon sequencing approach in four commercial salts: Ethiopian Afdera salt (EAS), Ethiopian rock salt (ERS), Korean Jangpan salt (KJS), and Korean Topan salt (KTS). Using domain-specific primers, a region of the 16S rRNA gene was amplified and sequenced using a Roche 454 instrument...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28539351/bacteriophage-transfer-during-faecal-microbiota-transplantation-in-clostridium-difficile-infection-is-associated-with-treatment-outcome
#17
Tao Zuo, Sunny H Wong, Kelvin Lam, Rashid Lui, Kitty Cheung, Whitney Tang, Jessica Y L Ching, Paul K S Chan, Martin C W Chan, Justin C Y Wu, Francis K L Chan, Jun Yu, Joseph J Y Sung, Siew C Ng
OBJECTIVE: Faecal microbiota transplantation (FMT) is effective for the treatment of recurrent Clostridium difficile infection (CDI). Studies have shown bacterial colonisation after FMT, but data on viral alterations in CDI are scarce. We investigated enteric virome alterations in CDI and the association between viral transfer and clinical outcome in patients with CDI. DESIGN: Ultra-deep metagenomic sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on stool samples from 24 subjects with CDI and 20 healthy controls...
May 24, 2017: Gut
https://www.readbyqxmd.com/read/28538678/effects-of-commercial-apple-varieties-on-human-gut-microbiota-composition-and-metabolic-output-using-an-in-vitro-colonic-model
#18
Athanasios Koutsos, Maria Lima, Lorenza Conterno, Mattia Gasperotti, Martina Bianchi, Francesca Fava, Urska Vrhovsek, Julie A Lovegrove, Kieran M Tuohy
Apples are a rich source of polyphenols and fiber. A major proportion of apple polyphenols escape absorption in the small intestine and together with non-digestible polysaccharides reach the colon, where they can serve as substrates for bacterial fermentation. Animal studies suggest a synergistic interaction between apple polyphenols and the soluble fiber pectin; however, the effects of whole apples on human gut microbiota are less extensively studied. Three commercial apple varieties-Renetta Canada, Golden Delicious and Pink Lady-were digested and fermented in vitro using a batch culture colonic model (pH 5...
May 24, 2017: Nutrients
https://www.readbyqxmd.com/read/28537545/paenibacillus-lacus-sp-nov-isolated-from-a-water-reservoir
#19
Wen-Ming Chen, Kai-Rou Lin, Shih-Yi Sheu
A bacterial strain, designated Agd-32T, was isolated from a water sample taken from the Agongdian Reservoir in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain Agd-32T were Gram-stain-variable, aerobic, motile by means of peritrichous flagella, endospore-forming, rod-shaped and surrounded by a thick capsule. Strain Agd-32T contained anteiso-C15 : 0 and C16 : 0 as the predominant fatty acids. The major isoprenoid quinone was MK-7, and the polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophosphoglycolipid, one unidentified glycolipid, one unidentified phospholipid and one unidentified lipid...
May 25, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28536926/structural-changes-of-gut-microbiota-in-parkinson-s-disease-and-its-correlation-with-clinical-features
#20
Wei Li, Xiaoli Wu, Xu Hu, Tao Wang, Shan Liang, Yunfeng Duan, Feng Jin, Bin Qin
The aim of this study was to compare the structure of gut microbiota in Parkinson's disease (PD) patients and healthy controls; and to explore correlations between gut microbiota and PD clinical features. We analyzed fecal bacterial composition of 24 PD patients and 14 healthy volunteers by using 16S rRNA sequencing. There were significant differences between PD and healthy controls, as well as among different PD stages. The putative cellulose degrading bacteria from the genera Blautia (P=0.018), Faecalibacterium (P=0...
May 20, 2017: Science China. Life Sciences
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