16S rRNA Clone Library The amount of sampled material was limited due to little faeces in the rectum of the polar bears, and only three faeces samples gave sufficient DNA yield to make 16S rRNA gene clone libraries. A 16S rRNA gene clone library was made with DNA extracted from CYC202 faeces from bear no. 6, 7 and 8. Total genomic DNA was extracted using the QIAmp DNA stool kit (Qiagen, Solna, Sweden) according to the protocol provided by the producer, and DNA quantified using a NanoDrop® ND-1000 Spectrophotometer (260 nm) (Thermo Fisher Scientific, Waltham, USA). Two parallel 16S rRNA gene PCR amplifications on DNA from each of the three animals were performed,

using primers 16S-27F and 16S-1494R (Table 6), in a reaction mixture containing 1× HotStartTaq DNA master mix (Qiagen), 0.3 μM of each primer, and 20 ng of extracted DNA solution in a final volume of 50 μl. PCR amplification was initiated by denaturation at 95°C for 15 min and then 30 cycles of 94°C for 30 s, 50°C for 30 s, and 72°C for 2 min, with a final extension at 72°C for 10 min. The 16S rRNA gene amplicons were pooled and cloned using the TOPO TA Cloning® Kit for Sequencing (Invitrogen, California, USA), and transformed by heat-shock into One Shot® Competent Escherichia coli cells (Invitrogen). Positive clones were randomly selected and recombinant plasmids extracted using QIA prep spin miniprep kit (Qiagen). Extracted DNA was quantified using

a NanoDrop ND-1000 Spectrophotometer (260 Dorsomorphin nm), and sequenced on a 3130 Genetic analyzer (Applied Biosystems, Foster City, USA) using the ABI BigDye Terminator G protein-coupled receptor kinase chemistry. The sequencing primers (Invitrogen) used were M13 forward primer, M13 reverse primer, and the universal bacterial 16S

rRNA primer Bact338, corresponding to nucleotide position 338-355 of E. coli (Table 6). Table 6 Primers used for PCR and sequencing Name Primer sequence (5′-3′) Gene target Reference BlaF CATTTCCGTGTCGCCCTTATTCC bla TEM [52] BlaR GGCACCTATCTCAGCGATCTGTCTA bla TEM [52] TemI3 TGGTTTATTGCTGATAAATCTGGAG bla TEM [15] TemI5a TTAAAAGTGCTCATCATTGGAAAAC bla TEM [15] TemI5b CTGTTGAGATCCAGTTCGATGTA bla TEM [15] 16S-27F AGAGTTTGATCCTGGCTCAG 16S rRNA [53] 16S-1494R CTACGGCTACCTTGTTACGA 16S rRNA [53] Bact338 GCTGCCTCCCGTAGGAGT 16S rRNA [54] Sequence analysis The 16S rRNA gene sequences were assembled using the program Lasergene™ Seqman v. 7.1.0. (DNASTAR Inc.). Putative chimeric sequences were evaluated using the Chimera Detection Program which is part of the SimRank 2.7 package available through the Ribosomal Database Project (RDP) [42]. Sequences generated were first compared to sequences obtained from the RDP II (Classifier: Naive Bayesian rRNA Classifier Version 1.0, November 2003; The nomenclature taxonomy of Garrity and Lilburn, release 6.0) and then compared to GenBank sequences using BLAST (Basic Local Alignment Search Tool) [43]. The 16S rRNA gene sequences were automatically aligned by CLUSTAL-W in the software package BioEdit (v. 5.0.9) to give a uniform length.