Draft genomes and descriptions of Urmitella timonensis gen. nov., sp. nov. and Marasmitruncus massiliensis gen. nov., sp. nov., isolated from severely malnourished African children using culturomics

Abstract

Two strains, designated as Marseille-P2918^T and Marseille-P3646^T, were isolated from a 14-week-old Senegalese girl using culturomics: Urmitella timonensis strain Marseille-P2918^T (= CSUR P2918, = DSM 103634) and Marasmitruncus massiliensis strain Marseille-P3646^T (= CSUR P3646, = CCUG72353). Both strains were rod-shaped, anaerobic, spore forming motile bacteria. The 16S rRNA gene sequences of strains Marseille-P2918^T (LT598554) and Marseille-P3646^T (LT725660) shared 93.25% and 94.34% identity with Tissierella praeacuta ATCC 25539^T and Anaerotruncus colihominis CIP 107754^T, their respective phylogenetically closest species with standing in nomenclature. Therefore, strain Marseille-P2918^T is classified within the family Tissierellaceae and order Tissierellales whereas strain Marseille-P3646^T is classified within the family Oscillospiraceae and order Eubacteriales. The genome of strain Marseille-P2918^T had a size of 2.13 Mb with a GC content of 50.52% and includes six scaffolds and six contigs, and that of strain Marseille-P3646^T was 3.76 Mbp long consisting of five contigs with a 50.04% GC content. The genomes of both strains presented a high percentage of genes encoding enzymes involved in genetic information and processing, suggesting a high growth rate and adaptability. These new taxa are extensively described and characterised in this paper, using the concept of taxono-genomic description.

Keywords: Culturomics; Human gut microbiota; Marasmitruncus massiliensis; New taxa; Taxono-genomics; Urmitella timonensis.

Fig. 1

Scanning electron microscopy of Urmitella timonensis gen. nov., sp. nov. (A, B) and Marasmitruncus massiliensis gen. nov., sp. nov. (C, D). Scale bars and acquisition settings are displayed on the figure

Fig. 2

Phylogenetic trees highlighting position of Urmitella timonensis strain Marseille-P2918^T (in red). Codon positions included were 1st + 2nd + 3rd + Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 1212 positions in the final dataset. Evolutionary analyses were conducted in MEGA7. Escherichia coli (NR_024570.1) were used as outgroup. A The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model [1]. The tree with the highest log likelihood (− 7626.34) is shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 20 nucleotide sequences. B The tree was built using the Neighbor-Joining method. The optimal tree with the sum of branch length = 966.65234375 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Tamura-Nei method and are in the units of the number of base substitutions per site. The analysis involved 19 nucleotide sequences.

Fig. 3

Phylogenetic trees highlighting position of Marasmitruncus massiliensis strain Marseille-P3646^T (in red). Codon positions included were 1st + 2nd + 3rd + Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 1336 positions in the final dataset. Evolutionary analyses were conducted in MEGA7. Christensenella minuta (NZ_CP029256.1) were used as outgroup. A The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model [1]. The tree with the highest log likelihood (− 6998.48) is shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. B The tree was built using the Neighbor-Joining method. The optimal tree with the sum of branch length = 827.00000000 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Tamura-Nei method and are in the units of the number of base substitutions per site. The analysis involved 17 nucleotide sequences

Fig. 4

Distribution of functional classes of predicted genes according to the COG of proteins (GOGs) for Urmitella timonensis gen. nov., sp. nov. and Marasmitruncus massiliensis gen. nov., sp. nov. among closely related bacterial taxa

Fig. 5

Heatmap generated with OrthoANI values calculated using the OAT software between Urmitella timonensis (A) and Marasmitruncus massiliensis (B), with their respective closely related taxa with standing in nomenclature