scholarly journals Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling

Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 221
Author(s):  
Ozlem Altay ◽  
Cheng Zhang ◽  
Hasan Turkez ◽  
Jens Nielsen ◽  
Mathias Uhlén ◽  
...  
Keyword(s):  
Systems Biology ◽  
Alternative Pathway ◽  
Growth Conditions ◽  
Pentose Phosphate ◽  
Burkholderia Cenocepacia ◽  
Bacterial Cells ◽  
Metabolic Remodeling ◽  
Transcriptomics Data ◽  
Biofilm Development ◽  
Genome Scale

Burkholderia cenocepacia is among the important pathogens isolated from cystic fibrosis (CF) patients. It has attracted considerable attention because of its capacity to evade host immune defenses during chronic infection. Advances in systems biology methodologies have led to the emergence of methods that integrate experimental transcriptomics data and genome-scale metabolic models (GEMs). Here, we integrated transcriptomics data of bacterial cells grown on exponential and biofilm conditions into a manually curated GEM of B. cenocepacia. We observed substantial differences in pathway response to different growth conditions and alternative pathway susceptibility to extracellular nutrient availability. For instance, we found that blockage of the reactions was vital through the lipid biosynthesis pathways in the exponential phase and the absence of microenvironmental lysine and tryptophan are essential for survival. During biofilm development, bacteria mostly had conserved lipid metabolism but altered pathway activities associated with several amino acids and pentose phosphate pathways. Furthermore, conversion of serine to pyruvate and 2,5-dioxopentanoate synthesis are also identified as potential targets for metabolic remodeling during biofilm development. Altogether, our integrative systems biology analysis revealed the interactions between the bacteria and its microenvironment and enabled the discovery of antimicrobial targets for biofilm-related diseases.

scholarly journals Biofilms as Promoters of Bacterial Antibiotic Resistance and Tolerance

Antibiotics ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 3
Author(s):  
Cristina Uruén ◽  
Gema Chopo-Escuin ◽  
Jan Tommassen ◽  
Raúl C. Mainar-Jaime ◽  
Jesús Arenas
Keyword(s):  
Close Contact ◽  
Animal Health ◽  
Deep Understanding ◽  
Growth Conditions ◽  
Multidrug Resistant ◽  
Extracellular Dna ◽  
Resistant Bacteria ◽  
Resistance To Antibiotics ◽  
Global Threat ◽  
Biofilm Development

Multidrug resistant bacteria are a global threat for human and animal health. However, they are only part of the problem of antibiotic failure. Another bacterial strategy that contributes to their capacity to withstand antimicrobials is the formation of biofilms. Biofilms are associations of microorganisms embedded a self-produced extracellular matrix. They create particular environments that confer bacterial tolerance and resistance to antibiotics by different mechanisms that depend upon factors such as biofilm composition, architecture, the stage of biofilm development, and growth conditions. The biofilm structure hinders the penetration of antibiotics and may prevent the accumulation of bactericidal concentrations throughout the entire biofilm. In addition, gradients of dispersion of nutrients and oxygen within the biofilm generate different metabolic states of individual cells and favor the development of antibiotic tolerance and bacterial persistence. Furthermore, antimicrobial resistance may develop within biofilms through a variety of mechanisms. The expression of efflux pumps may be induced in various parts of the biofilm and the mutation frequency is induced, while the presence of extracellular DNA and the close contact between cells favor horizontal gene transfer. A deep understanding of the mechanisms by which biofilms cause tolerance/resistance to antibiotics helps to develop novel strategies to fight these infections.

scholarly journals 616 Preventing Biofilms on BACTIGON® Coated Camstent Urinary Catheters in Patients Undergoing Elective Colorectal Surgery: A Single Centre Pilot Study

2021 ◽  
Vol 108 (Supplement_2) ◽  
Author(s):  
C Lewis-Lloyd ◽  
J Dubern ◽  
K Kalenderski ◽  
N Halliday ◽  
M Alexander ◽  
...  
Keyword(s):  
Environmental Scanning Electron Microscopy ◽  
Environmental Scanning ◽  
Bacterial Cells ◽  
Urinary Catheters ◽  
Elective Colorectal Surgery ◽  
Mineral Compositions ◽  
Microscopy Data ◽  
Tract Infections ◽  
Biofilm Development ◽  
Hospital Acquired

Abstract Introduction Catheter associated urinary tract infections account for 40% of hospital acquired infections. They are associated with biofilms consisting of bacterial cells enmeshed in a self-generated extracellular matrix adhering to catheter surfaces. We have developed a novel polymer family that, coated onto urinary catheters, creates a “non-stick” surface preventing biofilm development. Method Prospective cohort of elective colorectal patients recruited pre-operatively, received a standard silicone (SS) or Camstent (BACTIGON®) coated urinary catheter. After removal, catheters were cut longitudinally into 3 segments. Biomass and biomineralisation were analysed using confocal fluorescence microscopy. Data were normalised by square rooting the catheter indwelling duration. Environmental scanning electron microscopy and energy dispersive x-ray spectroscopy was performed. Results Of 40 patients, 20 each received a SS or coated catheter. Between SS and coated catheters, average indwelling duration was similar and biofilm biomass was 32.068µg/cm2 (95%CI ±21.950) vs. 1.948µg/cm2 (95%CI ±2.595) (P = 0.0111). Confocal microscopy suggested a 93.93% reduction in biofilm biomass on coated catheters. Mineral compositions were different with biofilm and struvite/apatite on SS and calcium oxalate, endogenously derived, on coated catheters. Conclusions Inert BACTIGON® coated catheters appear superior at preventing biofilm formation than SS catheters. Clinical trials are needed to determine the clinical and health economic benefit of this intervention.

PBP4 and PBP5 are involved in regulating exopolysaccharide synthesis during Escherichia coli biofilm formation

Microbiology ◽  
2021 ◽  
Vol 167 (3) ◽  
Author(s):  
Sathi Mallick ◽  
Shanti Kiran ◽  
Tapas Kumar Maiti ◽  
Anindya S. Ghosh
Keyword(s):  
Escherichia Coli ◽  
Biofilm Formation ◽  
Type Species ◽  
Pentose Phosphate ◽  
Bacterial Cells ◽  
Surface Adhesion ◽  
Content Type ◽  
Penicillin Binding Proteins ◽  
E Coli ◽  
Link Type

Escherichia coli low-molecular-mass (LMM) Penicillin-binding proteins (PBPs) help in hydrolysing the peptidoglycan fragments from their cell wall and recycling them back into the growing peptidoglycan matrix, in addition to their reported involvement in biofilm formation. Biofilms are external slime layers of extra-polymeric substances that sessile bacterial cells secrete to form a habitable niche for themselves. Here, we hypothesize the involvement of Escherichia coli LMM PBPs in regulating the nature of exopolysaccharides (EPS) prevailing in its extra-polymeric substances during biofilm formation. Therefore, this study includes the assessment of physiological characteristics of E. coli CS109 LMM PBP deletion mutants to address biofilm formation abilities, viability and surface adhesion. Finally, EPS from parent CS109 and its ΔPBP4 and ΔPBP5 mutants were purified and analysed for sugars present. Deletions of LMM PBP reduced biofilm formation, bacterial adhesion and their viability in biofilms. Deletions also diminished EPS production by ΔPBP4 and ΔPBP5 mutants, purification of which suggested an increased overall negative charge compared with their parent. Also, EPS analyses from both mutants revealed the appearance of an unusual sugar, xylose, that was absent in CS109. Accordingly, the reason for reduced biofilm formation in LMM PBP mutants may be speculated as the subsequent production of xylitol and a hindrance in the standard flow of the pentose phosphate pathway.

scholarly journals Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Neeraj Sinha ◽  
Evert M. van Schothorst ◽  
Guido J. E. J. Hooiveld ◽  
Jaap Keijer ◽  
Vitor A. P. Martins dos Santos ◽  
...  
Keyword(s):  
Metabolic Flux ◽  
Transcript Levels ◽  
Proportionality Constant ◽  
Model Predictions ◽  
Physiological Information ◽  
Highly Expressed Genes ◽  
Transcriptomics Data ◽  
Genome Scale ◽  
The Impact ◽  
Constraint Based Models

Abstract Background Several computational methods have been developed that integrate transcriptomics data with genome-scale metabolic reconstructions to increase accuracy of inferences of intracellular metabolic flux distributions. Even though existing methods use transcript abundances as a proxy for enzyme activity, each method uses a different hypothesis and assumptions. Most methods implicitly assume a proportionality between transcript levels and flux through the corresponding function, although these proportionality constant(s) are often not explicitly mentioned nor discussed in any of the published methods. E-Flux is one such method and, in this algorithm, flux bounds are related to expression data, so that reactions associated with highly expressed genes are allowed to carry higher flux values. Results Here, we extended E-Flux and systematically evaluated the impact of an assumed proportionality constant on model predictions. We used data from published experiments with Escherichia coli and Saccharomyces cerevisiae and we compared the predictions of the algorithm to measured extracellular and intracellular fluxes. Conclusion We showed that detailed modelling using a proportionality constant can greatly impact the outcome of the analysis. This increases accuracy and allows for extraction of better physiological information.

scholarly journals Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

2020 ◽  
Author(s):  
Colton J. Lloyd ◽  
Jonathan Monk ◽  
Laurence Yang ◽  
Ali Ebrahim ◽  
Bernhard O. Palsson
Keyword(s):  
Amino Acids ◽  
Growth Conditions ◽  
Anaerobic Growth ◽  
Metabolic Phenotype ◽  
E Coli ◽  
Scale Models ◽  
Protein Components ◽  
K 12 ◽  
Genome Scale ◽  
Prosthetic Groups

AbstractSustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated genome-scale models of metabolism and gene expression (ME-models) have the unique ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we use the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME model mostly agree with the standard biomass objective function used in models of metabolism alone (M models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of prebiotic amino acids in the proteins used to sustain anaerobic growth (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E. coli. Genome-scale models have thus reached a level of sophistication where they reveal intricate properties of functional proteomes and how they support different E. coli lifestyles.

The cis -2-dodecenoic acid (BDSF) quorum sensing system in Burkholderia cenocepacia

2022 ◽  
Author(s):  
Mingfang Wang ◽  
Xia Li ◽  
Shihao Song ◽  
Chaoyu Cui ◽  
Lian-Hui Zhang ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Bacterial Infections ◽  
Xanthomonas Campestris ◽  
Cell Communication ◽  
Burkholderia Cenocepacia ◽  
Bacterial Cells ◽  
Communication Signals ◽  
Signal Perception ◽  
Sensing System ◽  
Diffusible Signal Factor

It has been demonstrated that quorum sensing (QS) is widely employed by bacterial cells to coordinately regulate various group behaviors. Diffusible signal factor (DSF)-type signals have emerged as a growing family of conserved cell-cell communication signals. In addition to the DSF signal initially identified in Xanthomonas campestris pv. campestris, B urkholderia d iffusible s ignal f actor (BDSF, cis -2-dodecenoic acid) has been recognized as a conserved DSF-type signal with specific characteristics in both signal perception and transduction from DSF signals. Here, we review the history and current progress of the research of this type of signal, especially focusing on its biosynthesis, signaling pathways, and biological functions. We also discuss and explore the huge potential of targeting this kind of QS system as a new therapeutic strategy to control bacterial infections and diseases.

scholarly journals Recent Advances in Surface Nanoengineering for Biofilm Prevention and Control. Part I: Molecular Basis of Biofilm Recalcitrance. Passive Anti-Biofouling Nanocoatings

Nanomaterials ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1230 ◽  
Author(s):  
Paul Cătălin Balaure ◽  
Alexandru Mihai Grumezescu
Keyword(s):  
Life Cycle ◽  
Molecular Mechanisms ◽  
Antimicrobial Agents ◽  
Current Knowledge ◽  
Emergent Properties ◽  
Bacterial Cells ◽  
Life Cycle Stages ◽  
Fouling Release ◽  
Biofilm Development ◽  
And Control

Medical device-associated infections are becoming a leading cause of morbidity and mortality worldwide, prompting researchers to find new, more effective ways to control the bacterial colonisation of surfaces and biofilm development. Bacteria in biofilms exhibit a set of “emergent properties”, meaning those properties that are not predictable from the study of free-living bacterial cells. The social coordinated behaviour in the biofilm lifestyle involves intricate signaling pathways and molecular mechanisms underlying the gain in resistance and tolerance (recalcitrance) towards antimicrobial agents as compared to free-floating bacteria. Nanotechnology provides powerful tools to disrupt the processes responsible for recalcitrance development in all stages of the biofilm life cycle. The present paper is a state-of-the-art review of the surface nanoengineering strategies currently used to design antibiofilm coatings. The review is structurally organised in two parts according to the targeted biofilm life cycle stages and molecular mechanisms intervening in recalcitrance development. Therefore, in the present first part, we begin with a presentation of the current knowledge of the molecular mechanisms responsible for increased recalcitrance that have to be disrupted. Further, we deal with passive surface nanoengineering strategies that aim to prevent bacterial cells from settling onto a biotic or abiotic surface. Both “fouling-resistant” and “fouling release” strategies are addressed as well as their synergic combination in a single unique nanoplatform.

scholarly journals Clove Oil (Syzygium aromaticum L.) Activity against Alicyclobacillus acidoterrestris Biofilm on Technical Surfaces

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3334
Author(s):  
Alina Kunicka-Styczyńska ◽  
Agnieszka Tyfa ◽  
Dariusz Laskowski ◽  
Aleksandra Plucińska ◽  
Katarzyna Rajkowska ◽  
...  
Keyword(s):  
Essential Oil ◽  
Culture Conditions ◽  
Plate Count ◽  
Syzygium Aromaticum ◽  
Bacterial Cells ◽  
Clove Oil ◽  
Alicyclobacillus Acidoterrestris ◽  
Agitated Culture ◽  
Clove Essential Oil ◽  
Biofilm Development

Acidotermophilic bacteria Alicyclobacillus acidoterrestris is one of the main contaminants in the fruit industry forming biofilms which are difficult to remove from the production line by conventional methods. An alternative approach aims for the use of essential oils to prevent Alicyclobacillus biofilm development. The effect of clove essential oil on A. acidoterrestris biofilms on glass and polyvinyl chloride surfaces under static and agitated culture conditions was investigated by atomic force microscopy and the plate count method. The medium-flow and the type of technical surface significantly influenced A. acidoterrestris biofilm. The PVC was colonized in a greater extent comparing to glass. Clove essential oil in 0.05% (v/v) caused 25.1–65.0% reduction of biofilms on the technical surfaces along with substantial changes in their morphology by a decrease in the biofilm: height, surface roughness, and surface area difference. The oil also induced alteration in individual bacterial cells length and visible increase of their roughness. Clove essential oil seems to release EPS from biofilm and thus induce detachment of bacteria from the surface. Due to anti-A. acidoterrestris biofilm activity, the clove oil may be used in the juice industry to hinder a development of A. acidoterrestris biofilms on production surfaces.

Sign in / Sign up

Export Citation Format

Share Document