Biology subjects

Guillemin, K.

Publications and source records attributed to Guillemin, K..

18 recordsLinked to original sources

bioRxiv2026

Social modulation of activity and orientation fosters complex interactions in young zebrafish

Zebrafish are an important model organism for investigating collective behavior and neuropsychiatric disorders due to attributes such as fast development, high genetic homology with humans and a rich behavioral repertoire. Social behavior in zebrafish emerges as early as twelve days post-fertilization, building toward diverse, coordinated, and complex adult interactions. Most studies on social phenotypes, including in zebrafish, have focused on adult animals and assess isolated traits such as aggression, boldness, or social memory, leaving the critical period of early development when sociality emerges and the mechanisms underlying social behavior establishment largely unexplored. We present here a behavior analysis pipeline that identifies features describing general locomotion and social behavior based on simple geometric criteria. We apply this analysis to pairs of freely interacting two-week-old zebrafish and characterize nascent social preference. We find that young zebrafish favor a specific range of inter-fish distances, creating a social space characterized by specific modulation of locomotion features. Through quantitative analysis and modeling, we show that this proximity behavior is largely established through a turning bias toward counterparts and a socially induced suppression of the variance in turning angles over broader ranges of inter-fish distances. Furthermore, we describe how proximity fosters engagement by young zebrafish in transient, complex short-range physical interactions that include various forms of inter-fish contacts, reminiscent of patterns described in adult animals. Our approach has broad applications for understanding the ontogeny of sociality and collective behaviors and describing subtle phenotypes associated with various human disorders.

animal behavior and cognition↗

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↗

bioRxiv2022

A mucin-regulated adhesin determines the intestinal biogeography and inflammatory character of a bacterial symbiont.

In a healthy gut, microbes are often aggregated with host mucus, yet the molecular basis for this organization and its impact on intestinal health are unclear. Mucus is a viscous physical barrier separating resident microbes from epithelia, but also provides glycan cues that regulate microbial behaviors. Using experimental evolution, we discovered a mucin-sensing pathway in an Aeromonas symbiont of zebrafish, Aer01. In response to the mucin-associated glycan N-acetylglucosamine, a sensor kinase regulates expression of a mucin-binding adhesin we named MbpA. When MbpA is disrupted, Aer01 colonizes to normal levels, but is largely planktonic and elicits increased intestinal inflammation, traits which are reversed by increasing cell surface MpbA. MbpA-like adhesins are common in human-associated bacteria and expression of an Akkermansia muciniphila MbpA-like adhesin in MbpA-deficient Aer01 restored lumenal aggregation and reversed its pro-inflammatory character. Our work demonstrates how resident bacteria use mucin glycans to modulate behaviors congruent with host health.

microbiology↗

bioRxiv2022

Disaggregation as an interaction mechanism among intestinal bacteria

The gut microbiome contains hundreds of interacting species that together influence host health and development. The mechanisms by which intestinal microbes can interact, however, remain poorly mapped and are often modeled as spatially unstructured competitions for chemical resources. Recent imaging studies examining the zebrafish gut have shown that patterns of aggregation are central to bacterial population dynamics. In this study, we focus on bacterial species of genera Aeromonas and Enterobacter. Two zebrafish gut derived isolates, Aeromonas ZOR0001 (AE) and Enterobacter ZOR0014 (EN), when mono-associated with the host, are highly aggregated and located primarily in the intestinal midgut. An Aeromonas isolate derived from the commensal strain, Aeromonas-MB4 (AE-MB4), differs from the parental strain in that it is composed mostly of planktonic cells localized to the anterior gut. When challenged by AE-MB4, clusters of EN rapidly fragment into non-motile, slow-growing, dispersed individual cells with overall abundance two orders of magnitude lower than the mono-association value. In the presence of a certain set of additional gut bacterial species, these effects on EN are dampened. In particular, if AE-MB4 invades an already established multi-species community, EN persists in the form of large aggregates. These observations reveal an unanticipated competition mechanism based on manipulation of bacterial spatial organization, namely dissolution of aggregates, and provide evidence that multi-species communities may facilitate stable intestinal co-existence. SignificanceThe diverse microbial communities inhabiting vertebrate intestines influence many aspects of their hosts health and development. The rules governing community assembly and even the types of interactions that are possible among gut microbes remain poorly understood, however, with the role of spatial aggregation in interspecies dynamics being especially unclear. To address this, we performed live imaging studies of the larval zebrafish gut, focusing on two spatially distinct bacterial species that exhibit strong competition, discovering that the latter can induce a striking, rapid disintegration of aggregates of the former. This competition is attenuated in the presence of a particular set of additional bacterial species. Our findings reveal an unanticipated interaction mechanism and highlight that diverse communities may stabilize the gut microbiome.

microbiology↗

bioRxiv2022

Secreted Aeromonas GlcNAc binding protein GbpA stimulates epithelial cell proliferation in the zebrafish intestine

In response to microbiota colonization, the intestinal epithelia of many animals exhibit increased rates of cell proliferation. We used gnotobiotic larval zebrafish to identify a secreted factor from the mutualist Aeromonas veronii that is sufficient to promote intestinal epithelial cell proliferation. This secreted A. veronii protein is a homologue of the Vibrio cholerae GlcNAc binding protein GbpA, which was identified as a chitin-binding colonization factor in mice. GbpA was subsequently shown to be a lytic polysaccharide monooxygenase (LPMO) that can degrade recalcitrant chitin. Our phenotypic characterization of gbpA deficient A. veronii found no alterations in the mutant cells biogeography in the zebrafish intestine and only a modest competitive disadvantage in chitin-binding and colonization fitness when competed against the wild type strain. These results argue against the model of GbpA being a secreted adhesin that binds simultaneously to bacterial cells and GlcNAc, and instead suggests that GbpA is part of a bacterial GlcNAc utilization program. We show that the host proliferative response to GbpA occurs in the absence of bacteria upon exposure of germ-free zebrafish to preparations of native GbpA secreted from either A. veronii or V. cholerae or recombinant A. veronii GbpA. Furthermore, domain 1 of A. veronii GbpA, containing the predicted LPMO activity, is sufficient to stimulate intestinal epithelial proliferation. We conjecture that intestinal epithelia upregulate their rates of renewal in response to secreted bacterial GbpA proteins as an adaptive strategy for coexisting with bacteria that can degrade glycan constituents of the protective intestinal lining.

microbiology↗

bioRxiv2022

GLOBAL HOST RESPONSES TO THE MICROBIOTA AT SINGLE CELL RESOLUTION IN GNOTOBIOTIC ZEBRAFISH

Resident microbes are a feature of vertebrate animals that influence diverse aspects of their biology from tissue development to metabolism. Here we describe transcriptional responses to the microbiota across all the cells of a model developing vertebrate, the larval zebrafish. By performing single cell transcriptomic analysis of whole germ free and conventionalized larvae, we show that the impacts of the microbiota are sensed by all major organ systems but that responses are highly specific to different cell types. The presence of microbiota stimulates the expansion of progenitor-like cells in epithelial tissues and increases proliferation gene expression in progenitor-like cell populations of the immune and nervous systems. Across many cell types, including enterocytes, immune cells, and neurons, the microbiota upregulates expression of genes involved in microbial responses, cell type-specific activities, and cell type-specific deployment of ATP metabolism genes. These combined transcriptional patterns demonstrate how the microbiota simultaneously modulate cellular immune and metabolic programs. The impacts of the microbiota on tissue development are illustrated by the exocrine pancreas, which in the absence of the microbiota is smaller and composed of uniformly differentiated acinar cells. The presence of the microbiota results in exocrine pancreas enlargement and heterogeneous cellular expression of digestive enzyme and secretion genes, demonstrating how the microbiota promotes plasticity in tissue development and function. This single cell transcriptional dataset demonstrates the impacts of the microbiota on vertebrate development across the body and provides a foundation for dissecting cell type specific responses to microbial consortia members or molecules. SummaryAnimal development proceeds in the presence of intimate microbial associations, but the extent to which different host cells across the body respond to resident microbes remains to be fully explored. Using the vertebrate model organism, the larval zebrafish, we assessed transcriptional responses to the microbiota across the entire body at single cell resolution. We find that cell types across the body, not limited to tissues at host-microbe interfaces, respond to the microbiota. Responses are cell-type specific, but across many tissues the microbiota enhances cell proliferation, increases metabolism, and stimulates a diversity of cellular activities, revealing roles for the microbiota in promoting developmental plasticity. This work provides a resource for exploring transcriptional responses to the microbiota across all cell types of the vertebrate body and generating new hypotheses about the interactions between vertebrate hosts and their microbiota.

developmental biology↗

bioRxiv2022

A microbiota membrane disrupter disseminates to the pancreas and increases β-cell mass

Microbiome dysbiosis is a feature of diabetes, but how microbial products influence insulin production is poorly understood. Here we report the mechanism of BefA, a microbiome-derived protein that increases proliferation of insulin-producing {beta}-cells during pancreatic development in gnotobiotic zebrafish and mice. BefA disseminates systemically via multiple anatomic routes to act directly on pancreatic islets. We report the structure of BefA, containing a lipid-binding SYLF domain, and demonstrate that it permeabilizes synthetic liposomes and bacterial membranes. A BefA mutant impaired in membrane disruption fails to expand {beta}-cells whereas the pore-forming host defense protein, Reg3, stimulates {beta}-cell proliferation. Our work demonstrates that membrane permeabilization by microbiome-derived and host defense proteins is necessary and sufficient for {beta}-cell expansion during pancreas development, thereby connecting microbiome composition with diabetes risk.

molecular biology↗

bioRxiv2021

Enteric nervous system modulation of luminal pH modifies the microbial environment to promote intestinal health

The enteric nervous system (ENS) controls many aspects of intestinal homeostasis, including parameters that shape the habitat of microbial residents. Previously we showed that zebrafish lacking an ENS, due to deficiency of the sox10 gene, develop intestinal inflammation and bacterial dysbiosis, with an expansion of proinflammatory Vibrio strains. To understand the primary defects resulting in dysbiosis in sox10 mutants, we investigated how the ENS shapes the intestinal environment in the absence of microbiota and associated inflammatory responses. We found that intestinal transit, intestinal permeability, and luminal pH regulation are all aberrant in sox10 mutants, independent of microbially induced inflammation. Treatment with the proton pump inhibitor, omeprazole, corrected the more acidic luminal pH of sox10 mutants to wild type levels. Omeprazole treatment also prevented overabundance of Vibrio and ameliorated inflammation in sox10 mutant intestines. Treatment with the carbonic anhydrase inhibitor, acetazolamide, caused wild type luminal pH to become more acidic, and increased both Vibrio abundance and intestinal inflammation. We conclude that a primary function of the ENS is to regulate luminal pH, which plays a critical role in shaping the resident microbial community and regulating intestinal inflammation. Author SummaryThe intestinal microbiota is an important determinant of health and disease and is shaped by the environment of the gut lumen. The nervous system of the intestine, the enteric nervous system (ENS), helps maintain many aspects of intestinal health including a healthy microbiota. We used zebrafish with a genetic mutation that impedes ENS formation to investigate how the ENS prevents pathogenic shifts in the microbiota. We found that mutants lacking an ENS have a lower luminal pH, higher load of pathogenic bacteria, and intestinal inflammation. We showed that correcting the low pH, using the commonly prescribed pharmacological agent omeprazole, restored the microbiota and prevented intestinal inflammation. Conversely, we found that lowering the luminal pH of wild type animals, using the drug acetazolamide, caused expansion of pathogenic bacteria and increased intestinal inflammation. From these experiments, we conclude that a primary function of the ENS is to maintain normal luminal pH, thereby constraining intestinal microbiota community composition and promoting intestinal health.

microbiology↗

bioRxiv2021

The immunomodulatory dCache chemoreceptor TlpA of Helicobacter pylori binds multiple attractant and antagonistic ligands via distinct sites

The Helicobacter pylori chemoreceptor TlpA plays a role in dampening host inflammation during chronic stomach colonization. TlpA has a periplasmic dCache_1 domain, a structure that is capable of sensing many ligands; however, the only characterized TlpA signals are arginine, bicarbonate, and acid. To increase our understanding of TlpAs sensing profile, we screened for diverse TlpA ligands using ligand binding arrays. TlpA bound seven ligands with affinities in the low to middle micromolar ranges. Three of these ligands, arginine, fumarate, and cysteine, were TlpA-dependent chemoattractants, while the others elicited no response. Molecular docking experiments, site-directed point mutants, and competition surface plasmon resonance binding assays suggested that TlpA binds ligands via both the membrane-distal and -proximal dCache_1 binding pockets. Surprisingly, one of the non-active ligands, glucosamine, acted as a chemotaxis antagonist, preventing the chemotaxis response to chemoattractant ligands and acted to block binding of ligands irrespective of whether they bound the membrane-distal or -proximal dCache_1 subdomains. In total, these results suggest TlpA senses multiple attractant ligands as well as antagonist ones, an emerging theme in chemotaxis systems. ImportanceNumerous chemotactic bacterial pathogens depend on the ability to sense a diverse array of signals through chemoreceptors to achieve successful colonization and virulence within their host. The signals sensed by chemoreceptors, however, are not always fully understood. This is the case for TlpA, a dCache_1 chemoreceptor of H. pylori that enables the bacteria to induce less inflammation during chronic infections. H. pylori causes a significant global disease burden, which is driven by the development of gastric inflammation. Accordingly, it is essential to understand the processes by which H. pylori modulates host inflammation. This work uncovers the signals that TlpA can sense and highlights the underappreciated ability for regulating chemotactic responses by antagonistic chemoreceptor ligands, which is an emerging theme among other chemotactic systems.

microbiology↗

bioRxiv2020

Pseudocapillaria tomentosa, Mycoplasma spp., and intestinal lesions in experimentally infected zebrafish Danio rerio

Intestinal neoplasms and preneoplastic lesions are common in zebrafish research facilities. Previous studies have demonstrated that the neoplasms are caused by a transmissible agent, and two candidate agents have been implicated: a Mycoplasma sp. related to M. penetrans and the intestinal parasitic nematode, Pseudocapillaria tomentosa, and both agents are common in zebrafish facilities. To elucidate the role of these two agents in the occurrence and severity of the neoplasm and other intestinal lesions, we conducted two experimental inoculation studies. Exposed fish were examined at various time points over an 8 mo. period for intestinal histpathologic changes and the burden of Mycoplasma and nematodes. Fish exposed to a Mycoplasma isolate from zebrafish were associated with preneoplastic lesions. Fish exposed to the nematode alone or with the Mycoplasma isolate developed severe lesions and neoplasms. Both inflammation and neoplasm scores were associated with an increase in Mycoplasma burden. These results support the conclusions that P. tomentosa is a strong promoter of intestinal neoplasms in zebrafish, and that Mycoplasma alone can also cause intestinal lesions and accelerate cancer development in the context of nematode infection.

cancer biology↗

bioRxiv2020

A bacterial inflammation sensor regulates c-di-GMP signaling, adhesion, and biofilm formation.

The reactive oxygen species produced during inflammation through the neutrophilic respiratory burst play profound roles in combating bacterial pathogens and regulating the microbiota. Among these, the neutrophilic oxidant bleach, hypochlorous acid (HOCl), is the most prevalent and strongest oxidizer and kills bacteria through non-specific oxidation of proteins, lipids, and DNA. Thus, HOCl can be viewed as a host-specific cue that conveys important information about what bacterial physiology and lifestyle programs may be required for successful colonization. Nevertheless, bacteria that colonize animals face a molecular challenge in how to achieve highly selective detection of HOCl due to its reactive and transient nature and chemical similarity to more benign and non-host-specific oxidants like hydrogen peroxide (H2O2). Here, we report that in response to increasing HOCl levels E. coli regulates biofilm production via activation of the diguanylate cyclase DgcZ. We show the molecular mechanism of this activation to be specific oxidation of a conserved cysteine that coordinates the zinc of its regulatory chemoreceptor zinc-binding (CZB) domain, forming a zinc-cysteine redox switch 685-fold more sensitive to oxidation by HOCl over H2O2. Dissection of the signal transduction mechanism through quantum mechanics, molecular dynamics, and biochemical analyses reveal how the cysteine redox state alters the delicate equilibrium of competition for Zn++ between the CZB domain and other zinc binders to relay the presence of HOCl through activating the associated GGDEF domain to catalyze c-di-GMP. We find biofilm formation and HOCl-sensing in vivo to be regulated by the conserved cysteine, and point mutants that mimic oxidized CZB states increase production of the biofilm matrix polymer poly-N-acetylglucosamine and total biofilm. We observe CZB-regulated diguanylate cyclases and chemoreceptors in phyla in which host-associated bacteria are prevalent and are possessed by pathogens that manipulate host inflammation as part of their colonization strategy. A phylogenetic survey of all known CZB sequences shows these domains to be conserved and widespread across diverse phyla, suggesting CZB origin predates the bacterial last universal common ancestor. The ability of bacteria to use CZB protein domains to perceive and thwart the host neutrophilic respiratory burst has implications for understanding the mechanisms of diseases of chronic inflammation and gut dysbiosis.

microbiology↗

bioRxiv2019

Identification and characterization of zebrafish Tlr4 co-receptor Md-2

The zebrafish (Danio rerio) is a powerful model organism for studies of the innate immune system. One apparent difference between human and zebrafish innate immunity is the cellular machinery for LPS-sensing. In amniotes, the protein complex formed by Toll-like receptor 4 and myeloid differentiation factor 2 (Tlr4/Md-2) recognizes the bacterial molecule lipopolysaccharide (LPS) and triggers an inflammatory response. It is believed that zebrafish have neither Md-2 nor Tlr4: Md-2 has not been identified outside of amniotes, while the zebrafish tlr4 genes appear to be paralogs, not orthologs, of amniote TLR4s. We revisited these conclusions. We identified a zebrafish gene encoding Md-2, ly96. Using single-cell RNA-Seq, we found that ly96 is transcribed in cells that also transcribe genes diagnostic for innate immune cells, including the zebrafish tlr4-like genes. Unlike amniote LY96, zebrafish ly96 expression is restricted to a small number of macrophage-like cells. In a functional assay, zebrafish Md-2 and Tlr4a form a complex that activates NF-{kappa}B signaling in response to LPS, but ly96 loss-of-function mutations gave little protection against LPS-toxicity in larval zebrafish. Finally, by analyzing the genomic context of tlr4 genes in eleven jawed vertebrates, we found that tlr4 arose prior to the divergence of teleosts and tetrapods. Thus, an LPS-sensitive Tlr4/Md-2 complex is likely an ancestral feature shared by mammals and zebrafish, rather than a de novo invention on the tetrapod lineage. We hypothesize that zebrafish retain an ancestral, low-sensitivity Tlr4/Md-2 complex that confers LPS-responsiveness to a specific subset of innate immune cells.

immunology↗

bioRxiv2019

Swimming motility and chemotaxis control the spatial organization, persistence, and inflammatory activity of a model intestinal pathobiont

Understanding the processes that spatially restrict resident gut bacteria and the mechanisms by which disease-causing pathobionts escape this control will open new avenues for microbiome-based therapies. Using live imaging and genetically engineered bacteria, we discovered that flagella-based swimming motility and chemotaxis enable a model Vibrio pathobiont to govern its own spatial organization within the larval zebrafish gut and to persist in the face of the disruptive forces of intestinal flow. Bacterial mutants lacking motility traits became aggregated and lumenally confined, making them susceptible to periodic expulsion from the host. Consequently, non-motile and non-chemotactic mutants experienced large fluctuations in absolute abundance and impaired interbacterial competition. Further, we found that motile bacterial cells induce expression of the proinflammatory cytokine TNF in gut-associated macrophages and the liver. Using inducible genetic switches, we demonstrate that swimming motility can be manipulated in situ to modulate the spatial organization, persistence, and inflammatory activity of gut bacteria.

microbiology↗

bioRxiv2019

Zebrafish mbnl mutants model molecular and physical phenotypes of human MBNL loss of function disorders

The muscleblind RNA binding proteins (MBNL1, MBNL2, and MBNL3) are highly conserved across vertebrates and are important regulators of RNA alternative splicing. Loss of MBNL protein function through sequestration by CUG or CCUG RNA repeats is largely responsible for the phenotypes of the human genetic disorder myotonic dystrophy (DM). We generated the first stable zebrafish (Danio rerio) models of DM-associated MBNL loss of function through mutation of the three zebrafish mbnl genes. In contrast to mouse models, zebrafish double and triple homozygous mbnl mutants were viable to adulthood. Zebrafish mbnl mutants displayed disease-relevant physical phenotypes including decreased body size and impaired movement. They also exhibited widespread alternative splicing changes, including the misregulation of many DM-relevant exons. Physical and molecular phenotypes were more severe in compound mbnl mutants than in single mbnl mutants, suggesting partially redundant functions of Mbnl proteins. The high fecundity and larval optical transparency of this complete series of zebrafish mbnl mutants will make them useful for studying DM-related phenotypes and how individual Mbnl proteins contribute to them, and for testing potential therapeutics.

molecular biology↗

bioRxiv2019

Low-dose antibiotics can collapse gut bacterial populations via a gelation transition

Antibiotics can profoundly alter the intestinal microbiome even at the sublethal concentrations often encountered through environmental contamination. The mechanisms by which low-dose antibiotics induce large yet highly variable changes in gut communities have remained elusive. We therefore investigated the impact of antibiotics on intestinal bacteria using larval zebrafish, whose experimental tractability enables high-resolution in vivo examination of response dynamics. Live imaging revealed that sublethal doses of the common antibiotic ciprofloxacin lead to severe drops in bacterial abundance, coincident with changes in spatial organization that increase susceptibility to intestinal expulsion. Strikingly, our data can be mapped onto a physical model of living gels that links bacterial aggregation and expulsion to nonequilibrium abundance dynamics, providing a framework for predicting the impact of antibiotics on the intestinal microbiome.

microbiology↗

bioRxiv2018

Agent-Based Modeling Demonstrates How Local Chemotactic Behavior Can Shape Biofilm Architecture

Mature bacterial biofilms have elaborate three-dimensional architectures that endow these structures with their durability and resistance to environmental perturbations. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms of the human pathogen Helicobacter pylori. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterized H. pylori strains with varying AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger scale emergent properties of biofilms.\n\nImportanceMost bacteria exist in aggregated, three-dimensional structures called biofilms. Biofilms are resistant to antimicrobials and can pose societal problems, for example when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown that Helicobacter pylori bacteria are repulsed by high concentrations of a self-produced molecule, autoinducer-2 (AI-2) and that H. pylori mutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here we used computer simulations of biofilm formation to show that local H. pylori behavior of repulsion from high AI-2 could explain the overall architecture of H. pylori biofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.

microbiology↗

bioRxiv2018

Bacterial cohesion predicts spatial distribution in the larval zebrafish intestine

Are there general biophysical relationships governing the spatial organization of the gut microbiome? Despite growing realization that spatial structure is important for population stability, inter-bacterial competition, and host functions, it is unclear in any animal gut whether such structure is subject to predictive, unifying rules, or if it results from contextual, species-specific behaviors. To explore this, we used light sheet fluorescence microscopy to conduct a high-resolution comparative study of bacterial distribution patterns throughout the entire intestinal volume of live, larval zebrafish. Fluorescently tagged strains of seven bacterial symbionts, representing six different species native to zebrafish, were each separately mono-associated with animals that had been raised initially germ-free. The strains showed large differences in both cohesion--the degree to which they auto-aggregate--and spatial distribution. We uncovered a striking correlation between each strains mean position and its cohesion, whether quantified as the fraction of cells existing as planktonic individuals, the average aggregate size, or the total number of aggregates. Moreover, these correlations held within species as well; aggregates of different sizes localized as predicted from the pan-species observations. Together, our findings indicate that bacteria within the zebrafish intestine are subject to generic processes that organize populations by their cohesive properties. The likely drivers of this relationship, peristaltic fluid flow, tubular anatomy, and bacterial growth and aggregation kinetics, are common throughout animals. We therefore suggest that the framework introduced here, of biophysical links between bacterial cohesion and spatial organization, should be useful for directing explorations in other host-microbe systems, formulating detailed models that can quantitatively map onto experimental data, and developing new tools that manipulate cohesion to engineer microbiome function.

microbiology↗

bioRxiv2017

Modernized tools for streamlined genetic manipulation of wild and diverse symbiotic bacteria

The capacity to associate symbiotic bacteria with vital aspects of plant and animal biology is outpacing our understanding of the mechanisms shaping these interactions. A major barrier to mechanistic studies is the paucity of tools for genetically manipulating wild and diverse bacterial isolates. Solving this problem is crucial to elucidating the cellular and molecular rules that govern symbiotic relationships and ultimately harnessing them for agricultural and biomedical applications. Therefore, we constructed a series of vectors that expedite genetic knock-in and knock-out procedures across a range of bacterial lineages. This was accomplished by developing strategies for domestication-free bacterial conjugation, designing plasmids with customizable features, and streamlining allelic exchange using visual markers of homologous recombination. These tools enabled a comparative study based on live imaging of diverse bacterial symbionts native to the zebrafish intestine, with which we discovered heterogeneous colonization patterns and a striking correlation between bacterial population biogeography and cellular behavior.

genetics↗