Research Article: Establishment and characterization of a competitive exclusion bacterial culture derived from Nile tilapia (Oreochromis niloticus) gut microbiomes showing antibacterial activity against pathogenic Streptococcus agalactiae

Date Published: May 3, 2019

Publisher: Public Library of Science

Author(s): Javier Fernando Melo-Bolívar, Ruth Yolanda Ruiz Pardo, Michael E. Hume, David J. Nisbet, Fernando Rodríguez-Villamizar, Juan F. Alzate, Howard Junca, Luisa Marcela Villamil Díaz, Olivier Habimana.


This study reports the characterization of the microbial community composition, and the establishment and dynamics of a continuous-flow competitive exclusion culture (CFCEC) derived from gut microbiomes of Nile tilapia (Oreochromis niloticus) specimens reared on aquaculture farms in Colombia. 16S rRNA gene amplicon Illumina sequencing was used to identify taxonomical changes in the CFCEC microbial community over time. The CFCEC was developed from adult tilapia from two farms in Colombia, and CFCEC samples were collected over two months. The pH varied from 6.25 to 6.35 throughout culturing, while anaerobic and aerobic cell counts stabilized at day 9, at 109 CFU mL-1 and were maintained to day 68. A variation in the CFCEC bacterial composition was observed over time. Cetobacterium was the most abundant in the first two days and coincided with a higher CFCEC supernatant antimicrobial effect against the fish pathogen Streptococcus agalactiae. Antimicrobial activity against S. agalactiae disappeared by day 3. Changes in bacterial composition continued to day 33 with Lactococcus spp. becoming the most abundant member of the community. In conclusion, the study of the CFCEC from intestinal tract of Nile tilapia (Oreochromis niloticus) by 16S rRNA gene sequencing allowed identification of predominant bacterial genera in the continuous-flow competitive exclusion culture exhibiting antibacterial activity against the fish pathogen Streptococcus agalactiae.

Partial Text

The world population has been in continuous growth and it is expected to reach more than 9.6 million by 2050 [1]. Therefore, the United Nations proposed, among their sustainable development goals, the objective to reduce malnutrition (Zero Hunger) in the world’s human population. To achieve this goal, food industries are expected to increase production. Among them, the fish industry hopes to increase production by 19% in 2024 [2]. Wild-captured fishes have reached their production limit, therefore, aquaculture is one of the best alternatives to cover the demand for fish products [3].

From 1973, The Nurmi concept or competitive exclusion has been developed [34]. This concept considers that the administration of intestinal microbiota from an adult animal to young animals could give protection against pathogenic bacteria [35]. In the present study, we developed a CFCEC with antibacterial activity against S. agalactiae. It was maintained in TSB medium reported in the successful development of a competitive exclusion culture from different animals including fish culture [36,37]. This medium is relatively inexpensive, easily obtainable and easily reproducible from off-the-shelf-ingredients, also appropriate to support the growth of aerobic and anaerobic bacteria. We did not intend to use complex customized media to mimic intestinal conditions of the fish intestine as it will not have the aforementioned advantages, important in foreseen scaling-up applications, and TSB has proven to be suitable medium for the purposes of quickly enriching consortia from intestinal homogenates of O. niloticus allowing the isolation of bacteria with probiotic activity [37].