Soil metagenome datasets. Medical search. Frequent questions

Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. (biomedcentral.com)
Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. (biomedcentral.com)
MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. (biomedcentral.com)
The automatic binning software that we developed successfully classifies assembled sequences in metagenomic datasets into recovered individual genomes. (biomedcentral.com)
This work demonstrates that the processes required for recovering genomes from assembled metagenomic datasets can be readily automated, an important advance in understanding the metabolic potential of microbes in natural environments. (biomedcentral.com)
Due to the number, frequency, types and sizes of genomes present in highly diverse communities, additional sequencing of metagenome samples often captures novel genome fragments from increasingly rare members (or minor variants) of the community. (nature.com)
We further reconstructed a total of 18 genomes from both the original soil sample and the isolated consortium. (springeropen.com)
The analysis of both the metagenome of the consortium and the reconstructed metagenome-assembled genomes show that the most abundant bacterial genus in the consortium, Acidocella , possess many of the genes required for the degradation of diesel fuel aromatic hydrocarbons, which are often the most toxic component. (springeropen.com)
We reconstructed 18 metagenome-assembled genomes with potentials for bioremediation. (springeropen.com)
Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. (biomedcentral.com)

Therefore, the main objective of the present study was to evaluate the impact of vinasse amendment on the abundance of ARGs from soil resistome by analyzing metagenomic datasets from a previous study [ 9 ]. (biomedcentral.com)
Therefore, to address the objective proposed in the present study, we used eighteen metagenomic datasets, considering the V+ and V- treatments sampled in three different periods (7th, 157th and 217th dap) ( n = 3). (biomedcentral.com)
More details on how the metagenomic datasets were generated can be found in Navarrete et al. (biomedcentral.com)
MEGAN ("MEtaGenome ANalyzer") is a computer program that allows optimized analysis of large metagenomic datasets. (wikipedia.org)

Analysis of the genome dataset revealed that multiple organisms, including some from ~34 newly detected phyla, are often required to complete redox pathways. (nih.gov)
Application of MaxBin to metagenomes obtained from microbial consortia adapted to grow on cellulose allowed genomic analysis of new, uncultivated, cellulolytic bacterial populations, including an abundant myxobacterial population distantly related to Sorangium cellulosum that possessed a much smaller genome (5 MB versus 13 to 14 MB) but has a more extensive set of genes for biomass deconstruction. (biomedcentral.com)
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. (mbl.edu)
With approximately 30-40% of putative proteins encoded in any genome having no known function, environmental microbes represent a vast wealth of novel protein function and potential new biochemistry, the understanding of which will be critical to informing our understanding of the microbial component of soil biogeochemistry. (doe.gov)
His work combined the development of new bioinformatics tools for viral genome analysis, and coupled metagenome analysis with information derived from other newly developed experimental methods (e.g. single-cell genomics) as well as environmental virus-host model systems available at the Sullivan Lab. (ictv.global)
If you have a eukaryotic genome you're interested in, you could sketch it (sourmash sketch) and then use the branchwater tool to search most metagenomes in the SRA to see which ones have high containment with the genome your searched. (sciety.org)
In this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction pipeline). (biomedcentral.com)
16), E. coli c20 draft genome extracted from chicken gut and finally on 145 whole-metagenome data samples from human gut. (biomedcentral.com)

Fragments of DNA from an metagenomics sample, such as ocean waters or soil, are compared against databases of known DNA sequences using BLAST or another sequence comparison tool to assemble the segments into discrete comparable sequences. (wikipedia.org)
We developed an ensemble approach that exploits k-mer and reference-based strategies to improve eukaryotic sequence identification from metagenomes and identified MetaBAT2 as the best performing binning approach for clustering of eukaryotic sequences. (sciety.org)
In that work, we drew 16S rRNA sequences from more than 5000 publicly-available studies, including 16S amplicon libraries, metagenomes, and metatranscriptomes. (nature.com)
Within an hour and a half, Alex Crits-Christoph ( @acritschristoph ) analyzed a large 16S data set from soils to show that very few 16S sequences were closely related to cultures. (nature.com)
Virtifier: A deep learning-based identifier for viral sequences from metagenomes. (cdc.gov)
A curated dataset of peste des petits ruminants virus sequences for molecular epidemiological analyses. (cdc.gov)

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of the Solfatara Crater (Campi Flegrei, southern Italy). (mbl.edu)
In this study, we investigated the successional dynamics of a soil microbiome during. (pnnl.gov)
Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules" The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. (pnnl.gov)
The Bhatnagar lab studies soil microbiome variation in the context of changing environmental conditions. (bu.edu)

DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes" Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. (pnnl.gov)

Here, we investigated the effects of extreme drought and exotic plants, two of the most significant threats to Mediterranean-type ecosystems, on soil microbial community composition and carbon metabolic genes within a four-year field rainfall manipulation experiment. (nature.com)
Relationships found between microbial taxonomic groups and carbon metabolic genes support the interpretation that exotic plants change microbial carbon cycling by altering the soil microclimate and supplying easily decomposed high-quality litter. (nature.com)
Here we evaluate public datasets of soil metagenomes mining for changes in antibiotic resistance genes (ARGs) of soils from sugarcane mesocosms repeatedly amended with vinasse. (biomedcentral.com)
However, recent research has demonstrated that the utilization of organic compounds as fertilizers in agriculture soils can alter the selective pressure that drives antibiotic resistance genes (ARGs) on soil-borne microbial communities [ 4 ]. (biomedcentral.com)
While the sequencing of metagenomes provides an overview of the genes present in specific environments that can potentially play a role in adaptation, the analysis of expression provides a more precise picture of what functions are expressed and active in a particular moment of the environment. (biomedcentral.com)
A hot desert hypolith metagenomic DNA sequence dataset was screened in-silico for genes annotated as acetyl xylan esterases (AcXEs). (inrae.fr)
predict and recover novel enzyme encoding genes involved in Nitrogen (N) cycle from soil metagenomes. (kaabil.net)
The approach to be employed involves the cloning of large fragments of soil community DNA in an E. coli Bacterial Artificial Chromosome (BAC) expression vector, followed by screening of BAC clone libraries for expression of novel genes involved in the biotransformation of environmental contaminants associated with Superfund sites. (uidaho.edu)
This application is consistent with the NIH R21 mechanism of support in that the use of soil metagenomic expression libraries to discover novel biodegradation genes represents a new approach that is largely untested and has never before been applied to contaminant biotransformation research in a systematic manner as detailed here. (uidaho.edu)
We were able to identify numerous novel PKS I proteins, the highest density of which was found in Minnesota farm soil with 136 proteins out of 183,536 predicted genes. (embl.de)

Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. (pnnl.gov)
Pending Review Microbiomes contribute to multiple ecosystem services by transforming organic matter in soil. (pnnl.gov)
Moreover, ex situ methods are environmentally problematic as they alter the soil matrix and associated microbiomes. (springeropen.com)

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. (mbl.edu)
The contribution of microbial processes to soil biogeochemistry, particularly the management of soil carbon and nitrogen, is arguably one of the most important knowledge gaps in terrestrial ecology. (doe.gov)

Below the soil zone, the microorganisms that mediate transformations of nutrients, trace gases and contaminants are particularly poorly understood. (nih.gov)
Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. (pnnl.gov)
Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. (pnnl.gov)
Through successive enrichment of soil microorganisms from samples of an historic petroleum contaminated site in Wietze, Germany, we isolated a bacterial consortium using diesel fuel hydrocarbons as sole carbon and energy source. (springeropen.com)
Soil microorganisms perform a variety of essential roles, including acting as plant symbionts, animal pathogens, and free-living decomposers that recycle nutrients and carbon through the biosphere. (bu.edu)
This project will develop new bioinformatics tools to predict which soil microorganisms will endure and remain active over space and time. (bu.edu)
Soil Virus Offers Insight into Maintaining Microorganisms Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health. (doe.gov)

Invited speakers will provide their views of the challenges, as well as potential solutions, associated with protein identification, as well as integration with metagenome and metatranscriptome data, and, ultimately ecological characterization in soil environments. (doe.gov)
How can multi-omics analyses be used to define ecological properties of soil systems, e.g. by defining niche space, and niche diversification in spatial and temporal dynamics. (doe.gov)
Microbial DNA sequence data will be collected from soils obtained through a national sampling initiative - the National Ecological Observatory Network (NEON). (bu.edu)

HS are a complex and heterogeneous mixture of polymers formed in soils, sediments and natural waters by physico- and biochemical transformation of plant biomass (humification). (europa.eu)
Journal of Soils and Sediments. (rothamsted.ac.uk)

In addition, we surveyed the published metagenome data to find that the most abundant group of aromatic-degrading Methylobacterium in the environment is likely the group related to Methylobacterium nodulans, and they are especially common in soil and root environments. (figshare.com)

The life history strategies of soil bacteria remained poorly understood. (springernature.com)
By assessing genomic traits of soil bacteria using a global dataset of soil metagenomes, our study could be an important step towards filling this knowledge gap. (springernature.com)
In this study now published in Nature Microbiology , we decided to focus on bacteria that dominate the soil metagenomes. (springernature.com)
Our first goal was to define and calculate metagenomic metrics that we expected to capture the trait dimensions associated with the life history strategies of soil bacteria. (springernature.com)

Computational mining and modeling of complex multi-dimensional OMICS datasets using supervised and unsupervised learning, implement as databases and prediction tools. (kaabil.net)

The datasets were obtained using a MiSeq Personal Sequencing System (Illumina, San Diego, CA, USA) and are available through the Metagenomics Rapid Annotation (MG-RAST) server ( http://metagenomics.anl.gov/linkin.cgi?project=10854 ). (biomedcentral.com)
Cow Rumen and the Early Days of Metagenomics Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities. (doe.gov)

Soil microbial community responses to drought and exotic plants could potentially impact ecosystem C storage by producing a smaller, more vulnerable C pool of microbial biomass that is prone to increased pulses of heterotrophic respiration. (nature.com)

Co-occurrence network analysis revealed distinct patterns of interactions among ARGs, suggesting that nutrient amendment to soil microbial communities can impact on the coevolutionary dynamics of indigenous ARGs within soil resistome. (biomedcentral.com)

At the JGI, current projects in the Viral Genomics group revolve around the study of viral diversity and virus:host interactions in soil and freshwater environments, along with the development of new bioinformatics tools and experimental protocols to probe and characterize uncultivated viruses. (ictv.global)
Regardless of where they originate, however, steroids have been found to accumulate in soil, wastewater treatment plants, and aquatic environments, where even at low concentrations they have negative impacts on animals-including humans. (microbiomeinsights.com)
Despite this potential underestimation, this study is, according to researchers, "the first analysis of aerobic steroid degradation in diverse natural, engineered, and host-associated environments via bioinformatic analysis of an extensive metagenome data set. (microbiomeinsights.com)
Genomic fragments are directly sequenced from the microbial ecosystems, generating huge amounts of short reads from various environments, such as the human gut, soil, and ocean water [ 7 ]. (biomedcentral.com)

Soil ecosystems are considered to harbor a remarkable diversity of ARGs [ 4 ]. (biomedcentral.com)
Analysis of metagenomes from across the globe reveals the spectrum of soil microbial functional diversity based on community aggregated traits. (springernature.com)
Investigate diversity of enzymes in soil metagenomes and develop advanced tools. (kaabil.net)

However, even when sequencing reaches or surpasses one terabase, novel reads continue to be generated when sequencing the most complex communities, such as those in soil 4 . (nature.com)
Importantly, the graph is structured as a self-index that can be used for alignment and annotation of reads arising from metagenome sequencing experiments. (metasub.org)

The peat soils were subjected to DPH beginning in June of 2014 followed by WEW in August of 2015. (osti.gov)

2021. WA-TmG.2.0 (Metagenome, WA). (pnnl.gov)
2021. KS-TmG.2.0 (Metagenome, KS). (pnnl.gov)
2021. IA-TmG.2.0 (Metagenome, IA). (pnnl.gov)

First version is capable of analysing taxonomic content of a single dataset while the latest version can analyse multiple datasets including new features (query different databases, new algorithm etc. (wikipedia.org)

He received his PhD in 2013 from Université Blaise Pascal (Clermont-Ferrand, France), where he developed new bioinformatic tools for the analysis of "viral metagenomes", a new type of datasets at the time, and shared them through a web portal (MetaVir). (ictv.global)

We combined measurements of bulk microbial and soil properties with high-throughput microbial community analyses to elucidate microbial responses and microbial-mediated alterations to carbon cycling. (nature.com)
Soils under exotic plants had increased temperatures, enhanced infiltration during rainfall events, and decreased water retention and labile carbon in comparison to soils under native plants. (nature.com)

The goal of this workshop is to engage metaproteomics experts in a discussion with the "omics" community regarding the current status of soil metaproteomics, focusing on both the technical and informatics challenges encountered in the identification of the proteins isolated from soil samples. (doe.gov)

It provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses. (embl.de)

Members of both phyla coexist in wastewater, while species of Actinobacteria alone are found in soil and rhizospheres. (microbiomeinsights.com)

During my PhD, life history schemes of plants and soil microbes highly helped me to frame my research hypotheses 5,6 . (springernature.com)
However, I also realised that these theories were far less advanced for soil microbes than for plants. (springernature.com)
However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. (pnnl.gov)

Rakesh is an Assistant Professor of Bioinformatics in the Department of Plants, Soils, and Climate at Utah State University, and is the Director of Bioinformatics Facility at the Center for Integrated BioSystems, USU. (kaabil.net)

Using operonic data from metagenome to study secondary metabolic trends will significantly reduce the data volume to more precise data. (biomedcentral.com)
Furthermore, the identification of metabolic pathways associated with the occurrence of type 2 diabetes (T2D) also presents another dimension of analyzing the human gut metagenome. (biomedcentral.com)

The comparative studies of the potential protein content in many of these datasets have already provided interesting examples of specific functions that correlate with specific characteristics of the environment. (biomedcentral.com)

By the time of termination of this project, DNA from almost all samples has been extracted and sequencing of the first metagenomes was completed using either the Roche-454 or Illumina sequencing technology. (europa.eu)

Stands undergoing deciduous trajectories stored proportionally more of their C and N in aboveground stemwood and had 5-7 times faster rates of aboveground net primary productivity of trees compared to stands undergoing a black spruce trajectory, which stored more of their C and N in the soil organic layer (SOL), a thick layer of mostly undecomposed mosses. (nau.edu)

Within this context, we hypothesized that vinasse fertirrigation can impact the soil resistome dynamics. (biomedcentral.com)

Significant technical and informatics challenges exist for soil metaproteomics, some of which are being addressed with some success using current methods, while others will require novel approaches. (doe.gov)

Samples were collected in 2014 and 2019 to identify chemical changes occurring within peatland soils following five years of warming. (osti.gov)
Bulk soil samples were collected at the 7th day after vinasse application (7th, 157th and 217th days after planting, dap). (biomedcentral.com)
https://doi.org/10.25584/WATmG2/1770324 Soil samples were collected in triplicate in the fall of 2017 across the three grassland. (pnnl.gov)

however, time series ESOMs require multiple datasets for accurate binning. (biomedcentral.com)

MeGAMerge pipeline for metagenomes. (nature.com)

In the referred study, a greenhouse experiment was performed in which vinasse was repeatedly applied to sugarcane-cultivated soils in plastic pots (100 L) filled with 90 kg of soil ( n = 3). (biomedcentral.com)

Metagenome assembly, in contrast, often has an unclear definition of assembly quality. (nature.com)
Yet, it is unclear that soil microorgamisms will persist in a changing world. (bu.edu)

Among the functions with highest regulatory potential in each niche, we found significant enrichment of processes related to sensing and buffering external variable factors specific to each environment, like for example, the availability of co-factors in deep sea, of oligosaccharides in soil and the regulation of pH in the acid mine. (biomedcentral.com)

Their soil samples covered most of the global environmental range across biomes and they sequenced their metagenomes. (springernature.com)

Looking at available global datasets, I found the study by Bahram et al. (springernature.com)

Anatomy1

Organisms13

Chemicals and Drugs7

Analytical, Diagnostic and Therapeutic Techniques and Equipment10

Phenomena and Processes18

Disciplines and Occupations6

Technology, Industry, Agriculture1

Information Science14

Health Care16

Geographicals1

Genomes10

Metagenomic datasets4

Genome8

Sequences6

Microbiome4

Abundance1

Genes10

Microbiomes3

Nitrogen2

Microorganisms7

Ecological3

Sediments2

Abundant1

Bacteria4

Prediction1

Metagenomics2

Heterotrophic1

Microbial communities1

Environments4

Diversity3

Reads2

Peat1

20213

Taxonomic1

Bioinformatic1

Carbon2

Proteins1

Analyses1

Actinobacteria1

Microbes3

Plants1

Metabolic2

Protein1

Illumina1

Organic1

Dynamics1

Methods1

Samples were collected3

Multiple1

Pipeline1

Experiment1

Unclear2

Processes1

Environmental1

Found1