Microbiome Initiative Publications

Journal Publications

Cheng, A.G., Ho, P., Aranda-Díaz, A., Jain, S., Yu, F.B., Meng, X., Wang, M., Lakiviak, M., Nagashima, K., Zhao, A., Murugkar, P., Patil, A., Atabakhsh, K., Weakley, A., Yan, J., Brumbaugh, A.R., Higginbottom, S., Dimas, A., Shiver, A.L., Deutschbauer, A., Neff, N., Sonnenburg, J.L., Huang, K.C., Fischbach, M.A. (2022) Design, construction, and in vivo augmentation of a complex gut microbiome. Cell. September 15, 2022. Volume 185, Issue 19, Pages 3617-3636.e19, DOI:10.1016/j.cell.2022.08.003. PMID: 36070752.

Olm, M.R., Dahan, D., Carter, M.M., Merrill, B.D., Yu, F.B., Jain, S., Meng, X., Tripathi, S., Wastyk, H., Neff, N., Holmes, S., Sonnenburg, E.D., Jha, A.R., Sonnenburg, J.L. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles, Science. 2022 June 9. Volume 376, Issue 6598, Pages 1220-1223. DOI: 10.1126/science.abj2972.

Guthrie, L., Spencer, S.P., Perelman, D., Treuren, W.V., Han, S., Yu, F.B., Sonnenburg, E.D., Fischbach, M.A., Meyer, T.W., Sonnenburg, J.L. (2022) Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes. Cell Host Microbe. Volume 30, Issue 6, Pages 863-874.e4. 10.1016/j.chom.2022.05.003. PMID: 35643079.

Wong, E.O., Brownlie, E.J.E., Ng, K.M., Kathirgamanathan, S., Yu, F.B., Merrill, B.D., Huang, K.C., Martin, A., Tropini, C., Navarre, W.W. (2022) The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut. MBio 10.1128/mBio.02949-21. PMID: 35266814.

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) Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota. Cell Host Microbe. Volume 30, Issue 2, Pages 260-272.e5. 10.1016/j.chom.2021.12.008. PMID: 35051349.

Lam, K.N., Spanogiannopoulos, P., Soto-Perez, P., Alexander, M., Nalley, M.J., Bisanz, J.E., Yu, F.B., and Turnbaugh, P.J. Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome. Cell Reports, November 2, 2021. Volume 37, Issue 5, 109930, DOI: 10.1016/j.celrep.2021.109930.

Vasquez, K.S., Willis, L., Cira, N.J., Ng, K.M., Pedro, M.F., Aranda-Díaz, A., Rajendram, M., Yu, F.B., Higginbottom, S.K., Neff, N., Sherlock, G., Xavier, K.B., Quake, S.R., Sonnenburg, J.L., Good, B.H., Huang, K.C. (2021) Quantifying rapid bacterial evolution and transmission within the mouse intestine, Cell Host & Microbe. doi.org/10.1016/j.chom.2021.08.003

Wastyk, H.C., Fragiadakis, G.K., Perelman, D., Dahan, D., Merrill, B.D., Yu, F.B., Topf, M., Gonzalez, C.G., Treuren, W.V., Han, S., Robinson, J.L., Elias, J.E., Sonnenburg, E.D., Gardner, C.D., Sonnenburg, J.L. Gut-microbiota-targeted diets modulate human immune status,
Cell, July 6, 2021. Volume 184, Issue 16, Pages 4137-4153.e14, DOI: 10.1016/j.cell.2021.06.019.

West PT, Peters SL, Olm MR, Yu FB, Gause H, Lou YC, Firek BA, Baker R, Johnson AD, Morowitz MJ, Hettich RL, Banfield JF. Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics. Microbiome. 2021 Jun 21;9(1):142. DOI: 10.1186/s40168-021-01085-y. PMID: 34154658.

Cesar, S., Anjur-Dietrich, M., Yu, B., Li, E., Rojas, E., Neff, N., Cooper, T.F., and Huang, K.C. (2020) Bacterial Evolution in High-Osmolarity Environments. MBio 11. 10.1128/mBio.01191-20. PMID: 32753494.

Bisanz, J.E., Soto-Perez, P., Noecker, C., Aksenov, A.A., Lam, K.N., Kenney, G.E., Bess, E.N., Haiser, H.J., Kyaw, T.S., Yu, F.B., Rekdal, V.M., Ha, C.W.Y., Devkota, S., Balskus, E.P., Dorrestein, P.C., Allen-Vercoe, E., and Turnbaugh, P.J. (2020) A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria. Cell Host Microbe. 10.1016/j.chom.2020.04.006. PMID: 32348781.

Ng, K.M., Aranda-Díaz, A., Tropini, C., Frankel, M.R., Van Treuren, W., O’Laughlin, C.T., Merrill, B.D., Yu, F.B., Pruss, K.M., Oliveira, R.A., Higginbottom, S.K., Neff, N.F., Fischbach, M.A., Xavier, K.B., Sonnenburg, J.L., and Huang, K.C. (2019) Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs. Cell Host Microbe 26: 650-665.e654. 10.1016/j.chom.2019.10.011. PMID: 31726029.


Jin., X., Yu, F.B., Yan, J., Weakley, A., Pollard, K.S. (2022) Microcosm cultures of a complex synthetic community reveal ecology and genetics of gut microbial organization. bioRxiv. DOI: 10.1101/2022.09.13.507837