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Metagenomics

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https://www.readbyqxmd.com/read/28209840/genome-sequences-of-three-novel-bunyaviruses-two-novel-rhabdoviruses-and-one-novel-nyamivirus-from-washington-state-moths
#1
Negar Makhsous, Ryan C Shean, David Droppers, Jonathan Guan, Keith R Jerome, Alexander L Greninger
We report draft genome sequences of three novel bunyaviruses, two novel rhabdoviruses, and one novel nyamivirus identified metagenomically from 10 moths in Washington state.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28209833/metagenome-assembled-draft-genome-sequence-of-a-novel-microbial-stenotrophomonas-maltophilia-strain-isolated-from-caenorhabditisremanei-tissue
#2
Janna L Fierst, Duncan A Murdock, Chamali Thanthiriwatte, John H Willis, Patrick C Phillips
Stenotrophomonas maltophilia is a Gram-negative aerobic bacterium and emerging nosocomial pathogen. Here, we present a draft genome sequence for an S. maltophilia strain assembled from a metagenomic DNA extract isolated from a laboratory stock of the nematode worm Caenorhabditis remanei.
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28207851/impact-of-levels-of-total-digestible-nutrients-on-microbiome-enzyme-profile-and-degradation-of-feeds-in-buffalo-rumen
#3
Anju Kala, D N Kamra, Avinash Kumar, Neeta Agarwal, L C Chaudhary, C G Joshi
The present study was aimed at understanding a shift in rumen microbiome of buffaloes fed various levels of total digestible nutrients. To understand the process, the metagenomics of rumen microbes, in vivo and in vitro rumen fermentation studies were carried out. Three rumen fistulated adult male Murrah buffaloes were fed three isonitrogenous diets varying in total digestible nutrients (70, 85 and 100% of TDN requirement) in 3X3 switch over design. On dry matter basis, wheat straw/ roughage content were 81, 63 and 51% and that of maize grain was 8, 16 and 21% in three diets respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28205377/culture-independent-genomics-of-a-novel-chlamydial-pathogen-of-fish-provides-new-insight-into-host-specific-adaptations-utilised-by-these-intracellular-bacteria
#4
Alyce Taylor-Brown, Trestan Pillonel, Andrew Bridle, Weihong Qi, Nathan Bachmann, Terrence L Miller, Gilbert Greub, Barbara Nowak, Helena M B Seth-Smith, Lloyd Vaughan, Adam Polkinghorne
Several Chlamydiales families are associated with epitheliocystis, a common condition of the fish gill epithelium. These families share common ancestors with the Chlamydiaceae and environmental Chlamydiae. Due to the lack of culture systems, little is known about the biology of these chlamydial fish pathogens. We investigated epitheliocystis in cultured Orange-spotted grouper (Epinephelus coioides) from North Queensland, Australia. Basophilic inclusions were present in the gills of 22/31 fish and the presence of the chlamydial pathogen in the cysts was confirmed by in situ hybridisation...
February 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28204531/crystal-structure-of-metagenomic-%C3%AE-xylosidase-%C3%AE-l-arabinofuranosidase-activated-by-calcium
#5
Tomohiko Matsuzawa, Satoshi Kaneko, Naomi Kishine, Zui Fujimoto, Katsuro Yaoi
No abstract text is available yet for this article.
February 16, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28198672/integrated-metagenomic-data-analysis-demonstrates-that-a-loss-of-diversity-in-oral-microbiota-is-associated-with-periodontitis
#6
Dongmei Ai, Ruocheng Huang, Jin Wen, Chao Li, Jiangping Zhu, Li Charlie Xia
BACKGROUND: Periodontitis is an inflammatory disease affecting the tissues supporting teeth (periodontium). Integrative analysis of metagenomic samples from multiple periodontitis studies is a powerful way to examine microbiota diversity and interactions within host oral cavity. METHODS: A total of 43 subjects were recruited to participate in two previous studies profiling the microbial community of human subgingival plaque samples using shotgun metagenomic sequencing...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28198670/metatopics-an-integration-tool-to-analyze-microbial-community-profile-by-topic-model
#7
Jifang Yan, Guohui Chuai, Tao Qi, Fangyang Shao, Chi Zhou, Chenyu Zhu, Jing Yang, Yifei Yu, Cong Shi, Ning Kang, Yuan He, Qi Liu
BACKGROUND: Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial communities and their effect on a specific disease status. Even the relationships and interactions between different bacteria in a microbial community keep unknown. RESULTS: MetaTopics can efficiently extract the latent microbial communities which reflect the intrinsic relations or interactions among several major microbes...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28198609/an-unusual-flavin-dependent-halogenase-from-the-metagenome-of-the-marine-sponge-theonella-swinhoei-wa
#8
Duncan R M Smith, Agustinus R Robert Uria, Eric J N Helfrich, Daniela Milbredt, Karl-Heinz van-Pee, Joern Piel, Rebecca J M Goss
Uncultured bacteria from sponges have been demonstrated to be responsible for the generation of many potent, bioactive natural products including halogenated metabolites.1 The identification of gene clusters from the metagenomes of such bacterial communities enables the discovery of enzymes that mediate new and useful chemistries and allows insight to be gained into the biogenesis of potentially pharmacologically important natural products. Here we report a new pathway to the keramamides (krm); the first functional evidence for the existence of a distinct producer in the Theonella swinhoei WA chemotype is revealed, and a key enzyme on the pathway, a unique flavin dependent halogenase with a broad substrate specificity, and with potential as a useful new biocatalytic tool is described...
February 15, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28198423/discovery-of-genes-coding-for-carbohydrate-active-enzyme-by-metagenomic-analysis-of-lignocellulosic-biomasses
#9
Salvatore Montella, Valeria Ventorino, Vincent Lombard, Bernard Henrissat, Olimpia Pepe, Vincenza Faraco
In this study, a high-throughput sequencing approach was applied to discover novel biocatalysts for lignocellulose hydrolysis from three dedicated energy crops, Arundo donax, Eucalyptus camaldulensis and Populus nigra, after natural biodegradation. The microbiomes of the three lignocellulosic biomasses were dominated by bacterial species (approximately 90%) with the highest representation by the Streptomyces genus both in the total microbial community composition and in the microbial diversity related to GH families of predicted ORFs...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198087/meta-analysis-of-the-human-gut-microbiome-from-urbanized-and-pre-agricultural-populations
#10
REVIEW
Leonardo Mancabelli, Christian Milani, Gabriele Andrea Lugli, Francesca Turroni, Chiara Ferrario, Douwe van Sinderen, Marco Ventura
Metagenomic studies of the human gut microbiome have only recently begun to explore the differences in taxonomic composition between subjects from diverse geographical origins. Here, we compared taxonomy, resistome and functional metabolic properties of publicly available shotgun datasets of human fecal samples collected from different geographical regions (Europe, North America, Asia and Oceania). Such datasets encompassed gut microbiota information corresponding to 13 developed/industrialized societies, as well as two traditional hunter-gatherer, pre-agricultural communities (Tanzanian and Peruvian individuals)...
February 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28197141/metabolomic-and-metagenomic-analysis-of-two-crude-oil-production-pipelines-experiencing-differential-rates-of-corrosion
#11
Vincent Bonifay, Boris Wawrik, Jan Sunner, Emily C Snodgrass, Egemen Aydin, Kathleen E Duncan, Amy V Callaghan, Athenia Oldham, Turid Liengen, Iwona Beech
Corrosion processes in two North Sea oil production pipelines were studied by analyzing pig envelope samples via metagenomic and metabolomic techniques. Both production systems have similar physico-chemical properties and injection waters are treated with nitrate, but one pipeline experiences severe corrosion and the other does not. Early and late pigging material was collected to gain insight into the potential causes for differential corrosion rates. Metabolites were extracted and analyzed via ultra-high performance liquid chromatography/high-resolution mass spectrometry with electrospray ionization (ESI) in both positive and negative ion modes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28197136/characterization-of-the-genomic-diversity-of-norovirus-in-linked-patients-using-a-metagenomic-deep-sequencing-approach
#12
Neda Nasheri, Nicholas Petronella, Jennifer Ronholm, Sabah Bidawid, Nathalie Corneau
Norovirus (NoV) is the leading cause of gastroenteritis worldwide. A robust cell culture system does not exist for NoV and therefore detailed characterization of outbreak and sporadic strains relies on molecular techniques. In this study, we employed a metagenomic approach that uses non-specific amplification followed by next-generation sequencing to whole genome sequence NoV genomes directly from clinical samples obtained from 8 linked patients. Enough sequencing depth was obtained for each sample to use a de novo assembly of near-complete genome sequences...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28194314/evolutionary-and-functional-implications-of-hypervariable-loci-within-the-skin-virome
#13
Geoffrey D Hannigan, Qi Zheng, Jacquelyn S Meisel, Samuel S Minot, Frederick D Bushman, Elizabeth A Grice
Localized genomic variability is crucial for the ongoing conflicts between infectious microbes and their hosts. An understanding of evolutionary and adaptive patterns associated with genomic variability will help guide development of vaccines and antimicrobial agents. While most analyses of the human microbiome have focused on taxonomic classification and gene annotation, we investigated genomic variation of skin-associated viral communities. We evaluated patterns of viral genomic variation across 16 healthy human volunteers...
2017: PeerJ
https://www.readbyqxmd.com/read/28193877/origin-of-microbial-biomineralization-and-magnetotaxis-during-the-archean
#14
Wei Lin, Greig A Paterson, Qiyun Zhu, Yinzhao Wang, Evguenia Kopylova, Ying Li, Rob Knight, Dennis A Bazylinski, Rixiang Zhu, Joseph L Kirschvink, Yongxin Pan
Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28192251/antibiotic-induced-depletion-of-anti-inflammatory-clostridia-is-associated-with-the-development-of-gvhd-in-pediatric-stem-cell-transplant-patients
#15
Tiffany R Simms-Waldrip, Gauri Sunkersett, Laura A Coughlin, Milan R Savani, Carlos Arana, Jiwoong Kim, Minsoo Kim, Xiaowei Zhan, David E Greenberg, Yang Xie, Stella M Davies, Andrew Y Koh
Adult stem cell transplantation (SCT) patients with graft-versus-host-disease (GVHD) exhibit significant disruptions in gut microbial communities. These changes are associated with higher overall mortality and appear to be driven by specific antibiotic therapies. It is unclear whether pediatric SCT patients who develop GVHD exhibit similar antibiotic-induced gut microbiota community changes. Here, we show that pediatric SCT patients (from Children's Medical Center Dallas, n=8, and Cincinnati Children's Hospital, n=7) who develop GVHD show a significant decline, up to 10-log fold, in gut anti-inflammatory Clostridia (AIC), compared to those without GVHD...
February 9, 2017: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/28192164/origins-and-challenges-of-viral-dark-matter
#16
REVIEW
Siddharth R Krishnamurthy, David Wang
The accurate classification of viral dark matter - metagenomic sequences that originate from viruses but do not align to any reference virus sequences - is one of the major obstacles in comprehensively defining the virome. Depending on the sample, viral dark matter can make up from anywhere between 40-90% of sequences. This review focuses on the specific nature of dark matter as it relates to viral sequences. We identify three factors that contribute to the existence of viral dark matter: the divergence and length of virus sequences, the limitations of alignment based classification, and limited representation of viruses in reference sequence databases...
February 9, 2017: Virus Research
https://www.readbyqxmd.com/read/28191900/dimethylsulfoniopropionate-biosynthesis-in-marine-bacteria-and-identification-of-the-key-gene-in-this-process
#17
Andrew R J Curson, Ji Liu, Ana Bermejo Martínez, Robert T Green, Yohan Chan, Ornella Carrión, Beth T Williams, Sheng-Hui Zhang, Gui-Peng Yang, Philip C Bulman Page, Xiao-Hua Zhang, Jonathan D Todd
Dimethylsulfoniopropionate (DMSP) is one of the Earth's most abundant organosulfur molecules, a signalling molecule(1), a key nutrient for marine microorganisms(2,3) and the major precursor for gaseous dimethyl sulfide (DMS). DMS, another infochemical in signalling pathways(4), is important in global sulfur cycling(2) and affects the Earth's albedo, and potentially climate, via sulfate aerosol and cloud condensation nuclei production(5,6). It was thought that only eukaryotes produce significant amounts of DMSP(7-9), but here we demonstrate that many marine heterotrophic bacteria also produce DMSP, probably using the same methionine (Met) transamination pathway as macroalgae and phytoplankton(10)...
February 13, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28188902/dental-pulp-as-a-source-of-low-contaminated-dna
#18
Michel Drancourt, Gérard Aboudharam, Olivier Croce, Fabrice Armougom, Catherine Robert, Didier Raoult
The in-laboratory contamination of the ancient samples hinders the result interpretation of the investigations in the field of paleomicrobiology. We had promoted the dental pulp as a sample that limits the risks of in-laboratory contamination of the ancient material. In this work, we measured the contamination of the dental pulp manipulated according to paleomicrobiology protocol, used as a source of a total DNA for metagenomics. First, total DNA extracted from two dog canines was sequenced using next generation sequencing...
February 8, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28188205/metagenomic-and-metatranscriptomic-analyses-reveal-structure-and-dynamics-of-a-dechlorinating-community-containing-dehalococcoides-mccartyi-and-corrinoid-providing-microorganisms-under-cobalamin-limited-condition
#19
Yujie Men, Ke Yu, Jacob Bælum, Ying Gao, Julien Tremblay, Emmanuel Prestat, Ben Stenuit, Susannah G Tringe, Janet Jansson, Tong Zhang, Lisa Alvarez-Cohen
The aim of this study is to obtain a systems level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities and dynamics in trichloroethene (TCE) - dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 d), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment with exogenous cobalamin compared to the one without cobalamin addition...
February 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28187782/sputum-dna-sequencing-in-cystic-fibrosis-non-invasive-access-to-the-lung-microbiome-and-to-pathogen-details
#20
Rounak Feigelman, Christian R Kahlert, Florent Baty, Frank Rassouli, Rebekka L Kleiner, Philipp Kohler, Martin H Brutsche, Christian von Mering
BACKGROUND: Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typically involves regular respiratory-tract cultures in order to identify pathogens and to guide treatment. However, culture-based methods can miss atypical or slow-growing microbes. Furthermore, the isolated microbes are often not classified at the strain level due to limited taxonomic resolution...
February 10, 2017: Microbiome
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