Conventional diversity metrics underestimate gut microbiome disruption under florfenicol exposure in Nile tilapia (Oreochromis niloticus)
Abstract
The gut microbiome is an integral component of fish health and growth performance and therefore represents an important production factor in aquaculture. Antibiotics are a major stressor, not only by disturbing microbial diversity, but also by altering microbial interactions involved in digestion, colonization resistance and functional redundancy. Current risk assessments, however, rely largely on diversity-based evaluations and rarely consider changes in network topology. Here, we investigated the impact of florfenicol on the gut microbiome of Nile tilapia ( Oreochromis niloticus ) using 16S rRNA sequencing, combining conventional diversity metrics with microbial co-occurrence network modelling. While the microbial community remained overall stable at the diversity level, with treatment explaining only a minor proportion of the observed variation, network analysis revealed substantial fragmentation and a less robust network structure. Network connectivity was significantly reduced, with a near-complete turnover of central hub taxa in the florfenicol network. Our findings demonstrate that diversity-based assessments alone may substantially underestimate the extent of antibiotic-induced microbiome disturbance, with network analysis capturing changes within the community that are highly relevant for microbiome stability and would otherwise remain undetected when evaluations are restricted to diversity metrics.
Related
- Progressive Post-Acute Gut Microbiome Disruption Following SARS-CoV-2 Infection in Mice
- Comprehensive Proteomics Reveals Acute Osmoregulatory Responses in the Intestine of Oreochromis mossambicus Under Salinity, Alkalinity, and Combined Saline-Alkaline Stress.
- Chronic Erosive Dermatopathy (CED) Associated with Ectoparasite Infestation in Nile Tilapia Post-Larvae (Oreochromis niloticus Linnaeus, 1758).
- Effect of flaxseed oil in diet on fatty acid composition in the liver of Nile Tilapia (Oreochromis niloticus)
- Dietary Soybean and Kappaphycus sp. Differentially Modulate Gut Microbiota Diversity and Predicted Functional Profile in Nile Tilapia (Oreochromis niloticus).
BibTeX
@article{streb2026conventional,
title = {{Conventional diversity metrics underestimate gut microbiome disruption under florfenicol exposure in Nile tilapia (Oreochromis niloticus)}},
author = {Lisa-Marie Streb and Inácio Mateus Assane and Gabriela Freitas Pereira de Souza and Fabiana Pilarski and Anna Paula Queiroga and Susanne Walch and Susanne Rath and Michael Schloter},
journal = {Scientific Reports},
year = {2026},
month = oct,
doi = {10.1038/s41598-026-75240-6},
url = {https://www.nature.com/articles/s41598-026-75240-6},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Conventional diversity metrics underestimate gut microbiome disruption under florfenicol exposure in Nile tilapia (Oreochromis niloticus)
AU - Lisa-Marie Streb
AU - Inácio Mateus Assane
AU - Gabriela Freitas Pereira de Souza
AU - Fabiana Pilarski
AU - Anna Paula Queiroga
AU - Susanne Walch
AU - Susanne Rath
AU - Michael Schloter
PY - 2026
DA - 2026/10/12
JO - Scientific Reports
DO - 10.1038/s41598-026-75240-6
UR - https://www.nature.com/articles/s41598-026-75240-6
AB - The gut microbiome is an integral component of fish health and growth performance and therefore represents an important production factor in aquaculture. Antibiotics are a major stressor, not only by disturbing microbial diversity, but also by altering microbial interactions involved in digestion, colonization resistance and functional redundancy. Current risk assessments, however, rely largely on diversity-based evaluations and rarely consider changes in network topology. Here, we investigated the impact of florfenicol on the gut microbiome of Nile tilapia ( Oreochromis niloticus ) using 16S rRNA sequencing, combining conventional diversity metrics with microbial co-occurrence network modelling. While the microbial community remained overall stable at the diversity level, with treatment explaining only a minor proportion of the observed variation, network analysis revealed substantial fragmentation and a less robust network structure. Network connectivity was significantly reduced, with a near-complete turnover of central hub taxa in the florfenicol network. Our findings demonstrate that diversity-based assessments alone may substantially underestimate the extent of antibiotic-induced microbiome disturbance, with network analysis capturing changes within the community that are highly relevant for microbiome stability and would otherwise remain undetected when evaluations are restricted to diversity metrics.
SN - 2045-2322
ER -