Insights into the Geobacillus stearothermophilus species based on phylogenomic principles

Burgess, S. A.; Flint, S. H.; Lindsay, D.; Cox, M. P.; Biggs, P. J.

doi:10.1186/s12866-017-1047-x

Cited by 62Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyBacterial Identification and Susceptibility Testing

Insights into the Geobacillus stearothermophilus species based on phylogenomic principles

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Burgess, S. A., Flint, S. H., Lindsay, D., Cox, M. P., Biggs, P. J.·2017·BMC Microbiology

DOI 10.1186/s12866-017-1047-xPMC PMC5485677

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Abstract

BACKGROUND: The 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. RESULTS: This 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. CONCLUSIONS: The 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.

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Humans may not have as high a prevalence of antibodies against GeoCas9 as SpCas9 because Geobacillus stearothermophilus thrive in harsh environments.
“As Geobacillus stearothermophilus thrive in harsh environments such as hot spring cool soils [98], humans may not have as a high prevalence of antibodies against GeoCas9 as SpCas9.”
From Immune responses to gene editing by viral and non-viral delivery vectors used in retinal gene therapy (2022) · cites this paper as [98]

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Authors: Burgess, S. A., Flint, S. H., Lindsay, D., Cox, M. P., & Biggs, P. J.
Affiliations: Massey University (NZ)
Fonterra (New Zealand) (NZ)
Corresponding author: Burgess, S. A.
Biggs, P. J.
ORCID: Burgess, S. A.
Flint, S. H.
Lindsay, D.
Cox, M. P.
Biggs, P. J.
Venue: BMC Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2017-06-26
Volume: 17
Issue: 1
Pages: 140-140
ISSN: 1471-2180 (ISSN-L)
DOI: 10.1186/s12866-017-1047-x
PMC: PMC5485677
OpenAlex: W2676433822
Cited by: 62
References: 101
Citations by year: 2026: 4 · 2025: 7 · 2024: 10 · 2023: 4 · 2022: 8 · 2021: 7 · 2020: 10 · 2019: 6 · 2018: 4 · 2017: 1 · 2015: 1
FWCI: 2.35
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
Locations: BMC Microbiology (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Massey Research Online (Massey University) (submittedVersion, cc-by)
Funders: Broad Institute
Massey University
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
Keywords: Bacillus stearothermophilus, phylogenomics, average nucleotide identity, accessory genome, lactose utilization, lac operon, thermophilic bacteria, bacterial taxonomy, polyphasic taxonomy
MeSH terms: Animals, Geobacillus stearothermophilus, Food Microbiology, Milk, Phenotype, Phylogeny, Soil Microbiology, Water Microbiology, Genome, Bacterial, Genomics

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Insights into the Geobacillus stearothermophilus species based on phylogenomic principles

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