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Current Opinion in Microbiology

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https://www.readbyqxmd.com/read/28822274/emergent-properties-of-bacterial-chemotaxis-pathway
#1
REVIEW
Remy Colin, Victor Sourjik
The chemotaxis pathway of Escherichia coli is the most studied sensory system in prokaryotes. The highly conserved general architecture of this pathway consists of two modules which mediate signal transduction and adaptation. The signal transduction module detects and amplifies changes in environmental conditions and rapidly transmits these signals to control bacterial swimming behavior. The adaptation module gradually resets the activity and sensitivity of the first module after initial stimulation and thereby enables the temporal comparisons necessary for bacterial chemotaxis...
August 16, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28810194/towards-detecting-regulatory-protein-metabolite-interactions
#2
REVIEW
Maren Diether, Uwe Sauer
New mapping approaches have greatly expanded our view on the cellular landscape of protein-metabolite interactions. These methods either identify proteins interacting with a selected metabolite or vice versa. By reviewing recent developments, we found that comprehensive mapping of the protein-metabolite interaction space can be achieved eventually using existing methods, amongst which proteomics techniques to assess cell wide protein property changes in response to metabolite treatment currently offer the highest potential...
August 12, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28806587/elucidation-of-host-pathogen-protein-protein-interactions-to-uncover-mechanisms-of-host-cell-rewiring
#3
REVIEW
Charlotte Nicod, Amir Banaei-Esfahani, Ben C Collins
Infectious diseases are the result of molecular cross-talks between hosts and their pathogens. These cross-talks are in part mediated by host-pathogen protein-protein interactions (HP-PPI). HP-PPI play crucial roles in infections, as they may tilt the balance either in favor of the pathogens' spread or their clearance. The identification of host proteins targeted by viral or bacterial pathogenic proteins necessary for the infection can provide insights into their underlying molecular mechanisms of pathogenicity, and potentially even single out pharmacological intervention targets...
August 11, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28783509/dysbiotic-proteobacteria-expansion-a-microbial-signature-of-epithelial-dysfunction
#4
REVIEW
Yael Litvak, Mariana X Byndloss, Renée M Tsolis, Andreas J Bäumler
A balanced gut microbiota is important for health, but the mechanisms maintaining homeostasis are incompletely understood. Anaerobiosis of the healthy colon drives the composition of the gut microbiota towards a dominance of obligate anaerobes, while dysbiosis is often associated with a sustained increase in the abundance of facultative anaerobic Proteobacteria, indicative of a disruption in anaerobiosis. The colonic epithelium is hypoxic, but intestinal inflammation or antibiotic treatment increases epithelial oxygenation in the colon, thereby disrupting anaerobiosis to drive a dysbiotic expansion of facultative anaerobic Proteobacteria through aerobic respiration...
August 4, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28732267/understanding-the-holobiont-the-interdependence-of-plants-and-their-microbiome
#5
REVIEW
Carmen Sánchez-Cañizares, Beatriz Jorrín, Philip S Poole, Andrzej Tkacz
The holobiont is composed by the plant and its microbiome. In a similar way to ecological systems of higher organisms, the holobiont shows interdependent and complex dynamics [1,2]. While plants originate from seeds, the microbiome has a multitude of sources. The assemblage of these communities depends on the interaction between the emerging seedling and its surrounding environment, with soil being the main source. These microbial communities are controlled by the plant through different strategies, such as the specific profile of root exudates and its immune system...
July 18, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28709010/eco-aging-stem-cells-and-microbes-are-controlled-by-aging-antagonist-foxo
#6
REVIEW
Benedikt M Mortzfeld, Thomas Cg Bosch
The review highlights the dual role that the conserved master regulator FoxO has in aging by coordinating both stem cell proliferation and antimicrobial peptides, effector molecules of the innate immune system. As observed in non-senescent Hydra, continuously high activity of the transcription factor FoxO contributes to continuous stem cell proliferation and could support robust colonization of epithelia with a stable microbiome. The integration of research from stem cell biology, microbiology and ecology into aging concepts (Eco-Aging) acknowledges the multi-organismic nature of all living beings and presents a new conceptual framework for explaining the process of aging...
July 11, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28704686/a-three-act-play-pentachlorophenol-threats-to-the-cork-oak-forest-soils-mycobiome
#7
REVIEW
Adélia Varela, Celso Martins, Cristina Silva Pereira
Atmospheric release of persistent organic pollutants (POPs) constitutes a silent threat through chronic contamination of soils at global scale; yet fundamental understanding of their occurrence, sources and fate is still largely lacking. Similar to a three act play, this review comprises Setup, Confrontation and Resolution. The first emphasises the eighty years of the history of pentachlorophenol (PCP) usage, only recently classified as POP. The second focus on active sources of PCP pollution, including inside cork oak forests in N...
July 10, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28692866/linking-fungal-bacterial-co-occurrences-to-soil-ecosystem-function
#8
REVIEW
Alexandre B de Menezes, Alan E Richardson, Peter H Thrall
Fungi and bacteria are major players in soil biogeochemical cycles, however, most studies linking soil processes to microbial function ignore the potential role of interactions between these groups. A small number of studies have used correlation network analyses to investigate fungal-bacterial co-occurrences in soil, and revealed differences, as well as overlaps, in the ecosystem roles of these groups. These results contradict the view that fungi and bacteria are two distinct functional groups which can be studied in isolation...
July 7, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28689057/microbial-activity-and-the-dynamics-of-ecosystem-processes-in-forest-soils
#9
REVIEW
Petr Baldrian
Microbial activity in forest soils is driven by the dynamics of ecosystem processes, largely dependent on trees as the major primary producers. Diurnal variation of root activity, seasonality of photosynthate production or recalcitrance of decomposing plant biomass all affect microbial abundance, composition of their communities and activity. Due to low N content, fungi appear to be the major decomposers of complex plant biomass: litter and deadwood and to largely shape associated bacterial communities and their activity...
July 6, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28683354/known-knowns-known-unknowns-and-unknown-unknowns-in-prokaryotic-transposition
#10
REVIEW
Patricia Siguier, Edith Gourbeyre, Michael Chandler
Although the phenomenon of transposition has been known for over 60 years, its overarching importance in modifying and streamlining genomes took some time to recognize. In spite of a robust understanding of transposition of some TE, there remain a number of important TE groups with potential high genome impact and unknown transposition mechanisms and yet others, only recently identified by bioinformatics, yet to be formally confirmed as mobile. Here, we point to some areas of limited understanding concerning well established important TE groups with DDE Tpases, to address central gaps in our knowledge of characterised Tn with other types of Tpases and finally, to highlight new potentially mobile DNA species...
July 3, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28668769/microbial-influence-on-drosophila-biology
#11
REVIEW
M E Martino, D Ma, F Leulier
Commensal bacteria profoundly affect the biology of their animal partners. Drosophila melanogaster has been broadly used to study microbiota effects on invertebrates, whose findings are frequently applicable to translational studies. The beneficial role of commensal microbes on Drosophila biology is extensively described, ranging from growth to metabolism, immunity and even behaviour. However, the mechanisms underlying these effects are not well understood. Studies continue to discover new layers of complexity in the host-bacteria partnership that constantly changes depending on a plethora of different variables...
June 29, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28668720/inhibition-of-crispr-cas-systems-by-mobile-genetic-elements
#12
REVIEW
Erik J Sontheimer, Alan R Davidson
Clustered, regularly interspaced, short, palindromic repeats (CRISPR) loci, together with their CRISPR-associated (Cas) proteins, provide bacteria and archaea with adaptive immunity against invasion by bacteriophages, plasmids, and other mobile genetic elements. These host defenses impart selective pressure on phages and mobile elements to evolve countermeasures against CRISPR immunity. As a consequence of this pressure, phages and mobile elements have evolved 'anti-CRISPR' proteins that function as direct inhibitors of diverse CRISPR-Cas effector complexes...
June 29, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28646675/conformational-regulation-of-crispr-associated-nucleases
#13
REVIEW
Ryan N Jackson, Paul Bg van Erp, Samuel H Sternberg, Blake Wiedenheft
Adaptive immune systems in bacteria and archaea rely on small CRISPR-derived RNAs (crRNAs) to guide specialized nucleases to foreign nucleic acids. The activation of these nucleases is controlled by a series of molecular checkpoints that ensure precise cleavage of nucleic acid targets, while minimizing toxic off-target cleavage events. In this review, we highlight recent advances in understanding regulatory mechanisms responsible for controlling the activation of these nucleases and identify emerging regulatory themes conserved across diverse CRISPR systems...
June 21, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28645099/harnessing-the-natural-diversity-and-in-vitro-evolution-of-cas9-to-expand-the-genome-editing-toolbox
#14
REVIEW
Tautvydas Karvelis, Giedrius Gasiunas, Virginijus Siksnys
In the past few years, the Cas9 endonuclease from the type II CRISPR-Cas bacterial antiviral defense system has revolutionized the genome editing field. Guided by an RNA molecule, Cas9 can be reprogrammed to target almost any DNA sequence: the only limitation being the short nucleotide sequence in the vicinity of the target, termed the PAM, which is characteristic for each Cas9 protein. Streptococcus pyogenes Cas9 which recognizes the NGG PAM is currently most widely used for genome manipulation. However, Cas9 orthologues and engineered Cas9 variants offer expanded genome targeting capabilities, improved specificity and biochemical properties...
June 20, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28624690/toward-a-genetic-tool-development-pipeline-for-host-associated-bacteria
#15
REVIEW
Matthew C Waller, Josef R Bober, Nikhil U Nair, Chase L Beisel
Bacteria reside in externally accessible niches on and in multicellular organisms, often forming mutualistic relationships with their host. Recent studies have linked the composition of these microbial communities with alterations in the host's health, behavior, and development, yet the causative mediators of host-microbiota interactions remain poorly understood. Advances in understanding and engineering these interactions require the development of genetic tools to probe the molecular interactions driving the structure and function of microbial communities as well as their interactions with their host...
June 15, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28624689/from-complex-gut-communities-to-minimal-microbiomes-via-cultivation
#16
REVIEW
Thomas Clavel, Ilias Lagkouvardos, Bärbel Stecher
The mammalian gut microbiota is dominated by populations of bacteria, mostly strict anaerobes. Because these bacteria can influence the health of their host, it is important to investigate their diversity and functions, which can be done via culture-based or molecular approaches. In recent years, microbiologists have very often preferred the use of molecular techniques, as they do not limit the analysis to the fraction of communities that can be grown in the laboratory. In reality, cultivation and molecular methods are complementary, and we are now witnessing a period of unification...
June 15, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28623729/host-microbiota-interactions-in-caenorhabditis-elegans-and-their-significance
#17
REVIEW
Michael Shapira
As a useful genetic model, C. elegans can facilitate investigation of the genetic underpinnings of host-microbiota interactions. However, decades of feeding it with Escherichia coli left a gap in our understanding of its interactions with microbes, hindering such use. This is changing, with recent studies characterizing the gut microbiota of worms in their natural habitats, comparing them to those in their environment, and evaluating the significance of gut and environmental commensals. This work defined a shared core gut microbiota significantly influenced by host genetics, and unraveled bacterial contributions to life history traits...
June 14, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28623720/next-generation-precision-antimicrobials-towards-personalized-treatment-of-infectious-diseases
#18
REVIEW
Cesar de la Fuente-Nunez, Marcelo Dt Torres, Francisco Jm Mojica, Timothy K Lu
Antibiotics started to be used almost 90 years ago to eradicate life-threatening infections. The urgency of the problem required rapid, broad-spectrum elimination of infectious agents. Since their initial discovery, these antimicrobials have saved millions of lives. However, they are not exempt from side effects, which include the indiscriminate disruption of the beneficial microbiota. Recent technological advances have enabled the development of antimicrobials that can selectively target a gene, a cellular process, or a microbe of choice...
June 14, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28623719/the-crispr-cas-app-goes-viral
#19
REVIEW
Marie-Laurence Lemay, Philippe Horvath, Sylvain Moineau
If biology laboratories were smartphones, CRISPR-Cas would be the leading app. Nowadays, technology users rely on apps to communicate, get directions, entertain, and more. Likewise, many life scientists now rely on CRISPR-Cas systems to study the interactions between microbes and their viruses, to track strains as well as to modify and modulate genomes. Considering their high level of polymorphism, CRISPR arrays can increase the resolution of a microbial typing scheme. As dynamic systems, they allow the identification and the tracking of specific sequences, which is highly valuable for epidemiological studies...
June 14, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28622636/crispr-based-engineering-of-next-generation-lactic-acid-bacteria
#20
REVIEW
Claudio Hidalgo-Cantabrana, Sarah O'Flaherty, Rodolphe Barrangou
The advent of CRISPR-based technologies has opened new avenues for the development of next-generation food microorganisms and probiotics with enhanced functionalities. Building off two decades of functional genomics studies unraveling the genetic basis for food fermentations and host-probiotic interactions, CRISPR technologies offer a wide range of opportunities to engineer commercially-relevant Lactobacillus and Bifidobacteria. Endogenous CRISPR-Cas systems can be repurposed to enhance gene expression or provide new features to improve host colonization and promote human health...
June 13, 2017: Current Opinion in Microbiology
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