Networking strategies in streptomyces coelicolor

We are interested the soil dwelling bacteria Streptomyces coelicolor because its cells grow end to end in a line. New branches have the potential to extend from any point along this line and the result is a network of branches and connections. This is a novel form of colonisation in the bacterial world and it is advantageous for spreading through an environment resourcefully. Networking protocols for communication technologies have similar pressures to be resourceful in terms of time, computing power, and energy. In this preliminary investigation we design a computer model of the biological system to understand its limitations and strategies for survival. The decentralised capacity for organisation of both the bacterial system and the model reflects well on the now-popular conventions for path finding and ad hoc network building in human technologies. The project will ultimately become a comparison of strategies between nature and the man-made

Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom

Prevalence of three sulfonamide resistance genes, sul1, sul2 and sul3 and sulfachloropyridazine (SCP) resistance was determined in bacteria isolated from UK manured agricultural clay soils and slurry samples, over a two year period. Slurry from tylosin-fed pigs amended with SCP and oxytetracycline (OTC) was used for manuring. Sul gene positive isolates were further screened for the presence of class 1 and 2 integrons. Phenotypic resistance to SCP was significantly higher in pig slurry and post application soil than in pre-application soil. Of 5isolates, 23 % carried sul1, 18 % sul2 and 9 % sul3 only. Two percent of isolates contained all three sul genes. Class 1 and class 2 integrons were identified in 5 % and 11.7 % of sul positive isolates. In previous reports, sul1 was linked to class 1 integrons, but in this study only 8 % of sul1 positive isolates carried the intI1 gene. Sulfonamide resistant pathogens were identified in slurry amended soil and soil leachate, including Shigella flexneri, Aerococcus spp. and Acinetobacter baumanni, suggesting a potential environmental reservoir. Sulfonamide resistance in Psychrobacter, Enterococcus and Bacillus spp. is reported for the first time, and this study also provides the first description of the genotype sul1, sul2 and sul3 outside the Enterobacteriacae, and in the soil environment

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

Background The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constraint-based modeling and detailed transcriptomics time course observations. Results We reconstructed the stoichiometric matrix of S. coelicolor, including the major antibiotic biosynthesis pathways, and performed flux balance analysis to predict flux changes that occur when the cell switches from biomass to antibiotic production. We defined the model input based on observed fermenter culture data and used a dynamically varying objective function to represent the metabolic switch. The predicted fluxes of many genes show highly significant correlation to the time series of the corresponding gene expression data. Individual mispredictions identify novel links between antibiotic production and primary metabolism. Conclusion Our results show the usefulness of constraint-based modeling for providing a detailed interpretation of time course gene expression data

Integron prevalence and diversity in manured soil

Integron abundance and diversity were studied in soil amended with pig slurry. Real-time PCR illustrated a significant increase in class 1 integron prevalence post slurry-application with increased prevalence still evident at 10 months post-application. Culture dependent data revealed 10 genera, including putative human pathogens, carrying class 1 and 2 integrons

Environmental monitoring of Mycobacterium bovis in badger feces and badger sett soil by real-time PCR, as confirmed by immunofluorescence, immunocapture, and cultivation

Real-time PCR was used to detect and quantify Mycobacterium bovis cells in naturally infected soil and badger faeces. Immunomagnetic capture, immunofluorescence and selective culture confirmed species identification and cell viability. These techniques will prove useful for monitoring M. bovis in the environment and for elucidating transmission routes between wildlife and cattle

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels

Background Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. Results In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute >98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of >22000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database [1]. By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. Conclusions IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD

Bony ingrowth potential of 3D-printed porous titanium alloy: a direct comparison of interbody cage materials in an in vivo ovine lumbar fusion model.

Background contextThere is significant variability in the materials commonly used for interbody cages in spine surgery. It is theorized that three-dimensional (3D)-printed interbody cages using porous titanium material can provide more consistent bone ingrowth and biological fixation.PurposeThe purpose of this study was to provide an evidence-based approach to decision-making regarding interbody materials for spinal fusion.Study designA comparative animal study was performed.MethodsA skeletally mature ovine lumbar fusion model was used for this study. Interbody fusions were performed at L2-L3 and L4-L5 in 27 mature sheep using three different interbody cages (ie, polyetheretherketone [PEEK], plasma sprayed porous titanium-coated PEEK [PSP], and 3D-printed porous titanium alloy cage [PTA]). Non-destructive kinematic testing was performed in the three primary directions of motion. The specimens were then analyzed using micro-computed tomography (µ-CT); quantitative measures of the bony fusion were performed. Histomorphometric analyses were also performed in the sagittal plane through the interbody device. Outcome parameters were compared between cage designs and time points.ResultsFlexion-extension range of motion (ROM) was statistically reduced for the PTA group compared with the PEEK cages at 16 weeks (p-value=.02). Only the PTA cages demonstrated a statistically significant decrease in ROM and increase in stiffness across all three loading directions between the 8-week and 16-week sacrifice time points (p-value≤.01). Micro-CT data demonstrated significantly greater total bone volume within the graft window for the PTA cages at both 8 weeks and 16 weeks compared with the PEEK cages (p-value<.01).ConclusionsA direct comparison of interbody implants demonstrates significant and measurable differences in biomechanical, µ-CT, and histologic performance in an ovine model. The 3D-printed porous titanium interbody cage resulted in statistically significant reductions in ROM, increases in the bone ingrowth profile, as well as average construct stiffness compared with PEEK and PSP

A novel sulfonamide resistance mechanism by two-component flavin-dependent monooxygenase system in sulfonamide-degrading actinobacteria

Sulfonamide-degrading bacteria have been discovered in various environments, suggesting the presence of novel resistance mechanisms via drug inactivation. In this study, Microbacterium sp. CJ77 capable of utilizing various sulfonamides as a sole carbon source was isolated from a composting facility. Genome and proteome analyses revealed that a gene cluster containing a flavin-dependent monooxygenase and a flavin reductase was highly up-regulated in response to sulfonamides. Biochemical analysis showed that the two-component monooxygenase system was key enzymes for the initial cleavage of sulfonamides. Co-expression of the two-component system in Escherichia coli conferred decreased susceptibility to sulfamethoxazole, indicating that the genes encoding drug-inactivating enzymes are potential resistance determinants. Comparative genomic analysis revealed that the gene cluster containing sulfonamide monooxygenase (renamed as sulX) and flavin reductase (sulR) was highly conserved in a genomic island shared among sulfonamide-degrading actinobacteria, all of which also contained sul1-carrying class 1 integrons. These results suggest that the sulfonamide metabolism may have evolved in sulfonamide-resistant bacteria which had already acquired the class 1 integron under sulfonamide selection pressures. Furthermore, the presence of multiple insertion sequence elements and putative composite transposon structures containing the sulX gene cluster indicated potential mobilization. This is the first study to report that sulX responsible for both sulfonamide degradation and resistance is prevalent in sulfonamide-degrading actinobacteria and its genetic signatures indicate horizontal gene transfer of the novel resistance gene

Performance of an environmental test to detect Mycobacterium bovis infection in badger social groups

A study by Courtenay and others (2006) demonstrated that the probability of detecting Mycobacterium bovis by PCR in soil samples from the spoil heaps of main badger setts correlated with the prevalence of excretion (infectiousness) of captured badgers belonging to the social group. It has been proposed that such a test could be used to target badger culling to setts containing infectious animals (Anon 2007). This short communication discusses the issues surrounding this concept, with the intention of dispelling any misconceptions among relevant stakeholders (farmers, policy makers and conservationists)