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Microbiome

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https://www.readbyqxmd.com/read/29157308/characterization-of-the-upper-and-lower-respiratory-tract-microbiota-in-piedmontese-calves
#1
Isabella Nicola, Francesco Cerutti, Elena Grego, Iride Bertone, Paola Gianella, Antonio D'Angelo, Simone Peletto, Claudio Bellino
BACKGROUND: The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community composition of the upper and lower respiratory tracts in calves. RESULTS: The microbiota of the upper (nasal swab [NS]) and the lower (trans-tracheal aspiration [TTA]) respiratory tracts of 19 post-weaned Piedmontese calves with (8/19) and without (11/19) clinical signs of respiratory disease, coming from six different farms, was characterized by 16S rRNA gene metabarcoding...
November 21, 2017: Microbiome
https://www.readbyqxmd.com/read/29145893/normalization-of-the-microbiota-in-patients-after-treatment-for-colonic-lesions
#2
Marc A Sze, Nielson T Baxter, Mack T Ruffin, Mary A M Rogers, Patrick D Schloss
BACKGROUND: Colorectal cancer is a worldwide health problem. Despite growing evidence that members of the gut microbiota can drive tumorigenesis, little is known about what happens to it after treatment for an adenoma or carcinoma. This study tested the hypothesis that treatment for adenoma or carcinoma alters the abundance of bacterial populations associated with disease to those associated with a normal colon. We tested this hypothesis by sequencing the 16S rRNA genes in the feces of 67 individuals before and after treatment for adenoma (N = 22), advanced adenoma (N = 19), and carcinoma (N = 26)...
November 16, 2017: Microbiome
https://www.readbyqxmd.com/read/29145891/the-inuit-gut-microbiome-is-dynamic-over-time-and-shaped-by-traditional-foods
#3
Geneviève Dubois, Catherine Girard, François-Joseph Lapointe, B Jesse Shapiro
BACKGROUND: The human gut microbiome represents a diverse microbial community that varies across individuals and populations, and is influenced by factors such as host genetics and lifestyle. Diet is a major force shaping the gut microbiome, and the effects of dietary choices on microbiome composition are well documented. However, it remains poorly known how natural temporal variation in diet can affect the microbiome. The traditional Inuit diet is primarily based on animal products, which are thought to vary seasonally according to prey availability...
November 16, 2017: Microbiome
https://www.readbyqxmd.com/read/29141685/correction-to-towards-a-balanced-view-of-the-bacterial-tree-of-life
#4
Frederik Schulz, Emiley A Eloe-Fadrosh, Robert M Bowers, Jessica Jarett, Torben Nielsen, Natalia N Ivanova, Nikos C Kyrpides, Tanja Woyke
Following publication of the original article [1], the authors pointed out that the figure shown as figure S1 is actually figure S2 and vice versa. Figure S1 should show the barcharts, and figure S2 should shows the heatmaps. Figures captions are in the correct order. 1) "...SILVA-only OTUs (37,066 97% OTUs and 1266 85% clusters) (Additional file 3: Figure S2 )..." - > ...SILVA-only OTUs (37,066 97% OTUs and 1266 85% clusters) (Additional file 3: Figure S1 )..." 2) "...in groundwater and soil (Fig. 2, Additional file 2: Figure S1 )...
November 15, 2017: Microbiome
https://www.readbyqxmd.com/read/29132405/identifying-predictive-features-of-clostridium-difficile-infection-recurrence-before-during-and-after-primary-antibiotic-treatment
#5
Sepideh Pakpour, Amit Bhanvadia, Roger Zhu, Abhimanyu Amarnani, Sean M Gibbons, Thomas Gurry, Eric J Alm, Laura A Martello
BACKGROUND: Colonization by the pathogen Clostridium difficile often occurs in the background of a disrupted microbial community. Identifying specific organisms conferring resistance to invasion by C. difficile is desirable because diagnostic and therapeutic strategies based on the human microbiota have the potential to provide more precision to the management and treatment of Clostridium difficile infection (CDI) and its recurrence. METHODS: We conducted a longitudinal study of adult patients diagnosed with their first CDI...
November 13, 2017: Microbiome
https://www.readbyqxmd.com/read/29122007/pancreatic-cyst-fluid-harbors-a-unique-microbiome
#6
Shan Li, Gwenny M Fuhler, Nahush Bn, Tony Jose, Marco J Bruno, Maikel P Peppelenbosch, Sergey R Konstantinov
BACKGROUND: It is clear that specific intestinal bacteria are involved in the development of different premalignant conditions along the gastrointestinal tract. An analysis of the microbial constituents in the context of pancreatic cystic lesions has, however, as yet not been performed. This consideration prompted us to explore whether endoscopically obtained pancreatic cyst fluids (PCF) contain bacterial DNA and to determine the genera of bacteria present in such material. METHODS: Total DNA was isolated from 69 PCF samples...
November 9, 2017: Microbiome
https://www.readbyqxmd.com/read/29084611/morphological-and-genetic-factors-shape-the-microbiome-of-a-seabird-species-oceanodroma-leucorhoa-more-than-environmental-and-social-factors
#7
Douglas S Pearce, Brian A Hoover, Sarah Jennings, Gabrielle A Nevitt, Kathryn M Docherty
BACKGROUND: The microbiome provides multiple benefits to animal hosts that can profoundly impact health and behavior. Microbiomes are well-characterized in humans and other animals in controlled settings, yet assessments of wild bird microbial communities remain vastly understudied. This is particularly true for pelagic seabirds with unique life histories that differ from terrestrial bird species. This study was designed to examine how morphological, genetic, environmental, and social factors affect the microbiome of a burrow-nesting seabird species, Leach's storm petrel (Oceanodroma leucorhoa)...
October 30, 2017: Microbiome
https://www.readbyqxmd.com/read/29078812/dietary-changes-in-nutritional-studies-shape-the-structural-and-functional-composition-of-the-pigs-fecal-microbiome-from-days-to-weeks
#8
Bruno Tilocca, Katharina Burbach, Charlotte M E Heyer, Ludwig E Hoelzle, Rainer Mosenthin, Volker Stefanski, Amélia Camarinha-Silva, Jana Seifert
BACKGROUND: The possible impact of changes in diet composition on the intestinal microbiome is mostly studied after some days of adaptation to the diet of interest. The question arises if a few days are enough to reflect the microbial response to the diet by changing the community composition and function. The present study investigated the fecal microbiome of pigs during a time span of 4 weeks after a dietary change to obtain insights regarding the time required for adaptation. Four different diets were used differing in either protein source (field peas meal vs...
October 27, 2017: Microbiome
https://www.readbyqxmd.com/read/29078799/comparing-microbiotas-in-the-upper-aerodigestive-and-lower-respiratory-tracts-of-lambs
#9
Laura Glendinning, David Collie, Steven Wright, Kenny M D Rutherford, Gerry McLachlan
BACKGROUND: Recently, the importance of the lung microbiota during health and disease has been examined in humans and in small animal models. Whilst sheep have been proposed as an appropriate large animal model for studying the pathophysiology of a number of important human respiratory diseases, it is clearly important to continually define the limits of agreement between these systems as new concepts emerge. In humans, it has recently been established that the lung microbiota is seeded by microbes from the oral cavity...
October 27, 2017: Microbiome
https://www.readbyqxmd.com/read/29070062/microbial-biodiversity-assessment-of-the-european-space-agency-s-exomars-2016-mission
#10
Kaisa Koskinen, Petra Rettberg, Rüdiger Pukall, Anna Auerbach, Lisa Wink, Simon Barczyk, Alexandra Perras, Alexander Mahnert, Diana Margheritis, Gerhard Kminek, Christine Moissl-Eichinger
BACKGROUND: The ExoMars 2016 mission, consisting of the Trace Gas Orbiter and the Schiaparelli lander, was launched on March 14 2016 from Baikonur, Kazakhstan and reached its destination in October 2016. The Schiaparelli lander was subject to strict requirements for microbial cleanliness according to the obligatory planetary protection policy. To reach the required cleanliness, the ExoMars 2016 flight hardware was assembled in a newly built, biocontrolled cleanroom complex at Thales Alenia Space in Turin, Italy...
October 25, 2017: Microbiome
https://www.readbyqxmd.com/read/29041989/links-of-gut-microbiota-composition-with-alcohol-dependence-syndrome-and-alcoholic-liver-disease
#11
Veronika B Dubinkina, Alexander V Tyakht, Vera Y Odintsova, Konstantin S Yarygin, Boris A Kovarsky, Alexander V Pavlenko, Dmitry S Ischenko, Anna S Popenko, Dmitry G Alexeev, Anastasiya Y Taraskina, Regina F Nasyrova, Evgeny M Krupitsky, Nino V Shalikiani, Igor G Bakulin, Petr L Shcherbakov, Lyubov O Skorodumova, Andrei K Larin, Elena S Kostryukova, Rustam A Abdulkhakov, Sayar R Abdulkhakov, Sergey Y Malanin, Ruzilya K Ismagilova, Tatiana V Grigoryeva, Elena N Ilina, Vadim M Govorun
BACKGROUND: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29041965/enrichment-allows-identification-of-diverse-rare-elements-in-metagenomic-resistome-virulome-sequencing
#12
Noelle R Noyes, Maggie E Weinroth, Jennifer K Parker, Chris J Dean, Steven M Lakin, Robert A Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N Martin, Kenneth L Jones, Jaime Ruiz, Christina A Boucher, Keith E Belk, Paul S Morley
BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29041958/towards-a-balanced-view-of-the-bacterial-tree-of-life
#13
Frederik Schulz, Emiley A Eloe-Fadrosh, Robert M Bowers, Jessica Jarett, Torben Nielsen, Natalia N Ivanova, Nikos C Kyrpides, Tanja Woyke
The bacterial tree of life has recently undergone significant expansion, chiefly from candidate phyla retrieved through genome-resolved metagenomics. Bypassing the need for genome availability, we present a snapshot of bacterial phylogenetic diversity based on the recovery of high-quality SSU rRNA gene sequences extracted from nearly 7000 metagenomes and all available reference genomes. We illuminate taxonomic richness within established bacterial phyla together with environmental distribution patterns, providing a revised framework for future phylogeny-driven sequencing efforts...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29029638/indoor-microbiota-in-severely-moisture-damaged-homes-and-the-impact-of-interventions
#14
Balamuralikrishna Jayaprakash, Rachel I Adams, Pirkka Kirjavainen, Anne Karvonen, Asko Vepsäläinen, Maria Valkonen, Kati Järvi, Michael Sulyok, Juha Pekkanen, Anne Hyvärinen, Martin Täubel
BACKGROUND: The limited understanding of microbial characteristics in moisture-damaged buildings impedes efforts to clarify which adverse health effects in the occupants are associated with the damage and to develop effective building intervention strategies. The objectives of this current study were (i) to characterize fungal and bacterial microbiota in house dust of severely moisture-damaged residences, (ii) to identify microbial taxa associated with moisture damage renovations, and (iii) to test whether the associations between the identified taxa and moisture damage are replicable in another cohort of homes...
October 13, 2017: Microbiome
https://www.readbyqxmd.com/read/29029635/individual-signatures-and-environmental-factors-shape-skin-microbiota-in-healthy-dogs
#15
Anna Cuscó, Janelle M Belanger, Liza Gershony, Alma Islas-Trejo, Kerinne Levy, Juan F Medrano, Armand Sánchez, Anita M Oberbauer, Olga Francino
BACKGROUND: The individual, together with its environment, has been reported as the main force driving composition and structure of skin microbiota in healthy dogs. Therefore, one of the major concerns when analyzing canine skin microbiota is the likely influence of the environment. Despite the dense fur covering, certain skin diseases exhibit differential prevalence among skin sites, dog breeds, and individuals. RESULTS: We have characterized the normal variability of dog skin microbiota in a well-controlled cohort of a large number of Golden-Labrador Retriever crossed dogs (N = 35) with similar ages, related genetic background, and a shared environment...
October 13, 2017: Microbiome
https://www.readbyqxmd.com/read/29025421/correction-to-optimization-and-validation-of-sample-preparation-for-metagenomic-sequencing-of-viruses-in-clinical-samples
#16
Dagmara W Lewandowska, Osvaldo Zagordi, Fabienne-Desirée Geissberger, Verena Kufner, Stefan Schmutz, Jürg Böni, Karin J Metzner, Alexandra Trkola, Michael Huber
No abstract text is available yet for this article.
October 12, 2017: Microbiome
https://www.readbyqxmd.com/read/29020980/identification-of-76-novel-b1-metallo-%C3%AE-lactamases-through-large-scale-screening-of-genomic-and-metagenomic-data
#17
Fanny Berglund, Nachiket P Marathe, Tobias Österlund, Johan Bengtsson-Palme, Stathis Kotsakis, Carl-Fredrik Flach, D G Joakim Larsson, Erik Kristiansson
BACKGROUND: Metallo-β-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly problematic class of antibiotic resistance determinants. We hypothesized that there is a large and unexplored reservoir of unknown metallo-β-lactamases, some of which may spread to pathogens, thereby threatening public health...
October 12, 2017: Microbiome
https://www.readbyqxmd.com/read/29021001/correction-to-more-than-2500%C3%A2-years-of-oil-exposure-shape-sediment-microbiomes-with-the-potential-for-syntrophic-degradation-of-hydrocarbons-linked-to-methanogenesis
#18
Antonios Michas, Gisle Vestergaard, Kathleen Trautwein, Pavlos Avramidis, Dimitris G Hatzinikolaou, Constantinos E Vorgias, Heinz Wilkes, Ralf Rabus, Michael Schloter, Anne Schöler
No abstract text is available yet for this article.
October 11, 2017: Microbiome
https://www.readbyqxmd.com/read/29017607/non-digestible-oligosaccharides-directly-regulate-host-kinome-to-modulate-host-inflammatory-responses-without-alterations-in-the-gut-microbiota
#19
Richard Y Wu, Pekka Määttänen, Scott Napper, Erin Scruten, Bo Li, Yuhki Koike, Kathene C Johnson-Henry, Agostino Pierro, Laura Rossi, Steven R Botts, Michael G Surette, Philip M Sherman
BACKGROUND: Prebiotics are non-digestible food ingredients that enhance the growth of certain microbes within the gut microbiota. Prebiotic consumption generates immune-modulatory effects that are traditionally thought to reflect microbial interactions within the gut. However, recent evidence suggests they may also impart direct microbe-independent effects on the host, though the mechanisms of which are currently unclear. METHODS: Kinome arrays were used to profile the host intestinal signaling responses to prebiotic exposures in the absence of microbes...
October 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28978350/interactive-effects-of-temperature-organic-carbon-and-pipe-material-on-microbiota-composition-and-legionella-pneumophila-in-hot-water-plumbing-systems
#20
Caitlin R Proctor, Dongjuan Dai, Marc A Edwards, Amy Pruden
BACKGROUND: Several biotic and abiotic factors have been reported to influence the proliferation of microbes, including Legionella pneumophila, in hot water premise plumbing systems, but their combined effects have not been systematically evaluated. Here, we utilize simulated household water heaters to examine the effects of stepwise increases in temperature (32-53 °C), pipe material (copper vs. cross-linked polyethylene (PEX)), and influent assimilable organic carbon (0-700 μg/L) on opportunistic pathogen gene copy numbers and the microbiota composition, as determined by quantitative polymerase chain reaction and 16S rRNA gene amplicon sequencing...
October 4, 2017: Microbiome
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