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Microbiome

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https://www.readbyqxmd.com/read/29325581/haemophilus-is-overrepresented-in-the-nasopharynx-of-infants-hospitalized-with-rsv-infection-and-associated-with-increased-viral-load-and-enhanced-mucosal-cxcl8-responses
#1
Thomas H A Ederveen, Gerben Ferwerda, Inge M Ahout, Marloes Vissers, Ronald de Groot, Jos Boekhorst, Harro M Timmerman, Martijn A Huynen, Sacha A F T van Hijum, Marien I de Jonge
BACKGROUND: While almost all infants are infected with respiratory syncytial virus (RSV) before the age of 2 years, only a small percentage develops severe disease. Previous studies suggest that the nasopharyngeal microbiome affects disease development. We therefore studied the effect of the nasopharyngeal microbiome on viral load and mucosal cytokine responses, two important factors influencing the pathophysiology of RSV disease. To determine the relation between (i) the microbiome of the upper respiratory tract, (ii) viral load, and (iii) host mucosal inflammation during an RSV infection, nasopharyngeal microbiota profiles of RSV infected infants (< 6 months) with different levels of disease severity and age-matched healthy controls were determined by 16S rRNA marker gene sequencing...
January 11, 2018: Microbiome
https://www.readbyqxmd.com/read/29321060/-available-upon-request-not-good-enough-for-microbiome-data
#2
Morgan G I Langille, Jacques Ravel, W Florian Fricke
No abstract text is available yet for this article.
January 10, 2018: Microbiome
https://www.readbyqxmd.com/read/29321057/influenza-a-virus-infection-impacts-systemic-microbiota-dynamics-and-causes-quantitative-enteric-dysbiosis
#3
Soner Yildiz, Béryl Mazel-Sanchez, Matheswaran Kandasamy, Balaji Manicassamy, Mirco Schmolke
BACKGROUND: Microbiota integrity is essential for a growing number of physiological processes. Consequently, disruption of microbiota homeostasis correlates with a variety of pathological states. Importantly, commensal microbiota provide a shield against invading bacterial pathogens, probably by direct competition. The impact of viral infections on host microbiota composition and dynamics is poorly understood. Influenza A viruses (IAV) are common respiratory pathogens causing acute infections...
January 10, 2018: Microbiome
https://www.readbyqxmd.com/read/29316977/the-lung-tissue-microbiota-of-mild-and-moderate-chronic-obstructive-pulmonary-disease
#4
Alexa A Pragman, Tianmeng Lyu, Joshua A Baller, Trevor J Gould, Rosemary F Kelly, Cavan S Reilly, Richard E Isaacson, Chris H Wendt
BACKGROUND: Oral taxa are often found in the chronic obstructive pulmonary disease (COPD) lung microbiota, but it is not clear if this is due to a physiologic process such as aspiration or experimental contamination at the time of specimen collection. METHODS: Microbiota samples were obtained from nine subjects with mild or moderate COPD by swabbing lung tissue and upper airway sites during lung lobectomy. Lung specimens were not contaminated with upper airway taxa since they were obtained surgically...
January 9, 2018: Microbiome
https://www.readbyqxmd.com/read/29310713/an-imd-like-pathway-mediates-both-endosymbiont-control-and-host-immunity-in-the-cereal-weevil-sitophilus-spp
#5
Justin Maire, Carole Vincent-Monégat, Florent Masson, Anna Zaidman-Rémy, Abdelaziz Heddi
Many insects developing on nutritionally unbalanced diets have evolved symbiotic associations with vertically transmitted intracellular bacteria (endosymbionts) that provide them with metabolic components, thereby improving the host's abilities to thrive on such poor ecological niches. While host-endosymbiont coevolutionary constraints are known to entail massive genomic changes in the microbial partner, host's genomic evolution remains elusive, particularly with regard to the immune system. In the cereal weevil Sitophilus spp...
January 8, 2018: Microbiome
https://www.readbyqxmd.com/read/29304850/metabolic-capability-and-in-situ-activity-of-microorganisms-in-an-oil-reservoir
#6
Yi-Fan Liu, Daniela Domingos Galzerani, Serge Maurice Mbadinga, Livia S Zaramela, Ji-Dong Gu, Bo-Zhong Mu, Karsten Zengler
BACKGROUND: Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. RESULTS: Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach...
January 5, 2018: Microbiome
https://www.readbyqxmd.com/read/29301569/host-contributes-to-longitudinal-diversity-of-fecal-microbiota-in-swine-selected-for-lean-growth
#7
Duc Lu, Francesco Tiezzi, Constantino Schillebeeckx, Nathan P McNulty, Clint Schwab, Caleb Shull, Christian Maltecca
BACKGROUND: In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are normally reflected by fragments of 16S rRNA-encoding genes, has yet to be fully investigated. RESULTS: Fecal samples, collected from a population of crossbred pigs at three time points, including weaning, week 15 post weaning (hereafter "week 15"), and end-of-feeding test (hereafter "off-test"), were used to evaluate changes in the composition of the fecal microbiome of each animal over time...
January 4, 2018: Microbiome
https://www.readbyqxmd.com/read/29298732/the-association-between-anterior-nares-and-nasopharyngeal-microbiota-in-infants-hospitalized-for-bronchiolitis
#8
Pamela N Luna, Kohei Hasegawa, Nadim J Ajami, Janice A Espinola, David M Henke, Joseph F Petrosino, Pedro A Piedra, Ashley F Sullivan, Carlos A Camargo, Chad A Shaw, Jonathan M Mansbach
BACKGROUND: The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation between the microbiota found in the anterior nares and the microbiota found within the nasopharynx is unknown. We assessed the anterior nares and nasopharyngeal microbiota to determine (1) the relation of the microbiota from these two upper airway sites and (2) if associations were maintained between the microbiota from these two sites and two bronchiolitis severity outcomes...
January 3, 2018: Microbiome
https://www.readbyqxmd.com/read/29298729/grapevine-rootstocks-shape-underground-bacterial-microbiome-and-networking-but-not-potential-functionality
#9
Ramona Marasco, Eleonora Rolli, Marco Fusi, Grégoire Michoud, Daniele Daffonchio
BACKGROUND: The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit...
January 3, 2018: Microbiome
https://www.readbyqxmd.com/read/29291746/aerobic-proteobacterial-methylotrophs-in-movile-cave-genomic-and-metagenomic-analyses
#10
Deepak Kumaresan, Jason Stephenson, Andrew C Doxey, Hina Bandukwala, Elliot Brooks, Alexandra Hillebrand-Voiculescu, Andrew S Whiteley, J Colin Murrell
BACKGROUND: Movile Cave (Mangalia, Romania) is a unique ecosystem where the food web is sustained by microbial primary production, analogous to deep-sea hydrothermal vents. Specifically, chemoautotrophic microbes deriving energy from the oxidation of hydrogen sulphide and methane form the basis of the food web. RESULTS: Here, we report the isolation of the first methane-oxidizing bacterium from the Movile Cave ecosystem, Candidatus Methylomonas sp. LWB, a new species and representative of Movile Cave microbial mat samples...
January 2, 2018: Microbiome
https://www.readbyqxmd.com/read/29282153/under-control-how-a-dietary-additive-can-restore-the-gut-microbiome-and-proteomic-profile-and-improve-disease-resilience-in-a-marine-teleostean-fish-fed-vegetable-diets
#11
María Carla Piazzon, Josep Alvar Calduch-Giner, Belén Fouz, Itziar Estensoro, Paula Simó-Mirabet, Mónica Puyalto, Vasileios Karalazos, Oswaldo Palenzuela, Ariadna Sitjà-Bobadilla, Jaume Pérez-Sánchez
BACKGROUND: The constant increase of aquaculture production and wealthy seafood consumption has forced the industry to explore alternative and more sustainable raw aquafeed materials, and plant ingredients have been used to replace marine feedstuffs in many farmed fish. The objective of the present study was to assess whether plant-based diets can induce changes in the intestinal mucus proteome, gut autochthonous microbiota and disease susceptibility of fish, and whether these changes could be reversed by the addition of sodium butyrate to the diets...
December 28, 2017: Microbiome
https://www.readbyqxmd.com/read/29268781/wild-eel-microbiome-reveals-that-skin-mucus-of-fish-could-be-a-natural-niche-for-aquatic-mucosal-pathogen-evolution
#12
Miguel Carda-Diéguez, Rohit Ghai, Francisco Rodríguez-Valera, Carmen Amaro
BACKGROUND: Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host...
December 21, 2017: Microbiome
https://www.readbyqxmd.com/read/29268780/seasonal-spatial-and-maternal-effects-on-gut-microbiome-in-wild-red-squirrels
#13
Tiantian Ren, Stan Boutin, Murray M Humphries, Ben Dantzer, Jamieson C Gorrell, David W Coltman, Andrew G McAdam, Martin Wu
BACKGROUND: Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducted a comprehensive study of gut microbiota of a well-studied North American red squirrel (Tamiasciurus hudsonicus) population. Red squirrels are territorial, solitary, and live in a highly seasonal environment and therefore represent a very attractive system to study factors that drive the temporal and spatial dynamics of gut microbiota...
December 21, 2017: Microbiome
https://www.readbyqxmd.com/read/29262868/quinones-are-growth-factors-for-the-human-gut-microbiota
#14
Kathrin Fenn, Philip Strandwitz, Eric J Stewart, Eric Dimise, Sarah Rubin, Shreya Gurubacharya, Jon Clardy, Kim Lewis
BACKGROUND: The human gut microbiome has been linked to numerous components of health and disease. However, approximately 25% of the bacterial species in the gut remain uncultured, which limits our ability to properly understand, and exploit, the human microbiome. Previously, we found that growing environmental bacteria in situ in a diffusion chamber enables growth of uncultured species, suggesting the existence of growth factors in the natural environment not found in traditional cultivation media...
December 20, 2017: Microbiome
https://www.readbyqxmd.com/read/29246178/discovery-of-the-fourth-mobile-sulfonamide-resistance-gene
#15
Mohammad Razavi, Nachiket P Marathe, Michael R Gillings, Carl-Fredrik Flach, Erik Kristiansson, D G Joakim Larsson
BACKGROUND: Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long- and short-read technologies to maintain both accuracy and context...
December 15, 2017: Microbiome
https://www.readbyqxmd.com/read/29228991/the-rumen-microbiome-as-a-reservoir-of-antimicrobial-resistance-and-pathogenicity-genes-is-directly-affected-by-diet-in-beef-cattle
#16
Marc D Auffret, Richard J Dewhurst, Carol-Anne Duthie, John A Rooke, R John Wallace, Tom C Freeman, Robert Stewart, Mick Watson, Rainer Roehe
BACKGROUND: The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate...
December 11, 2017: Microbiome
https://www.readbyqxmd.com/read/29228972/impact-of-prematurity-and-nutrition-on-the-developing-gut-microbiome-and-preterm-infant-growth
#17
Alex Grier, Xing Qiu, Sanjukta Bandyopadhyay, Jeanne Holden-Wiltse, Haeja A Kessler, Ann L Gill, Brooke Hamilton, Heidie Huyck, Sara Misra, Thomas J Mariani, Rita M Ryan, Lori Scholer, Kristin M Scheible, Yi-Horng Lee, Mary T Caserta, Gloria S Pryhuber, Steven R Gill
BACKGROUND: Identification of factors that influence the neonatal gut microbiome is urgently needed to guide clinical practices that support growth of healthy preterm infants. Here, we examined the influence of nutrition and common practices on the gut microbiota and growth in a cohort of preterm infants. RESULTS: With weekly gut microbiota samples spanning postmenstrual age (PMA) 24 to 46 weeks, we developed two models to test associations between the microbiota, nutrition and growth: a categorical model with three successive microbiota phases (P1, P2, and P3) and a model with two periods (early and late PMA) defined by microbiota composition and PMA, respectively...
December 11, 2017: Microbiome
https://www.readbyqxmd.com/read/29197424/metalab-an-automated-pipeline-for-metaproteomic-data-analysis
#18
Kai Cheng, Zhibin Ning, Xu Zhang, Leyuan Li, Bo Liao, Janice Mayne, Alain Stintzi, Daniel Figeys
BACKGROUND: Research involving microbial ecosystems has drawn increasing attention in recent years. Studying microbe-microbe, host-microbe, and environment-microbe interactions are essential for the understanding of microbial ecosystems. Currently, metaproteomics provide qualitative and quantitative information of proteins, providing insights into the functional changes of microbial communities. However, computational analysis of large-scale data generated in metaproteomic studies remains a challenge...
December 2, 2017: Microbiome
https://www.readbyqxmd.com/read/29191217/multi-level-comparisons-of-cloacal-skin-feather-and-nest-associated-microbiota-suggest-considerable-influence-of-horizontal-acquisition-on-the-microbiota-assembly-of-sympatric-woodlarks-and-skylarks
#19
H Pieter J van Veelen, Joana Falcao Salles, B Irene Tieleman
BACKGROUND: Working toward a general framework to understand the role of microbiota in animal biology requires the characterisation of animal-associated microbial communities and identification of the evolutionary and ecological factors shaping their variation. In this study, we described the microbiota in the cloaca, brood patch skin and feathers of two species of birds and the microbial communities in their nest environment. We compared patterns of resemblance between these microbial communities at different levels of biological organisation (species, individual, body part) and investigated the phylogenetic structure to deduce potential microbial community assembly processes...
December 1, 2017: Microbiome
https://www.readbyqxmd.com/read/29179769/catalogue-of-antibiotic-resistome-and-host-tracking-in-drinking-water-deciphered-by-a-large-scale-survey
#20
Liping Ma, Bing Li, Xiao-Tao Jiang, Yu-Lin Wang, Yu Xia, An-Dong Li, Tong Zhang
BACKGROUND: Excesses of antibiotic resistance genes (ARGs), which are regarded as emerging environmental pollutants, have been observed in various environments. The incidence of ARGs in drinking water causes potential risks to human health and receives more attention from the public. However, ARGs harbored in drinking water remain largely unexplored. In this study, we aimed at establishing an antibiotic resistome catalogue in drinking water samples from a wide range of regions and to explore the potential hosts of ARGs...
November 28, 2017: Microbiome
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