Table 5 Observed composition of gut mock based on MinKNOW mappings. Species chosen for enrichment are highlighted in bold. Due to the large number of contigs (> 13,000) for C. albicans and S. cerevisiae, these references were not presented to the onboard alignment process, so data is not shown

Faecalibacterium prausnitzii

14

19.31

3428

Veillonella rogosae

14

15.04

14,353

Roseburia hominis

14

10.70

4412

Bacteroides fragilis

14

13.26

10,334

Prevotella corporis

6

6.50

9851

Bifidobacterium adolescentis

6

0.2

6699

Fusobacterium nucleatum

6

5.77

4928

Lactobacillus fermentum

6

7.38

866

Clostridioides difficile

1.5

1.72

8835

Akkermansia muciniphila

1.5

2.12

8765

Methanobrevibacter smithii

0.1

0.03

15,651

Salmonella enterica

0.01

0.03

8198

Enterococcus faecalis

0.0001

0.00

no reads

Clostridium perfringens

0.00001

0.00

no reads

Escherichia coli (JM109)

2.8

2.90

8782

Escherichia coli (B-3008)

2.8

3.44

7034

Escherichia coli (B-2207)

2.8

2.80

5895

Escherichia coli (B-766)

2.8

2.84

9007

Escherichia coli (B-1109)

2.8

3.10

8784

Candida albicans

1.5

n/a

n/a

Saccharomyces cerevisiae

1.4

n/a

n/a