Herptile Microbiomes

Research

Reptiles and amphibians are among the most threatened species on the planet, and an increasing number of their species must be managed in captive breeding programs. Understanding the biodiversity and function of microbes that are present in the digestive tracts of reptiles and amphibians is critical for insight into their role in host health. Early research suggests that the filamentous fungus Basidiobolus is an important member of reptile and amphibian gut microbiomes, and that this fungus influences what types of bacteria are present in the digestive tract. Genomic sequencing of Basidiobolus shows that genes have been transferred to the fungus from the gut bacteria. This transfer of genes between bacteria and fungi results in novel metabolism in the fungus that we propose plays important roles in regulating the reptile/amphibian host’s immune system, iron metabolism, and chemical communication with the gut bacteria. Below you will find a list of publications resulting from past research in this system.

2024

Lluvia Vargas-Gastélum, Alexander S Romer, Marjan Ghotbi, Jason W Dallas, N Reed Alexander, Kylie C Moe, Kerry L McPhail, George F Neuhaus, Leila Shadmani, Joseph W Spatafora, Jason E Stajich, Javier F Tabima, Donald M Walker
mSphere  ·  13 Feb 2024

2022

Aubree J. Hill, Matthew Grisnik, Donald M. Walker
Microbial Ecology  ·  01 Nov 2022

2021

Yuanning Li, Jacob L. Steenwyk, Ying Chang, Yan Wang, Timothy Y. James, Jason E. Stajich, Joseph W. Spatafora, Marizeth Groenewald, Casey W. Dunn, Chris Todd Hittinger, Xing-Xing Shen, Antonis Rokas
Current Biology  ·  06 Apr 2021
Ying Chang, D’Ann Rochon, Satoshi Sekimoto, Yan Wang, Mansi Chovatia, Laura Sandor, Asaf Salamov, Igor V. Grigoriev, Jason E. Stajich, Joseph W. Spatafora
Scientific Reports  ·  05 Feb 2021

2020

Javier F Tabima, Ian A Trautman, Ying Chang, Yan Wang, Stephen Mondo, Alan Kuo, Asaf Salamov, Igor V Grigoriev, Jason E Stajich, Joseph W Spatafora
G3 Genes|Genomes|Genetics  ·  01 Sep 2020
Alan K. Jarmusch, Mingxun Wang, Christine M. Aceves, Rohit S. Advani, Shaden Aguirre, Alexander A. Aksenov, Gajender Aleti, Allegra T. Aron, Anelize Bauermeister, Sanjana Bolleddu, Amina Bouslimani, Andres Mauricio Caraballo Rodriguez, Rama Chaar, Roxana Coras, Emmanuel O. Elijah, Madeleine Ernst, Julia M. Gauglitz, Emily C. Gentry, Makhai Husband, Scott A. Jarmusch, Kenneth L. Jones, Zdenek Kamenik, Audrey Le Gouellec, Aileen Lu, Laura-Isobel McCall, Kerry L. McPhail, Michael J. Meehan, Alexey V. Melnik, Riya C. Menezes, Yessica Alejandra Montoya Giraldo, Ngoc Hung Nguyen, Louis Felix Nothias, Mélissa Nothias-Esposito, Morgan Panitchpakdi, Daniel Petras, Robert A. Quinn, Nicole Sikora, Justin J. J. van der Hooft, Fernando Vargas, Alison Vrbanac, Kelly C. Weldon, Rob Knight, Nuno Bandeira, Pieter C. Dorrestein
Nature Methods  ·  17 Aug 2020
Allegra T. Aron, Emily C. Gentry, Kerry L. McPhail, Louis-Félix Nothias, Mélissa Nothias-Esposito, Amina Bouslimani, Daniel Petras, Julia M. Gauglitz, Nicole Sikora, Fernando Vargas, Justin J. J. van der Hooft, Madeleine Ernst, Kyo Bin Kang, Christine M. Aceves, Andrés Mauricio Caraballo-Rodríguez, Irina Koester, Kelly C. Weldon, Samuel Bertrand, Catherine Roullier, Kunyang Sun, Richard M. Tehan, Cristopher A. Boya P., Martin H. Christian, Marcelino Gutiérrez, Aldo Moreno Ulloa, Javier Andres Tejeda Mora, Randy Mojica-Flores, Johant Lakey-Beitia, Victor Vásquez-Chaves, Yilue Zhang, Angela I. Calderón, Nicole Tayler, Robert A. Keyzers, Fidele Tugizimana, Nombuso Ndlovu, Alexander A. Aksenov, Alan K. Jarmusch, Robin Schmid, Andrew W. Truman, Nuno Bandeira, Mingxun Wang, Pieter C. Dorrestein
Nature Protocols  ·  13 May 2020

2019

Donald M. Walker, Aubree J. Hill, Molly A. Albecker, Michael W. McCoy, Matthew Grisnik, Alexander Romer, Alejandro Grajal-Puche, Carlos Camp, Crystal Kelehear, Jessica Wooten, Justin Rheubert, Sean P. Graham
Microbial Ecology  ·  04 Dec 2019
Donald M. Walker, Jacob E. Leys, Matthew Grisnik, Alejandro Grajal-Puche, Christopher M. Murray, Matthew C. Allender
The ISME Journal  ·  07 May 2019

2018

Donald M Walker, Christopher M Murray, Doug Talbert, Paul Tinker, Sean P Graham, Thomas W Crowther
FEMS Microbiology Ecology  ·  20 Sep 2018

2017

Aubree J. Hill, Jacob E. Leys, Danny Bryan, Fantasia M. Erdman, Katherine S. Malone, Gabrielle N. Russell, Roger D. Applegate, Heather Fenton, Kevin Niedringhaus, Andrew N. Miller, Matthew C. Allender, Donald M. Walker
EcoHealth  ·  13 Nov 2017
Joseph W. Spatafora, Ying Chang, Gerald L. Benny, Katy Lazarus, Matthew E. Smith, Mary L. Berbee, Gregory Bonito, Nicolas Corradi, Igor Grigoriev, Andrii Gryganskyi, Timothy Y. James, Kerry O’Donnell, Robert W. Roberson, Thomas N. Taylor, Jessie Uehling, Rytas Vilgalys, Merlin M. White, Jason E. Stajich
Mycologia  ·  20 Jan 2017

2013

Kathryn E. Bushley, Rajani Raja, Pankaj Jaiswal, Jason S. Cumbie, Mariko Nonogaki, Alexander E. Boyd, C. Alisha Owensby, Brian J. Knaus, Justin Elser, Daniel Miller, Yanming Di, Kerry L. McPhail, Joseph W. Spatafora
PLoS Genetics  ·  20 Jun 2013