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International Journal of Systematic and... Nov 2020To clarify the evolutionary relationships and classification of species, comprehensive phylogenomic and comparative analyses were performed on >300 genomes. Multiple...
Robust demarcation of 17 distinct species clades, proposed as novel genera, by phylogenomics and comparative genomic analyses: description of sp. nov. and proposal for an emended genus limiting it only to the members of the Subtilis and Cereus clades of species.
To clarify the evolutionary relationships and classification of species, comprehensive phylogenomic and comparative analyses were performed on >300 genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some species reliably grouped with the genera and . The distinctness of identified species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 species clades should be recognized as novel genera, with the names gen. nov. gen. nov., gen. nov. gen. nov. gen. nov. gen. nov. gen. nov. gen. nov. gen. nov. gen. nov. gen. nov. gen. nov. gen. nov. gen. nov. gen. nov., gen. nov. and gen. nov. We also propose to transfer 's' to sp. nov. (type strain: NB22=JCM 17569=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species ) or the Cereus clade (containing and ). As most species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus to restrict it to only the members of the Subtilis and Cereus clades.
Topics: Amino Acid Sequence; Bacillaceae; Bacillus; Bacterial Typing Techniques; DNA, Bacterial; Genomics; INDEL Mutation; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 33112222
DOI: 10.1099/ijsem.0.004475 -
Trends in Microbiology Jul 2022
Topics: Bacillaceae; Bacillus
PubMed: 35165007
DOI: 10.1016/j.tim.2022.01.018 -
Peptides Mar 2018Members of the Bacillaceae family, including Bacillus spp., Brevibacillus spp., Paenibacillus spp., Aneurinibacillus sp., and Halobacillus sp., are an important source... (Review)
Review
Members of the Bacillaceae family, including Bacillus spp., Brevibacillus spp., Paenibacillus spp., Aneurinibacillus sp., and Halobacillus sp., are an important source of structurally diverse classes of short peptides of ∼ 30 residues or fewer possessing peculiar and rapid killing activity against various pathogens. Additionally, many have unique structures that enhance resistance to hydrolysis by proteases, and these are ideal therapeutic tools and potential alternatives to current antibiotics. The need for novel antibiotic lead compounds is urgent, and this review summarises 119 Bacillaceae compounds published since 2000, including 12 surfactin-like lipopeptides, 16 iturinic lipopeptides, fengycin C, 33 other cyclic lipopeptides, 26 linear lipopeptides, two thiopeptides, four 2,5-diketopiperazines, 20 typical cyclic peptides, and five standard linear peptides. The current and potential therapeutic applications of these peptides, including structure, antibacterial, antifungal, and antiviral activities, are discussed.
Topics: Animals; Anti-Bacterial Agents; Bacillaceae; Humans; Peptides
PubMed: 29269072
DOI: 10.1016/j.peptides.2017.12.018 -
Microbiology Spectrum Apr 2015Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed... (Review)
Review
Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.
Topics: Animals; Bacillaceae; Ecosystem; Genetic Variation; Humans; Microbial Interactions; Plants
PubMed: 26104706
DOI: 10.1128/microbiolspec.TBS-0017-2013 -
Sub-cellular Biochemistry 2021Thermostability is a key factor in the industrial and clinical application of enzymes, and understanding mechanisms of thermostability is valuable for molecular biology... (Review)
Review
Thermostability is a key factor in the industrial and clinical application of enzymes, and understanding mechanisms of thermostability is valuable for molecular biology and enzyme engineering. In this chapter, we focus on the thermostability of leucine dehydrogenase (LDH, EC 1.4.1.9), an amino acid-metabolizing enzyme that is an NAD-dependent oxidoreductase which catalyzes the deamination of branched-chain l-amino acids (BCAAs). LDH from Geobacillus stearothermophilus (GstLDH) is a highly thermostable enzyme that has already been applied to quantify the concentration of BCAAs in biological specimens. However, the molecular mechanism of its thermostability had been unknown because no high-resolution structure was available. Here, we discuss the thermostability of GstLDH on the basis of its structure determined by cryo-electron microscopy. Sequence comparison with other structurally characterized LDHs (from Lysinibacillus sphaericus and Sporosarcina psychrophila) indicated that non-conserved residues in GstLDH, including Ala94, Tyr127, and the C-terminal region, are crucial for oligomeric stability through intermolecular interactions between protomers. Furthermore, NAD binding to GstLDH increased the thermostability of the enzyme as additional intermolecular interactions formed on cofactor binding. This knowledge is important for further applications and development of amino acid metabolizing enzymes in industrial and clinical fields.
Topics: Bacillaceae; Cryoelectron Microscopy; Enzyme Stability; Geobacillus stearothermophilus; Leucine Dehydrogenase; Sporosarcina
PubMed: 33252736
DOI: 10.1007/978-3-030-58971-4_10 -
Microbiology Spectrum Oct 2014The family Bacillaceae constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to... (Review)
Review
The family Bacillaceae constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the Bacillaceae, the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.
Topics: Bacillaceae; Environmental Microbiology; Evolution, Molecular; Phylogeny
PubMed: 26104365
DOI: 10.1128/microbiolspec.TBS-0020-2014 -
Applied Microbiology and Biotechnology Jun 2023The aim of the present study was the characterisation of three true subtilisins and one phylogenetically intermediate subtilisin from halotolerant and halophilic...
The aim of the present study was the characterisation of three true subtilisins and one phylogenetically intermediate subtilisin from halotolerant and halophilic microorganisms. Considering the currently growing enzyme market for efficient and novel biocatalysts, data mining is a promising source for novel, as yet uncharacterised enzymes, especially from halophilic or halotolerant Bacillaceae, which offer great potential to meet industrial needs. Both halophilic bacteria Pontibacillus marinus DSM 16465 and Alkalibacillus haloalkaliphilus DSM 5271 and both halotolerant bacteria Metabacillus indicus DSM 16189 and Litchfieldia alkalitelluris DSM 16976 served as a source for the four new subtilisins SPPM, SPAH, SPMI and SPLA. The protease genes were cloned and expressed in Bacillus subtilis DB104. Purification to apparent homogeneity was achieved by ethanol precipitation, desalting and ion-exchange chromatography. Enzyme activity could be observed between pH 5.0-12.0 with an optimum for SPPM, SPMI and SPLA around pH 9.0 and for SPAH at pH 10.0. The optimal temperature for SPMI and SPLA was 70 °C and for SPPM and SPAH 55 °C and 50 °C, respectively. All proteases showed high stability towards 5% (w/v) SDS and were active even at NaCl concentrations of 5 M. The four proteases demonstrate potential for future biotechnological applications. KEY POINTS: • Halophilic and halotolerant Bacillaceae are a valuable source of new subtilisins. • Four new subtilisins were biochemically characterised in detail. • The four proteases show potential for future biotechnological applications.
Topics: Bacillaceae; Bacteria; Subtilisin; Peptide Hydrolases; Temperature
PubMed: 37160606
DOI: 10.1007/s00253-023-12553-w -
Short communication: Typing and tracking Bacillaceae in raw milk and milk powder using pyroprinting.Journal of Dairy Science Jan 2016Contamination of fluid and processed milk products with endospore-forming bacteria, such as Bacillaceae, affect milk quality and longevity. Contaminants come from a...
Contamination of fluid and processed milk products with endospore-forming bacteria, such as Bacillaceae, affect milk quality and longevity. Contaminants come from a variety of sources, including the dairy farm environment, transportation equipment, or milk processing machinery. Tracking the origin of bacterial contamination to allow specifically targeted remediation efforts depends on a reliable strain-typing method that is reproducible, fast, easy to use, and amenable to computerized analysis. Our objective was to adapt a recently developed genotype-based Escherichia coli strain-typing method, called pyroprinting, for use in a microbial source-tracking study to follow endospore-forming bacillus bacteria from raw milk to powdered milk. A collection of endospores was isolated from both raw milk and its finished powder, and, after germination, the vegetative cells were subject to the pyroprinting protocol. Briefly, a ribosomal DNA intergenic transcribed spacer present in multiple copies in Bacillaceae genomes was amplified by the PCR. This multicopy locus generated a mixed PCR product that was subsequently subject to pyrosequencing, a quantitative real-time sequencing method. Through a series of enzymatic reactions, each nucleotide incorporation event produces a photon of light that is quantified at each nucleotide dispensation. The pattern of light peaks generated from this mixed template reaction is called a pyroprint. Isolates with pyroprints that match with a Pearson correlation of 0.99 or greater are considered to be in the same group. The pyroprint also contains some sequence data useful for presumptive species-level identification. This method identified groups with isolates from raw milk only, from powdered milk only, or from both sources. This study confirms pyroprinting as a rapid, reproducible, automatically digitized tool that can be used to distinguish bacterial strains into taxonomically relevant groups and, thus, indicate probable origins of bacterial contamination in powdered milk.
Topics: Animals; Bacillaceae; Bacterial Typing Techniques; DNA, Bacterial; Food Handling; Milk; RNA, Ribosomal, 16S; Spores, Bacterial
PubMed: 26585475
DOI: 10.3168/jds.2015-9656 -
World Journal of Microbiology &... Mar 2023The Bacillaceae family members are considered to be a good source of microbial factories for biotechnological processes. In contrast to Bacillus and Geobacillus,... (Review)
Review
The Bacillaceae family members are considered to be a good source of microbial factories for biotechnological processes. In contrast to Bacillus and Geobacillus, Anoxybacillus, which would be thermophilic and spore-forming group of bacteria, is a relatively new genus firstly proposed in the year of 2000. The development of thermostable microbial enzymes, waste management and bioremediation processes would be a crucial parameter in the industrial sectors. There has been increasing interest in Anoxybacillus strains for biotechnological applications. Therefore, various Anoxybacillus strains isolated from different habitats have been explored and identified for biotechnological and industrial purposes such as enzyme production, bioremediation and biodegradation of toxic compounds. Certain strains have ability to produce exopolysaccharides possessing biological activities including antimicrobial, antioxidant and anticancer. This current review provides past and recent discoveries regarding Anoxybacillus strains and their potential biotechnological applications in enzyme industry, environmental processes and medicine.
Topics: Anoxybacillus; Bacillaceae; Biotechnology; Bacillus; Geobacillus
PubMed: 36995480
DOI: 10.1007/s11274-023-03583-7 -
Toxins Jul 2021Larvicides based on the bacteria svar. (Bti) and are effective and environmentally safe compounds for the control of dipteran insects of medical importance. They... (Review)
Review
Larvicides based on the bacteria svar. (Bti) and are effective and environmentally safe compounds for the control of dipteran insects of medical importance. They produce crystals that display specific and potent insecticidal activity against larvae. Bti crystals are composed of multiple protoxins: three from the three-domain Cry type family, which bind to different cell receptors in the midgut, and one cytolytic (Cyt1Aa) protoxin that can insert itself into the cell membrane and act as surrogate receptor of the Cry toxins. Together, those toxins display a complex mode of action that shows a low risk of resistance selection. crystals contain one major binary toxin that display an outstanding persistence in field conditions, which is superior to Bti. However, the action of the Bin toxin based on its interaction with a single receptor is vulnerable for resistance selection in insects. In this review we present the most recent data on the mode of action and synergism of these toxins, resistance issues, and examples of their use worldwide. Data reported in recent years improved our understanding of the mechanism of action of these toxins, showed that their combined use can enhance their activity and counteract resistance, and reinforced their relevance for mosquito control programs in the future years.
Topics: Animals; Bacillaceae; Bacillus thuringiensis; Bacterial Toxins; Culicidae; Mosquito Control; Pest Control, Biological
PubMed: 34437394
DOI: 10.3390/toxins13080523