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Microbial diversity

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https://www.readbyqxmd.com/read/28231697/the-fecal-microbiota-composition-of-boar-duroc-yorkshire-landrace-and-hampshire-pigs
#1
Yingping Xiao, Kaifeng Li, Yun Xiang, Weidong Zhou, Guohong Gui, Hua Yang
To investigate the effect of host genetics on gut microbial diversity, we performed a structural survey of the fecal microbiota of four purebred boar pig lines: Duroc, Landrace, Hampshire and Yorkshire. The V3-V4 regions of the 16S rRNA genes were amplified and sequenced. A total of 783 OTUs were shared by all breeds, whereas other OTUs were breed-specific. Firmicutes and Bacteroidetes dominated the majority of the fecal microbiota; Clostridia, Bacilli and Bacteroidia were the major classes. Nine predominant genera were observed in all breeds and eight of them can produce short-chain fatty acids (SCFAs)...
February 23, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28231613/genetic-determinism-vs-phenotypic-plasticity-in-protist-morphology
#2
Matthieu Mulot, Katarzyna Marcisz, Lara Grandgirard, Enrique Lara, Anush Kosakyan, Bjorn J M Robroek, Mariusz Lamentowicz, Richard J Payne, Edward A D Mitchell
Untangling the relationships between morphology and phylogeny is key to building a reliable taxonomy, but is especially challenging for protists, where the existence of cryptic or pseudocryptic species makes finding relevant discriminant traits difficult. Here we use Hyalosphenia papilio (a testate amoeba) as a model species to investigate the contribution of phylogeny and phenotypic plasticity in its morphology. We study the response of Hyalosphenia papilio morphology (shape and pores number) to environmental variables in 1) a manipulative experiment with controlled conditions (water level), 2) an observational study of a withinsite natural ecological gradient (water level), and 3) an observational study across 37 European peatlands (climate)...
February 23, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28229558/microbial-diversity-of-a-full-scale-uasb-reactor-applied-to-poultry-slaughterhouse-wastewater-treatment-integration-of-16s-rrna-gene-amplicon-and-shotgun-metagenomic-sequencing
#3
Tiago Palladino Delforno, Gileno Vieira Lacerda Júnior, Melline F Noronha, Isabel K Sakamoto, Maria Bernadete A Varesche, Valéria M Oliveira
The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset...
February 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28229543/developmental-trajectories-of-amphibian-microbiota-response-to-bacterial-therapy-depends-on-initial-community-structure
#4
Leyla R Davis, Laurent Bigler, Douglas C Woodhams
Improving host health through microbial manipulation requires untangling factors that shape the microbiome. There is currently little understanding of how initial community structure may drive the microbiota trajectory across host development or influence bacterial therapy. Probiotic baths of surface symbionts, Pseudomonas fluorescens and Flavobacterium johnsoniae were administered to 240 tadpoles of the midwife toad, Alytes obstetricans in semi-natural outdoor mesocosms originating from geographically and genetically distinct populations in Switzerland...
February 22, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28229521/microbial-potential-for-carbon-and-nutrient-cycling-in-a-geogenic-supercritical-carbon-dioxide-reservoir
#5
Adam J E Freedman, BoonFei Tan, Janelle R Thompson
Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO2 , harbor a "deep carbonated biosphere" with carbon cycling potential. We sampled subsurface fluids from scCO2 -water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content...
February 22, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28228075/challenges-in-dermal-delivery-of-therapeutic-antimicrobial-protein-and-peptides
#6
Rohan Aminbhai Lalani, Ambikanandan Misra, Jitendra Amrutiya, Hinal Patel, Priyanka Bhatt, Vivek Patel
BACKGROUND: Protein and peptides in biological system form an important part of innate immune system and are being explored for potential use in various diseases as therapeutics. Importance of proteins and peptides as a new class of antimicrobial agents have boosted research in the field of biotechnology as potential alternative to antibiotic agents. OBJECTIVE: Protein and peptides antimicrobial as a therapeutics class are structurally diverse and exhibit potent activity against microbes by various mechanisms...
February 22, 2017: Current Drug Metabolism
https://www.readbyqxmd.com/read/28228044/withaferin-a-protects-against-spinal-cord-injury-by-inhibiting-apoptosis-and-inflammation-in-mice
#7
Xianlei Yan, Guangxiang Huang, Quan Liu, Jiemin Zheng, Hongmou Chen, Qidan Huang, Jiakang Chen, Heqing Huang
CONTEXT: Withaferin A (WFA) exhibits diverse pharmaceutical applications on human diseases, including rheumatoid arthritis, cancers and microbial infection. OBJECTIVE: We evaluated the neuroprotective role of WFA using a mouse model of spinal cord injury (SCI). MATERIALS AND METHODS: BALB/c mice were administrated 10 mg/kg of WFA. Gene expression was measured by real-time PCR, western blot and immunohistochemistry. Cell morphology and apoptosis were determined by H&E staining and TUNEL assay...
December 2017: Pharmaceutical Biology
https://www.readbyqxmd.com/read/28225785/betel-nut-chewing-oral-premalignant-lesions-and-the-oral-microbiome
#8
Brenda Y Hernandez, Xuemei Zhu, Marc T Goodman, Robert Gatewood, Paul Mendiola, Katrina Quinata, Yvette C Paulino
Oral cancers are attributed to a number of causal agents including tobacco, alcohol, human papillomavirus (HPV), and areca (betel) nut. Although betel nut chewing has been established as an independent cause of oral cancer, the mechanisms of carcinogenesis are poorly understood. An investigation was undertaken to evaluate the influence of betel nut chewing on the oral microbiome and oral premalignant lesions. Study participants were recruited from a dental clinic in Guam. Structured interviews and oral examinations were performed...
2017: PloS One
https://www.readbyqxmd.com/read/28225587/compms2miner-an-automatable-metabolite-identification-visualization-and-data-sharing-r-package-for-high-resolution-lc-ms-datasets
#9
William Matthew Bell Edmands, Lauren M Petrick, Dinesh Kumar Barupal, Augustin Scalbert, Mark Wilson, Jeffrey Wickliffe, Stephen M Rappaport
A long-standing challenge of untargeted metabolomic profiling by ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) is efficient transition from unknown mass spectral features to confident metabolite annotations. The compMS2Miner (Comprehensive MS2 Miner) package was developed in the R language to facilitate rapid, comprehensive feature annotation using a peak-picker-output and MS2 data files as inputs. The number of MS2 spectra that can be collected during a metabolomic profiling experiment far outweigh the amount of time required for pain-staking manual interpretation, therefore a degree of software workflow autonomy is required for broad-scale metabolite annotation...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28223966/geological-and-geochemical-controls-on-subsurface-microbial-life-in-the-samail-ophiolite-oman
#10
Kaitlin R Rempfert, Hannah M Miller, Nicolas Bompard, Daniel Nothaft, Juerg M Matter, Peter Kelemen, Noah Fierer, Alexis S Templeton
Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28223733/impact-of-humic-acids-on-the-colonic-microbiome-in-healthy-volunteers
#11
Alexander Swidsinski, Yvonne Dörffel, Vera Loening-Baucke, Christoph Gille, Anne Reißhauer, Onder Göktas, Monika Krüger, Jürgen Neuhaus, Wieland Schrödl
AIM: To test the effects of humic acids on innate microbial communities of the colon. METHODS: We followed the effects of oral supplementation with humic acids (Activomin(®)) on concentrations and composition of colonic microbiome in 14 healthy volunteers for 45 d. 3 × 800 mg Activomin(®) were taken orally for 10 d followed by 3 × 400 mg for 35 d. Colonic microbiota were investigated using multicolor fluorescence in situ hybridization (FISH) of Carnoy fixated and paraffin embedded stool cylinders...
February 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28223725/gut-microbial-diversity-analysis-using-illumina-sequencing-for-functional-dyspepsia-with-liver-depression-spleen-deficiency-syndrome-and-the-interventional-xiaoyaosan-in-a-rat-model
#12
Juan-Juan Qiu, Zhe Liu, Peng Zhao, Xue-Jun Wang, Yu-Chun Li, Hua Sui, Lawrence Owusu, Hui-Shu Guo, Zheng-Xu Cai
AIM: To investigate gut microbial diversity and the interventional effect of Xiaoyaosan (XYS) in a rat model of functional dyspepsia (FD) with liver depression-spleen deficiency syndrome. METHODS: The FD with liver depression-spleen deficiency syndrome rat model was established through classic chronic mild unpredictable stimulation every day. XYS group rats received XYS 1 h before the stimulation. The models were assessed by parameters including state of the rat, weight, sucrose test result and open-field test result...
February 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28223457/the-source-and-evolutionary-history-of-a-microbial-contaminant-identified-through-soil-metagenomic-analysis
#13
Matthew R Olm, Cristina N Butterfield, Alex Copeland, T Christian Boles, Brian C Thomas, Jillian F Banfield
In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223452/heterogeneity-confounds-establishment-of-a-model-microbial-strain
#14
Nancy P Keller
Aspergillus fumigatus is a ubiquitous environmental mold and the leading cause of diverse human diseases ranging from allergenic bronchopulmonary aspergillosis (ABPA) to invasive pulmonary aspergillosis (IPA). Experimental investigations of the biology and virulence of this opportunistic pathogen have historically used a few type strains; however, it is increasingly observed with this fungus that heterogeneity among isolates potentially confounds the use of these reference isolates. Illustrating this point, Kowalski et al...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223257/the-fecal-microbiome-of-dogs-with-exocrine-pancreatic-insufficiency
#15
Anitha Isaiah, Joseph Cyrus Parambeth, Jörg M Steiner, Jonathan A Lidbury, Jan S Suchodolski
Exocrine pancreatic insufficiency (EPI) in dogs is a syndrome of inadequate synthesis and secretion of pancreatic enzymes. Small intestinal bacterial dysbiosis occurs in dogs with EPI, and is reversed with pancreatic enzyme therapy. However, there are no studies evaluating the fecal microbiome of dogs with EPI. The objective of this study was to evaluate the fecal microbiome of dogs with EPI. Three day pooled fecal samples were collected from healthy dogs (n = 18), untreated (n = 7) dogs with EPI, and dogs with EPI treated with enzyme replacement therapy (n = 19)...
February 18, 2017: Anaerobe
https://www.readbyqxmd.com/read/28222236/differential-sharing-and-distinct-co-occurrence-networks-among-spatially-close-bacterial-microbiota-of-bark-mosses-and-lichens%C3%A2-%C3%A2
#16
Ines Aline Aschenbrenner, Tomislav Cernava, Armin Erlacher, Gabriele Berg, Martin Grube
Knowledge of bacterial community host-specificity has increased greatly in recent years. However, the inter-microbiome relationships of unrelated but spatially close organisms remain little understood. Trunks of trees covered by epiphytes represent complex habitats with a mosaic of ecological niches. In this context, we investigated the structure, diversity and interactions of microbiota associated with lichens, mosses and the bare tree bark. Comparative analysis revealed significant differences in the habitat-associated community structures...
February 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28222161/the-distinct-features-of-microbial-dysbiosis-of-crohn-s-disease-do-not-occur-to-the-same-extent-in-their-unaffected-genetically-linked-kindred
#17
Umer Zeeshan Ijaz, Christopher Quince, Laura Hanske, Nick Loman, Szymon T Calus, Martin Bertz, Christine A Edwards, Daniel R Gaya, Richard Hansen, Paraic McGrogan, Richard K Russell, Konstantinos Gerasimidis
BACKGROUND/AIMS: Studying the gut microbiota in unaffected relatives of people with Crohn's disease (CD) may advance our understanding of the role of bacteria in disease aetiology. METHODS: Faecal microbiota composition (16S rRNA gene sequencing), genetic functional capacity (shotgun metagenomics) and faecal short chain fatty acids (SCFA) were compared in unaffected adult relatives of CD children (CDR, n = 17) and adult healthy controls, unrelated to CD patients (HUC, n = 14)...
2017: PloS One
https://www.readbyqxmd.com/read/28221910/influence-of-thawing-methods-and-storage-temperatures-on-bacterial-diversity-growth-kinetics-and-biogenic-amine-development-in-atlantic-mackerel
#18
S Onyango, H Palmadottir, T Tómason, V T Marteinsson, P M K Njage, E Reynisson
Limited knowledge is currently available on the influence of fish thawing and subsequent storage conditions on bacterial growth kinetics, succession, and diversity alongside the production of biogenic amines. This study aimed to address these factors during the thawing and subsequent storage of mackerel. Thawing was either done fast in 18°C water for 2 h or slowly at 30°C overnight. Subsequent storage was at 30°C (ambient) for 36 h and 2 to 5°C (refrigerated) for 12 days. The cultivation methods used were total viable counts, hydrogen sulfide-producing bacteria, and Pseudomonas ...
November 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28220693/aroma-precursors-in-grapes-and-wine-flavor-release-during-wine-production-and-consumption
#19
Mango Parker, Dimitra L Capone, I Leigh Francis, Markus J Herderich
Pioneering investigations into precursors to fruity and floral flavors established the importance of terpenoid and C13-norisoprenoid glycosides to the flavor of aromatic wines. Nowadays flavor precursors in grapes and wine are known to be structurally diverse, encompassing glycosides; amino acid conjugates; odorless volatiles; hydroxycinnamic acids and many others. Flavor precursors mainly originate in the grape berry, but also from oak or other materials involved in winemaking. Flavors are released from precursors during crushing and subsequent production steps by enzymatic and non-enzymatic transformations, via microbial glycosidases; esterases; C-S lyases and decarboxylases; and through acid catalysed hydrolysis and chemical rearrangements...
February 21, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28220514/randomised-clinical-trial-faecal-microbiota-transplantation-for-recurrent-clostridum-difficile-infection-fresh-or-frozen-or-lyophilised-microbiota-from-a-small-pool-of-healthy-donors-delivered-by-colonoscopy
#20
Z D Jiang, N J Ajami, J F Petrosino, G Jun, C L Hanis, M Shah, L Hochman, V Ankoma-Sey, A W DuPont, M C Wong, A Alexander, S Ke, H L DuPont
BACKGROUND: Faecal microbiota transplantation (FMT) has become routine in managing recurrent C. difficile infection (CDI) refractory to antibiotics. AIM: To compare clinical response and improvements in colonic microbiota diversity in subjects with recurrent CDI using different donor product. METHODS: Seventy-two subjects with ≥3 bouts of CDI were randomised in a double-blind study to receive fresh, frozen or lyophilised FMT product via colonoscopy from 50 g of stool per treatment from eight healthy donors...
February 21, 2017: Alimentary Pharmacology & Therapeutics
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