Presentation Title

Establishment of Coastal Microbe Culturing, Strain Collection, and Analytical Techniques with the Purpose of Developing a Coastal Microbial Community Standard

Faculty Mentor

Elinne Becket

Start Date

23-11-2019 12:30 PM

End Date

23-11-2019 12:45 PM

Location

Markstein 205

Session

oral 3

Type of Presentation

Oral Talk

Subject Area

biological_agricultural_sciences

Abstract

The development of mock microbial community standard (MCS) is crucial for standardizing microbiome analyses to detect workflow biases, which can cause inaccurate results in studying microbial populations. Such mock MCSs have been produced for a variety of microbial niches, but not for marine environments. As microbes have unique characteristics and therefore unique analytical biases in different niches, we sought to create a marine-specific MCS. In order to accurately create an MCS containing marine microbes, the development of culturing, strain collection, and analytical techniques on marine microbial strains were required. Culturing was done using modified marine media recipes to culture a larger number of strains and used to build a strain collection. Cultured isolates and total coastal microbiomes were analyzed using 16S rRNA sequencing (Sanger and Next-Generation Sequencing) in order to type isolates and establish community profiles, respectively. Although the microbial standard is still in development, multiple strains of bacteria have been isolated and characterized, such as Vibrio spp. and Rhodopseudomonas palustris, and a first-pass of a community profile has been created, revealing a roadmap for what strains should be included in the MCS. A combination of trypan blue staining and washing methods have also been established for the accurate counting of each culture to be included in the final standard. The developed marine MCS is to be used to standardize internal lab analytical pipelines, to check for chimeric sequences in sequencing library preparations, as well as to be made available to all CSU labs studying marine microbiomes.

This document is currently not available here.

Share

COinS
 
Nov 23rd, 12:30 PM Nov 23rd, 12:45 PM

Establishment of Coastal Microbe Culturing, Strain Collection, and Analytical Techniques with the Purpose of Developing a Coastal Microbial Community Standard

Markstein 205

The development of mock microbial community standard (MCS) is crucial for standardizing microbiome analyses to detect workflow biases, which can cause inaccurate results in studying microbial populations. Such mock MCSs have been produced for a variety of microbial niches, but not for marine environments. As microbes have unique characteristics and therefore unique analytical biases in different niches, we sought to create a marine-specific MCS. In order to accurately create an MCS containing marine microbes, the development of culturing, strain collection, and analytical techniques on marine microbial strains were required. Culturing was done using modified marine media recipes to culture a larger number of strains and used to build a strain collection. Cultured isolates and total coastal microbiomes were analyzed using 16S rRNA sequencing (Sanger and Next-Generation Sequencing) in order to type isolates and establish community profiles, respectively. Although the microbial standard is still in development, multiple strains of bacteria have been isolated and characterized, such as Vibrio spp. and Rhodopseudomonas palustris, and a first-pass of a community profile has been created, revealing a roadmap for what strains should be included in the MCS. A combination of trypan blue staining and washing methods have also been established for the accurate counting of each culture to be included in the final standard. The developed marine MCS is to be used to standardize internal lab analytical pipelines, to check for chimeric sequences in sequencing library preparations, as well as to be made available to all CSU labs studying marine microbiomes.