1. Supplementary data for:
Classification of culturable bifidobacterial population from colonic samples of wild pigs (Sus scrofa) based on three molecular genetic methods
Radko Pechar, Jiří Killer, Chahrazed Mekadim, Martina Geigerová, Vojtěch Rada

2. Bifidobacteriaceae strains
Table S1 NCBI accession numbers of genome regions in Bifidobacteriaceae strains encompassing thrS gene sequences which were used for designing of PCR primers
Bifidobacteriaceae strains
thrS (position)
Alloscardovia omnicolens DSM 21503T
NZATVB ( )
Parascardovia denticolens DSM 10105T
AEON ( )
Scardovia inopinata F0304
ADCX ( )
Scardovia wiggsiae F0424
AGZS ( )
Bifiddobacterium angulatum DSM 20098T
ABYS ( )
B. animalis subsp. animalis BCCM/LMG 10508T
CP ( )
B. animalis subsp. lactis DSM 10140T
NC ( )
B. asteroides DSM 20089T
NZJDTU ( )
B. bifidum BCCM/LMG 11041T
JGYO ( )
B. breve DSM 20213T
ACCG ( )
B. catenulatum DSM 16992T
ABXY ( )
B. dentium DSM 20436T
NZJDUY ( )
B. thermophilum JCM 1207T
NZJGZV ( )
Abbreviations: DSM - Deutsche Sammlung von Mikroorganismen (German Culture Collection); BCCM/LMG – Belgian Co-ordinated Collections of Microorganisms; JCM – Japan Collection of Microorganisms. T – type strain of (sub)species.

3. Table S2 Distribution of 149 F6PPK-positive bacterial isolates from fresh rectal contents of 22 wild pigs originating from four localities in the Czechia in DGGE groups and STs based on 16S rRNA comparative analysis
Locality
Individual
Sex
Number of F6PPK+ isolates
DGGE (G1-4) groups (number of isolates)
STs based on 16S rRNA comparative analysis (number of isolates)
Prague - Divoká Šárka 1
male 13
G1 (13)
ST1 (13) 2 11
G2 (11)
ST6 (11) 3
female
G1 (2)
ST1 (1), ST3 (1) 4
G1 (4)
ST1 (2), ST3 (2) 5 7
G1 (7)
ST1 (7) 6 8
G1 (8)
ST1 (6), ST5 (2)
G1 (3)
ST1 (2), ST5 (1)
ST1 (3) 9 26
G1 (22), G2 (3), G3 (1)
ST1 (16), ST3 (1), ST5 (5), ST8 (3), ST10 (1)
Boješice 10
G2 (6)
ST6 (2), ST8 (1), ST9 (3)
G1 (2), G2 (1)
ST1 (1), ST4 (1), ST9 (1) 12
G2 (3)
ST6 (2), ST9 (1) 14
Kouřim 15
ST2 (4) 16
ST2 (3) 17
G2 (9)
ST8 (9) 18
G1 (1), G2 (2), G4 (1)
ST3 (1), ST7 (1), ST8 (2) 19
G4 (3)
ST7 (3)
Hlavenec 20
G1 (1), G2 (1)
ST1 (1), ST8 (1) 21
G1 (14), G3 (6)
ST1 (3), ST3 (4), ST4 (1), ST5 (6), ST 10 (6) 22

4. Table S3 Classification of F6PPK-positive strains using the 16S rRNA comparative analysis
Most related (sub)species (pairwise similarities, %)
Classification
Lenght of fragment (nt)
GenBank accession no.
Number of isolates
DGGE group 1
B. boum DSM 20432T (98.44)
Bifidobacterium sp.
1347
KY194699 58 2
B. boum DSM 20432T (98.59)
KY194700 7 3
B. thermacidophilum subsp. thermacidophilum DSM 15837T (99.11)
Bifidobacterium thermacidophilum subsp. thermacidophilum
KY194701 8 4
B. boum DSM 20432T (98.40)
KY194702 5
B. thermacidophilum subsp. thermacidophilum DSM 15837T (99.30)
KY194703 14 6
B. boum DSM 20432T (99.71)
B. boum
1367
KY194704 17
B. pseudolongum subsp. globosum DSM 20092T (99.93)
B. pseudolongum subsp. globosum
1383
KY194705
B. thermacidophilum subsp. porcinum DSM 17755T (99.93)
Bifidobacterium thermacidophilum subsp. porcinum
1376
KY194706 25 9
B. thermacidophilum subsp. porcinum DSM 17755T (99.78)
KY194707 10
Pseudoscardovia suis DPTE4T (99.26)
Pseudoscardovia suis
1384
KY194708
DSM - Deutsche Sammlung von Mikroorganismen (German Culture Collection), BCCM/LMG – Belgian Co-ordinated Collections of Microorganisms. T – type strain of (sub)species

5. Table S4 Differentiation of F6PPK-positive strains using comparative analysis based on thrS gene sequences (length of 720 nt) ST
Most related (sub)species (pairwise similarities, %) / GeneBank accession number
Classification
GenBank accession no. 1
B. thermacidophilum subsp. porcinum DSM 17755T (89.72) / KY202679
Bifidobacterium spp.
KY202683 2
KY202684 3
B. thermacidophilum subsp. porcinum DSM 17755T (90.14) / KY202679
KY202685 4
B. thermacidophilum subsp. porcinum DSM 17755T (90.00) / KY202679
KY202686 5
KY202687 6
B. boum DSM 20432T (92.50) / NZJDUH
B. boum
KY202688 7
B. pseudolongum subsp. globosum DSM 20092T (98.75) / KY202681
B. pseudolongum subsp. globosum
KY202689 8
B. thermophilum DSM 20210T (99.58) / KY202678
B. thermophilum
KY202690 9
B. thermophilum DSM 20210T (99.86) / KY202678
KY202691 10
Pseudoscardovia suis DSM 24744T (98.19) / KY202676
Pseudoscardovia suis
KY202692 11
Pseudoscardovia suis DSM 24744T (99.30) / KY202676
KY202693

6. Table S5 Ability to ferment various carbohydrate substrates in randomly selected two strains classified into ten STs according to comparative analysis of 16S rRNA (Table S3). Two strains included in ST10 according to the thrS gene comparative analysis (Table S4) were used. All strains tested produced acids from D-glucose, D-fructose, maltose, melibiose, saccharose, raffinose, starch and glycogen. No strains were able to ferment glycerol, erythritol, D-arabinose, L-xylose, D-adonitol, methyl-βD-xylopyranoside, L-sorbose, L-rhamnose, dulcitol, inositol, D-mannitol, D-sorbitol, D-lyxose, D-tagatose, D-fucose, D-arabitol, L-arabitol, potassium gluconate, potassium 2-ketogluconate and potassium 5-ketogluconate. +, positive reaction; (+), weak positive reaction; -, negative reaction
Substrate
ST1
ST2
ST3
ST4
ST5
ST6
ST7
ST8
ST9
ST10
L-Arabinose - +
D-Ribose
D-Xylose
D-Galactose
(+)
D-Mannose
Methyl-αD-Mannopyranoside
Methyl-αD-Glucopyranoside
N-Acetylglucosamine
Amygdalin
Arbutin
Esculin
Salicin
Cellobiose
Lactose
Trehalose
Inulin
Melezitose
Xylitol
Gentiobiose
D-Turanose