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https://www.readbyqxmd.com/read/28822547/bacterial-diversity-in-goat-milk-from-the-guanzhong-area-of-china
#1
Fuxin Zhang, Zhaoxia Wang, Feiyan Lei, Bini Wang, Shuaiming Jiang, Qiannan Peng, Jiachao Zhang, Yuyu Shao
In this study, the V3 and V4 regions of the 16S rRNA gene from metagenomic DNA were sequenced to identify differences in microbial diversity in raw milk of Saanen and Guanzhong goats from the Guanzhong area of China. The results showed that Proteobacteria was the predominant phylum, accounting for 71.31% of all phyla identified in milk from the 2 breeds, and Enterobacter was the predominant genus (24.69%) within the microbial community. Microbial alpha diversity from Saanen goat milk was significantly higher than that of Guanzhong goat milk based on bioinformatic analysis of indices of Chao1, Shannon, Simpson, observed species, and the abundance-based coverage estimator...
August 16, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28821820/searching-for-signatures-across-microbial-communities-metagenomic-analysis-of-soil-samples-from-mangrove-and-other-ecosystems
#2
Madangchanok Imchen, Ranjith Kumavath, Debmalya Barh, Vasco Avezedo, Preetam Ghosh, Marcus Viana, Alice R Wattam
In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other known mangrove data, a tropical rainforest, and ocean sediment. An examination of the microbial communities from a large mangrove forest that stretches across southwestern India showed strong similarities across the higher taxonomic levels. When ocean sediment and a single isolate from a tropical rain forest were included in the analysis, a strong pattern emerged with Bacteria from the phylum Proteobacteria being the prominent taxon among the forest samples...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821731/stability-in-metabolic-phenotypes-and-inferred-metagenome-profiles-before-the-onset-of-colitis-induced-inflammation
#3
M Glymenaki, A Barnes, S O' Hagan, G Warhurst, A J McBain, I D Wilson, D B Kell, K J Else, S M Cruickshank
Inflammatory bowel disease (IBD) is associated with altered microbiota composition and metabolism, but it is unclear whether these changes precede inflammation or are the result of it since current studies have mainly focused on changes after the onset of disease. We previously showed differences in mucus gut microbiota composition preceded colitis-induced inflammation and stool microbial differences only became apparent at colitis onset. In the present study, we aimed to investigate whether microbial dysbiosis was associated with differences in both predicted microbial gene content and endogenous metabolite profiles...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821301/space-type-radiation-induces-multimodal-responses-in-the-mouse-gut-microbiome-and-metabolome
#4
David Casero, Kirandeep Gill, Vijayalakshmi Sridharan, Igor Koturbash, Gregory Nelson, Martin Hauer-Jensen, Marjan Boerma, Jonathan Braun, Amrita K Cheema
BACKGROUND: Space travel is associated with continuous low dose rate exposure to high linear energy transfer (LET) radiation. Pathophysiological manifestations after low dose radiation exposure are strongly influenced by non-cytocidal radiation effects, including changes in the microbiome and host gene expression. Although the importance of the gut microbiome in the maintenance of human health is well established, little is known about the role of radiation in altering the microbiome during deep-space travel...
August 18, 2017: Microbiome
https://www.readbyqxmd.com/read/28821012/multidomain-analyses-of-a-longitudinal-human-microbiome-intestinal-cleanout-perturbation-experiment
#5
Julia Fukuyama, Laurie Rumker, Kris Sankaran, Pratheepa Jeganathan, Les Dethlefsen, David A Relman, Susan P Holmes
Our work focuses on the stability, resilience, and response to perturbation of the bacterial communities in the human gut. Informative flash flood-like disturbances that eliminate most gastrointestinal biomass can be induced using a clinically-relevant iso-osmotic agent. We designed and executed such a disturbance in human volunteers using a dense longitudinal sampling scheme extending before and after induced diarrhea. This experiment has enabled a careful multidomain analysis of a controlled perturbation of the human gut microbiota with a new level of resolution...
August 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28818898/draft-genome-sequences-of-two-unclassified-chitinophagaceae-bacteria-ibvucb1-and-ibvucb2-isolated-from-environmental-samples
#6
Russell J S Orr, Stephane Rombauts, Yves Van de Peer, Kamran Shalchian-Tabrizi
We report here the draft genome sequences of two Chitinophagaceae bacteria, IBVUCB1 and IBVUCB2, assembled from metagenomes of surface samples from freshwater lakes. The genomes are >99% complete and may represent new genera within the Chitinophagaceae family, indicating a larger diversity than currently identified.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28817927/identification-of-biosynthetic-gene-clusters-from-metagenomic-libraries-using-pptase-complementation-in-a-streptomyces-host
#7
J Kipchirchir Bitok, Christophe Lemetre, Melinda A Ternei, Sean F Brady
The majority of environmental bacteria are not readily cultured in the lab, leaving the natural products they make inaccessible using culture-dependent discovery methods. Cloning and heterologous expression of DNA extracted from environmental samples (environmental DNA, eDNA) provides a means of circumventing this discovery bottleneck. To facilitate the identification of clones containing biosynthetic gene clusters, we developed a model heterologous expression reporter strain Streptomyces albus::bpsA ΔPPTase...
September 1, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28815469/metagenome-analysis-a-powerful-tool-for-enzyme-bioprospecting
#8
Aravind Madhavan, Raveendran Sindhu, Binod Parameswaran, Rajeev K Sukumaran, Ashok Pandey
Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The advent of metagenomics has revolutionized the field of microbial biotechnology. Metagenomics allow the recovery of genetic material directly from environmental niches without any cultivation techniques. Currently, metagenomic tools are widely employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the uncultivable component of microbial communities...
August 16, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28814344/microbial-phylogeny-determines-transcriptional-response-of-resistome-to-dynamic-composting-processes
#9
Cheng Wang, Da Dong, P J Strong, Weijing Zhu, Zhuang Ma, Yong Qin, Weixiang Wu
BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28813450/oral-microbial-community-assembly-under-the-influence-of-periodontitis
#10
Hongju Chen, Shuting Peng, Lin Dai, Quan Zou, Bin Yi, Xianghong Yang, Zhanshan Sam Ma
Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis...
2017: PloS One
https://www.readbyqxmd.com/read/28812643/a-submarine-volcanic-eruption-leads-to-a-novel-microbial-habitat
#11
Roberto Danovaro, Miquel Canals, Michael Tangherlini, Antonio Dell'Anno, Cristina Gambi, Galderic Lastras, David Amblas, Anna Sanchez-Vidal, Jaime Frigola, Antoni M Calafat, Rut Pedrosa-Pàmies, Jesus Rivera, Xavier Rayo, Cinzia Corinaldesi
Submarine volcanic eruptions are major catastrophic events that allow investigation of the colonization mechanisms of newly formed seabed. We explored the seafloor after the eruption of the Tagoro submarine volcano off El Hierro Island, Canary Archipelago. Near the summit of the volcanic cone, at about 130 m depth, we found massive mats of long, white filaments that we named Venus's hair. Microscopic and molecular analyses revealed that these filaments are made of bacterial trichomes enveloped within a sheath and colonized by epibiotic bacteria...
April 24, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811246/microbial-metagenomics-mock-scenario-based-sample-simulation-m3s3
#12
Yair Motro, Jacob Moran-Gilad
OBJECTIVES: Shotgun sequencing in increasingly applied in clinical microbiology for unbiased culture-independent diagnosis. While software solutions for metagenomics proliferate, integration of metagenomics in clinical care, requires method standardisation and validation. Virtual metagenomics samples could underpin validation by substituting real samples and thus we sought to develop a novel solution for simulation of metagenomics samples based on user-defined clinical scenarios. METHODS: We designed the Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3) workflow, which allows users to generate virtual samples from raw reads or assemblies...
August 12, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28811148/metagenomes-from-deep-baltic-sea-sediments-reveal-how-past-and-present-environmental-conditions-determine-microbial-community-composition
#13
Ian P G Marshall, Søren M Karst, Per H Nielsen, Bo Barker Jørgensen
Microbial communities that lived near the sediment surface in the past become slowly buried and are the source of deep subsurface communities thousands of years later. We used metagenomes to analyse how the composition of buried microbial communities may change to conform to altered environmental conditions at depth. Sediment samples were collected from down to 85m below sea floor during the Integrated Ocean Drilling Program Expedition 347, "Baltic Sea Paleoenvironment". The sediments vary in age, organic carbon content, porewater salinity, and other parameters that reflect the changing Baltic environment from the last ice age and throughout the Holocene...
August 12, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28810737/identification-of-the-colicin-v-bacteriocin-gene-cluster-by-functional-screening-of-a-human-microbiome-metagenomic-library
#14
Louis Cohen, Sun Han, Yun-Han Huang, Sean F Brady
The forces that shape human microbial ecology are complex. It is likely, that human microbiota, similarly to other microbiomes, use antibiotics as one way to establish an ecological niche. In this study, we use functional metagenomics to identify human microbial gene clusters that encode for antibiotic functions. Screening of a metagenomic library prepared from a healthy patient stool sample led to the identification of a family of clones with inserts that are 99% identical to a region of a virulence plasmid found in avian pathogenic Escherichia coli...
August 15, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28809851/grape-pomace-compost-harbors-organohalide-respiring-dehalogenimonas-species-with-novel-reductive-dehalogenase-genes
#15
Yi Yang, Steven A Higgins, Jun Yan, Burcu Şimşir, Karuna Chourey, Ramsunder Iyer, Robert L Hettich, Brett Baldwin, Dora M Ogles, Frank E Löffler
Organohalide-respiring bacteria have key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene...
August 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28809429/dissection-of-the-module-network-implementation-lemontree-enhancements-towards-applications-in-metagenomics-and-translation-in-autoimmune-maladies
#16
Youtao Lu, Xiaoyuan Zhou, Christine Nardini
Under the current deluge of omics, module networks distinctively emerge as methods capable of not only identifying inherently coherent groups (modules), thus reducing dimensionality, but also hypothesizing cause-effect relationships between modules and their regulators. Module networks were first designed in the transcriptomic era and further exploited in the multi-omic context to assess (for example) miRNA regulation of gene expression. Despite a number of available implementations, expansion of module networks to other omics is constrained by a limited characterization of the solutions' (modules plus regulators) accuracy and stability - an immediate need for the better characterization of molecular biology complexity in silico...
August 15, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28808691/fluoride-depletes-acidogenic-taxa-in-oral-but-not-gut-microbial-communities-in-mice
#17
Koji Yasuda, Tiffany Hsu, Carey A Gallini, Lauren J Mclver, Emma Schwager, Andy Shi, Casey R DuLong, Randall N Schwager, Galeb S Abu-Ali, Eric A Franzosa, Wendy S Garrett, Curtis Huttenhower, Xochitl C Morgan
Fluoridation of drinking water and dental products prevents dental caries primarily by inhibiting energy harvest in oral cariogenic bacteria (such as Streptococcus mutans and Streptococcus sanguinis), thus leading to their depletion. However, the extent to which oral and gut microbial communities are affected by host fluoride exposure has been underexplored. In this study, we modeled human fluoride exposures to municipal water and dental products by treating mice with low or high levels of fluoride over a 12-week period...
July 2017: MSystems
https://www.readbyqxmd.com/read/28808230/environmental-drivers-of-a-microbial-genomic-transition-zone-in-the-ocean-s-interior
#18
Daniel R Mende, Jessica A Bryant, Frank O Aylward, John M Eppley, Torben Nielsen, David M Karl, Edward F DeLong
The core properties of microbial genomes, including GC content and genome size, are known to vary widely among different bacteria and archaea (1,2) . Several hypotheses have been proposed to explain this genomic variability, but the fundamental drivers that shape bacterial and archaeal genomic properties remain uncertain (3-7) . Here, we report the existence of a sharp genomic transition zone below the photic zone, where bacterial and archaeal genomes and proteomes undergo a community-wide punctuated shift...
August 14, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28807044/metameta-integrating-metagenome-analysis-tools-to-improve-taxonomic-profiling
#19
Vitor C Piro, Marcel Matschkowski, Bernhard Y Renard
BACKGROUND: Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations...
August 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28806689/fungal-diversity-of-tomme-d-orchies-cheese-during-the-ripening-process-as-revealed-by-a-metagenomic-study
#20
Alexandre Ceugniez, Bernard Taminiau, Françoise Coucheney, Philippe Jacques, Véronique Delcenserie, Georges Daube, Djamel Drider
Tomme d'Orchies is an artisanal pressed and uncooked cheese produced and marketed in the north of France. This study aimed at showing the fungal microbiota evolution of this cheese using a metagenetic based Illumina technology targeting the ITS2 domain of 5.8S fungal rDNAs. To this end, samples were taken from the rind and the core of different cheeses, after 0, 1, 3, 7, 14 and 21days of ripening. The data underpinned the prevalence of Yarrowia lipolytica and Galactomyces geotrichum for both microbiotas. Unusual species including Clavispora lusitaniae, Kazachstania unispora and Cladosporium cladosporioides were also detected, but their origins remain to be ascertained...
July 25, 2017: International Journal of Food Microbiology
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