All animals exist in intimate associations with communities of microorganisms, which play important roles in animal development and fitness. The most numerically abundant microbial communities associated with vertebrate animals are the assemblages of microbes in the gut, or the gut microbiota. The mechanisms by which animal-associated microbial communities assemble and persist inside the host are poorly understood. Fundamental unanswered questions about the ecology of animal-associated microbial communities include the extent to which these communities are assembled by host selection or by stochastic processes. If host selection is important, what mechanisms by which this selection occurs? Do selective forces change as a function of host developmental stage? Do the host selective pressures that influence community assembly also contribute to community robustness? An understanding of the assembly principles of these communities is essential for beginning to design therapeutic strategies for humans to safely and effectively promote beneficial microbial communities and prevent or correct pathogenic ones. We propose to apply ecological theory and modeling to understand the assembly and persistence of the gut microbiota in the model vertebrate zebrafish. We have established methods to rear zebrafish under sterile conditions (""""""""germ-free"""""""") and associate them with defined microbial communities. The zebrafish offers many advantages for these studies. Their fecundity and rapid development allows us to rear thousands of germ-free individuals at a time and design experiments with a high degree of replication. The genetic tractability of zebrafish and their associated bacteria, permit experimental manipulation of host-microbiota associations from both sides of the interaction. The transparency of developing zebrafish allows us to monitor bacterial colonization of the gut in live animals and study spatial and temporal patterns of gut microbiota assembly. An overarching goal of this proposal is to advance the germ-free zebrafish model, through the improvement and standardization of germ-free nutrition and husbandry, and the development of defined zebrafish-associated microbial communities for reductionist analyses, such that this model can become widely used by microbial ecologists and developmental geneticists to study the dynamics of animal-associated microbial communities.
In Aim 1, we propose to use ecological theory to calculate the relative importance of host selection and stochastic processes in the assembly of the zebrafish gut microbiota. We will ask whether host selection varies as a function of host developmental stage and microbial taxonomy.
In Aim 2, we will determine the relative importance of diet and the immune system in host selection of the zebrafish microbiota. To address the role of diet, we will investigate gut microbiota assembly in fish reared on different diets. To address the role of the immune system, we will analyze gut microbiota assembly in zebrafish mutants with defect innate or adaptive immune systems, and in hosts vaccinated against members of their gut microbiota.
In Aim 3 we will investigate the mechanisms that underlie host selection. We will use defined microbial communities to determine the size of the initial colonizing population. We will use in vivo imaging to examine the spatial and temporal patterns of gut colonization. Finally we will determine how diet and immune system contribute to community robustness by monitoring invasion of established microbiota as a function of these host factors. Collectively these studies will provide a deeper mechanistic understanding of how host- associated microbial communities are established and sustained. Such knowledge is essential for the rational design of prebiotics, probiotics, and antibiotics to treat human pathologies associated with imbalances of the microbiota such as inflammatory bowel diseases and diabetes.

Public Health Relevance

The human gastrointestinal tract is colonized by approximately ten trillion microbial cells. This complex microbial community is important for normal human health and digestive physiology and is disrupted in many gastrointestinal disorders such as inflammatory bowel disease. The proposed experiments will provide new insights into the factors that direct the assembly and persistence of the gut microbial community. Such knowledge will advance the design of therapeutic strategies for humans to safely and effectively promote beneficial microbial communities and prevent or correct pathogenic ones.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1-GDB-2 (MC))
Program Officer
Sledjeski, Darren D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Oregon
Organized Research Units
United States
Zip Code
Melancon, E; Gomez De La Torre Canny, S; Sichel, S et al. (2017) Best practices for germ-free derivation and gnotobiotic zebrafish husbandry. Methods Cell Biol 138:61-100
Stagaman, Keaton; Burns, Adam R; Guillemin, Karen et al. (2017) The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish. ISME J 11:1630-1639
Burns, Adam R; Miller, Elizabeth; Agarwal, Meghna et al. (2017) Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model. Proc Natl Acad Sci U S A 114:11181-11186
Stephens, W Zac; Burns, Adam R; Stagaman, Keaton et al. (2016) The composition of the zebrafish intestinal microbial community varies across development. ISME J 10:644-54
Burns, Adam R; Stephens, W Zac; Stagaman, Keaton et al. (2016) Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. ISME J 10:655-64
Wong, Sandi; Stephens, W Zac; Burns, Adam R et al. (2015) Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut. MBio 6:e00687-15
Stephens, W Zac; Wiles, Travis J; Martinez, Emily S et al. (2015) Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine. MBio 6:e01163-15
Bomar, Lindsey; Stephens, W Zac; Nelson, Michael C et al. (2013) Draft Genome Sequence of Aeromonas veronii Hm21, a Symbiotic Isolate from the Medicinal Leech Digestive Tract. Genome Announc 1:
McFall-Ngai, Margaret; Hadfield, Michael G; Bosch, Thomas C G et al. (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A 110:3229-36
Sadler, Kirsten C; Rawls, John F; Farber, Steven A (2013) Getting the inside tract: new frontiers in zebrafish digestive system biology. Zebrafish 10:129-31

Showing the most recent 10 out of 14 publications