Biology subjects

Di Patti, F.

Publications and source records attributed to Di Patti, F..

5 recordsLinked to original sources

bioRxiv2026

Development of a stable microbial community for the study of plasmid-mediated antimicrobial resistance in a continuous culturing device

Horizontal gene transfer (HGT) is a major contributor to the spread of antimicrobial resistance (AMR) in microbial communities, particularly through conjugative plasmids. The dynamics of the spread of these plasmids in a susceptible microbial community requires a defined and controllable in vitro system, which is currently lacking from existing laboratory evolution systems. Here we describe the development of TriComm, an engineered microbial community of three strains with complementary amino acid auxotrophies, maintained in continuous culture under real-time optical and fluorescence monitoring. We show that two conjugative plasmids carrying resistance genes (blaOXA-48 and mcr-1) generally rescued TriComm from collapse under antimicrobial treatment, and that this protection was dependent on conjugative transfer. Community composition remained stable across most conditions, including after the AMR plasmid had spread through the population. Through mathematical modeling we predict that modulating both drug efficacy and conjugation rate can lead to the collapse of the community, suggesting potential strategies to limit the spread of AMR via HGT.

microbiology↗

bioRxiv2024

The acquisition of additional control over quorum sensing regulation buffers noise in microbial growth dynamics

Quorum sensing (QS) is a cell-to-cell communication system used by bacteria to act collectively. Often, bacteria possess more than one QS regulatory module that form complex regulatory networks. Presumably, these configurations have evolved through the integration of novel transcription factors into the native regulatory systems. The selective advantages provided by these alternative configurations on QS-related phenotypes is poorly predictable only based on their underlying network structure. Here we show that the acquisition of extra regulatory modules of QS has important consequences on the overall regulation of microbial growth dynamics by significantly reducing the variability in the final size of the population in Burkholderia. We mapped the distribution of horizontally transferred QS modules in extant bacterial genomes, finding that these tend to add up to already-present modules in the majority of cases, 63.32%. We then selected a strain harboring two intertwined QS modules and,using mathematical modelling, we predicted an intrinsic ability of the newly acquired module to buffer noise in growth dynamics. We experimentally validated this prediction choosing one strain possessing both systems, deleting one of the two and measuring key growth parameters and QS synthase expression. We extended such considerations on two other strains naturally implementing the two versions of the QS regulation studied herein. Finally, using transcriptomics, we show that the de-regulation of metabolism likely plays a key role in differentiating the two configurations. Our results shed light on the role of additional control over QS regulation and illuminate on the possible phenotypes that may arise after HGT events.

systems biology↗

bioRxiv2021

The acquisition of additional feedback loops may optimize and speed up the response of quorum sensing

1.Bacterial quorum sensing (QS) is a cell-to-cell communication system in which specific signals are activated to coordinate, for example, pathogenic behaviors and help bacteria collectively respond to perturbations. QS in Gram-negative bacteria is typically regulated by a N-acyl-homoserine lactone (AHL) molecules-mediated system, homologous of Vibrio fischeri LuxI-R. In many cases, bacteria possess more than one QS system, based on different types of molecules, that interact through a complex regulatory network. Presumably, these configurations have emerged over time from simpler ones through the acquisition of novel players (e.g. transcription factors) that have been successfully integrated into the native regulatory systems. However, the advantages provided by these alternative/additional configurations on QS-related phenotypes is poorly predictable only based on their underlying network structure. Here, we have adopted a modelling approach to infer the possible improvements conferred by the acquisition of additional control over bacterial regulation of QS. We use the Burkholderia genus as a case study because some of these strains, besides the LuxIR-like system (named CepIR), possess an integrated regulatory module named CciIR that interferes with the CepIR system through the implementation of several positive and negative control loops. Being associated to a genomic island (cci island), this additional module is prone to being horizontally transferred, giving rise to a potentially patchy genomic distribution and, in turn, to a complete (CepIR and CciIR systems together) vs. core (CepIR only) organization of QS regulation in this group of microorganisms. By using both deterministic and stochastic modelling we show that, upon their activation, the two regulatory schemes may lead to different phenotypes and to distinct responses to the extracellular concentration of signalling molecules. In particular, our simulations show that the presence of the additional regulatory module may confer specific improvements, including a faster response time and optimized control of QS regulation. Interestingly, some of these features may be particularly advantageous during host invasion, thus highlighting once more the importance of QS in the establishment and maintenance of bacterial infections.

systems biology↗

bioRxiv2019

Diauxie and co-utilization are not exclusive during growth in nutritionally complex environments

The classic view of microbial growth strategy when multiple carbon sources are available states that they either metabolize them sequentially (diauxic growth) or simultaneously (co-utilization). This perspective is biased by the fact that this process has been mainly analysed in over-simplified laboratory settings, i.e. using a few model microorganisms and growth media containing only two alternative compounds. Models concerning the mechanisms and the dynamics regulating nutrients assimilation strategies in conditions that are closer to the ones found in natural settings (i.e. with many alternative carbon/energy sources) are missing. Here, we show that bacterial co-utilization and sequential uptake of multiple substrates can coexist when multiple possible nutrients are provided in the same growth experiment, leading to an efficient exploitation of nutritionally complex settings. The order of nutrient uptake is determined by the actual biomass yield (and growth rate) that can be achieved when the same compounds are provided as single carbon sources. Finally, using two alternative theoretical models we show that this complex metabolic phenotype can be explained by a tight regulation process that allows microbes to actively modulate the different assimilatory pathways involved.

systems biology↗

bioRxiv2018

An synthetic microbial loop for modelling heterotroph-phototroph metabolic interactions

Marine ecosystems are characterized by an intricate set of interactions among their representatives. One of the most important occurs through the exchange of dissolved organic matter (DOM) provided by phototrophs and used by heterotrophic bacteria as their main carbon and energy source. This metabolic interaction represents the foundation of the entire ocean food-web.\n\nHere we have assembled a synthetic ecosystem to assist the systems-level investigation of this biological association. This was achieved building an integrated, genome-scale metabolic reconstruction using two model organisms (a diatom Phaeodactylum tricornutum and an heterotrophic bacterium, Pseudoalteromonas haloplanktis) to explore and predict their metabolic interdependencies. The model was initially analysed using a constraint-based approach (Flux Balance Analysis, FBA) and then turned into a dynamic (dFBA) model to simulate a diatom-bacteria co-culture and to study the effect of changes in growth parameters on such a system. Finally, we developed a simpler dynamic ODEs system that, fed with dFBA results, was able to qualitatively describe this synthetic ecosystem and allowed performing stochastic simulations to assess the effect of noise on the overall balance of this co-culture.\n\nWe show that our model recapitulates known metabolic cross-talks of a phototroph-heterotroph system, including mutualism and competition for inorganic ions (i.e. phosphate and sulphate). Further, the dynamic simulation predicts realistic growth rate for both the diatom and the bacterium and a steady state balance between diatom and bacterial cell concentration that matches those determined in experimental co-cultures. This steady state, however, is reached following an oscillatory trend, a behaviour that is typically observed in the presence of metabolic co-dependencies. Finally, we show that, at high diatom/bacteria cell concentration ratio, stochastic fluctuations can lead to the extinction of bacteria from the co-culture, causing the explosion of diatom population. We anticipate that the developed synthetic ecosystem will serve in the future as a basis for the generation of testable hypotheses and as a scaffold for integrating and interpreting-omics data from experimental co-cultures.

systems biology↗