Horizon scanning the application of probiotics for wildlife

Garcias-Bonet, Neus; Roik, Anna; Tierney, Braden; García, Francisca C.; Villela, Helena D.M.; Dungan, Ashley M.; Quigley, Kate M.; Sweet, Michael; Berg, Gabriele; Gram, Lone; Bourne, David G.; Ushijima, Blake; Sogin, Maggie; Hoj, Lone; Duarte, Gustavo; Hirt, Heribert; Smalla, Kornelia; Rosado, Alexandre S.; Carvalho, Susana; Thurber, Rebecca Vega; Ziegler, Maren; Mason, Christopher E.; van Oppen, Madeleine J.H.; Voolstra, Christian R.; Peixoto, Raquel S.

doi:10.1016/j.tim.2023.08.012

Cited by 26 publications

(20 citation statements)

References 149 publications

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“…Further studies are required to better understand these mechanisms and improve microbiome rehabilitation. Unraveling genomic-level mechanisms associated with BMCs and using omics to track the actual changes promoted by probiotics are crucial steps for addressing knowledge gaps on the functioning of coral probiotics 53 , as recently investigated 14,19,40 , and would improve the selection of BMCs based on targeted microbial traits.…”

Section: Discussionmentioning

confidence: 99%

“…This does not indicate “lack of success”: even in the absence of long-term manifestation of the probiotic strains at high abundance, microbial transfer can still trigger a “reboot” or “reset” of the microbiome that leads to a potentially more beneficial microbiome (as reviewed in ref. 53 ). Thus, the restructuring of the microbiome following probiotic treatment, in addition to (ideally) finding the treated bacterial strains in the restructured microbiome, are both indicators of successful treatment.…”

Section: Discussionmentioning

confidence: 99%

“…Other factors such as BMCs consortium composition, coral species, multi-host vs single-host bacterial donors, host-microbiome flexibility, and host health (i.e., bleaching state, diseases) likely influence host microbiome-probiotic interactions 10 , 11 . The potential mechanisms underlying probiotic action in the coral microbiome are likely multi-factorial 53 , and may include the enrichment of beneficial bacteria, indirect niche colonization by inoculated BMCs, antagonistic effects against pathogens 13 , predatory bacteria 109 , immune stimulation by allochthone strains triggered by the probiotic 14 , 110 , and support for coral heterotrophic feeding 36 . Further studies are required to better understand these mechanisms and improve microbiome rehabilitation.…”

Section: Discussionmentioning

confidence: 99%

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Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment

Delgadillo-Ordoñez,

Garcias-Bonet,

Raimundo

et al. 2024

Commun Biol

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Beneficial microorganisms for corals (BMCs), or probiotics, can enhance coral resilience against stressors in laboratory trials. However, the ability of probiotics to restructure the coral microbiome in situ is yet to be determined. As a first step to elucidate this, we inoculated putative probiotic bacteria (pBMCs) on healthy colonies of Pocillopora verrucosa in situ in the Red Sea, three times per week, during 3 months. pBMCs significantly influenced the coral microbiome, while bacteria of the surrounding seawater and sediment remained unchanged. The inoculated genera Halomonas, Pseudoalteromonas, and Bacillus were significantly enriched in probiotic-treated corals. Furthermore, the probiotic treatment also correlated with an increase in other beneficial groups (e.g., Ruegeria and Limosilactobacillus), and a decrease in potential coral pathogens, such as Vibrio. As all corals (treated and non-treated) remained healthy throughout the experiment, we could not track health improvements or protection against stress. Our data indicate that healthy, and therefore stable, coral microbiomes can be restructured in situ, although repeated and continuous inoculations may be required in these cases. Further, our study provides supporting evidence that, at the studied scale, pBMCs have no detectable off-target effects on the surrounding microbiomes of seawater and sediment near inoculated corals.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment

Delgadillo-Ordoñez,

Garcias-Bonet,

Raimundo

et al. 2024

Commun Biol

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“…For the placebo treatment, 1 mL of a sterile saline solution (0.85% NaCl) was applied, whereas 1 mL of a cell suspension in saline solution with 10 7 cells of probiotics was used in the BMC treatment (see below). The use of a placebo as a negative (and therefore inert) control is the gold standard for probiotic validations, as there is no current way to rule out bacterial cells as non-BMC (due to the lack of knowledge about all possible BMC mechanisms), and the use of dead cells could infer confounding factors since dead cells may act as postbiotics and trigger specific host responses ( 36 ). Inoculations were performed on the first day of the experiment (T0), on the 10th day of the experiment (T1), every 5 days between T1 and T2, and every 3 days between T2 and T3 ( Fig.…”

Section: Methodsmentioning

confidence: 99%

Localization and symbiotic status of probiotics in the coral holobiont

Cardoso,

Hill,

Villela

et al. 2024

mSystems

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Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis . Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome. IMPORTANCE Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.

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“…Probiotics, the supplementation of bene cial commensal bacteria to existing microbiomes, is of interest in both industrial and scienti c communities. For example, probiotics has been proposed as an alternative or supplement to antibiotics treatments for livestock and pets 29 as well as a potential avenue of increasing robustness of wildlife species which have become endangered due to anthropogenic factors 30 . Likewise, manipulation of speci c host bacteria has been proposed as a way to control pest insect species of importance in agriculture and human diseases 31 .…”

Section: Introductionmentioning

confidence: 99%

Feeding Drosophila gut microbiomes from young and old flies modifies the microbiome

Wesseltoft,

Danielsen,

Andersen

et al. 2024

Preprint

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It is becoming increasingly evident that the myriad of microbes in the gut, within cells and attached to body parts (or roots of plants), play crucial roles for the host. Although this has been known for decades, recent developments in molecular biology allow for expanded insight into the abundance and function of these microbes. Here we used the vinegar fly, Drosophila melanogaster, to investigate fitness measures across the lifetime of flies fed a suspension of gut microbes harvested from young or old flies, respectively. Our hypothesis was that flies constitutively enriched with a ‘Young microbiome’ would live longer and be more agile at old age (i.e. have increased healthspan) compared to flies enriched with an ‘Old microbiome’. Three major take home messages came out of our study: 1) the gut microbiomes of young and old flies differ markedly; 2) feeding flies with Young and Old microbiomes modulated the microbiome of recipient flies and 3) the two different microbial diets did not have any effect on locomotor activity nor lifespan of the recipient files, contradicting our working hypothesis. Combined, these results provide novel insight into the complex interplay between hosts and their microbiomes and clearly highlight that the phenotypic effects of gut transplants and probiotics are complex and unpredictable.

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Horizon scanning the application of probiotics for wildlife

Cited by 26 publications

References 149 publications

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment

Localization and symbiotic status of probiotics in the coral holobiont

Feeding Drosophila gut microbiomes from young and old flies modifies the microbiome

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