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)

Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of 'emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms - such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials - all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle.

Biofilms: an emergent form of bacterial life.

Universal sample preparation method for proteome analysis

Biofilm formation is a key virulence factor for a wide range of microorganisms that cause chronic infections. The multifactorial nature of biofilm development and drug tolerance imposes great challenges for the use of conventional antimicrobials and indicates the need for multi-targeted or combinatorial therapies. In this Review, we focus on current therapeutic strategies and those under development that target vital structural and functional traits of microbial biofilms and drug tolerance mechanisms, including the extracellular matrix and dormant cells. We emphasize strategies that are supported by in vivo or ex vivo studies, highlight emerging biofilm-targeting technologies and provide a rationale for multi-targeted therapies aimed at disrupting the complex biofilm microenvironment.

/pdf/targeting-microbial-biofilms-current-and-prospective-2br9buvtyz.pdf

Targeting microbial biofilms: current and prospective therapeutic strategies.

Clonal populations of microbial cells often show a high degree of phenotypic variability under homogeneous conditions. Stochastic fluctuations in the cellular components that determine cellular states can cause two distinct subpopulations, a property called bistability. Phenotypic heterogeneity can be readily obtained by interlinking multiple gene regulatory pathways, effectively resulting in a genetic logic-AND gate. Although switching between states can occur within the cells' lifetime, cells can also pass their cellular state over to the next generation by a mechanism known as epigenetic inheritance and thus perpetuate the phenotypic state. Importantly, heterogeneous populations can demonstrate increased fitness compared with homogeneous populations. This suggests that microbial cells employ bet-hedging strategies to maximize survival. Here, we discuss the possible roles of interlinked bistable networks, epigenetic inheritance, and bet-hedging in bacteria.

/pdf/bistability-epigenetics-and-bet-hedging-in-bacteria-nwb59xne6v.pdf

Bistability, epigenetics, and bet-hedging in bacteria.

Biofilms are communities of microbial cells that underpin diverse processes including sewage bioremediation, plant growth promotion, chronic infections and industrial biofouling. The cells resident in the biofilm are encased within a self-produced exopolymeric matrix that commonly comprises lipids, proteins that frequently exhibit amyloid-like properties, eDNA and exopolysaccharides. This matrix fulfils a variety of functions for the community, from providing structural rigidity and protection from the external environment to controlling gene regulation and nutrient adsorption. Critical to the development of novel strategies to control biofilm infections, or the capability to capitalize on the power of biofilm formation for industrial and biotechnological uses, is an in-depth knowledge of the biofilm matrix. This is with respect to the structure of the individual components, the nature of the interactions between the molecules and the three-dimensional spatial organization. We highlight recent advances in the understanding of the structural and functional role that carbohydrates and proteins play within the biofilm matrix to provide three-dimensional architectural integrity and functionality to the biofilm community. We highlight, where relevant, experimental techniques that are allowing the boundaries of our understanding of the biofilm matrix to be extended using Escherichia coli, Staphylococcus aureus, Vibrio cholerae, and Bacillus subtilis as exemplars.

https://pureadmin.qub.ac.uk/ws/files/15744307/femsre.fuv015.full.pdf

Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes

Biofilms represent the predominant mode of microbial growth in the natural environment. Bacillus subtilis is a ubiquitous Gram-positive soil bacterium that functions as an effective plant growth-promoting agent. The biofilm matrix is composed of an exopolysaccharide and an amyloid fiber-forming protein, TasA, and assembles with the aid of a small secreted protein, BslA. Here we show that natively synthesized and secreted BslA forms surface layers around the biofilm. Biophysical analysis demonstrates that BslA can self-assemble at interfaces, forming an elastic film. Molecular function is revealed from analysis of the crystal structure of BslA, which consists of an Ig-type fold with the addition of an unusual, extremely hydrophobic "cap" region. A combination of in vivo biofilm formation and in vitro biophysical analysis demonstrates that the central hydrophobic residues of the cap are essential to allow a hydrophobic, nonwetting biofilm to form as they control the surface activity of the BslA protein. The hydrophobic cap exhibits physiochemical properties remarkably similar to the hydrophobic surface found in fungal hydrophobins; thus, BslA is a structurally defined bacterial hydrophobin. We suggest that biofilms formed by other species of bacteria may have evolved similar mechanisms to provide protection to the resident bacterial community.

https://www.pnas.org/content/pnas/110/33/13600.full.pdf

BslA is a self-assembling bacterial hydrophobin that coats the Bacillus subtilis biofilm

Unicellular organisms use a variety of mechanisms to co-ordinate activity within a community and accomplish complex multicellular processes. Because some of the processes that are exhibited by one species can be physiologically incompatible, it raises the question of how entry into these different pathways is regulated. In the Gram-positive bacterium Bacillus subtilis, genetic competence, swarming motility, biofilm formation, complex colony architecture and protease production are all regulated by the response regulator DegU. DegU appears to integrate environmental signals and co-ordinate multicellular behaviours that are subsequently manifested at different levels of DegU phosphorylation. Data are presented which indicate that: (i) swarming motility is activated by very low levels of DegU approximately P that can be generated independently from its cognate sensor kinase DegS; (ii) complex colony architecture is activated by low levels of DegU approximately P that are produced in a DegS-dependent manner to activate transcription of yvcA, a novel gene required for complex colony architecture; and (iii) high levels of DegU approximately P inhibit complex colony architecture and swarming motility but are required prior to the activation of exoprotease production. A model is proposed to explain why such a system may have evolved within B. subtilis to control these multicellular processes through a single regulator.

DegU co-ordinates multicellular behaviour exhibited by Bacillus subtilis.

Biofilm formation is a social behaviour that generates favourable conditions for sustained survival in the natural environment. For the Gram-positive bacterium Bacillus subtilis the process involves the differentiation of cell fate within an isogenic population and the production of communal goods that form the biofilm matrix. Here we review recent progress in understanding the regulatory pathways that control biofilm formation and highlight developments in understanding the composition, function and structure of the biofilm matrix.

/pdf/biofilm-formation-by-bacillus-subtilis-new-insights-into-10124vm125.pdf

Biofilm formation by Bacillus subtilis: new insights into regulatory strategies and assembly mechanisms

https://backend.orbit.dtu.dk/ws/files/185297879/emss_80895.pdf

Nicola R. Stanley-Wall

Papers

Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes

BslA is a self-assembling bacterial hydrophobin that coats the Bacillus subtilis biofilm

DegU co-ordinates multicellular behaviour exhibited by Bacillus subtilis.

Biofilm formation by Bacillus subtilis: new insights into regulatory strategies and assembly mechanisms

Division of Labor during Biofilm Matrix Production.