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Shotgun metagenomics

Raffaella Mastrocola, Ilario Ferrocino, Erica Liberto, Fausto Chiazza, Alessia Sofia Cento, Debora Collotta, Giulia Querio, Debora Nigro, Valeria Bitonto, Juan Carlos Cutrin, Kalliopi Rantsiou, Mariaconcetta Durante, Emanuela Masini, Manuela Aragno, Chiara Cordero, Luca Cocolin, Massimo Collino
Despite clinical findings suggesting that the form (liquid versus solid) of the sugars may significantly affect the development of metabolic diseases, no experimental data are available on the impact of their formulations on gut microbiota, integrity and hepatic outcomes. In the present sudy, C57Bl/6j mice were fed a standard diet plus water (SD), a standard diet plus 60% fructose syrup (L-Fr) or a 60% fructose solid diet plus water (S-Fr) for 12 weeks. Gut microbiota was characterized through 16S rRNA phylogenetic profiling and shotgun sequencing of microbial genes in ileum content and related volatilome profiling...
February 13, 2018: Journal of Nutritional Biochemistry
Morgan Petrovich, Binh Chu, Dorothy Wright, Jim Griffin, Maryam Elfeki, Brian T Murphy, Rachel Poretsky, George Wells
Wastewater treatment plants (WWTPs) are known to harbor antibiotic resistance genes (ARGs) that are disseminated into the environment via effluent. However, few studies have compared abundance, mobilization, and selective pressures for ARGs in WWTPs as a function of variations in secondary treatment bioprocesses. We used shotgun metagenomics to provide a comprehensive analysis of ARG composition, relationship to mobile genetic elements, and co-occurrences with antibiotic production genes (APGs) throughout two full-scale municipal WWTPs, one of which employs biofilm-based secondary treatment and another that uses a suspended growth system...
March 9, 2018: FEMS Microbiology Ecology
Justin Wagner, Florin Chelaru, Jayaram Kancherla, Joseph N Paulson, Alexander Zhang, Victor Felix, Anup Mahurkar, Niklas Elmqvist, Héctor Corrada Bravo
Large studies profiling microbial communities and their association with healthy or disease phenotypes are now commonplace. Processed data from many of these studies are publicly available but significant effort is required for users to effectively organize, explore and integrate it, limiting the utility of these rich data resources. Effective integrative and interactive visual and statistical tools to analyze many metagenomic samples can greatly increase the value of these data for researchers. We present Metaviz, a tool for interactive exploratory data analysis of annotated microbiome taxonomic community profiles derived from marker gene or whole metagenome shotgun sequencing...
February 26, 2018: Nucleic Acids Research
Thomas C Jeffries, Smriti Rayu, Uffe N Nielsen, Kaitao Lai, Ali Ijaz, Loic Nazaries, Brajesh K Singh
Chemical contamination of natural and agricultural habitats is an increasing global problem and a major threat to sustainability and human health. Organophosphorus (OP) compounds are one major class of contaminant and can undergo microbial degradation, however, no studies have applied system-wide ecogenomic tools to investigate OP degradation or use metagenomics to understand the underlying mechanisms of biodegradation in situ and predict degradation potential. Thus, there is a lack of knowledge regarding the functional genes and genomic potential underpinning degradation and community responses to contamination...
2018: Frontiers in Microbiology
Roshonda B Jones, Xiangzhu Zhu, Emili Moan, Harvey J Murff, Reid M Ness, Douglas L Seidner, Shan Sun, Chang Yu, Qi Dai, Anthony A Fodor, M Andrea Azcarate-Peril, Martha J Shrubsole
The purpose of this study is to evaluate similarities and differences in gut bacterial measurements and stability in the microbial communities of three different types of samples that could be used to assess different niches of the gut microbiome: rectal swab, stool, and normal rectal mucosa samples. In swab-stool comparisons, there were substantial taxa differences with some taxa varying largely by sample type (e.g. Thermaceae), inter-individual subject variation (e.g. Desulfovibrionaceae), or by both sample type and participant (e...
March 7, 2018: Scientific Reports
Seungbum Kim, Ruby Goel, Ashok Kumar, Yanfei Qi, Gil Lobaton, Koji Hosaka, Mohammed Mohammed, Eileen M Handberg, Elaine M Richards, Carl J Pepine, Mohan K Raizada
Recent evidence indicates a link between gut pathology and microbiome with hypertension in animal models. However, whether this association exists in humans is unknown. Thus, our objectives in this study were to test the hypotheses that high blood pressure patients have distinct gut microbiomes and that gut epithelial barrier function markers and microbiome composition could predict systolic blood pressure. Fecal samples, analyzed by shotgun metagenomics, displayed taxonomic and functional changes, including altered butyrate production between patients with high blood pressure and reference subjects...
March 5, 2018: Clinical Science (1979-)
Wei Guo, Sudhanshu Mishra, Jiangchao Zhao, Jingsi Tang, Bo Zeng, Fanli Kong, Ruihong Ning, Miao Li, Hengzhi Zhang, Yutian Zeng, Yuanliangzi Tian, Yihang Zhong, Hongdi Luo, Yunhan Liu, Jiandong Yang, Mingyao Yang, Mingwang Zhang, Yan Li, Qingyong Ni, Caiwu Li, Chengdong Wang, Desheng Li, Hemin Zhang, Zhili Zuo, Ying Li
Bamboo-eating giant panda ( Ailuropoda melanoleuca ) is an enigmatic species, which possesses a carnivore-like short and simple gastrointestinal tract (GIT). Despite the remarkable studies on giant panda, its diet adaptability status continues to be a matter of debate. To resolve this puzzle, we investigated the functional potential of the giant panda gut microbiome using shotgun metagenomic sequencing of fecal samples. We also compared our data with similar data from other animal species representing herbivores, carnivores, and omnivores from current and earlier studies...
2018: Frontiers in Microbiology
Noelia Martínez, Roberto Luque, Christian Milani, Marco Ventura, Oscar Bañuelos, Abelardo Margolles
Bifidobacteria are mutualistic intestinal bacteria and their presence in the human gut has been associated with health-promoting activities. The presence of antibiotic resistance genes in this genus is controversial, since, although bifidobacteria are non-pathogenic microorganisms, they could serve as reservoirs of resistance for intestinal pathogens. However, until now, few antibiotic resistance determinants have been functionally characterized in this genus. In this work, we show that Bifidobacterium breve CECT7263 displays atypical resistance to erythromycin and clindamycin...
March 2, 2018: Applied and Environmental Microbiology
Daniel Garrido-Sanz, Javier Manzano, Marta Martín, Miguel Redondo-Nieto, Rafael Rivilla
Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source...
2018: Frontiers in Microbiology
Blanca Vera-Gargallo, Laura Navarro-Sampedro, Modesto Carballo, Antonio Ventosa
Two 454 shotgun metagenomes were sequenced from hypersaline soil samples collected in the Odiel salt marsh area in Huelva, southwestern Spain. Analysis of contigs and 16S rRNA-related sequences showed that Halobacteria , Balneolaeota , and Bacteroidetes were the dominant groups. Rhodothermaeota and Nanohaloarchaeota were also abundant.
March 1, 2018: Genome Announcements
Simone Rampelli, Silvia Turroni
ViromeScan is an innovative metagenomic analysis tool that allows the viral community characterization in terms of taxonomy from raw data of metagenomics sequencing. It efficiently denoises samples from reads of other microorganisms. Users can adopt the same shotgun metagenomic sequencing data to fully characterize complex microbial ecosystems, including bacteria and viruses. Here we apply ViromeScan pipeline to some examples, thus illustrating the processes computed from raw data to the final output.
2018: Methods in Molecular Biology
Gui-Hua Lu, Xiao-Mei Hua, Jing Cheng, Yin-Ling Zhu, Gu-Hao Wang, Yan-Jun Pang, Rong-Wu Yang, Lei Zhang, Huixia Shou, Xiao-Ming Wang, Jinliang Qi, Yong-Hua Yang
Background: The worldwide use of glyphosate has dramatically increased, but also has been raising concern over its impact on mineral nutrition, plant pathogen, and soil microbiota. To date, the bulk of previous studies still have shown different results on the effect of glyphosate application on soil rhizosphere microbial communities. Objective: This study aimed to clarify whether glyphosate has impact on nitrogen-fixation, pathogen or disease suppression, and rhizosphere microbial community of a soybean EPSPS-transgenic line ZUTS31 in one growth season...
January 2018: Current Genomics
Clarisse A Marotz, Jon G Sanders, Cristal Zuniga, Livia S Zaramela, Rob Knight, Karsten Zengler
BACKGROUND: Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencing approaches that assess taxonomy but not function and are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in microbial populations because few DNA sequence reads are from the microbial component. We developed and optimized a novel method for enriching microbial DNA from human oral samples and compared its efficiency and potential taxonomic bias with commercially available kits...
February 27, 2018: Microbiome
Raja Duraisamy, Jean Akiana, Bernard Davoust, Oleg Mediannikov, Caroline Michelle, Catherine Robert, Henri-Joseph Parra, Didier Raoult, Philippe Biagini, Christelle Desnues
Most of the emerging infectious diseases reported so far originated in wildlife. Therefore, virological surveillance of animals and particularly great apes is of great interest to establish the repertory of viruses associated with healthy hosts. This will further help to identify the emergence of new viruses and predict the possibility of interspecies transmission. In this study, we performed shotgun viral metagenomics on stool samples collected from seventeen free-living wild gorillas from the Republic of the Congo...
February 23, 2018: Virus Genes
Marc W Van Goethem, Rian Pierneef, Oliver K I Bezuidt, Yves Van De Peer, Don A Cowan, Thulani P Makhalanyane
BACKGROUND: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. METHODS: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region...
February 23, 2018: Microbiome
Federica Gigliucci, F A Bastiaan von Meijenfeldt, Arnold Knijn, Valeria Michelacci, Gaia Scavia, Fabio Minelli, Bas E Dutilh, Hamideh M Ahmad, Gerwin C Raangs, Alex W Friedrich, John W A Rossen, Stefano Morabito
The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E...
2018: Frontiers in Cellular and Infection Microbiology
Jincheng Wang, Lili Tang, Hongyuan Zhou, Jun Zhou, Travis C Glenn, Chwan-Li Shen, Jia-Sheng Wang
Green tea polyphenols (GTP) have been shown to exert a spectrum of health benefits to animals and humans. It is plausible that the beneficial effects of GTP are a result of its interaction with the gut microbiota. This study evaluated the effect of long-term treatment with GTP on the gut microbiota of experimental rats and the potential linkage between changes of the gut microbiota with the beneficial effects of GTP. Six-month-old Sprague-Dawley rats were randomly allocated into three dosing regimens (0, 0...
January 31, 2018: Journal of Nutritional Biochemistry
Erick Cardenas, Luis H Orellana, Konstantinos T Konstantinidis, William W Mohn
Forest ecosystems are critical to global biogeochemical cycles but under pressure from harvesting and climate change. We investigated the effects of organic matter (OM) removal during forest harvesting on the genetic potential of soil communities for biomass decomposition and nitrogen cycling in five ecozones across North America. We analyzed 107 samples, representing four treatments with varied levels of OM removal, at Long-Term Soil Productivity Study sites. Samples were collected more than ten years after harvesting and replanting and were analyzed via shotgun metagenomics...
February 16, 2018: Scientific Reports
Paul D Donovan, Gabriel Gonzalez, Desmond G Higgins, Geraldine Butler, Kimihito Ito
Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets...
2018: PloS One
Vicente Pérez-Brocal, Andrés Moya
We have analysed oral wash samples from 72 healthy young adults in Valencia (Spain) for a metagenomic analysis through the construction of shotgun libraries and high-throughput-sequencing. The oral viral communities have been taxonomically characterised as well as and the gene content from the latter. The majority of viruses are found in few individuals, with single occurrences being the most widespread ones, whereas universally distributed viruses, while present, are relatively rare, with bacteriophages from families Siphoviridae and Myoviridae, and Streptococcus phages, as well as the eukaryotic viral family Herpesviridae amongst the most widespread viruses...
2018: PloS One
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