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Current Opinion in Microbiology

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https://www.readbyqxmd.com/read/28624690/toward-a-genetic-tool-development-pipeline-for-host-associated-bacteria
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
https://www.readbyqxmd.com/read/28618368/the-scales-of-the-zebrafish-host-microbiota-interactions-from-proteins-to-populations
#7
REVIEW
Adam R Burns, Karen Guillemin
The interactions between animal hosts and their associated microbiota can be studied at multiple spatial and conceptual scales, with each providing unique perspectives on the processes structuring host-microbe systems. Recently, zebrafish, Danio rerio, has emerged as a powerful model in which to study these interactions at many different scales. Controlled but simplified gnotobiotic experiments enable discovery of the molecules and cellular dynamics that shape host-microbe system development, whereas population level investigations of bacterial dispersal and transmission are beginning to reveal the processes shaping microbiota assembly across hosts...
June 12, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28605718/diversity-classification-and-evolution-of-crispr-cas-systems
#8
REVIEW
Eugene V Koonin, Kira S Makarova, Feng Zhang
The bacterial and archaeal CRISPR-Cas systems of adaptive immunity show remarkable diversity of protein composition, effector complex structure, genome locus architecture and mechanisms of adaptation, pre-CRISPR (cr)RNA processing and interference. The CRISPR-Cas systems belong to two classes, with multi-subunit effector complexes in Class 1 and single-protein effector modules in Class 2. Concerted genomic and experimental efforts on comprehensive characterization of Class 2 CRISPR-Cas systems led to the identification of two new types and several subtypes...
June 9, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28600959/beyond-the-canonical-strategies-of-horizontal-gene-transfer-in-prokaryotes
#9
REVIEW
Cristina García-Aljaro, Elisenda Ballesté, Maite Muniesa
Efforts to identify and characterize strategies for horizontal gene transfer (HGT) in prokaryotes could have overlooked some mechanisms that do not entirely fit in with the canonical ones most often described (conjugation of plasmids, phage transduction and transformation). The difficulty in distinguishing the different HGT strategies could have contributed to underestimate their real extent. Here we review non classical HGT strategies: some that require mobile genetic elements (MGEs) and others independent of MGE...
June 7, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28599144/making-serine-integrases-work-for-us
#10
REVIEW
W Marshall Stark
DNA site-specific recombinases are enzymes (often associated with mobile DNA elements) that catalyse breaking and rejoining of DNA strands at specific points, thereby bringing about precise genetic rearrangements. Serine integrases are a group of recombinases derived from bacteriophages. Their unusual properties, including directionality of recombination and simple site requirements, are leading to their development as efficient, versatile tools for applications in experimental biology, biotechnology, synthetic biology and gene therapy...
June 6, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28599143/guaranteeing-a-captive-audience-coordinated-regulation-of-gene-transfer-agent-gta-production-and-recipient-capability-by-cellular-regulators
#11
REVIEW
Alexander B Westbye, J Thomas Beatty, Andrew S Lang
Gene transfer agents (GTAs) are bacteriophage-like particles produced by many prokaryotes. Several members of the Alphaproteobacteria produce a class of genetically-related GTAs that is best studied in Rhodobacter capsulatus. DNA transfer by the R. capsulatus GTA (RcGTA) combines aspects of both transduction and natural transformation, as recipient cells require a natural transformation-like system to incorporate donated DNA. The genes involved in RcGTA production and recipient capability are located at multiple loci in the bacterial genome; however, a conserved phosphorelay containing the response regulator CtrA and a quorum sensing system regulate both RcGTA production and recipient capability...
June 6, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28591676/evolution-of-commensal-bacteria-in-the-intestinal-tract-of-mice
#12
REVIEW
Ana Sousa, Nelson Frazão, Ricardo S Ramiro, Isabel Gordo
Hundreds of different bacterial species inhabit our intestines and contribute to our health status, with significant loss of species diversity typically observed in disease conditions. Within each microbial species a great deal of diversity is hidden and such intra-specific variation is also key to the proper homeostasis between the host and its microbial inhabitants. Indeed, it is at this level that new mechanisms of antibiotic resistance emerge and pathogenic characteristics evolve. Yet, our knowledge on intra-species variation in the gut is still limited and an understanding of the evolutionary mechanisms acting on it is extremely reduced...
June 4, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28586714/towards-a-taxonomy-of-conjugative-plasmids
#13
REVIEW
Raul Fernandez-Lopez, Santiago Redondo, M Pilar Garcillan-Barcia, Fernando de la Cruz
Conjugative plasmids are the keystone of horizontal gene transfer. Metagenomic research and clinical understanding of plasmid transmission beg for a taxonomical approach to conjugative plasmid classification. Up to now, a meaningful classification was difficult to achieve for lack of appropriate analytical tools. The advent of the genomic era revolutionized the landscape, offering a plethora of plasmid sequences as well as bioinformatic analytical tools. Given the need and the opportunity, in view of the available evidence, a taxonomy of conjugative plasmids is proposed in the hope that it will leverage plasmid studies...
June 3, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28578292/fungal-diversity-is-negatively-affected-by-habitat-fragmentation-a-meta-analysis
#14
REVIEW
G Grilli, S Longo, P Y Huais, M Pereyra, E Verga, C Urcelay, L Galetto
Fungi are ubiquitous organisms around the world with important roles in ecosystem functioning and services, but knowledge about how habitat fragmentation affect fungal diversity is spread in different trophic groups, studied regions and experimental approaches. We performed a meta-analysis to synthesize the available information to glimpse general patterns of habitat fragmentation effects on fungal diversity. The habitat fragmentation process consistently affect fungal diversity through isolation, area size and increasing edge proportion, albeit this trend may differ between both the type of response variable and fungal groups with different nutritional habits...
June 1, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28575802/themes-and-variations-in-gene-regulation-by-extracytoplasmic-function-ecf-sigma-factors
#15
REVIEW
Elena Sineva, Maria Savkina, Sarah E Ades
The ECF sigma family was identified 23 years ago as a distinct group of σ(70)-like factors. ECF sigma factors have since emerged as a major form of bacterial signal transduction that can be grouped into over 50 phylogenetically distinct subfamilies. Advances in our understanding of these sigma factors and the signaling pathways governing their activity have elucidated conserved features as well as aspects that have evolved over time. All ECF sigma factors are predicted to share a common streamlined domain structure and mode of promoter interaction...
May 30, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28551392/transposable-phages-dna-reorganization-and-transfer
#16
REVIEW
Ariane Toussaint, Phoebe A Rice
Transposable bacteriophages have long been known to necessarily and randomly integrate their DNA in their host genome, where they amplify by successive rounds of replicative transposition, profoundly reorganizing that genome. As a result of such transposition, a conjugative element (plasmid or genomic island), can either become integrated in the chromosome or receive chromosome segments, which can then be transferred to new hosts by conjugation. In recent years, more and more transposable phages have been isolated or detected by sequence similarity searches in a wide range of bacteria, supporting the idea that this mode of HGT may be pervasive in natural bacterial populations...
May 25, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28544996/temperate-bacteriophages-as-regulators-of-host-behavior
#17
REVIEW
Tal Argov, Gil Azulay, Anna Pasechnek, Olga Stadnyuk, Shai Ran-Sapir, Ilya Borovok, Nadejda Sigal, Anat A Herskovits
Bacteriophages are ubiquitous and affect most facets of life, from evolution of bacteria, through ecology and global biochemical cycling to human health. The interactions between phages and bacteria often lead to biological novelty and an important milestone in this process is the ability of phages to regulate their host's behavior. In this review article, we will focus on newly reported cases that demonstrate how temperate phages regulate bacterial gene expression and behavior in a variety of bacterial species, pathogenic and environmental...
May 23, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28538166/an-evolutionary-perspective-on-plasmid-lifestyle-modes
#18
REVIEW
Nils Hülter, Judith Ilhan, Tanita Wein, A Samer Kadibalban, Katrin Hammerschmidt, Tal Dagan
Plasmids are extra-chromosomal genetic elements whose ecology and evolution depend on their genetic repertoire and interaction with the host. We review the events that lead to transitions between plasmid lifestyle modes - invasion, host range, plasmid persistence and adaptation - from a plasmid perspective. Plasmid lifestyle is determined by various traits, including mobility, stability and indispensability that vary in their magnitude. Transitions between the plasmid lifestyles, invasion, host range, plasmid persistence and adpatation, are caused by the interplay between plasmid traits and host biology...
May 21, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28527384/embracing-the-enemy-the-diversification-of-microbial-gene-repertoires-by-phage-mediated-horizontal-gene-transfer
#19
REVIEW
Marie Touchon, Jorge A Moura de Sousa, Eduardo Pc Rocha
Bacteriophages and archaeal viruses contribute, through lysogenic conversion or transduction, to the horizontal transfer of genetic material between microbial genomes. Recent genomics, metagenomics, and single cell studies have shown that lysogenic conversion is widespread and provides hosts with adaptive traits often associated with biotic interactions. The quantification of the evolutionary impact of transduction has lagged behind and requires further theoretical and experimental work. Nevertheless, recent studies suggested that generalized transduction plays a role in the transfer of antibiotic resistance genes and in the acquisition of novel genes during intra-specific bacterial competition...
May 17, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28486162/the-impact-of-nutrition-on-intestinal-bacterial-communities
#20
REVIEW
Harry J Flint, Sylvia H Duncan, Petra Louis
What we eat influences the species composition of our gut microbiota. This is not only because diet composition determines the supply of substrates for microbial growth (in the form of dietary residue, mainly fibre, that reaches the large intestine) but also because of impacts on gut transit and the gut environment. In turn the metabolic activities of the gut microbiota, which have important health consequences, are influenced by diet and diet-driven changes in microbiota composition. Better understanding of the metabolic capabilities and host-interactions of dominant members of the gut microbiota will aid our ability to improve human health through diet...
May 6, 2017: Current Opinion in Microbiology
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