Harnessing the Potential of Killers and Altruists within the Microbial Community: A Possible Alternative to Antibiotic Therapy?

Uncovering the arsenal of class II bacteriocins in salivarius streptococci

Facing the antibiotic resistance crisis, bacteriocins are considered as a promising alternative to treat bacterial infections. In the human commensal Streptococcus salivarius, the production of unmodified bacteriocins (or salivaricins) is directly controlled at the transcriptional level by quorum-sensing. To discover hidden bacteriocins, we harnessed here the unique molecular signatures of salivaricins not yet used in available computational pipelines and performed genome mining followed by orthogonal reconstitution and expression. From 100 genomes of S. salivarius, we identified more than 50 bacteriocin candidates clustered into 21 groups. Strain-based analysis of bacteriocin combinations revealed significant diversity, reflecting the plasticity of seven independent loci. Activity tests showed both narrow and broad-spectrum bacteriocins with overlapping activities against a wide panel of Gram-positive bacteria, including notorious multidrug-resistant pathogens. Overall, this work provides a search-to-test generic pipeline for bacteriocin discovery with high impact for bacterial ecology and broad applications in the food and biomedical fields.

Electrogenetic signaling and information propagation for controlling microbial consortia via programmed lysis

To probe signal propagation and genetic actuation in microbial consortia, we have coopted the components of both redox and quorum sensing (QS) signaling into a communication network for guiding composition by "programming" cell lysis. Here, we use an electrode to generate hydrogen peroxide as a redox cue that determines consortia composition. The oxidative stress regulon of Escherichia coli, OxyR, is employed to receive and transform this signal into a QS signal that coordinates the lysis of a subpopulation of cells. We examine a suite of information transfer modalities including "monoculture" and "transmitter-receiver" models, as well as a series of genetic circuits that introduce time-delays for altering information relay, thereby expanding design space. A simple mathematical model aids in developing communication schemes that accommodate the transient nature of redox signals and the "collective" attributes of QS signals. We suggest this platform methodology will be useful in understanding and controlling synthetic microbial consortia for a variety of applications, including biomanufacturing and biocontainment.

Contact-Dependent Growth Inhibition in Bacteria: Do Not Get Too Close!

Over millions of years of evolution, bacteria have developed complex strategies for intra-and interspecies interactions and competition for ecological niches and resources. Contact-dependent growth inhibition systems (CDI) are designed to realize a direct physical contact of one bacterial cell with other cells in proximity via receptor-mediated toxin delivery. These systems are found in many microorganisms including clinically important human pathogens. The main purpose of these systems is to provide competitive advantages for the growth of the population. In addition, non-competitive roles for CDI toxin delivery systems including interbacterial signal transduction and mediators of bacterial collaboration have been suggested. In this review, our goal was to systematize the recent findings on the structure, mechanisms, and purpose of CDI systems in bacterial populations and discuss the potential biological and evolutionary impact of CDI-mediated interbacterial competition and/or cooperation.

Bacteriophage-mediated extracellular DNA release is important for the structural stability of aerobic granular sludge

The aim of this study was to investigate the microbial characteristics and the structural role of exDNA in different size AGSs. Metagenomic results showed that exDNA has a significantly lower GC content, ~46.0%, than the ~65.0% GC of intracellular DNA (inDNA). Taxonomic predictions showed most of the reads from the exDNA that could be taxonomically assigned were from members of the phyla Bacteroidetes (55.0-64.2% of the total exDNA reads). Assigned inDNA reads were mainly from Proteobacteria (50.9-57.8%) or Actinobacteria (18.0-28.0%). Reads mapping showed that exDNA read depths were similar across all predicted open reading frames from assembled genomes that were assigned as Bacteroidetes which is consistent with cell lysis as a source of exDNA. Enrichment of CRISPR-CAS proteins in exDNA reads and CRISPR spacers in Bacteroidetes associated draft genomes suggested that bacteriophage infection may be an important cause of lysis of these cells. A critical role for this exDNA was found using DNase I digestion experiments which showed that the exDNA was vital for the structural stability of relatively small sized AGS but not for the larger sized AGS. The characteristics of exDNA in AGSs revealed in this work provide a new perspective on AGS components and structural stability.