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Shotgun metagenomics

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https://www.readbyqxmd.com/read/28222161/the-distinct-features-of-microbial-dysbiosis-of-crohn-s-disease-do-not-occur-to-the-same-extent-in-their-unaffected-genetically-linked-kindred
#1
Umer Zeeshan Ijaz, Christopher Quince, Laura Hanske, Nick Loman, Szymon T Calus, Martin Bertz, Christine A Edwards, Daniel R Gaya, Richard Hansen, Paraic McGrogan, Richard K Russell, Konstantinos Gerasimidis
BACKGROUND/AIMS: Studying the gut microbiota in unaffected relatives of people with Crohn's disease (CD) may advance our understanding of the role of bacteria in disease aetiology. METHODS: Faecal microbiota composition (16S rRNA gene sequencing), genetic functional capacity (shotgun metagenomics) and faecal short chain fatty acids (SCFA) were compared in unaffected adult relatives of CD children (CDR, n = 17) and adult healthy controls, unrelated to CD patients (HUC, n = 14)...
2017: PloS One
https://www.readbyqxmd.com/read/28214713/comparative-analysis-of-metagenomes-of-italian-top-soil-improvers
#2
Federica Gigliucci, Gianfranco Brambilla, Rosangela Tozzoli, Valeria Michelacci, Stefano Morabito
Biosolids originating from Municipal Waste Water Treatment Plants are proposed as top soil improvers (TSI) for their beneficial input of organic carbon on agriculture lands. Their use to amend soil is controversial, as it may lead to the presence of emerging hazards of anthropogenic or animal origin in the environment devoted to food production. In this study, we used a shotgun metagenomics sequencing as a tool to perform a characterization of the hazards related with the TSIs. The samples showed the presence of many virulence genes associated to different diarrheagenic E...
February 16, 2017: Environmental Research
https://www.readbyqxmd.com/read/28198672/integrated-metagenomic-data-analysis-demonstrates-that-a-loss-of-diversity-in-oral-microbiota-is-associated-with-periodontitis
#3
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/28198087/meta-analysis-of-the-human-gut-microbiome-from-urbanized-and-pre-agricultural-populations
#4
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
#5
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/28192251/antibiotic-induced-depletion-of-anti-inflammatory-clostridia-is-associated-with-the-development-of-gvhd-in-pediatric-stem-cell-transplant-patients
#6
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/28176868/metagenomic-survey-of-the-taxonomic-and-functional-microbial-communities-of-seawater-and-sea-ice-from-the-canadian-arctic
#7
Etienne Yergeau, Christine Michel, Julien Tremblay, Andrea Niemi, Thomas L King, Joanne Wyglinski, Kenneth Lee, Charles W Greer
Climate change has resulted in an accelerated decline of Arctic sea ice since 2001 resulting in primary production increases and prolongation of the ice-free season within the Northwest Passage. The taxonomic and functional microbial community composition of the seawater and sea ice of the Canadian Arctic is not very well known. Bacterial communities from the bottom layer of sea ice cores and surface water from 23 locations around Cornwallis Island, NU, Canada, were extensively screened. The bacterial 16S rRNA gene was sequenced for all samples while shotgun metagenomics was performed on selected samples...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28176851/comparative-study-of-the-gut-microbiome-potentially-related-to-milk-protein-in-murrah-buffaloes-bubalus-bubalis-and-chinese-holstein-cattle
#8
Jiachao Zhang, Chuanbiao Xu, Dongxue Huo, Qisong Hu, Qiannan Peng
Previous studies suggested a close relationship between ruminant gut microbes and the mammary gland. In this study, shotgun metagenomic sequencing was used to reveal the differences in the intestinal microbiome potentially related to milk components in Murrah buffaloes and Chinese Holstein cattle. A PCoA based on the weighted Unifrac distances showed an apparent clustering pattern in the structure of intestinal microbiota between buffalo and cattle. We could attribute the structural difference to the genera of Sutterella, Coprococcus and Dorea...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28169558/validation-of-metagenomic-next-generation-sequencing-tests-for-universal-pathogen-detection
#9
Robert Schlaberg, Charles Y Chiu, Steve Miller, Gary W Procop, George Weinstock
CONTEXT: -Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients...
February 7, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28165194/diversity-and-functions-of-the-sheep-faecal-microbiota-a-multi-omic-characterization
#10
Alessandro Tanca, Cristina Fraumene, Valeria Manghina, Antonio Palomba, Marcello Abbondio, Massimo Deligios, Daniela Pagnozzi, Maria Filippa Addis, Sergio Uzzau
Little is currently known on the microbial populations colonizing the sheep large intestine, despite their expected key role in host metabolism, physiology and immunity. This study reports the first characterization of the sheep faecal microbiota composition and functions, obtained through the application of a multi-omic strategy. An optimized protocol was first devised for DNA extraction and amplification from sheep stool samples. Then, 16S rDNA sequencing, shotgun metagenomics and shotgun metaproteomics were applied to unravel taxonomy, genetic potential and actively expressed functions and pathways respectively...
February 6, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28159795/predominance-and-metabolic-potential-of-halanaerobium-in-produced-water-from-hydraulically-fractured-marcellus-shale-wells
#11
Daniel Lipus, Amit Vikram, Daniel Ross, Daniel Bain, Djuna Gulliver, Richard Hammack, Kyle Bibby
: Microbial activity in the produced water from hydraulically fractured oil and gas wells may potentially interfere with hydrocarbon production and cause damage to the well and surface infrastructure via corrosion, sulfide release, and fouling. In this study, we surveyed the microbial abundance and community structure of produced water sampled from 42 Marcellus Shale wells in southwestern Pennsylvania (well age ranged from 150 to 1846 days) to better understand the microbial diversity of produced water...
February 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28158639/paladin-protein-alignment-for-functional-profiling-whole-metagenome-shotgun-data
#12
Anthony Westbrook, Jordan Ramsdell, Taruna Schuelke, Louisa Normington, R Daniel Bergeron, W Kelley Thomas, Matthew MacManes
No abstract text is available yet for this article.
January 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28158392/large-scale-16s-gene-assembly-using-metagenomics-shotgun-sequences
#13
Feng Zeng, Zicheng Wang, Ying Wang, Jizhong Zhou, Ting Chen
No abstract text is available yet for this article.
January 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28155666/ribotagger-fast-and-unbiased-16s-18s-profiling-using-whole-community-shotgun-metagenomic-or-metatranscriptome-surveys
#14
Chao Xie, Chin Lui Wesley Goi, Daniel H Huson, Peter F R Little, Rohan B H Williams
BACKGROUND: Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis. RESULTS: Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion...
December 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28149696/antibiotic-resistance-potential-of-the-healthy-preterm-infant-gut-microbiome
#15
Graham Rose, Alexander G Shaw, Kathleen Sim, David J Wooldridge, Ming-Shi Li, Saheer Gharbia, Raju Misra, John Simon Kroll
BACKGROUND: Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. RESULTS: Dominant clinically important species identified within the microbiomes included C...
2017: PeerJ
https://www.readbyqxmd.com/read/28148977/survey-of-meta-genomic-approaches-for-understanding-microbial-community-dynamics
#16
REVIEW
Anukriti Sharma, Rup Lal
Advancement in the next generation sequencing technologies has led to evolution of the field of genomics and metagenomics in a slim duration with nominal cost at precipitous higher rate. While metagenomics and genomics can be separately used to reveal the culture-independent and culture-based microbial evolution, respectively, (meta)genomics together can be used to demonstrate results at population level revealing in-depth complex community interactions for specific ecotypes. The field of metagenomics which started with answering "who is out there?" based on 16S rRNA gene has evolved immensely with the precise organismal reconstruction at species/strain level from the deeply covered metagenome data outweighing the need to isolate bacteria of which 99% are de facto non-cultivable...
March 2017: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/28144631/studying-vertical-microbiome-transmission-from-mothers-to-infants-by-strain-level-metagenomic-profiling
#17
Francesco Asnicar, Serena Manara, Moreno Zolfo, Duy Tin Truong, Matthias Scholz, Federica Armanini, Pamela Ferretti, Valentina Gorfer, Anna Pedrotti, Adrian Tett, Nicola Segata
The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling...
January 2017: MSystems
https://www.readbyqxmd.com/read/28138508/data-on-gut-metagenomes-of-the-patients-with-alcoholic-dependence-syndrome-and-alcoholic-liver-cirrhosis
#18
Alexander V Tyakht, Veronika B Dubinkina, Vera Y Odintsova, Konstantin S Yarygin, Boris A Kovarsky, Alexander V Pavlenko, Dmitry S Ischenko, Anna S Popenko, Dmitry G Alexeev, Anastasiya Y Taraskina, Regina F Nasyrova, Evgeny M Krupitski, Nino V Shalikiani, Igor G Bakulin, Petr L Shcherbakov, Lyubov O Skorodumova, Andrei K Larin, Elena S Kostryukova, Rustam A Abdulkhakov, Sayar R Abdulkhakov, Sergey Y Malanin, Ruzilya K Ismagilova, Tatiana V Grigoryeva, Elena N Ilina, Vadim M Govorun
Alcoholism is associated with significant changes in gut microbiota composition. Metagenomic sequencing allows to assess the altered abundance levels of bacterial taxa and genes in a culture-independent way. We collected 99 stool samples from the patients with alcoholic dependence syndrome (n=72) and alcoholic liver cirrhosis (n=27). Each of the samples was surveyed using "shotgun" (whole-genome) sequencing on SOLiD platform. The reads are deposited in the ENA (project ID: PRJEB18041).
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28138506/data-on-gut-metagenomes-of-the-patients-with-helicobacter-pylori-infection-before-and-after-the-antibiotic-therapy
#19
Oksana E Glushchenko, Andrei E Samoilov, Evgenii I Olekhnovich, Boris A Kovarsky, Alexander V Tyakht, Alexander V Pavlenko, Vlad V Babenko, Andrei K Larin, Elena S Kostryukova, Maja V Malakhova, Elena N Ilina, Rustem A Abdulkhakov, Dilyara I Safina, Tatiana V Grigoryeva, Sayar R Abdulkhakov, Vadim M Govorun
Antibiotic therapy can lead to the disruption of gut microbiota community with possible negative outcomes for human health. One of the diseases for which the treatment scheme commonly included antibiotic intake is Helicobacter pylori infection. The changes in taxonomic and functional composition of microbiota in patients can be assessed using "shotgun" metagenomic sequencing. Ten stool samples were collected from 4 patients with Helicobacter pylori infection before and directly after the H. pylori eradication course...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28131445/in-vitro-fermentation-of-key-dietary-compounds-with-rumen-fluid-a-genome-centric-perspective
#20
Stefano Campanaro, Laura Treu, Mirko Cattani, Panagiotis G Kougias, Veronica Vendramin, Stefano Schiavon, Franco Tagliapietra, Alessio Giacomini, Viviana Corich
The anaerobic decomposition of organic substrates leads to the generation of gases, such as methane, which can either be a valuable energy carrier in industrial applications or can be considered as a main greenhouse gas when it is naturally emitted. In this study we investigated in vitro the effect of dietary compounds, such as starch and proteins, on the microbial community present in the rumen fluid. High throughput shotgun sequencing, followed by metagenomic assembly and binning allowed the extraction of 18 genome bins...
January 25, 2017: Science of the Total Environment
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