Bay Paul Publications

Recent Publications

Möller L., Vainshtein Y., Meyer B., Neidhardt J., Eren A. M., Sohn K., Rabus R. (2024). Rich microbial and depolymerising diversity in Antarctic krill gut.. Microbiology Spectrum. 12:e0403523. doi: 10.1128/spectrum.04035-23

Yu M. K., Fogarty E. C., Eren A. M. (2024). Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess. Nature Microbiology. 9:830-847. doi: 10.1038/s41564-024-01610-3

McMaken C. M., Gribble K. E. (2024). A free and user-friendly software protocol for the quantification of microfauna swimming behavior. Biotechniques. doi: 10.2144/btn-2024-0001

Rees J. M., Palmer M. A., Gillis J. A. (2024). Fgf signalling is required for gill slit formation in the skate, Leucoraja erinacea. Developmental Biology. 506:85-94. doi: 10.1016/j.ydbio.2023.11.008

Vineis J. H., Reznikoff W. S., Antonopoulos D. A., Koval J., Chang E., Fallon B. R., Paul B. G., Morrison H. G., Sogin M. L. (2024). A novel conjugative transposon carrying an autonomously amplified plasmid. Mbio. 15:e02787-e02723. doi: 10.1128/mbio.02787-23

Doré H., Eisenberg A. R., Junkins E. N., Leventhal G. E., Ganesh A., Cordero O. X., Paul B. G., Valentine D. L., O’Malley M. A., Wilbanks E. G. (2024). Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proceedings Of The National Academy Of Sciences Of The United States Of America. 121:e2316469121. doi: 10.1073/pnas.2316469121

Fogarty E. C., Schechter M. S., Lolans K., Sheahan M. L., Veseli I., Moore R. M., Kiefl E., Moody T., Rice P. A., Yu M. K., Mimee M., Chang E. B., Ruscheweyh H.-J., Sunagawa S., Mclellan S. L., Willis A. D., Comstock L. E., Eren A. M. (2024). A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell. 187:1206-1222.e16. doi: 10.1016/j.cell.2024.01.039

Hu S. K., Anderson R. E., Pachiadaki M. G., Edgcomb V. P., Serres M. H., Sylva S. P., German C. R., Seewald J. S., Lang S. Q., Huber J. A. (2024). Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents. The Isme Journal: Multidisciplinary Journal Of Microbial Ecology. 18:wrae004. doi: 10.1093/ismejo/wrae004

Mullowney M. W., Fiebig A., Schnizlein M. K., McMillin M., Rose A. R., Koval J., Rubin D., Dalal S., Sogin M. L., Chang E. B., Sidebottom A. M., Crosson S. (2024). Microbially catalyzed conjugation of GABA and tyramine to bile acids. Journal Of Bacteriology. 206:e00426-e00423. doi: 10.1128/jb.00426-23

Fiebig A., Schnizlein M. K., Pena-Rivera S., Trigodet F., Dubey A. A., Hennessy M. K., Basu A., Pott S., Dalal S., Rubin D., Sogin M. L., Eren A. M., Chang E. B., Crosson S. (2024). Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. Mbio. 15:e02830-e02823. doi: 10.1128/mbio.02830-23

Little A. S., Younker I. T., Schechter M. S., Bernardino P. N., Méheust R., Stemczynski J., Scorza K., Mullowney M. W., Sharan D., Waligurski E., Smith R., Ramanswamy R., Leiter W., Moran D., McMillin M., Odenwald M. A., Iavarone A. T., Sidebottom A. M., Sundararajan A., Pamer E. G., Eren A. M., Light S. H. (2024). Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Nature Microbiology. 9:55-69. doi: 10.1038/s41564-023-01560-2

Mark Welch D. B., Gould T. J., Olins A. L., Olins D. E. (2023). The transcriptome of acute dehydration in myeloid leukemic cells. Postepy Biochem. doi: 10.18388/pb.2021_507

Arkhipova I. R., Yushenova I. A. (2023). To Be Mobile or Not: The Variety of Reverse Transcriptases and Their Recruitment by Host Genomes. Biochemistry (Moscow). 88:1754-1762. doi: 10.1134/s000629792311007x

Arkhipova I. R., Burns K. H., Chiappinelli K. B., Chuong E. B., Goubert C., Guarné A., Larracuente A. M., Lee E. A., Levin H. L. (2023). Meeting report: transposable elements at the crossroads of evolution, health and disease 2023. Mobile Dna. 14:19. doi: 10.1186/s13100-023-00307-4

Castro S. P., Peredo E. L., Mason O. U., Vineis J., Bowen J. L., Mortazavi B., Ganesh A., Ruff S. E., Paul B. G., Giblin A. E., Cardon Z. G. (2023). Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes. Applied And Environmental Microbiology. 89:e00988-e00923. doi: 10.1128/aem.00988-23

Schrieke H., Duron O., Trouche B., Eren A. M., Reveillaud J. Multiple Wolbachia subpopulations co-occur in single Culex pipiens mosquito organs. doi: 10.21203/rs.3.rs-2179443/v2

Mendonça I. R. W., Theirlynck T., Zettler E. R., Amaral-Zettler L. A., Oliveira M. C. Microbiome changes in a stranding simulation of the holopelagic macroalgae Sargassum natans and Sargassum fluitans. doi: 10.21203/rs.3.rs-2556643/v2

Handa S., Biswas T., Chakraborty J., Paul B. G., Ghosh P. Structural Requirements for Reverse Transcription by a Diversity-generating Retroelement. doi: 10.1101/2023.10.23.563531

Jiang X., Gallager S., Pedrosa Pàmies R., Ruff S. E., Liu Z. Laboratory-Simulated Photoirradiation Reveals Strong Resistance of Primary Macroplastics to Weathering. doi: 10.26434/chemrxiv-2023-gdj7d

Schaible G. A., Jay Z. J., Cliff J., Schulz F., Gauvin C., Goudeau D., Malmstrom R. R., Ruff S. E., Edgcomb V., Hatzenpichler R. Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal. doi: 10.1101/2023.11.27.568837

Rees J. M., Kirk K., Gattoni G., Hockman D., Ritter D. J., Benito-Gutierrez È., Knapik E. W., Crump J. G., Fabian P., Gillis J. A. A pre-vertebrate endodermal origin of calcitonin-producing neuroendocrine cells. doi: 10.1101/2024.02.17.580846

Veseli I., Cooper Z. S., DeMers M. A., Schechter M. S., Miller S., Weber L., Smith C. B., Rodriguez L. T., Schroer W. F., McIlvin M. R., Lopez P. Z., Saito M., Dyhrman S., Eren A. M., Moran M. A., Braakman R. Digital Microbe: A Genome-Informed Data Integration Framework for Collaborative Research on Emerging Model Organisms. doi: 10.1101/2024.01.16.575828

Zhao Y., Zhou R., Xie B., Liu C. Y., Kalski M., Cham C. M., Koval J., Weber C. R., Rubin D. T., Sogin M., Crosson S., Huang J., Fiebig A., Dalal S., Chang E. B., Basu A., Pott S. Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients. doi: 10.1101/2023.11.11.23298309

Chandler T., Guo M., Su Y., Chen J., Wu Y., Liu J., Agashe A., Fischer R. S., Mehta S. B., Kumar A., Baskin T. I., Jamouilĺe V., Liu H., Swaminathan V., Nain A., Oldenbourg R., La Rivère P., Shroff H. Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM). doi: 10.1101/2024.03.09.584243

Shan Y., Lake J., Cham C. M., Zhu M., Kaur D., Ringus D., Fei N., Weber C. R., Spedale M., Theriault B., Dalal S., Rubin D. T., Fiebig A., Crosson S., Lolans K., Comstock L., Eren A. M., Basu A., Pott S., Sogin M., Liu C., Chang E. B. Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases. doi: 10.1101/2023.10.29.564605