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Ciona robusta (formerly C. intestinalis) as a model of gut host-microbe interactions

Recently Published:

Creasy A, Rosario K, Leigh BA,
Dishaw LJ, Breitbart M. Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta). Viruses. 2018 Jul 31;10(8). pii: E404. doi: 10.3390/v10080404. PubMed PMID: 30065169; PubMed Central PMCID: PMC6116155.
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Our lab at USF uses the protochordate, Ciona.
This is a very well-developed model system for many types of biosciences research.

Ciona are easy to propagate in the lab.
The genomes of two species of Ciona are sequenced.
The animal is a filter-feeder and siphons water 24/7 yet, we have shown, maintains distinct microbial communities in its gut.
Many labs around the world are available as collaborative partners.

Our lab is the first to develop this model specifically for the purposes of investigating host-bacterial dynamics within the gut.

We are also the first lab to develop germ-free studies of this model and the first to use bacteriophage to shape bacterial communities in the gut.

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Our lab uses the protochordate or urochordate model, Ciona robusta. There are many really good reasons to use Ciona, one of which is the fact that it has a simple (yet complex...) gut ecosystem that is colonized by distinct bacterial communities. The host, as well as other environmental factors, appears to be shaping the composition of the gut microbiome. We are interested in how the gut is colonized and, more specifically, characterizing the interface between host immunity and microbiomes. Secreted immune effectors serve critical roles at this interface...
Below are some examples of the specific topics we are investigating:


While Ciona siphons water 24/7, it can maintain distinct bacterial communities in its gut. We have been able to get many of these bacteria into culture; these isolates have become important study models for us both in vitro and for feeding germ-free animals that we culture in the lab.


Our lab is characterizing the role(s) that bacteriophages play in shaping the composition of host-associated microbiomes. We are also focusing on the role of prophages in the gut of Ciona.
Our work involves both in vivo and in vitro experiments and is supported by the NSF.

Some of our phage work involves a collaboration with Dr. Mya Breitbart.


Many of the bacterial isolates coming from the gut of starved Ciona grow very well as biofilms. This should not be too surprising considering that this is likely their 'normal' lifestyle in the gut. We are utilizing a variety of biofilm-based assays to study these isolates.

We have developed and utilize Ciona germ-free mariculture approaches.


Protochordates like Ciona possess a special immune-type molecule that is expressed almost exclusively in the gut. These variable region containing chitin-binding proteins (VCBPs) are Ig-like proteins that can bind bacteria, increase phagocytosis, and influence biofilms. They are a major aspect of our host-microbiome studies.

In vitro

We are developing a variety of in vitro assays to mimic conditions of the gut in our studies. Further, we are using 3D matrices to develop 'competition' assays. These 'microbial ecology' experiments are highly relevant to what is happening at the surface of the gut epithelium in Ciona.


What role(s) do fungi play in the gut? Why are they important?
We are now investigating fungi as an important player in the maintenance of gut microbiome homeostasis.
*This website is not an official University of South Florida website. Only the Dishaw Lab is responsible for its content.
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Ciona juveniles are like mini- guts on plastic dishes... by the hundreds or thousands!

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