Abstract
BackgroundA current focus of biofilm research is the chemical interaction between microorganisms within the biofilms. Prerequisites for this research are bioassay systems which integrate reliable tools for the planning of experiments with robot-assisted measurements and with rapid data processing. Here, data structures that are both human- and machine readable may be particularly useful.ResultsIn this report, we present several simplification and robotisation options for an assay of bacteria-induced biofilm formation by the freshwater diatom Achnanthidium minutissimum. We also tested several proof-of-concept robotisation methods for pipetting, as well as for measuring the biofilm absorbance directly in the multi-well plates. Furthermore, we exemplify the implementation of an improved data processing workflow for this assay using the Konstanz Information Miner (KNIME), a free and open source data analysis environment. The workflow integrates experiment planning files and absorbance read-out data, towards their automated processing for analysis.ConclusionsOur workflow lead to a substantial reduction of the measurement and data processing workload, while still reproducing previously obtained results in the A. minutissimum biofilm assay. The methods, scripts and files we designed are described here, offering adaptable options for other medium-throughput biofilm screenings.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0676-9) contains supplementary material, which is available to authorized users.
Highlights
A current focus of biofilm research is the chemical interaction between microorganisms within the biofilms
Human- and machine-readable data processing Regarding our use of the plate layout worksheets and Konstanz Information Miner (KNIME), we found that using such software for managing experimental workflows is advantageous [26, 27]
Because we show in several examples that staining with crystal violet is not strictly required for the detection of Achnanthidium minutissimum biofilms, our workflow may enable a broad range of existing plate-reading setups to be used for biofilm assays, while reducing chemical waste
Summary
A current focus of biofilm research is the chemical interaction between microorganisms within the biofilms. Many diatoms produce and secrete extracellular polymeric substances (EPS) which are a major component of their extracellular polymeric matrices, and which convey motility and substrate adherence [3, 4] Such aggregates of microbes that are embedded in a matrix of secreted EPS form so called biofilms [5]. Inspired by other biofilm assay approaches which include automated steps [13, 14], we aimed to improve the A. minutissimum bioassay described above with semiautomated pipetting and absorbance read-out methods. We wanted to improve the preparation of sample metadata and biofilm measurement data for analysis, adopting an already widely used tool in nucleotide sequencing and biochemical screening: the Konstanz Information Miner (https://www.knime.org/) (KNIME; [15, 16]). The objective of this study is to explain the above-mentioned automation options, and to present compelling evidence for their improvement potential using several examples from a laborious diatom biofilm assay
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
