co-occurrence network
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PLoS Computational Biology: Genetic Co-Occurrence Network across Sequenced Microbes

PLoS Computational Biology: Genetic Co-Occurrence Network across Sequenced Microbes | co-occurrence network | Scoop.it

"The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through the resulting phenotype. In this regard, contemporary genomes can be used as molecular records that reveal associations of various genes working in their natural lifestyles. By analyzing thousands of orthologs across ~600 bacterial species, we constructed a map of gene-gene co-occurrence across much of the sequenced biome. If genes preferentially co-occur in the same organisms, they were called herein correlogs; in the opposite case, called anti-correlogs. To quantify correlogy and anti-correlogy, we alleviated the contribution of indirect correlations between genes by adapting ideas developed for reverse engineering of transcriptional regulatory networks. Resultant correlogous associations are highly enriched for physically interacting proteins and for co-expressed transcripts, clearly differentiating a subgroup of functionally-obligatory protein interactions from conditional or transient interactions. Other biochemical and phylogenetic properties were also found to be reflected in correlogous and anti-correlogous relationships. Additionally, our study elucidates the global organization of the gene association map, in which various modules of correlogous genes are strikingly interconnected by anti-correlogous crosstalk between the modules. We then demonstrate the effectiveness of such associations along different domains of life and environmental microbial communities. These phylogenetic profiling approaches infer functional coupling of genes regardless of mechanistic details, and may be useful to guide exogenous gene import in synthetic biology."


Via Gerd Moe-Behrens
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Insights into the phylogeny and coding potential of microbial dark matter : Nature : Nature Publishing Group

Insights into the phylogeny and coding potential of microbial dark matter : Nature : Nature Publishing Group | co-occurrence network | Scoop.it

Genome sequencing is providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. Researchers have recently applied single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, they were able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. They uncovered unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This recent study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.

 

Microorganisms are the most diverse and abundant cellular life forms on Earth, occupying every possible metabolic niche. The large majority of these organisms have not been obtained in pure culture and we have only recently become aware of their presence mainly through cultivation-independent molecular surveys based on conserved marker genes (chiefly small subunit ribosomal RNA; SSU rRNA) or through shotgun sequencing (metagenomics). As an increasing number of environments are deeply sequenced using next-generation technologies, diversity estimates for Bacteria and Archaea continue to rise, with the number of microbial ‘species’ predicted to reach well into the millions. According to SSU rRNA-based phylogeny, these fall into at least 60 major lines of descent (phyla or divisions) within the bacterial and archaeal domains of which half have no cultivated representatives (so-called ‘candidate’ phyla). This biased representation is even more fundamentally skewed when considering that more than 88% of all microbial isolates belong to only four bacterial phyla, the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Genome sequencing of microbial isolates naturally reflects this cultivation bias. Recently, a systematic effort, the Genomic Encyclopaedia of Bacteria and Archaea (GEBA) Project, has been initiated to maximize coverage of the diversity captured in microbial isolates by phylogenetically targeted genome sequencing. However, GEBA does not address candidate phyla that represent a major unexplored portion of microbial diversity, and have been referred to as microbial dark matter (MDM).

 

Metagenomics can obtain genome sequences from uncultivated microorganisms through direct sequencing of DNA from the environment. In some instances, draft or even complete genomes of candidate phyla have been recovered solely from metagenomic data. A complementary cultivation-independent approach for obtaining genomes from candidate phyla is single-cell genomics; the amplification and sequencing of DNA from single cells obtained directly from environmental samples. This approach can be used for targeted recovery of genomes and has been applied to members of several candidate phyla. In particular, natural populations that have a high degree of genomic heterogeneity will be more accessible through single-cell genomics than through metagenomics as co-assembly of multiple strains is avoided. Despite these advances in obtaining genomic representation of MDM, no systematic effort has been made to obtain genomes from uncultivated candidate phyla using single-cell whole genome amplification approaches.

 


Via Dr. Stefan Gruenwald
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Infographics

Infographics | co-occurrence network | Scoop.it
The ISME Journal promotes diverse and integrated areas of microbial ecology spanning the breadth of microbial life, including bacteria, archaea, microbial eukaryotes, and viruses.

Via Clara Belzer
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Clara Belzer's curator insight, April 3, 2013 7:27 AM

ISMEJ also publishes Microbiota research of high quality

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What's in his kiss? 80 million bacteria, for starters - Today.com

What's in his kiss? 80 million bacteria, for starters - Today.com | co-occurrence network | Scoop.it
With every extended kiss we may be transferring as many as 80 million bacteria, scientists say. Eeewww. That knowledge certainly saps...
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Microbial Metagenomics Summer Course 2012 - MSU Metagenomics

Microbial Metagenomics Summer Course 2012 - MSU Metagenomics | co-occurrence network | Scoop.it

Microbial metagenomics course, June 3 - June 16th, Michigan State University: http://t.co/IXBu9RHO...


Via Elsevier Microbiol*, Ed Rybicki
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Australasian Biotechnology - The use of metagenomics to investigate the role of microbiota in animal health and productivity (APAFT) - Informit

Australasian Biotechnology - The use of metagenomics to investigate the role of microbiota in animal health and productivity (APAFT) - Informit | co-occurrence network | Scoop.it
Informit is an online service offering a wide range of database and full content publication products that deliver the vast majority of Australasian scholarly research to the education, research and business sectors.
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Broad Team Publishes RNA-seq Method for Lassa, Ebola Viruses - GenomeWeb

Broad Team Publishes RNA-seq Method for Lassa, Ebola Viruses - GenomeWeb | co-occurrence network | Scoop.it
The method may be deployed as part of the Broad's collaboration with Illumina and USAID to study Ebola in some West African countries hit by the outbreak.
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A Cross-Taxon Analysis of Insect-Associated Bacterial Diversity

A Cross-Taxon Analysis of Insect-Associated Bacterial Diversity | co-occurrence network | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.

Via Ashish Umre
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Metagenomics-Biology Beyond the Microscope (Mississippi Metagenomics at UMN)

Minnesota Mississippi Metagenome Project or M3P BioTechnology Institute and Department of Soil, Water and Climate Change at the University of Minnesota Dr. M...
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Environmental Microbiology: Methods and Protocols (Methods in Molecular Biology)

Environmental Microbiology: Methods and Protocols (Methods in Molecular Biology) | co-occurrence network | Scoop.it
Environmental Microbiology: Methods and Protocols (Methods in Molecular Biology) Offer Price $99.16 ISBN:162703711X Authors List Price : $119.00 Availablity Usually ships in 24 hours Publisher : Humana Press An up-to-date view of molecular...
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Precise measurements of microbial ecosystems - Science Codex

Precise measurements of microbial ecosystems - Science Codex | co-occurrence network | Scoop.it
The Luxembourg Centre for Systems Biomedicine (LCSB) has succeeded for the first time in describing the complex relationships within an ecosystem in unprecedented detail.
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Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats

Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats | co-occurrence network | Scoop.it
Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats Offer Price $260.32 ISBN:0470647191 Authors Frans J.
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Microbial Ecology at Harvard Forest - Harvard Forest

Microbial Ecology at Harvard Forest: A Synthesis of Past Work and Future Directions -- Serita Frey. Harvard Forest Symposium, March 15, 2011.
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Fast and sensitive protein alignment using DIAMOND : Nature Methods : Nature Publishing Group

The open-source DIAMOND software provides protein alignment that is 20,000 times faster on short reads than BLASTX at similar sensitivity, for rapid analysis of large metagenomics data sets on a desktop computer.

Via Mel Melendrez-Vallard
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Mass spectral molecular networking of living microbial colonies

Mass spectral molecular networking of living microbial colonies | co-occurrence network | Scoop.it

Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a “holy grail” in microbiology. This work describes a highly sensitive, broadly applicable, and cost-effective approach that allows metabolic profiling of live microbial colonies directly from a Petri dish without any sample preparation. Nanospray desorption electrospray ionization mass spectrometry (MS), combined with alignment of MS data and molecular networking, enabled monitoring of metabolite production from live microbial colonies from diverse bacterial genera, including Bacillus subtilis, Streptomyces coelicolor, Mycobacterium smegmatis, and Pseudomonas aeruginosa. This work demonstrates that, by using these tools to visualize small molecular changes within bacterial interactions, insights can be gained into bacterial developmental processes as a result of the improved organization of MS/MS data. To validate this experimental platform, metabolic profiling was performed on Pseudomonas sp. SH-C52, which protects sugar beet plants from infections by specific soil-borne fungi [R. Mendes et al. (2011) Science 332:1097–1100]. The antifungal effect of strain SH-C52 was attributed to thanamycin, a predicted lipopeptide encoded by a nonribosomal peptide synthetase gene cluster. Our technology, in combination with our recently developed peptidogenomics strategy, enabled the detection and partial characterization of thanamycin and showed that it is a monochlorinated lipopeptide that belongs to the syringomycin family of antifungal agents. In conclusion, the platform presented here provides a significant advancement in our ability to understand the spatiotemporal dynamics of metabolite production in live microbial colonies and communities.

 

Watrous J, et al. (2012) Mass spectral molecular networking
of living microbial colonies. Proc Natl Acad Sci
USA 109:E1743–E1752.

10.1073/pnas.1203689109

 

 


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The Tree of Life: CAMERA metagenomics resource is shutting down

The Tree of Life: CAMERA metagenomics resource is shutting down | co-occurrence network | Scoop.it
CAMERA metagenomics resource is shutting down. Just got this email and thought it would be of interest to many out there. Thank you for being a CAMERA user during its operation as a resource for environmental genomics.
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isoHunt - BitTorrent & P2P torrent search engine

isoHunt -  BitTorrent & P2P torrent search engine | co-occurrence network | Scoop.it
Download Metagenomics of the Human Body torrent from books category on Isohunt
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Frontiers | Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India | Antimicrobials, Resistance and Chemotherapy

There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining...
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Title Environmental Microbiology Microbiological

Pdf: Title Environmental Microbiology Microbiological, Backed by Science, #title #environmental #microbiology http://t.co/0UUldLobaC
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Aquatic microbial ecology through the lens of high-throughput DNA/RNA sequencing

Aquatic microbial ecology through the lens of high-throughput DNA/RNA sequencing - Aquatic microbial ecology through the lens of high-throughput DNA/RNA sequ...
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Just Wait Til You Get Home - GenomeWeb

Just Wait Til You Get Home - GenomeWeb | co-occurrence network | Scoop.it
Researchers have characterized the microbes living on four public bathroom surfaces over time.
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Behind the Bench: 16S rRNA Bacterial Community ...

Behind the Bench: 16S rRNA Bacterial Community ... | co-occurrence network | Scoop.it
.@CorrieMoreau FYI on the 16S comparison paper here’s a related @iontorrent post: http://t.co/rHlN5SQwfY
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Escherichia Coli in Microbial Ecology

Escherichia Coli in Microbial Ecology | co-occurrence network | Scoop.it
Escherichia Coli in Microbial Ecology The most complex ecosystems known in microbial ecology is the animal gastrointestinal tract, with over 1000 bacteria per gram of stool (Battistuzzi et al.,2004...
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One genome from many

One genome from many | co-occurrence network | Scoop.it
Researchers extract genome for single organism from water sample.

Via Gerd Moe-Behrens
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