All Publications

  • Resource competition predicts assembly of gut bacterial communities in vitro. Nature microbiology Ho, P., Nguyen, T. H., Sanchez, J. M., DeFelice, B. C., Huang, K. C. 2024


    Microbial community dynamics arise through interspecies interactions, including resource competition, cross-feeding and pH modulation. The individual contributions of these mechanisms to community structure are challenging to untangle. Here we develop a framework to estimate multispecies niche overlaps by combining metabolomics data of individual species, growth measurements in spent media and mathematical models. We applied our framework to an in vitro model system comprising 15 human gut commensals in complex media and showed that a simple model of resource competition accounted for most pairwise interactions. Next, we built a coarse-grained consumer-resource model by grouping metabolomic features depleted by the same set of species and showed that this model predicted the composition of 2-member to 15-member communities with reasonable accuracy. Furthermore, we found that incorporation of cross-feeding and pH-mediated interactions improved model predictions of species coexistence. Our theoretical model and experimental framework can be applied to characterize interspecies interactions in bacterial communities in vitro.

    View details for DOI 10.1038/s41564-024-01625-w

    View details for PubMedID 38486074

  • Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron. Nature chemical biology Keller, L. J., Nguyen, T. H., Liu, L. J., Hurysz, B. M., Lakemeyer, M., Guerra, M., Gelsinger, D. J., Chanin, R., Ngo, N., Lum, K. M., Faucher, F., Ipock, P., Niphakis, M. J., Bhatt, A. S., O'Donoghue, A. J., Huang, K. C., Bogyo, M. 2023


    Serine hydrolases have important roles in signaling and human metabolism, yet little is known about their functions in gut commensal bacteria. Using bioinformatics and chemoproteomics, we identify serine hydrolases in the gut commensal Bacteroides thetaiotaomicron that are specific to the Bacteroidetes phylum. Two are predicted homologs of the human dipeptidyl peptidase 4 (hDPP4), a key enzyme that regulates insulin signaling. Our functional studies reveal that BT4193 is a true homolog of hDPP4 that can be inhibited by FDA-approved type 2 diabetes medications targeting hDPP4, while the other is a misannotated proline-specific triaminopeptidase. We demonstrate that BT4193 is important for envelope integrity and that loss of BT4193 reduces B. thetaiotaomicron fitness during in vitro growth within a diverse community. However, neither function is dependent on BT4193 proteolytic activity, suggesting a scaffolding or signaling function for this bacterial protease.

    View details for DOI 10.1038/s41589-023-01357-8

    View details for PubMedID 37349583

    View details for PubMedCentralID 6108420

  • Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron. BMC biology Arjes, H. A., Sun, J., Liu, H., Nguyen, T. H., Culver, R. N., Celis, A. I., Walton, S. J., Vasquez, K. S., Yu, F. B., Xue, K. S., Newton, D., Zermeno, R., Weglarz, M., Deutschbauer, A., Huang, K. C., Shiver, A. L. 2022; 20 (1): 285


    Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development.Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data.We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.

    View details for DOI 10.1186/s12915-022-01481-2

    View details for PubMedID 36527020

  • Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota. Cell host & microbe Aranda-Díaz, A., Ng, K. M., Thomsen, T., Real-Ramírez, I., Dahan, D., Dittmar, S., Gonzalez, C. G., Chavez, T., Vasquez, K. S., Nguyen, T. H., Yu, F. B., Higginbottom, S. K., Neff, N. F., Elias, J. E., Sonnenburg, J. L., Huang, K. C. 2022


    Efforts to probe the role of the gut microbiota in disease would benefit from a system in which patient-derived bacterial communities can be studied at scale. We addressed this by validating a strategy to propagate phylogenetically complex, diverse, stable, and highly reproducible stool-derived communities in vitro. We generated hundreds of in vitro communities cultured from diverse stool samples in various media; certain media generally preserved inoculum composition, and inocula from different subjects yielded source-specific community compositions. Upon colonization of germ-free mice, community composition was maintained, and the host proteome resembled the host from which the community was derived. Treatment with ciprofloxacin in vivo increased susceptibility to Salmonella invasion in vitro, and the in vitro response to ciprofloxacin was predictive of compositional changes observed in vivo, including the resilience and sensitivity of each Bacteroides species. These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.

    View details for DOI 10.1016/j.chom.2021.12.008

    View details for PubMedID 35051349

  • Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics CELL SYSTEMS Chen, S. Y., Osimiri, L. C., Chevalier, M., Bugaj, L. J., Nguyen, T. H., Greenstein, R. A., Ng, A. H., Stewart-Ornstein, J., Neves, L. T., El-Samad, H. 2020; 11 (4): 336-+


    Gene expression is thought to be affected not only by the concentration of transcription factors (TFs) but also the dynamics of their nuclear translocation. Testing this hypothesis requires direct control of TF dynamics. Here, we engineer CLASP, an optogenetic tool for rapid and tunable translocation of a TF of interest. Using CLASP fused to Crz1, we observe that, for the same integrated concentration of nuclear TF over time, changing input dynamics changes target gene expression: pulsatile inputs yield higher expression than continuous inputs, or vice versa, depending on the target gene. Computational modeling reveals that a dose-response saturating at low TF input can yield higher gene expression for pulsatile versus continuous input, and that multi-state promoter activation can yield the opposite behavior. Our integrated tool development and modeling approach characterize promoter responses to Crz1 nuclear translocation dynamics, extracting quantitative features that may help explain the differential expression of target genes.

    View details for DOI 10.1016/j.cels.2020.08.009

    View details for Web of Science ID 000582118000003

    View details for PubMedID 32898473

    View details for PubMedCentralID PMC7648432

  • De novo design of bioactive protein switches NATURE Langan, R. A., Boyken, S. E., Ng, A. H., Samson, J. A., Dods, G., Westbrook, A. M., Nguyen, T. H., Lajoie, M. J., Chen, Z., Berger, S., Mulligan, V., Dueber, J. E., Novak, W. P., El-Samad, H., Baker, D. 2019; 572 (7768): 205-+


    Allosteric regulation of protein function is widespread in biology, but is challenging for de novo protein design as it requires the explicit design of multiple states with comparable free energies. Here we explore the possibility of designing switchable protein systems de novo, through the modulation of competing inter- and intramolecular interactions. We design a static, five-helix 'cage' with a single interface that can interact either intramolecularly with a terminal 'latch' helix or intermolecularly with a peptide 'key'. Encoded on the latch are functional motifs for binding, degradation or nuclear export that function only when the key displaces the latch from the cage. We describe orthogonal cage-key systems that function in vitro, in yeast and in mammalian cells with up to 40-fold activation of function by key. The ability to design switchable protein functions that are controlled by induced conformational change is a milestone for de novo protein design, and opens up new avenues for synthetic biology and cell engineering.

    View details for DOI 10.1038/s41586-019-1432-8

    View details for Web of Science ID 000479172800039

    View details for PubMedID 31341284

    View details for PubMedCentralID PMC6733528

  • Modular and tunable biological feedback control using a de novo protein switch NATURE Ng, A. H., Nguyen, T. H., Gomez-Schiavon, M., Dods, G., Langan, R. A., Boyken, S. E., Samson, J. A., Waldburger, L. M., Dueber, J. E., Baker, D., El-Samad, H. 2019; 572 (7768): 265-+


    De novo-designed proteins1-3 hold great promise as building blocks for synthetic circuits, and can complement the use of engineered variants of natural proteins4-7. One such designer protein-degronLOCKR, which is based on 'latching orthogonal cage-key proteins' (LOCKR) technology8-is a switch that degrades a protein of interest in vivo upon induction by a genetically encoded small peptide. Here we leverage the plug-and-play nature of degronLOCKR to implement feedback control of endogenous signalling pathways and synthetic gene circuits. We first generate synthetic negative and positive feedback in the yeast mating pathway by fusing degronLOCKR to endogenous signalling molecules, illustrating the ease with which this strategy can be used to rewire complex endogenous pathways. We next evaluate feedback control mediated by degronLOCKR on a synthetic gene circuit9, to quantify the feedback capabilities and operational range of the feedback control circuit. The designed nature of degronLOCKR proteins enables simple and rational modifications to tune feedback behaviour in both the synthetic circuit and the mating pathway. The ability to engineer feedback control into living cells represents an important milestone in achieving the full potential of synthetic biology10,11,12. More broadly, this work demonstrates the large and untapped potential of de novo design of proteins for generating tools that implement complex synthetic functionalities in cells for biotechnological and therapeutic applications.

    View details for DOI 10.1038/s41586-019-1425-7

    View details for Web of Science ID 000479172800051

    View details for PubMedID 31341280

  • Multi-directional dynamic model for traumatic brain injury detection. Journal of neurotrauma Laksari, K. n., Fanton, M. n., Wu, L. n., Nguyen, T. n., Kurt, M. n., Giordano, C. n., Kelly, E. n., O'Keeffe, E. n., Wallace, E. n., Doherty, C. n., Campbell, M. n., Tiernan, S. n., Grant, G. n., Ruan, J. n., Barbat, S. n., Camarillo, D. B. 2019


    Given the worldwide adverse impact of traumatic brain injury (TBI) on the human population, its diagnosis and prediction are of utmost importance. Historically, many studies have focused on associating head kinematics to brain injury risk. Recently, there has been a push towards using computationally expensive finite element (FE) models of the brain to create tissue deformation metrics of brain injury. Here, we develop a new brain injury metric, the Brain Angle Metric (BAM), based on the dynamics of a 3 degree-of-freedom lumped parameter brain model. The brain model is built based on the measured natural frequencies of an FE brain model simulated with live human impact data. We show it can be used to rapidly estimate peak brain strains experienced during head rotational accelerations that cause mild TBI. On our dataset, the simplified model correlates with peak principal FE strain (R2=0.82). Further, coronal and axial brain model displacement correlated with fiber-oriented peak strain in the corpus callosum (R2=0.77). Our proposed injury metric BAM uses the maximum angle predicted by our brain model and is compared against a number of existing rotational and translational kinematic injury metrics on a dataset of head kinematics from 27 clinically diagnosed injuries and 887 non-injuries. We found that BAM performed comparably to peak angular acceleration, translational acceleration, and angular velocity in classifying injury and non-injury events. Metrics which separated time traces into their directional components had improved model deviance to those which combined components into a single time trace magnitude. Our brain model can be used in future work to rapidly approximate the peak strain resulting from mild to moderate head impacts and to quickly assess brain injury risk.

    View details for DOI 10.1089/neu.2018.6340

    View details for PubMedID 31856650

  • MULTI-DIRECTIONAL DYNAMIC INJURY METRIC FOR MILD BRAIN TRAUMA DETECTION Laksari, K., Wu, L., Nguyen, T., Kurt, M., Fanton, M., Ruan, J., Barbat, S., Camarillo, D. MARY ANN LIEBERT, INC. 2017: A47