Phenotypic Characterization and Draft Genome Sequence Analyses of Two Novel Endospore-Forming Sporosarcina spp. Isolated from Canada Goose (Branta canadensis) Feces
Abstract
:1. Introduction
2. Materials and Methods
2.1. Isolation and Media Culture of Bacteria
2.2. Growth Inhibition Assays for Antibacterial Analyses of Isolates
2.3. Phenotype Analyses of Isolates
2.4. Bacterial DNA Purification and Draft Whole Genome Sequencing
2.5. Genome Sequence Analyses and Phylogenetic Analyses of Isolates’ Genomes
3. Results and Discussion
3.1. Phenotypic Characterization of Strains A4 and A15
3.2. Growth Inhibition Assays of Target Bacteria for Strains A4 and A15
3.3. Genome Analyses of Strains A4 and A15
3.4. Phylogenetic Relationships among the Sporosarcina spp. with Isolates A4 and A15
4. Summary and Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Genome1 | Genome2 | ANI1->2 | ANI2->1 | AF1->2 | AF2->1 |
---|---|---|---|---|---|
A4 | Sporosarcina newyorkensis DSM 23543 | 78.71 | 78.71 | 66.96 | 68.03 |
A4 | Sporosarcina newyorkensis 2681 | 78.67 | 78.67 | 67.05 | 67.49 |
A4 | Sporosarcina newyorkensis DSM 23966 | 78.65 | 78.65 | 70.14 | 71.90 |
A4 | Sporosarcina ureae P37 | 77.38 | 77.38 | 58.77 | 65.46 |
A4 | Sporosarcina ureae P33 | 77.35 | 77.35 | 58.64 | 67.62 |
A4 | Sporosarcina ureae S204 | 76.52 | 76.52 | 57.93 | 64.57 |
A4 | Sporosarcina ureae DSM 2281 | 76.49 | 76.49 | 58.85 | 65.85 |
A4 | Sporosarcina ureae P17a | 76.36 | 76.37 | 59.16 | 64.84 |
A4 | Sporosarcina ureae P8 | 76.32 | 76.32 | 58.18 | 65.07 |
A4 | Sporosarcina ureae P32a | 76.23 | 76.23 | 59.58 | 65.83 |
A4 | Sporosarcina sp. PTS2304 | 76.14 | 76.13 | 57.39 | 62.48 |
A4 | Sporosarcina pasteurii ATCC 11859 | 72.32 | 72.32 | 0.05 | 73.76 |
A4 | Sporosarcina koreensis Q1 | 71.27 | 71.26 | 39.81 | 34.46 |
A4 | Sporosarcina psychrophila DSM 6497 | 70.80 | 70.79 | 40.98 | 34.54 |
A4 | Sporosarcina sp. HYO08 | 70.79 | 70.77 | 36.45 | 43.88 |
A4 | Sporosarcina sp. ZBG7A | 70.65 | 70.65 | 36.44 | 38.27 |
A4 | Sporosarcina koreensis S-K12 | 70.56 | 70.55 | 34.08 | 42.44 |
A4 | Sporosarcina sp. D27 (unscreened) | 70.53 | 70.53 | 36.94 | 38.24 |
A4 | Sporosarcina sp. EUR3 2.2.2 | 69.03 | 69.04 | 24.35 | 26.61 |
A4 | Planococcus plakortidis DSM 23997 | 68.84 | 68.84 | 23.73 | 26.88 |
A4 | Sporosarcina globispora DSM 4 | 68.20 | 68.20 | 20.48 | 13.96 |
A4 | Sporosarcina pasteurii NCIM 2477 | 67.62 | 67.62 | 15.48 | 13.72 |
A4 | Bacillus thuringiensis YBT-1518 | 67.20 | 67.21 | 16.29 | 9.72 |
A4 | Clostridium scatologenes ATCC 25775 | 65.38 | 65.38 | 4.98 | 2.54 |
A4 | Flavobacterium reichenbachii LMG 25512 | 63.94 | 63.94 | 0.48 | 0.31 |
A4 | A15 | 78.08 | 78.08 | 68.39 | 69.72 |
A15 | Sporosarcina newyorkensis 2681 | 81.08 | 81.08 | 67.89 | 67.04 |
A15 | Sporosarcina newyorkensis DSM 23966 | 81.06 | 81.06 | 69.65 | 69.99 |
A15 | Sporosarcina newyorkensis DSM 23543 | 81.06 | 81.06 | 68.18 | 67.92 |
A15 | Sporosarcina sp. PTS2304 | 77.27 | 77.27 | 60.90 | 64.83 |
A15 | Sporosarcina ureae S204 | 77.09 | 77.10 | 59.43 | 64.98 |
A15 | Sporosarcina ureae P8 | 77.08 | 77.08 | 60.34 | 66.20 |
A15 | Sporosarcina ureae DSM 2281 | 77.07 | 77.07 | 60.28 | 66.16 |
A15 | Sporosarcina ureae P17a | 76.96 | 76.96 | 59.87 | 64.34 |
A15 | Sporosarcina ureae P32a | 76.95 | 76.95 | 60.72 | 65.85 |
A15 | Sporosarcina ureae P33 | 76.89 | 76.91 | 59.64 | 67.56 |
A15 | Sporosarcina ureae P37 | 76.88 | 76.88 | 60.14 | 65.70 |
A15 | Sporosarcina pasteurii ATCC 11859 | 72.88 | 72.88 | 0.05 | 74.11 |
A15 | Sporosarcina sp. HYO08 | 71.23 | 71.23 | 38.19 | 45.08 |
A15 | Sporosarcina psychrophila DSM 6497 | 71.07 | 71.07 | 42.06 | 34.78 |
A15 | Sporosarcina koreensis Q1 | 71.06 | 71.05 | 40.48 | 34.37 |
A15 | Sporosarcina sp. ZBG7A | 70.75 | 70.75 | 37.78 | 38.91 |
A15 | Sporosarcina sp. D27 (unscreened) | 70.68 | 70.68 | 37.84 | 38.42 |
A15 | Sporosarcina sp. EUR3 2.2.2 | 69.64 | 69.64 | 26.63 | 28.59 |
A15 | Sporosarcina koreensis S-K12 | 69.02 | 69.02 | 32.93 | 40.24 |
A15 | Bacillus thuringiensis YBT-1518 | 67.88 | 67.89 | 17.47 | 10.25 |
A15 | Planococcus plakortidis DSM 23997 | 67.87 | 67.87 | 23.39 | 25.99 |
A15 | Sporosarcina globispora DSM 4 | 67.65 | 67.65 | 20.85 | 13.93 |
A15 | Sporosarcina pasteurii NCIM 2477 | 67.22 | 67.22 | 15.66 | 13.61 |
A15 | Clostridium scatologenes ATCC 25775 | 65.99 | 65.99 | 5.91 | 2.96 |
A15 | Flavobacterium reichenbachii LMG 25512 | 64.45 | 64.45 | 0.47 | 0.30 |
Query Strain | Subject Strain | dDDH (d4, in %) | G+C Content Difference (in %) |
---|---|---|---|
A4 | Sporosarcina newyorkensis 2681a | 23.5 | 5.85 |
A4 | Sporosarcina sp. P33 | 20.5 | 1.64 |
A4 | Sporosarcina ureae P17a | 20 | 4.67 |
A4 | Sporosarcina ureae S204 | 19.4 | 4.66 |
A4 | Sporosarcina ureae DSM 2281a | 19.2 | 5.6 |
A4 | Sporosarcina sp. P7 | 19.2 | 3.68 |
A4 | Sporosarcina newyorkensis DSM 23966 | 15 | 3.99 |
A4 | Sporosarcina luteola NBRC 105378 | 13.5 | 2.77 |
A4 | Sporosarcina koreensis Q1a | 13.4 | 2.95 |
A4 | Sporosarcina koreensis S-K12 | 13.4 | 7.81 |
A4 | Sporosarcina psychrophila DSM 6497 | 13.3 | 5.84 |
A4 | Sporosarcina pasteurii BNCC 337394 | 13.3 | 7.01 |
A4 | Bacillus thuringiensis YBT-1518 529122.4 | 13.1 | 10.76 |
A4 | Planococcus plakortidis DSM 23997 | 13.1 | 3.8 |
A4 | Paenisporosarcina aarctica CGMCC 1.6503 | 13.1 | 9.18 |
A4 | Sporosarcina globispora DSM4 | 13.1 | 6.62 |
A4 | Clostridium scatologenes ATCC 25775 | 13 | 16.57 |
A4 | Flavobacterium reichenbachii LMG 25512a | 12.9 | 8.8 |
A4 | A15 | 24.2 | 0.36 |
A15 | Sporosarcina newyorkensis 2681a | 27.4 | 5.49 |
A15 | Sporosarcina sp. P33 | 20.7 | 1.28 |
A15 | Sporosarcina ureae S204 | 20.1 | 4.3 |
A15 | Sporoscarcina ureae DSM 2281a | 19.9 | 5.25 |
A15 | Sporosarcina sp. P7 | 19.8 | 3.32 |
A15 | Sporosarcina ureae P17a | 19.5 | 4.31 |
A15 | Sporosarcina newyorkensis DSM 23966 | 16.2 | 3.64 |
A15 | Sporosarcina luteola NBRC 105378 | 13.6 | 2.41 |
A15 | Sporosarcina psychrophila DSM 6497 | 13.5 | 5.48 |
A15 | Sporosarcina koreensis Q1a | 13.5 | 3.31 |
A15 | Sporosarcina pasteurii BNCC 337394 | 13.3 | 6.65 |
A15 | Sporosarcina koreensis S-K12 | 13.3 | 8.17 |
A15 | Bacillus thuringiensis YBT-1518 529122.4 | 13.2 | 10.4 |
A15 | Paenisporosarcina aarctica CGMCC 1.6503 | 13.2 | 8.82 |
A15 | Planococcus plakortidis DSM 23997 | 13.2 | 4.16 |
A15 | Sporosarcina globispora DSM4 | 13.1 | 6.26 |
A15 | Clostridium scatologenes ATCC 25775 | 13 | 16.21 |
A15 | Flavobacterium reichenbachii LMG 25512a | 12.9 | 8.45 |
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Keshri, J.; Smith, K.M.; Svendsen, M.K.; Keillor, H.R.; Moss, M.L.; Jordan, H.J.; Larkin, A.M.; Garrish, J.K.; Line, J.E.; Ball, P.N.; et al. Phenotypic Characterization and Draft Genome Sequence Analyses of Two Novel Endospore-Forming Sporosarcina spp. Isolated from Canada Goose (Branta canadensis) Feces. Microorganisms 2024, 12, 70. https://doi.org/10.3390/microorganisms12010070
Keshri J, Smith KM, Svendsen MK, Keillor HR, Moss ML, Jordan HJ, Larkin AM, Garrish JK, Line JE, Ball PN, et al. Phenotypic Characterization and Draft Genome Sequence Analyses of Two Novel Endospore-Forming Sporosarcina spp. Isolated from Canada Goose (Branta canadensis) Feces. Microorganisms. 2024; 12(1):70. https://doi.org/10.3390/microorganisms12010070
Chicago/Turabian StyleKeshri, Jitendra, Kristina M. Smith, Molly K. Svendsen, Haley R. Keillor, Madeline L. Moss, Haley J. Jordan, Abigail M. Larkin, Johnna K. Garrish, John Eric Line, Patrick N. Ball, and et al. 2024. "Phenotypic Characterization and Draft Genome Sequence Analyses of Two Novel Endospore-Forming Sporosarcina spp. Isolated from Canada Goose (Branta canadensis) Feces" Microorganisms 12, no. 1: 70. https://doi.org/10.3390/microorganisms12010070