The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

For a long time, superoxide generation by an NADPH oxidase was considered as an oddity only found in professional phagocytes. Over the last years, six homologs of the cytochrome subunit of the phag...

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The NOX Family of ROS-Generating NADPH Oxidases: Physiology and Pathophysiology

An expert panel was convened in October 2013 by the International Scientific Association for Probiotics and Prebiotics (ISAPP) to discuss the field of probiotics. It is now 13 years since the definition of probiotics and 12 years after guidelines were published for regulators, scientists and industry by the Food and Agriculture Organization of the United Nations and the WHO (FAO/WHO). The FAO/WHO definition of a probiotic--"live microorganisms which when administered in adequate amounts confer a health benefit on the host"--was reinforced as relevant and sufficiently accommodating for current and anticipated applications. However, inconsistencies between the FAO/WHO Expert Consultation Report and the FAO/WHO Guidelines were clarified to take into account advances in science and applications. A more precise use of the term 'probiotic' will be useful to guide clinicians and consumers in differentiating the diverse products on the market. This document represents the conclusions of the ISAPP consensus meeting on the appropriate use and scope of the term probiotic.

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Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic

Antimicrobial peptides are an abundant and diverse group of molecules that are produced by many tissues and cell types in a variety of invertebrate, plant and animal species. Their amino acid composition, amphipathicity, cationic charge and size allow them to attach to and insert into membrane bilayers to form pores by 'barrel-stave', 'carpet' or 'toroidal-pore' mechanisms. Although these models are helpful for defining mechanisms of antimicrobial peptide activity, their relevance to how peptides damage and kill microorganisms still need to be clarified. Recently, there has been speculation that transmembrane pore formation is not the only mechanism of microbial killing. In fact several observations suggest that translocated peptides can alter cytoplasmic membrane septum formation, inhibit cell-wall synthesis, inhibit nucleic-acid synthesis, inhibit protein synthesis or inhibit enzymatic activity. In this review the different models of antimicrobial-peptide-induced pore formation and cell killing are presented.

Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria?

Escherichia coli is the predominant nonpathogenic facultative flora of the human intestine. Some E. coli strains, however, have developed the ability to cause disease of the gastrointestinal, urinary, or central nervous system in even the most robust human hosts. Diarrheagenic strains of E. coli can be divided into at least six different categories with corresponding distinct pathogenic schemes. Taken together, these organisms probably represent the most common cause of pediatric diarrhea worldwide. Several distinct clinical syndromes accompany infection with diarrheagenic E. coli categories, including traveler’s diarrhea (enterotoxigenic E. coli), hemorrhagic colitis and hemolytic-uremic syndrome (enterohemorrhagic E. coli), persistent diarrhea (enteroaggregative E. coli), and watery diarrhea of infants (enteropathogenic E. coli). This review discusses the current level of understanding of the pathogenesis of the diarrheagenic E. coli strains and describes how their pathogenic schemes underlie the clinical manifestations, diagnostic approach, and epidemiologic investigation of these important pathogens.

Diarrheagenic Escherichia coli

Background Asthma is a chronic inflammatory disease characterized by bronchial hyper-responsiveness [1]. As the most endemic of all childhood diseases, asthma accounts for the majority of hospitalizations and school absences in children [2]. Exciting new research focuses on the involvement of the gut microbiome in asthma development. Murine studies support the hypothesis that the administration of probiotics or antibiotics during post-natal life alters the gut microbiome and ultimately the asthmatic symptoms of these mice [3-5]. This study will translate these findings into humans using stool samples obtained from the Canadian Healthy Infant Longitudinal Development (CHILD) study.

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The impact of the intestinal microbiome on human immune development and atopic disease

Background The MIND diet has been linked with prevention of Alzheimer’s disease and cognitive decline but has not been fully assessed in the context of Parkinson’s disease (PD). Objective To determine whether MIND diet adherence is associated with the age of Parkinson’s disease onset in a manner superior to that of the Mediterranean diet. Methods Food Frequency Questionnaires from 167 participants with PD and 119 controls were scored for MIND and two versions of Mediterranean diet adherence. Scores were compared between sex and disease subgroups, and PD diet adherence was correlated with age of onset using univariate and multivariate linear models. Results The female subgroup adhered more closely to the MIND diet than the males, and diet scores were not modified by disease status. Later age of onset correlated most strongly with MIND diet adherence in the female subgroup, corresponding to differences of up to 17.4 years (p Conclusions This cross-sectional study finds a strong correlation of age of onset of PD with dietary habits, suggesting that nutritional strategies may be an effective tool to delay PD onset. Further studies may help to elucidate potential nutrition-related sex-specific pathophysiological mechanisms and differential prevalence rates in PD.

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MIND diet associated with later onset of Parkinson’s disease

Crystal structure of enteropathogenic E.coli (EPEC) type III secretion system protein EscJ

Genome plasticity in Salmonella was first detected in Salmonella enterica serovar Typhi. It has been observed in a number of Salmonella serovars since then. Mechanisms that can lead to alterations in the genome include changes at the single-nucleotide level, gene loss, and genome rearrangements. Genome rearrangements including inversions and translocations can lead to genome plasticity, contributing to the divergence of Salmonella strains. Salmonella pathogenicity islands (SPIs) are large regions of DNA, which are most likely acquired as a result of horizontal gene transfer (HGT) and are often associated with virulence. The virulence plasmids of Salmonella strains contribute to the adaptation of the organism, and in some cases allow the transfer of genes. It appears that expansion of host range is linked to lateral gene transfer (LGT) of genes involved in host-pathogen interactions. A common theme for the variable regions between serovars was the diversity in sugar metabolism, highlighting the redundancy of these systems. The majority of coding regions unique to serovar Enteritidis encode prophage-related functions. Although the genome sequence of S. enterica serovar Pullorum is found to be very similar to those of other Salmonella serovars, the genetic arrangement was significantly different, with three major inversions and one translocation found between strains. Understanding the phenomenon of genome plasticity in this species is important to characterize the relationship between genetic variation and host adaptation, as well as the ability to cause a relatively minor gastrointestinal disease or a potentially life-threatening systemic fever.

Genome Plasticity in Salmonella enterica and Its Relevance to Host-Pathogen Interactions

The host-pathogen interaction involves a myriad of initiations and responses from both sides. Bacterial pathogens such as enteropathogenic Escherichia coli (EPEC) and Salmonella enterica have numerous virulence factors that interact with and alter signaling components of the host cell to initiate responses that are beneficial to pathogen survival and persistence. The study of Salmonella and EPEC infection reveals intricate connections between host signal transduction, cytoskeletal architecture, membrane trafficking, and cytokine gene expression. The emerging picture includes elements of molecular mimicry by bacterial effectors and bacterial subversion of typical host events, with the result that EPEC is able to survive and persist in an extracellular milieu, while Salmonella establishes an intracellular niche and is able to spread systemically throughout the host. This review focuses on recent advances in our understanding of the signaling events stemming from the host-pathogen interactions specific to Salmonella and EPEC.

B. Brett Finlay

Papers

The impact of the intestinal microbiome on human immune development and atopic disease

MIND diet associated with later onset of Parkinson’s disease

Crystal structure of enteropathogenic E.coli (EPEC) type III secretion system protein EscJ

Genome Plasticity in Salmonella enterica and Its Relevance to Host-Pathogen Interactions

Salmonella and Enteropathogenic Escherichia coli Interactions with Host Cells: Signaling Pathways.