Background
Methods
Determination of cultural, morphological and physiological properties
Cultural conditions and DNA isolation
Genome sequencing and assembly
Genome annotation
Comparative genomics
Results and discussion
Classification and unique features
Genome properties
Attribute | Genome (total) | |
---|---|---|
Value | % of totala | |
Size (bp) | 1,751,578 | |
G?+?C content (bp) | 653,105 | 37.29 |
Coding region (bp) | 1,457,159 | 83.19 |
Total genesb | 1,638 | |
RNA genes | 53 | 3.24 |
Protein-coding genes | 1,555 | 94.93 |
Genes assigned to COGs | 1,321 | 84.95 |
Genes with signal peptides | 29 | 1.86 |
Genes with transmembrane helices | 492 | 31.64 |
Genome of P. pentosaceus LI05 exhibits probiotic properties
Characterization | Locus_tag | Size (bp) | Product description | Identity (BLASTx) | Max. identity to proteins of other species (BLASTp) (%) | ||
---|---|---|---|---|---|---|---|
ATCC 25745 (%) | SL4 (%) | IE-3 (%) | |||||
Bile tolerance | BB06_RS0100955 | 1,026 | Choloylglycine hydrolase family protein | 99.05 | 99.25 | 100 | 69.50 |
Acid tolerance | BB06_RS0107040 | 1,518 | F0F1 ATP synthase subunit alpha | 99.74 | 99.60 | 95.39 | 92.46 |
BB06_RS0107025 | 420 | F0F1 ATP synthase subunit epsilon | 99.76 | 99.29 | 99.76 | 84.89 | |
BB06_RS0107030 | 1,410 | F0F1 ATP synthase subunit beta | 99.86 | 99.86 | 100 | 96.16 | |
BB06_RS0107035 | 921 | F0F1 ATP synthase subunit gamma | 99.89 | 99.78 | 99.89 | 87.95 | |
BB06_RS0107050 | 522 | F0F1 ATP synthase subunit B | 99.81 | 99.81 | 100 | 90.53 | |
BB06_RS0107055 | 213 | F0F1 ATP synthase subunit C | 100 | 100 | 100 | 87.14 | |
BB06_RS0107060 | 717 | F0F1 ATP synthase subunit A | 100 | 99.86 | 99.86 | 96.22 | |
Universal stress resistance | BB06_RS0103670 | 453 | Universal stress protein UspA | 99.12 | 99.34 | 99.12 | 68.42 |
BB06_RS0106945 | 456 | Universal stress protein UspA | 100 | 100 | 100 | 90.67 | |
BB06_RS0101810 | 474 | Universal stress protein UspA | 99.37 | 99.79 | 99.79 | 70.70 | |
BB06_RS0100900 | 432 | Universal stress protein UspA | 99.54 | 99.07 | 99.77 | 99.30 | |
BB06_RS0101815 | 450 | Universal stress protein UspA | 99.33 | 99.11 | 99.11 | 93.24 | |
BB06_RS0102220 | 453 | Universal stress protein UspA | 99.78 | 99.78 | 100 | 91.21 | |
Hyperosmotic and heat resistance | BB06_RS0104860 | 594 | GrpE protein | 98.32 | 98.82 | 99.83 | 72.60 |
BB06_RS0104870 | 1,131 | Molecular chaperone DnaJ | 99.03 | 98.85 | 99.82 | 88.56 | |
Environmental stress resistance | BB06_RS0102555 | 1,620 | Molecular chaperone GroEL | 100 | 99.26 | 100 | 94.81 |
Oxidative stress resistance | BB06_RS0105175 | 516 | Methionine sulfoxide reductase A | 99.22 | 99.22 | 99.61 | 81.87 |
Enterocin A resistance | BB06_RS0101010 | 279 | Enterocin A Immunity family protein | 99.64 | - | 100 | 38.89 |
Arsenate resistance | BB06_RS0105725 | 354 | Arsenate reductase | 99.15 | 98.87 | 100 | 83.76 |
Characterization | Locus_tag | Size (bp) | Product description | Identity (BLASTx) | Max. identity to proteins of other species (BLASTp) (%) | ||
---|---|---|---|---|---|---|---|
ATCC 25745 (%) | SL4 (%) | IE-3 (%) | |||||
Adhesion | BB06_RS0106620 | 306 | Competence protein ComGC | 99.67 | 99.67 | 100 | 76.47 |
BB06_RS0106150 | 1,188 | Elongation factor Tu | 99.92 | 99.92 | 100 | 95.69 | |
BB06_RS0102755 | 1,323 | Enolase | 99.92 | 99.85 | 100 | 91.82 | |
BB06_RS0107170 | 330 | Pilus biosynthesis protein HicB | 100 | 100 | 100 | 60.91 | |
BB06_RS0108295 | 660 | Sortase | 99.70 | 99.24 | 99.85 | 76.71 | |
BB06_RS0102750 | 756 | Triosephosphate isomerase | 100 | 99.47 | 100 | 93.23 | |
Antimicrobial | BB06_RS0101015 | 182 | Prebacteriocin | 100 | - | - | 96.30 |
BB06_RS0105320 | Lysin | 92.84 | 91.02 | - | 86.70 | ||
BB06_RS0100880 | 528 | Colicin V production family protein | 99.24 | 99.24 | 99.81 | 61.64 | |
Biosynthesis of peptidoglycans | BB06_RS0102815 | 903 | UDP-N-acetylenolpyruvoylglucosamine reductase | 100 | 98.9 | 100 | 84.62 |
BB06_RS0106375 | 1,368 | UDP-N-acetylmuramoylalanine-D-glutamate ligase | 99.05 | 98.90 | 100 | 74.23 | |
BB06_RS0107220 | 687 | Peptidoglycan-binding protein LysM | 99.85 | 99.71 | 99.85 | 67.54 | |
BB06_RS0100815 | 1,338 | Peptidoglycan-binding protein | 88.20 | 89.95 | 99.85 | 55.53 | |
Riboflavin synthesis | BB06_RS0100520 | 471 | Riboflavin synthase, beta subunit | 98.09 | 97.74 | 60.30 | 61.43 |
BB06_RS0100530 | 606 | Riboflavin synthase, alpha subunit | 98.84 | 97.85 | 100 | 61.14 | |
BB06_RS0100535 | 1,083 | Riboflavin biosynthesis protein RibD | 99.26 | 99.26 | 100 | 57.61 | |
BB06_RS0104850 | 945 | Riboflavin biosynthesis protein RibF | 97.46 | 99.26 | 100 | 74.84 | |
BB06_RS0105860 | 360 | Riboflavin biosynthesis acetyltransferase (GNAT) family | 100 | 99.72 | 100 | 84.14 | |
Folate | BB06_RS0106895 | 1,275 | Folylpolyglutamate synthase | 99.45 | 99.53 | - | 59.52 |
BB06_RS0105770 | 486 | Dihydrofolate reductase | 98.56 | 98.56 | 55.76 | 53.13 | |
Gamma-aminobutyrate | BB06_RS0107660 | 1,452 | Gamma-aminobutyrate permease | 99.38 | 99.66 | 100 | 85.45 |
Biotin | BB06_RS0108625 | 560 | Biotin biosynthesis protein BioY | 99.47 | 99.47 | 100 | 55.19 |
Thiamine | BB06_RS0106910 | 1,188 | Thiamine biosynthesis protein ThiI | 99.67 | 99.67 | 100 | 88.64 |
BB06_RS0107185 | 942 | Thiamine biosynthesis protein ApbE | 98.09 | 98.93 | 99.79 | 63.96 |
Comparisons with other fully sequenced genomes
Locus | Size (bp) | Predicted function | Best BLASTp hit | % Query cover | % Amino acid identity | |
---|---|---|---|---|---|---|
By BLASTp | Accession no. | Organism | ||||
BB06_RS0102945 | 1,110 | Type I restriction endonuclease subunit S | WP_000072560.1 |
Staphylococcus aureus
| 100 | 49.34 |
BB06_RS0102950 | 912 | Integrase | WP_006845852.1 |
Weissella koreensis
| 100 | 74.26 |
BB06_RS0102955 | 672 | Type I restriction-modification system, specificity subunit S | WP_003595917.1 |
Lactobacillus casei
| 100 | 54.71 |
BB06_RS0102980 | 936 | Daunorubicin resistance ATP-binding protein DrrA | YP_004841605.1 | Lactobacillus sanfranciscensis TMW 1.1304 | 100 | 62.06 |
BB06_RS0102995 | 678 | ThiJ/PfpI family protein | WP_010770374.1 |
Enterococcus caccae
| 99 | 71.42 |
BB06_RS0103035 | 633 | TraX family protein | YP_006726711.1 | Lactobacillus buchneri CD034 | 99 | 50.90 |
BB06_RS0103095 | 618 | Transposase | YP_005004471.1 | Pediococcusclaussenii ATCC BAA-344 | 100 | 98.05 |
BB06_RS0103100 | 2,268 | Daunorubicin resistance protein DrrC | WP_003680292.1 |
Lactobacillus coryniformis
| 100 | 99.07 |
BB06_RS0103110 | 591 | Integrase | WP_004906016.1 |
Leuconostoc citreum
| 99 | 97.96 |
BB06_RS0103120 | 468 | Ferritin-like DNA-binding protein | BAN08201.1 |
Lactobacillus plantarum 2025
| 100 | 99.35 |
BB06_RS0103125 | 744 | Glycosyltransferase family 2 | WP_027822873.1 |
Lactobacillus plantarum
| 100 | 99.60 |
BB06_RS0103130 | 1,248 | ABC transporter permease | WP_027822874.1 |
Lactobacillus plantarum
| 100 | 99.76 |
BB06_RS0103135 | 672 | TetR family transcriptional regulator | WP_027822875.1 |
Lactobacillus plantarum
| 100 | 99.55 |
BB06_RS0103140 | 339 | Transposase | WP_015474731.1 |
Lactobacillus brevis
| 95 | 99.07 |
BB06_RS0103155 | 1,308 | Excinuclease ABC subunit A | WP_024862991.1 | Pediococcus acidilactic i | 99 | 72.51 |
BB06_RS0103175 | 859 | Acetyl xylan esterase | WP_025478109.1 | Enterococcus saccharol yticus | 99 | 88.97 |
BB06_RS0103180 | 561 | PadR family transcriptional regulator | WP_017552090.1 |
Bacillus coagulans
| 100 | 99.43 |
BB06_RS0103200 | 906 | Membrane protein | 024625654.1 |
Lactobacillus fabifermentans
| 99 | 45.18 |
BB06_RS0103305 | 930 | Epimerase | WP_021357793.1 |
Lactobacillus plantarum
| 99 | 62.50 |
BB06_RS0103310 | 660 | Capsular polysaccharide biosynthesis protein | WP_003680917.1 |
Lactobacillus coryniformis
| 93 | 60.68 |
BB06_RS0103315 | 846 | Glycosyltransferase | WP_003638227.1 |
Lactobacillus pentosus
| 96 | 45.39 |
BB06_RS0103320 | 987 | Polysaccharide biosynthesis protein | YP_004889104.1 | Lactobacillus plantarum WCFS1 | 98 | 48.32 |
BB06_RS0104430 | 1,173 | Phage integrase family site-specific recombinase | WP_004165738.1 |
Pediococcus acidilactici DSM 20284
| 99 | 75.19 |
BB06_RS0104450 | 398 | Putative prophage repressor | WP_007289487.1 |
Thermosinus carboxydivorans
| 97 | 41.98 |
BB06_RS0104515 | 768 | Phage protein | ERL43462.1 | Lactobacillus plantarum JDM1 | 64 | 48 |
BB06_RS0104520 | 692 | Replisome organizer | WP_004165758.1 |
Pediococcus acidilactici
| 99 | 66.09 |
BB06_RS0104600 | 1,374 | Terminase | WP_002318686.1 |
Enterococcus faecium
| 100 | 60.18 |
BB06_RS0104605 | 1,548 | Minor capsid protein | WP_022638369.1 |
Lactobacillus plantarum
| 98 | 58.75 |
BB06_RS0104610 | 1,134 | Minor capsid protein | WP_016511174.1 |
Lactobacillus plantarum
| 99 | 49.47 |
BB06_RS0104645 | 462 | Capsid protein | WP_002314916.1 |
Enterococcus faecium
| 92 | 72.03 |
BB06_RS0104660 | 5,241 | Tail protein | WP_002820753.1 |
Oenococcus oeni
| 73 | 35.42 |
BB06_RS0105620 | 810 | Phage protein | WP_012678830.1 |
Streptococcus equi
| 92 | 33.46 |