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Johan S Sáenz, Tamires Valim Marques, Rafael Simões Coelho Barone, José Eurico Possebon Cyrino, Susanne Kublik, Joseph Nesme, Michael Schloter, Susanne Rath, Gisle Vestergaard
BACKGROUND: Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibiotic resistance. Yet, the effect of the oral administration of antibiotics on the mobility of microbial resistance genes in the fish gut is not well understood. In the present study, Piaractus mesopotamicus was used as a model to evaluate the effect of the antimicrobial florfenicol on the diversity of the gut microbiome as well as antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using a metagenomic approach...
February 18, 2019: Microbiome
Matthew R Olm, Patrick T West, Brandon Brooks, Brian A Firek, Robyn Baker, Michael J Morowitz, Jillian F Banfield
BACKGROUND: Fungal infections are a significant cause of mortality and morbidity in hospitalized preterm infants, yet little is known about eukaryotic colonization of infants and of the neonatal intensive care unit as a possible source of colonizing strains. This is partly because microbiome studies often utilize bacterial 16S rRNA marker gene sequencing, a technique that is blind to eukaryotic organisms. Knowledge gaps exist regarding the phylogeny and microdiversity of eukaryotes that colonize hospitalized infants, as well as potential reservoirs of eukaryotes in the hospital room built environment...
February 15, 2019: Microbiome
Rachael E Antwis, Katie L Edwards, Bryony Unwin, Susan L Walker, Susanne Shultz
BACKGROUND: Host microbiomes play a role in hormone production and subsequent fertility in humans, but this is less well understood in non-model organisms. This is of particular relevance to species in zoo-based conservation breeding programmes, as relationships between host microbiome composition and reproductive output may allow for the development of microbial augmentation strategies to improve success. Here, we characterise faecal bacterial communities of breeding and non-breeding eastern black rhino (Diceros bicornis michaeli) using 16S rRNA gene amplicon sequencing and quantify progestagen and glucocorticoid metabolite concentrations through enzyme immunoassays to identify such relationships...
February 15, 2019: Microbiome
Zhenwu Luo, Min Li, Yongxia Wu, Zhefeng Meng, Lisa Martin, Lumin Zhang, Elizabeth Ogunrinde, Zejun Zhou, Shenghui Qin, Zhuang Wan, Maria Anna Julia Westerink, Stephanie Warth, Hui Liu, Ping Jin, David Stroncek, Quan-Zhen Li, Ena Wang, Xueling Wu, Sonya L Heath, Zihai Li, Alexander V Alekseyenko, Wei Jiang
BACKGROUND: Increased autoreactive antibodies have been reported in HIV disease; however, the mechanism accounting for autoantibody induction in HIV remains unknown. RESULTS: Herein, we show that seasonal influenza vaccination induces autoantibody production (e.g., IgG anti-nuclear antibody (ANA) and anti-double-stranded DNA antibody (anti-dsDNA)) in some viral-suppressed antiretroviral therapy (ART)-treated HIV+ subjects, but not in healthy controls. These autoantibodies were not derived from antigen-specific B cells but from activated "bystander" B cells analyzed by single-cell assay and by study of purified polyclonal ANAs from plasma...
February 14, 2019: Microbiome
Robert A Quinn, Sandeep Adem, Robert H Mills, William Comstock, Lindsay DeRight Goldasich, Gregory Humphrey, Alexander A Aksenov, Alexei V Melnik, Ricardo da Silva, Gail Ackermann, Nuno Bandeira, David J Gonzalez, Doug Conrad, Anthony J O'Donoghue, Rob Knight, Pieter C Dorrestein
BACKGROUND: Studies of the cystic fibrosis (CF) lung microbiome have consistently shown that lung function decline is associated with decreased microbial diversity due to the dominance of opportunistic pathogens. However, how this phenomenon is reflected in the metabolites and chemical environment of lung secretions remains poorly understood. METHODS: Here we investigated the microbial and molecular composition of CF sputum samples using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry to determine their interrelationships and associations with clinical measures of disease severity...
February 13, 2019: Microbiome
Efrem S Lim, Cynthia Rodriguez, Lori R Holtz
How and when a newborn is first colonized by microbes continues to be of great interest due to its broad implications on human health and disease. Payne et al. express their opinion about our recent study in which we characterized the virome and bacterial microbiota of amniotic fluid from 24 uncomplicated term pregnancies. We conducted additional validation studies and respond to their comments. We conclude that in amniotic fluid from healthy term pregnancies, the bacterial microbiota is indistinguishable from contamination controls, and there is no evidence of a core virome...
February 12, 2019: Microbiome
Efrem S Lim, Cynthia Rodriguez, Lori R Holtz
Following publication of the original article [1], the authors reported a typographic error in the type of master mix kit used, the text should read as: "The qPCR was performed using Fast SYBR Green Master Mix (Thermo Fisher)."
February 12, 2019: Microbiome
M S Payne, J A Keelan, L F Stinson
A recent publication by Lim et al. 2018 (Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community) strongly concluded that the microbiome of amniotic fluid primarily originates from reagent contamination. However, upon closer inspection of the methods used and data presented in this study, in particular the supplementary data, such conclusions do not appear to be supported by the results. We outline such methodological/data interpretation concerns and invite the authors to discuss these...
February 12, 2019: Microbiome
Yiran Liang, Jing Zhan, Donghui Liu, Mai Luo, Jiajun Han, Xueke Liu, Chang Liu, Zheng Cheng, Zhiqiang Zhou, Peng Wang
BACKGROUND: Disruption of the gut microbiota homeostasis may induce low-grade inflammation leading to obesity-associated diseases. A major protective mechanism is to use the multi-layered mucus structures to keep a safe distance between gut epithelial cells and microbiota. To investigate whether pesticides would induce insulin resistance/obesity through interfering with mucus-bacterial interactions, we conducted a study to determine how long-term exposure to chlorpyrifos affected C57Bl/6 and CD-1 (ICR) mice fed high- or normal-fat diets...
February 11, 2019: Microbiome
J Alfredo Blakeley-Ruiz, Alison R Erickson, Brandi L Cantarel, Weili Xiong, Rachel Adams, Janet K Jansson, Claire M Fraser, Robert L Hettich
BACKGROUND: The gut microbiome plays a fundamental role in the human host's overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual, the gut microbiome co-exists within the human host in a symbiotic, non-inflammatory relationship that enables mutual benefits, such as microbial degradation of indigestible food products into small molecules that the host can utilize, and enhanced pathogen defense. In abnormal conditions, such as Crohn's disease, this favorable metabolic relationship breaks down and a variety of undesirable activities result, including chronic inflammation and other health-related issues...
February 11, 2019: Microbiome
Adrian Fritz, Peter Hofmann, Stephan Majda, Eik Dahms, Johannes Dröge, Jessika Fiedler, Till R Lesker, Peter Belmann, Matthew Z DeMaere, Aaron E Darling, Alexander Sczyrba, Andreas Bremges, Alice C McHardy
BACKGROUND: Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. RESULTS: We describe the CAMISIM microbial community and metagenome simulator...
February 8, 2019: Microbiome
Ke Yu, Shan Yi, Bing Li, Feng Guo, Xingxing Peng, Zhiping Wang, Yang Wu, Lisa Alvarez-Cohen, Tong Zhang
BACKGROUND: Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses...
February 6, 2019: Microbiome
Wencong Shi, Mingcong Li, Guangshan Wei, Renmao Tian, Cuiping Li, Bing Wang, Rongshan Lin, Chunyu Shi, Xiuli Chi, Bo Zhou, Zheng Gao
BACKGROUND: Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels...
February 1, 2019: Microbiome
Shuo Jiao, Yiqin Xu, Jie Zhang, Yahai Lu
BACKGROUND: Understanding the spatial distributions and ecological diversity of soil archaeal communities in agricultural ecosystems is crucial for improvements in crop productivity. Here, we conducted a comprehensive, continental-scale survey of soil archaeal communities in adjacent pairs of maize (dryland) and rice (wetland) fields in eastern China. RESULTS: We revealed the consequential roles of environmental filtering in driving archaeal community assembly for both maize and rice fields...
February 1, 2019: Microbiome
Tomislav Cernava, Armin Erlacher, Jung Soh, Christoph W Sensen, Martin Grube, Gabriele Berg
BACKGROUND: Arugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been also associated with high-profile outbreaks causing severe food-borne human diseases. A multiphasic approach integrating data from metagenomics, amplicon sequencing, and arugula-derived bacterial cultures was employed to understand the specificity of the indigenous microbiome and resistome of the edible plant parts...
January 29, 2019: Microbiome
Aleksei A Korzhenkov, Stepan V Toshchakov, Rafael Bargiela, Huw Gibbard, Manuel Ferrer, Alina V Teplyuk, David L Jones, Ilya V Kublanov, Peter N Golyshin, Olga V Golyshina
BACKGROUND: The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8-18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations...
January 28, 2019: Microbiome
Thomas D S Sutton, Adam G Clooney, Feargal J Ryan, R Paul Ross, Colin Hill
BACKGROUND: The viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members...
January 28, 2019: Microbiome
Christopher A Gaulke, Mauricio L Martins, Virginia G Watral, Ian R Humphreys, Sean T Spagnoli, Michael L Kent, Thomas J Sharpton
BACKGROUND: Helminth parasites represent a significant threat to the health of human and animal populations, and there is a growing need for tools to treat, diagnose, and prevent these infections. Recent work has turned to the gut microbiome as a utilitarian agent in this regard; components of the microbiome may interact with parasites to influence their success in the gut, meaning that the microbiome may encode new anthelmintic drugs. Moreover, parasite infections may restructure the microbiome's composition in consistent ways, implying that the microbiome may be useful for diagnosing infection...
January 24, 2019: Microbiome
Ziwei Song, Yuanyuan Cai, Xingzhen Lao, Xue Wang, Xiaoxuan Lin, Yingyun Cui, Praveen Kumar Kalavagunta, Jun Liao, Liang Jin, Jing Shang, Jing Li
BACKGROUND: Bile salt hydrolase plays an important role in bile acid-mediated signaling pathways, which regulate lipid absorption, glucose metabolism, and energy homeostasis. Several reports suggest that changes in the composition of bile acids are found in many diseases caused by dysbacteriosis. RESULTS: Here, we present the taxonomic identification of bile salt hydrolase (BSH) in human microbiota and elucidate the abundance and activity differences of various bacterial BSH among 11 different populations from six continents...
January 23, 2019: Microbiome
Renato Pedron, Alfonso Esposito, Irene Bianconi, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Mario Cristofolini, Nicola Segata, Olivier Jousson
BACKGROUND: Water springs provide important ecosystem services including drinking water supply, recreation, and balneotherapy, but their microbial communities remain largely unknown. In this study, we characterized the spring water microbiome of Comano Terme (Italy) at four sampling points of the thermal spa, including natural (spring and well) and human-built (storage tank, bathtubs) environments. We integrated large-scale culturing and metagenomic approaches, with the aim of comprehensively determining the spring water taxonomic composition and functional potential...
January 23, 2019: Microbiome
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