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Nahant Collection Related: NCBI ProjectPhage GenomesPhage Genome Plots [download pdf] – Talk)


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 HeThe 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. KauffmanPhages 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 populationEnvironmental 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 ironEarth 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 peopleCell 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 communitiesScientific 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] #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 populationApplied 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 bacterioplanktonThe 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 lobstersDiseases 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.