Genomic comparison of sporeforming bacilli isolated from milk

BMC Genomics

Table 1 Strains and genome description of strains used in this study

Strain	Species¹	*rpo* B allelic type (frequency of AT as reported by Ivy et al. (2012))²	Source (day of shelf life)	Total assembly size (number of contigs)³	N50	Mol% (G + C)⁴	GenBank accession number
FSL R5-860	Bacillus sp.⁵	158 (10.6%)	Pasteurized 2% milk (7 days)	5.6 Mb (106)	337,248	35.0	ASPZ00000000
FSL H7-687	Bacillus weihenstephanensis	3 (1.5%)	Pasteurized 2% milk (12 days)	5.6 Mb (112)	405,076	35.2	ASPY00000000
FSL R5-213	Viridibacillus arenosi	17(1.8%)	Pasteurized 2% milk (7 days)	4.4 Mb (47)	661,909	35.3	ASQA00000000
FSL H8-237	Paenibacillus odorifer	15 (9.5%)	Pasteurized 2% milk (21 days)	7.3 Mb (128)	256,380	44.0	ASPV00000000
FSL R7-277	Paenibacillus sp.⁶	45 (0.2%)	Pasteurized 2% milk (7 days)	7.6 Mb (122)	257,268	52.5	ASPX00000000
FSL R7-269	Paenibacillus sp.⁶	163 (0.7%)	Pasteurized 2% milk (7 days)	7.5 Mb (161)	252,603	51.8	ASPS00000000
FSL R5-192	Paenibacillus amylolyticus	23 (2.7%)	Pasteurized 2% milk (7 days)	7.0 Mb (80)	383,457	45.8	ASPR00000000
FSL H7-689	Paenibacillus amylolyticus	23 (2.7%)	Pasteurized 2% milk (12 days)	6.8 Mb (66)	525,446	45.9	ASPU00000000
FSL R5-808	Paenibacillus glucanolyticus	159 (0.5%)	Pasteurized 2% milk (1 day)	6.4 Mb (89)	316,677	48.8	ASPT00000000
FSL H8-457	Paenibacillus lautus	117 (0.1%)	Feed mix (N/A)	7.0 Mb (69)	696,553	51.2	ASPW00000000

¹Putative species were inferred based on 16S rRNA phylogenies (using 16S rRNA sequences extracted from the draft genome sequences) and confirmed using phylogenetic analysis of 31 protein sequences (Figure 1).
²Percentage of isolates with a given allelic type (AT) from a total of 1,288 isolates tested.
³Only contigs >199 bp are included.
⁴Inferred from genome sequence.
⁵FSL R5-860 was designated as Bacillus sp. as this strain clusters with B. cereus in a 16S rRNA phylogeny, but clusters with B. weihenstephanensis in the 31 protein phylogeny (Figure 1); while this is consistent with previous reports that B. cereus is polyphyletic, final species assignment of this isolate will require sequencing and analysis of further Bacillus isolates.
⁶Isolates FSL R7-277 and R7-269 were classified as Paenibacillus sp. as they could not be classified to species based on 16S rRNA sequences; in a 16S rRNA phylogeny both of these isolates clustered with P. caespitis (GenBank accession no. AM745263), but were not assigned this species name as this species has not yet been validly published.

ISSN: 1471-2164