148 (Part III) Pathogenic bacterial species (~10%) The selection of pathogenic bacterial species was based on a previously published study in which the 17 most-prevalent gut pathogens were chosen based on a report of the central laboratories of the Israeli Ministry of Health from 2015. Pathogenic species included were Salmonella enterica (subsp. Enterica serovar Enteritidis, Infantis and Muenchen), Campylobacter coli, Campylobacter jejuni (subsp. jejuni, ATCC 700819), Vibrio cholerae (AM-19226), Vibrio vulnificus, Shigella flexneri (2a str. 301), Shigella sonnei (53G), Listeria monocytogenes (serotypes 1/2a [str. 08-6569], 1/2b [str. 100810], 4b [str. F2365]), Escherichia coli (serotype O157:H7, str. Sakai), Staphylococcus aureus (subsp. aureus, MRSA252), Bacillus cereus (ATCC 14579), Enterococcus faecalis (V583) and Clostridium perfringens (ATCC 13124). (Part IV) Antibody-coated bacterial species (~9%) Antibody-coated bacterial species were selected based on a previous study that investigated IgA-coated microbiota in patients with IBD and healthy individuals.4 Antigens were incorporated into the phage library if the IgA coating index of the corresponding bacterial species was >10 and their relative abundances surpassed 10-6 in at least three patients with IBD or healthy individuals. Following this, nine bacterial species were selected: five from healthy individuals (Akkermansia muciniphila [ATCC BAA-835], Ruminococcus torques [ATCC 27756], Dorea formicigenerans [ATCC 27755], Ruminococcus bromii and Ruminococcus gnavus [AGR2154]) and four from patients with IBD (Blautia producta [ATCC 27340 = DSM 2950], Streptococcus lutetiensis [033], Bacteroides fragilis [YCH46], and Haemophilus parainfluenzae [T3T1]). (Part V) Probiotic bacterial species (~6%) The following probiotic bacterial species were rationally selected based on a recently published review:5 Lactobacillus rhamnosus GG, Lactobacillus acidophilus (NCFM), Lactobacillus plantarum (WCFS1), Lactobacillus salivarius (UCC118), Lactobacillus reuteri (DSM 20016), Escherichia coli Nissle (1917), Bifidobacterium breve (UCC2003), Bifidobacterium longum (35624), Bifidobacterium adolescentis (ATCC 15703), Bifidobacterium bifidum (PRL2010), Lactobacillus fermentum (IFO 3956), Lactobacillus gasseri (ATCC 33323 = JCM 1131) and Lactobacillus johnsonii (NCC 533). (Part VI) Virulence factors (~10%) Virulence factor antigen sequences were derived from the virulence factor database (VFDB), which contains antigens from pathogenic bacterial species.6 Sequences of 2,624 different genes of ‘set A’ of the VFDB were included, which represents established virulence factors confirmed by previous research. Chapter 4
RkJQdWJsaXNoZXIy MjY0ODMw