Influence of Medicated Feed on the Catfish Pond Microbiome:

Assessment from Two Farms with Different Management Strategies

Divya Rose1,2, Caitlin Older3, Brad Richardson3, Cyndi Ware1,2, Marsha Lewis1,2, Geoff Waldbieser3, Lester Khoo1,2, Hasan Tekedar4, Andy Perkins5, Larry Hanson4, T. Graham Rosser4, David Wise2,6 and Matt Griffin1,2.

1Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, MS 38776; 2Thad Cochran National Warmwater Aquaculture Center, Delta Research and Extension Center, Mississippi State University, Stoneville, MS 38776; 3Warmwater Aquaculture Research Unit, Agriculture Research Service, U.S. Department of Agriculture, Stoneville, MS 38776; 4Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762; 6Mississippi Agriculture and Forestry Experiment Station, College of Forest Resources, Mississippi State University, MS 38776

ABSTRACT

Mississippi is the largest catfish producer in the United States, producing 58% of U.S farm-raised catfish; with active aquaculture ponds covering >36,000 acres. The majority of Mississippi catfish production is in “The Delta” region in the western part of the state. Bacterial disease accounts for most disease related losses. Prophylactic vaccines exist for Edwardsiella ictaluri and Flavobacterium columnare, but at present, only the orally delivered E. ictaluri vaccine has gained widespread industry adoption.  Due to limited efficacious vaccines, feed restriction or antibiotic intervention are the most practiced management strategies to control bacterial outbreaks in catfish ponds. Reports from the Aquatic Research and Diagnostic Laboratory (ARDL) in Stoneville, MS, show an increase in antibiotic resistant (ABR) bacterial isolates over the past decade. Considering these developments, a metagenomic assessment was performed on pond water samples from two adjacent catfish farms (<4 miles apart): each employing different strategies for antibiotic use.  Both farms focus on channel catfish production and vaccinate their fingerling stocks using an orally delivered, live attenuated E. ictaluri vaccine.  Farm A uses medicated feed in response to disease outbreaks, while Farm B employs feed restriction and does not rely on antibiotic intervention.  Herein, the influence of on-farm antibiotic use on catfish pond microbial communities was assessed. High throughput 16S rRNA gene sequencing was performed on 56 pond water samples (33 from Farm A; 23 from Farm B) to assess bacterial community structure in ponds across both farms. Comparative analysis of relative abundance of multiple bacterial species revealed differences across the two farms. When analysis was limited to bacterial genera significant to fish health, Mycobacterium spp. were found to be the most abundant genera.  Similarly, Flavobacterium spp. were consistently present on both farms, with Farm A (routine antibiotic use) having a slightly higher relative abundance.  Interestingly, both Chryseobacterium spp. and Lactococcus spp. were observed with high relative abundance in some ponds on Farm B (no antibiotic use), both of which are considered potentially emergent fish pathogens. Visualization of beta diversity revealed differences in bacterial community structure between the two farms, while alpha diversity assessments demonstrated differences between medicated and non-medicated ponds. These analyses illustrate a possible difference in the bacterial community composition between farms that employ antibiotic interventions versus farms that rely on restricted feeding.  These data lay the foundation for further research investigating the biological significance of the varied bacterial communities observed on these two farms.