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. 2024 Dec 5;12(12):2507.
doi: 10.3390/microorganisms12122507.

Bacillus lumedeiriae sp. nov., a Gram-Positive, Spore-Forming Rod Isolated from a Pharmaceutical Facility Production Environment and Added to the MALDI Biotyper® Database

Luciana Veloso da Costa  1 , Juliana Nunes Ramos  2 , Leticia de Sousa Albuquerque  1 , Rebeca Vitória da Silva Lage de Miranda  1 , Talita Bernardo Valadão  1 , João Flávio Carneiro Veras  2 , Erica Miranda Damasio Vieira  2 , Stephen Forsythe  3 , Marcelo Luiz Lima Brandão  1 , Verônica Viana Vieira  2
Affiliations

Bacillus lumedeiriae sp. nov., a Gram-Positive, Spore-Forming Rod Isolated from a Pharmaceutical Facility Production Environment and Added to the MALDI Biotyper® Database

Luciana Veloso da Costa et al. Microorganisms. .

Abstract

A Gram-positive, aerobic, rod-shaped and spore-forming bacterium strain designation, B190/17, was isolated from an air monitoring sample of a Brazilian immunobiological production facility in 2017. The strain was not identifiable by biochemical methodology VITEK® 2 or by MALDI-TOF MS with VITEK® MS RUO and MALDI Biotyper®. The 16S rRNA gene sequencing results showed 98.51% similarity with Bacillus wudalianchiensis FJAT 27215T, 98.28% with 'Bacillus aerolatus' CX 253T, 97.96% with Bacillus badius MTCC 1458T, 97.63% with Bacillus xiapuensis FJAT 46582T and 97.21% with Bacillus thermotolerans SGZ8T. Biochemical data showed that the strain was alanine arylamidase-, Ala-Phe-Pro arylamidase-, ELLMAN (cysteine residues)-, leucine arylamidase-, phenyalanine arylamidase- and tyrosine arylamidase-positive. The genomic DNA G+C% content of B190/17 was 41.6 mol%. The phylogenetic, genomic taxonomy and biochemical tests suggested that B190/17 represents a novel species and should be classified as the type strain of a novel Bacillus species. The name Bacillus lumedeiriae sp. nov. was proposed. After characterization, B190/17 was added to the MALDI Biotyper® database as Bacillus lumedeiriae sp. nov.

Keywords: 16S rRNA; Bacillus lumedeiriae; MALDI-TOF MS; bacterial identification; genomic taxonomy; pharmaceutical industry.

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Conflict of interest statement

The author Stephen James Forsythe is the maintainer of Foodmicrobe.com Ltd. The remaining authors declare that this research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest.

Figures

Figure 1
Figure 1
Comparison between spectra provided by MALDI Biotyper® for B190/17 strain and B. badius. (a) Comparison between spectra of B190/17 and B. badius DSM 23T. (b) Comparison between spectra of B190/17 and B. badius DSM 30822. Ten closest matching classification results and their score values are displayed in box. Traffic-light colour-coding markers indicate closeness of match (green = full match; yellow = partial match; red = no match). Higher half of graphic displays peak list of B190/17, and its colour reflects degree of matching with reference main spectrum profile (MSP), whereas lower half displays peak list of selected MSP in blue using inverted scale.
Figure 2
Figure 2
Maximum likelihood phylogenetic tree showing position of B190/17 strain based on 16S rRNA gene sequences (22 strains with 1487 bp). SH-arLT/bootstrap values (>50%) based on 5000 repetitions are shown. Sequence of Bacillus smithii DSM 4216 was used as outgroup. Bar 0.01% estimated sequence divergence. GenBank accession number is given, and type strains are indicated (T). SH-aLRT = Shimodaira–Hasegawa approximate likelihood ratio test.
Figure 3
Figure 3
Maximum likelihood phylogenetic tree based on sequences of 16S rRNA, rpoB and gyrB showing position of B190/17 strain against most closely related strains (18 strains with 6973 nucleotides). SH-arLT/bootstrap values (>50%) based on 5000 repetitions are shown. Strain Bacillus smithii DSM 4216 was used as outgroup. Bar 0.06% estimated sequence divergence. Type strains are indicated (T). SH-aLRT = Shimodaira–Hasegawa approximate likelihood ratio test.
Figure 4
Figure 4
A phylotaxonomic genome tree showing the position of the B190/17 strain against the most closely related type strains based on whole-genome sequences. The genomic sequences were analyzed by type (strain) genome server (TYGS) with standard parameters. The tree was inferred with FastME 2.1.6.1 from GBDP distances calculated from genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values (>60%) from 100 replications, with an average branch support of 36.3%. Bacillus encimensis is synonym of Bacillus badius, and Bacillus aerolatus is not validly published [13]. The colour of the species and subspecies cluster are based on dDDH (digital DNA-DNA hybridization). The minimum percentage G+C is represented by white squares and the maximum by dark blue. The width of the black square/rectangle indicates the genome size in bp. The width of the beige square/rectangle indicates the protein count. The user strain is flagged with a blue cross.
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