Genus-wide Bacillus species identification through proper artificial neural network experiments on fatty acid profiles

Gas chromatographic fatty acid methyl ester analysis of bacteria is an easy, cheap and fast-automated identification tool routinely used in microbiological research. This paper reports on the application of artificial neural networks for genus-wide FAME-based identification of Bacillus species. Using 1,071 FAME profiles covering a genus-wide spectrum of 477 strains and 82 species, different balanced and imbalanced data sets have been created according to different validation methods and model parameters. Following training and validation, each classifier was evaluated on its ability to identify the profiles of a test set. Comparison of the classifiers showed a good identification rate favoring the imbalanced data sets. The presence of the Bacillus cereus and Bacillus subtilis groups made clear that it is of great importance to take into account the limitations of FAME analysis resolution for the construction of identification models. Indeed, as members of such a group cannot easily be distinguished from one another based upon FAME data alone, identification models built upon this data can neither be successful at keeping them apart. Comparison of the different experimental setups ultimately led to a few general recommendations. With respect to the routinely used commercial Sherlock Microbial Identification System (MIS, Microbial ID, Inc. (MIDI), Newark, Delaware, USA), the artificial neural network test results showed a significant improvement in Bacillus species identification. These results indicate that machine learning techniques such as artificial neural networks are most promising tools for FAME-based classification and identification of bacterial species.