Insights into Aquatic Biofilm Dynamics by High-Throughput Identification of Bacterial Isolates and Full-Length 16S rRNA Gene Surveys

C.E. Credits: P.A.C.E. CE Florida CE
Speaker

Abstract

Microbial biofilms form on all aquatic surfaces and can harbor pathogenic bacteria. In the aquaculture industry, Flavobacteria species can cause serious diseases and lead to high mortality. These disease outbreaks can reoccur on potential reservoir of these pathogens are biofilms. We characterized the biofilms in a commercial trout farm by filtering water entering and leaving the raceways and collecting surface swabs from walls and baffles. DNA was extracted and either the V4 region of the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq or the V1 to V9 regions were amplified and sequenced on a PacBio Sequel II. During the course of this study the raceways walls were not cleaned after stocking the fish, so the age of the fish reflects the age of the biofilm. The data analysis revealed the biofilms in raceways harboring the youngest fish had a simple community and in raceways that harbored older fish had more complex communities. We also cultured hundreds of bacteria from this site. 570 isolates were grown up in broth, their DNA extracted and the V1-V9 region of the 16S rRNA gene amplified using the Shoreline Biome DNA V1-V9 kit. Six different extraction plates were used and six SMRTbells with different barcodes were used to create libraries that were sequenced on a PacBio Sequel II. The data was analyzed using the SBanalyzer, DADA2 and Qiime2. This allowed the identification of the isolates. We identified bacteria that belonged to 22 families and 48 genera. In summary, PacBio, full-length 16S rRNA gene sequences provides high resolution insights into microbial communities and allows the rapid identification of bacteria.

Learning Objectives:

1. Gain an understanding of the changes in composition and complexity of microbial biofilms over time

2. Learn a novel approach for identifying hundreds of bacterial strains by sequencing the full-length 16S rRNA gene using a PacBio Sequel2


Show Resources
You May Also Like
SEP 14, 2021 7:00 AM PDT
C.E. CREDITS
SEP 14, 2021 7:00 AM PDT
Date: September 14, 2021 Time: 7am PDT, 10am EDT, 4pm CEST A conventional thermal cycler has long been a commodity product in the lab and end-point PCR techniques can be completed almost wit...
JUN 09, 2021 7:00 AM PDT
C.E. CREDITS
JUN 09, 2021 7:00 AM PDT
Date: June 9, 2021 Time: 09 June 2021, 7am PDT, 10am EDT, 4pm CEST cells with dramatic implications on the validity of past cell culture related research. The fact that at least 509 cell lin...
DEC 09, 2021 11:00 AM PST
C.E. CREDITS
DEC 09, 2021 11:00 AM PST
Date: December 09, 2021 Time: 11:00am (PDT), 2:00pm (EDT) The burden of antimicrobial resistance (AMR) has been acknowledged worldwide by leading health institutes. Besides the need for new...
NOV 30, 2021 10:00 AM PST
C.E. CREDITS
NOV 30, 2021 10:00 AM PST
Date: November 30, 2021 Time: 10:00am (PDT), 1:00pm (EDT) The prevalence of thyroid disease worldwide has served as a catalyst for healthcare providers to study various tools and methods to...
NOV 09, 2021 11:00 AM PST
C.E. CREDITS
NOV 09, 2021 11:00 AM PST
Date: November 09, 2021 Time: 11:00am (PDT), 02:00pm (EDT) Clinical translation of human pluripotent stem cells (hPSCs) requires advanced strategies that ensure safe and robust long-term gro...
JUN 22, 2021 10:00 AM PDT
C.E. CREDITS
JUN 22, 2021 10:00 AM PDT
Date: June 22, 2021 Time: 10:00am (PDT), 1:00pm (EDT) Antimicrobial resistance (AMR) has emerged as one of the principal public health problems of the 21st century. It threatens the effectiv...
Loading Comments...
Show Resources