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The Antibiotic Ciprofloxacin as a Full Tank Treatment for Saltwater Reef Aquariums.

Saltwater Reef Aquarium in Leawood, KS

I use full tank antibiotic treatments as a last resort. My initial concern was that a full tank antibiotic treatment would wipe out too much of the beneficial bacteria and compromise the microbiome. A healthy microbiome in a reef aquarium is crucial to its health, balance, and beauty. Without a well balanced microbiome, algae and disease are allowed to grow unchecked. 

The microbiome exists everywhere in the reef aquarium. It is present inside filter pipes, in the water column, on the rocks as a biofilm, and in between each and every coral polyp. The beneficial bacteria that helps make up the microbiome is paramount to coral health. 

For these reasons, it's important to not compromise the microbiome unless the situation is dire. If 50% of your coral are infected with a bacterial pathogen, and individually dipping is not possible, a full tank antibiotic treatment might be required.

I wanted to know, if I perform a full tank antibiotic treatment, will it not only help my coral, and reduce the pathogenic bacteria, but also not significantly compromise the beneficial microbiome? My results suggested they would. 

I experimented with dosing the antibiotic ciprofloxacin as a full tank treatment in three of my client’s saltwater reef aquariums. I also experimented with it as a dip by itself and as part of a cocktail of antibiotics. This article will focus on the three in-tank treatments. 

In each tank, I dosed 0.075 ml of ciprofloxacin per gallon, at a concentration of 10mg/ml of RODI water before the light came on, for 10 days in two tanks, and for six days in the third tank. 

I tested the microbiome, using Aquabiomics, of two of the aquariums that received the treatment. 

My results showed that ciprofloxacin did have incontrovertibly positive effects on the health of the infected and healthy corals, in some of the aquariums. The results also showed there was at least an average population and balance of the beneficial bacteria that make up a healthy microbiome after the treatment.

I would recommend a full tank ciprofloxacin treatment if you have (1) a robust, diverse, and balanced beneficial microbiome, (2) a rampant pathogenic bacterial infection that has affected multiple corals and is spreading, and (3) individual dipping is impractical. 


Types of Pathogenic Bacteria in Corals 

Corals host bacterial communities that are phylogenetically distinct, more active and more abundant than the bacterial communities in the surrounding seawater (Tout,, 2015). 

This means we can expect pathogenic and beneficial bacteria to be at a higher concentration within and next to coral polyps. This gives the bacteria a greater influence on the health of the coral, for better or worse. 

In the past few years, the scientific community has increased their efforts to identify specific groups of bacteria that cause disease in corals. This could be due to recent anthropogenic (human caused) influences on the increased nutrient load in the coral reefs. 

There is still relatively little known regarding which bacterial orders, families, and genera are pathogenic to corals. The few we are aware of include:




Peptostreptococcales–Tissierellales (NOAA, 2023)

In terms of the hobby, the best we can do is understand how these pathogens interact with healthy bacteria within the coral holobiont (the coral and the community of microorganisms that live amongst its tissue). 

Armed with the knowledge of what pathogens we are dealing with, and how they live and affect the organisms around them, we can create a plan to eradicate them, or at least control their population to a natural level. 

If we lose balance, and pathogenic bacteria are allowed to take over, this results in diseased corals, usually manifested as tissue necrosis. If multiple corals are infected and the entire aquarium is under threat, drastic measures may need to be taken. 

Misdiagnosing Issues as Bacterial Infections

A common practice, even amongst the most experienced reefers, is misdiagnosing the cause of poor coral health. I will not attempt to provide a guide on correctly diagnosing coral diseases. Be prepared to misdiagnose. 

Often in the aquarium hobby, we falsely correlate and causate unrelated events. This leads to improper solutions to problems. Sprung et. al. 2002, suggested all health issues related to Catalaphyllia problems were the cause of pathogenic bacteria. However, there may also be evidence, albeit anecdotal, that this family is prone to starving in the hobby. 

The reality is both the hobbyist and scientific community do not know enough about coral bacterial infections, trace element deficiency symptoms, and the effect of environmental changes to accurately diagnose coral diseases and health issues with perfect accuracy. 

However, not all is lost. We do know enough to use a trial and error approach to diagnosing and curing coral health problems. For example, if a coral is losing tissue rapidly, you assume it's the worst case scenario due to the severity of the symptom. You then dip with antibiotics. If it recovers, great, if not, you move on to the next possible cause. 

Taking all of this under consideration, you may decide a full tank treatment with ciprofloxacin is the best solution for your problem. Next, I'll detail exactly how I treated my client’s aquariums, and the results. 

Materials and Methods

The three subjects for this experiment are given the designations Aquarium A, B, and C. 

Aquarium A is a 180 gallon mixed reef running 50% water changes every 14 days, alkalinity and liquid carbon dosing, skimmer, refugium light, and two Neptune Skies. Temp is 78.3, pH is 8.13, alkalinity is 8.22, calcium is 385, and magnesium is 1430. This aquarium had five Euphyllia and two Acanthastrea specimens that were succumbing to rapid tissue necrosis. 

Aquarium B is a 116 gallon mixed reef running 30% water changes every 14 days, alkalinity and liquid carbon dosing, skimmer, and two AI Hydras. Temperature is 79.0, pH is 7.98, alkalinity is 8.0, calcium is 410, and magnesium is 1440. This aquarium had multiple Euphyllia with shrinking polyps that were pulled in for several weeks in a row. There were three cases of rapid tissue necrosis in this system as well. 

Aquarium C is a 110 gallon mixed reef running 15% water changes every 7 days, alkalinity, liquid carbon, AB+ dosing, skimmer, full refugium with light, and two Radion XR15s. Temperature is 79.1, pH is 8.25, alkalinity is 9.35, calcium is 420, and magnesium is 1505. This aquarium had two specimens showing signs of tissue necrosis and two more with shrinking polyps for several days in a row. 

I acquired 500 mg capsules of powdered ciprofloxacin from an online retailer. Some hobbyists have had success with acquiring antibiotics from their vet. This procedure works best with powdered capsules, not tablets. 

Determining the concentration of the liquid solution and then how much to dose is the first step. Several articles online have suggested different doses. I read through several case studies and found the average of all of them to be 10mg of ciprofloxacin per 1 ml of RODI water. 500 mg of ciprofloxacin would prepare 50 ml of solution at this concentration. 

I dosed each tank at 0.075 ml per gallon per day as the lights came on. I dosed for 10 days in aquariums A and B, and six days in aquarium C. I left the skimmer off for the entire duration of the dosing periods (10 days and 6 days). 

If you need to double the solution volume to make dosing small tanks easier, without using more ciprofloxacin, be sure to adjust the dosage as well. For example, if you use 500 mg of ciprofloxacin per 100 ml of RODI water to get 100 ml of solution, also double the dosage per gallon from 0.075 ml per gallon to 0.15 ml per gallon. 

On the morning of the 11th day for aquariums A and B, and the morning of the 7th day for aquarium C, I dosed 5 ml of Dr. Tim’s Eco Balance per 10 gallons of aquarium water volume. After 10 hours, I resumed the skimmer to normal function and schedule. 

Aquariums A and B got a repeat dose of 5 ml of Dr. Tim’s Eco Balance per 10 gallons of aquarium water volume at 14 days. The skimmer was turned off before the dose and resumed to a normal schedule after 10 hours. Aquarium C got a repeat dose of Dr. Tims at the same concentration after seven days. The skimmer was also turned off before the dose and resumed to normal schedule after 10 hours. 


Aquariums A and B showed marked improvement in coral polyp extension after the 10 day dosing period. One M. digittata species did not show improvement and continued to die off in Aquarium B. Some specimens from Aquarium B did not return to full extension, but did improve overall. 

Aquarium A exhibited by far the best results. Every coral recovered completely with full polyp extension and new growth after 2 months. 

Aquarium C had the most middling results. Two specimens (an Echinophyllia and a Euphyllia) stopped their tissue regression, but one other Euphyllia continued and a fourth was still not fully extended. 

Table 1. visual and microbiome results.

Aquarium A

Aquarium B

Aquarium C

Tissue Necrosis



3/4 Croals

Polyp Extension


3/4 of corals

½ Corals

Overall Recovery




Aquabiomics Balance




Aquabiomics Diversity




Coral Pathogens

None Detected

None Detected


As for the effect on the microbiome, I only have data from aquariums A and B for after the treatment regimens. I do not have microbiome data on these systems from before the treatment. 

However, the percentages are in relation to every other aquarium tested by Aquabiomics. This suggests some idea of how the microbiome was affected. 

Aquarium A is in the middle of most aquariums tested with average balance and diversity. There were no coral pathogens detected after the treatment. 

Aquarium B scored in the 96th percentile of aquariums tested for balance, but only 46% in diversity. There were also no coral pathogens detected. 

Due to the emergency nature of full tank antibiotic treatments, it is difficult to have data from before and after a full tank treatment unless your microbiome is sampled and tested semi-regularly. If you're considering a full tank antibiotic treatment, send in a sample of your aquarium to be tested before you start the treatment. 


I suspect Aquarium B’s lesser recovery compared to A had to do with two factors. The first being misdiagnosis of the issues affecting the coral. Antibiotics were a viable solution to only some of the coral. The specimens which continued to degrade may not have been affected by a bacterial infection, but were suffering from a different issue that antibiotics could not solve. 

The second factor may have been the consistency of the doses. My clients were responsible for dosing the aquariums each day. I am confident Aquarium A’s owner dosed correctly, as instructed. Aquarium B’s owner may have missed a dose. 

I believe aquarium A’s corals were all suffering from a bacterial infection, which is why they all responded so positively to the antibiotics. 

Six months ago, aquarium A could not keep a torch coral alive for more than a few weeks. They would rapidly succumb to tissue necrosis. As of the published date of this article, aquarium A’s corals are still going strong and three newly added torch corals are fully extended and could not be happier after being in the aquarium for nearly 2 months. 

Aquarium C’s lack of recovery may have been due to misdiagnosis. However, I believe the six day dosing period versus the 10 days had a larger impact on their poor recovery. 

In terms of the microbiome, with the limited data I have, I would say the microbiome was not significantly affected by the treatment long term. Corals did not relapse from a compromised microbiome. 

It should be noted, the sample for the microbiome tests were taken after two half doses of Dr. Tim’s Eco Balance was added to each aquarium. The samples were taken 14 days after the second dose of Dr. Tim’s, totaling 42 days after the last dose of antibiotic was added. 

I would recommend a full tank ciprofloxacin treatment under the following circumstances:

  1. You have massive die off or rapidly decaying tissue of multiple corals. 

  2. It is impractical to dip all the corals being affected separately. 

  3. You have correctly diagnosed the cause of the ailing corals as a bacterial infection. 

  4. You have a strong and established microbiome. 

  5. You have the ability to dose the proper concentration of antibiotic for the appropriate amount of time to ensure every pathogenic specimen is destroyed, thus preventing antibiotic resistant strains. 


We have to be our own veterinarians when it comes to diagnosing and curing our aquarium’s health problems. Trial and error is a part of this process as is misdiagnosing. The key is to only use treatments which affect the entire system if you're confident there is sound science and low risk behind it. 

Literature Cited

NOAA. “Researchers Find Key Bacteria in Disease Outbreak”. March 28, 2023 by AOML Communications to Corals, Ocean Chemistry and Ecosystems, Publication Stories.,progression%20of%20lesions%20on%20corals.

Tout, J. “Chemotaxis by natural populations of coral reef bacteria”. The ISME Journal. 9:1764-1777. 2015. 

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