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The ISME Journal - Abstract of article: Metagenomic mining for microbiologists

Microbial ecologists can now start digging into the accumulating mountains of metagenomic data to uncover the occurrence of functional genes and their correlations to microbial community members. Limitations and biases in DNA extraction and sequencing technologies impact sequence distributions, and therefore, have to be considered. However, when comparing metagenomes from widely differing environments, these fluctuations have a relatively minor role in microbial community discrimination. As a consequence, any functional gene or species distribution pattern can be compared among metagenomes originating from various environments and projects. In particular, global comparisons would help to define ecosystem specificities, such as involvement and response to climate change (for example, carbon and nitrogen cycle), human health risks (eg, presence of pathogen species, toxin genes and viruses) and biodegradation capacities. 

 

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getting ready to our first soil metagenome article

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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.
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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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My No-Soap, No-Shampoo, Bacteria-Rich Hygiene Experiment

My No-Soap, No-Shampoo, Bacteria-Rich Hygiene Experiment | Systems biology and bioinformatics | Scoop.it
What happens when you leave cleanliness up to your microbiome?
Dmitry Alexeev's insight:

I never heard it before on AObiome+ pructs

restoring innate ability to prouce fine fragrance is great

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Huang and Boushey provide their... - Journal of Allergy and Clinical Immunology | Facebook

Huang and Boushey provide their perspective on the findings of studies of differences in the airway microbiome in patients with asthma vs. healthy...
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Microbiomes of lungs
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Squid uses luminescent bacteria to match moonlight welling down from above to cancel out its own shadow

Squid uses luminescent bacteria to match moonlight welling down from above to cancel out its own shadow | Systems biology and bioinformatics | Scoop.it

The aquarium looks empty, but there is something in it. A pair of eyes stick out from the sandy floor, and their owner is easily scooped up into a glass bowl. At first, the creature looks like a hazelnut truffle — small, round and covered in tiny flecks. But with a gentle shake, the flecks of sand fall off to reveal a female Hawaiian bobtail squid (Euprymna scolopes), about the size of a thumb. As she jets furiously around the bowl, discs of pigment bloom and fade over her skin like a living pointillist painting.


There are no other animals in the bowl, but the squid is not alone. Its undersides contain a two-chambered light organ that is full of glowing bacteria called Vibrio fischeri. In the wild, their luminescence is thought to match the moonlight welling down from above and cancel out the squid's shadow, hiding the animal from predators. From below, the squid is invisible. From above, it is adorable. “They're just so beautiful,” says Margaret McFall-Ngai, a zoologist at the University of Wisconsin–Madison. “They're phenomenal lab animals.”


Few things excite McFall-Ngai more than the partnership between the bobtail squid and V. fischeri — and that is after studying it for more than 26 years. Over that time, she has shown that this symbiotic relationship is more intimate than anyone had imagined. She has found that the bacterium out-competes other microbes to establish an entirely faithful relationship with one host. It interacts with the squid's immune system, guides its body clock and shapes its early development by transforming its body.




Via Dr. Stefan Gruenwald
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cast no shadow

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Blood Work: Scientists Uncover Surprising New Tools to Rejuvenate the Brain | ucsf.edu

Blood Work: Scientists Uncover Surprising New Tools to Rejuvenate the Brain | ucsf.edu | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

its none systems biology non bioinformatics... yet)

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Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

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.
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looks amazing on our data

 

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Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome

Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome | Systems biology and bioinformatics | Scoop.it
eding/fasting cycle influence host metabolism and contribute to obesity and metabolic diseases. However, fundamental characteristics of this relationship between the feeding/fasting cycle and the gut microbiome are unknown. Our studies show that the gut microbiome is highly dynamic, exhibiting daily cyclical fluctuations in composition. Diet-induced obesity dampens the daily feeding/fasting rhythm and diminishes many of these cyclical fluctuations. Time-restricted feeding (TRF), in which feeding is consolidated to the nocturnal phase, partially restores these cyclical fluctuations. Furthermore, TRF, which protects against obesity and metabolic diseases, affects bacteria shown to influence host metabolism. Cyclical changes in the gut microbiome from feeding/fasting rhythms contribute to the diversity of gut microflora and likely represent a mechanism by which the gut microbiome affects host metabolism. Thus, feeding pattern and time of harvest, in addition to diet, are important parameters when assessing the microbiome’s contribution to host metabolism.
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fasting and microbiome dynamics

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Potential of fecal microbiota for early-stage detection of colorectal cancer - Zeller - 2014 - Molecular Systems Biology - Wiley Online Library

Potential of fecal microbiota for early-stage detection of colorectal cancer - Zeller - 2014 - Molecular Systems Biology - Wiley Online Library | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

not that systematic - but the point is 20 per cent more sensitivity

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SciCurve - Understand your Field of Research.

SciCurve - Understand your Field of Research. | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

exactly what I was looking for today - graphs of keyword publishsing and citing

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Kinetic competition during the transcription cycle results in stochastic RNA processing. - Abstract - Europe PubMed Central

Abstract: Synthesis of mRNA in eukaryotes involves the coordinated action of many enzymatic processes, including initiation, elongation, splicing and...
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looks just amazing how they can totally measure all the processes in one gene

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Genome Medicine | Abstract | Modules, networks and systems medicine for understanding disease and aiding diagnosis

Genome Medicine | Abstract | Modules, networks and systems medicine for understanding disease and aiding diagnosis | Systems biology and bioinformatics | Scoop.it
Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but functional understanding is a formidable challenge. Network-based analyses of omics data have identified modules of disease-associated genes that have been used to obtain both a systems level and a molecular understanding of disease mechanisms. For example, in allergy a module was used to find a novel candidate gene that was validated by functional and clinical studies. Such analyses play important roles in systems medicine. This is an emerging discipline that aims to gain a translational understanding of the complex mechanisms underlying common diseases. In this review, we will explain and provide examples of how network-based analyses of omics data, in combination with functional and clinical studies, are aiding our understanding of disease, as well as helping to prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve significant problems and limitations, which will be discussed. We also highlight the steps needed for clinical implementation.
Dmitry Alexeev's insight:

systems medicine in translation

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Rethinking “Enterotypes”

Rethinking “Enterotypes” | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

Took Rob Knight a while to publish work 

we ssaw it in 2012 in Paris

http://www.cell.com/cell-host-microbe/pdfExtended/S1931-3128(14)00346-1 - here is full version

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Separating the microbiome from the hyperbolome

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

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A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples | Systems biology and bioinformatics | Scoop.it
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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very very very fast tool)

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Voluntary and forced exercise differentially alter the gut microbiome in C57BL/6J mice

Dmitry Alexeev's insight:

taking excercises voluntarily is spmething different)

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A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes

A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

network science allows for new approaches to disease analysis

 

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Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches

Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches | Systems biology and bioinformatics | Scoop.it
Moderate consumption of wine seems to produce positive health effects derived from the occurrence of bioactive polyphenols. The gut microbiota is involved in the metabolism of phenolic compounds, and these compounds and/or their metabolites may modulate gut microbiota through the stimulation of the growth of beneficial bacteria and the inhibition of pathogenic bacteria. The characterization of bacterial metabolites derived from polyphenols is essential in order to understand their effects, inclu
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we just like wine and microbiota)

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping: Cell

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping: Cell | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

holy crap)

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Ben Althouse on Diseases as Complex Systems

Ben Althouse on Diseases as Complex Systems | Systems biology and bioinformatics | Scoop.it

щлThis is the first in a series of interviews highlighting the work of experts in the field of complex systems science. Dr. Ben Althouse, an Omidyar Fellow at the Santa Fe Institute, is a mathematical epidemiologist focusing on the dynamics of infectious disease transmission. Ben holds both an ScM in Biostatistics and a PhD in Epidemiology from the Johns Hopkins Bloomberg School of Public Health where he focused on understanding Dengue fever and other sylvatic mosquito-borne viruses (arboviruses) in Senegal using mechanistic modeling and the SIR model. Dr. Althouse also attended the Santa Fe Institute’s Complex Systems Summer School during his graduate studies.


Via Jorge Louçã
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An enteric virus can replace the beneficial function of commensal bacteria : Nature : Nature Publishing Group

An enteric virus can replace the beneficial function of commensal bacteria : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Intestinal microbial communities have profound effects on host physiology. Whereas the symbiotic contribution of commensal bacteria is well established, the role of eukaryotic viruses that are present in the gastrointestinal tract under homeostatic conditions is undefined. Here we demonstrate that a common enteric RNA virus can replace the beneficial function of commensal bacteria in the intestine. Murine norovirus (MNV) infection of germ-free or antibiotic-treated mice restored intestinal morphology and lymphocyte function without inducing overt inflammation and disease. The presence of MNV also suppressed an expansion of group 2 innate lymphoid cells observed in the absence of bacteria, and induced transcriptional changes in the intestine associated with immune development and type I interferon (IFN) signalling. Consistent with this observation, the IFN-[agr] receptor was essential for the ability of MNV to compensate for bacterial depletion. Importantly, MNV infection offset the deleterious effect of treatment with antibiotics in models of intestinal injury and pathogenic bacterial infection. These data indicate that eukaryotic viruses have the capacity to support intestinal homeostasis and shape mucosal immunity, similarly to commensal bacteria.
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viral

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The metacommunity concept: a framework for multi-scale community ecology - Leibold - 2004 - Ecology Letters - Wiley Online Library

The metacommunity concept: a framework for multi-scale community ecology - Leibold - 2004 - Ecology Letters - Wiley Online Library | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

we are quite excited about meta-community inside meta-community theory application to viruses living in bacteria living in human

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There Is No ‘Healthy’ Microbiome

There Is No ‘Healthy’ Microbiome | Systems biology and bioinformatics | Scoop.it

IN the late 17th century, the Dutch naturalist Anton van Leeuwenhoek looked at his own dental plaque through a microscope and saw a world of tiny cells “very prettily a-moving.” He could not have predicted that a few centuries later, the trillions of microbes that share our lives — collectively known as the microbiome — would rank among the hottest areas of biology.

These microscopic partners help us by digesting our food, training our immune systems and crowding out other harmful microbes that could cause disease. In return, everything from the food we eat to the medicines we take can shape our microbial communities — with important implications for our health. Studies have found that changes in our microbiome accompany medical problems from obesity to diabetes to colon cancer.


Via Complexity Digest
Dmitry Alexeev's insight:

Our microbes are truly part of us, and just as we are vast in our variety, so, too, are they. We must embrace this complexity if we hope to benefit from it.

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Rowan Norrie's curator insight, November 10, 2014 6:14 AM

The fascinating world of the microbiome and the opportunities it heralds for future medicine

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Biogeography and individuality shape function in the human skin metagenome : Nature : Nature Publishing Group

Biogeography and individuality shape function in the human skin metagenome : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

biogeography and reference free

 

we are getting deeper

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Abstract LB-155: Ovarian cancer-induced changes in the intestinal microbiota as potential biomarkers for early detection

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i actually doubt that microbiota can be a distinctive marker - unless we programm it

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