JBPC Publications 2022

Bronikowski, A. M., Meisel, R. P., Biga, P. R., Walters, J. R., Mank, J. E., Larschan, E., Wilkinson, G. S., Valenzuela, N., Conard, A. M., de Magalhaes, J. P., Duan, J. E., Elias, A. E., Gamble, T., Graze, R. M., Gribble, K. E., Kreiling, J. A., & Riddle, N. C. (2022). Sex-specific aging in animals: Perspective and future directions. Aging Cell, 21(2).https://doi.org/10.1111/acel.13542

Chaouni, B., Idrissi Azami, A., Essayeh, S., Arrafiqui, E., Bailal, A., Raoui, S., Amzazi, S., Twaddle, A., El Hamouti, C., Boukhatem, N., Timinouni, M., El Otmani, F., Chahboune, R., Barrijal, S., El Homani, A., Nejjari, C., Zaid, E., Hamamouch, N., Bakkali, F., Amaral-Zettler, L., … Ghazal, H. (2022). Moroccan Lagoon Microbiomes. Water, 14(11), 1715. https://doi.org/10.3390/w14111715

Chitale, P., Lemenze, A., Fogarty, E., Shah, A., Grady, C., Odom-Mabey, A., Johnson, W., Yang, J., Eren, A., Brosch, R., Kumar, P., & Alland, D. (2022). A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome. Nature Communications, 13(1), 7068. https://doi.org/10.1038/s41467-022-34853-x

Crognale, S., Venturi, S., Tassi, F., Simona, R., Cabassi, J., Capecchiacci, F., Bicocchi, G., Vaselli, O., Morrison, H., Sogin, M., & Fazi, S. (2022). Geochemical and microbiological profiles in hydrothermal extreme acidic environments (Pisciarelli Spring, Campi Flegrei, Italy). FEMS Microbiology Ecology. https://doi.org/10.1093/femsec/fiac088

Darras, H., De Souza Araujo, N., Baudry, L., Guiglielmoni, N., Lorite, P., Marbouty, M., Rodriguez, F., Arkhipova, I., Koszul, R., Flot, J.-F., & Aron, S. (2022). Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: Stepping stones towards genomic studies of hybridogenesis and thermal adaptation in desert ants. Peer Community Journal, 2. https://doi.org/10.24072/pcjournal.140

Delmont, T., Gaia, M., Hinsinger, D., Frémont, P., Vanni, C., Fernandez-Guerra, A., Eren, A., Kourlaiev, A., d’Agata, L., Clayssen, Q., Villar, E., Labadie, K., Cruaud, C., Poulain, J., Da Silva, C., Wessner, M., Noel, B., Aury, J.-M., Coordinators, T., … Jaillon, O. (2022). Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean. Cell Genomics, 2(5), 100123. https://doi.org/10.1016/j.xgen.2022.100123

Delmont, T. O., Karlusich, J. J. P., Veseli, I., Fuessel, J., Eren, A. M., Foster, R. A., Bowler, C., Wincker, P., & Pelletier, E. (2022). Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean. Isme Journal, 16(4), 927–936. https://doi.org/10.1038/s41396-021-01135-1

Delmont, T. O., Pierella Karlusich, J. J., Veseli, I., Fuessel, J., Eren, A. M., Foster, R. A., Bowler, C., Wincker, P., & Pelletier, E. (2022). Correction to: Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean. The ISME Journal, 16(4), 1203–1203. https://doi.org/10.1038/s41396-021-01173-9

Gillis, J., Bennett, S., Criswell, K., Rees, J., Sleight, V., Hirschberger, C., Calzarette, D., Kerr, S., & Dasen, J. (2022). Big insight from the little skate: Leucoraja erinacea as a developmental model system. In Emerging Model Systems in Developmental Biology (Vol. 147, pp. 595–630). Elsevier. https://doi.org/10.1016/bs.ctdb.2021.12.016.

Hirschberger, C., & Gillis, J. A. (2022). The pseudobranch of jawed vertebrates is a mandibular arch-derived gill. Development, 149(13). https://doi.org/10.1242/dev.200184

Klasek, S. A., Brock, M. T., Calder, W. J., Morrison, H. G., Weinig, C., & Maïgnien, L. (2022). Spatiotemporal Heterogeneity and Intragenus Variability in Rhizobacterial Associations with Brassica rapa Growth. mSystems, 0(0), e00060-22. https://doi.org/10.1128/msystems.00060-22

Kumar, A., Kerr, L., Shribak, M., Oldenbourg, R., & Patel, N. (2022). Reflecting on the Past and Building the Future of Imaging at MBL: Carrying Forward Shinya Inoué’s Legacy. Microscopy and Microanalysis, 28(S1), 1554–1556. https://doi.org/10.1017/s1431927622006249

Lebeaux, R. M., Madan, J. C., Nguyen, Q. P., Coker, M. O., Dade, E. F., Moroishi, Y., Palys, T. J., Ross, B. D., Pettigrew, M. M., Morrison, H. G., Karagas, M. R., & Hoen, A. G. (2022). Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies. Pediatric Research, 1–10. https://doi.org/10.1038/s41390-022-02104-w

Matute, J., Duan, J., Flak, M., Griebel, P., Tascon-Arcila, J., Doms, S., Hanley, T., Antanaviciute, A., Gundrum, J., Welch, J., Sit, B., Abtahi, S., Fuhler, G., Grootjans, J., Tran, F., Stengel, S., White, J., Krupka, N., Haller, D., … Blumberg, R. (2022). Intelectin-1 binds and alters the localization of the mucus barrier–modifying bacterium Akkermansia muciniphila. Journal of Experimental Medicine, 220(1), e20211938. https://doi.org/10.1084/jem.20211938

McLean, A., Torres‐Morales, J., Dewhirst, F., Borisy, G., & Welch, J. (2022). Site‐tropism of streptococci in the oral microbiome. Molecular Oral Microbiology. https://doi.org/10.1111/omi.12387

Miranda, K., Weigel, B., Fogarty, E., Veseli, I., Giblin, A., Eren, A., & Pfister, C. (2022). The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes. mSystems, e0059222. https://doi.org/10.1128/msystems.00592-22

Moran, M. A., Kujawinski, E. B., Schroer, W. F., Amin, S. A., Bates, N. R., Bertrand, E. M., Braakman, R., Brown, C. T., Covert, M. W., Doney, S. C., Dyhrman, S. T., Edison, A. S., Eren, A. M., Levine, N. M., Li, L., Ross, A. C., Saito, M. A., Santoro, A. E., Segre, D., … Vardi, A. (2022). Microbial metabolites in the marine carbon cycle. Nature Microbiology, 7(4), 508–523. https://doi.org/10.1038/s41564-022-01090-3

Morillo-Lopez, V., Sjaarda, A., Islam, I., Borisy, G., & Mark Welch, J. (2022). Corncob structures in dental plaque reveal microhabitat taxon specificity. Microbiome, 10(1). https://doi.org/10.1186/s40168-022-01323-x

Moroishi, Y., Gui, J., Hoen, A., Morrison, H., Baker, E., Nadeau, K., Li, H., Li, Z., Madan, J., & Karagas, M. (2022). The relationship between the gut microbiome and the risk of respiratory infections among newborns. Communications Medicine, 2(1), 87. https://doi.org/10.1038/s43856-022-00152-1

Moroishi, Y., Gui, J., Nadeau, K. C., Morrison, H. G., Madan, J., & Karagas, M. R. (2022). A prospective study of the infant gut microbiome in relation to vaccine response. Pediatric Research. https://doi.org/10.1038/s41390-022-02154-0

Niu, M., Deng, L., Su, L., Ruff, S., Yang, N., Luo, M., Qi, Q., Li, J., & Wang, F. (2022). Methane supply drives prokaryotic community assembly and network at cold seeps of the South China Sea. Molecular Ecology. https://doi.org/10.1111/mec.16786

Paul, B. G., & Eren, A. M. (2022). Eco-evolutionary significance of domesticated retroelements in microbial genomes. Mobile DNA, 13(1), 6. https://doi.org/10.1186/s13100-022-00262-6

Paul, B., Yushenova, I., & Arkhipova, I. (2022). The Diversity of Reverse Transcriptases. In Retrotransposons and Human Disease (pp. 1–28).

Ramirez-Puebla, S. T., Weigel, B. L., Jack, L., Schlundt, C., Pfister, C. A., & Welch, J. L. M. (2022). Spatial organization of the kelp microbiome at micron scales. Microbiome, 10(1), 52. https://doi.org/10.1186/s40168-022-01235-w

Richter, N., Russell, J. M., Amaral-Zettler, L., DeGroff, W., Raposeiro, P. M., Goncalves, V., de Boer, E. J., Pla-Rabes, S., Hernandez, A., Benavente, M., Ritter, C., Saez, A., Bao, R., Trigo, R. M., Prego, R., & Giralt, S. (2022). Long-term hydroclimate variability in the sub-tropical North Atlantic and anthropogenic impacts on lake ecosystems: A case study from Flores Island, the Azores. Quaternary Science Reviews, 285. https://doi.org/10.1016/j.quascirev.2022.107525

Rinaldi, G., Attenborough, T., Rawlinson, K., & Berriman, M. (2022). Schistosomes go single cell. Nature Reviews Microbiology, 20(12), 705–705. https://doi.org/10.1038/s41579-022-00810-0

Rodriguez, F., & Arkhipova, I. (2022). An overview of best practices for transposable element identification, classification, and annotation in eukaryotic genomes. In Transposable Elements (Vol. 2607, pp. 1–23). Humana Press. https://doi.org/10.1007/978-1-0716-2883-6_1

Rodriguez, F., Yushenova, I. A., DiCorpo, D., & Arkhipova, I. R. (2022). Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-28471-w

Roguet, A., Newton, R., Eren, A., & McLellan, S. (2022). Guts of the urban ecosystem: Microbial ecology of sewer infrastructure. mSystems, e00118–e00122. https://doi.org/10.1128/msystems.00118-22

Ruff, S. E. (2022). Editorial: Microbial Communities and Metabolisms Involved in the Degradation of Cellular and Extracellular Organic Biopolymers. Frontiers in Microbiology, 12, 802619. https://doi.org/10.3389/fmicb.2021.802619

Smith, J. J., Kenny, I. W., Wolff, C., Cray, R., Kumar, A., Sherwood, D. R., & Matus, D. Q. (2022). A light sheet fluorescence microscopy protocol for Caenorhabditis elegans larvae and adults. Frontiers in Cell and Developmental Biology, 10. https://www.frontiersin.org/articles/10.3389/fcell.2022.1012820

Thiruppathy, M., Fabian, P., Gillis, J. A., & Crump, J. G. (2022). Gill developmental program in the teleost mandibular arch. eLIFE, 11. https://doi.org/10.7554/eLife.78170

Trigodet, F., Lolans, K., Fogarty, E., Shaiber, A., Morrison, H. G., Barreiro, L., Jabri, B., & Eren, A. M. (2022). High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes. Molecular Ecology Resources, 22(5), 1786–1802. https://doi.org/10.1111/1755-0998.13588

Vanni, C., Schechter, M. S., Acinas, S. G., Barberan, A., Buttigieg, P. L., Casamayor, E. O., Delmont, T. O., Duarte, C. M., Eren, A. M., Finn, R. D., Kottmann, R., Mitchell, A., Sanchez, P., Siren, K., Steinegger, M., Gloeckner, F. O., & Fernandez-Guerra, A. (2022). Unifying the known and unknown microbial coding sequence space. eLIFE, 11. https://doi.org/10.7554/eLife.67667

Zhang, W., Foo, M., Eren, A. M., & Pan, T. (2022). tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes. Molecular Cell, 82(5), 891–906. https://doi.org/10.1016/j.molcel.2021.12.007

Zhao, S., Zettler, E., Bos, R., Lin, P., Amaral-Zettler, L., & Mincer, T. (2022). Large quantities of small microplastics permeate the surface ocean to abyssal depths in the South Atlantic Gyre. Global Change Biology, 28(9), 2991–3006. https://doi.org/10.1111/gcb.16089