Comparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains Culturing and Genome Sequencing
2.2. The Average Nucleotide Identity (ANI) Values and Phylogenetic Analyses
2.3. Pan-Genome and Core-Genome Analysis
2.4. Phylogenetic Comparison
2.5. Whole Genome Comparison
2.6. Genotype Analysis of Carbohydrate Metabolism
2.7. Genotype Analysis of Antibiotic Resistance
2.8. Prediction of the EPS and Surface Layer Protein Gene Operon
2.9. Prediction of Bacteriocin Operon
2.10. Identification of CRISPR-Cas Systems and Prophage
2.11. Ethics Statement
3. Results
3.1. Genome Characteristics of L. acidophilus
3.2. Pan-Genome and Core-Genome of L. acidophilus
3.3. ANI, Phylogenetic Analyses and Whole Genome Comparison of L. acidophilus
3.4. Genotype Analysis for Carbohydrates Utilization in L. acidophilus
3.5. Genotype Analysis for Antibiotic Resistance of L. acidophilus
3.6. Comparative Analysis of Functional Gene Composition of L. acidophilus
3.7. Prediction of the EPS Operon in L. acidophilus
3.8. Prediction of the Surface Layer Protein Operon in L. acidophilus
3.9. Prediction of the Bacteriocin Operon in L. acidophilus
3.10. Prediction of Prophages and CRISPR-Cas Systems in L. acidophilus
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Strain | BioSample | Size(Mb) | GC(%) | CDS no. | Source |
---|---|---|---|---|---|
ATCC 4356 | SAMN03105773 | 1.9567 | 34.6 | 1730 | Human |
ATCC 4796 | SAMN00001471 | 2.0205 | 34.7 | 1747 | Human |
ATCC 53544 | SAMN07357495 | 1.99191 | 34.7 | 1773 | Human |
BIO6307 | SAMN12856535 | 1.96977 | 34.6 | 1790 | Unknown |
CCFM137 | SAMN19655193 | 1.951495 | 34.58 | 1904 | Human |
CIP 76.13 | SAMEA2272342 | 1.95182 | 34.6 | 1741 | Human |
CIRM-BIA 442 | SAMEA2272381 | 1.98699 | 34.7 | 1787 | Dairy product |
CIRM-BIA 445 | SAMEA2272655 | 2.00201 | 34.6 | 1782 | Dairy product |
DS10_1A | SAMN05583778 | 1.97072 | 34.6 | 1787 | Commercial Probiotic Products |
DS13_1A | SAMN05583782 | 1.96427 | 34.6 | 1780 | Commercial Probiotic Products |
DS13_1B | SAMN05583783 | 1.96393 | 34.6 | 1785 | Commercial Probiotic Products |
DS2_1A | SAMN05583785 | 1.98202 | 34.6 | 1812 | Commercial Probiotic Products |
DS20_1 | SAMN06464087 | 1.96947 | 34.6 | 1795 | Commercial Probiotic Products |
DS24_1 | SAMN06464090 | 1.96837 | 34.6 | 1790 | Commercial Probiotic Products |
DS5_1A | SAMN05583788 | 1.96883 | 34.6 | 1784 | Commercial Probiotic Products |
DS8_1A | SAMN05583791 | 1.96757 | 34.6 | 1787 | Commercial Probiotic Products |
DS9_1A | SAMN05583792 | 1.96901 | 34.6 | 1792 | Commercial Probiotic Products |
DSM 20079 | SAMN06606133 | 2.00997 | 34.7 | 1760 | Human |
DSM 20242 | SAMEA2272474 | 2.04786 | 34.7 | 1814 | Unknown |
DSM 9126 | SAMEA2272239 | 1.99176 | 34.6 | 1790 | Unknown |
FAHWH11L56 | SAMN19655182 | 1.975822 | 34.591 | 1881 | Human |
FCQHC4LH1 | SAMN19655183 | 1.962741 | 34.569 | 1877 | Human |
FFJND6L5 | SAMN19655184 | 1.960445 | 34.562 | 1878 | Human |
FFJND7L5 | SAMN19655185 | 1.989652 | 34.581 | 1905 | Human |
FGSYC48L79 | SAMN19655186 | 1.990393 | 34.662 | 1984 | Human |
FHNXY41L162 | SAMN19655187 | 2.051142 | 34.733 | 2112 | Human |
FNMGHHHT12L40 | SAMN19655188 | 1.992905 | 34.658 | 1894 | Human |
FSHXBX32L130 | SAMN19655189 | 2.140788 | 34.893 | 2218 | Human |
FSI4 | SAMN03274004 | 1.99197 | 34.7 | 1790 | Fermented dairy product |
FXJSW24L139 | SAMN19655190 | 2.115801 | 34.647 | 2059 | Human |
FXJSW48L59 | SAMN19655191 | 2.048808 | 34.753 | 2100 | Human |
FZJTZ18L25 | SAMN19655192 | 2.115442 | 34.846 | 2170 | Human |
LA_AVK1 | SAMN13198235 | 1.96274 | 34.6 | 1690 | Unknown |
LA_AVK2 | SAMN13198280 | 1.96264 | 34.6 | 1690 | Unknown |
LA1 | SAMN05631052 | 1.9912 | 34.7 | 1787 | Fermented dairy product |
La-14 | SAMN02603216 | 1.99158 | 34.7 | 1781 | Human |
LA-G80-111 | SAMN15165794 | 1.99198 | 34.7 | 1788 | Unknown |
LMG P-21904 | SAMN07187785 | 1.96566 | 34.6 | 1780 | Commercial Probiotic Products |
NCFM | SAMN02603047 | 1.99356 | 34.7 | 1760 | Human |
P2 | SAMN07665576 | 2.04684 | 35.7 | 1904 | Commercial Probiotic Products |
s-13 | SAMN15579847 | 1.96575 | 34.6 | 1778 | Unknown |
s-4 | SAMN15579838 | 1.95327 | 34.6 | 1724 | Unknown |
UBLA-34 | SAMN10136005 | 1.95104 | 34.6 | 1762 | Fermented foods |
WG-LB-IV | SAMN04628015 | 1.95169 | 34.6 | 1780 | Fermented dairy product |
YT1 | SAMN08142761 | 2.09254 | 34.7 | 1878 | Unknown |
Strain | Age | Gender | Modernization |
---|---|---|---|
FAHWH11L56 | 3 | Female | City |
FCQHC4LH1 | 20 | Male | Rural |
FFJND6L5 | 24 | Male | City |
FFJND7L5 | 24 | Female | Rural |
FGSYC48L79 | NA | NA | Rural |
FHNXY41L162 | 80 | Female | Rural |
FNMGHHHT12L40 | 23 | Female | City |
FSHXBX32L130 | 59 | Female | Rural |
FXJSW24L139 | 2.3 | Female | Rural |
FXJSW48L59 | 12 | Female | Rural |
FZJTZ18L25 | 79 | Male | Rural |
Strain | CRISPR-Cas | Prophage |
---|---|---|
ATCC 4356 | incomplete | incomplete |
ATCC 4796 | incomplete | incomplete |
ATCC 53544 | incomplete | incomplete |
BIO6307 | incomplete | incomplete |
CCFM137 | incomplete | incomplete |
CIP 76.13 | incomplete | incomplete |
CIRM-BIA 442 | incomplete | incomplete |
CIRM-BIA 445 | incomplete | incomplete |
DS10_1A | incomplete | incomplete |
DS11_1A | incomplete | incomplete |
DS13_1A | incomplete | incomplete |
DS13_1B | incomplete | incomplete |
DS2_1A | incomplete | incomplete |
DS20_1 | incomplete | incomplete |
DS24_1 | incomplete | incomplete |
DS5_1A | incomplete | incomplete |
DS8_1A | incomplete | incomplete |
DS9_1A | incomplete | incomplete |
DSM 20079 | incomplete | incomplete |
DSM 20242 | incomplete | incomplete |
DSM 9126 | incomplete | incomplete |
FAHWH11L56 | incomplete | incomplete |
FCQHC4LH1 | incomplete | incomplete |
FFJND6L5 | incomplete | incomplete |
FFJND7L5 | incomplete | incomplete |
FGSYC48L79 | incomplete | intact |
FHNXY41L162 | complete | intact |
FNMGHHHT12L40 | incomplete | incomplete |
FSHXBX42L130 | incomplete | intact |
FSI4 | incomplete | incomplete |
FXJSW24L139 | incomplete | incomplete |
FXJSW48L59 | complete | intact |
FZJTZ18L25 | incomplete | intact |
LA_AVK1 | incomplete | incomplete |
LA_AVK2 | incomplete | incomplete |
LA1 | incomplete | incomplete |
La-14 | incomplete | incomplete |
LA-G80-111 | incomplete | incomplete |
LMG P-21904 | incomplete | incomplete |
NCFM | incomplete | incomplete |
P2 | incomplete | incomplete |
s-13 | incomplete | incomplete |
s-4 | incomplete | incomplete |
UBLA-34 | incomplete | incomplete |
WG-LB-IV | incomplete | incomplete |
YT1 | complete | intact |
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Huang, Z.; Zhou, X.; Stanton, C.; Ross, R.P.; Zhao, J.; Zhang, H.; Yang, B.; Chen, W. Comparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus. Microorganisms 2021, 9, 1992. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091992
Huang Z, Zhou X, Stanton C, Ross RP, Zhao J, Zhang H, Yang B, Chen W. Comparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus. Microorganisms. 2021; 9(9):1992. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091992
Chicago/Turabian StyleHuang, Zheng, Xingya Zhou, Catherine Stanton, Reynolds Paul Ross, Jianxin Zhao, Hao Zhang, Bo Yang, and Wei Chen. 2021. "Comparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus" Microorganisms 9, no. 9: 1992. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091992