Systems biology and bioinformatics
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Gene activity and transcript patterns visualized for the first time in thousands of single cells

Gene activity and transcript patterns visualized for the first time in thousands of single cells | Systems biology and bioinformatics | Scoop.it
Biologists of the University of Zurich have developed a method to visualize the activity of genes in single cells. The method is so efficient that, for the first time, a thousand genes can be studied in parallel in ten thousand single human cells.

 

Applications lie in fields of basic research and medical diagnostics. The new method shows that the activity of genes, and the spatial organization of the resulting transcript molecules, strongly vary between single cells. Whenever cells activate a gene, they produce gene specific transcript molecules, which make the function of the gene available to the cell. The measurement of gene activity is a routine activity in medical diagnostics, especially in cancer medicine. Today's technologies determine the activity of genes by measuring the amount of transcript molecules. However, these technologies can neither measure the amount of transcript molecules of one thousand genes in ten thousand single cells, nor the spatial organization of transcript molecules within a single cell. The fully automated procedure, developed by biologists of the University of Zurich under the supervision of Prof. Lucas Pelkmans, allows, for the first time, a parallel measurement of the amount and spatial organization of single transcript molecules in ten thousands single cells. The results, which were recently published in the scientific journal Nature Methods, provide completely novel insights into the variability of gene activity of single cells.

 

The method developed by Pelkmans' PhD students Nico Battich and Thomas Stoeger is based upon the combination of robots, an automated fluorescence microscope and a supercomputer. "When genes become active, specific transcript molecules are produced. We can stain them with the help of a robot", explains Stoeger. Subsequently, fluorescence microscope images of brightly glowing transcript molecules are generated. Those images were analyzed with the supercomputer Brutus, of the ETH Zurich. With this method, one thousand human genes can be studied in ten thousand single cells. According to Pelkmans, the advantages of this method are the high number of single cells and the possibility to study, for the first time, the spatial organization of the transcript molecules of many genes.

The analysis of the new data shows that individual cells distinguish themselves in the activity of their genes. While the scientists had been suspecting a high variability in the amount of transcript molecules, they were surprised to discover a strong variability in the spatial organization of transcript molecules within single cells and between multiple single cells. The transcript molecules adapted distinctive patterns.

 

The importance of these new insights was summarized by Pelkmans: "Our method will be of importance to basic research and the understanding of cancer tumors because it allows us to map the activity of genes within single tumor cells.


Via Dr. Stefan Gruenwald
Dmitry Alexeev's insight:

i would expect to find more tricky distributions of the gene expression pattern among cells - but... however it looks that the high throughputness is being reaching via automatization and robotization either then novell principles

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Understanding the interactions between bacteria in the human gut through metabolic modeling : Scientific Reports : Nature Publishing Group

Understanding the interactions between bacteria in the human gut through metabolic modeling : Scientific Reports : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
The human gut microbiome plays an influential role in maintaining human health, and it is a potential target for prevention and treatment of disease.
Dmitry Alexeev's insight:

little bit on metabolomic modelling from gurus. Surprising is the journal chosen for that

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Ex vivo systems to study host–microbiota interactions in the gastrointestinal tract

Ex vivo systems to study host–microbiota interactions in the gastrointestinal tract | Systems biology and bioinformatics | Scoop.it

It is increasingly apparent that the microbial ecosystems in the mammalian gastrointestinal tract play an intricate role in health and disease. There is a growing interest in the development of targeted strategies for modulating health through the modification of these microbiota.

Ecologists are faced with the challenge of understanding the structure and function of ecosystems, the component parts of which interact with each other in complex and diffuse ways. The human gut microbiota, with its high species richness and diversity (up to 1000 bacterial species per individual) including members of all three domains of life, situated in the dynamic environment of the gastrointestinal tract, is probably among the most complex ecosystems on this planet.

In order to elucidate the mechanistic foundations, and physiological significance, of beneficial or pathogenic relationships between the gut microbiota and their hosts, researchers require tractable model ecosystems that allow to recapitulate and investigate host–microbe and microbe–microbe interactions. This review discusses ex vivo gastrointestinal models systems that can be used to gain mechanistic insights into the emergent properties of the host–microbial superorganism.

Dmitry Alexeev's insight:

Do you think it is ever possible to construct an ex-vivo system for that?

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CoGe: Comparative Genomics

CoGe: Comparative Genomics | Systems biology and bioinformatics | Scoop.it
The CoGe Comparative Genomics Platform. A software suite of interlinked and interconnected web-based tools for easily visualizing, comparing, and understanding the evolution, struture and dynamics of genomes.
Dmitry Alexeev's insight:
Lets take a look at bac genome comparison?
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PLOS Computational Biology: Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation

PLOS Computational Biology: Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation | Systems biology and bioinformatics | Scoop.it

Several key proteins of the heat shock response became centers of heat shock-induced local communities, as well as bridges providing a residual connection of modules after heat shock. The observed changes resemble to a ‘stratus-cumulus’ type transition of the interactome structure, since the unstressed yeast interactome had a globally connected organization, similar to that of stratus clouds, whereas the heat shocked interactome had a multifocal organization, similar to that of cumulus clouds. Our results showed that heat shock induces a partial disintegration of the global organization of the yeast interactome. This change may be rather general occurring in many types of stresses. Moreover, other complex systems, such as single proteins, social networks and ecosystems may also decrease their inter-modular links, thus develop more compact modules, and display a partial disintegration of their global structure in the initial phase of crisis. Thus, our work may provide a model of a general, system-level adaptation mechanism to environmental changes.

  
Dmitry Alexeev's insight:

networks... heatshock,,, yummy)

 

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Network deconvolution as a general method to distinguish direct dependencies in networks

Network deconvolution as a general method to distinguish direct dependencies in networks | Systems biology and bioinformatics | Scoop.it

Recognizing direct relationships between variables connected in a network is a pervasive problem in biological, social and information sciences as correlation-based networks contain numerous indirect relationships. Here we present a general method for inferring direct effects from an observed correlation matrix containing both direct and indirect effects. We formulate the problem as the inverse of network convolution, and introduce an algorithm that removes the combined effect of all indirect paths of arbitrary length in a closed-form solution by exploiting eigen-decomposition and infinite-series sums. We demonstrate the effectiveness of our approach in several network applications: distinguishing direct targets in gene expression regulatory networks; recognizing directly interacting amino-acid residues for protein structure prediction from sequence alignments; and distinguishing strong collaborations in co-authorship social networks using connectivity information alone. In addition to its theoretical impact as a foundational graph theoretic tool, our results suggest network deconvolution is widely applicable for computing direct dependencies in network science across diverse disciplines.

 

Network deconvolution as a general method to distinguish direct dependencies in networks
Soheil Feizi, Daniel Marbach, Muriel Médard & Manolis Kellis

Nature Biotechnology 31, 726–733 (2013) http://dx.doi.org/10.1038/nbt.2635


Via Complexity Digest
Dmitry Alexeev's insight:

complexity is paving the way - now we look for directed graph

 

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Accurate and universal delineation of prokaryotic species

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The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool;http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.

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Earth is surrounded by a 'bubble' of live bacteria - at 33 000 feet

Earth is surrounded by a 'bubble' of live bacteria - at 33 000 feet | Systems biology and bioinformatics | Scoop.it

Earth’s upper atmosphere—below freezing, nearly without oxygen, flooded by UV radiation—is no place to live. But last winter, scientists from the Georgia Institute of Technology discovered that billions of bacteria actually thrive up there. Expecting only a smattering of microorganisms, the researchers flew six miles above Earth’s surface in a NASA jet plane. There, they pumped outside air through a filter to collect particles. Back on the ground, they tallied the organisms, and the count was staggering: 20 percent of what they had assumed to be just dust or other particles was alive. Earth, it seems, is surrounded by a bubble of bacteria.

 

Scientists don’t yet know what the bacteria are doing up there, but they may be essential to how the atmosphere functions, says Kostas Konstantinidis, an environmental microbiologist on the Georgia Tech team. For example, they could be responsible for recycling nutrients in the atmosphere, like they do on Earth. And similar to other particles, they could influence weather patterns by helping clouds form. However, they also may be transmitting diseases from one side of the globe to the other. The researchers found E. coli in their samples (which they think hurricanes lifted from cities), and they plan to investigate whether plagues are raining down on us. If we can find out more about the role of bacteria in the atmosphere, says Ann Womack, a microbial ecologist at the University of Oregon, scientists could even fight climate change by engineering the bacteria to break down greenhouse gases into other, less harmful compounds.


Via Dr. Stefan Gruenwald, Pedro Barbosa
Dmitry Alexeev's insight:

we'll have that one in our book as well

 

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Vloasis's curator insight, June 21, 2013 3:51 PM

Holy crap!  I never considered this...

Ed Rybicki's comment, June 25, 2013 3:39 AM
Hey, it's a microbial world - literally! From way above our heads, to way below our feet.
Dmitry Alexeev's curator insight, June 27, 2013 1:21 AM

we are everywhere)

Rescooped by Dmitry Alexeev from CBiB - Bordeaux Bioinformatics Center
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Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools | BMC Genomics

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools | BMC Genomics | Systems biology and bioinformatics | Scoop.it
De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity.

Via CBiB
Dmitry Alexeev's insight:

fine review and test for available techniques

 

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Dmitry Alexeev's curator insight, April 22, 2013 1:04 PM

a lot ... A LOT ... on genomic tools comparisons

 

Rescooped by Dmitry Alexeev from Complexity & Systems
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Amazing bead chain experiment in slow motion - Slo Mo #19 - Earth Unplugged

These beads seem to levitate, defy gravity and jump out of the beaker. But how and why do they act like this? We met up with Steve Mould, the science guy from Britain's Brightest, to explore the science behind the "self siphoning beads" - also known as "Newton's Beads".

To get a closer look at the phenomenon, we filmed them in slow motion to try to work out what exactly was happening, and how the behaviour changes with height.

 

 


Via Bernard Ryefield
Dmitry Alexeev's insight:

not that much of biology - so far (if we don't think of dna) 

however the slow motion is amazing

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PLOS Computational Biology: A Family of Algorithms for Computing Consensus about Node State from Network Data

PLOS Computational Biology: A Family of Algorithms for Computing Consensus about Node State from Network Data | Systems biology and bioinformatics | Scoop.it
PLOS Computational Biology is an open-access
Dmitry Alexeev's insight:

consensus of the network about this very node being meaningful

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The mycoplasma virulence factor lipoprotein MslA is a novel polynucleotide binding protein

Dmitry Alexeev's insight:

We are sure the function is not transport - but regulation

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Horizons in Social Sciences 2013

Horizons in Social Sciences 2013 | Systems biology and bioinformatics | Scoop.it

Nowadays there is an ongoing intense scientific debate around the definition of the foundational concepts as well as about the most appropriate methodological approaches to deal with the understanding of social dynamics. The challenge of understanding human behaviors is complex and intricate. Humans are intentional (and not necessarily rational) and the dynamics of social behavior are influenced by multitude of factors. In particular, with the advent of the Big Data era– i.e. the explosion of available datasets from technological mediated communication – that challenge has increased its complexity. If on the one hand we can have access to an enormous set of observable social and mobility traces, on the other hand there is a lack of theoretical concepts to ground and interpret data as an expression of individual and social behavior. The event is intended to gather the most proficient scientists and companies working at the edge of the computational social science and big data to detail the new frontiers and challenges with an interdisciplinary, tight and non reductionist approach.The symposium is open to all researchers, scientists and practitioners.

 

Invited Speakers: Alessandro Vespignani, David Lazer, Nicola Santoro

 

July 11, 2013 - IMT Lucca, Italy

http://networks.imtlucca.it/index.php/events


Via Complexity Digest
Dmitry Alexeev's insight:

this is what we will do when manage all current stuff - build a social bacteria network)

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Gene activity and transcript patterns visualized for the first time in thousands of single cells

Gene activity and transcript patterns visualized for the first time in thousands of single cells | Systems biology and bioinformatics | Scoop.it
Biologists of the University of Zurich have developed a method to visualize the activity of genes in single cells. The method is so efficient that, for the first time, a thousand genes can be studied in parallel in ten thousand single human cells.

 

Applications lie in fields of basic research and medical diagnostics. The new method shows that the activity of genes, and the spatial organization of the resulting transcript molecules, strongly vary between single cells. Whenever cells activate a gene, they produce gene specific transcript molecules, which make the function of the gene available to the cell. The measurement of gene activity is a routine activity in medical diagnostics, especially in cancer medicine. Today's technologies determine the activity of genes by measuring the amount of transcript molecules. However, these technologies can neither measure the amount of transcript molecules of one thousand genes in ten thousand single cells, nor the spatial organization of transcript molecules within a single cell. The fully automated procedure, developed by biologists of the University of Zurich under the supervision of Prof. Lucas Pelkmans, allows, for the first time, a parallel measurement of the amount and spatial organization of single transcript molecules in ten thousands single cells. The results, which were recently published in the scientific journal Nature Methods, provide completely novel insights into the variability of gene activity of single cells.

 

The method developed by Pelkmans' PhD students Nico Battich and Thomas Stoeger is based upon the combination of robots, an automated fluorescence microscope and a supercomputer. "When genes become active, specific transcript molecules are produced. We can stain them with the help of a robot", explains Stoeger. Subsequently, fluorescence microscope images of brightly glowing transcript molecules are generated. Those images were analyzed with the supercomputer Brutus, of the ETH Zurich. With this method, one thousand human genes can be studied in ten thousand single cells. According to Pelkmans, the advantages of this method are the high number of single cells and the possibility to study, for the first time, the spatial organization of the transcript molecules of many genes.

The analysis of the new data shows that individual cells distinguish themselves in the activity of their genes. While the scientists had been suspecting a high variability in the amount of transcript molecules, they were surprised to discover a strong variability in the spatial organization of transcript molecules within single cells and between multiple single cells. The transcript molecules adapted distinctive patterns.

 

The importance of these new insights was summarized by Pelkmans: "Our method will be of importance to basic research and the understanding of cancer tumors because it allows us to map the activity of genes within single tumor cells.


Via Dr. Stefan Gruenwald
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Dmitry Alexeev's curator insight, October 8, 2013 2:45 AM

i would expect to find more tricky distributions of the gene expression pattern among cells - but... however it looks that the high throughputness is being reaching via automatization and robotization either then novell principles

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Do You Know Jack? Look Inside: A Young Scientist’s Cancer Discovery

Do You Know Jack? Look Inside: A Young Scientist’s Cancer Discovery | Systems biology and bioinformatics | Scoop.it
At 15 years old, Andraka made a radical discovery. The invention was a novel paper sensor that could detect pancreatic cancer -- as well as ovarian and lung cancer -- in the early stages.
Dmitry Alexeev's insight:

well what to say - impresive and insipring

 

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Community-Analyzer: A platform for visualizing and comparing microbial community structure across microbiomes

Community-Analyzer: A platform for visualizing and comparing microbial community structure across microbiomes | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

community analyzer for bactrial biomes made in india

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Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review | BenthamScience

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review | BenthamScience | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into ‘cumulus-type’, i.e., those similar to puffy (white) clouds, and ‘stratus-type’, i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher rigidity of the individual units; there the conformational changes can be described by an ‘energy transfer’ mechanism. In the second class, the topology presents a compact structure with significant overlap between the modules; there the conformational changes can be described by ‘multi-trajectories’; that is, multiple highly populated pathways. We further propose that disordered protein regions evolved to help other protein segments reach ‘rarely visited’ but functionally-related states. We also show the role of disorder in ‘spatial games’ of amino acids; highlight the effects of intrinsically disordered proteins (IDPs) on cellular networks and list some possible studies linking protein disorder and protein structure networks

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ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality

ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality | Systems biology and bioinformatics | Scoop.it

Summary: The ModuLand plug-in provides Cytoscape users an algorithm for determining extensively overlapping network modules. Moreover, it identifies several hierarchical layers of modules, where meta-nodes of the higher hierarchical layer represent modules of the lower layer. The tool assigns module cores, which predict the function of the whole module, and determines key nodes bridging two or multiple modules. The plug-in has a detailed JAVA-based graphical interface with various colouring options. The ModuLand tool can run on Windows, Linux or Mac OS. We demonstrate its use on protein structure and metabolic networks.

Dmitry Alexeev's insight:

Makes sense for our data on networks

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3,500+ species discovered in Lake Vostok, underneath miles of ice, in conditions similar to Jupiter’s Europa | ExtremeTech

3,500+ species discovered in Lake Vostok, underneath miles of ice, in conditions similar to Jupiter’s Europa | ExtremeTech | Systems biology and bioinformatics | Scoop.it
After much controversy and an array of scientific challenges, researchers are finally ready to confirm that life in Lake Vostok doesn't just exist -- it thrives.

Via Pedro Barbosa
Dmitry Alexeev's insight:

this are heroes of our book - bacteria under ice - not power input and high pressure of ice - parallel evolution totally

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Rescooped by Dmitry Alexeev from Microbes Inside
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New immune system discovered - Medical Xpress - Medical Xpress

New immune system discovered - Medical Xpress - Medical Xpress | Systems biology and bioinformatics | Scoop.it
New immune system discovered - Medical Xpress Medical Xpress "We envision BAM influencing the prevention and treatment of mucosal infections seen in the gut and lungs, having applications for phage therapy and even directly interacting with the...

Via Gilbert C FAURE, Clara Belzer
Dmitry Alexeev's insight:

one of the ways various ways to control that wild kingdom of bacterias inside the gut)

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Cicada wings inspire new ideas for antibacterial products

Cicada wings inspire new ideas for antibacterial products | Systems biology and bioinformatics | Scoop.it
Here’s another reason to love cicadas: A new study has found that tiny structures on cicada wings can kill bacteria through physical and not chemical means.

Via Sakis Koukouvis
Dmitry Alexeev's insight:

bacterial membrane disruption through nano tech

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Greg Wurn's curator insight, March 4, 2014 9:20 PM

Interesting, could lead to some very important discoveries in future

Corie Rosen's curator insight, February 29, 2016 8:58 PM

Antibiotic resistance is nothing new; it is a very real threat in the world today. Bacteria are mutating and resisting our best tools at a rate that modern scientists can't keep up with. They say you learn something new everyday, and this was something I had no idea about until now! I flocked to this article because it is definitely an interesting concept. What is even cooler is the fact that a cicada's wings are able to kill gram-negative bacteria (gram-positive aren't affected), such as E. coli, through physical means and not chemical. This means the bacteria are unlikely to become resistant to the affects! Just imagine the ways scientists can utilize this!

 

This article, while not a scientific report, references the study done by scientists and provides links to it, therefore making the article a reliable source of information.

Janice Edgerly-Rooks's curator insight, September 12, 2016 9:36 PM
One wonders why bacteria would make a difference to a cicada's wings. They live underground as immatures which makes me think that antibacterial properties might derive from that part of their life cycle. But they don't have wings, so this is curious indeed.
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Illumina Announces Moleculo Long Read Technology and Phasing As Service

Illumina Announces Moleculo Long Read Technology and Phasing As Service | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

if your genome is over 100 m bp - the service is for you in only 12 weeks

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Ecological forces structure your body's personal mix of microbes - UW Today

Ecological forces structure your body's personal mix of microbes - UW Today | Systems biology and bioinformatics | Scoop.it
UW Today
Ecological forces structure your body's personal mix of microbes
UW Today
... Elhanan Borenstein, the lead scientist on the project.
Dmitry Alexeev's insight:

computation of microbial community and host interactio - tyakht is shooting an oral report this monday live)

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BMC Bioinformatics | Full text | MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information

A central challenge to understanding the ecological and biogeochemical roles of microorganisms in natural and human engineered ecosystems is the reconstruction of metabolic interaction networks from environmental sequence information.
Dmitry Alexeev's insight:

wonderful to know if this is applicable to gut microbiota

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With a little help from my phage friend

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Christina Tobin KåhrströmNature Reviews Genetics (2013) doi:10.1038/nrg3532Published online 25 June 2013
Mounting evidence suggests that the gut microbiota has a considerable impact on host physiology, but how the functional capacity of the microbiota is maintained after exposure to environmental stresses is unclear. Now, Collins and colleagues report that following antibiotic perturbation, the resident phage population provides the microbiota with a reservoir of advantageous genes, suggesting that the phage metagenome preserves the functional robustness of the microbiota on exposure to environmental stress. 
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