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Melo-Bolívar JF, Ruiz Pardo RY, Hume ME, Nisbet DJ, Rodríguez-Villamizar F, Alzate JF, Junca H, Villamil Díaz LM. Establishment and characterization of a competitive exclusion bacterial culture derived from Nile tilapia (Oreochromis niloticus) gut microbiomes showing antibacterial activity against pathogenic Streptococcus agalactiae. PLoS One 2019; 14:e0215375. [PMID: 31050668 PMCID: PMC6499431 DOI: 10.1371/journal.pone.0215375] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/01/2019] [Indexed: 12/28/2022] Open
Abstract
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.
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Affiliation(s)
- Javier Fernando Melo-Bolívar
- Universidad de La Sabana, Faculty of Engineering, Campus Universitario del Puente del Común, Km 7 Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Ruth Yolanda Ruiz Pardo
- Universidad de La Sabana, Faculty of Engineering, Campus Universitario del Puente del Común, Km 7 Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
- Universidad de La Sabana, Faculty of Engineering, Grupo de Investigación en Procesos Agroindustriales, Campus Universitario del Puente del Común, Km 7 Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Michael E. Hume
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX, United States of America
| | - David J. Nisbet
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX, United States of America
| | - Fernando Rodríguez-Villamizar
- Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Centro de investigación Tibaitatá, Mosquera, Cundinamarca, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica- CNSG, Sede de Investigación Universitaria SIU, Grupo de Parasitología, Facultad de Medicina Universidad de Antioquia, Medellín, Colombia
| | - Howard Junca
- Microbiomas Foundation, Div. Ecogenomics & Holobionts, RG Microbial Ecology: Metabolism, Genomics & Evolution, Chía, Colombia
| | - Luisa Marcela Villamil Díaz
- Universidad de La Sabana, Faculty of Engineering, Campus Universitario del Puente del Común, Km 7 Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
- Universidad de La Sabana, Faculty of Engineering, Grupo de Investigación en Procesos Agroindustriales, Campus Universitario del Puente del Común, Km 7 Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
- * E-mail:
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Golby S, Ceri H, Gieg LM, Chatterjee I, Marques LLR, Turner RJ. Evaluation of microbial biofilm communities from an Alberta oil sands tailings pond. FEMS Microbiol Ecol 2012; 79:240-50. [PMID: 22029695 DOI: 10.1111/j.1574-6941.2011.01212.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Bitumen extraction from the oil sands of Alberta has resulted in millions of cubic meters of waste stored on-site in tailings ponds. Unique microbial ecology is expected in these ponds, which may be key to their bioremediation potential. We considered that direct culturing of microbes from a tailings sample as biofilms could lead to the recovery of microbial communities that provide good representation of the ecology of the tailings. Culturing of mixed species biofilms in vitro using the Calgary Biofilm Device (CBD) under aerobic, microaerobic, and anaerobic growth conditions was successful both with and without the addition of various growth nutrients. Denaturant gradient gel electrophoresis and 16S rRNA gene pyrotag sequencing revealed that unique mixed biofilm communities were recovered under each incubation condition, with the dominant species belonging to Pseudomonas, Thauera, Hydrogenophaga, Rhodoferax, and Acidovorax. This work used an approach that allowed organisms to grow as a biofilm directly from a sample collected of their environment, and the biofilms cultivated in vitro were representative of the endogenous environmental community. For the first time, representative environmental mixed species biofilms have been isolated and grown under laboratory conditions from an oil sands tailings pond environment and a description of their composition is provided.
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Affiliation(s)
- Susanne Golby
- Department of Biological Sciences, University of Calgary, Calgary AB, Canada
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