Table S2. Information for antibiotic resistant fosmid inserts.

Clone
ID / No. of dupli-cates / Resis-tance
type / Resis-tancegene* / Best blastx hit for 5' end sequence / Best blastx hit for 3' end sequence / Taxonomic
assignment** / GenBank
ID
T4 / 1 / Tet / tetC / DNA topoisomerase I (Neisseria gonorrhoeae) / 3-isopropylmalate dehydrogenase (Neisseria mucosa) / S. alvi / JS807594
T8 / 7 / Tet / tetC / chaperonin HslO
(Neisseria polysaccharea) / No hit / S. alvi / JS807595
T9 / 2 / Tet / tetB / transposase, IS4 family (Escherichia coli) / No sequence / Unknown / JS807596
T13 / 1 / Tet / none / Single Strand Binding Protein (Bartonellahenselae) / 50S ribosomal protein L6
(Bartonellaschoenbuchensis) / Alpha1 / JS807558 JS807559
T2-5 / 3 / Tet / tetC / transport system
(Ochrobactrumintermedium) / No hit / Alpha1 / JS807560
TA1 / 2 / Tet / tetC / nitrilase (Neisseria mucosa) / No sequence / S. alvi / JS807607
TA3 / 3 / Tet / tetC / beta-N-acetylhexosaminidase (Simonsiella muelleri) / hypothetical protein NMB1087 (Neisseria meningitidis) / S. alvi / JS807599 JS807600
T3-2 / 1 / Tet / tetC / macrolide export ATP-binding macB (Neisseria mucosa) / putative fatty acid desaturase (Pectobacteriumatrosepticum) / S. alvi / JS807571 JS807572
T3-3 / 1 / Tet / tetC / tRNA pseudouridine synthase B (Neisseria mucosa) / peptidase M24
(Gallionella capsiferriformans) / S. alvi / JS807573 JS807574
T3-12 / 2 / Tet / none / bacteriophage transposase (Neisseria mucosa) / antetheine-phosphate adenylyltransferase (Neisseria sicca) / S. alvi / JS807586 JS807587
T3-7 / 2 / Tet / tetL / MATE efflux family protein (Sphingobiumchlorophenolicum) / Na+/H+ antiporter (Starkeya novella) / Alpha1 / JS807579 JS807580
T3-18 / 2 / Tet / tetC / FAD linked oxidase domain protein (Sinorhizobiummeliloti) / transposase InsB8 for insertion sequence IS26 (Yersinia pestis) / Alpha1 / JS807592 JS807593
T3-19 / 1 / Tet / tetC / polyribonucleotide nucleotidyltransferase
(Neisseria cinérea) / No hit / S. alvi / JS807563 JS807564
T3-21 / 1 / Tet / tetB / Ppx/GppA phosphatase (Ochrobactrumanthropi) / peptidyl-dipeptidaseDcp(Bartonellagrahamii) / Alpha1 / JS807565 JS807566
T3-28 / 3 / Tet / tetB / hypothetical protein
(Neisseria elongate) / TetB (Salmonella enterica) / S. alvi / JS807569
JS807570
Tc1 / 1 / Tet / tetB / hydroxyacylglutathione hydrolase (Neisseria wadsworthii) / No sequence / S. alvi / JS807613
Tc7 / 1 / Tet / tetC / No hit / No sequence / unknown / JS807611
Tc9 / 1 / Tet / tetB / DNA helicase RecG
(Neisseria wadsworthii) / No sequence / S. alvi / JS807610
Tc11 / 1 / Tet / tetC / M61 family peptidase
(Neisseria macacae) / No sequence / S. alvi / JS807614
Tc12 / 1 / Tet / tetB / 4-aminobutyrate transaminase (Neisseria shayeganii) / No sequence / S. alvi / JS807612
A1 / 4 / Amp/Tet / tetB / TetB (TETA(B) )
(Escherichia fergusonii) / pyruvate dehydrogenase
(Simonsiellamuelleri) / S. alvi / JS807616
A2-2 / 2 / Amp/Tet / tetB / coproporphyrinogen oxidase (Neisseria mucosa) / glutamine synthetase (Neisseria mucosa) / S. alvi / JS807617 JS807618
A2-5 / 2 / Amp/Tet / tetB / No hit / riboflavin synthase, (Neisseria sp.) / S. alvi / JS807619
A3-9 / 3 / Amp/Tet / tetB / No sequence / haemagluttinin protein (Escherichia coli) / G. apicola / JS807644
A3-11 / 1 / Amp / none / transglutaminase family (Neisseria elongate) / transposaseTnpA (Escherichia coli) / S. alvi / JS807620 JS807621
A3-15 / 1 / Amp/Tet / tetD / hypothetical protein (Eikenella corrodens) / No hit / S. alvi / JS807628 JS807629
A3-16 / 1 / Amp/Tet / tetB / hypothetical protein (Eikenella corrodens) / No hit / S. alvi / JS807630 JS807631
A3-17 / 1 / Amp/Tet / tetB / transposase Tn3 (Salmonella entérica) / hypothetical protein (Eikenella corrodens) / S. alvi / JS807632 JS807633
A3-24 / 1 / Amp/Tet / tetB / phosphatase (Neisseria meningitidis) / blaT protein (Escherichia coli) / S. alvi / JS807640 JS807641

*based on amplification with diagnostic primers and confirmed with sequencing. "none" indicates no PCR amplification.

**based on top blastx hits of end sequences and excluding mobile sequences or resistance gene sequences, which are poor indictors of taxonomic source.