Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12.

The genome of Bifidobacterium animalis subsp. lactis BB-12 was sequenced using Oxford Nanopore Technologies long-read and Illumina short-read sequencing platforms. A hybrid genome assembly approach was used to construct an updated complete genome sequence for BB-12 containing 1,944,152 bp, with a G+C content of 60.5% and 1,615 genes.

ANNOUNCEMENT

Bifidobacteria are often used as probiotics due to their health-promoting effects (1). Bifidobacterium animalis subsp. lactis BB-12 (2) has been associated with positive effects in areas such as immune function (3–5), gastrointestinal health (6), and the respiratory system (7, 8). Here, we present a second version of the BB-12 genome, generated through state-of-the-art sequencing technologies using both Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms.

BB-12 (DSM 15954) was obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ) (Braunschweig, Germany) in April 2004 and stored at −80°C. Cells were grown anaerobically at 37°C in MRS broth containing 0.05% l-cysteine hydrochloride monohydrate. Genomic DNA was extracted with the DNeasy blood and tissue kit on a QiaCube system (Qiagen, Germany). Sequencing libraries were generated using a KAPA HyperPlus library preparation kit and KAPA dual-indexed adapters (Roche, Switzerland), and AMPure XP beads (Beckman Coulter, USA) were used for library cleanup steps, following the manufacturers’ protocols. DNA concentrations were measured on a Qubit 3.0 fluorimeter using Qubit double-stranded DNA (dsDNA) broad-range and Qubit 1X dsDNA high-sensitivity (HS) assays (Thermo Fisher Scientific, USA). The average dsDNA library size distribution was determined using the Agilent HS next-generation sequencing (NGS) fragment (1 to 6,000 bp) kit on an Agilent fragment analyzer. Libraries were sequenced with the 600-cycle MiSeq reagent kit v3 on a MiSeq platform (Illumina Inc., USA) with a paired-end protocol and read lengths of 301 nucleotides (nt). Short-read sequencing yielded 686,356 read pairs with a total length of 255,784,736 nt. The reads were trimmed for quality using AdapterRemoval v2.2.4 (9) with parameters --minquality 20 --minlength 30 --trimqualities --trimns --trim5p 15.

For long-read sequencing, genomic DNA was extracted with a Genomic Maxi AX gravity column-based kit (A&A Biotechnology, Poland), prepared using a rapid barcoding sequencing kit (SQK-RBK004; ONT), and sequenced on a MinION flow cell (R9.4.1 FLO-MIN106; ONT) for 48 h. This yielded 72,175 reads with a total length of 374,342,567 nt and an N50 value of 10,185 nt. Base calling was performed with the Guppy base caller v3.2.10, and adapters were trimmed using ONT MinKNOW software.

The complete genome sequence of BB-12 was assembled using the long and short sequencing reads with Unicycler v0.4.7 (10) in conservative mode, resulting in one 1,944,152-bp circular chromosome with a G+C content of 60.5%. The genome sequence was annotated with Prokaryotic Genome Annotation Pipeline (PGAP) v4.13 (11), resulting in 1,615 genes.

To assess whether the genome sequenced here differs from the previously available BB-12 genome (GenBank accession number NC_017214.1), breseq v0.35.5 (12) with default settings was used to map Illumina reads from this work to both genome sequences. Mapping of Illumina reads to the genome sequence produced in this work did not yield any variants, while mapping to the previously available genome sequence resulted in 74 single-nucleotide differences and 235 small indels (Table 1).

TABLE 1

Overview of the genetic differences identified by comparing the newly generated reads to the previously available BB12 genome sequence (GenBank accession number NC_017214.1)

Nucleotide position	Mutation	Annotation	Gene(s)
469	C→A	Q49K (CAA→AAG)	BIF_00469 →
471	A→G	Q49K (CAA→AAG)	BIF_00469 →
21536	+A	Coding (867/927 nt)	BIF_02142 →
21540	3 bp→12 bp	Coding (871–873/927 nt)	BIF_02142 →
28398	+C	Intergenic (+28/−48)	BIF_00002 → / → BIF_02140
28414	A→T	Intergenic (+44/−32)	BIF_00002 → / → BIF_02140
28417	4 bp→18 bp	Intergenic (+47/−26)	BIF_00002 → / → BIF_02140
45995	+TGGAATTCCACGGGCCT	Intergenic (+95/+86)	BIF_01763 → / ← BIF_01079
93265	+CG	Intergenic (+43/+6)	BIF_01365 → / ← BIF_02171
93267	+AACC	Intergenic (+45/+4)	BIF_01365 → / ← BIF_02171
93268	T→A	Intergenic (+46/+3)	BIF_01365 → / ← BIF_02171
93270	+AT	Intergenic (+48/+1)	BIF_01365 → / ← BIF_02171
103949	4 bp→22 bp	Intergenic (+18/+56)	BIF_01186 → / ← BIF_02012
103961	C→A	Intergenic (+30/+47)	BIF_01186 → / ← BIF_02012
103963	Δ1 bp	Intergenic (+32/+45)	BIF_01186 → / ← BIF_02012
112686	+25 bp	Intergenic (−226/+31)	BIF_00107 ← / ← BIF_00801
132978	5 bp→19 bp	Intergenic (+14/−185)	BIF_01865 → / → BIF_02174
132990	+G	Intergenic (+26/−177)	BIF_01865 → / → BIF_02174
132999	+C	Intergenic (+35/−168)	BIF_01865 → / → BIF_02174
152141	21 bp→37 bp	Intergenic (+39/+16)	BIF_01884 → / ← BIF_00858
156687	+23 bp	Intergenic (+51/+2)	BIF_00548 → / ← BIF_00217
174620	+G	Coding (9/300 nt)	BIF_02178 →
174628	+G	Coding (17/300 nt)	BIF_02178 →
174796	3 bp→25 bp	Coding (185–187/300 nt)	BIF_02178 →
174847	+G	Coding (236/300 nt)	BIF_02178 →
174849	G→C	A80P (GCC→CCC)	BIF_02178 →
226865	+A	Coding (974/1,167 nt)	BIF_00004 ←
226867	G→C	S324S (TCC→TCG)	BIF_00004 ←
303227	+GGTGG	Intergenic (+30/+242)	BIF_01290 → / ← BIF_00983
332638	+GCATGCGGCGA	Intergenic (+65/+62)	BIF_00009 → / ← BIF_01572
332642	G→C	Intergenic (+69/+58)	BIF_00009 → / ← BIF_01572
348109	9 bp→32 bp	Intergenic (+13/+31)	BIF_01159 → / ← BIF_02184
374215	+32 bp	Intergenic (−158/+189)	BIF_00055 ← / ← BIF_01897
374264	+G	Intergenic (−207/+140)	BIF_00055 ← / ← BIF_01897
374286	2 bp→GC	Intergenic (−229/+117)	BIF_00055 ← / ← BIF_01897
395152	49 bp→66 bp	Intergenic (+77/+63)	BIF_01176 → / ← BIF_00941
395195	7 bp→19 bp	Intergenic (+120/+62)	BIF_01176 → / ← BIF_00941
412279	+CTGAGCACACGGGGGCCG	Intergenic (+8/−75)	BIF_01519 → / → BIF_01115
412281	G→T	Intergenic (+10/−73)	BIF_01519 → / → BIF_01115
412292	+A	Intergenic (+21/−62)	BIF_01519 → / → BIF_01115
412906	+54 bp	Intergenic (+25/+20)	BIF_01115 → / ← BIF_01114
416028	+C	Intergenic (+371/+25)	BIF_01112 → / ← BIF_02188
416031	+GA	Intergenic (+374/+22)	BIF_01112 → / ← BIF_02188
423866	1 bp→GG	Intergenic (+45/+26)	BIF_00671 → / ← BIF_00700
423877	1 bp→18 bp	Intergenic (+56/+15)	BIF_00671 → / ← BIF_00700
426071	+GGCGCCACACGCGAA	Intergenic (−149/+31)	BIF_00700 ← / ← BIF_01226
426073	+C	Intergenic (−151/+29)	BIF_00700 ← / ← BIF_01226
442719	Δ1 bp	Intergenic (−50/+31)	BIF_01320 ← / ← BIF_00999
442725	6 bp→19 bp	Intergenic (−56/+20)	BIF_01320 ← / ← BIF_00999
458009	+45 bp	Coding (13/132 nt)	BIF_02190 ←
479759	A→G	Intergenic (+44/+44)	BIF_01252 → / ← BIF_01632
512389	2 bp→GC	Coding (58–59/180 nt)	BIF_02194 ←
512406	+C	Coding (42/180 nt)	BIF_02194 ←
512414	+C	Coding (34/180 nt)	BIF_02194 ←
515142	2 bp→AA	Coding (116–117/2,316 nt)	BIF_02061 →
515145	G→A	W40* (TGG→TAG)	BIF_02061 →
515153	G→C	V43L (GTA→CTA)	BIF_02061 →
544458	A→G	T524T (ACA→ACG)	BIF_01621 →
544491	20 bp→35 bp	Coding (1,605–1,624/1,653 nt)	BIF_01621 →
551925	3 bp→17 bp	Coding (31–33/1,518 nt)	BIF_02058 →
551931	Δ1 bp	Coding (37/1,518 nt)	BIF_02058 →
555527	62 bp→77 bp	Intergenic (+44/+177)	BIF_00496 → / ← BIF_01682
574023	+AACCCGCCC	Intergenic (−880/+30)	BIF_16SrRNA12 ← / ← BIF_01549
601285	Δ1 bp	Coding (2/771 nt)	BIF_00943 ←
607329	+AC	Coding (148/159 nt)	BIF_02197 →
607331	G→C	A50P (GCG→CCC)	BIF_02197 →
627558	Δ1 bp	Intergenic (+54/−170)	BIF_01669 → / → BIF_02198
627563	+CCCGCCGGC	Intergenic (+59/−165)	BIF_01669 → / → BIF_02198
631554	+C	Intergenic (−383/+213)	BIF_00740 ← / ← BIF_00658
631589	+A	Intergenic (−418/+178)	BIF_00740 ← / ← BIF_00658
631599	Δ1 bp	Intergenic (−428/+168)	BIF_00740 ← / ← BIF_00658
631605	11 bp→48 bp	Intergenic (−434/+152)	BIF_00740 ← / ← BIF_00658
632722	+24 bp	Intergenic (−212/+219)	BIF_00658 ← / ← BIF_01209
632782	+G	Intergenic (−272/+159)	BIF_00658 ← / ← BIF_01209
690916	7 bp→28 bp	Intergenic (+28/+71)	BIF_01558 → / ← BIF_01474
795160	(G)8→9	Coding (834/1,299 nt)	BIF_01420 →
803347	+AGGTGGGG	Coding (433/435 nt)	BIF_02002 ←
803348	+AT	Coding (432/435 nt)	BIF_02002 ←
803350	A→C	S144A (TCG→GCA)	BIF_02002 ←
805769	+AGCA	Intergenic (−41/+271)	BIF_00477 ← / ← BIF_02124
813756	+C	Intergenic (+67/−63)	BIF_01190 → / → BIF_02126
889981	48 bp→76 bp	Intergenic (+42/+30)	BIF_01494 → / ← BIF_00763
890037	+G	Intergenic (+98/+21)	BIF_01494 → / ← BIF_00763
899064	+A	Intergenic (+234/−448)	BIF_01023 → / → BIF_01805
899066	C→A	Intergenic (+236/−446)	BIF_01023 → / → BIF_01805
899080	+G	Intergenic (+250/−432)	BIF_01023 → / → BIF_01805
899096	C→A	Intergenic (+266/−416)	BIF_01023 → / → BIF_01805
927296	+GGG	Intergenic (+878/+33)	BIF_01509 → / ← BIF_01083
980962	+G	Intergenic (−141/+180)	BIF_00863 ← / ← BIF_01247
996014	1 bp→CG	Intergenic (+36/−287)	BIF_02104 → / → BIF_01142
1054723	+29 bp	Intergenic (+134/−290)	BIF_00088 → / → BIF_02096
1054848	2 bp→21 bp	Intergenic (+259/−164)	BIF_00088 → / → BIF_02096
1054883	2 bp→GT	Intergenic (+294/−129)	BIF_00088 → / → BIF_02096
1151595	+C	Intergenic (+39/+27)	BIF_02003 → / ← BIF_tRNA28
1203020	(C)6→5	Intergenic (−170/−29)	BIF_02234 ← / → BIF_00647
1203058	(G)6→5	Coding (10/2,550 nt)	BIF_00647 →
1249797	15 bp→34 bp	Coding (32–46/126 nt)	BIF_02237 →
1254633	T→C	K65R (AAG→AGG)	BIF_00633 ←
1270898	+T	Intergenic (+15/+58)	BIF_00472 → / ← BIF_00205
1270906	+TGTGGGGCCCTACGG	Intergenic (+23/+50)	BIF_00472 → / ← BIF_00205
1270910	+C	Intergenic (+27/+46)	BIF_00472 → / ← BIF_00205
1283590	+TTCGGG	Intergenic (+24/−367)	BIF_00825 → / → BIF_00906
1283592	+CC	Intergenic (+26/−365)	BIF_00825 → / → BIF_00906
1291704	2 bp→11 bp	Intergenic (−1,307/+149)	BIF_01039 ← / ← BIF_00316
1291708	+T	Intergenic (−1,311/+146)	BIF_01039 ← / ← BIF_00316
1291709	G→C	Intergenic (−1,312/+145)	BIF_01039 ← / ← BIF_00316
1309076	+C	Coding (128/1,077 nt)	BIF_01009 ←
1309114	A→G	C30C (TGT→TGC)	BIF_01009 ←
1333145	+CC	Intergenic (+76/+16)	BIF_01182 → / ← BIF_00625
1333149	+ACGCA	Intergenic (+80/+12)	BIF_01182 → / ← BIF_00625
1333151	+A	Intergenic (+82/+10)	BIF_01182 → / ← BIF_00625
1333153	+C	Intergenic (+84/+8)	BIF_01182 → / ← BIF_00625
1345841	+A	Intergenic (+107/+54)	BIF_01862 → / ← BIF_00279
1345851	3 bp→18 bp	Intergenic (+117/+42)	BIF_01862 → / ← BIF_00279
1345877	+G	Intergenic (+143/+18)	BIF_01862 → / ← BIF_00279
1345918	+G	Coding (517/540 nt)	BIF_00279 ←
1345930	+T	Coding (505/540 nt)	BIF_00279 ←
1347684	+ACC	Intergenic (−32/−35)	BIF_02123 ← / → BIF_00396
1347686	+C	Intergenic (−34/−33)	BIF_02123 ← / → BIF_00396
1347687	+C	Intergenic (−35/−32)	BIF_02123 ← / → BIF_00396
1352581	G→A	Intergenic (+158/+131)	BIF_00072 → / ← BIF_00341
1352652	+ACAGAAGGGCGGT	Intergenic (+229/+60)	BIF_00072 → / ← BIF_00341
1352657	C→G	Intergenic (+234/+55)	BIF_00072 → / ← BIF_00341
1352659	A→C	Intergenic (+236/+53)	BIF_00072 → / ← BIF_00341
1360042	19 bp→35 bp	Intergenic (+28/+7)	BIF_00368 → / ← BIF_01760
1376069	14 bp→33 bp	Intergenic (+38/+27)	BIF_01846 → / ← BIF_00467
1414041	C→A	A373D (GCC→GAC)	BIF_00934 →
1414072	Δ1 bp	Coding (1,149/1,152 nt)	BIF_00934 →
1414079	+G	Intergenic (+4/+74)	BIF_00934 → / ← BIF_00718
1414090	8 bp→28 bp	Intergenic (+15/+56)	BIF_00934 → / ← BIF_00718
1419213	+G	Intergenic (+37/+331)	BIF_00332 → / ← BIF_02065
1419441	T→G	Intergenic (+265/+103)	BIF_00332 → / ← BIF_02065
1419443	C→T	Intergenic (+267/+101)	BIF_00332 → / ← BIF_02065
1419447	40 bp→53 bp	Intergenic (+271/+58)	BIF_00332 → / ← BIF_02065
1419488	T→G	Intergenic (+312/+56)	BIF_00332 → / ← BIF_02065
1419490	+TG	Intergenic (+314/+54)	BIF_00332 → / ← BIF_02065
1419492	1 bp→AC	Intergenic (+316/+52)	BIF_00332 → / ← BIF_02065
1419499	2 bp→GC	Intergenic (+323/+44)	BIF_00332 → / ← BIF_02065
1419504	+C	Intergenic (+328/+40)	BIF_00332 → / ← BIF_02065
1424409	4 bp→36 bp	Intergenic (+52/−47)	BIF_00028 → / → BIF_00780
1429003	1 bp→16 bp	Intergenic (+54/−44)	BIF_00776 → / → BIF_01792
1429006	T→G	Intergenic (+57/−41)	BIF_00776 → / → BIF_01792
1429008	C→T	Intergenic (+59/−39)	BIF_00776 → / → BIF_01792
1435740	10 bp→24 bp	Intergenic (+33/+22)	BIF_00308 → / ← BIF_00385
1435753	C→A	Intergenic (+46/+18)	BIF_00308 → / ← BIF_00385
1442201	+G	Intergenic (+56/+22)	BIF_00264 → / ← BIF_01752
1444091	1 bp→35 bp	Intergenic (−135/+100)	BIF_01751 ← / ← BIF_01116
1444149	+C	Intergenic (−193/+42)	BIF_01751 ← / ← BIF_01116
1444153	+C	Intergenic (−197/+38)	BIF_01751 ← / ← BIF_01116
1459986	14 bp→30 bp	Intergenic (+38/+3)	BIF_00179 → / ← BIF_00879
1466361	+TTGCGTTCCC	Intergenic (−140/+28)	BIF_01803 ← / ← BIF_00130
1466364	+C	Intergenic (−143/+25)	BIF_01803 ← / ← BIF_00130
1466365	G→T	Intergenic (−144/+24)	BIF_01803 ← / ← BIF_00130
1469891	+G	Intergenic (+56/−504)	BIF_00011 → / → BIF_02078
1469893	+G	Intergenic (+58/−502)	BIF_00011 → / → BIF_02078
1470155	A→C	Intergenic (+320/−240)	BIF_00011 → / → BIF_02078
1470159	T→C	Intergenic (+324/−236)	BIF_00011 → / → BIF_02078
1470162	+C	Intergenic (+327/−233)	BIF_00011 → / → BIF_02078
1470165	T→C	Intergenic (+330/−230)	BIF_00011 → / → BIF_02078
1470171	G→C	Intergenic (+336/−224)	BIF_00011 → / → BIF_02078
1470174	G→C	Intergenic (+339/−221)	BIF_00011 → / → BIF_02078
1470177	+C	Intergenic (+342/−218)	BIF_00011 → / → BIF_02078
1470183	1 bp→CC	Intergenic (+348/−212)	BIF_00011 → / → BIF_02078
1470187	+C	Intergenic (+352/−208)	BIF_00011 → / → BIF_02078
1470190	T→C	Intergenic (+355/−205)	BIF_00011 → / → BIF_02078
1470192	T→C	Intergenic (+357/−203)	BIF_00011 → / → BIF_02078
1470195	T→C	Intergenic (+360/−200)	BIF_00011 → / → BIF_02078
1470204	T→C	Intergenic (+369/−191)	BIF_00011 → / → BIF_02078
1470206	A→T	Intergenic (+371/−189)	BIF_00011 → / → BIF_02078
1470216	G→C	Intergenic (+381/−179)	BIF_00011 → / → BIF_02078
1470227	2 bp→GC	Intergenic (+392/−167)	BIF_00011 → / → BIF_02078
1470235	G→T	Intergenic (+400/−160)	BIF_00011 → / → BIF_02078
1470237	T→C	Intergenic (+402/−158)	BIF_00011 → / → BIF_02078
1470245	T→C	Intergenic (+410/−150)	BIF_00011 → / → BIF_02078
1470253	A→C	Intergenic (+418/−142)	BIF_00011 → / → BIF_02078
1470256	T→C	Intergenic (+421/−139)	BIF_00011 → / → BIF_02078
1470259	T→C	Intergenic (+424/−136)	BIF_00011 → / → BIF_02078
1470276	T→C	Intergenic (+441/−119)	BIF_00011 → / → BIF_02078
1470279	4 bp→CATT	Intergenic (+444/−113)	BIF_00011 → / → BIF_02078
1470308	4 bp→CCG	Intergenic (+473/−84)	BIF_00011 → / → BIF_02078
1470314	T→C	Intergenic (+479/−81)	BIF_00011 → / → BIF_02078
1470322	A→C	Intergenic (+487/−73)	BIF_00011 → / → BIF_02078
1470328	T→C	Intergenic (+493/−67)	BIF_00011 → / → BIF_02078
1474821	+G	Coding (7/2,349 nt)	BIF_00363 →
1474832	+C	Coding (18/2,349 nt)	BIF_00363 →
1494471	+TGAAGCGGC	Intergenic (+15/+59)	BIF_00354 → / ← BIF_02081
1494477	T→G	Intergenic (+21/+53)	BIF_00354 → / ← BIF_02081
1494479	1 bp→TG	Intergenic (+23/+51)	BIF_00354 → / ← BIF_02081
1507139	7 bp→21 bp	Intergenic (+39/+35)	BIF_00355 → / ← BIF_00882
1516347	Δ1 bp	Intergenic (+37/−88)	BIF_01797 → / → BIF_tRNA37
1516350	+TC	Intergenic (+40/−85)	BIF_01797 → / → BIF_tRNA37
1533794	C→A	Intergenic (−79/+25)	BIF_00836 ← / ← BIF_00445
1533800	3 bp→15 bp	Intergenic (−85/+17)	BIF_00836 ← / ← BIF_00445
1537535	G→A	Intergenic (+448/−131)	BIF_01766 → / → BIF_02245
1537566	C→G	Intergenic (+479/−100)	BIF_01766 → / → BIF_02245
1537568	G→C	Intergenic (+481/−98)	BIF_01766 → / → BIF_02245
1537618	C→T	Intergenic (+531/−48)	BIF_01766 → / → BIF_02245
1537650	2 bp→AT	Intergenic (+563/−15)	BIF_01766 → / → BIF_02245
1537653	1 bp→CG	Intergenic (+566/−13)	BIF_01766 → / → BIF_02245
1537688	A→C	N8T (AAC→ACC)	BIF_02245 →
1537694	A→T	E10V (GAG→GTG)	BIF_02245 →
1537708	C→T	P15S (CCT→TCC)	BIF_02245 →
1537710	T→C	P15S (CCT→TCC)	BIF_02245 →
1537719	2 bp→GC	Coding (54–55/99 nt)	BIF_02245 →
1537727	Δ1 bp	Coding (62/99 nt)	BIF_02245 →
1537733	+TG	Coding (68/99 nt)	BIF_02245 →
1537743	G→C	M26I (ATG→ATC)	BIF_02245 →
1541799	Δ1 bp	Coding (970/1,029 nt)	BIF_02111 →
1541804	69 bp→84 bp		[BIF_02111]
1541874	+C	Intergenic (+16/−107)	BIF_02111 → / → BIF_01915
1576870	+C	Intergenic (+277/+73)	BIF_00659 → / ← BIF_00506
1576890	2 bp→10 bp	Intergenic (+297/+52)	BIF_00659 → / ← BIF_00506
1589406	+ATGCGCCTGAC	Intergenic (−86/+44)	BIF_01830 ← / ← BIF_00522
1593487	2 bp→GC	Intergenic (−92/+36)	BIF_02016 ← / ← BIF_02017
1593511	+C	Intergenic (−116/+13)	BIF_02016 ← / ← BIF_02017
1593523	+G	Intergenic (−128/+1)	BIF_02016 ← / ← BIF_02017
1593561	+T	Coding (242/279 nt)	BIF_02017 ←
1595922	12 bp→22 bp	Intergenic (+63/+15)	BIF_00337 → / ← BIF_01744
1595936	+GA	Intergenic (+77/+12)	BIF_00337 → / ← BIF_01744
1595981	Δ1 bp	Coding (846/879 nt)	BIF_01744 ←
1595984	+AC	Coding (843/879 nt)	BIF_01744 ←
1595988	+C	Coding (839/879 nt)	BIF_01744 ←
1602531	3 bp→13 bp	Intergenic (+9/−74)	BIF_00963 → / → BIF_00287
1602535	1 bp→CC	Intergenic (+13/−72)	BIF_00963 → / → BIF_00287
1610137	Δ2 bp	Intergenic (−9/+26)	BIF_01901 ← / ← BIF_00277
1634778	+C	Intergenic (+137/−53)	BIF_01000 → / → BIF_00897
1657183	12 bp→30 bp	Intergenic (−58/+30)	BIF_01871 ← / ← BIF_00406
1671395	8 bp→29 bp	Intergenic (+22/+60)	BIF_00122 → / ← BIF_00441
1676721	+CGGGAGCCTTCCCATATCAA	Intergenic (+49/+5)	BIF_00162 → / ← BIF_00129
1685544	12 bp→38 bp	Intergenic (+9/+81)	BIF_00244 → / ← BIF_01784
1685646	Δ1 bp	Coding (515/525 nt)	BIF_01784 ←
1691786	2 bp→16 bp	Intergenic (−152/+40)	BIF_00694 ← / ← BIF_00758
1704247	+G	Intergenic (+37/+72)	BIF_00639 → / ← BIF_01823
1704249	38 bp→61 bp	Intergenic (+39/+33)	BIF_00639 → / ← BIF_01823
1704394	+G	Coding (414/489 nt)	BIF_01823 ←
1714609	+ATACGAAGAGGCCC	Intergenic (+15/+75)	BIF_02095 → / ← BIF_02255
1714612	A→G	Intergenic (+18/+72)	BIF_02095 → / ← BIF_02255
1714619	2 bp→TG	Intergenic (+25/+64)	BIF_02095 → / ← BIF_02255
1714622	G→C	Intergenic (+28/+62)	BIF_02095 → / ← BIF_02255
1720652	14 bp→29 bp		[BIF_02256]
1735437	17 bp→34 bp	Intergenic (−31/+299)	BIF_01975 ← / ← BIF_00492
1747481	Δ1 bp	Intergenic (+38/+25)	BIF_00693 → / ← BIF_00329
1747488	+A	Intergenic (+45/+18)	BIF_00693 → / ← BIF_00329
1747489	+CCCCTCACATTT	Intergenic (+46/+17)	BIF_00693 → / ← BIF_00329
1755127	C→G	M12I (ATG→ATC)	BIF_00612 ←
1755177	+C	Coding (2,001/2,019 nt)	BIF_00102 ←
1755247	2 bp→GC	Coding (1,930–1,931/2,019 nt)	BIF_00102 ←
1756978	+G	Coding (200/2,019 nt)	BIF_00102 ←
1757068	1 bp→GT	Coding (110/2,019 nt)	BIF_00102 ←
1757069	+C	Coding (109/2,019 nt)	BIF_00102 ←
1759022	+A	Intergenic (−66/+70)	BIF_tRNA49 ← / ← BIF_00125
1759023	+ATGGGGTGT	Intergenic (−67/+69)	BIF_tRNA49 ← / ← BIF_00125
1759024	+C	Intergenic (−68/+68)	BIF_tRNA49 ← / ← BIF_00125
1759026	G→T	Intergenic (−70/+66)	BIF_tRNA49 ← / ← BIF_00125
1759057	+C	Intergenic (−101/+35)	BIF_tRNA49 ← / ← BIF_00125
1770206	7 bp→20 bp	Intergenic (+28/+64)	BIF_01817 → / ← BIF_01834
1770224	G→C	Intergenic (+46/+52)	BIF_01817 → / ← BIF_01834
1787741	18 bp→50 bp	Intergenic (+6/+30)	BIF_02258 → / ← BIF_00170
1790308	Δ1 bp	Intergenic (+24/+44)	BIF_01753 → / ← BIF_01191
1790315	+GGGCCCGCGAACAC	Intergenic (+31/+37)	BIF_01753 → / ← BIF_01191
1790322	Δ1 bp	Intergenic (+38/+30)	BIF_01753 → / ← BIF_01191
1790332	+G	Intergenic (+48/+20)	BIF_01753 → / ← BIF_01191
1799928	6 bp→16 bp	Intergenic (+109/−49)	BIF_02068 → / → BIF_00066
1800775	2 bp→TA	Intergenic (+95/+64)	BIF_00066 → / ← BIF_01169
1800778	A→C	Intergenic (+98/+62)	BIF_00066 → / ← BIF_01169
1800781	Δ1 bp	Intergenic (+101/+59)	BIF_00066 → / ← BIF_01169
1800786	+C	Intergenic (+106/+54)	BIF_00066 → / ← BIF_01169
1800822	+AG	Intergenic (+142/+18)	BIF_00066 → / ← BIF_01169
1800824	6 bp→14 bp	Intergenic (+144/+11)	BIF_00066 → / ← BIF_01169
1800831	+CC	Intergenic (+151/+9)	BIF_00066 → / ← BIF_01169
1805672	13 bp→37 bp	Intergenic (−25/+12)	BIF_01167 ← / ← BIF_02259
1806026	+G	Coding (2,837/2,883 nt)	BIF_00729 ←
1809002	Δ1 bp	Coding (192/1,608 nt)	BIF_00491 →
1809008	+G	Coding (198/1,608 nt)	BIF_00491 →
1809045	25 bp→59 bp	Coding (235–259/1,608 nt)	BIF_00491 →
1815438	+GGAAGGGGC	Intergenic (−7/+29)	BIF_00256 ← / ← BIF_00796
1815443	A→C	Intergenic (−12/+24)	BIF_00256 ← / ← BIF_00796
1815446	Δ1 bp	Intergenic (−15/+21)	BIF_00256 ← / ← BIF_00796
1815449	Δ1 bp	Intergenic (−18/+18)	BIF_00256 ← / ← BIF_00796
1824017	+26 bp	Intergenic (+34/+19)	BIF_00792 → / ← BIF_01147
1832709	T→A	R51W (AGG→TGG)	BIF_02260 ←
1832733	Δ1 bp	Coding (127/180 nt)	BIF_02260 ←
1832760	Δ1 bp	Coding (100/180 nt)	BIF_02260 ←
1850719	3 bp→13 bp	Intergenic (−100/+17)	BIF_00078 ← / ← BIF_01879
1851378	+T	Coding (71/711 nt)	BIF_01879 ←
		Coding (163/216 nt)	BIF_02261 ←
1853256	Δ1 bp	Coding (63/195 nt)	BIF_02082 ←
1885096	10 bp→24 bp	Intergenic (+17/+55)	BIF_01746 → / ← BIF_01789
1885634	2 bp→GC	Coding (1,865–1,866/2,340 nt)	BIF_01789 ←
1885679	2 bp→CT	Coding (1,820–1,821/2,340 nt)	BIF_01789 ←
1885686	+G	Coding (1,814/2,340 nt)	BIF_01789 ←
1885711	+G	Coding (1,789/2,340 nt)	BIF_01789 ←
1885722	+A	Coding (1,778/2,340 nt)	BIF_01789 ←
1885787	2 bp→GC	Coding (1,712–1,713/2,340 nt)	BIF_01789 ←
1885792	+C	Coding (1,708/2,340 nt)	BIF_01789 ←
1885854	Δ1 bp	Coding (1,646/2,340 nt)	BIF_01789 ←
1893674	2 bp→TGC	Coding (2,445–2,446/2,673 nt)	BIF_00866 →
1893713	+G	Coding (2,484/2,673 nt)	BIF_00866 →
1893740	+G	Coding (2,511/2,673 nt)	BIF_00866 →
1893947	A→C	Intergenic (+45/+15)	BIF_00866 → / ← BIF_00684
1893952	3 bp→26 bp	Intergenic (+50/+8)	BIF_00866 → / ← BIF_00684
1903558	34 bp→73 bp	Intergenic (+2/+61)	BIF_00971 → / ← BIF_01033
1913433	C→T	Intergenic (+33/+59)	BIF_02085 → / ← BIF_01409
1914632	+AAGGGGCGCCG	Coding (60/1,200 nt)	BIF_01409 ←
1914636	A→G	V19A (GTA→GCA)	BIF_01409 ←
1932289	+G	Intergenic (+61/+53)	BIF_02266 → / ← BIF_00333
1932291	+T	Intergenic (+63/+51)	BIF_02266 → / ← BIF_00333
1932292	+G	Intergenic (+64/+50)	BIF_02266 → / ← BIF_00333
1932294	1 bp→GC	Intergenic (+66/+48)	BIF_02266 → / ← BIF_00333
1932295	+CA	Intergenic (+67/+47)	BIF_02266 → / ← BIF_00333
1932335	+CGCCT	Intergenic (+107/+7)	BIF_02266 → / ← BIF_00333

The nucleotide position column indicates the nucleotide position in GenBank accession number NC_017214.1, the mutation column indicates the genetic variant, the annotation column shows the effect of a variant on a gene (for intergenic variants, the numbers in parentheses indicate the variant’s position relative to the flanking genes, with positive numbers indicating that the variant is downstream and negative numbers indicating that the variant is upstream; for coding variants, the numbers in parentheses indicate the variant’s position in the affected gene and the gene's length), and the gene(s) column shows the locus tag(s) of the gene(s) in which or between which the variant occurs.

Data availability.

The genome sequence has been deposited in NCBI GenBank with accession number CP001853.2. The raw reads have been deposited in the SRA under BioProject number PRJNA42883 with accession numbers SRX9857028 (MiSeq) and SRX9857029 (MinION).