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https://www.readbyqxmd.com/read/29934437/human-gut-microbiome-hopes-threats-and-promises
#1
REVIEW
Patrice D Cani
The microbiome has received increasing attention over the last 15 years. Although gut microbes have been explored for several decades, investigations of the role of microorganisms that reside in the human gut has attracted much attention beyond classical infectious diseases. For example, numerous studies have reported changes in the gut microbiota during not only obesity, diabetes, and liver diseases but also cancer and even neurodegenerative diseases. The human gut microbiota is viewed as a potential source of novel therapeutics...
June 22, 2018: Gut
https://www.readbyqxmd.com/read/29934334/bacterial-methionine-metabolism-genes-influence-drosophila-melanogaster-starvation-resistance
#2
Alec M Judd, Melinda K Matthews, Rachel Hughes, Madeline Veloz, Corinne E Sexton, John M Chaston
Animal-associated microorganisms ('microbiota') dramatically influence nutritional and physiological traits of their hosts. To expand our understanding of such influences, we predicted bacterial genes that influence a quantitative animal trait by a comparative genomic approach and extended these predictions via mutant analysis. We focus on D. melanogaster starvation resistance (SR). We first confirmed that D. melanogaster SR responds to the microbiota by demonstrating that bacteria-free flies have greater SR than flies bearing a standard 5-species microbial community, and extended this analysis by revealing species-specific influence of 38 genome-sequenced bacterial species on D...
June 22, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29932624/assessing-the-efficiency-of-cultivation-techniques-to-recover-natural-product-biosynthetic-gene-populations-from-sediment
#3
Maryam Elfeki, Mohammad Alanjary, Stefan J Green, Nadine Ziemert, Brian T Murphy
Despite decades of cultivating microorganisms for use in drug discovery, few attempts have been made to measure the extent to which common cultivation techniques have accessed existing chemical space. Metagenomic studies have shown that cultivable bacteria represent a fraction of those that exist in the environment, and that uncultivated populations in sediment have genes that encode for a high diversity of novel natural product (NP) biosynthetic enzymes. Quantifying these genes in both sediment and cultivatable bacterial populations allows us to assess how much diversity is present on nutrient agar and is critical to guiding the trajectory of future NP discovery platforms...
June 22, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29930547/-in-silico-analysis-of-the-quorum-sensing-metagenome-in-environmental-biofilm-samples
#4
Jorge Barriuso, María J Martínez
Quorum sensing (QS) is a sophisticated cell to cell signaling mechanism mediated by small diffusible molecules called "autoinducers." This phenomenon is well studied in bacteria, where different QS systems are described that differ between Gram-negative and Gram-positive bacteria. However, a common system to these groups was discovered, the autoinducer 2. QS has implications in biofilm formation, where the application of metagenomic techniques to study these phenomena may be useful to understand the communication networks established by the different components of the community, and to discover new targets for microbial control...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29930350/dispersal-competition-tradeoff-in-microbiomes-in-the-quest-for-land-colonization
#5
Francisco Dini-Andreote, Jan Dirk van Elsas, Han Olff, Joana Falcão Salles
Ancestor microbes started colonizing inland habitats approximately 2.7 to 3.5 billion years ago. With some exceptions, the key physiological adaptations of microbiomes associated with marine-to-land transitions have remained elusive. This is essentially caused by the lack of suitable systems that depict changes in microbiomes across sufficiently large time scales. Here, we investigate the adaptive routes taken by microbiomes along a contemporary gradient of land formation. Using functional trait-based metagenomics, we show that a switch from a microbial 'dispersal' to a 'competition' response modus best characterizes the microbial trait changes during this eco-evolutionary trajectory...
June 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29930078/metagenome-sequences-of-a-thermophilic-anaerobic-digester-adapted-to-a-low-c-n-ratio-high-ammonia-feedstock-poultry-litter
#6
David H Huber, Jesus E Chavarria-Palma, Sridhar A Malkaram, Natalia A Montenegro-Garcia, Vadesse Lhilhi Noundou, Ifeoma R Ugwuanyi, Teodoro Espinosa-Solares
We sequenced the metagenome of a pilot-scale thermophilic digester with long-term, stable performance on poultry litter feedstock which has a very low C/N ratio, a high ammonia level, and high lignocellulose content. Firmicutes were the dominant phylum (68.9%). Other abundant phyla included Bacteroidetes , Euryarchaeota , and Thermotogae This microbiome represents a hydrogenotrophic methanogenic community with high diversity.
June 21, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29930077/characterization-of-the-microbiota-of-oyster-larvae-crassostrea-virginica-and-tank-water-from-an-aquaculture-system-with-high-and-low-larval-survival-rates
#7
Padmini Ramachandran, Elizabeth Reed, Seth Commichaux, Errol Strain, Angelo Depaola, Scott Rikard, Andrea Ottesen
Aquaculture plays an increasingly important role in the growing demand for seafood. Hatchery production of oyster larvae is an integral component of oyster farming, providing single seed for off-bottom farming or larvae for setting on larger substrates for on-bottom farming. Larvae from certain tanks in an established aquaculture enterprise were dying from an unknown etiologic agent. A metagenomic approach was used to examine oyster larvae and water from larval tanks with high and low survival rates to evaluate the epidemiological efficacy of this approach...
June 21, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29930056/complete-coding-sequences-of-five-dengue-virus-type-2-clinical-isolates-from-venezuela-obtained-through-shotgun-metagenomics
#8
Erley Lizarazo, Natacha Couto, Maria Vincenti-Gonzalez, Erwin C Raangs, Thomas Jaenisch, Alex W Friedrich, Adriana Tami, John W Rossen
Dengue is a disease endemic in Latin American countries, like Venezuela, and has become one of the most important public health problems. We report five complete coding sequences of dengue virus serotype 2 (DENV-2) isolated from DENV-infected patients in Venezuela. Phylogenetic analysis placed the isolates within the American/Asian genotype.
June 21, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29929823/bronchiolitis-obliterans-syndrome-susceptibility-and-the-pulmonary-microbiome
#9
Cody Schott, S Samuel Weigt, Benjamin A Turturice, Ahmed Metwally, John Belperio, Patricia W Finn, David L Perkins
BACKGROUND: Lung transplantation outcomes remain complicated by bronchiolitis obliterans syndrome (BOS), a major cause of mortality and retransplantation for patients. A variety of factors linking inflammation and BOS have emerged, meriting further exploration of the microbiome as a source of inflammation. In this analysis, we determined features of the pulmonary microbiome associated with BOS susceptibility. METHODS: Bronchoalveolar lavage (BAL) samples were collected from 25 patients during standard of care bronchoscopies before BOS onset...
April 26, 2018: Journal of Heart and Lung Transplantation
https://www.readbyqxmd.com/read/29929226/opportunities-and-risks-of-biofertilization-for-leek-production-in-urban-areas-influence-on-both-fungal-diversity-and-human-bioaccessibility-of-inorganic-pollutants
#10
Antoine Pierart, Camille Dumat, Arthur QuyManh Maes, Christophe Roux, Nathalie Sejalon-Delmas
The influence of biofertilization with arbuscular mycorrhizal fungi (AMF) on trace metal and metalloids (TM) - Pb, Cd and Sb - uptake by leek (Allium porrum L.) grown in contaminated soils was investigated. The effect of biofertilization on human bioaccessibility of the TM in the plants was also examined. Leek were cultivated in one soil with geogenic TM sources and one soil with anthropogenic TM, to assess the influence of pollutant origin on soil-plant transfer. Leek were grown for six months on these contaminated soils, with and without a local AMF based biofertilizer...
May 15, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29925949/a-distinct-abundant-group-of-microbial-rhodopsins-discovered-using-functional-metagenomics
#11
Alina Pushkarev, Keiichi Inoue, Shirley Larom, José Flores-Uribe, Manish Singh, Masae Konno, Sahoko Tomida, Shota Ito, Ryoko Nakamura, Satoshi P Tsunoda, Alon Philosof, Itai Sharon, Natalya Yutin, Eugene V Koonin, Hideki Kandori, Oded Béjà
Many organisms capture or sense sunlight using rhodopsin pigments1,2 , which are integral membrane proteins that bind retinal chromophores. Rhodopsins comprise two distinct protein families 1 , type-1 (microbial rhodopsins) and type-2 (animal rhodopsins). The two families share similar topologies and contain seven transmembrane helices that form a pocket in which retinal is linked covalently as a protonated Schiff base to a lysine at the seventh transmembrane helix2,3 . Type-1 and type-2 rhodopsins show little or no sequence similarity to each other, as a consequence of extensive divergence from a common ancestor or convergent evolution of similar structures 1 ...
June 20, 2018: Nature
https://www.readbyqxmd.com/read/29925880/a-strong-link-between-marine-microbial-community-composition-and-function-challenges-the-idea-of-functional-redundancy
#12
Pierre E Galand, Olivier Pereira, Corentin Hochart, Jean Christophe Auguet, Didier Debroas
Marine microbes have tremendous diversity, but a fundamental question remains unanswered: why are there so many microbial species in the sea? The idea of functional redundancy for microbial communities has long been assumed, so that the high level of richness is often explained by the presence of different taxa that are able to conduct the exact same set of metabolic processes and that can readily replace each other. Here, we refute the hypothesis of functional redundancy for marine microbial communities by showing that a shift in the community composition altered the overall functional attributes of communities across different temporal and spatial scales...
June 20, 2018: ISME Journal
https://www.readbyqxmd.com/read/29925824/coreprobe-a-novel-algorithm-for-estimating-relative-abundance-based-on-metagenomic-reads
#13
Dongmei Ai, Hongfei Pan, Ruocheng Huang, Li C Xia
With the rapid development of high-throughput sequencing technology, the analysis of metagenomic sequencing data and the accurate and efficient estimation of relative microbial abundance have become important ways to explore the microbial composition and function of microbes. In addition, the accuracy and efficiency of the relative microbial abundance estimation are closely related to the algorithm and the selection of the reference sequence for sequence alignment. We introduced the microbial core genome as the reference sequence for potential microbes in a metagenomic sample, and we constructed a finite mixture and latent Dirichlet models and used the Gibbs sampling algorithm to estimate the relative abundance of microorganisms...
June 20, 2018: Genes
https://www.readbyqxmd.com/read/29925614/ocean-warming-alters-predicted-microbiome-functionality-in-a-common-sea-urchin
#14
Cecilia J Brothers, William J Van Der Pol, Casey D Morrow, Joseph A Hakim, Hyunmin Koo, James B McClintock
The microbiome of sea urchins plays a role in maintaining digestive health and innate immunity. Here, we investigated the effects of long-term (90 day) exposure to elevated seawater temperatures on the microbiome of the common, subtropical sea urchin Lytechinus variegatus The community composition and diversity of microbes varied according to the type of sample collected from the sea urchin (seawater, feed, intestines, coelomic fluid, digested pellet and faeces), with the lowest microbial diversity (predominately the order Campylobacterales) located in the intestinal tissue...
June 27, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29925429/genomic-variation-and-biogeography-of-antarctic-haloarchaea
#15
Bernhard Tschitschko, Susanne Erdmann, Matthew Z DeMaere, Simon Roux, Pratibha Panwar, Michelle A Allen, Timothy J Williams, Sarah Brazendale, Alyce M Hancock, Emiley A Eloe-Fadrosh, Ricardo Cavicchioli
BACKGROUND: The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands)...
June 20, 2018: Microbiome
https://www.readbyqxmd.com/read/29925423/the-developing-premature-infant-gut-microbiome-is-a-major-factor-shaping-the-microbiome-of-neonatal-intensive-care-unit-rooms
#16
Brandon Brooks, Matthew R Olm, Brian A Firek, Robyn Baker, David Geller-McGrath, Sophia R Reimer, Karina R Soenjoyo, Jennifer S Yip, Dylan Dahan, Brian C Thomas, Michael J Morowitz, Jillian F Banfield
BACKGROUND: The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it has been previously shown that the gut microbiomes of these infants often resemble the microbes found in the NICU. Little is known, however, about the identity, persistence, and absolute abundance of NICU room-associated bacteria over long stretches of time. Here, we couple droplet digital PCR (ddPCR), 16S rRNA gene surveys, and recently published metagenomics data from infant gut samples to infer the extent to which the NICU microbiome is shaped by its room occupants...
June 20, 2018: Microbiome
https://www.readbyqxmd.com/read/29923801/screening-for-exotic-forest-pathogens-to-increase-survey-capacity-using-metagenomics
#17
Emilie D Tremblay, Marc-Olivier Duceppe, Jean A Berube, Troy Kimoto, Claude Lemieux, Guillaume J Bilodeau
Anthropogenic activities have a major impact on the global environment. Canada's natural resources are threatened by the spread of fungal pathogens, which is facilitated by agricultural practices and international trade. Fungi are introduced to new environments and sometimes become established, in which case they can cause disease outbreaks resulting in extensive forest decline. Here we describe how a nation-wide sample collection strategy coupled to Next-Generation sequencing (NGS) (i.e. metagenomics) can achieve fast and comprehensive screening for exotic invasive species...
June 20, 2018: Phytopathology
https://www.readbyqxmd.com/read/29922272/gut-microbiota-markers-in-obese-adolescent-and-adult-patients-age-dependent-differential-patterns
#18
Federica Del Chierico, Francesca Abbatini, Alessandra Russo, Andrea Quagliariello, Sofia Reddel, Danila Capoccia, Romina Caccamo, Stefano Ginanni Corradini, Valerio Nobili, Francesco De Peppo, Bruno Dallapiccola, Frida Leonetti, Gianfranco Silecchia, Lorenza Putignani
Obesity levels, especially in children, have dramatically increased over the last few decades. Recently, several studies highlighted the involvement of gut microbiota in the pathophysiology of obesity. We investigated the composition of gut microbiota in obese adolescents and adults compared to age-matched normal weight (NW) volunteers in order to assemble age- and obesity-related microbiota profiles. The composition of gut microbiota was analyzed by 16S rRNA-based metagenomics. Ecological representations of microbial communities were computed, and univariate, multivariate, and correlation analyses performed on bacterial profiles...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29922260/vigen-an-open-source-pipeline-for-the-detection-and-quantification-of-viral-rna-in-human-tumors
#19
Krithika Bhuvaneshwar, Lei Song, Subha Madhavan, Yuriy Gusev
An estimated 17% of cancers worldwide are associated with infectious causes. The extent and biological significance of viral presence/infection in actual tumor samples is generally unknown but could be measured using human transcriptome (RNA-seq) data from tumor samples. We present an open source bioinformatics pipeline viGEN, which allows for not only the detection and quantification of viral RNA, but also variants in the viral transcripts. The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29922239/dietary-deoxynivalenol-contamination-and-oral-lipopolysaccharide-challenge-alters-the-cecal-microbiota-of-broiler-chickens
#20
Annegret Lucke, Josef Böhm, Qendrim Zebeli, Barbara U Metzler-Zebeli
Dietary deoxynivalenol (DON) impairs the intestinal functions and performance in broiler chickens, whereas little is known about the effect of DON on the gastrointestinal microbiota. This study evaluated the impact of graded levels of dietary DON contamination on the cecal bacterial microbiota, their predicted metabolic abilities and short-chain fatty acid (SCFA) profiles in chickens. In using a single oral lipopolysaccharide (LPS) challenge we further assessed whether an additional intestinal stressor would potentiate DON-related effects on the cecal microbiota...
2018: Frontiers in Microbiology
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