Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity
Abstract
1. Introduction
2. Materials and Methods
2.1. Bacterial Growth Requirements
2.2. Antibiotic Resistance Screening
2.3. E. lenta Isolation from Human Faecal Samples
2.4. Bacterial Genomic DNA Extraction and Genome Sequencing
2.5. Bioinformatic Analysis of Bacterial Genomes
2.6. Prophage Features Identification, Phylogenetic and Protein Functional Analysis
2.7. Demonstration of DGR Functionality of Prophage DSM2243phi4
2.8. Detection of Circularised Prophage Genomes among Host Strain Cells
2.9. Detection of Virions in the Supernatant of Strain DSM2243
2.10. Data Processing and Visualisation
2.11. DDBJ/ENA/GenBank Submission Details
3. Results
3.1. Isolation of E. lenta from Human Faecal Samples
3.2. Genomes of E. lenta Isolates
3.3. Comparative Analysis of E. lenta Isolates
3.4. Identification and Diversity of Prophages
3.5. Gene Content of Prophages and Possible Impact on Host Infection
3.6. Taxonomic Placement of Prophages
3.7. Prophages and the CRISPR/cas System
3.8. Evidence That Prophages Are Functional
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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No. | Isolate | Accession (Genome; Plasmids) |
---|---|---|
1 | APC055-529-1D | CP089331; CP089332 |
2 | APC055-539-5C | CP089333 |
3 | APC055-920-1E | CP089334 |
4 | APC055-924-7B | CP089335 |
5 | APC055-928-H3-3 | CP089336 |
6 | APC055-943-4 | CP089337 |
7 | APC-F2-3 | CP089338; CP089339, CP089340 |
8 | DSM2243_R211 | JAJQIW000000000 |
9 | DSM2243_R611 | JAJQIX000000000 |
10 | DSM2243_R1011 | JAJQKW000000000 |
No. | Prophage | Host (Contig Accession) | Left Boundary | Right Boundary | Size (bp) | GC% | Integration Locus (Locus Tag) Relative to Strains DSM2243 or C529 | Clade |
---|---|---|---|---|---|---|---|---|
1 | 14Aphi1 | 14A (NZ_PPUR01000006.1) | 29,937 | 71,301 | 41,365 | 67 | tRNA-Leu (ELEN_RS15020) | 1 |
2 | MGYG-HGUT-02544phi1 | MGYG-HGUT-02544 (NZ_CABMOO010000006.1) | 29,956 | 71,302 | 41,347 | 67 | tRNA-Leu (ELEN_RS15020) | 1 |
3 | AB8_2phi1 | AB8 #2 (NZ_PPUJ01000004.1) | 191,735 | end of contig | >38,510 | 67 | tRNA-Leu (ELEN_RS15020) | 1 |
4 | APC055-529-1Dphi1 | APC055-529-1D (CP089331) | 3,240,976 | 3,282,082 | 41,106 | 67 | tRNA-Leu (ELEN_RS15020) | 1 |
5 | ResAG49phi1 | ResAG49 (NZ_WPON01000034.1) | full contig | full contig | >30,988 | 67 | unknown | 1 |
6 | MR1_12phi1 | MR1_#12 (NZ_PPTX01000022.1) | 3020 | 45,178 | 42,159 | 67 | tRNA-Leu (ELEN_RS02880) | 1 |
7 | 1001095IJ_161003_H5phi1 | 1001095IJ_161003_H5 (JADMUV010000007.1) | 137,112 | 178,204 | 41,092 | 67 | tRNA-Leu (ELEN_RS02880) | 1 |
8 | BSD2780120875_150330_C12phi1 | BSD2780120875_150330_C12 (JADMOT010000003.1) | 209,825 | 251,107 | 41,282 | 66 | tRNA-Leu (ELEN_RS15020) | 1 |
9 | Valenciaphi2 | Valencia (NZ_PPTV01000006.1) | 55,915 | 93,457 | 37,543 | 69 | tRNA-Ser (ELEN_RS00500) | 2 |
10 | 32-6-I_6_NAphi2 | 32-6-I_6_NA (NZ_PPUM01000011.1) | 26,284 | 63,686 | 37,403 | 69 | tRNA-Ser (ELEN_RS00500) | 2 |
11 | DSM15644phi3 | DSM15644 (NZ_PPUB01000019.1) | 32,924 | 69,743 | 36,820 | 67 | tRNA-Ala (ELEN_RS00055) | 3 |
12 | DSM15644phi4 | DSM15644 (NZ_PPUB01000037.1) | full contig | full contig | >36,317 | 63 | unknown | 4 |
13 | DSM2243phi4 | DSM2243 (NC_013204) | 3,031,719 | 3,068,586 | 36,618 | 63 | tRNA-Ala (C592_00654) | 4 |
14 | CC82_BHI2phi5 | CC82_BHI2 (NZ_PPUF01000005.1) | 22,245 | 56,042 | 33,798 | 65 | hypothetical protein (ELEN_RS14245) | 5 |
15 | C592phi5 | C592 (NZ_CP021140) | 500,864 | 534,671 | 33,808 | 65 | hypothetical protein (ELEN_RS14245) | 5 |
16 | J1101437_171009_A1phi5 | J1101437_171009_A1 (JADNJK010000003.1) | 299,175 | 333,022 | 33,847 | 65 | hypothetical protein (ELEN_RS14245) | 5 |
17 | J1101653_170612_H2phi5 | J1101653_170612_H2 (JADPDY010000015.1) | 27,299 | 61,125 | 33,826 | 65 | hypothetical protein (ELEN_RS14245) | 5 |
18 | 1-1-60AFAAphi6 | 1-1-60AFAA (NZ_KN214093.1) | 487,345 | 528,047 | 40,703 | 64 | unknown | 6 |
19 | APC055-529-1Dphi7 | APC055-529-1D (CP089331) | 3,337,687 | 3,371,357 | 33,670 | 59 | tRNA-Arg (ELEN_RS15245) | 7 |
20 | APC055-924-7Bphi7 | APC055-924-7B (CP089335) | 3,608,848 | 3,642,543 | 33,695 | 59 | tRNA-Arg (ELEN_RS15245) | 7 |
21 | 14Aphi7 | 14A (NZ_PPUR01000011.1) | 37,521 | 71,198 | 33,678 | 59 | tRNA-Arg (ELEN_RS15245) | 7 |
22 | MGYG-HGUT-02544phi7 | MGYG-HGUT-02544 (NZ_CABMOO010000011.1) | 37,518 | 71,195 | 33,678 | 59 | tRNA-Arg (ELEN_RS15245) | 7 |
23 | APC055-920-1Ephi7 | APC055-920-1E (CP089334) | 3,189,344 | 3,223,015 | 33,671 | 59 | tRNA-Arg (ELEN_RS15245) | 7 |
24 | MR1-F37phi7 | MRI-F37 (NZ_WPOI01000001.1) | 69,802 | 103,502 | 33,701 | 59 | tRNA-Arg (ELEN_RS15245) | 7 |
25 | MRI-F36phi7 | MRI-F36 (NZ_WPOJ01000009.1) | 49,797 | 83,505 | 33,709 | 59 | tRNA-Arg (ELEN_RS15245) | 7 |
26 | 32-6-1-6_NAphi7 | 32-6-I_6_NA (NZ_PPUM01000009.1) | 46,614 | 46,614 | 33,684 | 59 | tRNA-Arg (ELEN_RS15245) | 7 |
27 | MRI-F40phi7 | MRI-F40 (NZ_WPOH01000001.1) | 69,804 | 103,501 | 33,448 | 59 | tRNA-Arg (ELEN_RS15245) | 7 |
28 | J1100102_180507_G10phi7 | J1100102_180507_G10 (JADOZP010000001.1) | 109,609 | 145,440 | 35,831 | 58 | tRNA-Arg (ELEN_RS15245) | 7 |
29 | SECO-MT75m2phi8 | SECO-MT75m2 (NZ_VEVP01000036.1) | 3653 | end of contig | >28,901 | 63 | unknown | 8 |
30 | TF05-26B-4phi9 | TF05-26B-4 (NZ_QSSL01000026.1) | 16,687 | end of contig | >31,589 | 64 | unknown | 9 |
31 | J1100102_180507_G10phi9 | J1100102_180507_G10 (JADOZP010000013.1) | 10,288 | 46,514 | 36,226 | 65 | unknown | 9 |
32 | 1001302B_160321_A1phi9 | 1001302B_160321_A1 (JADNIO010000007.1) | 165,588 | 202,064 | 36,476 | 65 | unknown | 9 |
33 | 1001302B_160321_A1phi10 | 1001302B_160321_A1 (JADNIO010000005.1) | 220,405 | 252,147 | 31,742 | 58 | unknown | 10 |
Prophage | Predicted attP-Site | attB Relative to DSM2243 (Locus) |
---|---|---|
14Aphi1 | CAACCCCATGGAGGTTCAAGTCCTCTCGCCCGCACCATCTGAA | tRNA-Leu (ELEN_RS15020) |
MGYG-HGUT-02544phi1 | AACCCCATGGAGGTTCAAGTCCTCTCGCCCGCACCATCTGAA | tRNA-Leu (ELEN_RS15020) |
APC055-529-1Dphi1 | TTCAGATGGTGCGGGCGAGAGGACTTGAACCTCCATGGGGTT | tRNA-Leu (ELEN_RS15020) |
1001095IJ_161003_H5phi1 | ACTTAAAATCTTCCGGCTTCGGCCTTGCGGGTTCGAGTCCCGCCGCCCCTACCA | tRNA-Leu (ELEN_RS02880) |
BSD2780120875_150330_C12phi1 | TTCAGATGGTGCGGGCGAGAGGACTTGAACCTCCATGGGGTT | tRNA-Leu (ELEN_RS15020) |
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Buttimer, C.; Bottacini, F.; Shkoporov, A.N.; Draper, L.A.; Ross, P.; Hill, C. Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity. Microorganisms 2022, 10, 195. https://doi.org/10.3390/microorganisms10010195
Buttimer C, Bottacini F, Shkoporov AN, Draper LA, Ross P, Hill C. Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity. Microorganisms. 2022; 10(1):195. https://doi.org/10.3390/microorganisms10010195
Chicago/Turabian StyleButtimer, Colin, Francesca Bottacini, Andrey N. Shkoporov, Lorraine A. Draper, Paul Ross, and Colin Hill. 2022. "Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity" Microorganisms 10, no. 1: 195. https://doi.org/10.3390/microorganisms10010195
APA StyleButtimer, C., Bottacini, F., Shkoporov, A. N., Draper, L. A., Ross, P., & Hill, C. (2022). Selective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity. Microorganisms, 10(1), 195. https://doi.org/10.3390/microorganisms10010195