Publications These scientific publications are based on research from GutWorks. Metabolic rearrangement enables adaptation of microbial growth rate to temperature shifts.Knapp, B.D., Willis, L., Gonzalez, C., et al. Nat Microbiol 10(1), 185-201 (2025) https://doi.org/10.1038/s41564-024-01841-4 Improved mouse models of the small intestine microbiota using region-specific sampling from humans.Culver, R.N., Spencer, S.P., Violette, A., et al. bioRxiv [Preprint] 2024.04.24.590999 (2024) https://doi.org/10.1101/2024.04.24.590999 Pubmed Central An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity.Ryan, D., Bornet, E., Prezza, G., et al. Nat Microbiol 9(4), 1130-1144 (2024) https://doi.org/10.1038/s41564-024-01642-9 Pubmed Central Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction.Tripathi, S., Voogdt, C.G.P., Bassler, S.O., et al. Cell Rep 43(1), 113517 (2024) https://doi.org/10.1016/j.celrep.2023.113517 Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics.Voogdt, C.G.P., Tripathi, S., Bassler, S.O., et al. Cell Rep 43(1), 113519 (2024)https://doi.org/10.1016/j.celrep.2023.113519 Simvastatin induces human gut bacterial cell surface genes.Escalante, V., Nayak, R.R., Noecker, C., et al. Mol Microbiol 122(3), 372-386 (2024)https://doi.org/10.1111/mmi.15151 Resource competition predicts assembly of gut bacterial communities in vitro.Ho, P.Y., Nguyen, T.H., Sanchez, J.M., et al. Nat Microbiol 9(4),1036-1048 (2024)https://doi.org/10.1038/s41564-024-01625-w Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance.Huang, Y.Y., Price, M.N., Hung, A., et al. Nat Commun 15(1), 6618 (2024)https://doi.org/10.1038/s41467-024-50124-3 Pubmed Central Comprehensive double-mutant analysis of the Bacillus subtilis envelope using double-CRISPRi.Koo, B.M., Todor, H., Sun, J., et al.bioRxiv [Preprint] 2024.08.14.608006 (2024)https://doi.org/10.1101/2024.08.14.608006Pubmed Central Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.Lopez, J.A., McKeithen-Mead, S., Shi, H., et al. bioRxiv [Preprint] 2024.09.27.614587 (2024)https://doi.org/10.1101/2024.09.27.614587Pubmed Central A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions.Shiver, A.L., Sun, J., Culver, R., et al. bioRxiv [Preprint] 2023.08.29.555234 (2023)https://doi.org/10.1101/2023.08.29.555234 Pubmed Central Within-host evolution of the gut microbiome.Dapa, T., Wong, D.P., Vasquez, K.S., et al. Curr Opin Microbiol 71, 102258 (2023)https://doi.org/10.1016/j.mib.2022.102258 Pubmed Central Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities.Goldman, D.A., Xue, K.S., Parrott, A.B., et al.bioRxiv [Preprint] 11:2023.11.29.569120 (2023)https://doi.org/10.1101/2023.11.29.569120 Pubmed Central Modulation of antibiotic effects on microbial communities by resource competition.Newton, D.P., Ho, P.Y., Huang. K.C. Nat Commun 14(1), 2398 (2023)https://doi.org/10.1038/s41467-023-37895-xPubmed Central The impact of iron and heme availability on the healthy human gut microbiome in vivo and in vitro. Celis, A.I., Relman, D.A., Huang, K.C.Cell Chem Biol 30(1), 110-126.e3 (2023)https://doi.org/10.1016/j.chembiol.2022.12.001 Pubmed Central The impact of iron and heme availability on the healthy human gut microbiome in vivo and in vitro. Celis, A.I., Relman, D.A., Huang, K.C.Cell Chem Biol 30(1), 110-126.e3 (2023)https://doi.org/10.1016/j.chembiol.2022.12.001 Pubmed Central Recent Advancements in Electroporation Technologies: From Bench to Clinic.Campelo, S.N., Huang, P.H., Buie, C.R., Davalos, R.V. Annu Rev Biomed Eng 25, 77-100 (2023)https://doi.org/10.1146/annurev-bioeng-110220-023800 Pubmed Central Profiling the human intestinal environment under physiological conditions.Shalon, D., Culver, R.N., Grembi, J.A., et al. Nature 617(7961), 581-591 (2023)https://doi.org/10.1038/s41586-023-05989-7Pubmed Central Human metabolome variation along the upper intestinal tract. Folz, J., Culver, R.N., Morales, J.M., et al. Nat Metab 5(5):777-788 (2023)https://doi.org/10.1038/s42255-023-00777-z Pubmed Central Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron.Keller, L.J., Nguyen, T.H., Liu, L.J., et al. Nat Chem Biol 19(12):1469-1479 (2023)https://doi.org/10.1038/s41589-023-01357-8 Physiological and regulatory convergence between osmotic and nutrient stress responses in microbes.Brauer, A.M., Shi, H., Levin, P.A., Huang, K.C. Curr Opin Cell Biol 81, 102170 (2023)https://doi.org/10.1016/j.ceb.2023.102170Pubmed Central Previously uncharacterized rectangular bacterial structures in the dolphin mouth.Dudek, N.K., Galaz-Montoya, J.G., Shi, H., et al. Nat Commun 14(1) (2023)https://doi.org/10.1038/s41467-023-37638-y Pubmed Central M-TUBE enables large-volume bacterial gene delivery using a high-throughput microfluidic electroporation platform. Huang, P.H., Chen, S., Shiver, A.L., et al.PLoS Biol 20(9), e3001727 (2022)https://doi.org/10.1371/journal.pbio.3001727 Pubmed Central The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut.Wong, E.O., Brownlie, E.J.E., Ng, K.M., et al. mBio 13(2), e0294921 (2022)https://doi.org/10.1128/mbio.02949-21Pubmed Central Physical properties of the bacterial outer membrane.Sun, J., Rutherford, S.T., Silhavy, T.J., Huang, K.C. Nat Rev Microbiol 20(4), 236-248 (2022)https://doi.org/10.1038/s41579-021-00638-0Pubmed Central Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas.Ho, P.Y., Good, B.H., Huang, K.C. eLife 11, e75168 (2022)https://doi.org/10.7554/eLife.75168 Pubmed Central The Effects of Temperature on Cellular Physiology.Knapp, B.D., Huang, K.C. Annu Rev Biophys 51, 499-526 (2022)https://doi.org/10.1146/annurev-biophys-112221-074832 Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota.Aranda-Díaz, A., Ng, K.M., Thomsen, T., et al.Cell Host Microbe 30(2):260-272.e5 (2022)https://doi.org/10.1016/j.chom.2021.12.008 Pubmed Central Fatty Acid Synthesis Knockdown Promotes Biofilm Wrinkling and Inhibits Sporulation in Bacillus subtilis.Arjes, H.A., Gui, H., Porter, R., et al.mBio 13(5):e0138822 (2022)https://doi.org/10.1128/mbio.01388-22 Pubmed Central Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals.Celis, A.I., Aranda-Díaz, A., Culver, R., et al.iScience 25(4):103907 (2022)https://doi.org/10.1016/j.isci.2022.103907Pubmed Central Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron.Arjes, H.A., Sun, J., Liu, H., et al.BMC Biol 20(1), 285 (2022)https://doi.org/10.1186/s12915-022-01481-2 Pubmed Central Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria.Shiver, A.L., Culver, R., Deutschbauer, A.M., Huang, K.C.Nat Protoc 16(6), 3049-3071 (2021)https://doi.org/10.1038/s41596-021-00531-3 Pubmed Central Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments.Liu, H., Shiver, A.L., Price, M.N., et al. Cell Rep 34(9), 108789 (2021)https://doi.org/10.1016/j.celrep.2021.108789 Pubmed Central Effects of fixation on bacterial cellular dimensions and integrity.Zhu, L., Rajendram, M., Huang, K.C. iScience 24(4), 102348 (2021)https://doi.org/10.1016/j.isci.2021.102348 Pubmed Central Morphological and Transcriptional Responses to CRISPRi Knockdown of Essential Genes in Escherichia coli.Silvis, M.R., Rajendram, M., Shi, H., et al.mBio 12(5), e0256121 (2021)https://doi.org/10.1128/mBio.02561-21Pubmed Central Quantifying rapid bacterial evolution and transmission within the mouse intestine. Vasquez, K.S., Willis, L., Cira, N.J., et al.Cell Host Microbe 29(9), 1454-1468 (2021)https://doi.org/10.1016/j.chom.2021.08.003 Pubmed Central Straightening up for life in a biofilm.Arjes, H.A., Huang, K.C.Proc Natl Acad Sci U S A. 117(50), 31573-31574 (2020) https://doi.org/10.1073/pnas.2021127117 Pubmed Central
