scholarly journals Assessment of a metaviromic dataset generated from nearshore Lake Michigan

2016 ◽  
Vol 67 (11) ◽  
pp. 1700 ◽  
Author(s):  
Siobhan C. Watkins ◽  
Neil Kuehnle ◽  
C. Anthony Ruggeri ◽  
Kema Malki ◽  
Katherine Bruder ◽  
...  
Keyword(s):  
Lake Michigan ◽  
Global Scale ◽  
Metagenomic Data ◽  
Similar Data ◽  
Viral Ecology ◽  
Phage Ecology ◽  
Diverse Environment ◽  
Baseline Information ◽  
Diverse Community ◽  
Genome Level

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse similar data. Our results revealed a diverse community of DNA phages, largely comprising the order Caudovirales. Within the scope of the current study, the Lake Michigan virome demonstrates a distinct community. Although several phages appeared to hold dominance, further examination highlighted the importance of interrogating metagenomic data at the genome level. We present our study as baseline information for further examination of the ecology of the lake. In the current study we discuss our results and highlight issues of data analysis which may be important for freshwater studies particularly, in light of the complexities associated with examining phage ecology generally.

scholarly journals Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1Compound Oxidation

2015 ◽  
Vol 82 (5) ◽  
pp. 1423-1432 ◽  
Author(s):  
Vincent J. Denef ◽  
Ryan S. Mueller ◽  
Edna Chiang ◽  
James R. Liebig ◽  
Henry A. Vanderploeg
Keyword(s):  
Gene Expression ◽  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Water Column ◽  
Lake Michigan ◽  
Expression Patterns ◽  
Metagenomic Data ◽  
Type I ◽  
Deep Lake ◽  
Additional Energy

ABSTRACTTheChloroflexiCL500-11 clade contributes a large proportion of the bacterial biomass in the oxygenated hypolimnia of deep lakes worldwide, including the world's largest freshwater system, the Laurentian Great Lakes. Traits that allow CL500-11 to thrive and its biogeochemical role in these environments are currently unknown. Here, we found that a CL500-11 population was present mostly in offshore waters along a transect in ultraoligotrophic Lake Michigan (a Laurentian Great Lake). It occurred throughout the water column in spring and only in the hypolimnion during summer stratification, contributing up to 18.1% of all cells. Genome reconstruction from metagenomic data suggested an aerobic, motile, heterotrophic lifestyle, with additional energy being gained through carboxidovory and methylovory. Comparisons to other available streamlined freshwater genomes revealed that the CL500-11 genome contained a disproportionate number of cell wall/capsule biosynthesis genes and the most diverse spectrum of genes involved in the uptake of dissolved organic matter (DOM) substrates, particularly peptides.In situexpression patterns indicated the importance of DOM uptake and protein/peptide turnover, as well as type I and type II carbon monoxide dehydrogenase and flagellar motility. Its location in the water column influenced its gene expression patterns the most. We observed increased bacteriorhodopsin gene expression and a response to oxidative stress in surface waters compared to its response in deep waters. While CL500-11 carries multiple adaptations to an oligotrophic lifestyle, its investment in motility, its large cell size, and its distribution in both oligotrophic and mesotrophic lakes indicate its ability to thrive under conditions where resources are more plentiful. Our data indicate that CL500-11 plays an important role in nitrogen-rich DOM mineralization in the extensive deep-lake hypolimnion habitat.

scholarly journals Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples

2017 ◽  
Author(s):  
Feiqiao Brian Yu ◽  
Paul C. Blainey ◽  
Frederik Schulz ◽  
Tanja Woyke ◽  
Mark A. Horowitz ◽  
...  
Keyword(s):  
Single Cell ◽  
Statistical Power ◽  
Ad Hoc ◽  
Hot Spring ◽  
Genomic Structure ◽  
Metagenomic Data ◽  
Rigorous Approach ◽  
Environmental Selection ◽  
Wide Range ◽  
Genome Level

AbstractMetagenomics and single-cell genomics have enabled the discovery of many new genomes from previously unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and in many respects represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes from complex samples. In addition, by generating 96 sub-samples from each environmental sample, this method maintains high throughput, reduces sample complexity, and preserves single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes larger than 0.5 Mbps. These genomes represent novel lineages at different taxonomic levels, including three deeply branching lineages. Functional analysis revealed that these organisms utilize diverse pathways for energy metabolism. The resolution of this mini-metagenomic method enabled accurate quantification of genome abundance, even for genomes less than 1% in relative abundance. Our analyses also revealed a wide range of genome level single nucleotide polymorphism (SNP) distributions with nonsynonymous to synonymous ratio indicative of low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomic make it a powerful tool to dissect the genomic structure microbial communities while effectively preserving the fundamental unit of biology, the single cell.

Indicators of Information and Communication Technology

2019 ◽  
pp. 840-853
Author(s):  
Gulnara Abdrakhmanova ◽  
Leonid Gokhberg ◽  
Alexander Sokolov
Keyword(s):  
Information And Communication Technology ◽  
Communication Technology ◽  
Information Society ◽  
Practical Experience ◽  
Global Scale ◽  
Private Life ◽  
Similar Data ◽  
Public And Private ◽  
Leading Role ◽  
Information And Communication

Information and communication technology (ICT) has become a major driver of changes in economic, social, public, and private life, leading to emergence of the information society and digital economy. Identification of key trends and analysis of transformation processes can only be made on the basis of reliable statistical data. Development of relevant international statistics plays a leading role here; hence, via establishing and updating relevant standards, it allows to measure development of the information society in a global scale, and benchmark positions of individual countries in the worldwide economic environment. ICT indicators are based on general (definitions and classifications, similar data collection methodologies) and specialized statistical standards, whereas harmonized methodology provides highly compatible indicators for different countries. The objective of this chapter is to present a systemic overview of internationally accepted definitions of main ICT indicators based on accumulated methodological standards and practical experience.

scholarly journals A Literature Review of Neospora caninum Infection in Humans

2021 ◽  
Vol 8 (3) ◽  
pp. 113-116
Author(s):  
Jamal Gharekhani ◽  
Mohammad Yakhchali ◽  
Fariba Keramat ◽  
Reza Berahmat
Keyword(s):  
Neospora Caninum ◽  
Experimental Studies ◽  
Global Scale ◽  
Hiv Positive ◽  
Seroprevalence Rate ◽  
Caninum Infection ◽  
Obligate Intracellular ◽  
Factors Associated ◽  
Baseline Information ◽  
First Time

Background: Neosporosis is a parasitic disease caused by Neospora caninum. This parasite is an obligate intracellular coccidia similar to Toxoplasma gondii with a global distribution. With regard to the experimental studies, vertical transmission of the parasite in the monkey (non-human primates) has increased the concern about the zoonotic potential of this disease. The principal aim of the current research was to perform a mini-review on investigations regarding the Neospora infection in humans on a global scale for the first time. Methods: All peer-reviewed articles (published until April 2021) on the Neospora infection in humans were searched in English databases such as Google Scholar, ScienceDirect, Scopus, PubMed, and ProQuest. Results: Based on data in the available articles, the presence of antibodies against the Neospora infection was between 0 and 37.7% in people from different countries. The seroprevalence rate of this infection in HIV-positive individuals was higher (26.6% and 37.7%) compared to other cases. Finally, the genomic DNA of Neospora was detected up to 1% using molecular biology techniques. Conclusions: Overall, the detection of anti-Neospora antibodies in humans indicated that people have been exposed to the parasite. Comprehensive research studies are essential for clarifying the risk factors associated with the Neospora infection in humans. This report provides the baseline information for future researchers. Molecular investigations and genotypic works on N. caninum isolates are highly recommended as well.

scholarly journals nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

2021 ◽  
Author(s):  
Sabrina Krakau ◽  
Daniel Straub ◽  
Hadrien Gourlé ◽  
Gisela Gabernet ◽  
Sven Nahnsen
Keyword(s):  
Microbial Communities ◽  
Best Practice ◽  
Metagenomic Data ◽  
Hybrid Assembly ◽  
Individual Genome ◽  
Long Reads ◽  
Metagenome Assembly ◽  
Group Information ◽  
Genome Level ◽  
Reference Genomes

The analysis of shotgun metagenomic data provides valuable insights into microbial communities, while allowing resolution at individual genome level. In absence of complete reference genomes, this requires the reconstruction of metagenome assembled genomes (MAGs) from sequencing reads. We present the nf-core/mag pipeline for metagenome assembly, binning and taxonomic classification. It can optionally combine short and long reads to increase assembly continuity and utilize sample-wise group-information for co-assembly and genome binning. The pipeline is easy to install - all dependencies are provided within containers -, portable and reproducible. It is written in Nextflow and developed as part of the nf-core initiative for best-practice pipeline development. All code is hosted on GitHub under the nf-core organization https://github.com/nf-core/mag and released under the MIT license.

scholarly journals MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

2018 ◽  
Author(s):  
Gherman V Uritskiy ◽  
Jocelyne DiRuggiero ◽  
James Taylor
Keyword(s):  
Data Analysis ◽  
Shotgun Sequencing ◽  
Metagenomic Analysis ◽  
Metagenomic Data ◽  
Sequencing Data ◽  
High Quality ◽  
Single Genome ◽  
Significant Burden ◽  
Versatile Tool ◽  
Genome Level

AbstractBackground:The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization.Results:To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP’s hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real datasets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization.Conclusions:MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP.

scholarly journals Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

2016 ◽  
Author(s):  
Simon Roux ◽  
Jennifer R. Brum ◽  
Bas E. Dutilh ◽  
Shinichi Sunagawa ◽  
Melissa B. Duhaime ◽  
...  
Keyword(s):  
Deep Ocean ◽  
Global Scale ◽  
Host Community ◽  
Global Ocean ◽  
Trophic Networks ◽  
Evolutionary Trajectories ◽  
Genome Level ◽  
Dsdna Viruses ◽  
Auxiliary Metabolic Genes ◽  
Do So

AbstractOcean microbes drive global-scale biogeochemical cycling1, but do so under constraints imposed by viruses on host community composition, metabolism, and evolutionary trajectories2–5. Due to sampling and cultivation challenges, genome-level viral diversity remains poorly described and grossly understudied in nature such that <1% of observed surface ocean viruses, even those that are abundant and ubiquitous, are ‘known’5. Here we analyze a global map of abundant, double stranded DNA (dsDNA) viruses and viral-encoded auxiliary metabolic genes (AMGs) with genomic and ecological contexts through the Global Ocean Viromes (GOV) dataset, which includes complete genomes and large genomic fragments from both surface and deep ocean viruses sampled during the Tara Oceans and Malaspina research expeditions6,7. A total of 15,222 epi- and mesopelagic viral populations were identified that comprised 867 viral clusters (VCs, approximately genus-level groups8,9). This roughly triples known ocean viral populations10, doubles known candidate bacterial and archaeal virus genera9, and near-completely samples epipelagic communities at both the population and VC level. Thirty-eight of the 867 VCs were identified as the most impactful dsDNA viral groups in the oceans, as these were locally or globally abundant and accounted together for nearly half of the viral populations in any GOV sample. Most of these were predicted in silico to infect dominant, ecologically relevant microbes, while two thirds of them represent newly described viruses that lacked any cultivated representative. Beyond these taxon-specific ecological observations, we identified 243 viral-encoded AMGs in GOV, only 95 of which were known. Deeper analyses of 4 of these AMGs revealed that abundant viruses directly manipulate sulfur and nitrogen cycling, and do so throughout the epipelagic ocean. Together these data provide a critically-needed organismal catalog and functional context to begin meaningfully integrating viruses into ecosystem models as key players in nutrient cycling and trophic networks.

scholarly journals Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution

mBio ◽  
2018 ◽  
Vol 9 (2) ◽  
Author(s):  
Jason W. Shapiro ◽  
Catherine Putonti
Keyword(s):  
Host Range ◽  
Single Gene ◽  
Viral Ecology ◽  
Phage Ecology ◽  
Gene Level ◽  
Evolutionary Context ◽  
Gene Network Analysis ◽  
Rapid Pace ◽  
New Hosts ◽  
Biological Entities

ABSTRACTBacteriophages are the most abundant and diverse biological entities on the planet, and new phage genomes are being discovered at a rapid pace. As more phage genomes are published, new methods are needed for placing these genomes in an ecological and evolutionary context. Phages are difficult to study by phylogenetic methods, because they exchange genes regularly, and no single gene is conserved across all phages. Here, we demonstrate how gene-level networks can provide a high-resolution view of phage genetic diversity and offer a novel perspective on virus ecology. We focus our analyses on virus host range and show how network topology corresponds to host relatedness, how to find groups of genes with the strongest host-specific signatures, and how this perspective can complement phage host prediction tools. We discuss extensions of gene network analysis to predicting the emergence of phages on new hosts, as well as applications to features of phage biology beyond host range.IMPORTANCEBacteriophages (phages) are viruses that infect bacteria, and they are critical drivers of bacterial evolution and community structure. It is generally difficult to study phages by using tree-based methods, because gene exchange is common, and no single gene is shared among all phages. Instead, networks offer a means to compare phages while placing them in a broader ecological and evolutionary context. In this work, we build a network that summarizes gene sharing across phages and test how a key constraint on phage ecology, host range, corresponds to the structure of the network. We find that the network reflects the relatedness among phage hosts, and phages with genes that are closer in the network are likelier to infect similar hosts. This approach can also be used to identify genes that affect host range, and we discuss possible extensions to analyze other aspects of viral ecology.

scholarly journals Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Josephine E. S. Strange ◽  
Pimlapas Leekitcharoenphon ◽  
Frederik Duus Møller ◽  
Frank M. Aarestrup
Keyword(s):  
Antimicrobial Resistance ◽  
Economic Status ◽  
Bacterial Species ◽  
Regional Distribution ◽  
Geographic Origin ◽  
Global Scale ◽  
Metagenomic Data ◽  
Urban Sewage ◽  
Archaeal Viruses ◽  
Antimicrobial Resistance Gene

AbstractBacteriophages, or phages, are ubiquitous bacterial and archaeal viruses with an estimated total global population of 1031. It is well-known that wherever there are bacteria, their phage counterparts will be found, aiding in shaping the bacterial population. The present study used metagenomic data from global influent sewage in 79 cities in 60 countries to identify phages associated with bacteria and to explore their potential role in antimicrobial resistance gene (ARG) dissemination. The reads were mapped to known databases for bacteriophages and their abundances determined and correlated to geographic origin and the countries socio-economic status, as well as the abundances of bacterial species and ARG. We found that some phages were not equally distributed on a global scale, but their distribution was rather dictated by region and the socioeconomic status of the specific countries. This study provides a preliminary insight into the global and regional distribution of phages and their potential impact on the transmission of ARGs between bacteria. Moreover, the findings may indicate that phages in sewage could have adopted a lytic lifestyle, meaning that most may not be associated with bacteria and instead may be widely distributed as free-living phages, which are known to persist longer in the environment than their hosts. In addition, a significant correlation between phages and ARGs was obtained, indicating that phages may play a role in ARG dissemination. However, further analyses are needed to establish the true relationship between phages and ARGs due to a low abundance of the phages identified.

scholarly journals Salinity Drives Functional and Taxonomic Diversities in Global Water Metagenomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Huaihai Chen ◽  
Kayan Ma ◽  
Yu Huang ◽  
Yuchun Yang ◽  
Zilong Ma ◽  
...  
Keyword(s):  
Aquatic Ecosystems ◽  
Comprehensive Evaluation ◽  
Saline Water ◽  
Taxonomic Diversity ◽  
Functional Redundancy ◽  
Global Scale ◽  
Metagenomic Data ◽  
Functional Prediction ◽  
Functional Profiles ◽  
Global Water

A tight association between microbial function and taxonomy is the basis of functional prediction based on taxonomy, but such associations have been controversial in water biomes largely due to the probable prevalence of functional redundancy. However, previous studies on this topic used a relatively coarse resolution of ecosystem functioning, potentially inflating the estimated functional redundancy. Thus, a comprehensive evaluation of the association between high-resolution functional traits and taxonomic diversity obtained from fresh and saline water metagenomic data is urgently needed. Here, we examined 938 functionally and taxonomically annotated water metagenomes obtained worldwide to scrutinize the connection between function and taxonomy, and to identify the key driver of water metagenomes function or taxonomic composition at a global scale. We found that pairwise similarity of function was significantly associated with taxonomy, though taxonomy had higher global dissimilarity than function. Classification into six water biomes resulted in greater variation in taxonomic compositions than functional profiles, as the key regulating factor was salinity. Fresh water microbes harbored distinct functional and taxonomic structures from microbes in saline water biomes, despite that taxonomy was more susceptible to gradient of geography and climate than function. In summary, our results find a significant relationship between taxonomic diversity and microbial functioning in global water metagenomes, although microbial taxonomic compositions vary to a larger extent than functional profiles in aquatic ecosystems, suggesting the possibility and necessity for functional prediction of microorganisms based on taxonomy in global aquatic ecosystems.

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