Fig. 4

Metabolic functions represented by gene transcription activities that changed significantly in the L. fermentum genome. Y-axis: relative mRNA read abundance values in percent; x-axis: time points of biofilm maturation (x-axis). Upper panel: Metabolism of carbohydrates via the pentose pathway, pyruvate and glycerol oxidation, as well as the pH neutralizing arginine deiminase pathways were highly expressed during L. fermentum’s establishment as a secondary biofilm colonizer. Phage related proteins, and 67 transposases were also highly upexpressed suggesting that gene rearrangements and phage induction are of major importance in L. fermentum colonization success. Genes encoding two membrane proteins, a glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and a manganese transporter (MntH) were also highly upexpressed and suggest that: L. fermentum is capable of forming a Lactate-Mn(II) complex that assists in the intracellular removal of reactive oxygen species (ROS); and employs GADPH in glycolysis or for attaching to primary colonizers in the in vitro biofilm community, which supports its further colonization and growth