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Byunghan Lee, Hyeyoung Min, Sungroh Yoon
Motivation: Metagenomic sequencing has become a crucial tool for obtaining a gene catalogue of operational taxonomic units (OTUs) in a microbial community. A typical metagenomic sequencing produces a large amount of data (often in the order of terabytes or more), and computational tools are indispensable for efficient processing. In particular, error correction in metagenomics is crucial for accurate and robust genetic cataloging of microbial communities. However, many existing error-correction tools take a prohibitively long time and often bottleneck the whole analysis pipeline...
February 20, 2018: Bioinformatics
Tao Lu, Mingjing Ke, W J G M Peijnenburg, Youchao Zhu, Meng Zhang, Liwei Sun, Zhengwei Fu, Haifeng Qian
The plant rhizosphere microbiota plays multiple roles in plant growth. We investigated the taxonomic and functional variations in the rhizosphere microbial community, examining both prokaryotes and eukaryotes, of four crops at the seedling stage: wheat, barley and two rice varieties (indica and japonica) seeded in paddy soil. The diversity of rhizosphere communities in these four species were determined. Results showed that wheat and barley had much stronger selection effects than rice for the rhizosphere microbial community...
February 23, 2018: Journal of Agricultural and Food Chemistry
Jaison H Cuartas, Juan F Alzate, Claudia X Moreno-Herrera, Edna J Marquez
The endangered marine gastropod, Lobatus gigas, is an important fishery resource in the Caribbean region. Microbiological and parasitological research of this species have been poorly addressed despite its role in ecological fitness, conservation status and prevention of potential pathogenic infections. This study identified taxonomic groups associated with orange colored protrusions in the muscle of queen conchs using histological analysis, 454 pyrosequencing, and a combination of PCR amplification and automated Sanger sequencing...
2018: PeerJ
Vasim Ahmed, Manoj K Verma, Shashank Gupta, Vibha Mandhan, Nar S Chauhan
Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation...
2018: Frontiers in Microbiology
Neslihan Taş, Emmanuel Prestat, Shi Wang, Yuxin Wu, Craig Ulrich, Timothy Kneafsey, Susannah G Tringe, Margaret S Torn, Susan S Hubbard, Janet K Jansson
In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost...
February 22, 2018: Nature Communications
Anna-Louise Reysenbach, John A Donaho, Todd M Hinsch, John F Kelley, Kathleen Kouba, Mircea Podar, Matthew B Stott
A draft genome of a new Thermofilum sp. strain was obtained from an enrichment culture metagenome. Like its relatives, Thermofilum sp. strain NZ13 is adapted to organic-rich thermal environments and has to depend on other organisms and the environment for some key amino acids, purines, and cofactors.
February 22, 2018: Genome Announcements
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
A F C Leonard, X L Yin, T Zhang, M Hui, W H Gaze
Background: Antimicrobial resistance and the spread of antibiotic resistance genes (ARGs) poses a threat to human health. Community-acquired infections resistant to treatment with first-line antibiotics are increasing, and there are few studies investigating environmental exposures and transmission. Aim: To develop a novel targeted metagenomic method to quantify the abundance and diversity of ARGs in a faecal indicator bacterium, and to estimate human exposure to resistant bacteria in a natural environment...
February 19, 2018: FEMS Microbiology Ecology
A Lawan, F F A Jesse, U H Idris, M N Odhah, M Arsalan, N A Muhammad, K R Bhutto, Innocent Damudu Peter, G A Abraham, A H Wahid, M L Mohd-Azmi, M Zamri-Saad
Innumerable Escherichia coli of animal origin are identified, which are of economic significance, likewise, cattle, sheep and goats are the carrier of enterohaemorrhagic E. coli, which are less pathogenic, and can spread to people by way of direct contact and through the contamination of foodstuff or portable drinking water, causing serious illness. The immunization of ruminants has been carried out for ages and is largely acknowledged as the most economical and maintainable process of monitoring E. coli infection in ruminants...
February 19, 2018: Microbial Pathogenesis
Daniel F R Cleary, Ana R M Polónia, Nicole J de Voogd
Marine lakes are small bodies of landlocked seawater that are isolated from the open sea and have been shown to house numerous rare and unique taxa. The environmental conditions of the lakes are also characterised by lower pH and salinity and higher temperatures than generally found in the open sea. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach and a predictive metagenomic approach (PICRUSt) to examine bacterial composition and function in three distinct biotopes (sediment, water and the sponge species Biemna fortis) in three habitats (two marine lakes and the open sea) of the Berau reef system, Indonesia...
February 22, 2018: Microbial Ecology
M T Fountain, J Bennett, M Cobo-Medina, R Conde Ruiz, G Deakin, A Delgado, R Harrison, N Harrison
Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a damaging pest of fruit. Reproductively diapausing adults overwinter in woodlands and remain active on warmer winter days. It is unknown if this adult phase of the lifecycle feeds during the winter period, and what the food source may be. This study characterized the flora in the digestive tract of D. suzukii using a metagenomics approach. Live D. suzukii were trapped in four woodlands in the south of England and their guts dissected for DNA extraction and amplicon-based metagenomics sequencing (internal transcribed spacer and 16S rRNA)...
February 22, 2018: Insect Molecular Biology
Ping Lu, Xinwei Gao, Hao Dong, Zhen Liu, Francesco Secundo, Changhu Xue, Xiangzhao Mao
Astaxanthin is a pigment with various functions. Free astaxanthin is obtained mainly through saponification methods, which could result in many by-products. Enzymatic methods using lipases have been used in few cases, while there are no reports on the use of esterases for the production of free astaxanthin. Herein we present the screening and identification of a novel esterase (Est3-14) from a marine mud metagenomic library. Est3-14 is pH-sensitive and keeps good stability in akaline buffers (residual activity 94%, pH 8...
February 22, 2018: Journal of Agricultural and Food Chemistry
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
Mitsuhiro Yoshida, Tomohiro Mochizuki, Syun-Ichi Urayama, Yukari Yoshida-Takashima, Shinro Nishi, Miho Hirai, Hidetaka Nomaki, Yoshihiro Takaki, Takuro Nunoura, Ken Takai
Previous studies on marine environmental virology have primarily focused on double-stranded DNA (dsDNA) viruses; however, it has recently been suggested that single-stranded DNA (ssDNA) viruses are more abundant in marine ecosystems. In this study, we performed a quantitative viral community DNA analysis to estimate the relative abundance and composition of both ssDNA and dsDNA viruses in offshore upper bathyal sediment from Tohoku, Japan (water depth = 500 m). The estimated dsDNA viral abundance ranged from 3 × 106 to 5 × 106 genome copies per cm3 sediment, showing values similar to the range of fluorescence-based direct virus counts...
2018: Frontiers in Microbiology
Jacob H Munson-McGee, Shengyun Peng, Samantha Dewerff, Ramunas Stepanauskas, Rachel J Whitaker, Joshua S Weitz, Mark J Young
The application of viral and cellular metagenomics to natural environments has expanded our understanding of the structure, functioning, and diversity of microbial and viral communities. The high diversity of many communities, e.g., soils, surface ocean waters, and animal-associated microbiomes, make it difficult to establish virus-host associations at the single cell (rather than population) level, assign cellular hosts, or determine the extent of viral host range from metagenomics studies alone. Here, we combine single-cell sequencing with environmental metagenomics to characterize the structure of virus-host associations in a Yellowstone National Park (YNP) hot spring microbial community...
February 21, 2018: ISME Journal
Karthik Anantharaman, Bela Hausmann, Sean P Jungbluth, Rose S Kantor, Adi Lavy, Lesley A Warren, Michael S Rappé, Michael Pester, Alexander Loy, Brian C Thomas, Jillian F Banfield
A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive...
February 21, 2018: ISME Journal
Steven M Valles, Sanford D Porter, Luis A Calcaterra
Metagenomics and next generation sequencing were employed to discover new virus natural enemies of the fire ant, Solenopsis invicta Buren in its native range (i.e., Formosa, Argentina) with the ultimate goal of testing and releasing new viral pathogens into U.S. S. invicta populations to provide natural, sustainable control of this ant. RNA was purified from worker ants from 182 S. invicta colonies, which was pooled into 4 groups according to location. A library was created from each group and sequenced using Illumina Miseq technology...
2018: PloS One
Aonghus Lavelle, Harry Sokol
No abstract text is available yet for this article.
February 21, 2018: Nature Reviews. Gastroenterology & Hepatology
Nathálya Farias, Isabela Almeida, Carlos Meneses
Alkaline phytases from uncultured microorganisms, which hydrolyze phytate to less phosphorylated myo-inositols and inorganic phosphate, have great potential as additives in agricultural industry. The development of metagenomics has stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. In this study, a gene encoding a phytase was cloned from red rice crop residues and castor bean cake using a metagenomics strategy. The amino acid identity between this gene and its closest published counterparts is lower than 60%...
February 17, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Andrea Muras, Mario López-Pérez, Celia Mayer, Ana Parga, Jaime Amaro-Blanco, Ana Otero
There is increasing evidence being accumulated regarding the importance of N -acyl homoserine lactones (AHL)-mediated quorum-sensing (QS) and quorum-quenching (QQ) processes in the marine environment, but in most cases, data has been obtained from specific microhabitats, and subsequently little is known regarding these activities in free-living marine bacteria. The QS and QQ activities among 605 bacterial isolates obtained at 90 and 2000 m depths in the Mediterranean Sea were analyzed. Additionally, putative QS and QQ sequences were searched in metagenomic data obtained at different depths (15-2000 m) at the same sampling site...
February 16, 2018: Genes
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