Selected Publications

Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding

Published in Med, 2021

Access paper here

Recommended citation: Se Song, Jincheng Wang, Cameron Martino, Lingjing Jiang, Wesley Thompson, Liat Shenhav, Daniel McDonald, Clarisse Marotz, Paul Harris, Caroll Hernandez, Nora Henderson, Elizabeth Ackley, Deanna Nardella, Charles Gillihan, Valentina Montacuti, William Schweizer, Melanie Jay, Joan Combellick, Haipeng Sun, Izaskun Garcia-Mantrana, Fernando Raga, Maria Collado, Juana Rivera-Viñas, Maribel Campos-Rivera, Jean Ruiz-Calderon, Rob Knight, Maria Dominguez-Bello, "Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding." Med, 2021. http://dx.doi.org/10.1016/j.medj.2021.05.003

Multi-omics profiling of Earth’s biomes reveals that microbial and metabolite composition are shaped by the environment

Published in bioRxiv, 2021

Use Google Scholar for full citation

Recommended citation: Justin Shaffer, Louis-F{\'e}lix Nothias, Luke Thompson, Jon Sanders, Rodolfo Salido, Sneha Couvillion, Asker Brejnrod, Shi Huang, Franck Lejzerowicz, Holly Lutz, et. al"Multi-omics profiling of Earth’s biomes reveals that microbial and metabolite composition are shaped by the environment." bioRxiv, 2021.

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection

Published in Microbiome, 2021

Use Google Scholar for full citation

Recommended citation: Andre Mu, Daniel McDonald, Alan Jarmusch, Cameron Martino, Caitriona Brennan, Mackenzie Bryant, Gregory Humphrey, Julia Toronczak, Tara Schwartz, Dominic Nguyen, et. al"Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection." Microbiome, 2021.

Visualizing’omic feature rankings and log-ratios using Qurro

Published in NAR genomics and bioinformatics, 2020

Use Google Scholar for full citation

Recommended citation: Marcus Fedarko, Cameron Martino, James Morton, Antonio Gonz{\'a}lez, Gibraan Rahman, Clarisse Marotz, Jeremiah Minich, Eric Allen, Rob Knight, "Visualizing’omic feature rankings and log-ratios using Qurro." NAR genomics and bioinformatics, 2020.

SARS-CoV-2 infection depends on cellular heparan sulfate and ACE2

Published in Cell, 2020

Use Google Scholar for full citation

Recommended citation: Thomas Clausen, Daniel Sandoval, Charlotte Spliid, Jessica Pihl, Hailee Perrett, Chelsea Painter, Anoop Narayanan, Sydney Majowicz, Elizabeth Kwong, Rachael McVicar, et. al"SARS-CoV-2 infection depends on cellular heparan sulfate and ACE2." Cell, 2020.

QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

Published in Current protocols in bioinformatics, 2020

Use Google Scholar for full citation

Recommended citation: Mehrbod Estaki, Lingjing Jiang, Nicholas Bokulich, Daniel McDonald, Antonio Gonz{\'a}lez, Tomasz Kosciolek, Cameron Martino, Qiyun Zhu, Amanda Birmingham, Yoshiki V{\'a}zquez-Baeza, et. al"QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data." Current protocols in bioinformatics, 2020.

Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome

Published in Msystems, 2020

Use Google Scholar for full citation

Recommended citation: Bryn Taylor, Franck Lejzerowicz, Marion Poirel, Justin Shaffer, Lingjing Jiang, Alexander Aksenov, Nicole Litwin, Gregory Humphrey, Cameron Martino, Sandrine Miller-Montgomery, et. al"Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome." Msystems, 2020.

Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing

Published in Environment international, 2020

Use Google Scholar for full citation

Recommended citation: Farnaz Fouladi, Maximilian Bailey, William Patterson, Michael Sioda, Ivory Blakley, Anthony Fodor, Roshonda Jones, Zhanghua Chen, Jeniffer Kim, Frederick Lurmann, et. al"Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing." Environment international, 2020.

Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates

Published in Nature microbiology, 2019

Use Google Scholar for full citation

Recommended citation: Livia Zaramela, Cameron Martino, Frederico Alisson-Silva, Steven Rees, Sandra Diaz, L{\'e}a Chuzel, Mehul Ganatra, Christopher Taron, Patrick Secrest, Cristal Zu{\~n}iga, et. al"Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates." Nature microbiology, 2019.

Engineering the microbiome for animal health and conservation

Published in Experimental Biology and Medicine, 2019

Use Google Scholar for full citation

Recommended citation: Se Jin, Douglas Woodhams, Cameron Martino, Celeste Allaband, Andre Mu, Sandrine Javorschi-Miller-Montgomery, Jan Suchodolski, Rob Knight, "Engineering the microbiome for animal health and conservation." Experimental Biology and Medicine, 2019.

Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates

Published in Nature microbiology, 2019

Use Google Scholar for full citation

Recommended citation: Livia Zaramela, Cameron Martino, Frederico Alisson-Silva, Steven Rees, Sandra Diaz, L{\'e}a Chuzel, Mehul Ganatra, Christopher Taron, Patrick Secrest, Cristal Zu{\~n}iga, et. al"Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates." Nature microbiology, 2019.

Engineering the microbiome for animal health and conservation

Published in Experimental Biology and Medicine, 2019

Use Google Scholar for full citation

Recommended citation: Se Jin, Douglas Woodhams, Cameron Martino, Celeste Allaband, Andre Mu, Sandrine Javorschi-Miller-Montgomery, Jan Suchodolski, Rob Knight, "Engineering the microbiome for animal health and conservation." Experimental Biology and Medicine, 2019.

You can also find all my articles on my Google Scholar profile.