0379; LB: fRF, p = 0.0385; LB: uRF, p = 0.0381, dRF: fRF, p = 0.0121 and fRF: uRF, p = 0.0655; dRF: uRF, p = 0.1077. Proteomics analysis (i) Bottom-up LC-MS/MS analysis of the O157 cell pellet and lysate fractions

generated in Experiment I provided insights into the proteins being expressed by O157 in different media, under different growth conditions and at extended incubation time points. A total of 585 protein (2284 spectra) hits p38 MAPK signaling were identified by setting minimum characteristics for the identification confidence. However, of these only 218 O157 proteins matched a GS-1101 cell line higher threshold cut off, with 90% protein-80% peptide probability in the Scaffold Viewer, and RG7112 cost hence, were selected for analysis. The 218 O157 proteins were differentially expressed: 90 only under aerobic conditions, 37 only under anaerobic conditions and 91 under both conditions (data not shown), accounting for fewer proteins under anaerobic conditions. Interestingly, none of the O157 proteins expressed aerobically or anaerobically in either media were associated with direct virulence (e.g., the Locus of Enterocyte Effacement [LEE]-encoded proteins or Shiga toxins)

but were primarily associated with sequences homologous to other E. coli genomes (Backbone) (Additional file 1: Table S1). Considering that the rumen is an anaerobic microbiome, the 128/218 O157 proteins expressed anaerobically were examined in greater detail. www.selleck.co.jp/products/cetuximab.html These proteins were either unique to growth in LB (93/128), dRF (2/128), fRF (10/128) or, expressed in more than one media (14/128 in LB/dRF/fRF, 9/128 in dRF/fRF) (Figure 2). Specifically, the 35 proteins expressed anaerobically in fRF and dRF (unique and shared combined), were functionally associated with the osmotic adaptation pathway (OsmE), anaerobic respiration and oxidative stress pathway (YggE, MoaB, DmsB, FdoH), heat stress response (HchA), carbon starvation response (Slp),

energy metabolism and biosynthetic pathways (glycolytic/gluconeogenesis pathway, amino acid biosynthesis: AldoC, Crr, AnsB, PykF, Eno, GpmA, GadpH, CysK, Ttc, AhpC, YhcB), chaperones (DnaK, GroEL, HchA), transport (LamB, ManX, FadL, RbsB), outer membrane proteins/porins/channel (OmpC, TolC, YdeN, Slp, OmpA), tellurite resistance (TerD), lysozyme inhibitor (Ivy), chemotaxis (GgbP), and motility (FliC) (Table 3; Additional file 1: Table S1). Figure 2 Distribution of 128 anaerobically expressed O157 proteins, identified using bottom-up proteomics, amongst the media tested. LB, Luria-Bertani broth; dRF, depleted and filtered rumen fluid; fRF, filtered rumen fluid.