Antibiotic resistance is a growing global health threat. Although antibiotic activity is well studied in homogeneous liquid cultures, many infections are caused by spatially structured multicellular populations where consumption of scarce nutrients establishes strong spatial variations in their abundance. These nutrient variations have long been hypothesized to help bacterial populations tolerate antibiotics, since liquid culture studies link antibiotic tolerance to metabolic activity, and thus, local nutrient availability. Here, we test this hypothesis by visualizing cell death in structured Escherichia coli populations exposed to select nutrients and antibiotics. We find that nutrient availability acts as a bottleneck to antibiotic killing, causing death to propagate through the population as a traveling front. By integrating our measurements with biophysical theory and simulations, we establish quantitative principles that explain how collective nutrient consumption can limit the progression of this \"death front,\" protecting a population from a nominally deadly antibiotic dose. While increasing nutrient supply can overcome this bottleneck, in some cases, excess nutrient unexpectedly promotes the regrowth of resistant cells. Altogether, this work provides a key step toward predicting and controlling antibiotic treatment of spatially structured bacterial populations, yielding biophysical insights into collective behavior and guiding strategies for effective antibiotic stewardship.
", "doi": "10.1038/s41467-026-69625-4", "pmcid": "PMC13066622", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2026-04-09", "series_number": "1", "volume": "17", "issue": "1", "pages": "3337" }, { "id": "authors:y9n15-nmm43", "collection": "authors", "collection_id": "y9n15-nmm43", "cite_using_url": "https://authors.library.caltech.edu/records/y9n15-nmm43", "type": "article", "title": "Soil Texture Regulates Bacterial Motility and Chemotactic Recruitment to Plant Roots", "author": [ { "family_name": "Al Harraq", "given_name": "Ahmed", "orcid": "0000-0001-7679-348X" }, { "family_name": "Choi", "given_name": "Gayoung", "orcid": "0009-0004-8103-9552" }, { "family_name": "Datta", "given_name": "Sujit S.", "orcid": "0000-0003-2400-1561", "clpid": "Datta-Sujit-S" }, { "family_name": "Shaevitz", "given_name": "Joshua W.", "orcid": "0000-0001-8809-4723" } ], "abstract": "Soil microbial communities regulate critical ecological processes, including nutrient cycling, carbon sequestration, and plant growth. However, due to the opacity and structural complexity of soil, how physical constraints imposed by pore geometry influence bacterial motility and chemotactic recruitment to plant roots remains poorly understood. We use a transparent soil mimic composed of cryolite grains that replicates the structural characteristics of natural soils while enabling direct visualization of bacterial dynamics. Using as a model bacterium, we combine macroscopic spreading assays with microscopic tracking of cellular trajectories to characterize how soil texture affects motility across pore scales. We find that bacterial motility shifts from run-and-tumble behavior in large, open pores to frequent trapping in smaller, more confined spaces. This transition is governed by the pore size distribution and leads to reduced effective diffusivity and slower population-scale spreading. Moreover, pore-scale confinement hinders the chemotactic recruitment of bacteria to roots: recruitment is robust in sandy and loamy soils but negligible in highly confining textures. Our results establish soil texture as a critical factor regulating microbial dynamics and ecological interactions in the rhizosphere. This mechanistic understanding complements genomic surveys by identifying physical confinement as an ecological filter that shapes root-associated microbiomes. These findings highlight the essential and previously underappreciated role of soil texture, suggesting new strategies for managing microbial communities to promote plant health and sustainable agriculture.", "doi": "10.1103/56qk-s5zw", "issn": "2835-8279", "publisher": "American Physical Society", "publication": "PRX Life", "publication_date": "2026-03-19", "series_number": "1", "volume": "4", "issue": "1", "pages": "013034" }, { "id": "authors:1hzf1-nx962", "collection": "authors", "collection_id": "1hzf1-nx962", "cite_using_url": "https://authors.library.caltech.edu/records/1hzf1-nx962", "type": "article", "title": "Morphodynamics of surface-attached active drops", "author": [ { "family_name": "Mart\u00ednez-Calvo", "given_name": "Alejandro", "orcid": "0000-0002-2109-8145" }, { "family_name": "Datta", "given_name": "Sujit S.", "orcid": "0000-0003-2400-1561", "clpid": "Datta-Sujit-S" } ], "abstract": "Many biological and synthetic systems are suspensions of oriented actively-moving components. Unlike in passive suspensions, the interplay between orientational order, active flows, and interactions with boundaries gives rise to fascinating new phenomena in such active suspensions. Here, we examine the paradigmatic example of a surface-attached drop of an active fluid (an \"active drop\"), which has so far only been studied in the idealized limit of thin drops. We find that such surface-attached active drops can exhibit a wide array of stable steady-state shapes and internal flows that are far richer than those documented previously, depending on boundary conditions and the strength of active stresses. Our analysis uncovers quantitative principles to predict and even rationally control the conditions under which these different states arise—yielding design principles for next-generation active materials.
", "doi": "10.1038/s41467-025-68235-w", "pmcid": "PMC12905126", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2026-02-12", "series_number": "1", "volume": "17", "issue": "1", "pages": "1600" }, { "id": "authors:r3tnw-qdg62", "collection": "authors", "collection_id": "r3tnw-qdg62", "cite_using_url": "https://authors.library.caltech.edu/records/r3tnw-qdg62", "type": "article", "title": "Spatial self-organization of confined bacterial suspensions", "author": [ { "family_name": "Hokmabad", "given_name": "Babak Vajdi", "orcid": "0000-0001-5075-6357" }, { "family_name": "Mart\u00ednez-Calvo", "given_name": "Alejandro", "orcid": "0000-0002-2109-8145" }, { "family_name": "Gonzalez La Corte", "given_name": "Sebastian", "orcid": "0000-0003-1607-5632" }, { "family_name": "Datta", "given_name": "Sujit S.", "orcid": "0000-0003-2400-1561", "clpid": "Datta-Sujit-S" } ], "abstract": "Lab studies of bacteria usually focus on cells in spatially extended, nutrient-replete settings, such as in liquid cultures and on agar surfaces. By contrast, many biological and environmental settings\u2014ranging from mucus in the body to ocean sediments and the soil beneath our feet\u2014feature multicellular bacterial populations that are confined to tight spots where essential metabolic substrates (e.g., oxygen) are scarce. What influence does such confinement have on a bacterial population? Here, we address this question by studying suspensions of motile\n Escherichia coli\n confined to quasi two-dimensional (2D) droplets. We find that when the droplet size and cell concentration are both large enough, the initially uniform suspension spatially self-organizes into a concentrated, immotile inner \"core\" that coexists with a more dilute, highly motile surrounding \"shell.\" By simultaneously measuring cell concentration, oxygen concentration, and motility-generated fluid flow, we show that this behavior arises from the interplay between oxygen transport through the droplet from its boundary, uptake by the cells, and corresponding changes in their motility in response to oxygen variations. Furthermore, we use biophysical theory and simulations to quantitatively describe this interplay. Our work thus sheds light on the rich collective behaviors that emerge for bacterial populations in confined environments, with implications for understanding ecological niches and engineering artificial systems.", "doi": "10.1073/pnas.2503983122", "pmcid": "PMC12541401", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2025-10-14", "series_number": "41", "volume": "122", "issue": "41", "pages": "e2503983122" }, { "id": "authors:3cmyt-pqn75", "collection": "authors", "collection_id": "3cmyt-pqn75", "cite_using_url": "https://authors.library.caltech.edu/records/3cmyt-pqn75", "type": "article", "title": "Getting out of a tight spot: Cooperative unclogging of hydrogel particles in disordered porous media", "author": [ { "family_name": "Kamath", "given_name": "Sanjana", "orcid": "0009-0000-9352-0969" }, { "family_name": "Talon", "given_name": "Laurent", "orcid": "0000-0002-7965-2372" }, { "family_name": "Ramaswamy", "given_name": "Meera", "orcid": "0000-0001-9220-2256" }, { "family_name": "Browne", "given_name": "Christopher A.", "orcid": "0000-0002-3945-9906" }, { "family_name": "Datta", "given_name": "Sujit S.", "orcid": "0000-0003-2400-1561", "clpid": "Datta-Sujit-S" } ], "abstract": "We use event-driven pore network modeling to study the transport of hydrogel particles through disordered porous media\u2014a process that underlies diverse applications. By simulating particle advection, deformation, and clogging at the pore scale, we identify a dimensionless \"squeezing parameter\" that quantitatively predicts the depth to which particles penetrate into a given medium across diverse conditions. Our simulations also uncover a surprising cooperative effect: Adding more particles enables them to penetrate deeper into the medium. This phenomenon arises because individual particles redirect fluid to adjacent throats, forcing nearby particles through tight pores that they would otherwise clog. Altogether, these results help to establish a quantitative framework that connects microscopic particle mechanics to macroscopic transport behavior.\n \n \n \n \n Published by the American Physical Society\n 2025", "doi": "10.1103/j3jz-x97q", "issn": "2643-1564", "publisher": "American Physical Society", "publication": "Physical Review Research", "publication_date": "2025-07-11", "series_number": "3", "volume": "7", "issue": "3", "pages": "L032013" }, { "id": "authors:k1pxg-qdy13", "collection": "authors", "collection_id": "k1pxg-qdy13", "cite_using_url": "https://authors.library.caltech.edu/records/k1pxg-qdy13", "type": "article", "title": "Elastic instability of wormlike micelle solution flow in serpentine channels", "author": [ { "family_name": "Chen", "given_name": "Emily Y.", "orcid": "0009-0004-6007-3460" }, { "family_name": "Datta", "given_name": "Sujit S.", "orcid": "0000-0003-2400-1561", "clpid": "Datta-Sujit-S" } ], "abstract": "Wormlike micelle (WLM) solutions are abundant in energy, environmental, and industrial applications, which often rely on their flow through tortuous channels. How does the interplay between fluid rheology and channel geometry influence the flow behavior? Here, we address this question by experimentally visualizing and quantifying the flow of a semi-dilute WLM solution in millifluidic serpentine channels. At low flow rates, the base flow is steady and laminar, with strong asymmetry and wall slip. When the flow rate exceeds a critical threshold, the flow exhibits an elastic instability, producing spatially-heterogeneous, unsteady three-dimensional (3D) flow characterized by two notable features: (i) the formation and persistence of stagnant but strongly-fluctuating and multistable “dead zones” in channel bends, and (ii) intermittent 3D “twists” throughout the bulk flow. The geometry of these dead zones and twisting events can be rationalized by considering the minimization of local streamline curvature to reduce flow-generated elastic stresses. Altogether, our results shed new light into how the interplay between solution rheology and tortuous boundary geometry influences WLM flow behavior, with implications for predicting and controlling WLM flows in a broad range of complex environments.
", "doi": "10.1039/d5sm00344j", "issn": "1744-683X", "publisher": "Royal Society of Chemistry", "publication": "Soft Matter", "publication_date": "2025-07", "volume": "25", "pages": "4971-5164" }, { "id": "authors:787hm-66939", "collection": "authors", "collection_id": "787hm-66939", "cite_using_url": "https://authors.library.caltech.edu/records/787hm-66939", "type": "article", "title": "Interfacial Morphodynamics of Proliferating Microbial Communities", "author": [ { "family_name": "Mart\u00ednez-Calvo", "given_name": "Alejandro", "orcid": "0000-0002-2109-8145" }, { "family_name": "Trenado-Yuste", "given_name": "Carolina", "orcid": "0000-0002-7639-2181" }, { "family_name": "Lee", "given_name": "Hyunseok", "orcid": "0000-0003-1554-6228" }, { "family_name": "Gore", "given_name": "Jeff" }, { "family_name": "Wingreen", "given_name": "Ned S.", "orcid": "0000-0001-7384-2821" }, { "family_name": "Datta", "given_name": "Sujit S.", "orcid": "0000-0003-2400-1561", "clpid": "Datta-Sujit-S" } ], "abstract": "In microbial communities, various cell types often coexist by occupying distinct spatial domains. What determines the shape of the interface between such domains\u2014which, in turn, influences the interactions between cells and overall community function? Here, we address this question by developing a continuum model of a 2D spatially structured microbial community with two distinct cell types. We find that, depending on the balance of the different cell proliferation rates and substrate friction coefficients, the interface between domains is either stable and smooth or unstable and develops fingerlike protrusions. We establish quantitative principles describing when these different interfacial behaviors arise and find good agreement with both the results of previous experimental reports as well as new experiments performed here. Our work, thus, helps to provide a biophysical basis for understanding the interfacial morphodynamics of proliferating microbial communities as well as a broader range of proliferating active systems.\n \n \n \n \n Published by the American Physical Society\n 2025", "doi": "10.1103/physrevx.15.011016", "issn": "2160-3308", "publisher": "American Physical Society", "publication": "Physical Review X", "publication_date": "2025-01/2025-03", "series_number": "1", "volume": "15", "issue": "1", "pages": "011016" }, { "id": "authors:pmhk3-r5p55", "collection": "authors", "collection_id": "pmhk3-r5p55", "cite_using_url": "https://authors.library.caltech.edu/records/pmhk3-r5p55", "type": "article", "title": "Microbes get by with a little help from their friends", "author": [ { "family_name": "Datta", "given_name": "Sujit", "orcid": "0000-0003-2400-1561", "clpid": "Datta-Sujit-S" } ], "abstract": "Sujit Datta demonstrates how scaling arguments, thermodynamics and transport phenomena can be deployed to describe the motion of microbial collectives.", "doi": "10.1038/s44286-024-00164-9", "issn": "2948-1198", "publisher": "Nature Publishing Group", "publication": "Nature Chemical Engineering", "publication_date": "2025-01", "series_number": "1", "volume": "2", "issue": "1", "pages": "90" }, { "id": "authors:yvcat-rz898", "collection": "authors", "collection_id": "yvcat-rz898", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181210-140412486", "type": "article", "title": "High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine", "author": [ { "family_name": "Preska Steinberg", "given_name": "Asher", "orcid": "0000-0002-8694-7224", "clpid": "Preska-Steinberg-Asher" }, { "family_name": "Datta", "given_name": "Sujit S.", "orcid": "0000-0003-2400-1561", "clpid": "Datta-Sujit-S" }, { "family_name": "Naragon", "given_name": "Thomas", "orcid": "0000-0002-5373-4257", "clpid": "Naragon-Thomas-H" }, { "family_name": "Rolando", "given_name": "Justin C.", "orcid": "0000-0001-8948-319X", "clpid": "Rolando-Justin-C" }, { "family_name": "Bogatyrev", "given_name": "Said R.", "orcid": "0000-0003-0486-9451", "clpid": "Bogatyrev-Said-R" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "The lumen of the small intestine (SI) is filled with particulates: microbes, therapeutic particles, and food granules. The structure of this particulate suspension could impact uptake of drugs and nutrients and the function of microorganisms; however, little is understood about how this suspension is re-structured as it transits the gut. Here, we demonstrate that particles spontaneously aggregate in SI luminal fluid ex vivo. We find that mucins and immunoglobulins are not required for aggregation. Instead, aggregation can be controlled using polymers from dietary fiber in a manner that is qualitatively consistent with polymer-induced depletion interactions, which do not require specific chemical interactions. Furthermore, we find that aggregation is tunable; by feeding mice dietary fibers of different molecular weights, we can control aggregation in SI luminal fluid. This work suggests that the molecular weight and concentration of dietary polymers play an underappreciated role in shaping the physicochemical environment of the gut.", "doi": "10.7554/eLife.40387", "pmcid": "PMC6342521", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2019-01-22", "volume": "8", "pages": "Art. No. e40387" }, { "id": "authors:x2xza-km768", "collection": "authors", "collection_id": "x2xza-km768", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160614-141541328", "type": "article", "title": "Polymers in the gut compress the colonic mucus hydrogel", "author": [ { "family_name": "Datta", "given_name": "Sujit S.", "orcid": "0000-0003-2400-1561", "clpid": "Datta-Sujit-S" }, { "family_name": "Preska Steinberg", "given_name": "Asher", "orcid": "0000-0002-8694-7224", "clpid": "Preska-Steinberg-Asher" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "abstract": "Colonic mucus is a key biological hydrogel that protects the gut from infection and physical damage and mediates host\u2013microbe interactions and drug delivery. However, little is known about how its structure is influenced by materials it comes into contact with regularly. For example, the gut abounds in polymers such as dietary fibers or administered therapeutics, yet whether such polymers interact with the mucus hydrogel, and if so, how, remains unclear. Although several biological processes have been identified as potential regulators of mucus structure, the polymeric composition of the gut environment has been ignored. Here, we demonstrate that gut polymers do in fact regulate mucus hydrogel structure, and that polymer\u2013mucus interactions can be described using a thermodynamic model based on Flory\u2013Huggins solution theory. We found that both dietary and therapeutic polymers dramatically compressed murine colonic mucus ex vivo and in vivo. This behavior depended strongly on both polymer concentration and molecular weight, in agreement with the predictions of our thermodynamic model. Moreover, exposure to polymer-rich luminal fluid from germ-free mice strongly compressed the mucus hydrogel, whereas exposure to luminal fluid from specific-pathogen-free mice\u2014whose microbiota degrade gut polymers\u2014did not; this suggests that gut microbes modulate mucus structure by degrading polymers. These findings highlight the role of mucus as a responsive biomaterial, and reveal a mechanism of mucus restructuring that must be integrated into the design and interpretation of studies involving therapeutic polymers, dietary fibers, and fiber-degrading gut microbes.", "doi": "10.1073/pnas.1602789113", "pmcid": "PMC4932961", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2016-06-28", "series_number": "26", "volume": "113", "issue": "26", "pages": "7041-7046" } ]