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FEMS Microbiology Reviews

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https://www.readbyqxmd.com/read/28830097/editorial-lactic-acid-bacteria-a-continuing-journey-in-science-and-application
#1
Michiel Kleerebezem, Oscar P Kuipers, Eddy J Smid
No abstract text is available yet for this article.
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830096/using-murine-colitis-models-to-analyze-probiotics-host-interactions
#2
Rebeca Martín, Florian Chain, Sylvie Miquel, Jean-Paul Motta, Nathalie Vergnolle, Harry Sokol, Philippe Langella
Probiotics are defined as 'live microorganisms which when administered in adequate amounts confer a health benefit on the host'. So, to consider a microorganism as a probiotic, a demonstrable beneficial effect on the health host should be shown as well as an adequate defined safety status and the capacity to survive transit through the gastrointestinal tract and to storage conditions. In this review, we present an overview of the murine colitis models currently employed to test the beneficial effect of the probiotic strains as well as an overview of the probiotics already tested...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830095/oenococcus-oeni-and-the-genomic-era
#3
Eveline J Bartowsky
Oenococcus oeni is the main lactic acid bacteria species associated with grapes and wine. It is a bacterium that has adapted itself to the harsh conditions of wine, and demonstrated its importance in the production of quality wines. It has a small genome (1.8 Mb); over 200 strains have had their genome sequenced. Genomic analyses have proposed that there are two major branches of O. oeni strains that might be linked to wine style (sparkling wine versus white and red) and metagenomic studies have suggested a possible influence of terroir...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830094/physiology-ecology-and-industrial-applications-of-aroma-formation-in-yeast
#4
Maria C Dzialo, Rahel Park, Jan Steensels, Bart Lievens, Kevin J Verstrepen
Yeast cells are often employed in industrial fermentation processes for their ability to efficiently convert relatively high concentrations of sugars into ethanol and carbon dioxide. Additionally, fermenting yeast cells produce a wide range of other compounds, including various higher alcohols, carbonyl compounds, phenolic compounds, fatty acid derivatives and sulfur compounds. Interestingly, many of these secondary metabolites are volatile and have pungent aromas that are often vital for product quality. In this review, we summarize the different biochemical pathways underlying aroma production in yeast as well as the relevance of these compounds for industrial applications and the factors that influence their production during fermentation...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830093/the-evolution-of-gene-regulation-research-in-lactococcus-lactis
#5
Jan Kok, Lieke A van Gijtenbeek, Anne de Jong, Sjoerd B van der Meulen, Ana Solopova, Oscar P Kuipers
Lactococcus lactis is a major microbe. This lactic acid bacterium (LAB) is used worldwide in the production of safe, healthy, tasteful and nutritious milk fermentation products. Its huge industrial importance has led to an explosion of research on the organism, particularly since the early 1970s. The upsurge in the research on L. lactis coincided not accidentally with the advent of recombinant DNA technology in these years. The development of methods to take out and re-introduce DNA in L. lactis, to clone genes and to mutate the chromosome in a targeted way, to control (over)expression of proteins and, ultimately, the availability of the nucleotide sequence of its genome and the use of that information in transcriptomics and proteomics research have enabled to peek deep into the functioning of the organism...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830092/phase-variable-methylation-and-epigenetic-regulation-by-type-i-restriction-modification-systems
#6
Megan De Ste Croix, Irene Vacca, Min Jung Kwun, Joseph D Ralph, Stephen D Bentley, Richard Haigh, Nicholas J Croucher, Marco R Oggioni
Epigenetic modifications in bacteria, such as DNA methylation, have been shown to affect gene regulation, thereby generating cells that are isogenic but with distinctly different phenotypes. Restriction-modification (RM) systems contain prototypic methylases that are responsible for much of bacterial DNA methylation. This review focuses on a distinctive group of type I RM loci that , through phase variation, can modify their methylation target specificity and can thereby switch bacteria between alternative patterns of DNA methylation...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830091/bacteriocins-and-bacteriophage-a-narrow-minded-approach-to-food-and-gut-microbiology
#7
Susan Mills, R Paul Ross, Colin Hill
Bacteriocins and bacteriophage (phage) are biological tools which exhibit targeted microbial killing, a phenomenon which until recently was seen as a major drawback for their use as antimicrobial agents. However, in an age when the deleterious consequences of broad-spectrum antibiotics on human health have become apparent, there is an urgent need to develop narrow-spectrum substitutes. Indeed, disruption of the microbial communities which exist on and in our bodies can generate immediate and long-term negative effects and this is particularly borne out in the gut microbiota community whose disruption has been linked to a number of disorders reaching as far as the brain...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830090/practical-considerations-for-large-scale-gut-microbiome-studies
#8
Doris Vandeputte, Raul Y Tito, Rianne Vanleeuwen, Gwen Falony, Jeroen Raes
First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830089/unexpected-complexity-in-the-lactate-racemization-system-of-lactic-acid-bacteria
#9
Benoît Desguin, Patrice Soumillion, Robert P Hausinger, Pascal Hols
Analysis of lactate racemase (Lar) in lactic acid bacteria (LAB) has been a scientific challenge for many years, as indicated by the numerous contradictory reports on this activity. Recently, genetic and biochemical studies of the Lar system of Lactobacillus plantarum have unveiled the complexity of this particular enzymatic system. Lar activity is associated with LarA and its nickel-containing cofactor, synthesized from nicotinic acid adenine dinucleotide by the three biosynthetic enzymes: LarB, LarC, and LarE...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830088/host-recognition-by-lactic-acid-bacterial-phages
#10
Jennifer Mahony, Christian Cambillau, Douwe van Sinderen
Bacteriophage infection of lactic acid bacteria (LAB) is one of the most significant causes of inconsistencies in the manufacture of fermented foods, affecting production schedules and organoleptic properties of the final product. Consequently, LAB phages, and particularly those infecting Lactococcus lactis, have been the focus of intensive research efforts. During the past decade, multidisciplinary scientific approaches have uncovered molecular details on the exquisite process of how a lactococcal phage recognises and binds to its host...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830087/polysaccharide-production-by-lactic-acid-bacteria-from-genes-to-industrial-applications
#11
Ahmad A Zeidan, Vera Kuzina Poulsen, Thomas Janzen, Patrizia Buldo, Patrick M F Derkx, Gunnar Øregaard, Ana Rute Neves
The ability to produce polysaccharides with diverse biological functions is widespread in bacteria. In lactic acid bacteria (LAB), production of polysaccharides has long been associated with the technological, functional and health-promoting benefits of these microorganisms. In particular, the capsular polysaccharides and exopolysaccharides have been implicated in modulation of the rheological properties of fermented products. For this reason, screening and selection of exocellular polysaccharide-producing LAB has been extensively carried out by academia and industry...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28673043/lifestyles-in-transition-evolution-and-natural-history-of-the-genus-lactobacillus
#12
Rebbeca M Duar, Xiaoxi B Lin, Jinshui Zheng, Maria Elena Martino, Théodore Grenier, María Elisa Pérez-Muñoz, François Leulier, Michael Gänzle, Jens Walter
Lactobacillus species are found in nutrient-rich habitats associated with food, feed, plants, animals and humans. Due to their economic importance, the metabolism, genetics and phylogeny of lactobacilli have been extensively studied. However, past research primarily examined lactobacilli in experimental settings abstracted from any natural history, and the ecological context in which these bacteria exist and evolve has received less attention. In this review, we synthesize phylogenetic, genomic and metabolic metadata of the Lactobacillus genus with findings from fine-scale phylogenetic and functional analyses of representative species to elucidate the evolution and natural history of its members...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28633473/experimental-evolution-and-the-adjustment-of-metabolic-strategies-in-lactic-acid-bacteria
#13
Herwig Bachmann, Douwe Molenaar, Filipe Branco Dos Santos, Bas Teusink
Experimental evolution of microbes has gained lots of interest in recent years, mainly due to the ease of strain characterisation through next-generation sequencing. While evolutionary and systems biologists use experimental evolution to address fundamental questions in their respective fields, studies with lactic acid bacteria are often more directed by applied questions. Insight into population and genome dynamics are valuable for experimental design and data interpretation, and it is becoming increasingly apparent how different constraints limit and govern the outcome of microbial adaptation to a selective environment...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28591840/novel-approaches-in-function-driven-single-cell-genomics
#14
Devin F R Doud, Tanja Woyke
Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology...
July 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28486655/microbial-processes-driving-coral-reef-organic-carbon-flow
#15
Cynthia B Silveira, Giselle S Cavalcanti, Juline M Walter, Arthur W Silva-Lima, Elizabeth A Dinsdale, David G Bourne, Cristiane C Thompson, Fabiano L Thompson
Coral reefs are one of the most productive ecosystems on the planet, with primary production rates compared to that of rain forests. Benthic organisms release 10-50% of their gross organic production as mucus that stimulates heterotrophic microbial metabolism in the water column. As a result, coral reef microbes grow up to 50 times faster than open ocean communities. Anthropogenic disturbances cause once coral-dominated reefs to become dominated by fleshy organisms, with several outcomes for trophic relationships...
July 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28430946/forgotten-fungi-the-gut-mycobiome-in-human-health-and-disease
#16
Chloe E Huseyin, Paul W O'Toole, Paul D Cotter, Pauline D Scanlan
The human body is home to a complex and diverse microbial ecosystem that plays a central role in host health. This includes a diversity of fungal species that is collectively referred to as our 'mycobiome'. Although research into the mycobiome is still in its infancy, its potential role in human disease is increasingly recognised. Here we review the existing literature available on the human mycobiota with an emphasis on the gut mycobiome, including how fungi interact with the human host and other microbes...
July 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28402413/regulation-of-heat-shock-genes-in-bacteria-from-signal-sensing-to-gene-expression-output
#17
Davide Roncarati, Vincenzo Scarlato
The heat-shock response is a mechanism of cellular protection against sudden adverse environmental growth conditions and results in the prompt production of various heat-shock proteins. In bacteria, specific sensory biomolecules sense temperature fluctuations and transduce intercellular signals that coordinate gene expression outputs. Sensory biomolecules, also known as thermosensors, include nucleic acids (DNA or RNA) and proteins. Once a stress signal is perceived, it is transduced to invoke specific molecular mechanisms controlling transcription of genes coding for heat-shock proteins...
July 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28369623/the-hidden-life-of-integrative-and-conjugative-elements
#18
François Delavat, Ryo Miyazaki, Nicolas Carraro, Nicolas Pradervand, Jan Roelof van der Meer
Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE-host partnership...
July 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28333226/exploring-the-human-microbiome-from-multiple-perspectives-factors-altering-its-composition-and-function
#19
David Rojo, Celia Méndez-García, Beata Anna Raczkowska, Rafael Bargiela, Andrés Moya, Manuel Ferrer, Coral Barbas
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors...
July 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28531298/evolution-of-bacterial-virulence
#20
Médéric Diard, Wolf-Dietrich Hardt
Bacterial virulence is highly dynamic and context-dependent. For this reason, it is challenging to predict how molecular changes affect the growth of a pathogen in a host and its spread in host population. Two schools of thought have taken quite different directions to decipher the underlying principles of bacterial virulence. While molecular infection biology is focusing on the basic mechanisms of the pathogen-host interaction, evolution biology takes virulence as one of several parameters affecting pathogen spread in a host population...
May 22, 2017: FEMS Microbiology Reviews
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