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Nahant Collection Related: NCBI Project – Phage Genomes – Phage Genome Plots [download pdf] – Talk)
Preprints
2024 | Charmaine C.M. Yung, Rachel L. Kelly, Kathryn M Kauffman, Brady Cunningham, Amy Zimmerman, Alexandra Worden, Seth Greeley John. Iron limitation differentially affects viral replication in key marine microbes. [bioRxiv July 22, 2024]. #Vibrio #Phages
Peer reviewed
2023 | Jonathon Baker, Jessica Mark Welch, Kathryn M. Kauffman, Jeffrey McLean, Xuesong He. The oral microbiome: diversity, biogeography, and human health. Nature Reviews Microbiology Sep 12, 2023] #Review
2023 | Cole B. Matrishin, Elaine M. Haase, Floyd E. Dewhirst, Jessica L. Mark Welch, Fabiola Miranda-Sanchez, Donald C. MacFarland, Kathryn M. Kauffman. Phages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis. Microbiome July 25, 2023 [bioRxiv Dec 31, 2022]. #Porphyromonas #Pg #Phages [associated dataset at zenodo]
2022 | Damien Piel, Maxime Bruto, Yannick Labreuche, Francois Blanquart, Sabine Chenivesse, Sophie Lepanse, Adèle James, Rubén Barcia-Cruz, Javier Dubert, Bruno Petton, Erica Lieberman, K. Mathias Wegner, Fatima A. Hussain, Kathryn M. Kauffman, Martin F. Polz, David Bikard, Sylvain Gandon, Frédérique Le Roux. Phage-host coevolution in natural populations . Nature Microbiology June 27, 2022 [bioRxiv May 6, 2021]. #Vibrio #Phages
2022 | Kathryn M. Kauffman*, William K. Chang*, Julia M. Brown, Fatima Aysha Hussain, Joy Y. Yang, Martin Polz, Libusha Kelly. Resolving the structure of phage-bacteria interactions in the context of natural diversity. Nature Communications January 18, 2022 [biorxiv June 28, 2021]. #NahantCollection #Vibrio #Phages
2021 | Fatima Aysha Hussain*, Javier Dubert*, Joseph Elsherbini, Mikayla Murphy, David VanInsberghe, Philip Arevalo, Kathryn Kauffman, Bruno Kotska Rodino-Janeiro, Martin Polz. Rapid evolutionary turnover of mobile genetic elements drives microbial resistance to viruses Science October 22, 2021 [biorxiv March 28, 2021]. See related Perspective article by Meaden & Fineran, here. #NahantCollection #Vibrio #Phages
2021 | Joy Y. Yang, Wenwen Fang, Fabiola Miranda-Sanchez, Julia M. Brown, Kathryn M. Kauffman, Chantel M. Acevero, David P. Bartel, Martin F. Polz, Libusha Kelly. Degradation of host translational machinery drives tRNA acquisition in viruses. Cell Systems. #NahantCollection #Vibrio #Phages
2020 | Fuqing Wu, Jianbo Zhang, Amy Xiao, Xiaoqiong Gu, Wei Lin Lee, Federica Armas, Kathryn Kauffman, William Hanage, Mariana Matus, Newsha Ghaeli, Noriko Endo, Claire Duvallet, Mathilde Poyet, Katya Moniz, Alex D. Washburne, Timothy B. Erickson, Peter R. Chai, Janelle Thompson, Eric J. Alm. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems 5(4:e00614-20). #Humans #Viruses
2020 | Paul C. Kirchberger, Fabini D. Orata, Tania Nasreen, Kathryn M. Kauffman, Rebecca J. Case, Martin F. Polz and Yan Boucher. Culture-independent tracking of Vibrio cholerae lineages reveals complex spatiotemporal dynamics in a natural population. Environmental Microbiology. #Vibrio
2019 | Ruifeng Zhang, Rachel L. Kelly, Kathryn M. Kauffman, Amber K. Reid, Jonathan M. Lauderdale, Michael J. Follows, and Seth G. John. Growth of marine Vibrio in oligotrophic environments is not stimulated by the addition of inorganic iron. Earth and Planetary Science Letters (516: 148-155). #Vibrio
2019 | Shijie Zhao, Tami D. Lieberman, Mathilde Poyet, Kathryn M. Kauffman, Sean M. Gibbons, Mathieu Groussin, Ramnik J. Xavier, Eric J. Alm. Adaptive evolution within the gut microbiomes of healthy people. Cell Host & Microbe 25(5: 656-667). #Prophages #Humans
2018 | Kathryn M. Kauffman, Fatima A. Hussain, Joy Yang, Phil Arevalo, Julia M. Brown, William K. Chang, David VanInsberghe, Joseph Elsherbini, Radhey S. Sharma, Michael B. Cutler, Libusha Kelly, Martin F. Polz. A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature, 554(118). #NahantCollection #Vibrio #Phages
2018 | Kathryn M. Kauffman*, Julia M. Brown*, Radhey S. Sharma, David VanInsberghe, Joseph Elsherbini, Martin Polz, Libusha Kelly. Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses. Scientific Data, 5(180114). * = authors contributed equally #NahantCollection #Vibrio #Phages
2018 | Antonio M. Martin-Platero*, Brian Cleary*, Kathryn M. Kauffman, Sarah P. Preheim, Dennis J. McGillicuddy, Eric J. Alm, Martin F. Polz. High resolution time series reveals cohesive but short-lived communities in coastal plankton. Nature Communications, 9(266). #NahantCollection #Vibrio #Phages
2018 | Daniel Castillo, Kathryn Kauffman, Fatima Hussain, Panos Kalatzis, Nanna Rørbo, Martin Polz, Mathias Middelboe. Widespread distribution of prophage-encoded virulence factors in marine Vibrio communities. Scientific Reports 8(9973). #Vibrio #Prophages
2018 | Yan-Jiun Lee, Nan Dai, Shannon E. Walsh, Stephanie Müller, Morgan E. Fraser, Kathryn M. Kauffman, Chudi Guan, Ivan R. Corrêa and Peter R. Weigele. Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses. PNAS, 115(14). #NahantCollection #Vibrio #Phages
2018 | Kathryn M. Kauffman, Martin F. Polz. Streamlining standard bacteriophage methods for higher throughput. MethodsX, 5(159-172). [also available as protocols on protocols.io] #Methods #Phages
2017 | David J. Burks, Stephen Norris, Kathryn M. Kauffman, Abigail Joy, Philip Arevalo, Rajeev K. Azad, Hans Wildschutte. Environmental vibrios represent a source of antagonistic compounds that inhibit pathogenic Vibrio cholera and Vibrio parahaemolyticus strains. MicrobiologyOpen, 6(5: e504). #NahantCollection #Vibrio
2016 | Paul C. Kirchberger, Fabini D. Orata, E. Jed Barlow, Kathryn M. Kauffman, Rebecca J. Case, Martin F. Polz, Yan Boucher. A small number of phylogenetically distinct clonal complexes dominate a coastal Vibrio cholerae population. Applied and Environmental Microbiology. #Vibrio
2012 | Gitta Szabo, Sarah P. Preheim, Kathryn M. Kauffman, Lawrence A. David, Jesse Shapiro, Eric J. Alm, and Martin F. Polz. Reproducibility of Vibrionaceae population structure in coastal bacterioplankton. The ISME Journal 7(3: 509-519). #Vibrio
2011 | Seth G. John, Carolina B. Mendez, Li Deng, Bonnie Poulos, Anne Kathryn M. Kauffman, Suzanne Kern, Jennifer Brum, Martin F. Polz, Edward A. Boyle, and Matthew B. Sullivan. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environmental Microbiology Reports 3(2: 195-202). #Methods #Phages #Viruses
2007 | Megan M. Montgomery-Fullerton, Roland A. Cooper, Kathryn M. Kauffman, Jeffrey D. Shields, and Robert E. Ratzlaff. Detection of Panulirus argus Virus 1 in Caribbean spiny lobsters. Diseases of Aquatic Organisms 76(1: 1-6). #Viruses
non-Peer Reviewed
2020 | Jessica Sacher, Kathryn Kauffman. Phages to Treat Secondary Bacterial Infections in COVID-19 Patients? Capsid & Tail, (69) March 29, 2020.
