Genomic Analysis of Limosilactobacillus fermentum ATCC 23271, a Potential Probiotic Strain with Anti-Candida Activity
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains and Growth Conditions
2.2. Whole-Genome Sequencing of Limosilactobacillus fermentum ATCC 23271
2.3. Genome Analysis
2.4. Antagonism Assay
2.5. Interference on Cell Adhesion
2.6. Tolerance to Gastrointestinal Conditions
2.7. Antibiotic Susceptibility Test
2.8. Ethical Aspects
2.9. Statistical Analysis
3. Results
3.1. General Genome Features and Comparative Analysis
3.2. Putative Genes Associated with Probiotic Properties
3.3. Antagonism Activity
3.4. Interference in Pathogen Cell Adhesion
3.5. Tolerance to Bile Salts and Acidic pH
3.6. Antibiotic Susceptibility Assay
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Attribute * | Indicators |
---|---|
Genome size (bp) | 2,193,335 |
G + C content (%) | 50.9 |
N50 | 33,843 |
L50 | 22 |
Number of contigs (with PEGs) | 223 |
Number of subsystems | 312 |
Prophage-like clusters | 2 |
CDS | 2387 |
CDS (with proteins) | 2123 |
N° of RNAs | 79 |
N° of tmRNA operons | 1 |
N° of tRNA | 55 |
N° of rRNA | 21 |
N° of CRISPR loci | 2 |
RAST/BLAST Description | Query Length | Accession Length | Query Cover | E Value | Per Ident | Accession |
---|---|---|---|---|---|---|
ATP synthase F0 sector subunit a/F0F1 ATP synthase subunit A | 711 pb | 236 aa | 100% | 7 × 10−167 | 100% | WP_003682740.1 |
ATP synthase F0 sector subunit b/F0F1 ATP synthase subunit B | 507 pb | 168 aa | 100% | 6 × 10−116 | 100% | WP_054173734.1 |
ATP synthase F0 sector subunit c/MULTISPECIES: F0F1 ATP synthase subunit C | 213 pb | 70 aa | 100% | 1 × 10–38 | 100% | WP_003682741.1 |
ATP synthase alpha chain/F0F1 ATP synthase subunit alpha | 1539 pb | 512 aa | 100% | 0.0 | 99.80% | WP_086439482.1 |
ATP synthase beta chain/F0F1 ATP synthase subunit beta | 1422 pb | 473 aa | 100% | 0.0 | 99.79% | WP_057194567.1 |
ATP synthase delta chain/F0F1 ATP synthase subunit delta | 546 pb | 181 aa | 100% | 3 × 10–126 | 99.45% | WP_057194565.1 |
ATP synthase gamma chain/F0F1 ATP synthase subunit gamma | 936 pb | 311 aa | 100% | 0.0 | 99.68% | WP_088460387.1 |
ATP synthase epsilon chain/ | 423 pb | 140 aa | 100% | 3 × 10–95 | 99.29% | WP_003685876.1 |
L-lactate dehydrogenase (EC 1.1.1.27)/L-lactate dehydrogenase | 954 bp | 317 aa | 100% | 0.0 | 99.68% | WP_012391154.1 |
L-lactate dehydrogenase (EC 1.1.1.27)/L-lactate dehydrogenase | 942 bp | 313 aa | 100% | 0.0 | 100% | WP_138464682.1 |
L-lactate dehydrogenase (EC 1.1.1.27)/L-lactate dehydrogenase | 933 bp | 310 aa | 100% | 0.0 | 100% | WP_046948611.1 |
PTS system, cellobiose-specific IIC component/PTS system oligo-beta-mannoside-specific EIIC component | 1311 bp | 436 aa | 100% | 0.0 | 100% | QIX58800.1 |
ATP-dependent Clp protease ATP-binding subunit ClpX/ATP-dependent Clp protease ATP-binding subunit ClpX | 1251 bp | 416 aa | 100% | 0.0 | 99.52% | WP_096493701.1 |
Glucose-6-phosphate isomerase (EC 5.3.1.9)/glucose-6-phosphate isomerase | 525 bp | 174 aa | 100% | 1 × 10–124 | 99.43% | RGW51862.1 |
Glucose-6-phosphate isomerase (EC 5.3.1.9)/glucose-6-phosphate isomerase | 1353 bp | 450 aa | 100% | 0.0 | 99.56% | WP_021815746.1 |
GTP pyrophosphokinase (EC 2.7.6.5)/GTP pyrophosphokinase | 612 bp | 203 aa | 100% | 8 × 10–150 | 99.51% | WP_100184301.1 |
Pyruvate kinase/pyruvate kinase | 1422 bp | 473 aa | 100% | 0.0 | 100% | WP_003684953.1 |
Arginine/ornithine antiporter ArcD/Amino acid transporter | 1419 bp | 472 aa | 100% | 0.0 | 100% | AOR74635.1 |
Phosphoglycerate mutase/2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 678 bp | 225 aa | 100% | 4 × 10–166 | 100% | WP_004562727.1 |
Choloylglycine hydrolase/choloylglycine hydrolase family protein | 978 bp | 325 aa | 100% | 0.0 | 100% | WP_035436617.1 |
CTP synthase/CTP synthase | 1602 bp | 533 aa | 100% | 0.0 | 99.81% | WP_003684004.1 |
RAST/BLAST Description | Function | Query Length | Accession Length | Query Cover | E Value | Per Ident | Accession |
---|---|---|---|---|---|---|---|
Aggregation substance precursor | Aggregation | 1842 pb | 613 aa | 99% | 0.0 | 99.84% | AKM50933.1 |
LysM peptidoglycan-binding domain-containing protein | 591 pb | 196 aa | 99% | 9 × 10–85 | 100.00% | WP_021815732.1 | |
LysM peptidoglycan-binding domain-containing protein | 816 pb | 315 aa | 48% | 1 × 10–40 | 100.00% | WP_168183590.1 | |
Exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase | Exopolysaccharide production | 666 pb | 229 aa | 99% | 3 × 10–159 | 98.64% | WP_104877738.1 |
Exopolysaccharide biosynthesis protein | 771 pb | 256 aa | 99% | 0.0 | 99.22% | WP_163601282.1 | |
CpsD/CapB family tyrosine-protein kinase | 741 pb | 247 aa | 91% | 3 × 10–160 | 99.12% | WP_062813522.1 | |
Exopolysaccharide biosynthesis protein | 771 pb | 256 aa | 99% | 5 × 10–174 | 99.61% | KPH03198.1 | |
Fibronectin-binding domain-containing protein | Adhesion | 1692 pb | 563 aa | 99% | 0.0 | 99.82% | WP_103205388.1 |
Algorithms * | Results |
---|---|
SVM | 1.000 |
DA | 1.000 |
RF | 0.957 |
ANN | NAMP |
RAST/BLAST Description | Query Length | Accession Length | Query Cover | E Value | Per Ident | Accession |
---|---|---|---|---|---|---|
Penicillin-binding protein | 1017 | 338 | 99% | 0.0 | 99.41% | EQC60084.1 |
Class A beta-lactamase-related serine hydrolase | 1020 | 339 | 99% | 0.0 | 99.12% | MBD9348952.1 |
Cation diffusion facilitator family transporter | 906 | 301 | 99% | 0.0 | 100.00% | WP_015639412.1 |
Elongation factor G | 2085 | 694 | 99% | 0.0 | 99.86% | KPH03387.1 |
DNA topoisomerase IV subunit B | 1998 | 665 | 99% | 0.0 | 99.85% | WP_003683141.1 |
Topoisomerase IV subunit A | 2478 | 825 | 99% | 0.0 | 100.00% | BAG27240.1 |
MerR family transcriptional regulator | 423 | 140 | 99% | 1 × 10–97 | 100.00% | WP_003682036.1 |
Multidrug resistance protein MdtG | 342 | 113 | 99% | 2 × 10–61 | 99.12% | QIX57855.1 |
MFS transporter | 123 | 160 | 97% | 2 × 10–17 | 97.50% | WP_155762340.1 |
GTP-binding protein | 1935 | 644 | 99% | 0.0 | 100.00% | WP_112296957.1 |
Multidrug transporter | 1227 | 413 | 99% | 0.0 | 99.75% | AKM51464.1 |
DNA topoisomerase (ATP-hydrolyzing) subunit B | 1950 | 649 | 99% | 0.0 | 99.85% | WP_023465959.1 |
DNA gyrase subunit A | 2511 | 836 | 99% | 0.0 | 99.76% | WP_160229810.1 |
MerR family transcriptional regulator | 423 | 151 | 99% | 3 × 10–98 | 100.00% | CDI69999.1 |
Multidrug transporter MatE | 1317 | 438 | 99% | 0.0 | 99.77% | WP_042513988.1 |
Heavy metal translocating P-type ATPase | 1929 | 642 | 99% | 0.0 | 99.84% | WP_112297009.1 |
MATE family efflux transporter | 1320 | 439 | 99% | 0.0 | 97.95% | WP_135252410.1 |
FAD-dependent oxidoreductase | 1350 | 449 | 99% | 0.0 | 100.00% | WP_100184414.1 |
Cation transporter | 552 | 207 | 99% | 4 × 10–98 | 100.00% | WP_114684362.1 |
Pathogen | Inhibition Zone in mm ± SD * |
---|---|
E. faecalis (ATCC 29212) | In situ |
E. coli enteroaggregative 17.2 | In situ |
Salmonella enterica (ATCC 13076) | In situ |
C. albicans (ATCC 90028) | 17 ± 1.41 |
C. albicans (SC 5314) | 16.5 ± 1.12 |
C. albicans 44 | 14 ± 1.4 |
C. albicans CAS | 20 ± 0 |
C. krusei (ATCC 6258) | − |
C. krusei GJFD | − |
Candida parapsilosis (ATCC 22019) | 26.5 ± 2.1 |
C. parapsilosis FSG | 13.5 ± 2.1 |
C. parapsilosis RCL | 14.5 ± 0.7 |
Conditions | % of L. fermentum Survival (±SD) 1 | p-Value 2 |
---|---|---|
pH 2.0 | 60.88 ± 0.9569 | 0.0043 |
pH 4.0 | 105.0 ± 5909 | |
Bile salt 0.5% | 109.7 ± 4434 | 0.0348 |
Bile salt 1% | 94.13 ± 1244 |
Antibiotics | L. fermentum ATCC 23271 | |
---|---|---|
Zone Inhibition in mm | Interpretation * | |
Cefazolin | 22 | Susceptible |
Chloramphenicol | 34 | |
Ciprofloxacin | 21 | |
Clindamycin | 31 | |
Erythromycin | 39 | |
Linezolid | 40 | |
Nitrofurantoin | 30 | |
Rifampicin | 34 | |
Penicillin G | 41 | |
Tetracycline | 38 | |
Tigecillin | 40 | |
Cefoxitin | 15 | Moderately susceptible |
Norfloxacin | 14 | |
Gentamycin | 12 | Resistant |
Sulfazotrim | 0 | |
Vancomycin | 0 |
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dos Santos, C.I.; Campos, C.D.L.; Nunes-Neto, W.R.; do Carmo, M.S.; Nogueira, F.A.B.; Ferreira, R.M.; Costa, E.P.S.; Gonzaga, L.F.; Araújo, J.M.M.; Monteiro, J.M.; et al. Genomic Analysis of Limosilactobacillus fermentum ATCC 23271, a Potential Probiotic Strain with Anti-Candida Activity. J. Fungi 2021, 7, 794. https://doi.org/10.3390/jof7100794
dos Santos CI, Campos CDL, Nunes-Neto WR, do Carmo MS, Nogueira FAB, Ferreira RM, Costa EPS, Gonzaga LF, Araújo JMM, Monteiro JM, et al. Genomic Analysis of Limosilactobacillus fermentum ATCC 23271, a Potential Probiotic Strain with Anti-Candida Activity. Journal of Fungi. 2021; 7(10):794. https://doi.org/10.3390/jof7100794
Chicago/Turabian Styledos Santos, Camilla I., Carmem D. L. Campos, Wallace R. Nunes-Neto, Monique S. do Carmo, Flávio A. B. Nogueira, Rômulo M. Ferreira, Ennio P. S. Costa, Laoane F. Gonzaga, Jéssica M. M. Araújo, Joveliane M. Monteiro, and et al. 2021. "Genomic Analysis of Limosilactobacillus fermentum ATCC 23271, a Potential Probiotic Strain with Anti-Candida Activity" Journal of Fungi 7, no. 10: 794. https://doi.org/10.3390/jof7100794