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Shotgun sequence microbes

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https://www.readbyqxmd.com/read/29743119/profiling-microbial-strains-in-urban-environments-using-metagenomic-sequencing-data
#1
Moreno Zolfo, Francesco Asnicar, Paolo Manghi, Edoardo Pasolli, Adrian Tett, Nicola Segata
BACKGROUND: The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context...
May 9, 2018: Biology Direct
https://www.readbyqxmd.com/read/29686086/myb72-dependent-coumarin-exudation-shapes-root-microbiome-assembly-to-promote-plant-health
#2
Ioannis A Stringlis, Ke Yu, Kirstin Feussner, Ronnie de Jonge, Sietske Van Bentum, Marcel C Van Verk, Roeland L Berendsen, Peter A H M Bakker, Ivo Feussner, Corné M J Pieterse
Plant roots nurture a tremendous diversity of microbes via exudation of photosynthetically fixed carbon sources. In turn, probiotic members of the root microbiome promote plant growth and protect the host plant against pathogens and pests. In the Arabidopsis thaliana - Pseudomonas simiae WCS417 model system the root-specific transcription factor MYB72 and the MYB72-controlled β-glucosidase BGLU42 emerged as important regulators of beneficial rhizobacteria-induced systemic resistance (ISR) and iron-uptake responses...
April 23, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29676472/the-first-taxus-rhizosphere-microbiome-revealed-by-shotgun-metagenomic-sequencing
#3
Da-Cheng Hao, Cai-Rong Zhang, Pei-Gen Xiao
In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539)...
April 20, 2018: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/29560821/vitcomic2-visualization-tool-for-the-phylogenetic-composition-of-microbial-communities-based-on-16s-rrna-gene-amplicons-and-metagenomic-shotgun-sequencing
#4
Hiroshi Mori, Takayuki Maruyama, Masahiro Yano, Takuji Yamada, Ken Kurokawa
BACKGROUND: The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary relationships among taxa are inferred by a phylogenetic tree. Thus, the combined representation of taxonomic composition and phylogenetic relationships among taxa is a powerful method for understanding microbial community structure; however, applying phylogenetic tree-based representation with information on the abundance of thousands or more taxa in each community is a difficult task...
March 19, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29335008/multi-omics-differentially-classify-disease-state-and-treatment-outcome-in-pediatric-crohn-s-disease
#5
Gavin M Douglas, Richard Hansen, Casey M A Jones, Katherine A Dunn, André M Comeau, Joseph P Bielawski, Rachel Tayler, Emad M El-Omar, Richard K Russell, Georgina L Hold, Morgan G I Langille, Johan Van Limbergen
BACKGROUND: Crohn's disease (CD) has an unclear etiology, but there is growing evidence of a direct link with a dysbiotic microbiome. Many gut microbes have previously been associated with CD, but these have mainly been confounded with patients' ongoing treatments. Additionally, most analyses of CD patients' microbiomes have focused on microbes in stool samples, which yield different insights than profiling biopsy samples. RESULTS: We sequenced the 16S rRNA gene (16S) and carried out shotgun metagenomics (MGS) from the intestinal biopsies of 20 treatment-naïve CD and 20 control pediatric patients...
January 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29235707/tales-from-the-tomb-the-microbial-ecology-of-exposed-rock-surfaces
#6
Tess E Brewer, Noah Fierer
Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analysed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing...
December 13, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29165844/oral-microbiomes-from-hunter-gatherers-and-traditional-farmers-reveal-shifts-in-commensal-balance-and-pathogen-load-linked-to-diet
#7
Florent Lassalle, Matteo Spagnoletti, Matteo Fumagalli, Liam Shaw, Mark Dyble, Catherine Walker, Mark G Thomas, Andrea Bamberg Migliano, Francois Balloux
Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29156542/computational-approaches-for-integrative-analysis-of-the-metabolome-and-microbiome
#8
REVIEW
Jasmine Chong, Jianguo Xia
The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years. The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health. In this context, metabolomics is increasingly applied to complement sequencing-based approaches (marker genes or shotgun metagenomics) to enable resolution of microbiome-conferred functionalities associated with health. However, analyzing the resulting multi-omics data remains a significant challenge in current microbiome studies...
November 18, 2017: Metabolites
https://www.readbyqxmd.com/read/28959368/a-model-based-approach-for-species-abundance-quantification-based-on-shotgun-metagenomic-data
#9
Eric Z Chen, Frederic D Bushman, Hongzhe Li
The human microbiome, which includes the collective microbes residing in or on the human body, has a profound influence on the human health. DNA sequencing technology has made the large-scale human microbiome studies possible by using shotgun metagenomic sequencing. One important aspect of data analysis of such metagenomic data is to quantify the bacterial abundances based on the metagenomic sequencing data. Existing methods almost always quantify such abundances one sample at a time, which ignore certain systematic differences in read coverage along the genomes due to GC contents, copy number variation and the bacterial origin of replication...
June 2017: Statistics in Biosciences
https://www.readbyqxmd.com/read/28954247/microbiome-dynamics-and-adaptation-of-expression-signatures-during-methane-production-failure-and-process-recovery
#10
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/28938903/metagenomic-characterization-of-ambulances-across-the-usa
#11
Niamh B O'Hara, Harry J Reed, Ebrahim Afshinnekoo, Donell Harvin, Nora Caplan, Gail Rosen, Brook Frye, Stephen Woloszynek, Rachid Ounit, Shawn Levy, Erin Butler, Christopher E Mason
BACKGROUND: Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in pre-hospital settings, such as ambulances, an important first point-of-contact between patients and hospitals. RESULTS: We sequenced 398 samples from 137 ambulances across the USA using shotgun sequencing...
September 22, 2017: Microbiome
https://www.readbyqxmd.com/read/28936203/modulation-of-gut-microbiome-composition-and-function-in-experimental-colitis-treated-with-sulfasalazine
#12
Haihui Zheng, Mingyi Chen, Yuan Li, Yuanyuan Wang, Lin Wei, Ziqiong Liao, Mengxia Wang, Fangli Ma, Qiongfeng Liao, Zhiyong Xie
Inflammatory bowel disease (IBD) results from alterations in intestinal flora and the immune system. Sulfasalazine (SASP) is a sulfa antimicrobial used to treat IBD in clinic for years. However, how SASP affects gut microbes and its potential functions remains unclear. To investigate the relationships of SASP, IBD, and gut microbiome, we used 2,4,6-trinitrobenzenesulfonic acid (TNBS) to induce experimental colitis in rats, and analyzed the microbiota in the fecal samples, which come from the control group (treated with ethanol + saline), the model group (treated with TNBS-ethanol + saline) and the SASP group (treated with TNBS-ethanol + SASP), with 16S gene sequencing and followed up a subset sample using shotgun sequencing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28898207/shotgun-metagenomics-from-sampling-to-analysis
#13
REVIEW
Christopher Quince, Alan W Walker, Jared T Simpson, Nicholas J Loman, Nicola Segata
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples or environments containing organisms with limited similarity to sequenced genomes, are needed...
September 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28884091/alterations-of-the-gut-microbiome-in-hypertension
#14
Qiulong Yan, Yifang Gu, Xiangchun Li, Wei Yang, Liqiu Jia, Changming Chen, Xiuyan Han, Yukun Huang, Lizhe Zhao, Peng Li, Zhiwei Fang, Junpeng Zhou, Xiuru Guan, Yanchun Ding, Shaopeng Wang, Muhammad Khan, Yi Xin, Shenghui Li, Yufang Ma
Introduction: Human gut microbiota is believed to be directly or indirectly involved in cardiovascular diseases and hypertension. However, the identification and functional status of the hypertension-related gut microbe(s) have not yet been surveyed in a comprehensive manner. Methods: Here we characterized the gut microbiome in hypertension status by comparing fecal samples of 60 patients with primary hypertension and 60 gender-, age-, and body weight-matched healthy controls based on whole-metagenome shotgun sequencing...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28846439/microbial-lineages-in-sarcoidosis-a-metagenomic-analysis-tailored-for-low-microbial-content-samples
#15
Erik L Clarke, Abigail P Lauder, Casey E Hofstaedter, Young Hwang, Ayannah S Fitzgerald, Ize Imai, Wojciech Biernat, Bartłomiej Rękawiecki, Hanna Majewska, Anna Dubaniewicz, Leslie A Litzky, Michael D Feldman, Kyle Bittinger, Milton D Rossman, Karen C Patterson, Frederic D Bushman, Ronald G Collman
RATIONALE: The etiology of sarcoidosis is unknown, but microbial agents are suspected as triggers. OBJECTIVES: We sought to identify bacterial, fungal, or viral lineages in specimens from patients with sarcoidosis enriched relative to control subjects using metagenomic DNA sequencing. Because DNA from environmental contamination contributes disproportionately to samples with low authentic microbial content, we developed improved methods for filtering environmental contamination...
January 15, 2018: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28830999/numerous-uncharacterized-and-highly-divergent-microbes-which-colonize-humans-are-revealed-by-circulating-cell-free-dna
#16
Mark Kowarsky, Joan Camunas-Soler, Michael Kertesz, Iwijn De Vlaminck, Winston Koh, Wenying Pan, Lance Martin, Norma F Neff, Jennifer Okamoto, Ronald J Wong, Sandhya Kharbanda, Yasser El-Sayed, Yair Blumenfeld, David K Stevenson, Gary M Shaw, Nathan D Wolfe, Stephen R Quake
Blood circulates throughout the human body and contains molecules drawn from virtually every tissue, including the microbes and viruses which colonize the body. Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome. Analyzing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little or no sequence homology in any existing databases...
September 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28769920/unraveling-the-microbial-interactions-and-metabolic-potentials-in-pre-and-post-treated-sludge-from-a-wastewater-treatment-plant-using-metagenomic-studies
#17
Chandni Sidhu, Surendra Vikram, Anil Kumar Pinnaka
Sewage waste represents an ecosystem of complex and interactive microbial consortia which proliferate with different kinetics according to their individual genetic as well as metabolic potential. We performed metagenomic shotgun sequencing on Ion-Torrent platform, to explore the microbial community structure, their biological interactions and associated functional capacity of pre-treated/raw sludge (RS) and post-treated/dried sludge (DS) of wastewater treatment plant. Bacterial phylotypes belonging to Epsilonproteobacteria (∼45...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28758937/a-different-microbiome-gene-repertoire-in-the-airways-of-cystic-fibrosis-patients-with-severe-lung-disease
#18
Giovanni Bacci, Alessio Mengoni, Ersilia Fiscarelli, Nicola Segata, Giovanni Taccetti, Daniela Dolce, Patrizia Paganin, Patrizia Morelli, Vanessa Tuccio, Alessandra De Alessandri, Vincenzina Lucidi, Annamaria Bevivino
In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing...
July 29, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28747705/soil-nutritional-status-and-biogeography-influence-rhizosphere-microbial-communities-associated-with-the-invasive-tree-acacia-dealbata
#19
Casper N Kamutando, Surendra Vikram, Gilbert Kamgan-Nkuekam, Thulani P Makhalanyane, Michelle Greve, Johannes J Le Roux, David M Richardson, Don Cowan, Angel Valverde
Invasiveness and the impacts of introduced plants are known to be mediated by plant-microbe interactions. Yet, the microbial communities associated with invasive plants are generally poorly understood. Here we report on the first comprehensive investigation of the bacterial and fungal communities inhabiting the rhizosphere and the surrounding bulk soil of a widespread invasive tree, Acacia dealbata. Amplicon sequencing data indicated that rhizospheric microbial communities differed significantly in structure and composition from those of the bulk soil...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28530140/associations-of-nasopharyngeal-metabolome-and-microbiome-with-severity-among-infants-with-bronchiolitis-a-multiomic-analysis
#20
MULTICENTER STUDY
Christopher J Stewart, Jonathan M Mansbach, Matthew C Wong, Nadim J Ajami, Joseph F Petrosino, Carlos A Camargo, Kohei Hasegawa
RATIONALE: Bronchiolitis is the most common lower respiratory infection in infants; however, it remains unclear which infants with bronchiolitis will develop severe illness. In addition, although emerging evidence indicates associations of the upper-airway microbiome with bronchiolitis severity, little is known about the mechanisms linking airway microbes and host response to disease severity. OBJECTIVES: To determine the relations among the nasopharyngeal airway metabolome profiles, microbiome profiles, and severity in infants with bronchiolitis...
October 1, 2017: American Journal of Respiratory and Critical Care Medicine
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