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Rescooped by Dmitry Alexeev from Microbes Inside
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Bacterial colonization factors control specificity and stability of the gut microbiota : Nature : Nature Publishing Group

Bacterial colonization factors control specificity and stability of the gut microbiota : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Mammals harbour a complex gut microbiome, comprising bacteria that confer immunological, metabolic and neurological benefits.

Via Clara Belzer
Dmitry Alexeev's insight:

polysaccharide utilization loci found resposible for success of colonization


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Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee : Nature Communications : Nature Publishing Group

Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee : Nature Communications : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
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should we look for coffee degrading bugs in starbucks customers?)

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PLOS Pathogens: Risks of Antibiotic Exposures Early in Life on the Developing Microbiome

PLOS Pathogens: Risks of Antibiotic Exposures Early in Life on the Developing Microbiome | Systems biology and bioinformatics | Scoop.it
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altered microbiome and tissue development in infants

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Conducting a Microbiome Study

Conducting a Microbiome Study | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

Starting a micorbiome study?

Don't forget to do read through

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Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota | Systems biology and bioinformatics | Scoop.it
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before mismatch diseases we were like this)

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Ranking in interconnected multilayer networks reveals versatile nodes

Ranking in interconnected multilayer networks reveals versatile nodes | Systems biology and bioinformatics | Scoop.it

The determination of the most central agents in complex networks is important because they are responsible for a faster propagation of information, epidemics, failures and congestion, among others. A challenging problem is to identify them in networked systems characterized by different types of interactions, forming interconnected multilayer networks. Here we describe a mathematical framework that allows us to calculate centrality in such networks and rank nodes accordingly, finding the ones that play the most central roles in the cohesion of the whole structure, bridging together different types of relations. These nodes are the most versatile in the multilayer network. We investigate empirical interconnected multilayer networks and show that the approaches based on aggregating—or neglecting—the multilayer structure lead to a wrong identification of the most versatile nodes, overestimating the importance of more marginal agents and demonstrating the power of versatility in predicting their role in diffusive and congestion processes.

 

Ranking in interconnected multilayer networks reveals versatile nodes
Manlio De Domenico, Albert Solé-Ribalta, Elisa Omodei, Sergio Gómez & Alex Arenas

Nature Communications 6, Article number: 6868 http://dx.doi.org/10.1038/ncomms7868 ;


Via Complexity Digest
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 insight on the networks

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Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes - Sanders - 2014 - Molecular Ecology - Wiley Online Library

Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes - Sanders - 2014 - Molecular Ecology - Wiley Online Library | Systems biology and bioinformatics | Scoop.it
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RNA chaperones buffer deleterious mutations in E. coli

RNA chaperones buffer deleterious mutations in E. coli | Systems biology and bioinformatics | Scoop.it

тумукBoth proteins and RNAs can misfold into non-functional conformations. Protein chaperones promote native folding of nascent polypeptides and re-folding of misfolded species, thereby buffering mutations that compromise protein structure and function. Here we show that RNA chaperones can also act as mutation buffers that enhance organismal fitness. Using competition assays, we demonstrate that overexpression of select RNA chaperones, including three DEAD box RNA helicases (CsdA, SrmB, RhlB) and the cold shock protein CspA, improves fitness of two independently evolved E. coli mutator strains that have accumulated deleterious mutations during short- and long-term laboratory evolution. We identify strain-specific mutations that are deleterious and subject to buffering when introduced individually into the ancestral genotype. For DEAD box RNA helicases we show that buffering requires helicase activity, implicating RNA structural remodelling in the buffering process. Our results suggest that RNA chaperones might play a fundamental role in RNA evolution and evolvability.

Dmitry Alexeev's insight:

never heard it before - RNA chaperones - they buffer the mutations

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Home : npj Biofilms and Microbiomes

Home : npj Biofilms and Microbiomes | Systems biology and bioinformatics | Scoop.it
npj Biofilms and Microbiomes is a new open-access, online only multi- and interdisciplinary journal dedicated to publishing the finest research on microbial biofilms and microbiomes.
Dmitry Alexeev's insight:

new journal on microbiomes

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PLOS Computational Biology: Ten Simple Rules for Lifelong Learning, According to Hamming

PLOS Computational Biology: Ten Simple Rules for Lifelong Learning, According to Hamming | Systems biology and bioinformatics | Scoop.it
life of trying to achieve excellence in some area is in itself a worthy goal for your life.…[A] life without a struggle…is hardly a life worth living.”
Dmitry Alexeev's insight:

amazing

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Collective unconscious: how gut microbes shape human behavior

Collective unconscious: how gut microbes shape human behavior | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

root of uncosciousness

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Protein Complexes in Bacteria

Protein Complexes in Bacteria | Systems biology and bioinformatics | Scoop.it
Author Summary Though more than 20,000 binary protein-protein interactions have been published for a few well-studied bacterial species, the results rarely capture the full extent to which proteins take part in complexes. Here, we use experimentally-observed protein complexes from E . coli or Mycoplasma pneumoniae , as well as gene orthology, to predict protein complexes across many species of bacteria. Surprisingly, the majority of protein complexes is not conserved, demonstrating an une
Dmitry Alexeev's insight:

conservation of protein complex content is not constant in bacteria - is it because the places of some preitein in complexes were overtaken by other proteins?

how does it correspond to phylogeny and evolution?

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Frontiers | Macromolecular networks and intelligence in microorganisms | Microbiotechnology, Ecotoxicology and Bioremediation

Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of Information and Communication Technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity – particularly activity of the human brain – with a phenomenon we call “intelligence”. Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as “human” and “brain” out of the defining features of “intelligence”, all forms of life – from microbes to humans – exhibit some or all characteristics consistent with “intelligence”. We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo.
Dmitry Alexeev's insight:

Level of intelligence and computational mechanisms for intracellular calculations

 

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Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome : Nature : Nature Publishing Group

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
The intestinal tract is inhabited by a large and diverse community of microbes collectively referred to as the gut microbiota. While the gut microbiota provides important benefits to its host, especially in metabolism and immune development, disturbance of the microbiota-host relationship is associated with numerous chronic inflammatory diseases, including inflammatory bowel disease and the group of obesity-associated diseases collectively referred to as metabolic syndrome. A primary means by which the intestine is protected from its microbiota is via multi-layered mucus structures that cover the intestinal surface, thereby allowing the vast majority of gut bacteria to be kept at a safe distance from epithelial cells that line the intestine. Thus, agents that disrupt mucus-bacterial interactions might have the potential to promote diseases associated with gut inflammation. Consequently, it has been hypothesized that emulsifiers, detergent-like molecules that are a ubiquitous component of processed foods and that can increase bacterial translocation across epithelia in vitro, might be promoting the increase in inflammatory bowel disease observed since the mid-twentieth century. Here we report that, in mice, relatively low concentrations of two commonly used emulsifiers, namely carboxymethylcellulose and polysorbate-80, induced low-grade inflammation and obesity/metabolic syndrome in wild-type hosts and promoted robust colitis in mice predisposed to this disorder. Emulsifier-induced metabolic syndrome was associated with microbiota encroachment, altered species composition and increased pro-inflammatory potential. Use of germ-free mice and faecal transplants indicated that such changes in microbiota were necessary and sufficient for both low-grade inflammation and metabolic syndrome. These results support the emerging concept that perturbed host-microbiota interactions resulting in low-grade inflammation can promote adiposity and its associated metabolic effects. Moreover, they suggest that the broad use of emulsifying agents might be contributing to an increased societal incidence of obesity/metabolic syndrome and other chronic inflammatory diseases.
Dmitry Alexeev's insight:

should we test the chemicals one by one - or finally have a preassumption of thier influence on gut?

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Obesity: Medicinal mushroom reduces obesity by modulating microbiota : Nature Reviews Endocrinology : Nature Publishing Group

Obesity: Medicinal mushroom reduces obesity by modulating microbiota : Nature Reviews Endocrinology : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Ganoderma lucidum
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i've just ordered one )

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Genome Biology | Full text | Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

Average genome size is an important, yet often overlooked, property of microbial communities. We developed MicrobeCensus to rapidly and accurately estimate average genome size from shotgun metagenomic data and applied our tool to 1,352 human microbiome samples. We found that average genome size differs significantly within and between body sites and tracks with major functional and taxonomic differences. In the gut, average genome size is positively correlated with the abundance of Bacteroides and genes related to carbohydrate metabolism. Importantly, we found that average genome size variation can bias comparative analyses, and that normalization improves detection of differentially abundant genes.
Dmitry Alexeev's insight:

well size matters isn't it?

i enjoyed the difference in genome sizes between body habitats

 

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Frontiers | The Intestinal Microbiome in Early Life: Health and Disease | Immunotherapies and Vaccines

Frontiers | The Intestinal Microbiome in Early Life: Health and Disease | Immunotherapies and Vaccines | Systems biology and bioinformatics | Scoop.it
Human microbial colonization begins at birth and continues to develop and modulate in species abundance for about three years, until the microbiota becomes adult-like. During the same time period, ...
Dmitry Alexeev's insight:

i just like the infographics)

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Enterotoxigenic Bacteroides fragilis induces oncogenic regulatory T cells (TUM9P.1000)

Dmitry Alexeev's insight:

it is seen well because toxin is stromg, but what about other less strong toxins? from other gut bacteria

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Sanders: Disentangling the coevolutionary histories of animal gut microbiota - YouTube

Jon Sanders
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Manipulative Microbiomes | The Scientist Magazine®

Manipulative Microbiomes | The Scientist Magazine® | Systems biology and bioinformatics | Scoop.it
Cancer Cell
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one more idea on micorbial command center

 

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Primary transcripts of microRNAs encode regulatory peptides : Nature : Nature Publishing Group

Primary transcripts of microRNAs encode regulatory peptides : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
MicroRNAs (miRNAs) are small regulatory RNA molecules that inhibit the expression of specific target genes by binding to and cleaving their messenger RNAs or otherwise inhibiting their translation into proteins. miRNAs are transcribed as much larger primary transcripts (pri-miRNAs), the function of which is not fully understood. Here we show that plant pri-miRNAs contain short open reading frame sequences that encode regulatory peptides. The pri-miR171b of Medicago truncatula and the pri-miR165a of Arabidopsis thaliana produce peptides, which we term miPEP171b and miPEP165a, respectively, that enhance the accumulation of their corresponding mature miRNAs, resulting in downregulation of target genes involved in root development. The mechanism of miRNA-encoded peptide (miPEP) action involves increasing transcription of the pri-miRNA. Five other pri-miRNAs of A. thaliana and M. truncatula encode active miPEPs, suggesting that miPEPs are widespread throughout the plant kingdom. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications.
Dmitry Alexeev's insight:

miRNA peptides found active in plants

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New drug for Crohn's disease targets RNA

New drug for Crohn's disease targets RNA | Systems biology and bioinformatics | Scoop.it
If eventually approved, treatment would be among a handful of its kind
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Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics

Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics | Systems biology and bioinformatics | Scoop.it
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ribust genetic engeneering platform for gene function elucidation in vivo

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Restriction-Modification Systems as Mobile Epigenetic Elements - Madame Curie Bioscience Database - NCBI Bookshelf

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RM systems review 

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An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks

An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks | Systems biology and bioinformatics | Scoop.it
Author Summary The ever growing amount of genomic data enables the assembly of large-scale network models that can provide important new insights into living systems. However, assembly and validation of such large-scale models can be challenging, since we often lack sufficient information to make accurate predictions. This work describes a new approach for constructing large-scale transcriptional regulatory networks of individual cells. We show that the reconstructed network captures a signif
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guide for trn reconstruction in bacteria

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Separating the microbiome from the hyperbolome

Dmitry Alexeev's insight:

comprehensive point of view on translation in microbiome - nothing has been ever translated so quickly - indeed

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