Fig. 2

2D SDS-PAGE of proteins extracted from ruminal digesta. Digesta samples were obtained from different host species using different sampling methods, mixed with PBS/glycerol buffer and stored at −80 °C. In all gels size standards range from 10–250 kDa from bottom to top, isoelectric points (pI) range from pH 4–7 from left to right. a. Reindeer from Finland (MTT) fed silage forage based diet. Samples were obtained manually via ruminal cannulae. Protein extraction was carried out after bacterial enrichment by differential centrifugation and wash dilution stages. The gel shows severe protein degradation and spots are obscured by co-staining of humic compounds. b. Dairy cows from Sweden (SLU) fed a high protein diet. Samples were taken by intubation via ruminal cannula. Protein was extracted with no sample pre-processing. Spots identified: 1. Actin, Entodinium caudatum, GI: 3377675. Based on eight peptide matches, 36% coverage, theoretical size 41.7 kDa. 2. Actin, E. caudatum, GI: 3386579. Based on eight peptide matches, 34% coverage, theoretical size 41.7 kDa. c. Beef cattle from Scotland on a fattening high concentrate diet. Samples were taken by nasogastric intubation. Large particles were separated and removed by settling for 5 min before continuing to the protein extraction stages. Spots identified: 1. Methyl-CoM reductase McrA, Methanobrevibacter smithii, GI: 518094697. Based on five peptide matches, 12% coverage, theoretical size 61.1 kDa. 2. Methyl-CoM reductase beta subunit McrB, M. ruminantium M1, GI:288561184. Based on three peptide matches, 8% coverage, theoretical size 47.2 kDa. 3. 5,10-methylenetetrahydromethanopterin reductase, M. ruminantium M1 GI:288559826. Based on five peptide matches, 22% coverage, theoretical size 33.1 kDa. Additional proteins identified are described in Tables 1 and 2. d. Post-mortem digesta from lambs from Scotland fed on a finishing concentrate diet. Protein extraction was carried out on fresh samples after bacterial enrichment by differential centrifugation and wash dilution stages. Proteins identified are described in Tables 1 and 2