| 1. |
- Abadikhah, Marie, 1992, et al.
(author)
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Effect of anode material and dispersal limitation on the performance and biofilm community in microbial electrolysis cells
- 2023
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In: Biofilm. - 2590-2075. ; 6
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Journal article (peer-reviewed)abstract
- In a microbial electrolysis cell (MEC), the oxidization of organic compounds is facilitated by an electrogenic biofilm on the anode surface. The biofilm community composition determines the function of the system. Both deterministic and stochastic factors affect the community, but the relative importance of different factors is poorly understood. Anode material is a deterministic factor as materials with different properties may select for different microorganisms. Ecological drift is a stochastic factor, which is amplified by dispersal limitation between communities. Here, we compared the effects of three anode materials (graphene, carbon cloth, and nickel) with the effect of dispersal limitation on the function and biofilm community assembly. Twelve MECs were operated for 56 days in four hydraulically connected loops and shotgun metagenomic sequencing was used to analyse the microbial community composition on the anode surfaces at the end of the experiment. The anode material was the most important factor affecting the performance of the MECs, explaining 54–80 % of the variance observed in peak current density, total electric charge generation, and start-up lag time, while dispersal limitation explained 10–16 % of the variance. Carbon cloth anodes had the highest current generation and shortest lag time. However, dispersal limitation was the most important factor affecting microbial community structure, explaining 61–98 % of the variance in community diversity, evenness, and the relative abundance of the most abundant taxa, while anode material explained 0–20 % of the variance. The biofilms contained nine Desulfobacterota metagenome-assembled genomes (MAGs), which made up 64–89 % of the communities and were likely responsible for electricity generation in the MECs. Different MAGs dominated in different MECs. Particularly two different genotypes related to Geobacter benzoatilyticus competed for dominance on the anodes and reached relative abundances up to 83 %. The winning genotype was the same in all MECs that were hydraulically connected irrespective of anode material used.
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| 2. |
- Abadikhah, Marie, 1992, et al.
(author)
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Evidence of competition between electrogens shaping electroactive microbial communities in microbial electrolysis cells
- 2022
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In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 13
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Journal article (peer-reviewed)abstract
- In single-chamber microbial electrolysis cells (MECs), organic compounds are oxidized at the anode, liberating electrons that are used for hydrogen evolution at the cathode. Microbial communities on the anode and cathode surfaces and in the bulk liquid determine the function of the MEC. The communities are complex, and their assembly processes are poorly understood. We investigated MEC performance and community composition in nine MECs with a carbon cloth anode and a cathode of carbon nanoparticles, titanium, or stainless steel. Differences in lag time during the startup of replicate MECs suggested that the initial colonization by electrogenic bacteria was stochastic. A network analysis revealed negative correlations between different putatively electrogenic Deltaproteobacteria on the anode. Proximity to the conductive anode surface is important for electrogens, so the competition for space could explain the observed negative correlations. The cathode communities were dominated by hydrogen-utilizing taxa such as Methanobacterium and had a much lower proportion of negative correlations than the anodes. This could be explained by the diffusion of hydrogen throughout the cathode biofilms, reducing the need to compete for space.
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| 3. |
- Alalam, Hanna, et al.
(author)
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A High-Throughput Method for Screening for Genes Controlling Bacterial Conjugation of Antibiotic Resistance.
- 2020
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In: mSystems. - 2379-5077. ; 5:6
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Journal article (peer-reviewed)abstract
- The rapid horizontal transmission of antibiotic resistance genes on conjugative plasmids between bacterial host cells is a major cause of the accelerating antibiotic resistance crisis. There are currently no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation, which prevents understanding and targeting conjugation. We introduce a novel experimental framework to screen for conjugation-based horizontal transmission of antibiotic resistance between >60,000 pairs of cell populations in parallel. Plasmid-carrying donor strains are constructed in high-throughput. We then mix the resistance plasmid-carrying donors with recipients in a design where only transconjugants can reproduce, measure growth in dense intervals, and extract transmission times as the growth lag. As proof-of-principle, we exhaustively explore chromosomal genes controlling F-plasmid donation within Escherichia coli populations, by screening the Keio deletion collection in high replication. We recover all seven known chromosomal gene mutants affecting conjugation as donors and identify many novel mutants, all of which diminish antibiotic resistance transmission. We validate nine of the novel genes' effects in liquid mating assays and complement one of the novel genes' effect on conjugation (rseA). The new framework holds great potential for exhaustive disclosing of candidate targets for helper drugs that delay resistance development in patients and societies and improve the longevity of current and future antibiotics. Further, the platform can easily be adapted to explore interspecies conjugation, plasmid-borne factors, and experimental evolution and be used for rapid construction of strains.IMPORTANCE The rapid transmission of antibiotic resistance genes on conjugative plasmids between bacterial host cells is a major cause of the accelerating antibiotic resistance crisis. There are currently no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation, which prevents understanding and targeting conjugation. We introduce a novel experimental framework to screen for conjugation-based horizontal transmission of antibiotic resistance between >60,000 pairs of cell populations in parallel. As proof-of-principle, we exhaustively explore chromosomal genes controlling F-plasmid donation within E. coli populations. We recover all previously known and many novel chromosomal gene mutants that affect conjugation efficiency. The new framework holds great potential for rapid screening of compounds that decrease transmission. Further, the platform can easily be adapted to explore interspecies conjugation, plasmid-borne factors, and experimental evolution and be used for rapid construction of strains.
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| 4. |
- Benkwitz-Bedford, Sam, et al.
(author)
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Machine Learning Prediction of Resistance to Subinhibitory Antimicrobial Concentrations from Escherichia coli Genomes.
- 2021
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In: mSystems. - 2379-5077. ; 6:4
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Journal article (peer-reviewed)abstract
- Escherichia coli is an important cause of bacterial infections worldwide, with multidrug-resistant strains incurring substantial costs on human lives. Besides therapeutic concentrations of antimicrobials in health care settings, the presence of subinhibitory antimicrobial residues in the environment and in clinics selects for antimicrobial resistance (AMR), but the underlying genetic repertoire is less well understood. Here, we used machine learning to predict the population doubling time and cell growth yield of 1,407 genetically diverse E. coli strains expanding under exposure to three subinhibitory concentrations of six classes of antimicrobials from single-nucleotide genetic variants, accessory gene variation, and the presence of known AMR genes. We predicted cell growth yields in the held-out test data with an average correlation (Spearman's ρ) of 0.63 (0.36 to 0.81 across concentrations) and cell doubling times with an average correlation of 0.59 (0.32 to 0.92 across concentrations), with moderate increases in sample size unlikely to improve predictions further. This finding points to the remaining missing heritability of growth under antimicrobial exposure being explained by effects that are too rare or weak to be captured unless sample size is dramatically increased, or by effects other than those conferred by the presence of individual single-nucleotide polymorphisms (SNPs) and genes. Predictions based on whole-genome information were generally superior to those based only on known AMR genes and were accurate for AMR resistance at therapeutic concentrations. We pinpointed genes and SNPs determining the predicted growth and thereby recapitulated many known AMR determinants. Finally, we estimated the effect sizes of resistance genes across the entire collection of strains, disclosing the growth effects for known resistance genes in each individual strain. Our results underscore the potential of predictive modeling of growth patterns from genomic data under subinhibitory concentrations of antimicrobials, although the remaining missing heritability poses a challenge for achieving the accuracy and precision required for clinical use. IMPORTANCE Predicting bacterial growth from genome sequences is important for a rapid characterization of strains in clinical diagnostics and to disclose candidate novel targets for anti-infective drugs. Previous studies have dissected the relationship between bacterial growth and genotype in mutant libraries for laboratory strains, yet no study so far has examined the predictive power of genome sequence in natural strains. In this study, we used a high-throughput phenotypic assay to measure the growth of a systematic collection of natural Escherichia coli strains and then employed machine learning models to predict bacterial growth from genomic data under nontherapeutic subinhibitory concentrations of antimicrobials that are common in nonclinical settings. We found a moderate to strong correlation between predicted and actual values for the different collected data sets. Moreover, we observed that the known resistance genes are still effective at sublethal concentrations, pointing to clinical implications of these concentrations.
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| 5. |
- Bourgard, Catarina, 1985, et al.
(author)
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Development of Dicationic Bisguanidine-Arylfuran Derivatives as Potent Agents against Gram-Negative Bacteria.
- 2022
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In: Antibiotics. - : MDPI AG. - 2079-6382. ; 11:8
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Journal article (peer-reviewed)abstract
- Antibiotic resistance among bacteria is a growing global challenge. A major reason for this is the limited progress in developing new classes of antibiotics active against Gram-negative bacteria. Here, we investigate the antibacterial activity of a dicationic bisguanidine-arylfuran, originally developed as an antitrypanosomal agent, and new derivatives thereof. The compounds showed good activity (EC50 2-20 µM) against antibiotic-resistant isolates of the Gram-negative members of the ESKAPE group (Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) and Escherichia coli with different antibiotic susceptibility patterns, including ESBL isolates. Cytotoxicity was moderate, and several of the new derivatives were less cytotoxic than the lead molecule, offering better selectivity indices (40-80 for several ESKAPE isolates). The molecular mechanism for the antibacterial activity of these molecules is unknown, but sensitivity profiling against human ESKAPE isolates and E. coli collections with known susceptibility patterns against established antibiotics indicates that it is distinct from lactam and quinolone antibiotics.
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| 6. |
- Gamfeldt, Lars, 1975, et al.
(author)
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Scaling-up the biodiversity-ecosystem functioning relationship: the effect of environmental heterogeneity on transgressive overyielding
- 2023
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In: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 2023:3
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Journal article (peer-reviewed)abstract
- Knowledge of how biodiversity sustains ecosystem function comes predominantly from studies focused on small spatial scales. Thus, we know relatively little about the role of biodiversity at larger scales of space and time where habitats become increasingly heterogeneous. Efforts to upscale the relationship between biodiversity and function have yielded inconclusive results. Given that increasing habitat heterogeneity is a ubiquitous consequence of increasing spatial scale, we asked: as habitat heterogeneity increases, can single species continue to maintain ecosystem function? Or, does transgressive overyielding (functioning of species mixture divided by the functioning of the highest functioning single species) change with habitat heterogeneity? We addressed this using a combination of computer simulations, an experiment and a meta-analysis. The three parts followed the same rationale: habitat heterogeneity was increased by aggregating local habitats with different conditions into larger and more heterogeneous landscapes. The computer simulations showed that, on average, transgressive overyielding increased with habitat heterogeneity because monoculture functioning decreased with habitat heterogeneity. We tested this expectation experimentally by varying the strain richness from one to five species across 10800 bacterial communities in five different habitats defined by sub-inhibitory concentrations of antibiotics. On average, the experimental results concurred with the simulations. We tested the generality of this result using a meta-analysis of 26 published experiments that manipulated habitat conditions and species richness. This confirmed that transgressive overyielding tended to increase with habitat heterogeneity but only when species were specialised to different habitats and were not inhibited in mixtures by negative species interactions. This was not the case in several experiments used in our meta-analysis where one species maximised functioning across all habitats, contrary to the assumptions of many ecological models. Our results illustrate the importance of biodiversity at larger spatial scales with more heterogeneity but also highlights contingencies that this pattern depends on.
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| 7. |
- Gholami, Asma, et al.
(author)
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Discovery of novel inhibitors for Pseudomonas aeruginosa lipase enzyme from in silico and in vitro studies
- 2024
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In: Journal of Biomolecular Structure & Dynamics. - 0739-1102. ; 42:5, s. 2197-2210
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Journal article (peer-reviewed)abstract
- Pseudomonas aeruginosa is an opportunistic pathogen prone to developing drug-resistance and is a major cause of infection for burn patients and patients suffering from cystic fibrosis or are hospitalized in intensive care units. One of the virulence factors of this bacterium is the lipase enzyme that degrades the extracellular matrix of the host tissue and promotes invasion. Bromhexine is a mucolytic drug and has recently been reported to function as a competitive inhibitor of lipase with an IC50 value of 49 mu M. In the present study, an attempt was made to identify stronger inhibitors from the ChEMBL database of bioactive compounds, as compared to the reference compound Bromhexine. Following docking and MD simulations, four hit compounds (N1-N4) were selected that showed promising binding modes and low RMSD values indicative of stable protein-ligand complexes. From subsequent binding pose metadynamics (BPMD) simulations, two of these (N2 and N4) stood out as more potent than Bromhexine, displaying stable interactions with residues in the catalytic site of the enzyme. Biological investigations were performed for all four compounds. Among them, the same two hit compounds were found to be the most effective binders with IC50 values of 22.1 and 27.5 mu M, respectively; i.e. roughly twice as efficient as the reference Bromhexine. Taken together, our results show that these hits can be promising new candidates to use as leads for the development of drugs targeting the P. aeruginosa lipase enzyme.Communicated by Ramaswamy H. Sarma
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| 8. |
- Jutkina, Jekaterina, et al.
(author)
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Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli
- 2022
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In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 13
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Journal article (peer-reviewed)abstract
- Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.
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| 9. |
- Kvint, Kristian, 1964, et al.
(author)
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Teaching about antibiotic resistance to a broad audience: a multidisciplinary approach.
- 2020
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In: FEMS microbiology letters. - : Oxford University Press (OUP). - 1574-6968. ; 367:14, s. 1-6
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Journal article (peer-reviewed)abstract
- Education for the general public about antibiotic resistance is advocated as a key component of our response to this crisis. Since this is a multidisciplinary problem encompassing natural, medical and social sciences, it is an educational challenge as both students and lecturers will have vastly different backgrounds in the topics. Here we describe an online multidisciplinary course on antibiotic resistance spanning topics as diverse as chemistry and practical philosophy. The target group was any post-secondary school student and the participating students had different occupations and educational experience. Although as many as 38% of the students were currently studying natural sciences at university, the course included a diverse group with medical professionals (16%) and teachers (6%) making up a significant fraction of the class. The outcomes based on examination and the course evaluations were very positive and we have indications that the information students gained from this course has been spread to others.Unlike other online courses addressing antibiotic resistance, this course is both accessible to a wide range of students and covers a broad range of topics. We advocate courses like ours as an effective tool in educating the public about this crisis.
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| 10. |
- Mamedov, Ibrahim, et al.
(author)
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Antibacterial activity of 2-amino-3-cyanopyridine derivatives
- 2020
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In: Mendeleev Communications. - : Elsevier BV. - 0959-9436 .- 1364-551X. ; 30:4, s. 498-499
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Journal article (peer-reviewed)abstract
- © 2020 New 2-amino-4-aryl-3-cyanopyridines were obtained by the three-component condensation of arylidenemalononitriles, malononitrile and (di)amine system or acetoacetanilide. Antibacterial activity of all synthesized compounds against the Gram-negative bacteria E. coli and the Gram-positive B. subtilis was tested, the only representative showed a substantial antimicrobial effect.
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