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FEMS Microbiology Reviews

Marines du Teil Espina, Giorgio Gabarrini, Hermie J M Harmsen, Johanna Westra, Arie Jan van Winkelhoff, Jan Maarten van Dijl
Microbial communities inhabiting the human body, collectively called the microbiome, are critical modulators of immunity. This notion is underpinned by associations between changes in the microbiome and particular autoimmune disorders. Specifically, in rheumatoid arthritis, one of the most frequently occurring autoimmune disorders worldwide, changes in the oral and gut microbiomes have been implicated in the loss of tolerance against self-antigens and in increased inflammatory events promoting the damage of joints...
September 14, 2018: FEMS Microbiology Reviews
Annika Gillis, Nancy Fayad, Lionel Makart, Alexander Bolotin, Alexei Sorokin, Mireille Kallassy, Jacques Mahillon
Bacillus thuringiensis is a well-known biopesticide that has been used for more than 80 years. This spore-forming bacterium belongs to the group of Bacillus cereus that also includes, among others, emetic and diarrheic pathotypes of B. cereus, the animal pathogen Bacillus anthracis and the psychrotolerant Bacillus weihenstephanensis. B. thuringiensis is rather unique since it has adapted its lifestyle as an efficient pathogen of specific insect larvae. One of the peculiarities of B. thuringiensis strains is the extent of their extrachromosomal pool, with strains harbouring more than 10 distinct plasmid molecules...
September 7, 2018: FEMS Microbiology Reviews
Mecky Pohlschroder, Sonja-Verena Albers
No abstract text is available yet for this article.
August 22, 2018: FEMS Microbiology Reviews
Jeella Z Acedo, Sorina Chiorean, John C Vederas, Marco J van Belkum
Bacteria use various strategies to compete in an ecological niche, including the production of bacteriocins. Bacteriocins are ribosomally synthesized antibacterial peptides and it has been postulated that the majority of Gram-positive bacteria produce one or more of these natural products. Bacteriocins can be used in food preservation and are also considered as potential alternatives to antibiotics. The majority of bacteriocins from Gram-positive bacteria had been traditionally divided into two major classes, namely lantibiotics, which are post-translationally modified bacteriocins, and unmodified bacteriocins...
August 1, 2018: FEMS Microbiology Reviews
Lisa Röttjers, Karoline Faust
Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these networks is not straightforward, and the biological implications of network properties are unclear. Analysis of microbial networks allows researchers to predict hub species and species interactions. Additionally, such analyses can help identify alternative community states and niches. Here, we review factors that can result in spurious predictions and address emergent properties that may be meaningful in the context of the microbiome...
July 30, 2018: FEMS Microbiology Reviews
Michelle M C Buckner, Maria Laura Ciusa, Laura J V Piddock
Antimicrobial resistance (AMR) is a global problem hindering treatment of bacterial infections, rendering many aspects of modern medicine less effective. AMR genes (ARGs), are frequently located on plasmids, which are self-replicating elements of DNA. They are often transmissible between bacteria, and some have spread globally. Novel strategies to combat AMR are needed, and plasmid curing and anti-plasmid approaches could reduce ARG prevalence, and sensitize bacteria to antibiotics. We discuss the use of curing agents as laboratory tools including chemicals (e...
July 30, 2018: FEMS Microbiology Reviews
Sandra Wiegand, Mareike Jogler, Christian Jogler
Planctomycetes are ubiquitous, environmentally and biotechnologically important bacteria that are key-players in global carbon- and nitrogen cycles. Ever since their first discovery in the 1920s they seemed to blur the prokaryote/eukaryote dichotomy. After initially being described as fungi and reclassified as bacteria later, they were still thought to feature a nucleus-like compartment surrounding their highly condensed DNA. Also, an endocytosis-like uptake mechanism for macromolecules was described. Besides these eukaryotic hallmark traits, Planctomycetes seemed to lack typical bacterial features such as a peptidoglycan cell wall or the universal bacterial cell division protein FtsZ, while mostly dividing by polar budding instead of binary fission...
July 24, 2018: FEMS Microbiology Reviews
Colin R Harwood, Jean-Marie Mouillon, Susanne Pohl, José Arnau
Members of the 'B. subtilis group' include some of the most commercially important bacteria, used for the production of a wide range of industrial enzymes and fine biochemicals. Increasingly, group members have been developed for use as animal feed enhancers and antifungal biocontrol agents. The group have long been recognized to produce a range of secondary metabolites and, despite their long history of safe usage, this has resulted in an increased focus on their safety. Traditional methods used to detect the production of secondary metabolites and other potentially harmful compounds have relied on phenotypic tests...
July 19, 2018: FEMS Microbiology Reviews
Christopher T Straub, James A Counts, Diep M N Nguyen, Chang-Hao Wu, Benjamin M Zeldes, James R Crosby, Jonathan M Conway, Jonathan K Otten, Gina L Lipscomb, Gerrit J Schut, Michael W W Adams, Robert M Kelly
Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores...
September 1, 2018: FEMS Microbiology Reviews
Mechthild Pohlschroder, Friedhelm Pfeiffer, Stefan Schulze, Mohd Farid Abdul Halim
Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between domains, others are shared with bacteria or eukaryotes or both. Based on recent studies completed on a phylogenetically diverse array of archaea, from a wide variety of habitats, here we discuss advances in the characterization of mechanisms underpinning archaeal cell surface biogenesis...
September 1, 2018: FEMS Microbiology Reviews
Callum J D Lee, Phillip E McMullan, Callum J O'Kane, Andrew Stevenson, Inês C Santos, Chayan Roy, Wriddhiman Ghosh, Rocco L Mancinelli, Melanie R Mormile, Geoffrey McMullan, Horia L Banciu, Mario A Fares, Kathleen C Benison, Aharon Oren, Mike L Dyall-Smith, John E Hallsworth
NaCl-saturated brines such as saltern crystalliser ponds, inland salt lakes, deep-sea brines and liquids-of-deliquescence on halite are commonly regarded as a paradigm for the limit of life on Earth. There are, however, other habitats that are thermodynamically more extreme. Typically, NaCl-saturated environments contain all domains of life and perform complete biogeochemical cycling. Despite their reduced water activity, ∼0.755 at 5 M NaCl, some halophiles belonging to the Archaea and Bacteria exhibit optimum growth/metabolism in these brines...
September 1, 2018: FEMS Microbiology Reviews
Fatemeh Askarian, Theresa Wagner, Mona Johannessen, Victor Nizet
Early recognition of pathogens by the innate immune system is crucial for bacterial clearance. Many pattern recognition receptors (PRRs) such as Toll-like (TLRs) and (NOD)-like (NLRs) receptors have been implicated in initial sensing of bacterial components. The intracellular signaling cascades triggered by these receptors result in transcriptional upregulation of inflammatory pathways. Although this step is crucial for bacterial elimination, it is also associated with the potential for substantial immunopathology, which underscores the need for tight control of inflammatory responses...
September 1, 2018: FEMS Microbiology Reviews
Zhichao Zhou, Jie Pan, Fengping Wang, Ji-Dong Gu, Meng Li
Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-coenzyme A-centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, and/or (v) potentially other organic matter...
September 1, 2018: FEMS Microbiology Reviews
Jorge Barriuso, Deborah A Hogan, Tajalli Keshavarz, María Jesús Martínez
Microbial cells do not live in isolation in their environment, but rather they communicate with each other using chemical signals. This sophisticated mode of cell-to-cell signalling, known as quorum sensing, was first discovered in bacteria, and coordinates the behaviour of microbial population behaviour in a cell-density-dependent manner. More recently, these mechanisms have been described in eukaryotes, particularly in fungi, where they regulate processes such as pathogenesis, morphological differentiation, secondary metabolite production and biofilm formation...
September 1, 2018: FEMS Microbiology Reviews
Christelle Bressuire-Isoard, Véronique Broussolle, Frédéric Carlin
Bacterial spores are resistant to physical and chemical insults, which makes them a major concern for public health and industry. Spores help bacteria to survive extreme environmental conditions that vegetative cells cannot tolerate. Spore resistance and dormancy are important properties for applications in medicine, veterinary health, food safety, crop protection and other domains. The resistance of bacterial spores results from a protective multilayered structure and from the unique composition of the spore core...
September 1, 2018: FEMS Microbiology Reviews
Béatrice Clouet-d'Orval, Manon Batista, Marie Bouvier, Yves Quentin, Gwennaele Fichant, Anita Marchfelder, Lisa-Katharina Maier
RNA-processing pathways are at the centre of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes are still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya...
September 1, 2018: FEMS Microbiology Reviews
Hadar Neuman, Paul Forsythe, Atara Uzan, Orly Avni, Omry Koren
Antibiotics are the most common type of medication prescribed to children, including infants, in the Western world. While use of antibiotics has transformed previously lethal infections into relatively minor diseases, antibiotic treatments can have adverse effects as well. It has been shown in children, adults and animal models that antibiotics dramatically alter the gut microbial composition. Since the gut microbiota plays crucial roles in immunity, metabolism and endocrinology, the effects of antibiotics on the microbiota may lead to further health complications...
July 1, 2018: FEMS Microbiology Reviews
Emilia M F Mauriello, Christopher Jones, Audrey Moine, Judith P Armitage
The bacterial cytoplasm is not a homogeneous solution of macromolecules, but rather a highly organized and compartmentalized space where the clustering and segregation of macromolecular complexes in certain cell regions confers functional efficiency. Bacterial chemoreceptors represent a versatile model system to study the subcellular localization of macromolecules, as they are present in almost all motile bacterial and archaeal species, where they tend to form highly ordered arrays that occupy distinct positions in cells...
July 1, 2018: FEMS Microbiology Reviews
Kelly M Zatopek, Andrew F Gardner, Zvi Kelman
DNA replication and repair are essential biological processes needed for the survival of all organisms. Although these processes are fundamentally conserved in the three domains, archaea, bacteria and eukarya, the proteins and complexes involved differ. The genetic and biophysical tools developed for archaea in the last several years have accelerated the study of DNA replication and repair in this domain. In this review, the current knowledge of DNA replication and repair processes in archaea will be summarized, with emphasis on the contribution of genetics and other recently developed biophysical and molecular tools, including capillary gel electrophoresis, next-generation sequencing and single-molecule approaches...
July 1, 2018: FEMS Microbiology Reviews
Hirotaka Hiyoshi, Connor R Tiffany, Denise N Bronner, Andreas J Bäumler
Typhoid and paratyphoid fever are severe systemic infections caused by human-adapted typhoidal Salmonella serovars that are indistinguishable in their clinical presentation, but differ from human gastroenteritis caused by zoonotic non-typhoidal Salmonella serovars. Typhoidal Salmonella serovars evolved from ancestral gastrointestinal pathogens through genetic changes that supported a change in pathogen ecology. Typhoidal Salmonella serovars share virulence properties that were acquired through convergent evolution and therefore this group is not defined by the presence of shared virulence genes that are absent from non-typhoidal Salmonella serovars...
July 1, 2018: FEMS Microbiology Reviews
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