keyword
MENU ▼
Read by QxMD icon Read
search

Shotgun metagenomics

keyword
https://www.readbyqxmd.com/read/29141885/a-role-for-bacterial-urease-in-gut-dysbiosis-and-crohn-s-disease
#1
Josephine Ni, Ting-Chin David Shen, Eric Z Chen, Kyle Bittinger, Aubrey Bailey, Manuela Roggiani, Alexandra Sirota-Madi, Elliot S Friedman, Lillian Chau, Andrew Lin, Ilana Nissim, Justin Scott, Abigail Lauder, Christopher Hoffmann, Gloriany Rivas, Lindsey Albenberg, Robert N Baldassano, Jonathan Braun, Ramnik J Xavier, Clary B Clish, Marc Yudkoff, Hongzhe Li, Mark Goulian, Frederic D Bushman, James D Lewis, Gary D Wu
Gut dysbiosis during inflammatory bowel disease involves alterations in the gut microbiota associated with inflammation of the host gut. We used a combination of shotgun metagenomic sequencing and metabolomics to analyze fecal samples from pediatric patients with Crohn's disease and found an association between disease severity, gut dysbiosis, and bacterial production of free amino acids. Nitrogen flux studies using (15)N in mice showed that activity of bacterial urease, an enzyme that releases ammonia by hydrolysis of host urea, led to the transfer of murine host-derived nitrogen to the gut microbiota where it was used for amino acid synthesis...
November 15, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/29123512/alternative-growth-promoters-modulate-broiler-gut-microbiome-and-enhance-body-weight-gain
#2
Serajus Salaheen, Seon-Woo Kim, Bradd J Haley, Jo Ann S Van Kessel, Debabrata Biswas
Antibiotic growth promoters (AGPs) are frequently used to enhance weight-gain in poultry production. However, there has been increasing concern over the impact of AGP on the emergence of antibiotic resistance in zoonotic bacterial pathogens in the microbial community of the poultry gut. In this study, we adopted mass-spectrophotometric, phylogenetic, and shotgun-metagenomic approaches to evaluate bioactive phenolic extracts (BPE) from blueberry (Vaccinium corymbosum) and blackberry (Rubus fruticosus) pomaces as AGP alternatives in broilers...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29112136/gut-microbiome-and-putative-resistome-of-inca-and-italian-nobility-mummies
#3
Tasha M Santiago-Rodriguez, Gino Fornaciari, Stefania Luciani, Gary A Toranzos, Isolina Marota, Valentina Giuffra, Raul J Cano
Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacterial diversity as compared to the Inca mummies when using 16S ribosomal (rRNA) gene amplicon sequencing, but both groups showed bacterial and fungal taxa when using shotgun metagenomic sequencing that may resemble both the thanatomicrobiome and extant human gut microbiomes...
November 7, 2017: Genes
https://www.readbyqxmd.com/read/29104938/vitamin-and-amino-acid-auxotrophy-in-anaerobic-consortia-operating-under-methanogenic-conditions
#4
Valerie Hubalek, Moritz Buck, BoonFei Tan, Julia Foght, Annelie Wendeberg, David Berry, Stefan Bertilsson, Alexander Eiler
Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions...
September 2017: MSystems
https://www.readbyqxmd.com/read/29101194/year-round-shotgun-metagenomes-reveal-stable-microbial-communities-in-agricultural-soils-and-novel-ammonia-oxidizers-responding-to-fertilization
#5
Luis H Orellana, Joanne C Chee-Sanford, Robert A Sanford, Frank E Löffler, Konstantinos T Konstantinidis
The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for better understanding nutrient cycling. Here, we analyzed 20 short-read metagenomes collected at four time points across one year from two depths (0-5 and 20-30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty-loam), with similar cropping histories. Although microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural water-based ecosystems...
November 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29097759/sequencing-genomes-from-mixed-dna-samples-evaluating-the-metagenome-skimming-approach-in-lichenized-fungi
#6
Anjuli Meiser, Jürgen Otte, Imke Schmitt, Francesco Dal Grande
The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi...
November 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29097220/the-organophosphate-malathion-disturbs-gut-microbiome-development-and-the-quorum-sensing-system
#7
Bei Gao, Liang Chi, Pengcheng Tu, Xiaoming Bian, Jesse Thomas, Hongyu Ru, Kun Lu
The gut microbiome has tremendous potential to impact health and disease. Various environmental toxicants, including insecticides, have been shown to alter gut microbiome community structures. However, the mechanism that compositionally and functionally regulates gut microbiota remains unclear. Quorum sensing is known to modulate intra- and interspecies gene expression and coordinate population responses. It is unknown whether quorum sensing is disrupted when environmental toxicants cause perturbations in the gut microbiome community structure...
October 30, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/29096601/optimisation-of-16s-rrna-gut-microbiota-profiling-of-extremely-low-birth-weight-infants
#8
Cristina Alcon-Giner, Shabhonam Caim, Suparna Mitra, Jennifer Ketskemety, Udo Wegmann, John Wain, Gusztav Belteki, Paul Clarke, Lindsay J Hall
BACKGROUND: Infants born prematurely, particularly extremely low birth weight infants (ELBW) have altered gut microbial communities. Factors such as maternal health, gut immaturity, delivery mode, and antibiotic treatments are associated with microbiota disturbances, and are linked to an increased risk of certain diseases such as necrotising enterocolitis. Therefore, there is a requirement to optimally characterise microbial profiles in this at-risk cohort, via standardisation of methods, particularly for studying the influence of microbiota therapies (e...
November 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29092015/metacherchant-analyzing-genomic-context-of-antibiotic-resistance-genes-in-gut-microbiota
#9
Evgenii I Olekhnovich, Artem T Vasilyev, Vladimir I Ulyantsev, Elena S Kostryukova, Alexander V Tyakht
Motivation: Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens. Results: We developed MetaCherchant - an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph...
October 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29065388/targeted-sequencing-of-clade-specific-markers-from-skin-microbiomes-for-forensic-human-identification
#10
Sarah E Schmedes, August E Woerner, Nicole M M Novroski, Frank R Wendt, Jonathan L King, Kathryn M Stephens, Bruce Budowle
The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals...
October 18, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29053714/atopic-asthmatic-immune-phenotypes-associated-with-airway-microbiota-and-airway-obstruction
#11
Benjamin A Turturice, Halvor S McGee, Brian Oliver, Melissa Baraket, Brian T Nguyen, Christian Ascoli, Ravi Ranjan, Asha Rani, David L Perkins, Patricia W Finn
BACKGROUND: Differences in asthma severity may be related to inflammation in the airways. The lower airway microbiota has been associated with clinical features such as airway obstruction, symptom control, and response to corticosteroids. OBJECTIVE: To assess the relationship between local airway inflammation, severity of disease, and the lower airway microbiota in atopic asthmatics. METHODS: A cohort of young adult, atopic asthmatics with intermittent or mild/moderate persistent symptoms (n = 13) were assessed via bronchoscopy, lavage, and spirometry...
2017: PloS One
https://www.readbyqxmd.com/read/29049378/immune-modulatory-genomic-properties-differentiate-gut-microbiota-of-infants-with-and-without-eczema
#12
Seungdae Oh, Gaik Chin Yap, Pei-Ying Hong, Chiung-Hui Huang, Marion M Aw, Lynette Pei-Chi Shek, Wen-Tso Liu, Bee Wah Lee
Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months...
2017: PloS One
https://www.readbyqxmd.com/read/29041989/links-of-gut-microbiota-composition-with-alcohol-dependence-syndrome-and-alcoholic-liver-disease
#13
Veronika B Dubinkina, Alexander V Tyakht, 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 Krupitsky, 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
BACKGROUND: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29041965/enrichment-allows-identification-of-diverse-rare-elements-in-metagenomic-resistome-virulome-sequencing
#14
Noelle R Noyes, Maggie E Weinroth, Jennifer K Parker, Chris J Dean, Steven M Lakin, Robert A Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N Martin, Kenneth L Jones, Jaime Ruiz, Christina A Boucher, Keith E Belk, Paul S Morley
BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28989277/a-metagenomic-analysis-of-bacterial-microbiota-in-the-digestive-tract-of-triatomines
#15
Nicolas Carels, Marcial Gumiel, Fabio Faria da Mota, Carlos José de Carvalho Moreira, Patricia Azambuja
The digestive tract of triatomines (DTT) is an ecological niche favored by microbiota whose enzymatic profile is adapted to the specific substrate availability in this medium. This report describes the molecular enzymatic properties that promote bacterial prominence in the DTT. The microbiota composition was assessed previously based on 16S ribosomal DNA, and whole sequenced genomes of bacteria from the same genera were used to calculate the GC level of rare and prominent bacterial species in the DTT. The enzymatic reactions encoded by coding sequences of both rare and common bacterial species were then compared and revealed key functions explaining why some genera outcompete others in the DTT...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28969654/viral-metagenomics-of-aphids-present-in-bean-and-maize-plots-on-mixed-use-farms-in-kenya-reveals-the-presence-of-three-dicistroviruses-including-a-novel-big-sioux-river-virus-like-dicistrovirus
#16
Francis O Wamonje, George N Michuki, Luke A Braidwood, Joyce N Njuguna, J Musembi Mutuku, Appolinaire Djikeng, Jagger J W Harvey, John P Carr
BACKGROUND: Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farmers to provide fixed nitrogen for cultivation of starch crops such as maize. We used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples...
October 2, 2017: Virology Journal
https://www.readbyqxmd.com/read/28962671/tools-for-metagenomic-analysis-at-wastewater-treatment-plants-application-to-a-foaming-episode
#17
(no author information available yet)
Metagenomic analysis is a powerful approach for wholesale characterizations of microbial populations like those that operate within municipal wastewater treatment plant. It is well-known that many problems are associated with the overgrowth or undergrowth of specific bacterial genera. We describe a database of the combined metagenomes of activated sludge aeration basins from around the globe and use it as a reference to study the population of a foamy activated sludge aeration basin. We show that foam production is associated with blooms of mycolic acid producing genera, especially Mycobacterium...
September 29, 2017: Water Environment Research: a Research Publication of the Water Environment Federation
https://www.readbyqxmd.com/read/28961809/soil-microbial-community-dynamics-and-assembly-under-long-term-land-use-change
#18
Dennis Goss-Souza, Lucas William Mendes, Clovis Daniel Borges, Dilmar Baretta, Siu Mui Tsai, Jorge L M Rodrigues
We evaluated the bacterial and archaeal community dynamics and assembly in soils under forest, grassland and no-till cropping, using a high-throughput shotgun metagenomics approach. No significant alterations in alpha diversity were observed among different land uses, but beta diversity in grassland was lower than that observed in forest and no-till soils. Grassland communities showed assembly that predominantly followed the neutral model, i.e. high homogenizing selection with moderate dispersion, leading to biotic homogenization...
October 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28961782/metacache-context-aware-classification-of-metagenomic-reads-using-minhashing
#19
André Müller, Christian Hundt, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
Motivation: Metagenomic shotgun sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification, i.e., the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes corresponding software tools suffer from either long runtimes, large memory requirements, or low accuracy...
August 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28959368/a-model-based-approach-for-species-abundance-quantification-based-on-shotgun-metagenomic-data
#20
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
keyword
keyword
72454
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"