keyword
MENU ▼
Read by QxMD icon Read
search

Shotgun sequence metagenome

keyword
https://www.readbyqxmd.com/read/27900686/shotgun-metagenomic-sequencing-analysis-of-soft-rot-enterobacteriaceae-in-polymicrobial-communities
#1
James Doonan, Sandra Denman, James E McDonald, Peter N Golyshin
Shotgun metagenomic sequencing of bacterial communities in necrotic plant lesions allows insights of host-pathogen molecular interactions. Soft-rot Enterobacteriaceae are significant crop pathogens with a wide host range. Reconstructed polymicrobial community DNA from soft-rot affected crops provides details of species relative abundance and functional potential, enabling significant insights into their lifestyle. Here, we describe a workflow for DNA recovery, metagenomic shotgun sequencing and in particular, an in silico analysis of bacterial isolates from affected plant tissue...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896068/metagenomic-investigation-of-the-microbial-diversity-in-a-chrysotile-asbestos-mine-pit-pond-lowell-vermont-usa
#2
Heather E Driscoll, James J Vincent, Erika L English, Elizabeth D Dolci
Here we report on a metagenomics investigation of the microbial diversity in a serpentine-hosted aquatic habitat created by chrysotile asbestos mining activity at the Vermont Asbestos Group (VAG) Mine in northern Vermont, USA. The now-abandoned VAG Mine on Belvidere Mountain in the towns of Eden and Lowell includes three open-pit quarries, a flooded pit, mill buildings, roads, and > 26 million metric tons of eroding mine waste that contribute alkaline mine drainage to the surrounding watershed. Metagenomes and water chemistry originated from aquatic samples taken at three depths (0...
December 2016: Genomics Data
https://www.readbyqxmd.com/read/27889153/metagenomics-reveals-flavour-metabolic-network-of-cereal-vinegar-microbiota
#3
Lin-Huan Wu, Zhen-Ming Lu, Xiao-Juan Zhang, Zong-Min Wang, Yong-Jian Yu, Jin-Song Shi, Zheng-Hong Xu
Multispecies microbial community formed through centuries of repeated batch acetic acid fermentation (AAF) is crucial for the flavour quality of traditional vinegar produced from cereals. However, the metabolism to generate and/or formulate the essential flavours by the multispecies microbial community is hardly understood. Here we used metagenomic approach to clarify in situ metabolic network of key microbes responsible for flavour synthesis of a typical cereal vinegar, Zhenjiang aromatic vinegar, produced by solid-state fermentation...
April 2017: Food Microbiology
https://www.readbyqxmd.com/read/27888291/whole-genome-enrichment-provides-deep-insights-into-vibrio-cholerae-metagenome-from-an-african-river
#4
L Vezzulli, C Grande, G Tassistro, I Brettar, M G Höfle, R P A Pereira, D Mushi, A Pallavicini, P Vassallo, C Pruzzo
The detection and typing of Vibrio cholerae in natural aquatic environments encounter major methodological challenges related to the fact that the bacterium is often present in environmental matrices at very low abundance in nonculturable state. This study applied, for the first time to our knowledge, a whole-genome enrichment (WGE) and next-generation sequencing (NGS) approach for direct genotyping and metagenomic analysis of low abundant V. cholerae DNA (<50 genome unit/L) from natural water collected in the Morogoro river (Tanzania)...
November 25, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27881416/metagenomics-of-two-severe-foodborne-outbreaks-provides-diagnostic-signatures-and-signs-of-co-infection-not-attainable-by-traditional-methods
#5
Andrew D Huang, Chengwei Luo, Angela Pena-Gonzalez, Michael R Weigand, Cheryl Tarr, Konstantinos T Konstantinidis
: Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based, culture-independent approaches such as shotgun metagenomics could sidestep these limitations, and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology...
November 23, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27876765/pre-and-post-weaning-diet-alters-the-faecal-metagenome-in-the-cat-with-differences-vitamin-and-carbohydrate-metabolism-gene-abundances
#6
Wayne Young, Christina D Moon, David G Thomas, Nick J Cave, Emma N Bermingham
Dietary format, and its role in pet nutrition, is of interest to pet food manufacturers and pet owners alike. The aim of the present study was to investigate the effects of pre- and post-weaning diets (kibbled or canned) on the composition and function of faecal microbiota in the domestic cat by shotgun metagenomic sequencing and gene taxonomic and functional assignment using MG-RAST. Post-weaning diet had a dramatic effect on community composition; 147 of the 195 bacterial species identified had significantly different mean relative abundances between kittens fed kibbled and canned diets...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27852235/enrichment-dynamics-of-listeria-monocytogenes-and-the-associated-microbiome-from-naturally-contaminated-ice-cream-linked-to-a-listeriosis-outbreak
#7
Andrea Ottesen, Padmini Ramachandran, Elizabeth Reed, James R White, Nur Hasan, Poorani Subramanian, Gina Ryan, Karen Jarvis, Christopher Grim, Ninalynn Daquiqan, Darcy Hanes, Marc Allard, Rita Colwell, Eric Brown, Yi Chen
BACKGROUND: Microbiota that co-enrich during efforts to recover pathogens from foodborne outbreaks interfere with efficient detection and recovery. Here, dynamics of co-enriching microbiota during recovery of Listeria monocytogenes from naturally contaminated ice cream samples linked to an outbreak are described for three different initial enrichment formulations used by the Food and Drug Administration (FDA), the International Organization of Standardization (ISO), and the United States Department of Agriculture (USDA)...
November 16, 2016: BMC Microbiology
https://www.readbyqxmd.com/read/27822556/impact-of-sample-type-and-dna-isolation-procedure-on-genomic-inference-of-microbiome-composition
#8
Berith E Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank M Aarestrup, Sünje J Pamp
Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822529/thermus-and-the-pink-discoloration-defect-in-cheese
#9
Lisa Quigley, Daniel J O'Sullivan, David Daly, Orla O'Sullivan, Zuzana Burdikova, Rostislav Vana, Tom P Beresford, R Paul Ross, Gerald F Fitzgerald, Paul L H McSweeney, Linda Giblin, Jeremiah J Sheehan, Paul D Cotter
A DNA sequencing-based strategy was applied to study the microbiology of Continental-type cheeses with a pink discoloration defect. The basis for this phenomenon has remained elusive, despite decades of research. The bacterial composition of cheese containing the defect was compared to that of control cheese using 16S rRNA gene and shotgun metagenomic sequencing as well as quantitative PCR (qPCR). Throughout, it was apparent that Thermus, a carotenoid-producing genus, was present at higher levels in defect-associated cheeses than in control cheeses...
May 2016: MSystems
https://www.readbyqxmd.com/read/27822528/urban-transit-system-microbial-communities-differ-by-surface-type-and-interaction-with-humans-and-the-environment
#10
Tiffany Hsu, Regina Joice, Jose Vallarino, Galeb Abu-Ali, Erica M Hartmann, Afrah Shafquat, Casey DuLong, Catherine Baranowski, Dirk Gevers, Jessica L Green, Xochitl C Morgan, John D Spengler, Curtis Huttenhower
Public transit systems are ideal for studying the urban microbiome and interindividual community transfer. In this study, we used 16S amplicon and shotgun metagenomic sequencing to profile microbial communities on multiple transit surfaces across train lines and stations in the Boston metropolitan transit system. The greatest determinant of microbial community structure was the transit surface type. In contrast, little variation was observed between geographically distinct train lines and stations serving different demographics...
May 2016: MSystems
https://www.readbyqxmd.com/read/27818083/shotgun-metagenomics-of-250-adult-twins-reveals-genetic-and-environmental-impacts-on-the-gut-microbiome
#11
Hailiang Xie, Ruijin Guo, Huanzi Zhong, Qiang Feng, Zhou Lan, Bingcai Qin, Kirsten J Ward, Matthew A Jackson, Yan Xia, Xu Chen, Bing Chen, Huihua Xia, Changlu Xu, Fei Li, Xun Xu, Jumana Yousuf Al-Aama, Huanming Yang, Jian Wang, Karsten Kristiansen, Jun Wang, Claire J Steves, Jordana T Bell, Junhua Li, Timothy D Spector, Huijue Jia
The gut microbiota has been typically viewed as an environmental factor for human health. Twins are well suited for investigating the concordance of their gut microbiomes and decomposing genetic and environmental influences. However, existing twin studies utilizing metagenomic shotgun sequencing have included only a few samples. Here, we sequenced fecal samples from 250 adult twins in the TwinsUK registry and constructed a comprehensive gut microbial reference gene catalog. We demonstrate heritability of many microbial taxa and functional modules in the gut microbiome, including those associated with diseases...
November 2, 2016: Cell Systems
https://www.readbyqxmd.com/read/27807621/microbial-community-analysis-of-ph-4-thermal-springs-in-yellowstone-national-park
#12
Xiaoben Jiang, Cristina D Takacs-Vesbach
The pH of the majority of thermal springs in Yellowstone National Park (YNP) is from 1 to 3 and 6 to 10; relatively few springs (~5%) have a pH range of 4-5. We used 16S rRNA gene pyrosequencing to investigate microbial communities sampled from four pH 4 thermal springs collected from four regions of YNP that differed in their fluid temperature and geochemistry. Our results revealed that the composition of bacterial communities varied among the sites, despite sharing similar pH values. The taxonomic composition and metabolic functional potential of the site with the lowest temperature (55 °C), a thermal spring from the Seven Mile Hole (SMH) area, were further investigated using shotgun metagenome sequencing...
November 2, 2016: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/27781166/the-single-species-metagenome-subtyping-staphylococcus-aureus-core-genome-sequences-from-shotgun-metagenomic-data
#13
Sandeep J Joseph, Ben Li, Robert A Petit Iii, Zhaohui S Qin, Lyndsey Darrow, Timothy D Read
In this study we developed a genome-based method for detecting Staphylococcus aureus subtypes from metagenome shotgun sequence data. We used a binomial mixture model and the coverage counts at >100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of 40 subtypes in metagenome samples. We were able to obtain >87% sensitivity and >94% specificity at 0.025X coverage for S. aureus. We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S...
2016: PeerJ
https://www.readbyqxmd.com/read/27773914/diet-dependent-modular-dynamic-interactions-of-the-equine-cecal-microbiota
#14
Camilla Kristoffersen, Rasmus B Jensen, Ekaterina Avershina, Dag Austbø, Anne-Helene Tauson, Knut Rudi
Knowledge on dynamic interactions in microbiota is pivotal for understanding the role of bacteria in the gut. We herein present comprehensive dynamic models of the horse cecal microbiota, which include short-chained fatty acids, carbohydrate metabolic networks, and taxonomy. Dynamic models were derived from time-series data in a crossover experiment in which four cecum-cannulated horses were fed a starch-rich diet of hay supplemented with barley (starch intake 2 g kg(-1) body weight per day) and a fiber-rich diet of only hay...
October 21, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27760854/sequence-based-classification-and-identification-of-fungi
#15
David Hibbett, Kessy Abarenkov, Urmas Koljalg, Maarja Opik, Benli Chai, James R Cole, Qiong Wang, Pedro W Crous, Vincent A R G Robert, Thorunn Helgason, Josh Herr, Paul Kirk, Shiloh Lueschow, Kerry O'Donnell, Henrik Nilsson, Ryoko Oono, Conrad L Schoch, Christopher Smyth, Donny Walker, Andrea Porras-Alfaro, John W Taylor, David M Geiser
Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes...
October 19, 2016: Mycologia
https://www.readbyqxmd.com/read/27760173/filtration-and-normalization-of-sequencing-read-data-in-whole-metagenome-shotgun-samples
#16
Philippe Chouvarine, Lutz Wiehlmann, Patricia Moran Losada, David S DeLuca, Burkhard Tümmler
Ever-increasing affordability of next-generation sequencing makes whole-metagenome sequencing an attractive alternative to traditional 16S rDNA, RFLP, or culturing approaches for the analysis of microbiome samples. The advantage of whole-metagenome sequencing is that it allows direct inference of the metabolic capacity and physiological features of the studied metagenome without reliance on the knowledge of genotypes and phenotypes of the members of the bacterial community. It also makes it possible to overcome problems of 16S rDNA sequencing, such as unknown copy number of the 16S gene and lack of sufficient sequence similarity of the "universal" 16S primers to some of the target 16S genes...
2016: PloS One
https://www.readbyqxmd.com/read/27738970/differential-changes-in-gut-microbiota-after-gastric-bypass-and-sleeve-gastrectomy-bariatric-surgery-vary-according-to-diabetes-remission
#17
Rinki Murphy, Peter Tsai, Mia Jüllig, Amy Liu, Lindsay Plank, Michael Booth
BACKGROUND: It is unclear whether specific gut microbiota is associated with remission of type 2 diabetes (T2D) after distinct types of bariatric surgery. AIMS: The aim of this study is to examine gut microbiota changes after laparoscopic Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG) surgery in obese patients with T2D. METHODS: Whole-metagenome shotgun sequencing of DNA fragments using Illumina HiSeq2000 was obtained from stool samples collected from 14 obese T2D patients pre-operatively (while on very low calorie diet) and 1 year after randomisation to laparoscopic SG (n = 7) or RYGB (n = 7)...
October 13, 2016: Obesity Surgery
https://www.readbyqxmd.com/read/27731934/the-perioperative-lung-transplant-virome-torque-teno-viruses-are-elevated-in-donor-lungs-and-show-divergent-dynamics-in-primary-graft-dysfunction
#18
A A Abbas, J M Diamond, C Chehoud, B Chang, J J Kotzin, J C Young, I Imai, A R Haas, E Cantu, D J Lederer, K Meyer, R K Milewski, K M Olthoff, A Shaked, J D Christie, F D Bushman, R G Collman
Primary graft dysfunction (PGD) is a principal cause of early morbidity and mortality after lung transplantation, but its pathogenic mechanisms are not fully clarified. Thus far, studies using standard clinical assays have not linked microbial factors to PGD. We previously used comprehensive metagenomic methods to characterize viruses in lung allografts >1 month post-transplant and found that levels of Anellovirus, mainly Torque teno viruses (TTV), were significantly higher than in non-transplant healthy controls...
October 12, 2016: American Journal of Transplantation
https://www.readbyqxmd.com/read/27726782/paleomicrobiology-of-human-tuberculosis
#19
Helen D Donoghue
Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections...
August 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/27708392/unique-features-of-ethnic-mongolian-gut-microbiome-revealed-by-metagenomic-analysis
#20
Wenjun Liu, Jiachao Zhang, Chunyan Wu, Shunfeng Cai, Weiqiang Huang, Jing Chen, Xiaoxia Xi, Zebin Liang, Qiangchuan Hou, Bing Zhou, Nan Qin, Heping Zhang
The human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status. Here we characterized 110 healthy Mongolian adults gut microbiota by shotgun metagenomic sequencing and compared the intestinal microbiome among Mongolians, the Hans and European cohorts. The results showed that the taxonomic profile of intestinal microbiome among cohorts revealed the Actinobaceria and Bifidobacterium were the key microbes contributing to the differences among Mongolians, the Hans and Europeans at the phylum level and genus level, respectively...
October 6, 2016: Scientific Reports
keyword
keyword
62282
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"