Biology subjects

Amitabh, P.

Publications and source records attributed to Amitabh, P..

3 recordsLinked to original sources

bioRxiv2026

Imaging the impact of rotifer consumption on bacterial behaviors in the zebrafish gut

The gut microbiota influence many aspects of their hosts health and physiology including the digestion of food, and food intake in turn influences the composition of the gut microbiome. However, the ways in which food can alter the behavior of intestinal bacteria remain largely unknown, due in large part to the difficulty of assessing behavior in situ. Larval zebrafish provide a model for addressing this gap because of their optical transparency and their ability to be prepared germ-free and then associated with specific microbial species. Using light sheet fluorescence microscopy to visualize bacteria inside the intestines of live zebrafish larvae, we examine the properties of two commensal strains with markedly different physical characteristics. One is a zebrafish-commensal Enterobacter species that forms large aggregates in unfed larvae, and the other is a pathobiont Vibrio species that is motile and planktonic. Following host consumption of rotifers, a common food, Enterobacter clusters disintegrate into motile individuals. Vibrio remains planktonic in fed larvae but decreases the activity of its Type VI Secretion System, leading to a strong decrease in damage to host tissue. Our results reveal that feeding can have major impacts on bacterial behavior that should be considered in models of normal gut microbiome dynamics as well as pathogenesis.

microbiology↗

bioRxiv2025

Characterizing trajectories of innate immune cells in larval zebrafish

It is well established from in vitro studies of immune cells that stimulation by a wide range of potential signals leads to motility and morphology changes. How these physical behaviors manifest inside a living animal remains unclear due to limitations of conventional imaging and analysis approaches. Here, we establish a quantitative framework for imaging and tracking neutrophil and macrophage dynamics in larval zebrafish, spanning a large fraction of the animal for multi-hour timescales with few-minute temporal resolution. We focus especially on the gut, examining innate immune responses to different preparations of the intestinal microbiome. Using light sheet fluorescence microscopy and trajectory analysis of hundreds of individual cells, we characterize speeds, directional persistence measures, and cellular morphology to reveal distinct population behaviors. Individual immune cells exhibit stable motility phenotypes, favoring predominantly motile or non-motile states rather than frequent transitions between them. Gut architecture constrains migration patterns as demonstrated by preferential anterior-posterior movement and a high probability of cells remaining in the vicinity of the gut throughout the imaging duration. Macrophages display significantly reduced sphericity during motile periods compared to non-motile periods, providing a morphological signature that may enable inference of dynamic behavior from static snapshots. Surprisingly, migration patterns remain consistent across diverse microbial conditions - germ-free, conventionally reared, and colonized by two strains of a zebrafish-native Vibrio species - indicating that tissue structure exerts a stronger influence than bacterial stimuli on immune surveillance dynamics. Previously observed tissue damage by the wild-type Vibrio strain, and the resulting recruitment of immune cells towards the damage site, provided the only microbe-specific cellular behavior. These findings reveal innate immune surveillance as a stereotyped process whose characteristics reflect both cellular decision-making and larger-scale anatomical structure.

biophysics↗

bioRxiv2024

Bacterial Modulation of Intestinal Motility through Macrophage Redistribution

Intestinal microbes, whether resident or transient, influence the physiology of their hosts, altering both the chemical and the physical characteristics of the gut. An example of the latter is the human pathogen Vibrio choleraes ability to induce strong mechanical contractions, discovered in zebrafish. The underlying mechanism has remained unknown, but the phenomenon requires the actin crosslinking domain (ACD) of Vibrios Type VI Secretion System (T6SS), a multicomponent protein syringe that pierces adjacent cells and delivers toxins. By using a zebrafish-native Vibrio and imaging-based assays of host intestinal mechanics and immune responses, we find that macrophages mediate the connection between the T6SS ACD and intestinal activity: ACD-dependent tissue damage activates macrophages and recruits them from their unperturbed positions near enteric neurons lining the midgut, spurring strong gut contractions resembling those resulting from genetic depletion of macrophages. In addition to illuminating host-directed actions of the widespread T6SS protein apparatus, our findings highlight how localized bacteria-induced injury can reshape neuro-immune cellular dynamics to impact whole-organ physiology.

microbiology↗