Developing Gut-Healthy Strains for Pets: Probiotic Potential and Genomic Insights of Canine-Derived Lactobacillus acidophilus GLA09
Abstract
:1. Introduction
2. Materials and Methods
2.1. Main Reagents and Instruments
2.2. Strain Source and Culture
2.3. WGS, Assembly and Annotation
2.3.1. Strain DNA Extraction and Detection
2.3.2. WGS and Genome Assembly
2.3.3. Functional Annotation of Genomes
2.3.4. Secondary Metabolites
2.3.5. Comparative Genomes
2.4. Biogenic Amines Detection
2.5. In Vitro Probiotic Potential of Strain
2.5.1. Cell Surface Hydrophobicity and Auto-Aggregation
2.5.2. Antibacterial Activity
2.5.3. Low pH and Bile Salt Tolerance
2.5.4. Data Analysis
3. Results
3.1. Genomic Characterization of L. acidophilus GLA09
3.2. Functional Annotation Analysis of the L. acidophilus GLA09
3.2.1. COG Annotations
3.2.2. GO Annotations
3.2.3. KEGG Annotations
3.2.4. TCDB Functional Notes and Pathogen Host Interactions
3.2.5. Non-Redundant Protein Database
3.2.6. CAZy Functional Notes
3.3. L. acidophilus GLA09 Tolerance-Related Genes
3.4. L. acidophilus GLA09 Safety-Related Gene
3.5. Biogenic Amine Content of L. acidophilus GLA09
3.6. Secondary Metabolite Prediction and Comparative Genome
3.7. Results of In Vitro Probiotic Potential Test of the Strain
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
WGS | Whole-genome sequencing |
MRS | MRS broth medium |
LB | Luria-Bertani |
GO | Gene Ontology |
KEGG | Kyoto Encyclopaedia of Genes and Genomes |
COG | Cluster of Orthologous Groups of Proteins |
CAZy | Carbohydrate-Active EnZymes database |
PHI | Pathogen Host Interactions Database |
CARD | Comprehensive Antibiotic Research Database |
VFDB | Virulence Factor Database |
SD | Standard deviation |
G + C | Guanine + Cytosine |
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Items | Values |
---|---|
Chromosome size (bp) | 2,042,740 |
Plasmid size (bp) | 59,983 |
G + C content of chromosome (%) | 34.94 |
G + C content of plasmid (%) | 33.38 |
tRNA | 64 |
23S rRNA | 5 |
16S rRNA | 5 |
5S rRNA | 5 |
Gene islands | 8 |
Prophage | 10 |
Gene | Gene Name | Gene Function |
---|---|---|
Universal stress family protein | ||
ctg_02003 | YaaA | peroxide stress protein |
ctg_00159 | - | universal stress protein |
ctg_01392 | - | universal stress protein |
Heat stress resistance | ||
ctg_00883 | DnaK | molecular chaperone DnaK |
ctg_00884 | DnaJ | molecular chaperone DnaJ |
ctg_00882 | GrpE | nucleotide exchange factor GrpE |
ctg_00881 | HrcA | heat-inducible transcriptional repressor |
ctg_00290 | HslO | Hsp33 family molecular chaperone |
ctg_00427 | GroES | co-chaperone GroES |
ctg_00428 | groEL | chaperonin GroEL |
ctg_01187 | HslU | ATP-dependent protease ATPase subunit |
Cold-shock stress resistance | ||
ctg_01357 | - | cold-shock protein |
ctg_00502 | CSD | cold-shock domain |
ctg_01357 | CspA | cold-shock protein |
Bile salt resistance | ||
ctg_01277 | BSH | bile salt hydrolase |
ctg_01002 | ppaC | manganese-dependent inorganic pyrophosphatase |
ctg_01277 | cbh | choloylglycine hydrolase |
ctg_00059 | ldhA | D-lactate dehydrogenase |
ctg_00379 | pstB1 | phosphate import ATP-binding protein |
pH stress resistance | ||
ctg_00826 | Asp23 | alkaline shock protein (Asp23) family |
ctg_00805 | Asp23 | alkaline shock protein (Asp23) family |
ctg_02131 | ClcA | H+/Cl− antiporter ClcA |
ctg_01406 | atpH | F-type H+-transporting ATPase subunit delta |
ctg_01402 | atpC | F-type H+-transporting ATPase subunit epsilon |
ctg_01405 | atpA | F0F1 ATP synthase subunit alpha |
ctg_01403 | atpD | F-type H+/Na+-transporting ATPase subunit beta |
ctg_01404 | atpG | F-type H+-transporting ATPase subunit gamma |
ctg_01408 | atpE | F-type H+-transporting ATPase subunit c |
ctg_01409 | atpB | F-type H+-transporting ATPase subunit a |
ctg_01407 | atpF | F-type H+-transporting ATPase subunit b |
ctg_01705 | nhaC | Na+/H+ antiporter NhaC |
Oxidative stress | ||
ctg_00443 | trxA | thioredoxin 1 |
ctg_01044 | - | putative NADH-flavin reductase |
ctg_00417 | - | NADH/NAD ratio-sensing transcriptional regulator Rex |
ctg_01569 | mvaA | hydroxymethylglutaryl-CoA reductase |
ctg_01520 | trxB, TRR | thioredoxin reductase (NADPH) |
ctg_00566 | - | thiol-disulfide isomerase or thioredoxin |
ctg_01776 | pcaC | 4-carboxymuconolactone decarboxylase |
ctg_00730 | - | NADPH-dependent 2,4-dienoyl-CoA reductase |
ctg_01536 | - | OAR1`3-oxoacyl-[acyl-carrier protein] reductase |
ctg_00527 | - | NADH dehydrogenase |
ctg_00526 | - | NADH dehydrogenase |
ctg_00711 | - | NADH oxidase |
ctg_01020 | GSR, gor | glutathione reductase (NADPH) |
ctg_01536 | fabG | OAR1`3-oxoacyl-[acyl-carrier protein] reductase |
Drug Class | Resistance Gene | Identities% | Percentage Length of Reference Sequence | AMR Gene Family |
---|---|---|---|---|
Lincosamide antibiotic | Lnu(C) | 97.56 | 100 | Lincosamide nucleotidyltransferase (LNU) |
VFDB ID | Virulence Factor Names | Related Genes |
---|---|---|
VFG016490 | EF-Tu | (Tuf) elongation factor Tu |
VFG000077 | clpP | (clpP) ATP-dependent Clp protease proteolytic subunit |
VFG006826 | lisR | (lisR) two-component response regulator |
VFG012103 | groEL | (groEL) chaperonin GroEL |
VFG005865 | galU | (galU) UTP--glucose-1-phosphate uridylyltransferase GalU |
VFG006041 | rfbA | (rfbA) glucose-1-phosphate thymidylyltransferase RfbA |
VFG037099 | msrA/B | (msrA/B(pilB)) trifunctional thioredoxin/methionine sulfoxide reductase A/B protein |
VFG026980 | sigA | (sigA/rpoV) RNA polymerase sigma factor |
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Zhao, M.; Zhang, Y.; Li, Y.; Li, G. Developing Gut-Healthy Strains for Pets: Probiotic Potential and Genomic Insights of Canine-Derived Lactobacillus acidophilus GLA09. Microorganisms 2025, 13, 350. https://doi.org/10.3390/microorganisms13020350
Zhao M, Zhang Y, Li Y, Li G. Developing Gut-Healthy Strains for Pets: Probiotic Potential and Genomic Insights of Canine-Derived Lactobacillus acidophilus GLA09. Microorganisms. 2025; 13(2):350. https://doi.org/10.3390/microorganisms13020350
Chicago/Turabian StyleZhao, Mengdi, Yuanyuan Zhang, Yueyao Li, and Guangyu Li. 2025. "Developing Gut-Healthy Strains for Pets: Probiotic Potential and Genomic Insights of Canine-Derived Lactobacillus acidophilus GLA09" Microorganisms 13, no. 2: 350. https://doi.org/10.3390/microorganisms13020350
APA StyleZhao, M., Zhang, Y., Li, Y., & Li, G. (2025). Developing Gut-Healthy Strains for Pets: Probiotic Potential and Genomic Insights of Canine-Derived Lactobacillus acidophilus GLA09. Microorganisms, 13(2), 350. https://doi.org/10.3390/microorganisms13020350