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Probiotics and microbiome manipulation in coral restoration. Effective solution or just a dream?

Updated: May 25

-by Ioana Stanca.

With the powerful and devastating extent of the coral bleaching on The Great Barrier Reef, the health of corals has become a much bigger concern in the scientific world. Climate change is not without consequences, the constant modification in ocean temperature levels has triggered an imbalance in the microbiome and led to a state of dysbacteriosis which has exposed the corals to diseases and bleaching through the emergence of pathogenic species.

Currently, coral restoration programs are divided into passive restoration and active restoration.

Passive restoration consists of heat stress protection through cooling and shading techniques. The new techniques regarding microbiome manipulation are a part of active restoration with human involvement. With this in mind, it is important to consider the major role of the microbiome in coral reef restoration, as any disturbances to the normal function of the ecosystem are shown early by irregular behavior in the microbial communities leading to the bleaching effect. I believe that by enhancing the natural immunity of the corals with probiotics, along with outside help consisting of shading techniques, the reefs will be able to survive the heat waves.

The main concern of using probiotics is the effects it can have on the physiological and metabolic responses of the corals as well as possible changes in the genome of the bacteria and symbiont. The symbiotic relationship between corals and Symbiodinium is maintained by the microbiome inside the corals. Any disturbance to the natural order of the microbial system leads to the expulsion of Symbiodinium out of the corals and resulting in bleaching.

Probiotics are created from bacteria already inside the coral or surrounding them, in order to increase or supplement their loss of beneficial microorganisms for corals during heat stress. Probiotics consisting of a diverse amount of bacteria existent in the natural microbiome of the corals have been tested on different species of corals and have been proven effective (Zhang et al.,2021; Santoro et al., 2021; Rosado et al ,2019).

Manipulation of the coral microbiome and the introduction of probiotics for corals have shown big improvements in the research aquariums by enhancing their resistance to heat and stress. The corals were exposed to rising temperatures in water reaching 32 degrees Celsius and tested for color changes, altering of the microbiome, and possible differences in the genome.

Production and administration of probiotics (source: Thatcher et al. 2022)

Nevertheless, the question still stands, is microbiome manipulation safe? In a study done by Zhang et al. (2021) by manipulating the bacterial population, no negative change in the physiology of the corals was noticed, however, there was a rise in the protein, lipids, and carbohydrate levels in the treated corals. From this concept, we can further analyze the idea that by inoculating a mix of specific bacteria, we can enhance the health of the corals during the heat waves.

In addition, an increase chlorophyll a levels was noticed which proves a bigger efficiency of Symbiodinium`s photosystem. By using the bacteria Pocillopora damicornis, the effects of the heat stress were reduced significantly (Zhang et al.,2021). Furthermore, the probiotic treatment diminishes the expression of inflammatory responses in the immune system of the corals concerning post heat stress disorder (PHSD). Additionally no irregularities in chromosome condensation or DNA methylation were observed meaning that by treating corals with probiotics no alterations are produced to the coral genes or its symbiont. During this particular study, Santoro et al. (2021) noticed that the beneficial microorganisms for corals treatment has resulted in blockage of the symptoms of PHSD and thermal stress protection (Santoro et al., 2021).

In another study done by Rosado et al.(2019), the bacterial strains used as probiotics were collected from coral tissue and the water surrounding them. This study challenged the effects of the probiotics by not only testing the healthy coral's reaction to heat stress but also it`s susceptibility to opportunistic pathogens. The scientist tested the effects of the opportunistic virus Vibrio coralliilyticus with and without probiotics maintaining a temperature of 30 degrees Celsius in the aquariums. The results showed that the color of the corals without probiotics decreased considerably during the 26 days of the study, going from dark brown colors to almost white. However, kept under the same environmental conditions the corals treated with probiotics displayed a one-unit decrease on the color scale. This study showed that by manipulating the microbiome of corals, one could decrease the susceptibility of said corals to opportunistic pathogens.

After analyzing these experimental procedures we must ask ourselves, is microbiome manipulation an effective solution concerning the protection of corals or is it just a dream? I believe it is an effective solution, at least for the short term. However, even by enhancing the natural immune system of the corals, climate change will still affect them, so by combining microbial manipulation and effective temperature control in the ocean there might be hope for a healthy reef. While the introduction of probiotics does have some concerns for the future development of the reefs, it has many more beneficial outcomes because depending on the species of bacteria introduced into the probiotics, the health of the corals has improved by enhancing their natural immunity system. Microbiome manipulation has been proven to be effective in fighting opportunistic bacteria and helping in post-heat stress disorder.


1. Rosado, P.M., Leite, D.C.A., Duarte, G.A.S., et al. Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME J 13, 921–936 (2019).

2. Santoro EP, Borges RM, Espinoza JL, Freire M, Messias CSMA, Villela HDM, Pereira LM, Vilela CLS, Rosado JG, Cardoso PM, Rosado PM, Assis JM, Duarte GAS, Perna G, Rosado AS, Macrae A, Dupont CL, Nelson KE, Sweet MJ, Voolstra CR, Peixoto RS. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Sci Adv. 2021 Aug 13;7(33):eabg3088. doi: 10.1126/sciadv.abg3088. PMID: 34389536; PMCID: PMC8363143.

3. Thatcher C., Høj L., Bourne D.G., Probiotics for coral aquaculture: challenges and considerations, Current Opinion in Biotechnology, Volume 73, 2022, Pages 380-386, ISSN 0958-1669,

4. Zhang, Y., Yang, Q., Ling, J. et al. Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium. BMC Microbiol 21, 130 (2021).


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