Antimicrobial Effects of Potential Probiotics of Bacillus spp. Isolated from Human Microbiota: In Vitro and In Silico Methods

Alfonso Torres-Sánchez, Jesús Pardo-Cacho, Ana López-Moreno, Ángel Ruiz-Moreno, Klara Cerk, Margarita Aguilera, Alfonso Torres-Sánchez, Jesús Pardo-Cacho, Ana López-Moreno, Ángel Ruiz-Moreno, Klara Cerk, Margarita Aguilera

Abstract

The variable taxa components of human gut microbiota seem to have an enormous biotechnological potential that is not yet well explored. To investigate the usefulness and applications of its biocompounds and/or bioactive substances would have a dual impact, allowing us to better understand the ecology of these microbiota consortia and to obtain resources for extended uses. Our research team has obtained a catalogue of isolated and typified strains from microbiota showing resistance to dietary contaminants and obesogens. Special attention was paid to cultivable Bacillus species as potential next-generation probiotics (NGP) together with their antimicrobial production and ecological impacts. The objective of the present work focused on bioinformatic genome data mining and phenotypic analyses for antimicrobial production. In silico methods were applied over the phylogenetically closest type strain genomes of the microbiota Bacillus spp. isolates and standardized antimicrobial production procedures were used. The main results showed partial and complete gene identification and presence of polyketide (PK) clusters on the whole genome sequences (WGS) analysed. Moreover, specific antimicrobial effects against B. cereus, B. circulans, Staphylococcus aureus, Streptococcus pyogenes, Escherichia coli, Serratia marcescens, Klebsiella spp., Pseudomonas spp., and Salmonella spp. confirmed their capacity of antimicrobial production. In conclusion, Bacillus strains isolated from human gut microbiota and taxonomic group, resistant to Bisphenols as xenobiotics type endocrine disruptors, showed parallel PKS biosynthesis and a phenotypic antimicrobial effect. This could modulate the composition of human gut microbiota and therefore its functionalities, becoming a predominant group when high contaminant exposure conditions are present.

Keywords: Bacillus; antimicrobial effect; in silico methods; in vitro methods; probiotics.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Conserved PKs proteins and functions in Bacillus modified from Straight et al. [37].
Figure 2
Figure 2
BPA relative percentage of degradation by human fecal specimens. (LC-MS/MS) system was used for BPA quantification; SN: Supernatant.
Figure 3
Figure 3
Phylogenetic tree based on gene sequences of isolated gut microbiota strains. The tree was obtained by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach and Kimura 2-parameter model. The species and strain names are shown. Bootstrap values shown after 1000 resamplings. Main clusters are highlighted: in green close to B.subtilis group and yellow close to B.cereus group.

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