Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i

Antimicrobially active microorganisms associated with marine bryozoans

Bryozoans are sessile colonial animals that can be found in various aquatic and mainly in marine environments. Due to their sessile nature, bryozoans compete for surfaces they can colonize but, on the other hand, are confronted with microbial colonizers on their surfaces. Interactions of the bryozoan with its associates, as well as within the microbial community, are mediated chemically. Biofilm formation and composition is mainly influenced by the use of chemical compounds. Studies on the bryozoan-associated microbial diversity are scarce, and surveys on the antimicrobial potential of these associated bacteria are missing. The present study focused on isolating bryozoan-associated bacteria, assessing their antimicrobial properties and classifying them phylogenetically. Various bryozoan specimens were collected in the Baltic (10 specimens) and the Mediterranean Sea (11 specimens). Bacteria were isolated using a variety of nutrient media and tested for their antimicrobial abilities against Gram-positive and Gram-negative indicator strains, as well as against the yeast Candida glabrata. 30% of all isolates displayed activity and were phylogenetically classified on the basis of 16S rDNA gene sequences. Whereas all isolates were active against Gram-positive indicators, four isolates exhibited additional anti-Escherichia coli activity, the phylogenetic analysis revealed affiliation to Gram-negative phyla (Flavobacteria, Alpha- and Gammaproteobacteria). One isolate belonged to the Gram-positive Actinobacteria. Both species- and strain-specific activity patterns were revealed. Furthermore, site-specific distribution patterns of associated bacteria were found. Of these antibiotically active isolates, the strain B390 was described as type strain of the novel species Tenacibaculum adriaticum. Also, specimens of the bryozoan Membranipora membranacea were sampled in the Baltic Sea for the first more detailed analysis on antimicrobially active isolates. Low-nutrient media featuring “artificial” or “natural” ingredients were used for isolation of bacteria. Additionally, the antibiotic test panel was extended to six different production media. The impact of these media on the phylogenetic diversity, as well as on activity patterns was determined. Although bacteria were affiliated with same phyla (Alpha- and Gammaproteobacteria, Actinobacteria, additionally Bacilli), the isolates of this sampling were more diverse as far as genus or phylotype affiliation was concerned. Especially within the Alphaproteobacteria, several probably novel bacterial species were found. Furthermore, the use of six different media for activity testing resulted in a more than twofold higher hit rate of active isolates in comparison to only one single medium

Rapid (<5 min) identification of pathogen in human blood by electrokinetic concentration and surface-enhanced Raman spectroscopy.

This study reports a novel microfluidic platform for rapid and long-ranged concentration of rare-pathogen from human blood for subsequent on-chip surface-enhanced Raman spectroscopy (SERS) identification/discrimination of bacteria based on their detected fingerprints. Using a hybrid electrokinetic mechanism, bacteria can be concentrated at the stagnation area on the SERS-active roughened electrode, while blood cells were excluded away from this region at the center of concentric circular electrodes. This electrokinetic approach performs isolation and concentration of bacteria in about three minutes; the density factor is increased approximately a thousand fold in a local area of ~5000 μm(2) from a low bacteria concentration of 5 × 10(3) CFU/ml. Besides, three genera of bacteria, S. aureus, E. coli, and P. aeruginosa that are found in most of the isolated infections in bacteremia were successfully identified in less than one minute on-chip without the use of any antibody/chemical immobilization and reaction processes

The potential of Symbiont Ba cteria in Melo melo Gastropod found in Pekalongan Waters as a source of MDR antibacterial active compound

The increasing resistance of many pathogenic microorganisms against antibiotics compounds creates an alarming issue in medical world. This concern has created research opportunities in new antibiotics compounds as alternative options. The gastropod Melo melo is a species whose main diet consists of other smaller gastropods. However, Melo-melo does not have any self-defense mechanism save for its thin shell. To protect itself from various pathogenic bacteria existing in its food, Melo melo produces secondary metabolites, which are suspected to contain bioactive compounds with antibacterial properties. This fact puts Melo melo as a marine biota with potential as a source of new antibacterial compounds. This research aims to discover the potency of symbiont bacteria in the gastropod Melo melo with capabilities in producing Multi-drug resistant (MDR) antibacterial compounds. Samples of Melo melo are collected from the vicinity of Pekalongan waters, Central Java, Indonesia. This research begins with the isolation of symbiont bacteria, screening of symbiont bacteria with potency in MDR antibacterial activities, antibacterial test, and isolation of MDR clinical pathogenic bacteria. These protocols are then followed by antibacterial sensitivity test, and identification of bacterial species active against MDR by biochemical test and molecular analysis. Molecular analyses are carried out sequentially by DNA extraction, DNA amplification by PCR, and DNA sequencing. Results of 16S rDNA are analyzed using Genetix program and then followed by sequence analysis of the 16S rDNA. In this research, 11 bacteria in Melo melo are isolated and there are 4 isolates which show antibacterial activities against MDR bacteria from Pseudomonas sp. and Enterobacter sp species. Molecular analysis of the most active isolates identifies that isolate PM 26 matches in characteristics with Brevibacterium celere strain KMM 3637 with 89% homology match. On the other hand, biochemical test shows that isolate PM 26 is identical with Bacillus sp. This research concludes that symbiont bacteria found in Melo melo possess antibacterial activities against bacteria of MDR strain

A Drop of Active Matter

We study theoretically the hydrodynamics of a fluid drop containing oriented filaments endowed with active contractile or extensile stresses and placed on a solid surface. The active stresses alter qualitatively the wetting properties of the drop, leading to new spreading laws and novel static drop shapes. Candidate systems for testing our predictions include cytoskeletal extracts with motors and ATP, suspensions of bacteria or pulsatile cells, or fluids laden with artificial self-propelled colloids.Comment: submitted to J Fluid Mec

Phase separation and rotor self-assembly in active particle suspensions

Adding a non-adsorbing polymer to passive colloids induces an attraction between the particles via the `depletion' mechanism. High enough polymer concentrations lead to phase separation. We combine experiments, theory and simulations to demonstrate that using active colloids (such as motile bacteria) dramatically changes the physics of such mixtures. First, significantly stronger inter-particle attraction is needed to cause phase separation. Secondly, the finite size aggregates formed at lower inter-particle attraction show unidirectional rotation. These micro-rotors demonstrate the self assembly of functional structures using active particles. The angular speed of the rotating clusters scales approximately as the inverse of their size, which may be understood theoretically by assuming that the torques exerted by the outermost bacteria in a cluster add up randomly. Our simulations suggest that both the suppression of phase separation and the self assembly of rotors are generic features of aggregating swimmers, and should therefore occur in a variety of biological and synthetic active particle systems.Comment: Main text: 6 pages, 5 figures. Supplementary information: 5 pages, 4 figures. Supplementary movies available from httP://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1116334109/-/DCSupplementa

Metabolic network analysis reveals microbial community interactions in anammox granules.

Microbial communities mediating anaerobic ammonium oxidation (anammox) represent one of the most energy-efficient environmental biotechnologies for nitrogen removal from wastewater. However, little is known about the functional role heterotrophic bacteria play in anammox granules. Here, we use genome-centric metagenomics to recover 17 draft genomes of anammox and heterotrophic bacteria from a laboratory-scale anammox bioreactor. We combine metabolic network reconstruction with metatranscriptomics to examine the gene expression of anammox and heterotrophic bacteria and to identify their potential interactions. We find that Chlorobi-affiliated bacteria may be highly active protein degraders, catabolizing extracellular peptides while recycling nitrate to nitrite. Other heterotrophs may also contribute to scavenging of detritus and peptides produced by anammox bacteria, and potentially use alternative electron donors, such as H2, acetate and formate. Our findings improve the understanding of metabolic activities and interactions between anammox and heterotrophic bacteria and offer the first transcriptional insights on ecosystem function in anammox granules

The role of Bursaphelenchus xylophilus associated bacteria in pine wilt disease

Pine wilt disease (PWD) is a complex disease integrating three major factors: the causal agent, the pinewood nematode Bursaphelenchus xylophilus; the insect-vector Monochamus spp.; and the host pine tree, Pinus sp. Since the early 80’s, the notion that another pathogenic agent involved, namely bacteria, may play a role in PWD has been gaining traction, however the role of bacteria in PWD is still unknown. The present work suggests the intriguing possibility that some B. xylophilus-associated bacteria may play a significant role in the development of this disease. This is inferred as a consequence of: (i) the phenotypic characterization, of a collection of 35 isolates of B. xylophilus-associated bacteria, in different tests broadly used to test plant pathogenic and plant growth promoting bacteria, and (ii) greenhouse experiments that infer pathogenicity of these bacteria in in maritime pine, Pinus pinaster. The results illustrate the presence of a heterogeneous microbial community associated with B. xylophilus and the traits exhibited by at least some of these bacteria appear to be related to PWD symptoms. The inoculation of four specific B. xylophilus-associated bacteria in P. pinaster seedlings resulted in the development of some PWD symptoms suggesting that these bacteria likely play an active role with B. xylophilus in PWD

Characterization of the corrosion resistance of several alloys to dilute biologically active solutions

Sulfate reducing bacteria and acid producing bacteria/fungi detected in hygiene waters increased the corrosion rate in aluminum alloy. Biologically active media enhanced the formation of pits on metal coupons. Direct observation of gas evolved at the corrosion sample, coupled with scanning electron microscopy (SEM) and energy dispersive x-ray analysis of the corrosion products indicates that the corrosion rate is increased because the presence of bacteria favor the reduction of hydrogen as the cathodic reaction through the reaction of oxygen and water. SEM verifies the presence of microbes in a biofilm on the surface of corroding samples. The bacterial consortia are associated with anodic sites on the metal surface, aggressive pitting occurs adjacent to biofilms. Many pits are associated with triple points and inclusions in the aluminum alloy microstructure. Similar bacterial colonization was found on the stainless steel samples. Fourier transform Infrared Spectroscopy confirmed the presence of carbonyl groups in pitted areas of samples exposed to biologically active waters