Publications by authors named "Matthew B Sullivan"

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Glacier ice archives nearly 15,000-year-old microbes and phages.
Zhi-Ping Zhong, Funing Tian, Simon Roux, M Consuelo Gazitúa, Natalie E Solonenko, Yueh-Fen Li, Mary E Davis, James L Van Etten, Ellen Mosley-Thompson, Virginia I Rich

Microbiome· July 2021

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Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study.
Dae-Wook Kang, James B Adams, Ann C Gregory, Thomas Borody, Lauren Chittick, Alessio Fasano, Alexander Khoruts, Elizabeth Geis, Juan Maldonado, Sharon McDonough-Means

January 2017

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STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies.
Julia M Kelliher, Chloe Mirzayi, Sarah R Bordenstein, Aaron Oliver, Christina A Kellogg, Matthew B Sullivan

Nat Microbiol· December 2025

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Phage resistance mutations in a marine bacterium impact biogeochemically relevant cellular processes.
Marion Urvoy, Cristina Howard-Varona, Carlos Owusu-Ansah, Andrew J Stai, John A Bouranis, Matthew B Sullivan

Nat Microbiol· December 2025

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Seasonal enhancement of the viral shunt catalyzes a subsurface oxygen maximum in the Sargasso Sea.
Naomi E Gilbert, Daniel Muratore, Camelia Shopen Gochev, Gary R LeCleir, Shelby M Cagle, Matthew B Sullivan

Nat Commun· December 2025

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Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.
Gareth Trubl, Simon Roux, Mikayla A Borton, Arvind Varsani, Yueh-Fen Li, Matthew B Sullivan

Nat Commun· December 2025

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Machine learning enables scalable and systematic hierarchical virus taxonomy.
Benjamin Bolduc, Olivier Zablocki, Dann Turner, Ho Bin Jang, Jiarong Guo, Matthew B Sullivan

Nat Biotechnol· December 2025

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Precision Prediction of Microbial Ecosystem Impact on Host Metabolism Using Genome-Resolved Metagenomics.
Mohamed Mohssen, Ahmed A Zayed, Kristina A Kigerl, Jingjie Du, Garrett J Smith, Matthew B Sullivan

bioRxiv· November 2025

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CLAE: A High-Fidelity Nanopore Sequencing Strategy for Read-Level Viral Variant Detection and Environmental RNA Virus Discovery.
Hannah Yu, Sarah Golconda, Ga-Eun Lee, Dantong Xue, Guillermo Domínguez-Huerta, Matthew B Sullivan

Adv Sci (Weinh)· November 2025

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Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking.
Rokaiya Nurani Shatadru, Natalie E Solonenko, Christine L Sun, Matthew B Sullivan

PLoS Biol· November 2025

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Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences.
Rokaiya Nurani Shatadru, Natalie E Solonenko, Christine L Sun, Matthew B Sullivan

bioRxiv· September 2025

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The cervicovaginal microbiome of pregnant people living with HIV on antiretroviral therapy in the Democratic Republic of Congo: A Pilot Study and Global Meta-analysis.
Kimberley S Ndlovu, Ricardo R Pavan, Jacqueline Corry, Ann C Gregory, Samia Mahamed, Matthew B Sullivan

bioRxiv· August 2025

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Disruption of The Spinal Cord-Gut Axis Alters Gut Microbial Dynamics and Carbohydrate Cross-feeding.
Mohamed Mohssen, Ahmed A Zayed, Kristina A Kigerl, Jingjie Du, Garrett J Smith, Matthew B Sullivan

bioRxiv· July 2025

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Virocell resource manipulation under nutrient limitation.
Morgan M Lindback, Cristina Howard-Varona, Jane Fudyma, Malak Tfaily, Matthew B Sullivan

mSystems· July 2025

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Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al.
Marissa R Gittrich, Courtney M Sanderson, James M Wainaina, Cara M Noel, Jonathan E Leopold, Matthew B Sullivan

PLoS One· May 2025

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Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.
Julia M Kelliher, Mashael Aljumaah, Sarah R Bordenstein, J Rodney Brister, Patrick S G Chain, Matthew B Sullivan

Environ Microbiome· April 2025

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Unveiling plasmid diversity and functionality in pristine groundwater.
Olga María Pérez-Carrascal, Akbar Adjie Pratama, Matthew B Sullivan, Kirsten Küsel

Environ Microbiome· April 2025

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A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry.
Zhen Li, William J Riley, Gianna L Marschmann, Ulas Karaoz, Ian A Shirley, Matthew B Sullivan

Nat Commun· March 2025

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Virocell Necromass Provides Limited Plant Nitrogen and Elicits Rhizosphere Metabolites That Affect Phage Dynamics.
Vlastimil Novak, Michelle C M van Winden, Thomas V Harwood, Rachel Neurath, Suzanne M Kosina, Matthew B Sullivan

Plant Cell Environ· March 2025

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Infection and Genomic Properties of Single- and Double-Stranded DNA Phages.
Cristina Howard-Varona, Natalie E Solonenko, Marie Burris, Marion Urvoy, Courtney M Sanderson, Matthew B Sullivan

Viruses· March 2025

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A functional microbiome catalogue crowdsourced from North American rivers.
Mikayla A Borton, Bridget B McGivern, Kathryn R Willi, Ben J Woodcroft, Annika C Mosier, Matthew B Sullivan

Nature· January 2025

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Polyphenol rewiring of the microbiome reduces methane emissions.
Bridget B McGivern, Jared B Ellenbogen, David W Hoyt, John A Bouranis, Brooke P Stemple, Matthew B Sullivan

ISME J· January 2025

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Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.
Viviana Freire-Zapata, Hannah Holland-Moritz, Dylan R Cronin, Sam Aroney, Derek A Smith, Matthew B Sullivan

Nat Microbiol· November 2024

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Polyphenol rewiring of the microbiome reduces methane emissions.
Bridget B McGivern, Jared B Ellenbogen, David W Hoyt, John A Bouranis, Brooke P Stemple, Matthew B Sullivan

bioRxiv· October 2024

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Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals.
Thomas W Crowther, Rino Rappuoli, Cinzia Corinaldesi, Roberto Danovaro, Timothy J Donohue, Matthew B Sullivan

Cell· September 2024

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Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.
Funing Tian, James M Wainaina, Cristina Howard-Varona, Guillermo Domínguez-Huerta, Benjamin Bolduc, Matthew B Sullivan

Microbiome· August 2024

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Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient.
Christine L Sun, Akbar Adjie Pratama, Maria Consuelo Gazitúa, Dylan Cronin, Bridget B McGivern, Matthew B Sullivan

Environ Microbiol· July 2024

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