Experiments to investigate the expression and function of these genes in vivo are in progress. Methods Bacterial strains and culture conditions Capmatinib purchase Bacteroides fragilis strains used in this study are presented in Table 7. All strains were purchased from the United Kingdom National Culture Collection (UKNCC) except

638R which was a kind gift from Dr Sheila Patrick, Queen’s University, Belfast. Both B. fragilis strains and B. thetaiotaomicron VPI-5482 [42] were grown in an anaerobic chamber at 37°C. Cultures were grown without shaking in Brain Heart Infusion (BHI) broth supplemented with 50 μg/ml hemin and 0.5 μg/ml menadione. Media for plating was made from Brain Heart Infusion agar supplemented with 5% defibrinated sheep blood, 50 μg/ml

hemin and 0.5 μg/ml menadione. Bioinformatics and sequence analysis Members of the C10 protease family in B. fragilis were detected by BLAST analysis [43]. Sequences were aligned by CLUSTAL W [44] or T-Coffee [45]. Protein secondary structure was predicted using GorIV [46] and JPred [47]. Protein export signals were identified using the Geneticin algorithms using LipPred [23], LipoP [48], SignalP [25] and PSORTb [26]. Phylogenetic and molecular evolutionary analyses were conducted using VE-822 genetic-distance-based neighbour-joining algorithms [49] within MEGA Version 4.0 http://​www.​megasoftware.​net/​. Bootstrap analysis for 1000 replicates was performed to estimate the confidence of tree topology [50]. MegaBLAST [51] was used to search all NCBI genomes for Bfgi1 and Bfgi2. Molecular techniques Standard techniques were employed for molecular analysis [52]. Bacteroides genomic Pregnenolone DNA was prepared as described by [53]. Total microbial DNA was extracted from human faeces, collected under an ethically approved protocol, by a glass beads-Qiagen Stool kit method previously described [54]. PCR reactions were carried using 10-30 ng of genomic DNA from B. fragilis 638R as template and using Phusion Polymerase (New England Biolabs).

The primers Bfp3_F and Bfgi2_Int_F (Table 4) were used for detecting the attP sites for Bfgi2. Bfgi2_attB_F and Bfgi2_attB_R (Table 4) were used for determining the attB attachment sites for Bfgi2 integration. The primers TraQ_F and Int_F were used in testing for the presence of the circular intermediate for Bfgi1. Primers to detect the circular intermediate for both Bfgi1 and Bfgi2 were designed, pointing outwards, flanking the ends of each predicted element. Primers to detect the attB site in Bfgi2 were designed, pointing inwards, flanking the proposed excision point for the Bfgi2 prophage DNA. Total RNA isolation for Reverse Transcription analysis B. fragilis 638R and B. thetaiotaomicron VPI-5482 were cultured under anaerobic conditions until early logarithmic phase and the cultures were then immediately centrifuged for 15 minutes at 4000 × g. Total RNA extraction from B. fragilis 638R and B.