Comparative Genomic Analysis Reveals Intestinal Habitat Adaptation of Ligilactobacillus equi Rich in Prophage and Degrading Cellulase
Abstract
:1. Introduction
2. Results and Discussion
2.1. L. equi Genome Characteristics
2.2. Analysis of the Average Nucleotide Identity and Total Nucleotide Identity of Ligilactobacillus Type Strains
2.3. Core Gene Set to Construct Phylogenetic Tree
2.4. Gene Prediction and Annotation
2.5. Construction of the Core Gene Set, Pan-Gene Set, and Unique Gene Analysis of L. equi
2.5.1. Construction of Pan-Core Gene Set
2.5.2. Analysis of Specific Functional Genes
2.6. Carbohydrate-Active Enzyme Analysis
2.7. Identification of the Presence of Prophages in L. equi
2.8. Synteny Analysis
3. Materials and Methods
3.1. Experimental Strain
3.2. Main Reagents and Instruments
3.3. Strain Culture
3.4. DNA Extraction and Genome Sequencing
3.5. Genome Assembly of Strains
3.6. Calculation of Total Nucleotide Consistency (TNI) and Average Nucleotide Consistency (ANI)
3.7. Analysis of Core Gene Set and Phylogenetic Tree
3.8. RAST Notes
3.9. Analysis of Carbohydrate-Active Enzymes
3.10. Prediction of Prophage
3.11. Commonality Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Strain | Isolation Source | Genome Size (Mbp) | GC Content (%) | CDS | tRNA | rRNA | Accession NCBI |
---|---|---|---|---|---|---|---|
L. acidipiscis DSM 15353T | Fermented fish | 2.22 | 39.07 | 2230 | 32 | 2 | AZFI01000000 |
L. agilis DSM 20509T | Municipal sewage | 1.96 | 41.74 | 2025 | 40 | 3 | AYYP01000000 |
L. animalis DSM 20602T | Dental plaque of baboon | 1.79 | 41.07 | 1812 | 34 | 4 | AYYW01000000 |
L. apodemi DSM 16634T | Feces, wild Japanese wood mouse | 1.99 | 38.60 | 2032 | 49 | 4 | AZFT01000000 |
L. aviarius DSM 20655T | Feces of chicken | 1.60 | 40.12 | 1585 | 37 | 3 | AYZA01000000 |
L.ceti DSM 22408T | Lungs of a beaked whale | 1.33 | 33.73 | 1273 | 51 | 3 | AUHP01000000 |
L.hayakitensis DSM 18933T | Feces of horse | 1.60 | 34.03 | 1583 | 36 | 2 | AZGD00000000 |
L. murinus DSM 20452T | Intestine of rat | 2.08 | 40.03 | 2040 | 24 | 4 | AYYN01000000 |
L. pobuzihii NBRC 103219T | Pobuzihi (fermented cummingcordia) | 2.23 | 37.70 | 2121 | 46 | 4 | JQCN01000000 |
L. ruminis DSM 20403T | Bovine rumen | 1.94 | 43.37 | 1912 | 40 | 7 | AYYL01000000 |
L. saerimneri DSM 16049T | Pig feces | 1.64 | 42.54 | 1726 | 35 | 4 | AZFP01000000 |
L. salivarius DSM 20555T | Saliva | 1.89 | 32.5 | 1920 | 25 | 4 | AYYT01000000 |
L. equi DPC 6820 | Feces of horses | 2.07 | 39.21 | 2077 | 44 | 2 | AWWH01000000 |
L. equi DSM 15833T | Feces of horses | 2.18 | 39.03 | 2188 | 50 | 2 | AZFH01000000 |
L. equi JCM 10991T | Feces of horses | 2.14 | 38.99 | 2425 | 18 | 4 | BAMI01000000 |
L. equi IMAU81196 | Feces of horses | 1.95 | 39.48 | 1905 | 33 | 4 | JAKGTO000000000 |
IMAU81196 | Function | JCM 10991T | Function | DSM 15833T | Function | DPC 6820 | Function |
---|---|---|---|---|---|---|---|
aroA | 3-phosphoshikimate 1-carboxyvinyltransferase | gltX | Glutamate—RNA ligase | fruA | Fructan beta-fructosidase precursor | cysE | Serine acetyltransferase |
aroC | Chorismate synthase | alaS | Alanine—tRNA ligase | trpF | N-(5’-phosphoribosyl) anthranilate isomerase | ||
aroK | Shikimate kinase | proS | Proline—tRNA ligase | yhdJ | DNA adenine methyltransferase | ||
bglF | PTS system beta-glucoside-specific EIIBCA component | leuS | Leucine—tRNA ligase | psuK | Pseudouridine kinase | ||
bglH | Aryl-phospho-beta-D-glucosidase | valS | Valine—tRNA ligase | ||||
bglG | Cryptic beta-glucoside bgl operon antiterminator | aspS | Aspartate—tRNA ligase | ||||
dhaM | PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit | argS | Arginine—tRNA ligase | ||||
dhaL | PTS-dependent dihydroxyacetone kinase, ADP-binding subunit | ileS | Isoleucine—tRNA ligase | ||||
dhaK | PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit | cycA | D-serine/D-alanine/glycine transporter | ||||
dhaQ | DhaKLM operon coactivator | folT | Folate transporter | ||||
dhaS | HTH-type dhaKLM operon transcriptional activator | znuB | High-affinity zinc uptake system membrane protein |
Strains | Prophage Region | Completeness | Region Length(kb) | Total Proteins | GC % | Most Common Phage (Number of Genes) |
---|---|---|---|---|---|---|
JCM 10991T | 1 | Incomplete | 11.60 | 21 | 40.00 | PHAGE_Lactob_phiPYB5_NC_027982(3) |
2 | Questionable | 22.40 | 37 | 41.53 | PHAGE_Lister_B054_NC_009813 (6) | |
3 | Intact | 36.00 | 62 | 39.51 | PHAGE_Lactob_LF1_NC_019486 (15) | |
4 | Incomplete | 10.90 | 14 | 37.55 | PHAGE_Clostr_c_st_NC_007581 (2) | |
DSM 15833T | 1 | Questionable | 31.10 | 15 | 38.21 | PHAGE_Clostr_c_st_NC_007581 (3) |
2 | Intact | 42.70 | 63 | 40.54 | PHAGE_Lister_B054_NC_009813 (11) | |
3 | Intact | 38.40 | 62 | 39.34 | PHAGE_Lactob_LF1_NC_019486 (15) | |
IMAU81196 | 1 | Intact | 14.90 | 21 | 34.14 | PHAGE_Lactob_JCL1032_NC_019456 (4) |
DPC 6820 | 1 | Intact | 18.50 | 19 | 40.10 | PHAGE_Lactob_phig1e_NC_004305 (13) |
2 | Questionable | 15.80 | 20 | 43.33 | PHAGE_Lactob_LfeSau_NC_029068 (8) | |
3 | Incomplete | 11.90 | 20 | 36.54 | PHAGE_Lactob_PLE3_NC_031125 (3) | |
4 | Questionable | 16.0 | 17 | 39.84 | PHAGE_Lister_LP_101_NC_024387 (8) | |
5 | Questionable | 5.40 | 10 | 36.88 | PHAGE_Clostr_c_st_NC_007581 (2) | |
6 | Incomplete | 13.90 | 20 | 39.65 | PHAGE_Lactob_phig1e_NC_004305 (3) |
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Li, Y.; Liu, C.; Liu, Q.; Liu, W. Comparative Genomic Analysis Reveals Intestinal Habitat Adaptation of Ligilactobacillus equi Rich in Prophage and Degrading Cellulase. Molecules 2022, 27, 1867. https://doi.org/10.3390/molecules27061867
Li Y, Liu C, Liu Q, Liu W. Comparative Genomic Analysis Reveals Intestinal Habitat Adaptation of Ligilactobacillus equi Rich in Prophage and Degrading Cellulase. Molecules. 2022; 27(6):1867. https://doi.org/10.3390/molecules27061867
Chicago/Turabian StyleLi, Yu, Chen Liu, Qing Liu, and Wenjun Liu. 2022. "Comparative Genomic Analysis Reveals Intestinal Habitat Adaptation of Ligilactobacillus equi Rich in Prophage and Degrading Cellulase" Molecules 27, no. 6: 1867. https://doi.org/10.3390/molecules27061867