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Whole genome sequence microbiome

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https://www.readbyqxmd.com/read/29227468/metagenomic-binning-and-association-of-plasmids-with-bacterial-host-genomes-using-dna-methylation
#1
John Beaulaurier, Shijia Zhu, Gintaras Deikus, Ilaria Mogno, Xue-Song Zhang, Austin Davis-Richardson, Ronald Canepa, Eric W Triplett, Jeremiah J Faith, Robert Sebra, Eric E Schadt, Gang Fang
Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29211769/arsenic-exposure-and-intestinal-microbiota-in-children-from-sirajdikhan-bangladesh
#2
Xiaoxi Dong, Natalia Shulzhenko, Julien Lemaitre, Renee L Greer, Kate Peremyslova, Quazi Quamruzzaman, Mahmudar Rahman, Omar Sharif Ibn Hasan, Sakila Afroz Joya, Mostofa Golam, David C Christiani, Andriy Morgun, Molly L Kile
BACKGROUND: Arsenic has antimicrobial properties at high doses yet few studies have examined its effect on gut microbiota. This warrants investigation since arsenic exposure increases the risk of many diseases in which gut microbiota have been shown to play a role. We examined the association between arsenic exposure from drinking water and the composition of intestinal microbiota in children exposed to low and high arsenic levels during prenatal development and early life. RESULTS: 16S rRNA gene sequencing revealed that children with high arsenic exposure had a higher abundance of Proteobacteria in their stool compared to matched controls with low arsenic exposure...
2017: PloS One
https://www.readbyqxmd.com/read/29177251/a-concurrent-subtractive-assembly-approach-for-identification-of-disease-associated-sub-metagenomes
#3
Wontack Han, Mingjie Wang, Yuzhen Ye
Comparative analysis of metagenomes can be used to detect sub-metagenomes (species or gene sets) that are associated with specific phenotypes (e.g., host status). The typical workflow is to assemble and annotate metagenomic datasets individually or as a whole, followed by statistical tests to identify differentially abundant species/genes. We previously developed subtractive assembly (SA), a de novo assembly approach for comparative metagenomics that first detects differential reads that distinguish between two groups of metagenomes and then only assembles these reads...
2017: Research in Computational Molecular Biology: ... Annual International Conference, RECOMB ...: Proceedings
https://www.readbyqxmd.com/read/29176730/the-microbiomes-of-blowflies-and-houseflies-as-bacterial-transmission-reservoirs
#4
Ana Carolina M Junqueira, Aakrosh Ratan, Enzo Acerbi, Daniela I Drautz-Moses, Balakrishnan N V Premkrishnan, Paul I Costea, Bodo Linz, Rikky W Purbojati, Daniel F Paulo, Nicolas E Gaultier, Poorani Subramanian, Nur A Hasan, Rita R Colwell, Peer Bork, Ana Maria L Azeredo-Espin, Donald A Bryant, Stephan C Schuster
Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome...
November 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29167663/metagenomic-analysis-of-the-gut-microbiome-of-the-common-black-slug-arion-ater-in-search-of-novel-lignocellulose-degrading-enzymes
#5
Ryan Joynson, Leighton Pritchard, Ekenakema Osemwekha, Natalie Ferry
Some eukaryotes are able to gain access to well-protected carbon sources in plant biomass by exploiting microorganisms in the environment or harbored in their digestive system. One is the land pulmonate Arion ater, which takes advantage of a gut microbial consortium that can break down the widely available, but difficult to digest, carbohydrate polymers in lignocellulose, enabling them to digest a broad range of fresh and partially degraded plant material efficiently. This ability is considered one of the major factors that have enabled A...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29145425/statistical-analysis-of-co-occurrence-patterns-in-microbial-presence-absence-datasets
#6
Kumar P Mainali, Sharon Bewick, Peter Thielen, Thomas Mehoke, Florian P Breitwieser, Shishir Paudel, Arjun Adhikari, Joshua Wolfe, Eric V Slud, David Karig, William F Fagan
Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy...
2017: PloS One
https://www.readbyqxmd.com/read/29106455/virapipe-scalable-parallel-pipeline-for-viral-metagenome-analysis-from-next-generation-sequencing-reads
#7
Altti Ilari Maarala, Zurab Bzhalava, Joakim Dillner, Keijo Heljanko, Davit Bzhalava
Motivation: Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments...
November 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29051233/high-quality-whole-genome-sequences-of-the-oligo-mouse-microbiota-bacterial-community
#8
Debora Garzetti, Sandrine Brugiroux, Boyke Bunk, Rüdiger Pukall, Kathy D McCoy, Andrew J Macpherson, Bärbel Stecher
The Oligo-Mouse-Microbiota (Oligo-MM(12)) is a community of 12 mouse intestinal bacteria to be used for microbiome research in gnotobiotic mice. We present here the high-quality whole genome sequences of the Oligo-MM(12) strains, which were obtained by combining the accuracy of the Illumina platforms with the long reads of the PacBio technology.
October 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29047329/genome-sequencing-of-39-akkermansia-muciniphila-isolates-reveals-its-population-structure-genomic-and-functional-diverisity-and-global-distribution-in-mammalian-gut-microbiotas
#9
Xianfeng Guo, Shenghui Li, Jiachun Zhang, Feifan Wu, Xiangchun Li, Dan Wu, Min Zhang, Zihao Ou, Zhuye Jie, Qiulong Yan, Peng Li, Jiangfeng Yi, Yongzheng Peng
BACKGROUND: Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its genomic content. RESULTS: Herein, we for the first time characterized the genomic architecture of A. muciniphila based on whole-genome sequencing, assembling, and annotating of 39 isolates derived from human and mouse feces. We revealed a flexible open pangenome of A. muciniphila currently consisting of 5644 unique proteins...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29018426/transfer-and-persistence-of-a-multi-drug-resistance-plasmid-in-situ-of-the-infant-gut-microbiota-in-the-absence-of-antibiotic-treatment
#10
Heidi Gumpert, Jessica Z Kubicek-Sutherland, Andreas Porse, Nahid Karami, Christian Munck, Marius Linkevicius, Ingegerd Adlerberth, Agnes E Wold, Dan I Andersson, Morten O A Sommer
The microbial ecosystem residing in the human gut is believed to play an important role in horizontal exchange of virulence and antibiotic resistance genes that threatens human health. While the diversity of gut-microorganisms and their genetic content has been studied extensively, high-resolution insight into the plasticity, and selective forces shaping individual genomes is scarce. In a longitudinal study, we followed the dynamics of co-existing Escherichia coli lineages in an infant not receiving antibiotics...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28983469/population-genomic-insights-into-variation-in-prevotella-intermedia-and-prevotella-nigrescens-isolates-and-its-association-with-periodontal-disease
#11
Yifei Zhang, Min Zhen, Yalin Zhan, Yeqing Song, Qian Zhang, Jinfeng Wang
High-throughput sequencing has helped to reveal the close relationship between Prevotella and periodontal disease, but the roles of subspecies diversity and genomic variation within this genus in periodontal diseases still need to be investigated. We performed a comparative genome analysis of 48 Prevotella intermedia and Prevotella nigrescens isolates that from the same cohort of subjects to identify the main drivers of their pathogenicity and adaptation to different environments. The comparisons were done between two species and between disease and health based on pooled sequences...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28954247/microbiome-dynamics-and-adaptation-of-expression-signatures-during-methane-production-failure-and-process-recovery
#12
Anja Grohmann, Steffen Fehrmann, Yevhen Vainshtein, Nicola L Haag, Franziska Wiese, Philip Stevens, Hans-Joachim Naegele, Hans Oechsner, Thomas Hartsch, Kai Sohn, Christian Grumaz
This study aimed to uncover microbial dynamics and transcriptional adaptations during mesophilic AD of maize silage and slurry. While one digester performed under optimal conditions, the investigations also evaluated the microbiome during a temperature drop mediated process failure accompanied by acidification and how it contributed to a process recovery. Composition and pathway activities were analyzed by whole genome shotgun (WGS) and metatranscriptome sequencing, respectively. A biodiversity of 112 species was observed with noticeable shifts over process time...
September 4, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28948844/next-generation-sequencing-an-application-in-forensic-sciences
#13
Maria Jesus Alvarez-Cubero, Maria Saiz, Belén Martínez-García, Sara M Sayalero, Carmen Entrala, Jose Antonio Lorente, Luis Javier Martinez-Gonzalez
CONTEXT: Over the last few decades, advances in sequencing have improved greatly. One of the most important achievements of Next Generation Sequencing (NGS) is to produce millions of sequence reads in a short period of time, and to produce large sequences of DNA in fragments of any size. Libraries can be generated from whole genomes or any DNA or RNA region of interest without the need to know its sequence beforehand. This allows for looking for variations and facilitating genetic identification...
September 26, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28887527/pan-genome-analysis-of-bacillus-for-microbiome-profiling
#14
Yihwan Kim, InSong Koh, Mi Young Lim, Won-Hyong Chung, Mina Rho
Recent advances in high-throughput sequencing technology allow for in-depth studies on microbial genomes and their communities. While multiple strains of the same species could display genomic variations with different gene contents in diverse habitats and hosts, the essential functions for a specific species are conserved as core genes that are shared among strains. We have comprehensively analyzed 238 strains of five different Bacillus species to identify the properties of core and strain-specific genes. Core and strain-specific genes in each Bacillus species show significant differences in their functions and genomic signatures...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28831408/shotgun-metagenomic-data-on-the-human-stool-samples-to-characterize-shifts-of-the-gut-microbial-profile-after-the-helicobacter-pylori-eradication-therapy
#15
Eugenia A Boulygina, Maria I Markelova, Dilyara R Khusnutdinova, Maria N Siniagina, Sergey Yu Malanin, Rustam A Abdulkhakov, Sayar R Abdulkhakov, Vladislav M Chernov, Tatiana V Grigoryeva
The shotgun sequencing data presented in this report are related to the research article named "Gut microbiome shotgun sequencing in assessment of microbial community changes associated with H. pylori eradication therapy" (Khusnutdinova et al., 2016) [1]. Typically, the H. pylori eradication protocol includes a prolonged two-week use of the broad-spectrum antibiotics. The presented data on the whole-genome sequencing of the total DNA from stool samples of patients before the start of the eradication, immediately after eradication and several weeks after the end of treatment could help to profile the gut microbiota both taxonomically and functionally...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28797298/community-characteristics-of-the-gut-microbiomes-of-competitive-cyclists
#16
Lauren M Petersen, Eddy J Bautista, Hoan Nguyen, Blake M Hanson, Lei Chen, Sai H Lek, Erica Sodergren, George M Weinstock
BACKGROUND: Changes in diet and exercise can alter the gut microbiome of humans and mice; however, few studies to date have assessed the microbiomes of highly fit athletes. In this pilot study, we used metagenomic whole genome shotgun (mWGS) and metatranscriptomic (RNA-Seq) sequencing to show what organisms are both present and active in the gut microbiomes of both professional and amateur level competitive cyclists and to determine if any significant differences exist between these two groups...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28790208/pathogenicity-locus-core-genome-and-accessory-gene-contributions-to-clostridium-difficile-virulence
#17
Brittany B Lewis, Rebecca A Carter, Lilan Ling, Ingrid Leiner, Ying Taur, Mini Kamboj, Erik R Dubberke, Joao Xavier, Eric G Pamer
Clostridium difficile is a spore-forming anaerobic bacterium that causes colitis in patients with disrupted colonic microbiota. While some individuals are asymptomatic C. difficile carriers, symptomatic disease ranges from mild diarrhea to potentially lethal toxic megacolon. The wide disease spectrum has been attributed to the infected host's age, underlying diseases, immune status, and microbiome composition. However, strain-specific differences in C. difficile virulence have also been implicated in determining colitis severity...
August 8, 2017: MBio
https://www.readbyqxmd.com/read/28774671/complete-genome-sequence-of-ruminococcaceae-bacterium-cpb6-a-newly-isolated-culture-for-efficient-n-caproic-acid-production-from-lactate
#18
Yong Tao, Xiaoyu Zhu, Han Wang, Yi Wang, Xiangzhen Li, Hong Jin, Junpeng Rui
n-caproic acid (CA) is a valuable chemical feedstock for various industrial applications. Biological production of CA from renewable carbon sources has attracted a lot of attentions recently. We lately reported the new culture Ruminococcaceae bacterium CPB6, which was isolated from a microbiome for efficient CA production from lactate. To further elucidate its metabolism, we sequenced the whole genome of the strain. The size of the complete genome is 2,069,994bp with 50.58% GC content; no plasmid was identified...
July 31, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28771533/mechanisms-by-which-porphyromonas-gingivalis-evades-innate-immunity
#19
Kaveh Abdi, Tsute Chen, Brian A Klein, Albert K Tai, Jill Coursen, Xiangdong Liu, Jeff Skinner, Saravanan Periasamy, Youngnim Choi, Benedikt M Kessler, Robert J Palmer, Apostolos Gittis, Polly Matzinger, Margaret J Duncan, Nevil J Singh
The oral cavity is home to unique resident microbial communities whose interactions with host immunity are less frequently studied than those of the intestinal microbiome. We examined the stimulatory capacity and the interactions of two oral bacteria, Porphyromonas gingivalis (P. gingivalis) and Fusobacterium nucleatum (F. nucleatum), on Dendritic Cell (DC) activation, comparing them to the effects of the well-studied intestinal microbe Escherichia coli (E. coli). Unlike F. nucleatum and E. coli, P. gingivalis failed to activate DCs, and in fact silenced DC responses induced by F...
2017: PloS One
https://www.readbyqxmd.com/read/28714965/a-wellness-study-of-108-individuals-using-personal-dense-dynamic-data-clouds
#20
Nathan D Price, Andrew T Magis, John C Earls, Gustavo Glusman, Roie Levy, Christopher Lausted, Daniel T McDonald, Ulrike Kusebauch, Christopher L Moss, Yong Zhou, Shizhen Qin, Robert L Moritz, Kristin Brogaard, Gilbert S Omenn, Jennifer C Lovejoy, Leroy Hood
Personal data for 108 individuals were collected during a 9-month period, including whole genome sequences; clinical tests, metabolomes, proteomes, and microbiomes at three time points; and daily activity tracking. Using all of these data, we generated a correlation network that revealed communities of related analytes associated with physiology and disease. Connectivity within analyte communities enabled the identification of known and candidate biomarkers (e.g., gamma-glutamyltyrosine was densely interconnected with clinical analytes for cardiometabolic disease)...
August 2017: Nature Biotechnology
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