Biology subjects

Secchi, E.

Publications and source records attributed to Secchi, E..

10 recordsLinked to original sources

bioRxiv2026

bioRheoFlow A Rheometric Platform for In Situ Biofilm Mechanics Under Controlled Flow Conditions

Biofilm mechanics depend strongly on growth history, hydration, nutrient availability, and interfacial attachment, yet conventional rheology requires harvesting and transfer that can perturb the as-grown structure. Here, we introduce bioRheoFlow, a 3D-printed rheometer-mounted platform for cultivation and mechanical characterization without sample transfer. The platform combines evaporation compensation with static or axial nutrient flow, and benchmark measurements validate its rheometric performance. Applied to Pseudomonas putida and Pantoea sp., bioRheoFlow reveals that biofilms cultivated in situ under axial flow exhibit substantially higher elastic moduli than conventionally grown and scraped samples. Despite similar linear-viscoelastic stress ranges, the species show distinct nonlinear responses: P. putida exhibits a lower crossover stress and more abrupt failure, whereas Pantoea sp. sustains larger stresses and deformations. Creep suggests contributions from bulk deformation and biofilm-substrate interactions. bioRheoFlow provides a controlled framework for probing growth-conditioned mechanics in living biofilms.

biophysics↗

bioRxiv2025

Emergent spatial structure in the gut microbiota is driven by bacterial growth and gut contractions

Spatial structure can determine function and evolution of bacterial communities. The gut microbiota is known to be spatially structured longitudinally along the many meters of the gastrointestinal tract, but micro-scale structure in the gut lumen has not been extensively explored. In samples from mice and humans, we show that upper large-intestinal content behaves as a non-Newtonian fluid that changes its viscoelastic properties under the force of gut contractions. This phenomenon is sufficient to explain micro-scale bacterial clustering in the murine cecum, resulting from growth within the gel-like structure of cecum content, and periodic disruption due to peristalsis-driven shear-thinning and clearance. Shear-thinning can also explain the surprising observation that fed beads enter the tip of the mouse cecum by flow along the epithelial cell layer before being mixed into the cecum content. Our study shows mechanistically how spatial structure in the gut emerges through the interplay of microbial and host physiology and highlights the possibility of host control over gut microbiota distribution via gut contractions. One sentence summaryWe show how spatial structure emerges in the gut microbiota through bacterial growth in the matrix of gut content.

systems biology↗

bioRxiv2024

Stress-hardening behaviour of biofilm streamers

Bacterias ability to withstand mechanical challenges is enhanced in their biofilm lifestyle, where they are encased in a viscoelastic polymer matrix [1]. Under fluid flow, biofilms can form as streamers - slender filaments tethered to solid surfaces and suspended in the flowing fluid [2, 3]. Streamers thrive in environments subjected to intense hydrodynamic stresses, such as medical devices and water filters, often resulting in catastrophic clogging [4]. Their colonisation success may depend on a highly adaptable mechanical response to varying stress conditions, though the evidence and underlying mechanisms of this adaptation remain elusive. Here, we demonstrate that biofilm streamers exhibit a stress-hardening behaviour, with both differential elastic modulus and effective viscosity increasing linearly with external stress. This stress-hardening is consistent across biofilms with different matrix compositions, formed by various bacterial species, and under diverse growth conditions. We further demonstrate that this mechanical response originates from the properties of extracellular DNA (eDNA) molecules [5], which constitute the structural backbone of the streamers. In addition, our results identify extracellular RNA (eRNA) as a modulator of the matrix network, contributing to both the structure and rheological properties of the eDNA backbone. Our findings reveal an instantaneous, purely physical mechanism enabling streamers to adapt to hydrodynamic stresses. Given the ubiquity of extracellular nucleic acids (eNA) in biofilms [1, 6], this discovery prompts a re-evaluation of their functional role in biofilm mechanics, with potential implications for biofilm structural integrity, ecological resilience, and colonisation dynamics.

biophysics↗

bioRxiv2024

Single-cell approach dissecting agr quorum sensing dynamics in Staphylococcus aureus

Staphylococcus aureus both colonizes humans and causes severe virulent infections. Virulence is regulated by the agr quorum sensing system and its autoinducing peptide (AIP), with dynamics at the single-cell level across four agr-types - each defined by distinct AIP sequences and capable of cross-inhibition - remaining elusive. Employing microfluidics, time-lapse microscopy, and deep-learning image analysis, we uncovered significant differences in AIP sensitivity among agr-types. We observed bimodal agr activation, attributed to intergenerational phenotypic stability and influenced by AIP concentration. Upon AIP stimulation, agr-III showed AIP insensitivity, while agr-II exhibited increased sensitivity and prolonged generation time. Beyond expected cross-inhibition of agr-I by heterologous AIP-II and -III, the presumably cross-activating AIP-IV also inhibited agr-I. Community interactions across different agr-type pairings revealed four main patterns: stable or switched dominance, and delayed or stable dual activation, influenced by community characteristics. These insights underscore the potential of personalized treatment strategies considering virulence and genetic diversity.

microbiology↗

bioRxiv2023

Tunable living bacterial networks: A multi-scaled description of their self-assembly and mechanical behaviour

Bacterial aggregate formation and surface accumulation are increasingly viewed as alternative pathways for biofilm colonization. However, little is known about the dynamics of bacterial aggregate cluster-cluster assembly and their subsequent microstructural and mechanical properties. To this end, we studied experimentally and computationally an aggregating bacterial system that forms a space-spanning interconnected network via cluster-cluster assembly. By controllably inducing bacterial filamentation, we aimed to understand how cell length distribution and cell surface hydrophobicity control the dynamics of aggregation and sedimentation, as well as the microstructure and mechanics of the settled bacterial networks. We found that filamentation lowers the percolation threshold, leading to gelation at a lower number density with distinct assembly dynamics and lower network connectivity. Furthermore, we analyzed the mechanical properties of the bacterial networks. Static stress tests reveal three yielding modes: discrete cluster-cluster disassembly, collective delamination, and sub-regional network fracture. The yielding modes are consistent with the gel-like viscoelastic properties of the cluster-cluster assembled networks observed during macroscale rheometry. In particular, we observe a scaling relationship between the storage modulus and the volume fraction, characteristic of an attractive rod gel. Our experimental observations are supported by Langevin dynamic simulations, providing mechanistic insights into the factors determining network self-assembly and connectivity. Our findings elucidate the gel-like structure-function dynamics in cluster-cluster aggregated bacterial systems and underscore the fundamental importance of filamentation in their properties and mechanical behavior.

biophysics↗

bioRxiv2022

A microfluidic platform for characterizing the structure and rheology of biofilm streamers

Biofilm formation is the most successful survival strategy for bacterial communities. In the biofilm lifestyle, bacteria embed themselves in a self-secreted matrix of extracellular polymeric substances (EPS), which acts as a shield against mechanical and chemical insults. When ambient flow is present, this viscoelastic scaffold can take a streamlined shape, forming biofilm filaments suspended in flow, called streamers. Streamers significantly disrupt the fluid flow by causing rapid clogging and affect transport in aquatic environments. Despite their relevance, the structural and rheological characterization of biofilm streamers is still at an early stage. In this work, we present a microfluidic platform that allows the reproducible growth of biofilm streamers in controlled physico-chemical conditions and the characterization of their biochemical composition, morphology, and rheology in situ. We employed isolated micropillars as nucleation sites for the growth of single biofilm streamers under the continuous flow of a diluted bacterial suspension. By combining fluorescent staining of the EPS components and epifluorescence microscopy, we were able to characterize the biochemical composition and morphology of the streamers. Additionally, we optimized a protocol to perform hydrodynamic stress tests in situ, by inducing controlled variations of the fluid shear stress exerted on the streamers by the flow. Thus, the reproducibility of the formation process and the testing protocol make it possible to perform several consistent experimental replicates that provide statistically significant information. By allowing the systematic investigation of the role of biochemical composition on the structure and rheology of streamers, this platform will advance our understanding of biofilm formation.

biophysics↗

bioRxiv2021

The role of surface adhesion on the macroscopic wrinkling of biofilms

Biofilms, bacterial communities of cells encased by a self-produced matrix, exhibit a variety of three-dimensional structures. Specifically, channel networks formed within the bulk of the biofilm have been identified to play an important role in the colonies viability by promoting the transport of nutrients and chemicals. Here, we study channel formation and focus on the role of the adhesion of the biofilm matrix to the substrate in Pseudomonas aeruginosa biofilms grown under constant flow in microfluidic channels. We perform phase contrast and confocal laser scanning microscopy to examine the development of the biofilm structure as a function of the substrates surface energy. The formation of the wrinkles and folds is triggered by a mechanical buckling instability, controlled by biofilm growth rate and the films adhesion to the substrate. The three-dimensional folding gives rise to hollow channels that rapidly increase the overall volume occupied by the biofilm and facilitate bacterial movement inside them. The experiments and analysis on mechanical instabilities for the relevant case of a bacterial biofilm grown during flow enable us to predict and control the biofilm morphology.

biophysics↗

bioRxiv2021

The structural role of bacterial eDNA in the formation of biofilm streamers

Across diverse habitats, bacteria are mainly found as biofilms, surface-attached communities embedded in a self-secreted matrix of extracellular polymeric substances (EPS), which enhances bacterial resistance to antimicrobial treatment and mechanical stresses. In the presence of flow and geometric constraints such as corners or constrictions, biofilms take the form of long, suspended threads known as streamers, which bear important consequences in industrial and clinical settings by causing clogging and fouling. The formation of streamers is thought to be driven by the viscoelastic nature of the biofilm matrix. Yet, little is known about the structural composition of streamers and how it affects their mechanical properties. Here, using a microfluidic platform that allows growing and precisely examining biofilm streamers, we show that extracellular DNA (eDNA) constitutes the backbone and is essential for the mechanical stability of Pseudomonas aeruginosa s streamers. This finding is supported by the observations that DNA-degrading enzymes prevent the formation of streamers and clear already formed ones, and that the antibiotic ciprofloxacin promotes their formation by increasing the release of eDNA. Furthermore, using mutants for production of the exopolysaccharide Pel, an important component of P. aeruginosa s EPS, we reveal a new, although indirect role of Pel, in tuning the mechanical properties of the streamers. Taken together, these results highlight the importance of eDNA and of its interplay with Pel in determining the mechanical properties of P. aeruginosa streamers, and suggest that targeting the composition of streamers can be an effective approach to control the formation of these biofilm structures.

biophysics↗

bioRxiv2021

Dynamic arrest and aging of biomolecular condensates are regulated by low-complexity domains, RNA and biochemical activity

Biomolecular condensates require suitable material properties to properly carry out their function. Yet, modulators that affect the material properties of condensates have remained largely unexplored. Here we apply Differential Dynamic Microscopy (DDM) to probe the material properties of an in vitro model of processing bodies (P-bodies) consisting of condensates formed by the DEAD-box ATPase Dhh1 in the presence of ATP and RNA. DDM allows us to measure the viscosity of liquid droplets and to distinguish between liquid-like and gel- or glass-like condensates. By applying this single-droplet technique we show that condensates within the same population exhibit a distribution of material properties, which can be drastically affected by several modulators such as the low-complexity domains (LCDs) of the protein, the protein/RNA ratio, the type of RNA as well as the enzymatic activity. In particular, we show that structured RNA leads to a large fraction of dynamically arrested condensates with respect to unstructured polyuridylic acid (polyU), emphasizing the role of RNA structure in condensate dynamics. We further demonstrate that the ageing of the condensates and the formation of gel or glass-like structures is reduced by promoting the enzymatic ATPase activity of Dhh1 and the rate of droplet formation and dissolution. Our study shows that not only the reversible formation and dissolution of condensates but also their material properties are regulated on several levels, and that biochemical activity and material turnover can be important to maintain fluid-like properties over time.

biophysics↗

bioRxiv2019

The effect of flow on swimming bacteria controls the initial colonization of curved surfaces

The colonization of solid surfaces by bacteria is a widespread phenomenon with major consequences on environmental processes, biotechnology and human health. While much is known about the molecular mechanisms of surface colonization, the influence of the physical environment remains poorly understood. Here we show that the magnitude and location of colonization of non-planar surfaces by motile bacteria is largely controlled by the local flow conditions. Using microfluidic experiments with Pseudomonas aeruginosa and Escherichia coli, we demonstrate that the velocity gradients created by a curved surface drive preferential attachment to specific regions of the collecting surface, namely the leeward side of cylinders and immediately downstream of apexes on corrugated surfaces, locations that are in stark contrast to where non-motile cells attach. The preferential attachment location depends on the local hydrodynamic conditions and, as revealed by a mathematical model benchmarked on the observations, on cell morphology and swimming traits, while it is independent of the physicochemical properties of the surface. The interplay between imposed flow and bacterial motility further affects the overall attachment rate, increasing it by up to two orders of magnitude compared to the non-motile case at moderate flow velocities of up to twenty times the bacterial swimming speed. These results highlight the importance of fluid flow on the magnitude and location of bacterial colonization of surfaces and provide a mechanistic model to predict colonization in flow for a wide range of applications, from infection biology to bioremediation and biofouling.

biophysics↗