Bacillus kwashiorkori sp nov., a new bacterial species isolated from a malnourished child using culturomics

El Hadji Seck (1) , Mamadou Beye (1) , Sory Ibrahima Traore (1) , Saber Khelaifia (2, 3) , Caroline Michelle (3) , Carine Couderc (3) , Souleymane Brah , Pierre-Edouard Fournier (4) , Didier Raoult (3) , Fadi Bittar (3)

1 URMITE - Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes
2 IHU Marseille - Institut Hospitalier Universitaire Méditerranée Infection
3 MEPHI - Microbes évolution phylogénie et infections
4 VITROME - Vecteurs - Infections tropicales et méditerranéennes

Strain SIT6(T) was isolated from the fecal flora of a severely malnourished child as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of the human microbiota. An analysis of the 16S rRNA gene sequence showed that strain SIT6(T) shared 94.1% 16S rRNA gene sequence similarity with Bacillus thermoamylovorans DKPT (NR\₀29151), the phylogenetically closest type species. Colonies are creamy white, circular, 4-5 mm in diameter after cultivation at 37 degrees C for 24 hr on 5% sheep blood-enriched Colombia agar. Growth occurs at temperatures in the range of 25-56 degrees C (optimally at 37 degrees C). Strain SIT6(T) is a gram-positive, facultative anaerobic rod and motile by means of peritrichous flagella and sporulating; it is catalase and oxidase positive. The 2,784,637-bp-long genome, composed of 16 contigs, has a G+C content of 35.19%. Of the 2,646 predicted genes, 2,572 were protein-coding genes and 74 were RNAs. The major fatty acids are saturated species (15:0 iso, 16:0 and 17:0 anteiso). Of the 14 detected fatty acids, 11 are saturated, either linear or branched (iso and anteiso). Digital DNA-DNA hybridization (dDDH) estimation and average genomic identity of orthologous gene sequences (AGIOS) of the strain SIT6(T) against genomes of the type strains of related species ranged between 18.6% and 38.3% and between 54.77% and 65.50%, respectively. According to our taxonogenomics results, we propose the creation of Bacillus kwashiorkori sp. nov. that contains the type strain SIT6(T) (=CSUR P2452(T), =DSM 29059(T)).

Mots clés: Bacillus kwashiorkori; culturomics; genome; taxonogenomics

Domaines: Maladies infectieuses; Bactériologie

El Hadji Seck, Mamadou Beye, Sory Ibrahima Traore, Saber Khelaifia, Caroline Michelle, et al.. Bacillus kwashiorkori sp nov., a new bacterial species isolated from a malnourished child using culturomics. MicrobiologyOpen, 2018, 7 (1), pp.e00535. ⟨10.1002/mbo3.535⟩. ⟨hal-01780644⟩