Abstract
Strain SIT6T 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 SIT6T 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°C for 24 hr on 5% sheep blood‐enriched Colombia agar. Growth occurs at temperatures in the range of 25–56°C (optimally at 37°C). Strain SIT6T 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 SIT6T 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 SIT6T (=CSUR P2452T, =DSM 29059T).
Highlights
The human intestinal flora is intrinsically associated with the host genotype and age, many external factors can affect and modify this microbiota, such as antibiotics, probiotics, and diet (Angelakis, Armougom, Million, & Raoult, 2012; Chen, He, & Huang, 2014; Moreno-Indias, Cardona, Tinahones, & Queipo-Ortuño, 2014)
In our laboratory we have developed a new strategy called culturomics, which is based on the application of various culture conditions followed by rapid identification using matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to explore the bacterial composition (Lagier et al, 2012)
Average nucleotide identity at the genome level between B. kwashiorkori (CTDX00000000) and the other species B. firmus (BCUY00000000), B. shackletonii (LJJC00000000), B. smithii (BCVY00000000), B. aquimaris (LQXM00000000), B. thermoamylovorans (CCRF00000000), B. coagulans (CP003056), B. alveayuensis (JYCE00000000), B. sporothermodurans (LQYN00000000), B. acidicola (LWJG00000000), and B. ginsengihumi (JAGM00000000) was estimated using BLASTN and a home made software, following the algorithm described by Ouk, Chun, Lee, and Park (2016)
Summary
The human intestinal flora is intrinsically associated with the host genotype and age, many external factors can affect and modify this microbiota, such as antibiotics, probiotics, and diet (Angelakis, Armougom, Million, & Raoult, 2012; Chen, He, & Huang, 2014; Moreno-Indias, Cardona, Tinahones, & Queipo-Ortuño, 2014). For this reason, in our laboratory we have developed a new strategy called culturomics, which is based on the application of various culture conditions followed by rapid identification using matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to explore the bacterial composition (Lagier et al, 2012). In our laboratory we have developed a new strategy called culturomics, which is based on the application of various culture conditions followed by rapid identification using matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to explore the bacterial composition (Lagier et al, 2012) This new concept has allowed us to significantly increase the bacterial species associated with the human digestive tract and to find many new species (Lagier et al, 2016). We describe the strain SIT6T (=CSUR P2452T, =DSM 29059T) isolated from the stool sample of a kwashiorkor patient
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