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...

/pdf/the-nox-family-of-ros-generating-nadph-oxidases-physiology-zjc88zvh59.pdf

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

https://www.cell.com/immunity/pdf/S1074-7613(15)00450-1.pdf

Worming Their Way into the Picture: Microbiota Help Helminths Modulate Host Immunity

Models to study enteropathogenic bacteria: lessons learned from Shigella

There is a tremendous history of capitalizing on the biodiversity of our natural environment for molecules to treat diseases and regulate host physiology (e.g. penicillin, acetylsalicylic acid). However, until recently we have failed to probe the therapeutic potential of our microbial symbionts: a biodiverse population of bacteria, archaea, viruses, protists, and fungi that reside on and within us. Recently there has been an increased realization that the microbiota significantly impact many of our physiological and immunological processes (Fig. 1), suggesting that there is great opportunity for therapeutic discoveries.



Figure 1

Some of the many mechanisms through which gut microbes and their signals can affect host health. SFB, segmented filamentous bacteria.



The potential of the microbiota to affect the host is vast, considering its impressive genetic composition. The collective genomes of our resident microbes, referred to as the metagenome, represent a gene set which is estimated to be 150-fold greater than the human genetic complement [1]. Many of these genes are the product of co-evolution and have been selected on the basis of improving host fitness rather than the fitness of the microbe itself. As we begin to understand previously unidentified properties and molecules of the microbiota, we will be able to “mine” these for potential therapeutic benefit. Here, we discuss some of the avenues of discovery that present opportunities for further exploitation. Possibilities discussed include strategies for excluding pathogens, manipulation of the immune system and regulation of non-intestinal sites.

Harvesting the biological potential of the human gut microbiome

Many bacterial pathogens interact with surfaces on the body resulting in disease. These interactions are usually tightly regulated. Several of these pathogens also exploit host processed which contribute to their pathogenesis. Enteropathogenic existing epithelial cells using sophisticated mechanisms that exploit existing epithelial signal transduction pathways and host cytoskeleton components. Unlike EPEC, Salmonella species actually enter into epithelial cells (invade) and function as intracellular parasites. During invasion Salmonella exploit various host signal transduction pathways and cause cytoskeletal rearrangements. Salmonella enter an intracellular vacuole which remains separated from the main epithelial cell, Salmonella species trigger the formation of a novel intracellular organelle which is associated with intracellular growth. Comparison of the virulence mechanisms used by these two pathogens and their exploitation of epithelial cells illustrates several principles used by bacterial pathogens to cause disease.

B. Brett Finlay

Papers

Worming Their Way into the Picture: Microbiota Help Helminths Modulate Host Immunity

Models to study enteropathogenic bacteria: lessons learned from Shigella

Harvesting the biological potential of the human gut microbiome

Interactions of Enteric Pathogens with Human Epithelial Cells

Crowd control: quorum sensing in pathogenic E. coli.