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Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plant Echinacea purpurea

Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plant Echinacea purpurea | Microbiome | Scoop.it

In this work we have studied the antagonistic interactions existing among cultivable bacteria isolated from three ecological niches (rhizospheric soil, roots, and stem/leaves) of the traditional natural medicinal plant Echinacea purpurea. The three compartments harbored different taxonomic assemblages of strains, which were previously reported to display different antibiotic resistance patterns, suggesting the presence of differential selective pressure due to antagonistic molecules in the three compartments. Antagonistic interactions were assayed by the cross-streak method and interpreted using a network-based analysis. In particular “within-niche inhibition” and “cross-niche inhibition'’ were evaluated among isolates associated with each compartment as well as between isolates retrieved from the three different compartments, respectively. Data obtained indicated that bacteria isolated from the stem/leaves compartment were much more sensitive to the antagonistic activity than bacteria from roots and rhizospheric soil. Moreover, both the taxonomical position and the ecological niche might influence the antagonistic ability/sensitivity of different strains. Antagonism could play a significant role in contributing to the differentiation and structuring of plant-associated bacterial communities.


Via Kemen Lab, Nina Dombrowski, Stéphane Hacquard
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Nutrient cross-feeding in the microbial world

Nutrient cross-feeding in the microbial world | Microbiome | Scoop.it

The stability and function of a microbial community depends on nutritional interactions among community members such as the cross-feeding of essential small molecules synthesized by a subset of the population. In this review, we describe examples of microbe–microbe and microbe–host cofactor cross-feeding, a type of interaction that influences the forms of metabolism carried out within a community. Cofactor cross-feeding can contribute to both the health and nutrition of a host organism, the virulence and persistence of pathogens, and the composition and function of environmental communities. By examining the impact of shared cofactors on microbes from pure culture to natural communities, we stand to gain a better understanding of the interactions that link microbes together, which may ultimately be a key to developing strategies for manipulating microbial communities with human health, agricultural, and environmental implications.


Via Kemen Lab, Stéphane Hacquard
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The Ecological Genomics of Fungi - Francis Martin

The Ecological Genomics of Fungi - Francis Martin | Microbiome | Scoop.it
This unique book covers a broad diversity of fungal systems and provides unique insight into the functions of those fungi in various ecosystems – from soil, to plant, to human. Bringing together fungal genomic information on a variety of lifestyles and traits, the book covers saprotrophism, pathogenesis (including biotrophs, hemibiotrophs, necrotrophs) and symbiosis. Advances in high-throughput sequencing now offer unprecedented opportunities for identification of novel key molecular mechanisms controlling plant-microbe interactions, evolution of fungi and developmentally- and ecologically-relevant traits, this book explores how these massive streams of fungal sequences can be exploited to gain a deeper understanding of the evolution of fungi and their ecological role. Although tremendous progress has been made in recent years in fungal genomics, thanks to the sequencing of over one hundred fungal genomes, until now no book has used this information to bridge fungal genomics, molecular ecology and ecology. Edited by a recognized leader in fungal genomics and soil metagenomics with over a decade of experience, Genomics & Metagenomics for Harnessing the Ecology of Fungi will be a useful resource for the experienced as well as the new researchers entering the field.
Via Plant Breeding and Genomics News
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Plant–microbe interactions as drivers of ecosystem functions relevant for the biodegradation of organic contaminants

Plant–microbe interactions as drivers of ecosystem functions relevant for the biodegradation of organic contaminants | Microbiome | Scoop.it

Highlights• Biotransformation is an ecosystem property.• Microbes are the main drivers in biotransformation.• Dispersal of chemicals and bacteria drives degradation effectiveness.• Ecosystem stability is increased by plant–microbe interactions


Via Francis Martin
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Tackling soil diversity with the assembly of large, complex metagenomes

The large volumes of sequencing data required to sample deeply the microbial communities of complex environments pose new challenges to sequence analysis. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires substantial computational resources. We combine two preassembly filtering approaches—digital normalization and partitioning—to generate previously intractable large metagenome assemblies. Using a human-gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes totaling 398 billion bp (equivalent to 88,000 Escherichia coli genomes) from matched Iowa corn and native prairie soils. The resulting assembled contigs could be used to identify molecular interactions and reaction networks of known metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes Orthology database. Nonetheless, more than 60% of predicted proteins in assemblies could not be annotated against known databases. Many of these unknown proteins were abundant in both corn and prairie soils, highlighting the benefits of assembly for the discovery and characterization of novelty in soil biodiversity. Moreover, 80% of the sequencing data could not be assembled because of low coverage, suggesting that considerably more sequencing data are needed to characterize the functional content of soil.
Via Stéphane Hacquard
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Rice bioengineers invent light tube array to debug genetic circuits

Rice bioengineers invent light tube array to debug genetic circuits | Microbiome | Scoop.it
Rice University bioengineers have created a toolkit that uses colored lights and engineered bacteria to bring both mathematical predictability and cut-and-paste simplicity to the world of genetic circuit design.“Life is controlled by DNA-based circuits, and these are similar to the circuits found in electronic devices like smartphones and computers,” said Rice bioengineer Jeffrey Tabor, the lead researcher on the project.“A major difference is that electrical engineers measure the signals flowing into and out of electronic circuits as voltage, whereas bioengineers measure genetic circuit signals as genes turning on and off.”In a paper appearing online in the journal Nature Methods, Tabor and colleagues, including graduate student and lead author Evan Olson, describe a new, ultra high-precision method for creating and measuring gene expression signals in bacteria by combining light-sensing proteins from photosynthetic algae with a simple array of red and green LED lights and standard fluorescent reporter genes.By varying the timing and intensity of the lights, the researchers were able to control exactly when and how much different genes were expressed. “Light provides us a powerful new method for reliably measuring genetic circuit activity,” said Tabor, an assistant professor of bioengineering who also teaches in Rice’s Ph.D. program in systems, synthetic and physical biology.“Our work was inspired by the methods that are used to study electronic circuits. Electrical engineers have tools likeoscilloscopes and function generators that allow them to measure how voltage signals flow through electrical circuits. Those measurements are essential for making multiple circuits work together properly, so that more complex devices can be built. We have used our light-based tools as a biological function generator and oscilloscope in order to similarly analyze genetic circuits.”If a gene is not “expressed,” it is turned off, and its product is not produced. The bacteria used in Tabor’s study have about 4,000 genes, while humans have about 20,000. The processes of life are coordinated by different combinations and timings of genes turning on and off.Each component of a genetic circuit acts on the input it receives — which may be one or more gene-expression products from other components — and produces its own gene-expression product as an output.By linking the right genetic components together, synthetic biologists like Tabor and his students construct genetic circuits that program cells to carry out complex functions, such as counting, having memory, growing into tissues, or diagnosing the signatures of disease in the body.

Via Dr. Stefan Gruenwald
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NutraIngredients: What's on our editorial calendar for 2014? - NutraIngredients.com

NutraIngredients: What's on our editorial calendar for 2014? - NutraIngredients.com | Microbiome | Scoop.it
NutraIngredients.com
NutraIngredients: What's on our editorial calendar for 2014?
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Weill Cornell Nets $75M for Cancer Center, Clinical Research - GenomeWeb

Weill Cornell Nets $75M for Cancer Center, Clinical Research - GenomeWeb | Microbiome | Scoop.it
Weill Cornell Nets $75M for Cancer Center, Clinical Research
GenomeWeb
The center also plans to use the gift to continue its efforts to recruit researchers and clinicians and to provide seed funding for innovative research projects.
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New Biomarker Development Alliance Aims to Address 'Urgent' Need for ... - GenomeWeb

New Biomarker Development Alliance Aims to Address 'Urgent' Need for ... - GenomeWeb | Microbiome | Scoop.it
New Biomarker Development Alliance Aims to Address 'Urgent' Need for ...
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New Projects Use Novel Techniques to Research Causes and Prevention of Preterm Birth

New Projects Use Novel Techniques to Research Causes and Prevention of Preterm Birth | Microbiome | Scoop.it
This article was originally published by GAPPS   (RT @gdarmsta: Univ Washingtron researchers will examine the role of the vaginal microbiome in preterm birth, http://t.co/MkWt6Jzt6I #BornTo…)...
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Is it really worth having your gut bacteria tested? - io9

Is it really worth having your gut bacteria tested? - io9 | Microbiome | Scoop.it
Is it really worth having your gut bacteria tested?
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Different Sponge Species Have Highly Specific, Stable Microbiomes - Science Daily (press release)

Different Sponge Species Have Highly Specific, Stable Microbiomes - Science Daily (press release) | Microbiome | Scoop.it
Different Sponge Species Have Highly Specific, Stable Microbiomes Science Daily (press release) 21, 2014 — The sea sponge is about as simple as an animal can get, but its associated bacterial community -- its microbiome -- is known to approach the...
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Cheese Made From Bacteria Between Your Toes and Other Bizarre Bio Art - Smithsonian

Cheese Made From Bacteria Between Your Toes and Other Bizarre Bio Art Smithsonian “Grow Your Own…Life After Nature,” an exhibition recently at Trinity College Dublin's Science Gallery, features 20 works—all art projects as much as science...
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More than 99 percent of microbes and viruses populating the oceans have not yet been cultivated in the lab

More than 99 percent of microbes and viruses populating the oceans have not yet been cultivated in the lab | Microbiome | Scoop.it
A fishing expedition of microscopic proportions led by University of Arizona ecologists revealed that the lines between virus types in nature are less blurred than previously thought.

 

Using lab-cultured bacteria as "bait," a team of scientists led by Matthew Sullivan has sequenced complete and partial genomes of about 10 million viruses from an ocean water sample in a single experiment.

 

The study, published online on July 14 by the journal Nature, revealed that the genomes of viruses in natural ecosystems fall into more distinct categories than previously thought. This enables scientists to recognize actual populations of viruses in nature for the first time.

 

"You could count the number of viruses from a soil or water sample in a microscope, but you would have no idea what hosts they infect or what their genomes were like," said Sullivan, an associate professor in the UA's Department of Ecology and Evolutionary Biology and member of the UA's BIO5 Institute. "Our new approach for the first time links those same viruses to their host cells. In doing so, we gain access to viral genomes in a way that opens up a window into the roles these viruses play in nature."

 

Sullivan's team developed a new approach called viral tagging, which uses cultivated bacterial hosts as "bait" to fish for viruses that infect that host. The scientists then isolate the DNA of those viruses and decipher their sequence.

 

"Instead of a continuum, we found at least 17 distinct types of viruses in a single sample of Pacific Ocean seawater, including several that are new to science – all associated with the single 'bait' host used in the experiment," Sullivan said.


"Microbes are now recognized as drivers of the biogeochemical engines that fuel Earth, and the viruses that infect them control these processes by transferring genes between microbes, killing them in great numbers and reprogramming their metabolisms," explained the first author of the study, Li Deng, a former postdoctoral researcher in Sullivan's lab who now is a research scientist at the Helmholtz Research Center for Environmental Health in Neuherberg, Germany. "Our study for the first time provides the methodology needed to match viruses to their host microbes at scales relevant to nature."

 

Getting a grip on the diversity of viruses infecting a particular host is critical beyond environmental sciences, Deng said, and has implications for understanding how viruses affect pathogens that cause human disease, which in turn is relevant for vaccine design and antiviral drug therapy.

 

Sullivan estimates that up to 99 percent of microbes that populate the oceans and drive global processes such as nutrient cycles and climate have not yet been cultivated in the lab, which makes their viruses similarly inaccessible.


Via Dr. Stefan Gruenwald
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Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution | Microbiome | Scoop.it

Abstract

 

Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant–microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.


Via Pierre-Marc Delaux, Jean-Michel Ané, Stéphane Hacquard
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Pierre-Marc Delaux's curator insight, July 17, 2014 2:57 PM

Yeah!! Online finally :)

Jean-Michel Ané's curator insight, July 17, 2014 3:28 PM

Paper from our lab!

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Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction | Microbiome | Scoop.it
Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.

Via Niklaus Grunwald, Francis Martin
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Steve Marek's curator insight, March 6, 2014 1:35 AM

this looks useful

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Nature's microbiome: introduction - Molecular Ecology Special Issue

Nature's microbiome: introduction - Molecular Ecology Special Issue | Microbiome | Scoop.it

In this special issue of Molecular Ecology, we present 28 articles incorporating molecular and bioinformatics tools to dissect the intimate and prolonged associations that define symbioses. We have organized these studies into three sections, focused on (i) the composition of symbiotic communities and how this varies across hosts, tissues and development, and in response to environmental change (‘The Dynamic Microbiome’); (ii) the roles that microbes play for their hosts and the underlying mechanisms behind these functions (‘Microbiome Function’); and (iii) the nature and mechanisms of interactions between hosts and symbionts and between the co-inhabiting symbionts themselves (‘The Interactive Microbiome’). These articles highlight the state-of-the-art in microbiome research, with novel discoveries for well-developed models and for other budding systems beyond the human realm.


Via Francis Martin
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Electro-Diet: Rhodopseudomonas palustris can pull electrons from minerals located deep inside soil and sediment

Electro-Diet: Rhodopseudomonas palustris can pull electrons from minerals located deep inside soil and sediment | Microbiome | Scoop.it
“Researchers have shown that the commonly found bacterium Rhodopseudomonas palustris can use natural conductivity to pull electrons from minerals located remotely in soil and sediment while remaining at the surface, where they absorb the sunlight needed to produce energy.”Led by Peter Girguis, the John L. Loeb Associate Professor of the Natural Sciences, and Arpita Bose, a post-doctoral fellow in Organismic and Evolutionary Biology, a team of researchers showed that the commonly found bacterium Rhodopseudomonas palustris can use natural conductivity to pull electrons from minerals located deep in soil and sediment while remaining at the surface, where they absorb the sunlight needed to produce energy. The study is described in a February 26 paper in Nature Communications."When you think about electricity and living organisms, most people default to Mary Shelley's Frankenstein, but we've long understood that all organisms actually use electrons -- what constitutes electricity -- to do work," Girguis said. "At the heart of this paper is a process called extracellular electron transfer (EET), which involves moving electrons in and out of cells. What we were able to show is that these microbes take up electricity, which goes into their central metabolism, and we were able to describe some of the systems that are involved in that process."In the wild, the microbes rely on iron to provide the electrons they need to fuel energy generation, but tests in the lab suggest the iron itself isn't critical for this process. By attaching an electrode to colonies of the microbes in the lab, researchers observed that they could take up electrons from a non-ferrous source, suggesting they might also use other electron-rich minerals -- such as other metals and sulfur compounds -- in the wild."That's a game-changer," Girguis said. "We have understood for a long time that the aerobic and anaerobic worlds interact mainly through the diffusion of chemicals into and out of those domains. Accordingly, we also believe this process of diffusion governs the rates of many biogeochemical cycles. But this research indicates…that this ability to do EET is, in a sense, an end-run around diffusion. That could change the way we think about the interactions between the aerobic and anaerobic worlds, and might change the way we calculate the rates of biogeochemical cycling."Using genetic tools, researchers were also able to identify a gene that is critical to the ability to take up electrons. When the gene was turned off, Girguis said, the microbes' ability to take up electrons dropped by about a third."We are very interested in understanding exactly what that role that gene plays in electron uptake," Girguis said. "Related genes are found throughout other microbes in nature, and we aren't exactly sure what they're doing in those microbes. This offers some tantalizing evidence that other microbes carry out this process as well."
Via Dr. Stefan Gruenwald
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Uncovering the secret world of the Plastisphere

Uncovering the secret world of the Plastisphere | Microbiome | Scoop.it
Scientists are revealing how microbes living on floating pieces of plastic marine debris affect the ocean ecosystem, and the potential harm they pose to invertebrates, humans and other animals. New research being presented here today delves deeper into the largely unexplored world of the 'Plastisphere' ...
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'Detox? Quite the opposite' - Regina Leader-Post

'Detox? Quite the opposite' - Regina Leader-Post | Microbiome | Scoop.it
Regina Leader-Post
'Detox? Quite the opposite' Regina Leader-Post Just as the Human Genome Project was created to identify every gene and its associated function, the Human Microbiome Project (HMP), started six years ago in the US, was created to...
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Amgen Partners with Broad, Mass General on IBD Drug Discovery - GenomeWeb

Amgen Partners with Broad, Mass General on IBD Drug Discovery - GenomeWeb | Microbiome | Scoop.it
Amgen Partners with Broad, Mass General on IBD Drug Discovery
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The partners will form a joint steering committee to select and guide projects. Financial ...
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uBiome Crowdfunded Over $350000 on Indiegogo, Now They are Raising ... - Crowdfund Insider

uBiome Crowdfunded Over $350000 on Indiegogo, Now They are Raising ... - Crowdfund Insider | Microbiome | Scoop.it
uBiome Crowdfunded Over $350000 on Indiegogo, Now They are Raising ...
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Different sponge species have highly specific, stable microbiomes - Phys.Org

Different sponge species have highly specific, stable microbiomes - Phys.Org | Microbiome | Scoop.it
Different sponge species have highly specific, stable microbiomes
Phys.Org
Credit: Map provided by the project Hotspot Ecosystems Research and Man's Impact on European Seas (HERMOINE).
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Damon Runyon's $2.3M Backs High-Risk, High-Reward Cancer Projects - GenomeWeb

Damon Runyon's $2.3M Backs High-Risk, High-Reward Cancer Projects - GenomeWeb | Microbiome | Scoop.it
Damon Runyon's $2.3M Backs High-Risk, High-Reward Cancer Projects
GenomeWeb
Researchers in Portugal report on their characterization of the grapevine microbiome.
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The Hospital Microbiome Project | Micro Blog

The Hospital Microbiome Project | Micro Blog | Microbiome | Scoop.it
I recently came across the Hospital Microbiome Project, a multidisciplinary, multinational project designed to investigate the hospital microbiome. The.
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