Table 2 Details of bacterial species-derived DNA sequences identified in each patient*

ReA

   1

45

10 × Stenotrophomonas maltophilia, 7 × Shigella species, 6 × Propionibacterium acnes, 3 × Ralstonia species, 3 × Shigella sonnei, 3 × uncultured bacterium, 2 × Bradyrhizobium elkanii, 1 × uncultured γ proteobacterium, 1 × uncultured γ proteobacterium, 2 × uncultured Sphingobacterium species, 1 × Aranicola species, 1 × Agrobacterium species, 1 × Burkholderia species, 1 × Escherichia coli, 1 × Paenibacillus humicus, 1 × Pantoea ananatis, 1 × uncultured β proteobacterium.

   2

47

13 × Stenotrophomonas maltophilia, 4× Shigella species, 3 × Aranicola species, 3 × Ralstonia species, 2 × β proteobacterium, 2 × γ proteobacterium, 2 × uncultured β proteobacterium, 1 × Agrobacterium species,, 1 × Bacteroidetes bacterium, 1 × Escherichia coli, 1 × Escherichia species, 1 × Flavobacterium mizutaii, 1 × Pantoea ananatis, 1 × Paenibacillus humicus, 1 × Paenibacillus species, 1 × Propionibacterium acnes, 3 × Shigella sonnei 1 × Streptococcus mitis, 1 × swine manure bacterium, 1 × uncultured α proteobacterium, 1 × uncultured Bacteroidetes bacterium, 1 × uncultured Flavobacterium species, 1 × uncultured soil bacterium.

   3

42

10 × Shigella species, 9 × Stenotrophomonas maltophilia, 3 × Aranicola species, 3 × uncultured bacterium,, 2 × Escherichia species, 2 × Paenibacillus humicus, 2 × Streptococcus mitis, 1 × Achromobacter xylosoxidans, 1 × Bradyrhizobium elkanii, 1 × Bacteroidetes bacterium, 1 × Flavobacterium mizutaii, 1 × γ proteobacterium, 1 × Propionibacterium acnes, 1 × Shigella sonnei, 1 × Streptococcus mitis, 1 × uncultured Flavobacterium species, 1 × uncultured Methylococcaceae bacterium, 1 × uncultured Bacteroidetes bacterium

   4

49

11 × Stenotrophomonas maltophilia, 6 × γ proteobacterium, 5 × Shigella species, 5 × Shigella sonnei, 3 × Aranicola species, 3 × Comamonas testosteroni, 3 × uncultured bacterium, 2 × Escherichia species, 2× Propionibacterium acnes, 2 × uncultured Flavobacterium species, 2 × uncultured β proteobacterium, 1 × Alcaligenes faecalis, 1 × Flavobacterium mizutaii, 1 × Paenibacillus humicus 1 × Pelomonas saccharophila, 1 × Pseudomonas species.

   5

31

5 × Escherichia coli, 4 × Stenotrophomonas maltophilia, 3 × Escherichia coli, 2 × Pseudomonas species, 2 × Shigella species, 2 × Sphingomonas faeni, 1 × Alcaligenes faecalis, 1 × β proteobacterium, 1 × Comamonas testosteroni, 1 × Diaphorobacter species, 1 × Delftia acidovorans, 1 ×Flavobacterium mizutaii, 1 × γ proteobacterium, 1 × uncultured bacterium, 1 × uncultured β proteobacterium, 1 × Pantoea ananatis, 1 × Propionibacterium acnes, 1 × Ralstonia species, 1 × Shigella sonnei,

UA

   6

47

13 × Stenotrophomonas maltophilia, 9 × Shigella species, 7 × γ proteobacterium, 2 × uncultured bacterium, 2 × uncultured Veillonella species, 1 × Alcaligenes faecalis, 1× Agrobacterium species, 1 × Escherichia species, 1 × Streptococcus thermophilus, 1 × Flavobacterium mizutaii, 1 × Propionibacterium acnes, 1 × uncultured β proteobacterium, 1 × uncultured bacterium, 1 × uncultured candidate division OP10 bacterium, 1 × Pantoea ananatis, 1 × Shigella sonnei, 1 × unidentiefied bacterium, 1 × uncultured Flavobacterium species, 1 × uncultured Sphingobacterium species.

   7

30

8 × Stenotrophomonas maltophilia, 3 × Shigella species, 2 × Comamonas testosteroni, 2 × Paenibacillus humicus, 2 × Ralstonia species, 2 × uncultured bacterium, 2 × uncultured β proteobacterium, 2 × uncultured Flavobacterium species, 1 × Burkholderia species, 1 × Bradyrhizobium elkanii, 1 × Bacteroidetes bacterium, 1 × Escherichia coli, 1 × Flavobacterium mizutaii, 1 × γ proteobacterium, 1 × Shigella sonnei

   8

43

15 × Stenotrophomonas maltophilia, 5 × Shigella species, 3 × Escherichia species, 3 × Paenibacillus humicus, 2 × uncultured bacterium, 2 × uncultured β proteobacterium, 1 × Alcaligenes faecalis, 1 × Aranicola species, 1 × Bradyrhizobium elkanii, 1 × Flavobacterium mizutaii, 1 × γ proteobacterium, 1 × Ralstonia species, 1 × Staphylococcus pasteuri, 1 × Streptococcus mitis, 1 × Streptococcus pneumoniae, 1 × Streptococcus species, 1 × uncultured candidate division OP10 bacterium, 1 × uncultured Streptococcus species, 1 × uncultured Veillonella species.

   9

38

11 × Aquabacterium commune, 8 × Shigella species, 3 × Aranicola species, 3 × Paenibacillus humicus, 2 × Alcaligenes faecalis, 2 uncultured bacterium, 1 × β proteobacterium, 1 × Comamonas testosteroni, 1× Escherichia species, 1 × Kocuria species, 1 × Pseudomonas species, 1 × Paracoccus species, 1 × Streptococcus thermophilus, 1 × Streptococcus species, 1 × uncultured β proteobacterium

   10

41

13 × Stenotrophomonas maltophilia, 4 × Shigella species, 3 × γ proteobacterium, 3 × Shigella sonnei, 1 × Aranicola species, 1 × Alcaligenes faecalis, 1× Aeromonas species, 1× Burkholderia species, 1 × Bradyrhizobium elkanii, 1 × Comamonas testosteroni, 1 × Capnocytophaga sputigena 1 × Enterococcus faecium, 1× Escherichia species, 1 × Enterobacter hormaechei, 1 × Pseudomonas poae, 1 × Pantoea ananatis, 1 × Paenibacillus humicus, 1 × Rhodococcus species, 1 × Ralstonia species, 1 uncultured bacterium, 1 × uncultured γ proteobacterium, 1 × uncultured Flavobacterium species.

   11

36

6 × Stenotrophomonas maltophilia, 5 × Shigella species, 4 × γ proteobacterium, 4 × Ralstonia species, 3 × Escherichia coli, 2 × Bradyrhizobium elkanii, 2 × Comamonas testosteroni, 2 × uncultured bacterium, 1 × Achromobacter xylosoxidans, 1 × Alcaligenes faecalis, 1 × Bacteroidetes bacterium, 1 × Flavobacterium mizutaii, 1 × Rhizobium radiobacter, 1 × Rhodococcus species, 1 × uncultured β proteobacterium, 1 × uncultured organism.

   12

22

4 × Shigella species, 4 × Stenotrophomonas maltophilia, 3 × Alcaligenes faecalis, 2 × Shigella sonnei, 2 × uncultured β proteobacterium, 2 × uncultured bacterium, 1 × Aminobacter aminovorans, 1 × Achromobacter xylosoxidans, 1 × Paenibacillus humicus, 1 × Ralstonia species, 1 × uncultured organism.

   13

37

12 × Stenotrophomonas maltophilia, 3 × Shigella species, 3 × uncultured bacterium, 2 × Bacillus niacini, 2 × Ralstonia species, 1 × β proteobacterium, 1 × Bradyrhizobium japonicum, 1 × Burkholderia cepacia, 1 × Corynebacterium durum, 1 × Comamonas testosteroni, 1 × Flavobacterium mizutaii, 1 × γ proteobacterium, 1 × uncultured β proteobacterium, 1 × uncultured Sphingobacterium species, 1 × Mycobacterium aubagnense, 1 × Shigella sonnei., 1 × Sphingomonas species, 1 × Sphingomonas species, 1 × Pseudomonas poae, 1 × Pantoea ananatis.

   14

36

10 × Stenotrophomonas maltophilia, 7 × Ralstonia species, 3 × Comamonas testosteroni, 3 × uncultured bacterium, 2 × γ proteobacterium, 1 × Escherichia species, 1 × Flavobacterium mizutaii, 1 × Methylomicrobium species, 1 × Paenibacillus humicus, 1 × Pantoea ananatis, 1 × Photorhabdus luminescens, 1 × Streptococcus pneumoniae, 1 × uncultured Sphingobacterium species, 1 × uncultured Flavobacterium species, 1 × uncultured β proteobacterium, 1 × uncultured Firmicutes bacterium.

RA

   15

24

10 × Stenotrophomonas maltophilia, 3 × uncultured Flavobacterium species, 2 × Comamonas testosteroni, 2 × uncultured bacterium, 1 × Aranicola species, 1 × Flavobacterium mizutaii, 1 × Paenibacillus humicus, 1 × Shigella species, 1 × Staphylococcus cohnii, 1 × Sphingobacterium thalpophilum, 1 × uncultured Sphingobacterium species.

   16

13

5 × uncultured β proteobacterium, 4 × uncultured Flavobacterium species, 2 × uncultured Sphingobacterium species, 1 × Comamonas testosterone, 1 × uncultured bacterium.

   17

8

3 × Escherichia species, 2 × uncultured bacterium, 1 × Alcaligenes faecalis, 1 × Comamonas testosteroni, 1 × Shigella species.

OA

   18

18

4 × Stenotrophomonas maltophilia, 4 × Shigella species, 2 × Flavobacterium mizutaii, 2 × uncultured Flavobacterium species, 2 × uncultured Sphingobacterium species, 1 × Acinetobacter junii, 1 × Escherichia coli O157, 2 × uncultured bacterium.

   19

16

5 × Stenotrophomonas maltophilia, 3 × Shigella species, 3 × uncultured bacterium, 1 × Alcaligenes faecalis, 1 × Comamonas testosteroni, 1 × Flavobacterium mizutaii, 1 × Paenibacillus humicus, 1 × Ralstonia species.

   20

17

4 × Stenotrophomonas maltophilia, 3 × Shigella species, 3 × uncultured bacterium, 1 × Achromobacter xylosoxidans, 1 × Alcaligenes faecalis, 1 × Bacillus cereus, 1 × Escherichia species, 1 × Rothia mucilaginosa, 2 × uncultured β proteobacterium