Interaction between atypical microorganisms and E. coli in catheter-associated urinary tract biofilms

Most biofilms involved in catheter-associated urinary tract infections (CAUTIs) are polymicrobial, with disease causing (eg Escherichia coli) and atypical microorganisms (eg Delftia tsuruhatensis) frequently inhabiting the same catheter. Nevertheless, there is a lack of knowledge about the role of atypical microorganisms. Here, single and dual-species biofilms consisting of E. coli and atypical bacteria (D. tsuruhatensis and Achromobacter xylosoxidans), were evaluated. All species were good biofilm producers (Log 5.84–7.25 CFU cm−2 at 192 h) in artificial urine. The ability of atypical species to form a biofilm appeared to be hampered by the presence of E. coli. Additionally, when E. coli was added to a pre-formed biofilm of the atypical species, it seemed to take advantage of the first colonizers to accelerate adhesion, even when added at lower concentrations. The results suggest a greater ability of E. coli to form biofilms in conditions mimicking the CAUTIs, whatever the pre-existing microbiota and the inoculum concentration.This work was supported by the Portuguese Science Foundation (FCT), DNA mimics Research Project [Ref. PIC/IC/82815/2007] from the FCT and MCTES; PhD Fellowship [SFRH/BD/82663/2011]; and Postdoctoral Fellowship [SFRH/BPD/74480/2010]. The authors would like to thank to M. Fenice M and A. Steinbuchel for kindly providing the Delftia tsuruhatensis BM90 and Achromobacter xylosoxidans B3 species, respectively

Cooperation or conflict? Impact of intraspecific diversity on Escherichia coli biofilms

Intraspecific diversity in biofilm communities is associated with enhanced survival and growth of the individual biofilm populations. In here, we assess if this apparent cooperative behavior still holds as the number of different strains in a biofilm increases. Using E. coli as a model organism, the influence of intraspecific diversity in biofilm populations composed of up to six different E. coli strains, was assessed. Biofilm quantification was evaluated by crystal violet (CV) staining and colony forming units (CFU) counts. In general, with the increasing number of strains in a biofilm, an increase in cell counts and a decrease in matrix production was observed. This observation was confirmed by cluster analysis that indicated that after 24h of biofilm formation the best model, according to the Bayesian information criterion (BIC), consisted of three clusters that grouped together biofilms with an equal number of strains. It hence appears that increased genotypic diversity in a biofilm leads E. coli to maximize the production of its offspring, in detriment of the production of public goods (i.e. matrix components), that would be beneficial to all strains individually and the consortium as a whole. Apart from the ecological implications, these results can be explored in the area of clinical biofilms, as a decrease in matrix production might render these intraspecies biofilms more sensitive to antimicrobial agents

Impact of Delftia tsuruhatensis and Achromobacter xylosoxidans on Escherichia coli dual-species biofilms treated with antibiotic agents

Recently it was demonstrated that for urinary tract infections species with a lower or unproven pathogenic potential, such as Delftia tsuruhatensis and Achromobacter xylosoxidans, might interact with conventional pathogenic agents such as Escherichia coli. Here, single- and dual-species biofilms of these microorganisms were characterized in terms of microbial composition over time, the average fitness of E. coli, the spatial organization and the biofilm antimicrobial profile. The results revealed a positive impact of these species on the fitness of E. coli and a greater tolerance to the antibiotic agents. In dual-species biofilms exposed to antibiotics, E. coli was able to dominate the microbial consortia in spite of being the most sensitive strain. This is the first study demonstrating the protective effect of less common species over E. coli under adverse conditions imposed by the use of antibiotic agents.This work was financially supported by the FCT/MEC with national funds and when applicable co-funded by FEDER in the scope of the P2020 Partnership Agreement [Project UID/ EQU/00511/2013-LEPABE]; FEDER funds through the Operational Programme for Competitiveness Factors – COMPETE, O Novo Norte–North Portugal Regional Operational Programme – ON2 and National Funds through Foundation for Science and Technology – FCT [Project NORTE-07-0124- FEDER-000025–RL2_ Environment&Health and Project ‘DNAmimics’ PIC/IC/82815/2007]; PhD fellowship [SFRH/ BD/82663/2011]; and postdoctoral fellowship [SFRH/ BPD/74480/2010]

Increased intraspecies diversity in Escherichia coli biofilms promotes cellular growth at the expense of matrix production

Intraspecies diversity in biofilm communities is associated with enhanced survival and growth of the individual biofilm populations. Studies on the subject are scarce, namely, when more than three strains are present. Hence, in this study, the influence of intraspecies diversity in biofilm populations composed of up to six different Escherichia coli strains isolated from urine was evaluated in conditions mimicking the ones observed in urinary tract infections and catheter-associated urinary tract infections. In general, with the increasing number of strains in a biofilm, an increase in cell cultivability and a decrease in matrix production were observed. For instance, single-strain biofilms produced an average of 73.1 µg·cm−2 of extracellular polymeric substances (EPS), while six strains biofilms produced 19.9 µg·cm−2. Hence, it appears that increased genotypic diversity in a biofilm leads E. coli to direct energy towards the production of its offspring, in detriment of the production of public goods (i.e., matrix components). Apart from ecological implications, these results can be explored as another strategy to reduce the biofilm burden, as a decrease in EPS matrix production may render these intraspecies biofilms more sensitive to antimicrobial agents.This work was financially supported by Base Funding—UIDB/00511/2020 of the Laboratory for Process Engineering, Environment, Biotechnology and Energy—LEPABE—funded by national funds through the FCT/MCTES (PIDDAC); Project POCI-01-0145-FEDER-030431 (CLASInVivo) and project POCI-01-0145-FEDER-029841 (POLY-PREVENTT), funded by FEDER funds through COMPETE2020—Programa Operacional Competitividade e Internacionalização (POCI) and by national funds (PIDDAC) through FCT/MCTES; Strategic funding of UIDB/04469/2020 of the Centre of Biological Engineering–CEB–funded by national funds through the FCT; Project BeMundus Brazil Europe/Erasmus Mundus scholarship granted by BM13DF0014.info:eu-repo/semantics/publishedVersio

#126. Nova estratégia para detetar e localizar patogénicos periodontais: a técnica de PNA-FISH

[Excerto] Objetivos: A compreensão da dinâmica periodontal biofilme-hospedeiro, in situ, é crucial para melhorar o diagnóstico e definir tratamentos mais racionais e eficazes. Este trabalho tem como objetivo o desenvolvimento de sondas de ácido peptídico nucleico (PNA), um mímico do DNA, para a identificac¸ão e localizac¸ão de Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans)ePorphyromonas gingivalis (P.gingivalis)emamostrasdeplacasubgengivalebiópsiasgengivais, pelo método de hibridac¸ão fluorescente in situ (FISH). [...]info:eu-repo/semantics/publishedVersio

Particle size effect of integral carob flour on bioaccessibility of bioactive compounds during simulated gastrointestinal digestion

Carob fruit is native to the Mediterranean region and produced mainly in Portugal, Italy, Morocco and Turkey. The production of the carob fruit in Portugal is highly extensive and sustainable. Currently, carob flour (CF) production is mainly achieved after pulp separation, despite it having been demonstrated that the seeds improve the extraction efficiency of bioactive compounds such as polyphenols, promoting human health. This study aimed to produce an integral CF through an innovative process and assess its physicochemical and bioactive properties at different particle sizes throughout simulated gastrointestinal tract (GIT) digestion. The sugar content profile obtained throughout GIT digestion indicated that sucrose, the sugar present at the highest concentration in undigested CF, was digested and broken down into simple sugars, namely glucose and fructose. The total phenolic content (TPC) and antioxidant activity obtained for the ≤100 µm fraction were in accordance and gastric digestion promoted an increase in the TPC value compared to the undigested sample. The >100 µm fractions displayed a distinct profile from the ≤100 µm fraction. This study showed that the particle size affects the sugar, antioxidant and total phenolic content of CFs and also their gastrointestinal tract digestion. The ≤100 µm fraction demonstrated the most suitable profile as a functional food ingredient.info:eu-repo/semantics/publishedVersio

BiofOmics: A Web Platform for the Systematic and Standardized Collection of High-Throughput Biofilm Data

Background: Consortia of microorganisms, commonly known as biofilms, are attracting much attention from the scientific community due to their impact in human activity. As biofilm research grows to be a data-intensive discipline, the need for suitable bioinformatics approaches becomes compelling to manage and validate individual experiments, and also execute inter-laboratory large-scale comparisons. However, biofilm data is widespread across ad hoc, non-standardized individual files and, thus, data interchange among researchers, or any attempt of cross-laboratory experimentation or analysis, is hardly possible or even attempted. Methodology/Principal findings This paper presents BiofOmics, the first publicly accessible Web platform specialized in the management and analysis of data derived from biofilm high-throughput studies. The aim is to promote data interchange across laboratories, implementing collaborative experiments, and enable the development of bioinformatics tools in support of the processing and analysis of the increasing volumes of experimental biofilm data that are being generated. BiofOmics data deposition facility enforces data structuring and standardization, supported by controlled vocabulary. Researchers are responsible for the description of the experiments, their results and conclusions. BiofOmics curators interact with submitters only to enforce data structuring and the use of controlled vocabulary. Then, BiofOmics search facility makes publicly available the profile and data associated with a submitted study so that any researcher can profit from these standardization efforts to compare similar studies, generate new hypotheses to be tested or even extend the conditions experimented in the study. Significance BiofOmics novelty lays on its support to standardized data deposition, the availability of computerizable data files and the free-of-charge dissemination of biofilm studies across the community. Hopefully, this will open promising research possibilities, namely: the comparison of results between different laboratories, the reproducibility of methods within and between laboratories, and the development of guidelines and standardized protocols for biofilm formation devices and analytical methods.The financial support from the Institute of Biotechnology and Bioengineering - Center of Biological Engineering (IBB-CEB), Fundacao para a Ciencia e Tecnologia (FCT) and European Community fund FEDER (Program COMPETE), project PTDC/SAU-ESA/646091/2006/FCOMP-01-0124-FEDER-007480 and PhD grant of Idalina Machado (SFRH/BD/31065/2006) are gratefully acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

C2-phytoceramide perturbs lipid rafts and cell integrity in Saccharomyces cerevisiae in a sterol-dependent manner

Specific ceramides are key regulators of cell fate, and extensive studies aimed to develop therapies based on ceramide-induced cell death. However, the mechanisms regulating ceramide cytotoxicity are not yet fully elucidated. Since ceramides also regulate growth and stress responses in yeast, we studied how different exogenous ceramides affect yeast cells. C2-phytoceramide, a soluble form of phytoceramides, the yeast counterparts of mammalian ceramides, greatly reduced clonogenic survival, particularly in the G2/M phase, but did not induce autophagy nor increase apoptotic markers. Rather, the loss of clonogenic survival was associated with PI positive staining, disorganization of lipid rafts and cell wall weakening. Sensitivity to C2-phytoceramide was exacerbated in mutants lacking Hog1p, the MAP kinase homolog of human p38 kinase. Decreasing sterol membrane content reduced sensitivity to C2-phytoceramide, suggesting sterols are the targets of this compound. This study identified a new function of C2-phytoceramide through disorganization of lipid rafts and induction of a necrotic cell death under hypo-osmotic conditions. Since lipid rafts are important in mammalian cell signaling and adhesion, our findings further support pursuing the exploitation of yeast to understand the basis of synthetic ceramides' cytotoxicity to provide novel strategies for therapeutic intervention in cancer and other diseases.This work was supported by Fundacao para a Ciencia e Tecnologia through projects PTDC/BIA-BCM/69448/2006 and PEst-C/BIA/UI4050/2011, and fellowships to A. P. (SFRH/BPD/65003) and F. A. (SFRH/BD/80934/2011), as well as by FEDER through POFC - COMPETE. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.Peer Reviewe