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https://www.readbyqxmd.com/read/28545131/major-changes-in-microbial-diversity-and-community-composition-across-gut-sections-of-a-juvenile-panchlora-cockroach
#1
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
#2
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/28544806/can-soil-microbial-diversity-influence-plant-metabolites-and-life-history-traits-of-a-rhizophagous-insect-a-demonstration-in-oilseed-rape
#3
Tom Lachaise, Morgane Ourry, Lionel Lebreton, Anne-Yvonne Guillerm-Erckelboudt, Juliette Linglin, Chrystelle Paty, Valérie Chaminade, Nathalie Marnet, Julie Aubert, Denis Poinsot, Anne-Marie Cortesero, Christophe Mougel
Interactions between plants and phytophagous insects play an important part in shaping the biochemical composition of plants. Reciprocally plant metabolites can influence major life history traits in these insects and largely contribute to their fitness. Plant rhizospheric microorganisms are an important biotic factor modulating plant metabolites and adaptation to stress. While plant-insects or plant-microorganisms interactions and their consequences on the plant metabolite signature are well-documented, the impact of soil microbial communities on plant defenses against phytophagous insects remains poorly known...
May 23, 2017: Insect Science
https://www.readbyqxmd.com/read/28544522/metagenomic-potential-for-and-diversity-of-n-cycle-driving-microorganisms-in-the-bothnian-sea-sediment
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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/28542313/environmental-dna-edna-metabarcoding-assays-to-detect-invasive-invertebrate-species-in-the-great-lakes
#11
Katy E Klymus, Nathaniel T Marshall, Carol A Stepien
Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA) demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and resources spent on traditional survey methods. The literature emphasizes the importance of genetic marker development, as the markers dictate the applicability, sensitivity and resolution ability of an eDNA assay. The present study developed two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways, with a focus for use on invasive bivalve and gastropod species monitoring...
2017: PloS One
https://www.readbyqxmd.com/read/28541746/the-evolving-cystic-fibrosis-microbiome-a-comparative-cohort-study-spanning-sixteen-years
#12
Nicole Acosta, Fiona J Whelan, Ranjani Somayaji, Ali Poonja, Michael G Surette, Harvey R Rabin, Michael D Parkins
RATIONALE: The cystic fibrosis (CF) airways are infected with a diverse polymicrobial community. OBJECTIVES: Understanding how changes in the CF microbiome have occurred over time, similar to the observed changes in the prevalence of cultured pathogens, is key in understanding the microbiome's role in disease. METHODS: Drawing from a prospectively collected and maintained sputum biobank, we identified 45 patients with sputum samples collected between the ages of 18-21 years in three successive cohorts of adults transitioning to our CF clinic: A(1997-2000), B(2004-2007), and C(2010-2013)...
May 25, 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/28541458/microbiome-analysis-of-a-disease-affecting-the-deep-sea-sponge-geodia-barretti
#13
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
#14
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
#15
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/28539260/phylogenetic-relationships-of-the-tribe-toxotrypanini-diptera-tephritidae-based-on-molecular-characters
#16
Ximo Mengual, Peter Kerr, Allen L Norrbom, Norman B Barr, Matthew L Lewis, Anna M Stapelfeldt, Sonja J Scheffer, Patrick Woods, Md-Sajedul Islam, Cheslavo A Korytkowski, Keiko Uramoto, Erick J Rodriguez, Bruce D Sutton, Norma Nolazco, Gary J Steck, Stephen Gaimari
Current hypotheses of relationship among the species of the fruit fly genera Anastrepha and Toxotrypana are tested using sequence data from six DNA regions: the mitochondrial regions 16S, CAD, and COI, and the nuclear regions EF1a, PER, and PGD. DNA sequences were obtained from 146 species of Anastrepha, representing 19 of the 21 species groups as well as five of the six clades of the robusta group, and four species of Toxotrypana in addition to species of Hexachaeta, Pseudophorellia, Alujamyia, and 13 other tephritid genera used as outgroups...
May 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28538949/the-follicular-skin-microbiome-in-patients-with-hidradenitis-suppurativa-and-healthy-controls
#17
Hans Christian Ring, Jonathan Thorsen, Ditte M Saunte, Berit Lilje, Lene Bay, Peter Theut Riis, Niels Larsen, Lee O'Brien Andersen, Henrik V Nielsen, Iben M Miller, Thomas Bjarnsholt, Kurt Fuursted, Gregor Borut Jemec
Importance: Although the pathogenesis of hidradenitis suppurativa (HS) remains enigmatic, several factors point to potential involvement of the cutaneous microbiome. Insight into the cutaneous microbiome in HS using next-generation sequencing may provide novel data on the microbiological diversity of the skin. Objective: To investigate the follicular skin microbiome in patients with HS and in healthy controls. Design, Setting, and Participants: This case-control study obtained punch biopsy specimens from patients with HS (lesional and nonlesional) and healthy controls between October 1, 2014, and August 1, 2016...
May 24, 2017: JAMA Dermatology
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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