Think Horses, Not Zebras: Antibiotics and the Gut Microbiome of Zebrafish

Chemicals in the Water:

As the modern world has developed, anthropogenic chemical leaching has increased, which can cause contamination within surface and groundwater. Anthropogenic chemicals refer to chemicals originating from human activities and these common contaminating chemicals include nitrates, phosphates, pesticides, mercury, Polychlorinated biphenyls (PCBs), and legacy pesticides, , among others (Gavrilaș et al., 2025; Office of Environmental Health Hazard Assessment, 2020). While it’s fairly common knowledge that chemical pollution comes from agricultural, natural resource extraction, and manufacturing activities, another source of chemical contamination comes from pharmaceuticals, or medications. These chemicals can range from antibiotics to birth control to heart medications and more and are also common contaminants found in water sources.

While it might seem unlikely that medications, which are prescribed to improve our health, could be damaging to the ecosystem, it’s actually quite true – taking medications when you’re a healthy person can actually be quite harmful and this is the same for the animals that encounter pharmaceutical contamination! For example, a study in Florida looked at the effects of anthropogenic chemical exposure on bonefish and found that 56% of the sampled fish had quantities of medications above levels that can cause harmful effects (Castillo et al., 2024). For example, Atenolol, a beta-blocker prescribed to manage high blood pressure was found in 72% of the sampled fish. But why is this such a big deal? Well, other studies have found that animal exposure to human medications can alter behavior, reproduction, and survival, For example, fish exposure to 17-β-estradiol, a chemical in birth control pills, can cause delayed reflexes in minnow larvae, which can harm their ability to escape predators (Lovett, 2012).

Of human medications, antimicrobial agents are an increasing worry, which is commonly recognised in the rise in antibiotic resistance. But here’s where we dive into the true complexity of this issue. Some medications, like antibiotics pose a threat not only in terms of antibiotic resistance, but can also pose a threat to the health of our gut microbiome and this does not only affect us as humans but also animals. But why does our gut microbiome matter? Well, the gut microbiome refers to the community of bacteria that live within the intestinal tract andis incredibly important in many ways: It influences metabolism, weight, the immune system, nutrient absorption, disease, and the brain, among many other things. The microbes in the gut form complex relationships and networks with each other that benefit them, keeping the community strong, and their host (the host being a human, dog, fish, etc.). A disturbance to gut microbiome, such as antibiotic use, can alter the abundances, or amounts, of different microbial species, the richness, or the number of species, the diversity, and the connections and relationships between species, which can have a detrimental effect on the host. For example, Patangia et al. (2022) found that antibiotic use rapidly decreased the microbial diversity of the gut and shifted the abundances of species. This issue is what leads us to the focus of this article: The effect of triclosan exposure on the microbiomes of zebrafish.

The Basics:

Before we jump into the discoveries of Gaulke et al.’s 2016 study, Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish, let’s cover some background information. First, this study looked at the effect of triclosan on the gut microbiome of zebrafish. Triclosan is a common antimicrobial agent found in soaps, toothpastes, deodorant, cosmetics, and detergents, to name a few and is readily absorbed through the skin, mouth, and intestinal tract (Cleveland Clinic, 2022). However, triclosan was mostly banned in 2016 due to antibiotic resistance concerns and since it was not more effective than soap and water. This sets this study up to be a great model for future research in this field, though, because the effects of triclosan are known. Second, zebrafish are a commonly used species in science and are referred to as a model organism because they have been extensively studied, are easily housed, reproduce quickly, and easily manipulated for experiments. Zebrafish are commonly used in toxicology studies due to these factors, which is another reason why this study is such a great model for future research.

The Central Question:

Gaulke et al.’s 2016 investigated the dynamics of the gut microbiome in fish and the effect of chemical exposure to the microbiome’s composition and stability. Additionally, the authors wanted to identify a reliable and reproducible means for similar studies on the effects of other chemicals on the fish microbiome.

The Methods:

The study design of this experiment was relatively simple so let’s do a quick overview. The authors had 15 fish in each treatment group that were fed a particular diet for one week. There were three treatment groups that either received 7 days of triclosan-laddened food, triclosan-laddened food for 4 days followed by triclosan-free food for 3 days, or 7 days of triclosan-free food. After the seventh day, feces were collected immediately for analysis of the gut microbiome. The analysis consisted of identifying the microbial species present and the community networks of the microbiome. The authors identified the microbial species by reading a specific sequence of DNA called the 16S rRNA gene, which is a very common technique because this section of DNA contains highly conserved sequences, meaning that sections are the same across almost all species, and highly variable sequences, meaning that these sections are different between species.

The Findings:

Gaulke et al.’s 2016 study found that Proteobacteria and Fusobacteria were the major phyla found and the genera Cetobacterium, Shewanella, Aeromonas, the family Aeromonadaceae, and the class CK-1C4-19 were also highly abundant, which is consistent with previous studies on zebrafish (Roeselers et al., 2011). Proteobacteria and Fusobacteria are broad categories encompassing microbes involved in metabolism, detoxification, and inflammatory responses, respectively. Cetobacterium, Shewanella, Aeromonas, are involved in metabolism and Cetobacterium also play a role in maintaining and strengthening the immune system of the gut. Further, the study found that the triclosan fed fish had significantly more variation in their microbiomes and that the diversity and species richness were decreased in the fish fed triclosan-laddened food for 7 days.

The change in species richness and diversity was due to whether the microbes were susceptible or resistant to triclosan. For example, bacteria of the family Enterobacteriaceae, family Aeromonadaceae, and genus Plesiomonas decreased in abundance, relatively, because they were vulnerable to the effects of triclosan whereas bacteria in the genus Pseudomonas and order Rhizobiales increased in relative abundance because they are triclosan resistant.

Most importantly, the study found that triclosan exposure decreased the size of the microbial communities and increased the connectivity, or the interconnectedness and complexity of the microbial relationships, of the microbial networks. This means that the decrease in the number of species caused the entire community to shrink due to the loss of species diversity and, further, for relationships between the microbes to rearrange and become more interconnected. While greater interconnectedness may sound beneficial, the study identified that this caused more negative relationships to occur between microbes, meaning the relationships were likely of a combative nature, likely due to competition and an overlap in roles. Figure 1 below illustrates this finding, where each panel (A, B, and C) shows the microbial communities of each treatment group, the colored shapes represent the species that are associated with each other, and the lines represent a relationship (positive/beneficial or negative/harmful) between species.

Figure 1: A) Unexposed fish, B) four-day exposure, C) seven-day exposure (Figure 5 from Gaulke et al., 2016)

Looking to the Future:

This study leaves me wondering, what are the effects of other, more common, antibiotics on fish? Does the decrease in communities cause the loss of vital functions of the microbiome? Can the microbiome recover from the disturbance? Does the decrease in diversity and loss of community networks make the host more susceptible to disease?

Further research is needed to understand the answers to these questions. The logical next steps in my mind would be to generate more studies with this design, using the same species, and testing different antibiotics and other common pharmaceutical contaminants. Another step would be to assess what the effects of the community changes are to the host. For example, are the products produced by these microbes decreased? Are vital functions, such as nutrient absorption compromised?

What questions does this study raise for you?

References:

Castillo, N. A., Santos, R. O., James, W. R., Rezek, R., Cerveny, D., Boucek, R. E., Adams, A. J., Fick, J., Brodin, T., & Rehage, J. S. (2024). Widespread pharmaceutical exposure at concentrations of concern for a subtropical coastal fishery: Bonefish (Albula vulpes). Marine Pollution Bulletin, 209, 117143. https://doi.org/10.1016/j.marpolbul.2024.117143

Cleveland Clinic. (2022, October 10). Triclosan: What It Is & Effects. Cleveland Clinic. https://my.clevelandclinic.org/health/articles/24280-triclosan

Gavrilaș, S., Burescu, F.-L., Chereji, B.-D., & Munteanu, F.-D. (2025). The Impact of Anthropogenic Activities on the Catchment’s Water Quality Parameters. Water, 17(12), 1791. https://doi.org/10.3390/w17121791

Gaulke, C. A., Barton, C. L., Proffitt, S., Tanguay, R. L., & Sharpton, T. J. (2016). Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish. PLOS ONE, 11(5), e0154632. https://doi.org/10.1371/journal.pone.0154632

Lovett, R. A. (2012). Human drugs make fish flounder. Nature. https://doi.org/10.1038/nature.2012.11843

Roeselers, G., Mittge, E. K., Stephens, W. Z., Parichy, D. M., Cavanaugh, C. M., Guillemin, K., & Rawls, J. F. (2011). Evidence for a core gut microbiota in the zebrafish. The ISME Journal, 5(10), 1595–1608. https://doi.org/10.1038/ismej.2011.38

Office of Environmental Health Hazard Assessment. (2020). Chemicals in Fish. Ca.gov. https://oehha.ca.gov/fish/chemicals-fish

Patangia, D. V., Anthony Ryan, C., Dempsey, E., Paul Ross, R., & Stanton, C. (2022). Impact of antibiotics on the human microbiome and consequences for host health. MicrobiologyOpen, 11(1), e1260. https://doi.org/10.1002/mbo3.1260