Insights into the Geobacillus stearothermophilus species based on phylogenomic principles

Abstract

BackgroundThe genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species. For example, G. stearothermophilus was traditionally defined as a species that does not utilise lactose, but the ability of dairy strains of G. stearothermophilus to use lactose has now been well established.ResultsThis study compared the genome sequences of 63 Geobacillus isolates and showed that based on two different genomic approaches (core genome comparisons and average nucleotide identity) the Geobacillus genus could be divided into sixteen taxa for those Geobacillus strains that have genome sequences available thus far. In addition, using Geobacillus stearothermophilus as an example, we show that inclusion of the accessory genome, as well as phenotypic characteristics, is not suitable for defining this species. For example, this is the first study to provide evidence of dairy adaptation in G. stearothermophilus - a phenotypic feature not typically considered standard in this species - by identifying the presence of a putative lac operon in four dairy strains.ConclusionsThe traditional polyphasic approach of combining both genotypic and phenotypic characteristics to define a bacterial species could not be used for G. stearothermophilus where many phenotypic characteristics vary within this taxon. Further evidence of this discordant use of phenotypic traits was provided by analysis of the accessory genome, where the dairy strains contained a putative lac operon. Based on the findings from this study, we recommend that novel bacterial species should be defined using a core genome approach.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-1047-x) contains supplementary material, which is available to authorized users.

The impact of skin care products on skin chemistry and microbiome dynamics

“…This finding is in agreement with our previous data from the 3D cartographical skin maps that revealed the presence of co-localized chloroplast and lotion molecules [18]. Other low-abundant microbial signatures found in the sunscreen lotion include additional plant-associated bacteria: mitochondria [73], Bacillaceae [74,75], Planococcaceae [76], and Ruminococcaceae family [77], but all these bacteria are not responsible for microbial changes associated to beauty product use, as they were poorly detected in the armpits and feet (Fig. 7).…”

Identification of a New Heavy-Metal-Resistant Strain of Geobacillus stearothermophilus Isolated from a Hydrothermally Active Volcanic Area in Southern Italy

“…Multiple alignment of 16S rRNA sequence of the novel G. stearothermophilus isolate (GF16) with those of other Geobacilli and Bacilli with identities from 99% to 97% was performed to build the phylogenetic tree shown in Figure 2. The results confirmed the difficulty in determining a threshold for defining species within the Geobacillus genus and supported the concept that a combination of genotypic and phenotypic characteristics could be not sufficient for describing a new species [60].…”

“…The interest toward microorganisms of the Geobacillus genus prompted us to combine two different experimental approaches such as MALDI-TOF MS analysis and 16S rRNA sequencing to try to unambiguously identify the species. Indeed, the classification of the different species within the Geobacillus genus is challenging since the sequence similarity of the 16S rRNA can be higher than 97% even among species [60]. On the other hand, MALDI-TOF MS analysis has been proposed as a powerful bioanalytical method to detect profiles of proteins derived from whole bacterial cells to be used for bacteria identification [61].…”

Diversity and enzymatic potential of thermophilic bacteria associated with terrestrial hot springs in Algeria

“…Although 16S rRNA gene sequencing is highly accurate and useful regarding bacterial classification, it may be insufficient to distinguish between some closely related species and has low discriminatory power for some genera [78]. This is the case for species within some genera, like Bacillus, Anoxibacillus, Aeribacillus, and Geobacillus [79][80][81]. Thus, the identification of bacteria, and specifically thermophiles, could benefit from the addition of other fingerprinting methods for strain and species discrimination [10,.…”