Supplementary Table 2

List of primers used for qRT-PCR experiments

Name / Specificity / Forward (5’ è 3’) / Reverse (5’ è 3’) / Target / Reference
rpoB / rpoB / aacatcggtttgatcaac / cgttgcatgttggtacccat / rpoB / 27
Lachno / Lachnospiraceae / cggtacctgactaagaagc / agtttyattcttgcgaacg / 16S rDNA / 27
Eub338 / All Bacteria / ACTCCTACGGGAGGCAGCAG / ATTACCGCGGCTGCTGG / 16S rDNA / S1
Bact934 / Bacteroidetes / GGARCATGTGGTTTAATTCGATGAT / AGCTGACGACAACCATGCAG / 16S rDNA / S1
Firm / Firmicutes / GGAGYATGTGGTTTAATTCGAAGCA / AGCTGACGACAACCATGCAC / 16S rDNA / S1
Bac32 / Bacteroides-Prevotella / AACGCTAGCTACAGGCTT / CCAATGTGGGGGACCTTC / 16S rDNA / S1
W102-W105 / All Bacteria / CGGTGAATACGTTCYCGG / GGWTACCTTGTTACGACTT / 16S rDNA / S2
ASF 360 / Lactobacillus / CGGCGGATGGGTGAGTAAC / GTATTAGCACCTGTTTCCAAGTGGTA / 16S rDNA / S3
ASF 361 / Lactobacillus murinus / GTGGCGAACGGGTGAGTAA / GCACCTGTTTCCAAGTGTTATCC / 16S rDNA / S3
ASF 519 / Bacteroides / ATTGCCGTTGGAAATGTTATCC / CCTTCGCAATCGGAGTTCTG / 16S rDNA / S3
ASF 457 / Flexistipes / TGCAAGAATGAAACTCAAAGGAAT / TAAGGTTCTTCGGTTAGCATCGA / 16S rDNA / S3
ASF 356 / Clostridium / AACGCCGCGTGAAGGAA / ACGCTTGCCCCCTACGTATT / 16S rDNA / S3
ASF 492 / Eubacterium plexicaudatum / TGGAGCATGTGGTTTAATTCGA / TGCACCACCTGTCTGCAATG / 16S rDNA / S3
ASF 500 / Firmicutes / GCTGCTAATACCGCATGATATGTC / CAGACGCGAGTCCATCTCAGA / 16S rDNA / S3
ASF 502 / Clostridium / GCTACAATGGCGTAAACAAAGAGA / TCCGAACTGAGACGTTATTTTTGA / 16S rDNA / S3
Bacteroides / Bacteroides / GAGAGGAAGGTCCCCCAC / CGCTACTTGGCTGGTTCAG / 16S rDNA / S4
Bacillus / Bacillus / GCGGCGTGCCTAATACATGC / CTTCATCACTCACGCGGCGT / 16S rDNA / 25
A.baum16S / Acinetobacter Baumanni / GGAACTTTAAGGATACTGCCAGTG / GGTCGTAAGGGCCATGATGAC / 16S rDNA / S5
Ac436-676 / Acinetobacter / TTTAAGCGAGGAGGAGG / ATTCTACCATCCTCTCCC / 16S rDNA / S6

List of probes used for FISH experiments

Name / Specificity / Sequence (5’ è 3’) / Target position / Reference
Eub338 / Eubacteria / GCTGCCTCCCGTAGGAGT / 16S rRNA, 338-355 / S7
Non338 / None / ACTCCTACGGGAGGCAGC / None / S8
ACA652 / Acinetobacter / atcctctcccatactcta / 16S rRNA, 652-669 / S9
CteA / Comamonas testosteroni / catgacccggggatattagc / 16S rRNA, 462-481 / S10
ALF968 / Alphaproteobacteria / ggtaaggttctgcgcgtt / 16S rRNA, 968-985 / S11
BET42a / Betaproteobacteria / gccttcccacttcgttt / 23S rRNA, 1027-1043 / S12
GAM42a / Gammaproteobacteria / gccttcccacatcgttt / 23S rRNA, 1027-1043 / S12
CF319a / Flavobacteria / tggtccgtgtctcagtac / 16S rRNA, 319-336 / S13
BAC303 / Bacteroidaceae, Prevotellaceae / ccaatgtgggggacctt / 16S rRNA, 303-319 / S13
Pce / Burkholderia / cccatcgcatctaacaat / 23S rRNA, 1406-1423 / S14
COM1424 / Comamonas / acctcattctggcgaga / 16S rRNA, 1424-1440 / S15
LGC354A / Firmicutes / tggaagattccctactgc / 16S rRNA, 354-371 / S16
LGC354B / Firmicutes / cggaagattccctactgc / 16S rRNA, 354-371 / S16
LGC254C / Firmicutes / ccgaagattccctactgc / 16S rRNA, 354-371 / S16

Supplementary references

S1. Rehman, A., et al. 2011. Nod2 is essential for temporal development of intestinal microbial communities Gut. doi:10.1136.

S2. Moletta-Denat, M., et al. 2010. Selective microbial aerosolization in biogas demonstrated by quantitative PCR. Bioresour. Technol. 101:7252-7257.

S3. Deloris-Alexander, A., et al. 2006 Quantitative PCR assays for mouse enteric microbiota reveal strain-dependent differences in composition that are influenced by the microenvironment. Mammalian Genome. 17:1093-1104.

S4. Guo, X., et al. 2008. Development of a real-time PCR method for Firmicutes and Bacteroidetes in faeces and its application to quantify intestinal population of obese and lean pigs. Lett. Appl. Microbiol. 47:367-373.

S5. Rios-Licea, M. M., F. J. Bosques, A. C. Arroliga, J. O. Galindo-Galindo, and E. Garza-Gonzalez. 2010. Quadruplex real-time quantitative PCR assay for the detection of pathogens related to late-onset ventilator-associated pneumonia: a preliminary report. J. Microbiol. Methods. 81:232-234.

S6. Vanbroekhoven, K., A. Ryngaert, P. Wattiau, R. Mot, and D. Springael. 2004. Acinetobacter diversity in environmental samples assessed by 16S rRNA gene PCR-DGGE fingerprinting. FEMS Microbiol. Ecol. 50:37-50.

S7. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.

S8. Manz, W., et al. 1993. In situ identification of bacteria in drinking water and adjoining biofilms by hybridization with 16S and 23S rRNA-directed fluorescent oligonucleotide probes. Appl. Environ. Microbiol. 59:2293-2298.

S9. Wagner, M., et al. 1994. Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 60:792-800.

S10. Bathe, S., and M. Hausner. 2006. Design and evaluation of 16S rRNA sequence based oligonucleotide probes for the detection and quantification of Comamonas testosteroni in mixed microbial communities. BMC Microbiol. 6:54.

S11. Neef, A., et al. 1996. Population analysis in a denitrifying sand filter: conventional and in situ identification of Paracoccus spp. in methanol-fed biofilms. Appl. Environ. Microbiol. 62:4329-4339.

S12. Manz, W., R. Amann, W. Ludwig, M. Wagner, and K. H. Schleifer. 1992. Phylogenetic oligonucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15:593–600.

S13. Manz, W., R. Amann, W. Ludwig, M. Vancanneyt, and K. H. Schleifer. 1996. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology. 142:1097-1106.

S14. Schleifer, K. H., et al. 1992. Nucleic acid probes for the identification and in situ detection of pseudomonads. Pseudomonas: Molecular Biology and Biotechnology (Galli E, Silver S & Witholt B, ed), pp. 127–134.

S15. Amann, R., J. Snaidr, M. Wagner, W. Ludwig, and K. H. Schleifer. 1996. In situ visualization of high genetic diversity in a natural microbial community. J. Bacteriol. 178:3496–3500.

S16. Meier, H., R. Amann, W. Ludwig, and K. H. Schleifer. 1999. Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G + C content. Syst. Appl. Microbiol. 22:186-196.