Effect of the growth medium on the cellular fatty acid composition of aeromonads: consequences for the chemotaxonomic differentiation of DNA hybridization groups in the genus Aeromonas

Mining fatty acid databases for detection of novel compounds in aerobic bacteria

This study examines how the discriminatory power of an automated bacterial whole-cell fatty acid identification system can be significantly enhanced by exploring the vast amounts of information accumulated during 15 years of routine gas chromatographic analysis of the fatty acid content of aerobic bacteria. Construction of a global peak occurrence histogram based upon a large fatty acid database is shown to serve as a highly informative tool for assessing the delineation of the naming windows used during the automatic recognition of fatty acid compounds. Along the lines of this data mining application, it is suggested that several naming windows of the Sherlock MIS TSBA50 peak naming method may need to be re-evaluated in order to fit more closely with the bulk of observed fatty acid profiles. At the same time, the global peak occurrence histogram has put forward the delineation of 32 new peak naming windows, accounting for a 26% increase in the total number of fatty acid features taken into account for bacterial identification. By scrutinizing the relationships between the newly delineated naming windows and the many taxonomic units covered within a proprietary fatty acid database, all new naming windows were proven to correspond with stable features of some specific groups of microorganisms. This latter analysis clearly underscores the impact of incorporating the new fatty acid compounds for improving the resolution of the bacterial identification system and endorses the applicability of knowledge discovery in databases within the field of microbiology.

Characterization of Escherichia coli isolates from different fecal sources by means of classification tree analysis of fatty acid methyl ester (FAME) profiles

Microbial source tracking (MST) methods need to be rapid, inexpensive and accurate. Unfortunately, many MST methods provide a wealth of information that is difficult to interpret by the regulators who use this information to make decisions. This paper describes the use of classification tree analysis to interpret the results of a MST method based on fatty acid methyl ester (FAME) profiles of Escherichia coli isolates, and to present results in a format readily interpretable by water quality managers. Raw sewage E. coli isolates and animal E. coli isolates from cow, dog, gull, and horse were isolated and their FAME profiles collected. Correct classification rates determined with leaveone-out cross-validation resulted in an overall low correct classification rate of 61%. A higher overall correct classification rate of 85% was obtained when the animal isolates were pooled together and compared to the raw sewage isolates. Bootstrap aggregation or adaptive resampling and combining of the FAME profile data increased correct classification rates substantially. Other MST methods may be better suited to differentiate between different fecal sources but classification tree analysis has enabled us to distinguish raw sewage from animal E. coli isolates, which previously had not been possible with other multivariate methods such as principal component analysis and cluster analysis.

Adaptational changes in cellular fatty acid branching and unsaturation of Aeromonas species as a response to growth temperature and salinity

The effects of growth temperature and salinity on the cellular fatty acids were investigated on Aeromonas caviae, Aeromonas hydrophila and Aeromonas sobria. Under optimal growth conditions, fatty acids patterns were dominated by even-numbered chains C(16:0), C(16:1cis9), C(18:1cis11), C(12:0) and C(14:0). Growth temperature modifications induced, in the three Aeromonas species, important changes in fatty acid (i) unsaturation, (ii) branching and (iii) chain length. An important decrease in the C(18:1cis11) fatty acid content was observed for the three species below 15 degrees C and above 25 degrees C. The evolution of C(18:1cis11) and C(16:0) showed a mirror image for the three Aeromonas species. Low NaCl concentrations did not elicit significant changes in the fatty acids content of the three Aeromonas species. However, for high NaCl concentration in the medium, the growth ability was related to an important decrease of the unsaturated to saturated fatty acids ratio indicating a membrane rigidification. Thermal and salinity adaptations were branched fatty acid-dependent for A. caviae, whereas this phenomenon was less significant for A. hydrophila and A. sobria.

Isolation of small-subunit rRNA for stable isotopic characterization

Small-subunit ribosomal RNA (SSU rRNA) has several characteristics making it a good candidate biomarker compound: it is found in bacteria, archaea and eukaryotes; it is quickly degraded extracellularly, hence SSU rRNA extracted from a sample probably derives from the currently active population; it includes both conserved and variable regions, allowing the design of capture probes at various levels of phylogenetic discrimination; and rRNA sequences from uncultured species can be classified by comparison with the large and growing public database. Here we present a method for isolation of specific classes of rRNAs from mixtures of total RNA, employing biotin-labelled oligonucleotide probes and streptavidin-coated paramagnetic beads. We also show that the stable carbon isotope composition of Escherichia coli total RNA and SSU rRNA reflects that of the growth substrate for cells grown on LB, M9 glucose and M9 acetate media. SSU rRNA is therefore a promising biomarker for following the flow of carbon, and potentially nitrogen, in natural microbial populations. Some possible applications are discussed.

Growth medium affects the cellular fatty acid composition of Pasteurellaceae

We studied the cellular fatty acid composition of 10 Actinobacillus (A.) and Pasteurella (P.) reference strains grown on 2 types of agar by the MIDI Microbial Identification System (MIS). A. capsulatus, A. equuli, A. lignieresii, A. ureae, A. dagmatis, P. gallinarum, P. haemolytica, P. multocida, P. pneumotropica biotypes Heyl and Jawetz were grown on GC agar supplemented with ascitic fluid and X and V factor (Levinthal's agar = LA agar) or GC agar supplemented with vitox and hemoglobin (VH agar) on 3 to 7 and 7 to 16 occasions respectively and fatty acid methylester (FAME) profiles were submitted to principal component analysis (PCA). All Pasteurellaceae strains showed FAME profiles typical for the family. Maximum coefficients of variation of the percentage of the 3 major FAMEs 14:0, 16:0, and 16:1 cis were 0.03, 0.03 and 0.03 for Pasteurellaceae strains grown on VH agar and 0.09, 0.17 and 0.09 respectively for strains grown on LA agar. PCA of FAME profiles obtained with growth from LA agar generally did not allow species separation of the Pasteurellaceae but most species were clearly discriminated by PCA when they were grown on VH agar. Our findings indicate that the growth medium had a significant effect on the reproducibility of fatty acid profiling in Pasteurellaceae and that PCA of fatty acid data obtained under standardized growth conditions may discriminate Pasteurellaceae species.