Negativibacillus massiliensis gen. nov., sp. nov., a New Bacterial Genus Isolated from a Human Left Colon Sample
Abstract
:1. Introduction
2. Material and Methods
2.1. Sample Collection
2.2. Bacterial Strain and Identification
2.3. Phenotypic Characteristics
2.3.1. Optimal Growth Conditions
2.3.2. Morphologic and Biochemical Characteristics, and Antibiotic Susceptibility
2.3.3. Fatty Acid Methyl Ester (FAME) Analysis by GC/MS
2.4. Genomic Characteristics
2.4.1. Genome Sequencing
2.4.2. Genome Assemblage, Annotation and Comparison
3. Results
3.1. Strain Identification
3.2. Phenotypic Description
3.2.1. Morphologic and Biochemical Characteristics
3.2.2. Optimal Growth Conditions
3.2.3. Antibiotic Susceptivity
3.3. Genomic Characteristics
3.3.1. Genome Properties
3.3.2. Genomic Comparison
4. Conclusions
4.1. Nucleotide Sequence Accession Number
4.2. Deposit in Culture Collections
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Fatty Acids | Name | Mean Relative % (a) |
---|---|---|
16:0 | Hexadecanoic acid | 49.8 ± 0.5 |
14:0 | Tetradecanoic acid | 21.0 ± 0.8 |
18:1n9 | 9-Octadecenoic acid | 9.0 ± 0.3 |
18:2n6 | 9,12-Octadecadienoic acid | 8.4 ± 0.1 |
18:0 | Octadecanoic acid | 7.4 ± 0.1 |
12:0 | Dodecanoic acid | 1.6 ± 0.2 |
18:1n7 | 11-Octadecenoic acid | 1.5 ± 0.1 |
15:0 | Pentadecanoic acid | TR |
17:0 | Heptadecanoic acid | TR |
16:1n7 | 9-Hexadecenoic acid | TR |
15:0 iso | 13-methyl-tetradecanoic acid | TR |
Attribute | Genome (Total) | |
---|---|---|
Value | % of Total | |
Size | 2,876,881 | 100 |
G + C content (%) | 1,306,499 | 45.41 |
Coding region (bp) | 2,512,042 | 87.31 |
Total genes | 2779 | 100 |
RNA genes | 63 | 2.27 |
Protein-coding genes | 2716 | 97.73 |
Genes with function prediction | 2453 | 90.32 |
Genes assigned to COGs | 1827 | 65.74 |
Genes with peptide signals | 345 | 12.70 |
Genes with transmembrane helices | 631 | 23.23 |
CRISPR repeats | ||
ORFans genes | 21 | 0.77 |
Genes associated with PKS or NRPS | 4 | 0.15 |
N° of antibiotic resistance genes | 2 | 0.074 |
Name of Organisms | RefSeq | Size (Mb) | G + C (%) | Protein-Coding Genes | Total Genes (ORFs) |
---|---|---|---|---|---|
Anaerotruncus colihominis | NZ_DS544194 | 3.72 | 54.2 | 3525 | 3704 |
Ruminococcus champanellensis | NC_021039 | 2.57 | 53.3 | 2276 | 2383 |
Harryflintia acetispora | NZ_SLUK01000001 | 2.93 | 60.0 | 2704 | 2786 |
Negativibacillus massiliensis | NZ_FTRU01000008 | 2.88 | 45.4 | 268 | 2781 |
Hydrogenoanaerobcaterium saccharovorans | NZ_RKRD01000001 | 3.18 | 42.7 | 2906 | 2994 |
Caprociproducens galactitovorans | NZ_SRMQ01000001 | 2.58 | 48.1 | 2413 | 2535 |
Ruminococcus albus | NZ_FOAT01000022 | 3.85 | 45.2 | 3334 | 3484 |
Clostridium methylpentosum | PRJNA30029 | 3.48 | 50.7 | 3907 | 3964 |
Massiliimalia massiliensis | NZ_FUHT00000000.1 | 2.84 | 47.2 | 2681 | 2769 |
Ruminococcus callidus | PRJNA18185 | 3.1 | 49.0 | 2719 | 2866 |
Negativibacillus massiliensis | |||
---|---|---|---|
Code | Description | Value | % of Total |
[A] | Rna processing and modification | 0 | 0.00 |
[B] | Chromatin structure and dynamics | 0 | 0.00 |
[C] | Energy production and conversion | 91 | 4.53 |
[D] | Cell cycle control. mitosis and meiosis | 26 | 1.29 |
[E] | Amino acid transport and metabolism | 156 | 7.77 |
[F] | Nucleotide transport and metabolism | 58 | 2.89 |
[G] | Carbohydrate transport and metabolism | 89 | 4.43 |
[H] | Coenzyme transport and metabolism | 59 | 2.94 |
[I] | Lipid transport and metabolism | 33 | 1.64 |
[J] | Translation | 159 | 7.91 |
[K] | Transcription | 172 | 8.56 |
[L] | Replication. recombination and repair | 126 | 6.27 |
[M] | Cell wall/membrane biogenesis | 94 | 4.68 |
[N] | Cell motility | 2 | 0.10 |
[O] | Posttanslational modification. protein turnover.chaperones | 51 | 2.54 |
[P] | Inorganic ion transport and metabolism | 107 | 5.33 |
[Q] | Secondary metabolites biosynthesis. transport and catabolism | 10 | 0.50 |
[R] | General function prediction only | 232 | 11.55 |
[T] | Signal transduction mechanisms | 49 | 2.44 |
[U] | Intracellular trafficking and secretion | 24 | 1.19 |
[V] | Defense mechanisms | 95 | 4.73 |
[W] | Extracellular structures | 0 | 0.00 |
[Y] | Nuclear structure | 0 | 0.00 |
[Z] | Cytoskeleton | 0 | 0.00 |
[S] | Function unknown | 194 | 9.66 |
_ | Not in COGs | 182 | 9.06 |
Acetanaerobacterium elongatum | Anaerotruncus colihominis | Caproiciproducens galactitolivorans | Clostridium methylpentosum | Ethanoligenens harbinense | Harryflintia acetispora | Hydrogenoanaerobacterium saccharovorans | Massilimaliae massiliensis | Negativibacillus massiliensis | Ruminococcus albus | Ruminococcus callidus | Ruminococcus champanellensis | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Acetanaerobacterium elongatum | 20.60% | 23% | 17.50% | 20% | 18.70% | 19.40% | 37.50% | 24% | 26.60% | 29.40% | 33.80% | |
Anaerotruncus colihominis | 35% | 21.10% | 19.60% | 22.60% | 27.20% | 33.90% | 32.30% | 28.80% | 26.80% | 35.90% | ||
Caproiciproducens galactitolivorans | 25.10% | 23.60% | 30.20% | 27.80% | 32.90% | 28.60% | 26% | 31.30% | 27.70% | |||
Clostridium methylpentosum | 18.20% | 20.30% | 21.10% | 22.90% | 27.80% | 25.80% | 24% | 28.10% | ||||
Ethanoligenens harbinense | 18.80% | 25.50% | 31.40% | 27.90% | 27.90% | 29.70% | 30.40% | |||||
Harryflintia acetispora | 24.20% | 24.50% | 35.60% | 29.30% | 23.40% | 20.2% | ||||||
Hydrogenoanaerobacterium saccharovorans | 23.70% | 26.20% | 27.50% | 21.90% | 35.50% | |||||||
Massilimaliae massiliensis | 25.20% | 34.90% | 20.20% | 29.70% | ||||||||
Negativibacillus massiliensis | 24.30% | 25.50% | 24.40% | |||||||||
Ruminococcus albus | 22.70% | 24.50% | ||||||||||
Ruminococcus callidus | 20.90% | |||||||||||
Ruminococcus champanellensis |
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Valles, C.; Mailhe, M.; Ricaboni, D.; Armstrong, N.; Alibar, S.; Vitton, V.; Lagier, J.-C.; Raoult, D.; Tidjani Alou, M. Negativibacillus massiliensis gen. nov., sp. nov., a New Bacterial Genus Isolated from a Human Left Colon Sample. Microbiol. Res. 2021, 12, 29-42. https://doi.org/10.3390/microbiolres12010004
Valles C, Mailhe M, Ricaboni D, Armstrong N, Alibar S, Vitton V, Lagier J-C, Raoult D, Tidjani Alou M. Negativibacillus massiliensis gen. nov., sp. nov., a New Bacterial Genus Isolated from a Human Left Colon Sample. Microbiology Research. 2021; 12(1):29-42. https://doi.org/10.3390/microbiolres12010004
Chicago/Turabian StyleValles, Camille, Morgane Mailhe, Davide Ricaboni, Nicholas Armstrong, Stéphane Alibar, Véronique Vitton, Jean-Christophe Lagier, Didier Raoult, and Maryam Tidjani Alou. 2021. "Negativibacillus massiliensis gen. nov., sp. nov., a New Bacterial Genus Isolated from a Human Left Colon Sample" Microbiology Research 12, no. 1: 29-42. https://doi.org/10.3390/microbiolres12010004