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  • Microbial Ninja Warriors: Bacterial Immune Evasion
    12/15/2018
  • Microbial Minutes: Bacterial Speciation, Ancient Bacteria, and Drug-Resistant Infection Deaths
    12/11/2018
  • May I borrow a cup of catalase? Prochlorococcus and its helpful neighbors.
    12/07/2018
  • ASM Career Development Grant Helps A Postdoc Develop Science Policy Skills
    12/06/2018
  • Just the Facts: Role of Evidence-Based Medicine in Clinical Microbiology
    12/03/2018
  • Temperature Adaptation as a Virulence Determinant for Fungal Pathogens
    11/30/2018
  • Microbiology Resource of the Month: the Red Mite Genome
    11/28/2018
  • ASM Career Development Grant Helps With Studying Ocean Health in Puerto Rico
    11/28/2018
  • Microbial Minutes: Diabetes, Malaria, and a New Kingdom of Life
    11/27/2018
  • Food Safety Part I: Foods to avoid at your next holiday potluck
    11/21/2018

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  • Sunday, 16 December 2018

    Staphylococcus aureus is a major human pathogen that can cause infections that range from superficial skin and mucosal infections to life threatening disseminated infections. S. aureus can attach to medical devices and host tissues and form biofilms that allow the bacteria to evade the host immune system and provide protection from antimicrobial agents. To counter host-generated oxidative and nitrosative stress mechanisms that are part of the normal host responses to invading pathogens, S. aureus utilizes low molecular weight (LMW) thiols, such as bacillithiol (BSH). Additionally, S. aureus synthesizes its own nitric oxide (NO), which combined with its downstream metabolites may...

  • Sunday, 16 December 2018

    The study of cell biology is limited by the difficulty in visualizing cellular structures at high spatial resolution within their native milieu. Here, we have visualized sporulation in Bacillus subtilis using cryo-electron tomography coupled with cryo-focused ion beam milling, a technique that allows the 3D reconstruction of cellular structures in near-native state at molecular resolution. During sporulation, an asymmetrically-positioned septum divides the cell into a larger mother cell and a smaller forespore. Subsequently, the mother cell phagocytoses the forespore in a process called engulfment, which entails a dramatic rearrangement of the peptidoglycan (PG) cell wall around the forespore. By imaging...

  • Friday, 14 December 2018

    Rapid antibiotic susceptibility testing (AST) is urgently needed for treating infections with correct antibiotics and slowing down the emergence of antibiotic resistant bacteria. Current clinical methods reply on culture and take at least 16 h. Here, using P. aeruginosa, E. coli and S. aureus as models, we show that the AST can be finished in 10 minutes by stimulated Raman scattering (SRS) imaging of D2O metabolic activities. The metabolic incorporation of D2O, which is used for biomolecule synthesis, can be monitored in a single bacterium. Time lapse experiments show that the C-D vibrational signal can be observed in a single...

  • Friday, 14 December 2018

    Genus Frankia is comprised primarily of nitrogen-fixing actinobacteria that form root nodule symbioses with a group of hosts known as the actinorhizal plants. These plants are evolutionarily closely related to the legumes, which are nodulated by the rhizobia. Both host groups utilize homologs of nodulation genes for root-nodule symbiosis, derived from common plant ancestors. However the corresponding endosymbionts, Frankia and the rhizobia, are distantly related groups of bacteria, leading to questions of their symbiotic mechanisms and evolutionary history. To date, a stable system of genetic transformation has been lacking in Frankia. Here, we report the successful electrotransformation of Frankia alni...

  • Friday, 14 December 2018

    Competence for genetic transformation allows the opportunistic human pathogen Streptococcus pneumoniae to take up exogenous DNA for incorporation into its own genome. This ability may account for the extraordinary genomic plasticity of this bacterium, leading to antigenic variation, vaccine escape, and the spread of antibiotic resistance markers. The competence system has been thoroughly studied and its regulation is well-understood. Additionally, over the last decade, several stress factors have been shown to trigger the competent state, leading to the activation of several stress response regulons. The arrival of next-generation sequencing techniques allowed us to update the competence regulon, the latest report...

  • Friday, 14 December 2018

    Lyme borreliosis is a systemic infection caused by tick-borne pathogenic borreliae of the Borrelia burgdorferi sensu lato complex or of the more heterogeneous relapsing fever borrelia group. Clinical distinction of the infections due to different borrelia species is difficult. Accurate knowledge of the prevalence and the species of borreliae in the infected ticks in the endemic areas is valuable for formulating appropriate guidelines for proper management of this infectious disease. The purpose of this research was to design a readily implementable protocol to detect the divergent species of borreliae known to exist in Europe, using Irish samples of Ixodes ricinus...

  • Thursday, 13 December 2018

    The anaerobic gut pathogen, Clostridioides difficile, forms adherent biofilms that may play an important role in recurrent C. difficile infections. The mechanisms underlying C. difficile community formation and inter-bacterial interactions are nevertheless poorly understood. C. difficile produces AI-2, a quorum sensing molecule that modulates biofilm formation across many bacterial species. We found that a strain defective in LuxS, the enzyme that mediates AI-2 production, is defective in biofilm development in vitro. Transcriptomic analyses of biofilms formed by wild type (WT) and luxS mutant (luxS) strains revealed a downregulation of prophage loci in the luxS mutant biofilms compared to the WT....

  • Thursday, 13 December 2018

    The progressive reduction of gut microbiome (GM) biodiversity along human evolutionary history has been found to be particularly exacerbated in Western urban compared to traditional rural populations, and supposed to contribute to the increasing incidence of chronic non-communicable diseases. Together with sanitation, antibiotics and C-section, the Western diets, low in microbiota-accessible carbohydrates (MACs) while rich in industrialized and processed foods, are considered one of the leading causes of this shrinkage. However, significant questions remain unanswered, especially whether high-MAC low-processed diets may be sufficient to recover GM diversity in Western urban populations. Here, we profiled the GM structure of urban Italian...

  • Thursday, 13 December 2018

    Chronic rhinosinusitis (CRS) is a heterogeneous condition characterised by persistent sinus inflammation and microbial dysbiosis. This study aimed to identify clinically relevant sub-groups of CRS patients based on distinct microbial signatures, with a comparison to the commonly used phenotypic subgrouping approach. The underlying drivers of these distinct microbial clusters were also investigated, together with associations with epithelial barrier integrity. Sinus biopsies were collected from CRS patients (n=23), and disease controls (n=8). Expression of 42 tight junction genes was evaluated using quantitative PCR, together with microbiota analysis and immunohistochemistry for measuring mucosal integrity and inflammation. CRS patients clustered into two distinct...

  • Thursday, 13 December 2018

    Pseudomonas aeruginosa is a common cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. An attenuated PAO1 strain and its derivatives are widely used to study the biology of this bacterium, however recent studies indicated an ongoing evolution of the laboratory strains, highlighted by changes in the genomes of PAO1 sublines and derivatives used in different laboratories worldwide. Here we have sequenced the genome of Pseudomonas aeruginosa PAO1161 strain, a leu-, RifR, restriction-modification defective PAO1 derivative. This strain is described as the host of IncP-8 plasmid FP2, conferring the resistance to mercury and used in the...

  • Thursday, 13 December 2018

    Small proteins likely abound in prokaryotes, and may mediate much of the communication that occurs between organisms within a microbiome and their host. Unfortunately, small proteins are traditionally overlooked in biology, in part due to the computational and experimental difficulties in detecting them. To systematically identify novel small proteins, we carried out a large comparative genomics study on 1,773 HMP human-associated metagenomes from four different body sites (mouth, gut, skin and vagina). We describe more than four thousand conserved protein families, the majority of which are novel; ~30% of these protein families are predicted to be secreted or transmembrane. Over...

  • Thursday, 13 December 2018

    Dispersal is a critical yet poorly understood factor underlying macroecological patterns in microbial communities. Airborne microbial transport is assumed to occupy a central role in determining dispersal outcomes and extra-range dispersal has important implications for predicting ecosystem resilience and response to environmental change. One of the most pertinent biomes in this regard is Antarctica given its geographic isolation and vulnerability to climate change and human disturbance. Here we report the first characterisation of microbial diversity in near-ground and high-altitude air above a typical Antarctic Dry Valley as well as that of underlying soil microbial communities. We found that persistent airborne...

  • Thursday, 13 December 2018

    Metschnikowia pulcherrima synthesizes the red pigment pulcherrimin, from cyclodileucine (cyclo(Leu-Leu)) as a precursor, and exhibits strong antifungal activity against notorious plant pathogenic fungi such as Botrytis and Gibberella (i.e., Fusarium). This yeast therefore has great potential for biocontrol applications against fungal diseases; particularly in the phyllosphere where this species is frequently found. To elucidate the molecular basis of the antifungal activity of M. pulcherrima, we compared a wildtype strain with a spontaneously occurring, pigmentless, weakly antagonistic mutant derivative. Whole genome sequencing of the wildtype and mutant strains identified a point mutation that creates a premature stop codon in the transcriptional...

  • Thursday, 13 December 2018

    Most urinary tract infections (UTIs) are caused by uropathogenic Escherichia coli (UPEC), which depend on an extracellular organelle (Type 1 pili) for adherence to bladder cells during infection. Type 1 pilus expression is partially regulated by inversion of a piece of DNA referred to as fimS, which contains the promoter for the fim operon encoding Type 1 pili. fimS inversion is regulated by up to five recombinases collectively known as Fim recombinases. These Fim recombinases are currently known to regulate two other switches: the ipuS and hyxS switches. A long-standing question has been whether the Fim recombinases regulate the inversion...

  • Thursday, 13 December 2018

    Multi-targeting antibiotics, i.e. single compounds capable to inhibit two or more bacterial targets offer a promising therapeutic strategy, but information on resistance evolution against such drugs is scarce. Gepotidacin is an antibiotic candidate that selectively inhibits both bacterial DNA gyrase and topoisomerase IV. In a susceptible organism, Klebsiella pneumoniae, a combination of two specific mutations in these target proteins provide an over 2000-fold increment in resistance, while individually none of these mutations affect resistance significantly. Alarmingly, gepotidacin-resistant strains are found to be as virulent as the wild-type K. pneumoniae strain in a murine model, and extensive cross-resistance was demonstrated between...

  • Thursday, 13 December 2018

    Wolbachia (Alphaproteobacteria, Rickettsiales) is an intraovarially-transmitted symbiont of insects able to exert striking phenotypes, including reproductive manipulations and pathogen blocking. These phenotypes make Wolbachia a promising tool to combat mosquito-borne diseases. Although Wolbachia is present in the majority of terrestrial arthropods, including many disease vectors, it was considered absent from Anopheles gambiae mosquitos, the main vectors of malaria in sub-Saharan Africa. In 2014, Wolbachia sequences were detected in A. gambiae samples collected in Burkina Faso. Subsequently, similar evidence came from collections all over Africa, revealing a high Wolbachia 16S sequence diversity, low abundance, and a lack of congruence between host...

  • Thursday, 13 December 2018

    Biofilms are closely packed cells held and shielded by extracellular matrix composed of structural proteins and exopolysaccharides (EPS). As matrix components are costly to produce and shared within the population, EPS-deficient cells can act as cheaters by gaining benefits from the cooperative nature of EPS producers. Remarkably, genetically programmed EPS producers can also exhibit phenotypic heterogeneity at single cell level. For instance, mature biofilms of Bacillus subtilis contain cells in an "ON" state, expressing extracellular matrix genes, as well as cells in an "OFF" state. Previous studies have shown that spatial structure of biofilms limits the spread of cheaters, but...

  • Thursday, 13 December 2018

    Molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with universal PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. Unfortunately both amplicon-based and shotgun sequencing approaches have significant shortcomings that limit the ability to study microbiome dynamics. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. This new method generates a quantitative, pan-Domain community profile...

  • Thursday, 13 December 2018

    The rational discovery of new specialized metabolites by genome mining represents a very promising strategy in the quest for new bioactive molecules. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural product that derive from genetically encoded precursor peptides. However, RiPP gene clusters are particularly refractory to reliable bioinformatic predictions due to the absence of a common biosynthetic feature across all pathways. Here, we describe RiPPER, a new tool for the family-independent identification of RiPP precursor peptides and apply this methodology to search for novel thioamidated RiPPs in Actinobacteria. Until now, thioamidation was believed to be...

  • Thursday, 13 December 2018

    HBsAg and HBeAg have gained traction as biomarkers of control and clearance during monitoring of chronic hepatitis B virus infection (CHB). An improved understanding of the correlates of clearance of these proteins could help inform improvements in patient-stratified care and advance insights into the underlying mechanisms of disease control, thus underpinning new cure strategies. We collected electronic clinical data via an electronic pipeline supported by the National Institute for Health Research Health Informatics Collaborative (NIHR-HIC), adopting an unbiased approach to generating a robust longitudinal dataset for adults testing HBsAg-positive from a large UK teaching hospital over a six year period...

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