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Shotgun metagenomics

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https://www.readbyqxmd.com/read/29790949/fecal-microbiota-composition-changes-after-a-body-weight-loss-diet-in-beagle-dogs
#1
A Salas, I Jeusette, I Castillo, C L Manuelian, C Lionnet, N Iraculis, N Sanchez, S Fernández, L L Vilaseca, C Torre
In developed countries, dogs and cats frequently suffer from obesity. Recently, gut microbiota composition in humans has been related to obesity and metabolic diseases. This study aimed to evaluate changes in body composition, and gut microbiota composition in obese Beagle dogs after a 17-week body weight (BW) loss program. A total of six neutered adult Beagle dogs with an average initial BW of 16.34 ± 1.52 kg and BCS of 7.8 ± 0.1 points (9-point scale) were restrictedly fed with a hypocaloric, low-fat and high-fiber dry-type diet...
May 22, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29788417/poor-feed-efficiency-in-sheep-is-associated-with-several-structural-abnormalities-in-the-community-metabolic-network-of-their-ruminal-microbes
#2
Rocky D Patil, Melinda J Ellison, Sara M Wolff, Courtney Shearer, Anna M Wright, Rebecca R Cockrum, Kathy J Austin, William R Lamberson, Kristi M Cammack, Gavin C Conant
Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not...
May 18, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29769358/resolving-the-phylogenetic-position-of-darwin-s-extinct-ground-sloth-mylodon-darwinii-using-mitogenomic-and-nuclear-exon-data
#3
Frédéric Delsuc, Melanie Kuch, Gillian C Gibb, Jonathan Hughes, Paul Szpak, John Southon, Jacob Enk, Ana T Duggan, Hendrik N Poinar
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12 880-year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient subfossil, probably the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra...
May 16, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29768437/oral-health-status-in-historic-population-macroscopic-and-metagenomic-evidence
#4
Claire Willmann, Xavier Mata, Kristian Hanghoej, Laure Tonasso, Lenka Tisseyre, Céline Jeziorski, Elodie Cabot, Pierre Chevet, Eric Crubézy, Ludovic Orlando, Rémi Esclassan, Catherine Thèves
Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked...
2018: PloS One
https://www.readbyqxmd.com/read/29753103/genetic-diversity-of-human-sapovirus-across-the-americas
#5
Marta Diez-Valcarce, Christina J Castro, Rachel L Marine, Natasha Halasa, Holger Mayta, Mayuko Saito, Laura Tsaknaridis, Chao-Yang Pan, Filemon Bucardo, Sylvia Becker-Dreps, Maria Renee Lopez, Laura Cristal Magaña, Terry Fei Fan Ng, Jan Vinjé
BACKGROUND: Sapoviruses are responsible for sporadic and epidemic acute gastroenteritis worldwide. Sapovirus typing protocols have a success rate as low as 43% and relatively few complete sapovirus genome sequences are available to improve current typing protocols. OBJECTIVE/STUDY DESIGN: To increase the number of complete sapovirus genomes to better understand the molecular epidemiology of human sapovirus and to improve the success rate of current sapovirus typing methods, we used deep metagenomics shotgun sequencing to obtain the complete genomes of 68 sapovirus samples from four different countries across the Americas (Guatemala, Nicaragua, Peru and the US)...
May 6, 2018: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/29743119/profiling-microbial-strains-in-urban-environments-using-metagenomic-sequencing-data
#6
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/29742642/successful-brincidofovir-treatment-of-metagenomics-detected-adenovirus-infection-in-a-severely-ill-stat1-deficient-patient
#7
Diana Averbuch, Rifaat Safadi, Daniel Dar, Dana Wolf, Meir Cherniak, Rotem Sorek, Sharon Amit
A STAT1-deficient patient presented with prolonged fever, cachexia, anemia, hypoalbuminemia and finally relapsing debilitating mycobacterial osteomyelitis while receiving a previously effective antimycobacterial treatment. Progression despite rigorous workup and multiple antibiotics prompted shotgun metagenomics revealing adenovirus in liver samples. Brincidofovir led to a complete, sustained clinical recovery, including of osteomyelitis, probably attributed to reversal of adenovirus-induced immune dysregulation...
May 4, 2018: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/29741366/metagenomic-characterization-of-antibiotic-resistance-genes-in-full-scale-reclaimed-water-distribution-systems-and-corresponding-potable-systems
#8
Emily Garner, Chaoqi Chen, Kang Xia, Jolene Bowers, David Engelthaler, Jean McLain, Marc A Edwards, Amy Pruden
Water reclamation provides a valuable resource for meeting non-potable water demands. However, little is known about the potential for wastewater reuse to disseminate antibiotic resistance genes (ARGs). Here, samples were collected seasonally in 2014-2015 from four U.S. utilities' reclaimed and potable water distribution systems before treatment, after treatment, and at five points of use (POU). Shotgun metagenomic sequencing was used to profile the resistome (i.e., full contingent of ARGs) of a subset (n=38) of samples...
May 9, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29732327/microbiological-profile-of-chicken-carcasses-a-comparative-analysis-using-shotgun-metagenomic-sequencing
#9
Alessandra De Cesare, Federica Palma, Alex Lucchi, Frederique Pasquali, Gerardo Manfreda
In the last few years metagenomic and 16S rRNA sequencing have completly changed the microbiological investigations of food products. In this preliminary study, the microbiological profile of chicken carcasses collected from animals fed with different diets were tested by using shotgun metagenomic sequencing. A total of 15 carcasses have been collected at the slaughetrhouse at the end of the refrigeration tunnel from chickens reared for 35 days and fed with a control diet (n=5), a diet supplemented with 1500 FTU/kg of commercial phytase (n=5) and a diet supplemented with 1500 FTU/kg of commercial phytase and 3g/kg of inositol (n=5)...
March 31, 2018: Italian Journal of Food Safety
https://www.readbyqxmd.com/read/29732264/algorithms-and-strategies-in-short-read-shotgun-metagenomic-reconstruction-of-plant-communities
#10
Robert S Harbert
Premise of the Study: DNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants. Methods: To establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants...
March 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29728379/effects-of-ceftiofur-and-chlortetracycline-on-the-resistome-of-feedlot-cattle
#11
Margaret D Weinroth, H Morgan Scott, Bo Norby, Guy H Loneragan, Noelle R Noyes, Pablo Rovira, Enrique Doster, Xiang Yang, Dale R Woerner, Paul S Morley, Keith E Belk
Treatment of food producing animals with antimicrobial drugs (AMD) is controversial because of concerns regarding promotion of antimicrobial resistance (AMR). To investigate this concern, resistance genes in metagenomic bovine fecal samples during a clinical trial were analyzed to assess the impacts of treatment on beef feedlot cattle resistomes. Four groups of cattle were exposed, using a 2x2 factorial design, to different regimens of antimicrobial treatment. Injections of ceftiofur crystalline free acid (a third generation cephalosporin) were used to treat all cattle in treated pens vs...
May 4, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29727057/raman-activated-cell-sorting-and-metagenomic-sequencing-revealing-carbon-fixing-bacteria-in-the-ocean
#12
Xiaoyan Jing, Honglei Gou, Yanhai Gong, Xiaolu Su, La Xu, Yuetong Ji, Yizhi Song, Ian P Thompson, Jian Xu, Wei E Huang
It is of great significance to understand CO2 fixation in the oceans. Using single cell Raman spectra (SCRS) as biochemical profiles, Raman activated cell ejection (RACE) was able to link phenotypes and genotypes of cells. Here we show that mini-metagenomic sequences from RACE can be used as a reference to reconstruct nearly complete genomes of key functional bacteria by binning shotgun metagenomic sequencing data. By applying this approach to 13 C-bicarbonate spiked seawater from euphotic zone of the Yellow Sea of China, the dominant bacteria Synechococcus spp...
May 4, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29718191/metacompare-a-computational-pipeline-for-prioritizing-environmental-resistome-risk
#13
Min Oh, Amy Pruden, Chaoqi Chen, Lenwood S Heath, Kang Xia, Liqing Zhang
The spread of antibiotic resistance is a growing public health concern. While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means of comparing and prioritizing risks represented by various environmental compartments is lacking. Here we introduce MetaCompare, a publicly-available tool for ranking 'resistome risk,' which we define as the potential for antibiotic resistance genes (ARGs) to be associated with mobile genetic elements (MGEs) and mobilize to pathogens based on metagenomic data...
April 26, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29709640/metagenome-based-diversity-analyses-suggest-a-strong-locality-signal-for-bacterial-communities-associated-with-oyster-aquaculture-farms-in-ofunato-bay
#14
Atsushi Kobiyama, Kazuho Ikeo, Md Shaheed Reza, Jonaira Rashid, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda, Nanami Mizusawa, Shigeru Sato, Takehiko Ogata, Mitsuru Jimbo, Toshiaki Kudo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Katsuhiko Mineta, Vladimir Bajic, Takashi Gojobori, Shugo Watabe
Ofunato Bay, in Japan, is the home of buoy-and-rope-type oyster aquaculture activities. Since the oysters filter suspended materials and excrete organic matter into the seawater, bacterial communities residing in its vicinity may show dynamic changes depending on the oyster culture activities. We employed a shotgun metagenomic technique to study bacterial communities near oyster aquaculture facilities at the center of the bay (KSt. 2) and compared the results with those of two other localities far from the station, one to the northeast (innermost bay, KSt...
April 27, 2018: Gene
https://www.readbyqxmd.com/read/29709637/seasonal-changes-in-the-communities-of-photosynthetic-picoeukaryotes-in-ofunato-bay-as-revealed-by-shotgun-metagenomic-sequencing
#15
Jonaira Rashid, Atsushi Kobiyama, Md Shaheed Reza, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda, Nanami Mizusawa, Kazuho Ikeo, Shigeru Sato, Takehiko Ogata, Toshiaki Kudo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Katsuhiko Mineta, Vladimir Bajic, Takashi Gojobori, Shugo Watabe
Small photosynthetic eukaryotes play important roles in oceanic food webs in coastal regions. We investigated seasonal changes in the communities of photosynthetic picoeukaryotes (PPEs) of the class Mamiellophyceae, including the genera Bathycoccus, Micromonas and Ostreococcus, in Ofunato Bay, which is located in northeastern Japan and faces the Pacific Ocean. The abundances of PPEs were assessed over a period of one year in 2015 at three sampling stations, KSt. 1 (innermost bay area), KSt. 2 (middle bay area) and KSt...
April 27, 2018: Gene
https://www.readbyqxmd.com/read/29705728/understanding-the-gut-kidney-axis-in-nephrolithiasis-an-analysis-of-the-gut-microbiota-composition-and-functionality-of-stone-formers
#16
Andrea Ticinesi, Christian Milani, Angela Guerra, Franca Allegri, Fulvio Lauretani, Antonio Nouvenne, Leonardo Mancabelli, Gabriele Andrea Lugli, Francesca Turroni, Sabrina Duranti, Marta Mangifesta, Alice Viappiani, Chiara Ferrario, Rossella Dodi, Margherita Dall'Asta, Daniele Del Rio, Marco Ventura, Tiziana Meschi
OBJECTIVES: The involvement of the gut microbiota in the pathogenesis of calcium nephrolithiasis has been hypothesised since the discovery of the oxalate-degrading activity of Oxalobacter formigenes , but never comprehensively studied with metagenomics. The aim of this case-control study was to compare the faecal microbiota composition and functionality between recurrent idiopathic calcium stone formers (SFs) and controls. DESIGN: Faecal samples were collected from 52 SFs and 48 controls (mean age 48±11)...
April 28, 2018: Gut
https://www.readbyqxmd.com/read/29705130/seasonal-changes-in-the-abundance-of-bacterial-genes-related-to-dimethylsulfoniopropionate-catabolism-in-seawater-from-ofunato-bay-revealed-by-metagenomic-analysis
#17
Toshiaki Kudo, Atsushi Kobiyama, Jonaira Rashid, Shaheed Reza, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda, Nanami Mizusawa, Kazuho Ikeo, Shigeru Sato, Takehiko Ogata, Mitsuru Jimbo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Satoshi Segawa, Katsuhiko Mineta, Vladimir Bajic, Takashi Gojobori, Shugo Watabe
Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH)...
April 26, 2018: Gene
https://www.readbyqxmd.com/read/29705129/basin-scale-seasonal-changes-in-marine-free-living-bacterioplankton-community-in-the-ofunato-bay
#18
Md Shaheed Reza, Atsushi Kobiyama, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda, Nanami Mizusawa, Kazuho Ikeo, Shigeru Sato, Takehiko Ogata, Mitsuru Jimbo, Toshiaki Kudo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Katsuhiko Mineta, Vladimir Bajic, Takashi Gojobori, Shugo Watabe
The Ofunato Bay in the northeastern Pacific Ocean area of Japan possesses the highest biodiversity of marine organisms in the world and has attracted much attention due to its economic and environmental importance. We report here a shotgun metagenomic analysis of the year-round variation in free-living bacterioplankton collected across the entire length of the bay. Phylogenetic differences among spring, summer, autumn and winter bacterioplankton suggested that members of Proteobacteria tended to decrease at high water temperatures and increase at low temperatures...
April 26, 2018: Gene
https://www.readbyqxmd.com/read/29704804/selective-concentration-for-ciprofloxacin-resistance-in-escherichia-coli-grown-in-complex-aquatic-bacterial-biofilms
#19
Nadine Kraupner, Stefan Ebmeyer, Johan Bengtsson-Palme, Jerker Fick, Erik Kristiansson, Carl-Fredrik Flach, D G Joakim Larsson
There is concern that antibiotics in the environment can select for and enrich bacteria carrying acquired antibiotic resistance genes, thus increasing the potential of those genes to emerge in a clinical context. A critical question for understanding and managing such risks is what levels of antibiotics are needed to select for resistance in complex bacterial communities. Here, we address this question by examining the phenotypic and genotypic profiles of aquatic communities exposed to ciprofloxacin, also evaluating the within-species selection of resistant E...
April 25, 2018: Environment International
https://www.readbyqxmd.com/read/29691633/emdunifrac-exact-linear-time-computation-of-the-unifrac-metric-and-identification-of-differentially-abundant-organisms
#20
Jason McClelland, David Koslicki
Both the weighted and unweighted UniFrac distances have been very successfully employed to assess if two communities differ, but do not give any information about how two communities differ. We take advantage of recent observations that the UniFrac metric is equivalent to the so-called earth mover's distance (also known as the Kantorovich-Rubinstein metric) to develop an algorithm that not only computes the UniFrac distance in linear time and space, but also simultaneously finds which operational taxonomic units are responsible for the observed differences between samples...
April 25, 2018: Journal of Mathematical Biology
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