Scientific Literature

New discoveries in the world of microbial ecology are being made every day. See below for a deeper dive into current research being done into the impact of microbiomes on human, animal and ocean health.

Project Publications

Aquarium Viromes: Viromes of Human-Managed Aquatic Systems. Kim Yiseul, William Van Bonn, Tiong G. Aw, and Joan B. Rose, Frontiers in microbiology 2017 8:1231.


Environmental sources of bacteria differentially influence host-associated microbial dynamics. Cesar Cardona, Simon Lax, Peter Larsen, Brent Stephens, Jarrad Hampton-Marcell, Christian F. Edwardson, Christopher Henry, William Van Bonn, and Jack A. Gilbert. Manuscript in review, Microbiome.


Drivers of Microbial Community Dynamics in a Managed Artificial Seawater System. Christian F. Edwardson, Frank Oliaro, Allen La Pointe, William Van Bonn, Angela Kent. American Society of Limnology and Oceanography, Annual Conference 2018, abstract accepted 2017.


Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management. William Van Bonn, Allen LaPointe, Sean M. Gibbons, Angel Frazier, Jarrad Hampton-Marcell, and Jack Gilbert, Zoo Biology 2015  34: 360–367.


Evaluation of Health Parameters in Cownose Rays (Rhinoptera Bonasus) Housed in a Seasonal Touch Pool Habitat Compared with an Off-Exhibit Habitat. James G. Johnson III, Lisa M. Naples, William G. Van Bonn, Angela D. Kent, Mark A. Mitchell, and Matthew C. Allender, Journal of Zoo and Wildlife Medicine 2017 48(4):954-960.

Further Reading

Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish. Victor Schmidt, Marta Gomez-Chiarri, Chelsea, Katherine Smith, and Linda Amaral-Zettler, MSystems 2017 2(6):e00133-17.


Early-life disruption of amphibian microbiota decreases later-life resistance to parasites. Sarah A. Knutie, Christina L. Wilkinson, Kevin D. Kohl, and Jason R. Rohr, Nature communications 2017 8:86.


The environment as a driver of immune and endocrine responses in dolphins (Tursiops truncatus). Patricia A. Fair, Adam M. Schaefer, Dorian S. Houser, Gregory D. Bossart, Tracy A. Romano, Cory D. Champagne, Jeffrey L. Stott, Charles D. Rice, Natasha White, and John S. Reif, PLoS ONE 2017 12:e0176202.


Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean. Amy Apprill, Frontiers in Marine Science 2017 4:222.


Walleye Autochthonous Bacteria as Promising Probiotic Candidates against Flavobacterium columnare. Hamza Seghouani, Carlos-Enrique Garcia-Rangel, Jérémie Füller, Jeff Gauthier, and Nicolas Derome, Frontiers in microbiology 2017 8:1349.


Innate immunity and asthma risk in Amish and Hutterite farm children. Michelle M. Stein, Cara L. Hrusch, Justyna Gozdz, Catherine Igartua, Vadim Pivniouk, Sean E. Murray, Julie G. Ledford, Mauricius Marques dos Santos, Rebecca L. Anderson, Nervana Metwali, Julia W. Neilson, Raina M. Maier, Jack A. Gilbert, Mark Holbreich, Peter S. Thorne, Fernando D. Martinez, Erika von Mutius, Donata Vercelli, Carole Ober, and Anne I. Sperling, New England Journal of Medicine 2016 375(5):411–421.


The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat. Embriette R. Hyde, Jose A. Navas-Molina, Se Jin Song, Jordan G. Kueneman, Gail Ackermann, Cesar Cardona, Gregory Humphrey, Don Boyer, Tom Weaver, Joseph R. Mendelson III, Valerie J. McKenzie, Jack A. Gilbert, and Rob Knight, mSystems 20161(4):e00046-16.


How colonization by microbiota in early life shapes the immune system. Thomas Gensollen, Shankar S. Iyer, Dennis L. Kasper, and Richard S. Blumberg, Science 2016 352(6285):539-544.


Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History. Andrew W. Brooks, Kevin D. Kohl, Robert M. Brucker, Edward J. van Opstal, and Seth R. Bordenstein, PLoS Biology 2016 14(11):e2000225.


Marine mammals harbour unique microbiotas shaped by and yet distinct from the sea. Elisabeth M. Bik, Elizabeth K. Costello, Alexandra D. Switzer, Benjamin J. Callahan, Susan P. Holmes, Randall S. Wells, Kevin P. Carlin, Eric D. Jensen, Stephanie Venn-Watson, and David A. Relman, Nature communications 2016 7:10516.


Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Tommi Vatanen, Aleksandar D. Kostic, Eva d’Hennezel, Heli Siljander, Eric A. Franzosa, Moran Yassour, Raivo Kolde, Hera Vlamakis, Timothy D. Arthur, Anu-Maaria Hämäläinen, Aleksandr Peet, Vallo Tillmann, Raivo Uibo, Sergei Mokurov, Natalya Dorshakova, Jorma Ilonen, Suvi M. Virtanen, Susanne J. Szabo, Jeffrey A. Porter, Harri Lähdesmäki, Curtis Huttenhower, Dirk Gevers, Thomas W. Cullen, Mikael Knip, and Ramnik J. Xavier, Cell 2016 165:842-853.


The geomicrobiology of CO2 geosequestration: a focused review on prokaryotic community responses to field-scale CO2 injection. Andre Mu and John W. Moreau, Frontiers in Microbiology 2015 Apr 9;6:263.


Stable-isotope probing and metagenomics reveal predation by protozoa drives E.coli removal in slow sand filters. S. J. Haig, M. Schirmer, R. D'Amore, J. Gibbs, R. L. Davies, G. Collins, C. Quince, International Society for Microbial Ecology Journal 2015 Mar 17;9(4):797-808.


Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. BoonFei Tan, Charmaine Ng, Jean Pierre Nshimyimana, Lay Leng Loh, Karina Y.-H. Gin, and Janelle R. Thompson, Frontiers in microbiology 2015 6:1027.


Ecology and exploration of the rare biosphere. Michael D. J. Lynch and Josh D. Neufeld, Nature Reviews Microbiology 2015 13:217–229.


Increased Biodiversity in the Environment Improves the Humoral Response of Rats. C. Pi, E. H. Allott, D. Ren, S. Poulton, S. Y. R. Lee, S. Perkins, M. L. Everett, Z. E. Holzknecht, S. S. Lin, and W. Parker, PLoS ONE 2015 10(4): e0120255.


The Earth Microbiome project: successes and aspirations. Jack A. Gilbert, Janet K. Jansson, and Rob Knight, BMC Biology 2014 12:69.


Characterization of the gut microbiota of three commercially valuable warmwater fish species. Andrea M. Larsen, Haitham H. Mohammed, and Covadonga R. Arias, Journal of Applied Microbiology 2014 116: 1396-1404.


Animals in a bacterial world, a new imperative for the life sciences. Margaret McFall-Ngai, Michael G. Hadfield, Thomas C. G. Bosch, Hannah V. Carey, Tomislav Domazet-Lošo, Angela E. Douglas, Nicole Dubilier, Gerard Eberl, Tadashi Fukami, Scott F. Gilbert, Ute Hentschel, Nicole King, Staffan Kjelleberg, Andrew H. Knoll, Natacha Kremer, Sarkis K. Mazmanian, Jessica L. Metcalf, Kenneth Nealson, Naomi E. Pierce, John F. Rawls, Ann Reid, Edward G. Ruby, Mary Rumpho, Jon G. Sanders, Diethard Tautz, and Jennifer J. Wernegreen, Proceedings of the National Academy of Sciences 2013 110(9):3229-3236.


Maintaining health by balancing microbial exposure and prevention of infection: the hygiene hypothesis versus the hypothesis of early immune challenge. A. Kramer, S. Bekeschus, B. M. Bröker, H. Schleibinger, B. Razavi, and O. Assadian, Journal of Hospital Infection 2013 83:S29-S34.


Triclosan Exposure Increases Triclosan Resistance and Influences Taxonomic Composition of Benthic Bacterial Communities. Bradley Drury, John Scott, Emma J. Rosi-Marshall, and John J. Kelly, Environmental Science & Technology 2013 47(15):8923-8930.


Taking Stock of the Human Microbiome and Disease. Michael Balter, Science 2012 Jun 8;336(6086):1246-1247.


The 'hygiene hypothesis' for autoimmune and allergic diseases: an update. H. Okada, C. Kuhn, H. Feillet, and J. F. Bach, Clinical & Experimental Immunology 2010 Apr;160(1):1-9. 


Microbial diversity in the deep sea and the underexplored "rare biosphere". Mitchell L. Sogin, Hilary G. Morrison, Julie A. Huber, David Mark Welch, Susan M. Huse, Phillip R. Neal, Jesus M. Arrieta, and Gerhard J. Herndl, Proceedings of the National Academy of Sciences, USA 2006 103(32):12115-20.


Unseen forces: the influence of bacteria on animal development. Margaret J. McFall-Ngai, Developmental Biology 2002 Feb 1;242(1):1-14.

The Shedd Aquarium Microbiome Project is made possible in part by the generosity of The Grainger Foundation.

The Grainger Foundation