Suspension‐feeding bivalves are critical members of aquatic ecosystems worldwide, which is why research into their host‐associated microbiota is growing. Experiments that artificially diminish the native microbial communities of bivalves
An understanding of the mechanistic drivers of animal‐microbial symbiosis and associations generally requires experiments that manipulate specific symbionts or microbial communities. As part of an ongoing study of the mechanisms that drive microbial communities in coral reef fishes, and specifically the role of cleanerfish in microbial transmission, we tested the effects of the commonly used antibiotics Enrofloxacin and Nitrofurazone on the skin microbiome of three ornamental reef fish species: the four‐eyed butterflyfish,
- PAR ID:
- 10518591
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Aquaculture, Fish and Fisheries
- Volume:
- 4
- Issue:
- 3
- ISSN:
- 2693-8847
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract in vivo will be increasingly necessary to evaluate the functional role of microbes within their hosts. Previous methods to manipulate the microbiome of bivalves lack standardization and, often, verification of successful disturbance. The goal of this study was to evaluate antibiotic administration as a method for perturbing the gut microbiome of bivalves in two separate, but related, experiments. In the first, a mixture of antibiotics was delivered to eastern oysters for 4 days to probe effects on gut microbial carbon usage, diversity, and taxonomic composition. In the second, the same antibiotic mixture was administered to blue mussels for 21 days to probe effects on microbial abundance, diversity, and taxonomic composition. In both experiments, animals were administered antibiotics in isolation, and stringent sterilization methods were employed, which included sterilized seawater and microalgal food. The results of the oyster experiment revealed that antibiotics substantially reduced microbial carbon usage and perturbed community composition. In the mussel experiment, antibiotics lowered microbial abundance and species richness and significantly altered community composition. Taken together, results from the two experiments demonstrate that antibiotics can be used to effectively alter the function and composition of the gut microbial community of bivalves. Future research that aims to perturb the microbiomes of suspension‐feeding animals should incorporate aspects similar to the protocols described herein. Additionally, future studies must include verification, ideally high‐throughput DNA sequencing coupled with microbial quantification, that the antibiotic perturbation was successful. -
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Abstract Background Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and methods to mitigate associated negative effects remain poorly understood, particularly outside of human-clinical and model-rodent studies that focus on outcome over process. To improve conceptual understanding of host-microbe symbiosis in more naturalistic contexts, we applied an ecological framework to a non-traditional, strepsirrhine primate model via long-term, multi-faceted study of microbial community structure before, during, and following two experimental manipulations. Specifically, we administered a broad-spectrum antibiotic, either alone or with subsequent fecal transfaunation, to healthy, male ring-tailed lemurs (
Lemur catta ), then used 16S rRNA and shotgun metagenomic sequencing to longitudinally track the diversity, composition, associations, and resistomes of their gut microbiota both within and across baseline, treatment, and recovery phases.Results Antibiotic treatment resulted in a drastic decline in microbial diversity and a dramatic alteration in community composition. Whereas microbial diversity recovered rapidly regardless of experimental group, patterns of microbial community composition reflected long-term instability following treatment with antibiotics alone, a pattern that was attenuated by fecal transfaunation. Covariation analysis revealed that certain taxa dominated bacterial associations, representing potential keystone species in lemur gut microbiota. Antibiotic resistance genes, which were universally present, including in lemurs that had never been administered antibiotics, varied across individuals and treatment groups.
Conclusions Long-term, integrated study post antibiotic-induced microbial imbalance revealed differential, metric-dependent evidence of recovery, with beneficial effects of fecal transfaunation on recovering community composition, and potentially negative consequences to lemur resistomes. Beyond providing new perspectives on the dynamics that govern host-associated communities, particularly in the Anthropocene era, our holistic study in an endangered species is a first step in addressing the recent, interdisciplinary calls for greater integration of microbiome science into animal care and conservation.
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Abstract Antibiotic treatment significantly impacts the human gut microbiota, but quantitative understanding of how antibiotics affect community diversity is lacking. Here, we build on classical ecological models of resource competition to investigate community responses to species-specific death rates, as induced by antibiotic activity or other growth-inhibiting factors such as bacteriophages. Our analyses highlight the complex dependence of species coexistence that can arise from the interplay of resource competition and antibiotic activity, independent of other biological mechanisms. In particular, we identify resource competition structures that cause richness to depend on the order of sequential application of antibiotics (non-transitivity), and the emergence of synergistic and antagonistic effects under simultaneous application of multiple antibiotics (non-additivity). These complex behaviors can be prevalent, especially when generalist consumers are targeted. Communities can be prone to either synergism or antagonism, but typically not both, and antagonism is more common. Furthermore, we identify a striking overlap in competition structures that lead to non-transitivity during antibiotic sequences and those that lead to non-additivity during antibiotic combination. In sum, our results establish a broadly applicable framework for predicting microbial community dynamics under deleterious perturbations.
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