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Deep learning reveals functional archetypes in the adult human gut microbiome that underlie interindividual variability and confound disease signals

Meawad, M., Singh, D., Deng, A., Sonthalia, R., Cai, E., Dumeaux, V.

10.1101/2025.01.29.635381 — Posted: 2025-01-29 — Discussion: 2025-12-22

Live biotherapeutic product exhibits similar efficacy and superior engraftment to same donor fecal microbiota transplant for recurrent Clostridioides difficile infection

Bethlehem, L., Bartu, L., Marke, G., Mar, P., Feldman, S., Eggers, J., Ruprecht, C., Britton, G., Aggarwala, V., Bongers, G., Li, Z., Yang, N., Hohmann, E., Mogno, I., Faith, J. J., Grinspan, A.

10.1101/2025.09.08.25335342 — Posted: 2025-09-12 — Discussion: 2025-12-22

Chakraborty, M., Shi, S. M., Porter, I. E., Richard, D. J., Marinov, G. K., Moore, A. A., Blum, J. L. E., Natarajan, A., Jahng, J. W., Wu, J. C., Lu, S. X., Davidson, S. M., Greenleaf, W. J., Saw, N. L., Shamloo, M., Brunet, A., Wyss-Coray, T., Bhatt, A. S.

10.1101/2025.10.03.680371 — Posted: 2025-10-05 — Discussion: 2025-12-22

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Bouras, G., Grigson, S. R., Mirdita, M., Heinzinger, M., Papudeshi, B., Mallawaarachchi, V., Green, R., Kim, R. S., Mihalia, V., Psaltis, A. J., Wormald, P.-J., Vreugde, S., Steinegger, M., Edwards, R. A.

10.1101/2025.08.05.668817 — Posted: 2025-08-06 — Discussion: 2025-10-27

Principles of protein abundance regulation across single cells in a mammalian tissue

Leduc, A., Shipkovenska, G., Xu, Y., Franks, A., Slavov, N.

10.1101/2025.09.17.676955 — Posted: 2025-09-20 — Discussion: 2025-09-21 Single Cell Proteomics

Protein degradation and growth dependent dilution substantially shape mammalian proteomes

Leduc, A., Slavov, N.

10.1101/2025.02.10.637566 — Posted: 2025-02-12 — Discussion: 2025-09-05 Single Cell Proteomics

Uniform bacterial genetic diversity along the guts of mice inoculated with human stool

Wasney, M., Briscoe, L., Wolff, R., Ghezzi, H., Tropini, C., Garud, N. R.

10.1101/2025.01.28.635365 — Posted: 2025-01-29 — Discussion: 2025-06-16

Genomic analysis of cultivated infant microbiomes identifies Bifidobacterium 2'-fucosyllactose utilization can be facilitated by co-existing species

Lou, Y. C., Rubin, B. E., Schoelmerich, M. C., DiMarco, K., Borges, A. L., Rovinsky, R., Song, L., Doudna, J. A., Banfield, J. F.

10.1101/2023.03.10.532136 — Posted: 2023-03-11 — Discussion: 2025-02-26

BMI and BPH correlate with urinary microbiome diversity and lower urinary tract symptoms in men

Bowie, K., Garzotto, M., Orwoll, E., Karstens, L.

10.1101/2023.12.14.571758 — Posted: 2023-12-15 — Discussion: 2025-02-26

Viroid-like colonists of human microbiomes

Zheludev, I. N., Edgar, R. C., Galiano, M. J. L., De la Pena, M., Babaian, A., Bhatt, A. S., Fire, A. Z.

10.1101/2024.01.20.576352 — Posted: 2024-01-21 — Discussion: 2025-02-25