Bacterial accumulation in intestinal folds induced by physical and biological factors.

BACKGROUND: The gut microbiota, vital for host health, influences metabolism, immune function, and development. Understanding the dynamic processes of bacterial accumulation within the gut is crucial, as it is closely related to immune responses, antibiotic resistance, and colorectal cancer. We investigated Escherichia coli behavior and distribution in zebrafish larval intestines, focusing on the gut microenvironment. RESULTS: We discovered that E. coli spread was considerably suppressed within the intestinal folds, leading to a strong physical accumulation in the folds. Moreover, a higher concentration of E. coli on the dorsal side than on the ventral side was observed. Our in vitro microfluidic experiments and theoretical analysis revealed that the overall distribution of E. coli in the intestines was established by a combination of physical factor and bacterial taxis. CONCLUSIONS: Our findings provide valuable insight into how the intestinal microenvironment affects bacterial motility and accumulation, enhancing our understanding of the behavioral and ecological dynamics of the intestinal microbiota.

Glucose stockpile in the intestinal apical brush border in C. elegans.

Revealing the mechanisms of glucose transport is crucial for studying pathological diseases caused by glucose toxicities. Numerous studies have revealed molecular functions involved in glucose transport in the nematode Caenorhabditis elegans, a commonly used model organism. However, the behavior of glucose in the intestinal lumen-to-cell remains elusive. To address that, we evaluated the diffusion coefficient of glucose in the intestinal apical brush border of C. elegans by using fluorescent glucose and fluorescence recovery after photobleaching. Fluorescent glucose taken in the intestine of worms accumulates in the apical brush border, and its diffusion coefficient of ∼10-8 cm2/s is two orders of magnitude slower than that in bulk. This result indicates that the intestinal brush border is a viscous layer. ERM-1 point mutations at the phosphorylation site, which shorten the microvilli length, did not significantly affect the diffusion coefficient of fluorescent glucose in the brush border. Our findings imply that glucose enrichment is dominantly maintained by the viscous layer composed of the glycocalyx and molecular complexes on the apical surface.

Swimming, Feeding, and Inversion of Multicellular Choanoflagellate Sheets.

The recent discovery of the striking sheetlike multicellular choanoflagellate species Choanoeca flexa that dynamically interconverts between two hemispherical forms of opposite orientation raises fundamental questions in cell and evolutionary biology, as choanoflagellates are the closest living relatives of animals. It similarly motivates questions in fluid and solid mechanics concerning the differential swimming speeds in the two states and the mechanism of curvature inversion triggered by changes in the geometry of microvilli emanating from each cell. Here we develop fluid dynamical and mechanical models to address these observations and show that they capture the main features of the swimming, feeding, and inversion of C. flexa colonies, which can be viewed as active, shape-shifting polymerized membranes.

50-year history and perspective on biomechanics of swimming microorganisms: Part II. Collective behaviours.

The paired review papers in Parts I and II describe the 50-year history of research on the biomechanics of swimming microorganisms and its prospects in the next 50 years. Parts I and II are divided not by the period covered, but by the content of the research: Part I explains the behaviours of individual microorganisms, and Part II explains collective behaviour. In the 1990s, the description of microbial suspensions as a continuum progressed, and macroscopic flow structures such as bioconvection were analysed. The continuum model was later extended to analyse various phenomena such as flow induced trapping of microorganisms and accumulation of cells at interfaces. In the 2000s, the collective behaviour of swimming microorganisms came into the limelight, and physicists as well as biomechanics researchers carried out many studies probing microorganism collectivity. In particular, research on the turbulence-like flow structure of dense bacterial suspensions has led to dramatic developments in the field of microbial biomechanics. Efforts to bridge the cellular scale to the macroscopic scale by extracting macroscopic physical quantities from the microstructure of cell suspensions are also underway. This Part II reviews these collective behaviours of swimming microorganisms and discusses future prospects of the field.

Endotracheal tube, by the venturi effect, reduces the efficacy of increasing inlet pressure in improving pendelluft.

In mechanically ventilated severe acute respiratory distress syndrome patients, spontaneous inspiratory effort generates more negative pressure in the dorsal lung than in the ventral lung. The airflow caused by this pressure difference is called pendelluft, which is a possible mechanisms of patient self-inflicted lung injury. This study aimed to use computer simulation to understand how the endotracheal tube and insufficient ventilatory support contribute to pendelluft. We established two models. In the invasive model, an endotracheal tube was connected to the tracheobronchial tree with 34 outlets grouped into six locations: the right and left upper, lower, and middle lobes. In the non-invasive model, the upper airway, including the glottis, was connected to the tracheobronchial tree. To recreate the inspiratory effort of acute respiratory distress syndrome patients, the lower lobe pressure was set at -13 cmH2O, while the upper and middle lobe pressure was set at -6.4 cmH2O. The inlet pressure was set from 10 to 30 cmH2O to recreate ventilatory support. Using the finite volume method, the total flow rates through each model and toward each lobe were calculated. The invasive model had half the total flow rate of the non-invasive model (1.92 L/s versus 3.73 L/s under 10 cmH2O, respectively). More pendelluft (gas flow into the model from the outlets) was observed in the invasive model than in the non-invasive model. The inlet pressure increase from 10 to 30 cmH2O decreased pendelluft by 11% and 29% in the invasive and non-invasive models, respectively. In the invasive model, a faster jet flowed from the tip of the endotracheal tube toward the lower lobes, consequently entraining gas from the upper and middle lobes. Increasing ventilatory support intensifies the jet from the endotracheal tube, causing a venturi effect at the bifurcation in the tracheobronchial tree. Clinically acceptable ventilatory support cannot completely prevent pendelluft.

50-year History and perspective on biomechanics of swimming microorganisms: Part I. Individual behaviours.

The paired review papers in Parts I and II describe the 50-year history of research on the biomechanics of swimming microorganisms and its prospects in the next 50 years: Part I explains the behaviour of individual microorganisms, and Part II explains collective behaviour. Since the discovery of microorganisms by van Leeuwenhoek in the 17th century, many natural scientists have been interested in their motility because it is directly associated with biological function. A research upsurge occurred in the 1970s, with the elucidation of swimming mechanisms among individual microorganisms and the theoretical derivation of swimming speeds. Various swimming strategies of three types of microorganisms, i.e. bacteria, ciliates and microalgae, are explained in this Part I. We show that some of the behaviours of microorganisms can be described by biomechanical equations and are to some extent predictable. Recent researches have revealed the behaviour of microorganisms in more complex environments and more realistic settings, which are also reviewed in the paper. Last, we provide future prospects for research on microbial behaviour.

Biophysical Analysis of Mechanical Signals in Immotile Cilia of Mouse Embryonic Nodes Using Advanced Microscopic Techniques.

Immotile cilia of crown cells at the node of mouse embryos are required for sensing leftward fluid flow that gives rise to the breaking of left-right (L-R) symmetry. The flow-sensing mechanism has long remained elusive, mainly because of difficulties inherent in manipulating and precisely analyzing the cilium. Recent progress in optical microscopy and biophysical analysis has allowed us to study the mechanical signals involving primary cilia. In this study, we used high-resolution imaging with mechanical modeling to assess the membrane tension in a single cilium. Optical tweezers, a technique used to trap sub-micron-sized particles with a highly focused laser beam, allowed us to manipulate individual cilia. Super-resolution microscopy allowed us to discern the precise localization of ciliary proteins. Using this protocol, we provide a method for applying these techniques to cilia in mouse embryonic nodes. This method is widely applicable to the determination of mechanical signals in other cilia.

Effectiveness of substantial shortening of the endotracheal tube for decreasing airway resistance and increasing tidal volume during pressure-controlled ventilation in pediatric patients: a prospective observational study.

The endotracheal tubes (ETTs) used for children have a smaller inner diameter. Accordingly, the resistance across ETT (RETT) is higher. Theoretically, shortening the ETTs can decrease total airway resistance (Rtotal), because Rtotal is sum of RETT and patient's airway resistance. However, the effectiveness of ETT shortening for mechanical ventilation in the clinical setting has not been reported. We assessed the effectiveness of shortening a cuffed ETT for decreasing Rtotal, and increasing tidal volume (TV), and estimated the RETT/Rtotal ratio in children. In anesthetized children in a constant pressure-controlled ventilation setting, Rtotal and TV were measured with a pneumotachometer before and after shortening a cuffed ETT. In a laboratory experiment, the pressure gradient across the original length, shortened length, and the slip joint alone of the ETT were measured. We then determined the RETT/Rtotal ratio using the above results. The clinical study included 22 children. The median ETT percent shortening was 21.7%. Median Rtotal was decreased from 26 to 24 cmH2O/L/s, and median TV was increased by 6% after ETT shortening. The laboratory experiment showed that ETT length and the pressure gradient across ETT are linearly related under a certain flow rate, and approximately 40% of the pressure gradient across the ETT at its original length was generated by the slip joint. Median RETT/Rtotal ratio were calculated as 0.69. The effectiveness of ETT shortening on Rtotal and TV was very limited, because the resistance of the slip joint was very large.

Immotile cilia mechanically sense the direction of fluid flow for left-right determination.

Immotile cilia at the ventral node of mouse embryos are required for sensing leftward fluid flow that breaks left-right symmetry of the body. However, the flow-sensing mechanism has long remained elusive. In this work, we show that immotile cilia at the node undergo asymmetric deformation along the dorsoventral axis in response to the flow. Application of mechanical stimuli to immotile cilia by optical tweezers induced calcium ion transients and degradation of Dand5 messenger RNA (mRNA) in the targeted cells. The Pkd2 channel protein was preferentially localized to the dorsal side of immotile cilia, and calcium ion transients were preferentially induced by mechanical stimuli directed toward the ventral side. Our results uncover the biophysical mechanism by which immotile cilia at the node sense the direction of fluid flow.

Reciprocating intestinal flows enhance glucose uptake in C. elegans.

Despite its physiological and pathological importance, the mechanical relationship between glucose uptake in the intestine and intestinal flows is unclear. In the intestine of the nematode Caenorhabditis elegans, the defecation motor program (DMP) causes reciprocating intestinal flows. Although the DMP is frequently activated in the intestines, its physiological function is unknown. We evaluated the mechanical signature of enhanced glucose uptake by the DMP in worms. Glucose uptake tended to increase with increasing flow velocity during the DMP because of mechanical mixing and transport. However, the increase in input energy required for the DMP was low compared with the calorie intake. The findings suggest that animals with gastrointestinal motility exploit the reciprocating intestinal flows caused by peristalsis to promote nutrient absorption by intestinal cells.

Influence of Respiratory Gas Density on Tidal Volume during Mechanical Ventilation: A Laboratory Investigation and Observational Study in Children.

Fluid mechanics show that high-density gases need more energy while flowing through a tube. Thus, high-density anesthetic gases consume more energy to flow and less energy for lung inflation during general anesthesia. However, its impact has not been studied. Therefore, this study aimed to investigate the effects of high-density anesthetic gases on tidal volume in laboratory and clinical settings. In the laboratory study, a test lung was ventilated at the same pressure-controlled ventilation with 22 different gas compositions (density range, 1.22-2.27 kg/m3) using an anesthesia machine. A pneumotachometer was used to record the tidal volume of the test lung and the respiratory gas composition; it showed that the tidal volume of the test lung decreased as the respiratory gas density increased. In the clinical study, the change in tidal volume per body weight, accompanied by gas composition change (2% sevoflurane in oxygen and with 0-30-60% of N2O), was recorded in 30 pediatric patients. The median tidal volume per body weight decreased by 10% when the respiratory gas density increased from 1.41 kg/m3 to 1.70 kg/m3, indicating a significant between-group difference (P < 0.0001). In both settings, an increase in respiratory gas density decreased the tidal volume during pressure-controlled ventilation, which could be explained by the fluid dynamics theory. This study clarified the detailed mechanism of high-density anesthetic gas reduced the tidal volume during mechanical ventilation and revealed that this phenomenon occurs during pediatric anesthesia, which facilitates further understanding of the mechanics of ventilation during anesthesia practice and respiratory physiology.

Impact of rheological properties on bacterial streamer formation.

Bacterial biofilms, which can be found wherever there is water and a substrate, can cause chronic infections and clogging of industrial flow systems. Despite intensive investigation of the dynamics and rheological properties of biofilms, the impact of their rheological properties on streamer growth remains unknown. We numerically simulated biofilm growth in a pillar-flow and investigated the effects of rheological properties of a filamentous flow-shaped biofilm, called a 'streamer', on its formation by varying the viscoelasticity. The flow-field is assumed to be a Stokes flow and is solved by a boundary element method. A Maxwell model is used for extracellular matrix-mediated streamer growth to express the fluidity of streamer formations. Both high elastic modulus and viscosity are needed for streamer formation, and high viscosity promotes streamer growth at low cell concentrations. Our findings are consistent with experimental observations and can explain the relationship between the cell concentrations and viscosity at which streamers form.

Near-wall rheotaxis of the ciliate Tetrahymena induced by the kinesthetic sensing of cilia.

To survive in harsh environments, single-celled microorganisms autonomously respond to external stimuli, such as light, heat, and flow. Here, we elucidate the flow response of Tetrahymena, a well-known single-celled freshwater microorganism. Tetrahymena moves upstream against an external flow via a behavior called rheotaxis. While micrometer-sized particles are swept away downstream in a viscous flow, what dynamics underlie the rheotaxis of the ciliate? Our experiments reveal that Tetrahymena slides along walls during upstream movement, which indicates that the cells receive rotational torque from shear flow to control cell orientation. To evaluate the effects of the shear torque and propelling speed, we perform a numerical simulation with a hydrodynamic model swimmer adopting cilia dynamics in a shear flow. The swimmer orientations converge to an upstream alignment, and the swimmer slides upstream along a boundary wall. The results suggest that Tetrahymena automatically responds to shear flow by performing rheotaxis using cilia-stalling mechanics.

Microbial Brazil nut effect.

The Brazil nut effect (BNE) is a counter-intuitive process of segregation of a large object inside a vibrated granular medium (GM), which has been studied widely by subjecting GMs to various kinds of shears and vibrations. In this article, we report a new kind of BNE which occurs as a consequence of granular fluctuations induced by microbe-generated gas bubbles. We call it the 'microbial Brazil nut effect'. The paper demonstrates microbial BNE for a bidisperse granular mixture as well as for intruder segregation. Furthermore, using X-ray µCT and a simple scaling argument for segregation velocity, the paper clarifies the transport mechanics of an intruder inside a bubbly granular bed. We think the reported phenomenon should be ubiquitous in the microbe-populated wet sandy floors of waterbodies and may have some implication on the distribution of material near the floors.

Non-biodegradable objects may boost microbial growth in water bodies by harnessing bubbles.

Given the ubiquity of bubbles and non-biodegradable wastes in aqueous environments, their transport through bubbles should be widely extant in water bodies. In this study, we investigate the effect of bubble-induced waste transport on microbial growth by using yeasts as model microbes and a silicone rubber object as model waste. Noteworthily, this object repeatedly rises and sinks in fluid through fluctuations in bubble-acquired buoyant forces produced by cyclic nucleation, growth and release of bubbles from object's surface. The rise-sink movement of the object gives rise to a strong bulk mixing and an enhanced resuspension of cells from the floor. Such spatially dynamic contaminant inside a nutrient-rich medium also leads to an increment in the total microbe concentration in the fluid. The enhanced concentration is caused by strong nutrient mixing generated by the object's movement which increases the nutrient supply to growing microbes and thereby, prolonging their growth phases. We confirm these findings through a theoretical model for cell concentration and nutrient distribution in fluid medium. The model is based on the continuum hypothesis and it uses the general conservation law which takes an advection-diffusion growth form. We conclude the study with the demonstration of bubble-induced digging of objects from model sand.

Cilia and centrosomes: Ultrastructural and mechanical perspectives.

Cilia and centrosomes of eukaryotic cells play important roles in cell movement, fluid transport, extracellular sensing, and chromosome division. The physiological functions of cilia and centrosomes are generated by their dynamics, motions, and forces controlled by the physical, chemical, and biological environments. How an individual cilium achieves its beat pattern and induces fluid flow is governed by its ultrastructure as well as the coordination of associated molecular motors. Thus, a bottom-up understanding of the physiological functions of cilia and centrosomes from the molecular to tissue levels is required. Correlations between the structure and motion can be understood in terms of mechanics. This review first focuses on cilia and centrosomes at the molecular level, introducing their ultrastructure. We then shift to the organelle level and introduce the kinematics and mechanics of cilia and centrosomes. Next, at the tissue level, we introduce nodal ciliary dynamics and nodal flow, which play crucial roles in the organogenetic process of left-right asymmetry. We also introduce respiratory ciliary dynamics and mucous flow, which are critical for protecting the epithelium from drying and exposure to harmful particles and viruses, i.e., respiratory clearance function. Finally, we discuss the future research directions in this field.

Bacterial biomechanics-From individual behaviors to biofilm and the gut flora.

Bacteria inhabit a variety of locations and play important roles in the environment and health. Our understanding of bacterial biomechanics has improved markedly in the last decade and has revealed that biomechanics play a significant role in microbial biology. The obtained knowledge has enabled investigation of complex phenomena, such as biofilm formation and the dynamics of the gut flora. A bottom-up strategy, i.e., from the cellular to the macroscale, facilitates understanding of macroscopic bacterial phenomena. In this Review, we first cover the biomechanics of individual bacteria in the bulk liquid and on surfaces as the base of complex phenomena. The collective behaviors of bacteria in simple environments are next introduced. We then introduce recent advances in biofilm biomechanics, in which adhesion force and the flow environment play crucial roles. We also review transport phenomena in the intestine and the dynamics of the gut flora, focusing on that in zebrafish. Finally, we provide an overview of the future prospects for the field.

Swimming microorganisms acquire optimal efficiency with multiple cilia.

Planktonic microorganisms are ubiquitous in water, and their population dynamics are essential for forecasting the behavior of global aquatic ecosystems. Their population dynamics are strongly affected by these organisms' motility, which is generated by their hair-like organelles, called cilia or flagella. However, because of the complexity of ciliary dynamics, the precise role of ciliary flow in microbial life remains unclear. Here, we have used ciliary hydrodynamics to show that ciliates acquire the optimal propulsion efficiency. We found that ciliary flow highly resists an organism's propulsion and that the swimming velocity rapidly decreases with body size, proportional to the power of minus two. Accordingly, the propulsion efficiency decreases as the cube of body length. By increasing the number of cilia, however, efficiency can be significantly improved, up to 100-fold. We found that there exists an optimal number density of cilia, which provides the maximum propulsion efficiency for all ciliates. The propulsion efficiency in this case decreases inversely proportionally to body length. Our estimated optimal density of cilia corresponds to those of actual microorganisms, including species of ciliates and microalgae, which suggests that now-existing motile ciliates and microalgae have survived by acquiring the optimal propulsion efficiency. These conclusions are helpful for better understanding the ecology of microorganisms, such as the energetic costs and benefits of multicellularity in Volvocaceae, as well as for the optimal design of artificial microswimmers.