Isolation and Description of Catonella massiliensis sp. nov., a Novel Catonella Species, Isolated from a Stable Periodontitis Subject
Abstract
:1. Introduction
2. Results
2.1. Strain Isolation and Phenotypic Characteristics
2.2. Genome Sequencing Information and Genome Properties
2.3. Comparison with Closely Related Bacterial Strains
2.4. Description of Catonella Massiliensis sp. nov.
3. Discussion
4. Materials and Methods
4.1. Strain Isolation and Phenotypic Tests
4.2. Extraction and Genome Sequencing
4.3. Assembly and Annotation of the Genome Sequence
4.4. Phylogenetic Analysis and Genome Comparison
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Characteristic | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
---|---|---|---|---|---|---|---|---|
Gram stain | - | + | + | + | + | + | - | + |
Spore formation | - | - | + | - | - | + | - | - |
Temperature (°C) | 28–41.5 | 37 | 20–40 | 20–40 | 20–40 | 15–40 | 37 | 40–65 |
pH | 6.5–8.5 | 7.0 | 6.0–8.0 | 6.0–8.0 | 6.0–8.0 | 6.2–8.5 | 5.0–5.6 | 6.5–8.5 |
Catalase activity | - | ND | ND | ND | - | - | - | - |
Oxidase activity | - | ND | ND | ND | ND | - | ND | ND |
Acid produced from: | ||||||||
L-Arabinose | + | + | + | + | + | + | - | + |
Cellobiose | + | - | + | + | - | + | + | + |
Lactose | + | - | + | + | - | + | + | - |
Maltose | + | - | + | + | + | + | + | ND |
D-Mannitol | + | - | + | - | - | - | - | ND |
D-Mannose | + | - | + | + | + | + | - | + |
Raffinose | + | - | + | + | - | - | + | ND |
L-Rhamnose | + | + | + | + | + | - | + | ND |
D-Sorbitol | + | - | + | - | - | - | - | - |
Enzyme activity: | ||||||||
Alkaline phosphatase | + | - | - | - | - | ND | ND | ND |
C4 esterase | - | ND | w | w | w | ND | ND | ND |
C8 esterase lipase | - | ND | w | w | - | ND | ND | ND |
C14 lipase | - | ND | - | - | - | - | ND | ND |
Leucine arylamidase | + | - | - | - | - | ND | ND | ND |
Valine arylamidase | - | ND | - | - | - | ND | ND | ND |
Cystine arylamidase | - | ND | - | - | - | ND | ND | ND |
Trypsin | - | ND | - | - | - | ND | ND | ND |
α-Chymotrypsin | - | ND | - | - | - | ND | ND | ND |
Acid phosphatase | + | ND | + | + | w | ND | ND | ND |
Naphthol-AS-BI-phosphohydrolase | + | ND | w | w | w | ND | ND | ND |
α-Galactosidase | + | + | + | + | + | ND | ND | ND |
β-Galactosidase | + | + | + | + | - | ND | ND | ND |
β-Glucuronidase | - | + | + | - | - | ND | ND | ND |
α-Glucosidase | + | + | + | w | + | ND | ND | ND |
β-Glucosidase | + | + | + | - | - | ND | ND | ND |
N-Acetyl-β-glucosaminidase | + | - | - | - | - | ND | ND | ND |
α-Mannosidase | - | ND | - | - | - | ND | ND | ND |
α-Fucosidase | - | - | + | - | - | ND | ND | ND |
Fatty Acid | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
---|---|---|---|---|---|---|---|---|
C12:0 | TR | ND | 1.6 | 3.3 | 2.6 | ND | ND | ND |
C13:0 | TR | ND | - | - | - | ND | ND | ND |
C14:0 | 6.4 | 6.2 | 6.0 | 9.3 | 9.2 | 0.6 | 42 | 14.0 |
C14:0 DMA | ND | ND | - | - | - | 1.5 | 14 | 9.1 |
C15:0 | TR | ND | - | - | - | ND | ND | ND |
C16:0 | 64.2 | 43.4 | 12.0 | 15.6 | 15.6 | 5.5 | 12 | 19.9 |
C16:0 ALDE | - | ND | - | - | - | 20.6 | ND | 2.9 |
C16:0 DMA | ND | ND | 2.0 | 3.4 | 3.4 | 17.4 | ND | 5.3 |
C16:0 3-OH | - | ND | ND | ND | ND | 1.2 | ND | ND |
C16:1ω9c DMA | ND | ND | ND | ND | ND | 3.8 | ND | ND |
C16:1n9 | - | ND | ND | ND | ND | ND | 2 | 1.2 |
C17:0 | TR | ND | - | - | - | ND | ND | ND |
C17:1 ω8c | ND | 8.3 | ND | ND | ND | ND | ND | ND |
C18:0 | 6.6 | ND | 1.4 | - | 3.9 | ND | 4 | 1.2 |
C18:1n7 | 1.3 | ND | ND | ND | ND | ND | ND | ND |
C18:1n9 | 12.5 | ND | 25.9 | 21.9 | 22.9 | ND | 5 | ND |
C18:1ω9C DMA | ND | ND | 37.0 | 36.3 | 28.6 | 3.1 | ND | ND |
C18:1ω7C DMA | ND | ND | 2.4 | - | 4.0 | 9.0 | ND | ND |
C18:2n6 | 7.8 | ND | ND | ND | ND | ND | ND | ND |
C19:0 cyclo 9,10 DMA | ND | ND | ND | ND | ND | ND | ND | 38.3 |
C19:0 cyclo 11,12 DMA | ND | ND | ND | ND | ND | 1.4 | ND | ND |
Code | Strain Marseille-Q4567 T | Description |
---|---|---|
[J] | 145 | Translation, ribosomal structure, and biogenesis |
[A] | 0 | RNA processing and modification |
[K] | 150 | Transcription |
[L] | 137 | Replication, recombination, and repair |
[B] | 0 | Chromatin structure and dynamics |
[D] | 29 | Cell cycle control, cell division, chromosome partitioning |
[Y] | 0 | Nuclear structure |
[V] | 76 | Defense mechanisms |
[T] | 82 | Signal transduction mechanisms |
[M] | 64 | Cell wall/membrane/envelope biogenesis |
[N] | 49 | Cell motility |
[Z] | 0 | Cytoskeleton |
[W] | 0 | Extracellular structures |
[U] | 38 | Intracellular trafficking, secretion, and vesicular transport |
[O] | 60 | Posttranslational modification, protein turnover, chaperones |
[X] | 0 | Mobilome: Prophages, transposons |
[C] | 74 | Energy production and conversion |
[G] | 183 | Carbohydrate transport and metabolism |
[E] | 141 | Amino acid transport and metabolism |
[F] | 51 | Nucleotide transport and metabolism |
[H] | 31 | Coenzyme transport and metabolism |
[I] | 47 | Lipid transport and metabolism |
[P] | 86 | Inorganic ion transport and metabolism |
[Q] | 21 | Secondary metabolites biosynthesis, transport, and catabolism |
[R] | 214 | General function prediction only |
[S] | 134 | Function unknown |
Species | Genome Size (bp) | Number of Contigs | G+C Content (%) | Gene Content |
---|---|---|---|---|
Catonella massiliensis Marseille-Q4567T | 3,122,925 | 3 | 38.8 | 2849 |
Cuneatibacter caecimuris DSM 29486T (NZ_SGXF01000001.1) | 3,462,725 | 16 | 49.1 | 3268 |
Eubacterium oxidoreducens DSM 3217T (NZ_FMXR01000031.1) | 2,912,287 | 33 | 39.8 | 2700 |
Faecalicatena orotica strain NLAE-zl-C242 (NZ_QGDL01000001.1) | 5,717,637 | 33 | 44.7 | 5174 |
Roseburia hominis A2-183T (NC_015977.1) | 3,592,125 | 1 | 48.5 | 3349 |
Faecalicatena contorta 2789STDY5834876 (NZ_CYZU01000001.1) | 5,545,490 | 139 | 45.9 | 5148 |
Faecalicatena fissicatena KCTC 15010 (NZ_LDAQ01000001.1) | 5,014,239 | 184 | 45.6 | 4411 |
Anaerocolumna cellulosilytica strain SN021T (NZ_AP023367.1) | 5,430,627 | 1 | 36.7 | 4545 |
Catonella morbi ATCC 51271T (NZ_KI535366.1) | 3,479,204 | 8 | 37.1 | 3155 |
Herbinix luporum strain SD1DT (NZ_LN879430.1) | 2,609,352 | 1 | 35.3 | 2430 |
Species | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
---|---|---|---|---|---|---|---|---|---|---|
1 Catonella massiliensis Marseille-Q4567T | 100.00 | 28.4 [26.1–30.9] | 27.0 [24.6–29.5] | 26.0 [23.7–28.5] | 24.8 [22.5–27.3 | 24.7 [22.3–27.1] | 24.60 [22.3–27.1] | 24.5 [22.2–27] | 23.80 [21.5–26.2] | 22.9 [20.6–25.3] |
2 Cuneatibacter caecimuris DSM 29486T (NZ_SGXF01000001.1) | 100.00 | 25.7 [23.3–28.1] | 23.0 [20.7–25.4] | 25.8 [23.5–28.3] | 19.2 [17–21.6] | 19.0 [16.8–21.4] | 25.4 [23.1–27.9] | 23.1 [20.8–25.5] | 30.1 [27.7–32.6] | |
3 Eubacterium oxidoreducens DSM 3217T (NZ_FMXR01000031.1) | 100.00 | 22.6 [20.3–25] | 23.2 [20.9–25.7] | 26.1 [23.8–28.6] | 22.9 [20.6–25.3] | 28.8 [26.4–31.3] | 29.3 [26.9–31.8] | 20.7 [18.4–23.1] | ||
4 Faecalicatena orotica strain NLAE-zl-C242 (NZ_QGDL01000001.1) | 100.00 | 22.0 [19.7–24.4] | 21.6 [19.4–24.1] | 21.7 [19.4–24.1 | 22.2 [20–24.7] | 22.2 [19.9–24.6] | 25.5 [23.2–28] | |||
5 Roseburia hominis A2-183T (NC_015977.1) | 100.00 | 24.0 [21.7–26.5] | 24.6 [22.3–27.1] | 32.9 [30.5–35.4] | 23.70 [21.4–26.1] | 29.2 [26.9–31.7] | ||||
6 Faecalicatena contorta 2789STDY5834876 (NZ_CYZU01000001.1) | 100.00 | 28.5 [26.2–31] | 28.5 [26.1–31] | 26.4 [24–28.8] | 25.8 [23.5–28.3] | |||||
7 Faecalicatena fissicatena KCTC 15010 (NZ_LDAQ01000001.1) | 100.00 | 26.4 [24.1–28.9] | 25.3 [22.9–27.8] | 23.1 [20.9–25.6] | ||||||
8 Anaerocolumna cellulosilytica strain SN021T (NZ_AP023367.1) | 100.00 | 24.1 [21.8–26.5] | 26.5 [24.1–29] | |||||||
9 Catonella morbi ATCC 51271T (NZ_KI535366.1) | 100.00 | 21.0 [18.8–23.4] | ||||||||
10 Herbinix luporum strain SD1DT (NZ_LN879430.1) | 100.00 |
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Antezack, A.; Boxberger, M.; La Scola, B.; Monnet-Corti, V. Isolation and Description of Catonella massiliensis sp. nov., a Novel Catonella Species, Isolated from a Stable Periodontitis Subject. Pathogens 2021, 10, 367. https://doi.org/10.3390/pathogens10030367
Antezack A, Boxberger M, La Scola B, Monnet-Corti V. Isolation and Description of Catonella massiliensis sp. nov., a Novel Catonella Species, Isolated from a Stable Periodontitis Subject. Pathogens. 2021; 10(3):367. https://doi.org/10.3390/pathogens10030367
Chicago/Turabian StyleAntezack, Angéline, Manon Boxberger, Bernard La Scola, and Virginie Monnet-Corti. 2021. "Isolation and Description of Catonella massiliensis sp. nov., a Novel Catonella Species, Isolated from a Stable Periodontitis Subject" Pathogens 10, no. 3: 367. https://doi.org/10.3390/pathogens10030367