Publications

Google Scholar | Protocols.IO

Non-Reviewed

2021 | 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. bioRxiv June 28, 2021.

2021 | 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. Genetic determinism of phage-bacteria coevolution in natural populations. bioRxiv May 6, 2021.

2020 | Jessica Sacher, Kathryn Kauffman. Phages to Treat Secondary Bacterial Infections in COVID-19 Patients? Capsid & Tail, (69) March 29, 2020.

Peer Reviewed

Nahant Collection Related (more infos: NCBI ProjectPhage GenomesRecorded Talk)

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.

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.

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).

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

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).

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).

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).

Methods

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]

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).

Vibrionaceae dynamics & population structure

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.

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).

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.

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).

Prophages

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).

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).

Animal viruses

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).

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).