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BMC Microbiology Sep 2022Probiotics contain beneficial live bacteria that confer several health benefits to the host. For the past 50 years, spore-forming Bacillus species have been used in...
Probiotics contain beneficial live bacteria that confer several health benefits to the host. For the past 50 years, spore-forming Bacillus species have been used in the form of probiotics. Among these, Bacillus clausii strains are used for the management of acute and antibiotic-associated diarrhoea. In the present work, we have evaluated the asserted label information on randomly chosen commercial Bacillus clausii spore suspension of probiotic products. The quality and number of viable bacteria were evaluated based on the colony count, antibiotic resistance, and hemolytic activity assays. The colony fingerprinting and 16S rRNA gene-sequencing techniques were used to confirm the presence of a univariate strain (Bacillus clausii). Our results corroborated the label count of 2 × 10 CFU/5 mL in BACIPRO®, ENTEROGERMINA®, and TUFPRO® products. However, vegetative spore count was not found to match with the given label count in BENEGUT®, PROALANA-B®, β-LOCK®, and PROCILLUS® Bacillus clausii brands. In the hemolytic activity assay, except for β-LOCK®, the other 6 products showed gamma-hemolysis activity. Bacillus clausii isolated from all 7 probiotic products demonstrated resistance to several broad-spectrum antibiotics. The 16S rRNA gene-sequencing data detected genera of Bacillus and Bacillus clausii strain in the BACIPRO®, ENTEROGERMINA®, PROALANA-B®, BENEGUT®, and TUFPRO® products; however, Ralstonia mannitolilytica and Paenibacillus dendritiformis species were identified in β-LOCK® and PROCILLUS®, respectively. As correct label information was observed only in BACIPRO®, ENTEROGERMINA®, and TUFPRO® products, it is proposed that a more stringent quality check would minimize the possibility of mismatch concerning the label information.
Topics: Anti-Bacterial Agents; Bacillus; Bacillus clausii; Probiotics; RNA, Ribosomal, 16S; Spores, Bacterial
PubMed: 36114449
DOI: 10.1186/s12866-022-02631-w -
Journal of Natural Products Jan 2021Chemical investigation of a marine sponge-associated sp. led to the discovery of bacillibactins E and F ( and ). Despite containing the well-established cyclic triester...
Chemical investigation of a marine sponge-associated sp. led to the discovery of bacillibactins E and F ( and ). Despite containing the well-established cyclic triester core of iron-binding natural products such as enterobactin, bacillibactins E and F ( and ) are the first bacterial siderophores that contain nicotinic and benzoic acid moieties. The structures of the new compounds, including their absolute configurations, were determined by extensive spectroscopic analyses and Marfey's method. A plausible biosynthetic pathway to and is proposed; this route bears great similarity to other previously established bacillibactin-like pathways but appears to differentiate itself by a promiscuous DhbE, which likely installs the nicotinic moiety of and the benzoic acid group of .
Topics: Animals; Bacillus; Enterobactin; Iron; Molecular Structure; Oligopeptides; Porifera; Siderophores
PubMed: 33337146
DOI: 10.1021/acs.jnatprod.0c01170 -
Microbiology Spectrum Feb 2022Bacillus velezensis HNA3, a potential plant growth promoter and biocontrol rhizobacterium, was isolated from plant rhizosphere soils in our previous work. Here, we... (Comparative Study)
Comparative Study
Bacillus velezensis HNA3, a potential plant growth promoter and biocontrol rhizobacterium, was isolated from plant rhizosphere soils in our previous work. Here, we sequenced the entire genome of the HNA3 strain and performed a comparative genome analysis. We found that HNA3 has a 3,929-kb chromosome with 46.5% GC content and 4,080 CDSs. We reclassified HNA3 as a Bacillus velezensis strain by core genome analysis between HNA3 and 74 previously defined strains in the evolutionary tree. A comparative genomic analysis among Bacillus velezensis HNA3, Bacillus velezensis FZB42, Bacillus amyloliquefaciens DSM7, and Bacillus subtilis 168 showed that only HNA3 has one predicated secretory protein feruloyl esterase that catalyzes the hydrolysis of plant cell wall polysaccharides. The analysis of gene clusters revealed that whole biosynthetic gene clusters type Lanthipeptide was exclusively identified in HNA3 and might lead to the synthesis of new bioactive compounds. Twelve gene clusters were detected in HNA3 responsible for the synthesis of 14 secondary metabolites including Bacillaene, Fengycin, Bacillomycin D, Surfactin, Plipastatin, Mycosubtilin, Paenilarvins, Macrolactin, Difficidin, Amylocyclicin, Bacilysin, Iturin, Bacillibactin, Paenibactin, and others. HNA3 has 77 genes encoding for possible antifungal and antibacterial secreting carbohydrate active enzymes. It also contains genes involved in plant growth promotion, such as 11 putative indole acetic acid (IAA)-producing genes, spermidine and polyamine synthase genes, volatile compound producing genes, and multiple biofilm related genes. HNA3 also has 19 phosphatase genes involved in phosphorus solubilization. Our results provide insights into the genetic characteristics responsible for the bioactivities and potential application of HNA3 as plant growth-promoting strain in ecological agriculture. This study is the primary initiative to identify Bacillus velezensis HNA3 whole genome sequence and reveal its genomic properties as an effective biocontrol agent against plant pathogens and a plant growth stimulator. HNA3 genetic profile can be used as a reference for future studies that can be applied as a highly effective biofertilizer and biofungicide inoculum to improve agriculture productivity. HNA3 reclassified in the phylogenetic tree which may be helpful for highly effective strain engineering and taxonomy. The genetic comparison among HNA3 and closely similar species B. velezensis FZB42, DSM7, and B. subtilis 168 demonstrates some distinctive genetic properties of HNA3 and provides a basis for the genetic diversity of the genus, which allows developing more effective eco-friendly resources for agriculture and separation of Bacillus velezensis as distinct species in the phylogenetic tree.
Topics: Antifungal Agents; Bacillus; Bacterial Proteins; Biological Control Agents; Genome, Bacterial; Genomics; Multigene Family; Phylogeny; Plant Growth Regulators; Secondary Metabolism
PubMed: 35107331
DOI: 10.1128/spectrum.02169-21 -
Journal of Controlled Release :... Mar 2023Biofilm-associated diseases such as periodontitis are widespread and challenging to treat which calls for new strategies for their effective management. Probiotics...
Biofilm-associated diseases such as periodontitis are widespread and challenging to treat which calls for new strategies for their effective management. Probiotics represent a promising approach for targeted treatment of dysbiosis in biofilm and modulation of host immune response. In this interdisciplinary study, nanofibers with two autochthonous Bacillus strains 27.3.Z and 25.2.M were developed. The strains were isolated from the oral microbiota of healthy individuals, and their genomes were sequenced and screened for genes associated with antimicrobial and immunomodulatory activities, virulence factors, and transferability of resistance to antibiotics. Spores of two Bacillus strains were incorporated individually or in combination into hydrophilic poly(ethylene oxide) (PEO) and composite PEO/alginate nanofibers. The nanofiber mats were characterised by a high loading of viable spores (> 7 log CFU/mg) and they maintained viability during electrospinning and 6 months of storage at room temperature. Spores were rapidly released from PEO nanofibers, while presence of alginate in the nanofibers prolonged their release. All formulations exhibited swelling, followed by transformation of the nanofiber mat into a hydrogel and polymer erosion mediating spore release kinetics. The investigated Bacillus strains released metabolites, which were not cytotoxic to peripheral blood mononuclear cells (PBMCs) in vitro. Moreover, their metabolites exhibited antibacterial activity against two periodontopathogens, an antiproliferative effect on PBMCs, and inhibition of PBMC expression of proinflammatory cytokines. In summary, the developed nanofiber-based delivery system represents a promising therapeutic approach to combat biofilm-associated disease on two fronts, namely via modulation of the local microbiota with probiotic bacteria and host immune response with their metabolites.
Topics: Humans; Nanofibers; Leukocytes, Mononuclear; Bacillus; Anti-Bacterial Agents; Polyethylene Glycols; Alginates
PubMed: 36738969
DOI: 10.1016/j.jconrel.2023.01.082 -
Scientific Reports Mar 2021To date, a large number of Bacillus species from different sources have been identified. However, there are few investigations on genome information and evolutionary...
To date, a large number of Bacillus species from different sources have been identified. However, there are few investigations on genome information and evolutionary insights of Bacillus species from cold environments. Bacillus sp. TK-2, isolated from the soil of Changbai Mountain, is a gram-positive bacterium with cold adaptation characteristics. In this study, we present the annotated complete genome sequence of Bacillus sp. TK-2. The genome comprised 5,286,177 bp with a GC content of 35.88%, 5293 protein-encoding genes, 32 rRNA, and 77 tRNA. Numerous genes related to cold adaptation were detected in the genome of Bacillus sp. TK-2, mainly involving in energy supply, regulation of cell membrane fluidity, antioxidant, and molecular chaperones. In addition, the strain TK-2 classified in the Bacillus groups was distributed on a terminal branch with Bacillus cereus A1 by Blastn and phylogenetic analysis in NCBI database. Complete genome sequences of the strain TK-2 and Bacillus cereus A1 were compared by the online tool "Average Nucleotide Identity", showing that the average nucleotide identity of these two strains was 98.26%. In parallel, A comparative analysis of the genomes of both Bacillus sp. TK-2 and Bacillus cereus A1 was conducted. Through the analysis of core and specific genes with cd-hit, it was found that the two strains had 5691 pan gene, 4524 core gene, and 1167 specific gene clusters. Among the 624 specific gene clusters of Bacillus sp. TK-2, some cold tolerance genes were detected, which implied the unique adaptability of Bacillus sp. TK-2 in long-term low temperature environments. Importantly, enzyme-encoding genes related to the degradation of polysaccharides such as cellulose and hemicellulose were detected in the 477 CAZyme genes of this genome. This work on sequencing and bioinformatics analysis of the complete sequence of Bacillus sp. TK-2 promote the application and in-depth research of low-temperature biotechnology.
Topics: Acclimatization; Bacillus; Cold Temperature; Evolution, Molecular; Genome, Bacterial; Phylogeny; Whole Genome Sequencing
PubMed: 33649356
DOI: 10.1038/s41598-021-84286-7 -
Microbiology Spectrum Dec 2021Some species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge...
Some species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent confrontation, a multifaceted macroscopic outcome was observed and characterized by growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera. Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.
Topics: Bacillus; Lipopeptides; Microbial Interactions; Pseudomonas; Secondary Metabolism; Soil Microbiology
PubMed: 34878336
DOI: 10.1128/spectrum.02038-21 -
Molekuliarnaia Biologiia 2020Bacillus subtilis bacteria play an important role in veterinary medicine, medicine, and biotechnology, and the permanently growing demand for biotechnological products... (Review)
Review
Bacillus subtilis bacteria play an important role in veterinary medicine, medicine, and biotechnology, and the permanently growing demand for biotechnological products fuels the improvement of the properties of biotechnological strains. B. subtilis strains with improved characteristics maybe obtained by rational design and the directed evolution technologies, or be found among newly described strains. In the course of the long-term microbiome composition studies in the Russian segment of the International Space Station, the B. subtilis 20 strain was isolated, this strain shows the capacity for rapid growth and considerable biomass accumulation, as well as increased resistance to acidification of the environment in comparison to the "terrestrial" B. subtilis 168 strain. What is more, B. subtilis 20 is hyperresistant to the DNA and protein damaging factors that are linked to the overexpression of the genes controlling DNA repair, hydrogen sulfide production, and reactive oxygen species neutralization. The described properties of B. subtilis 20 are indicative of its considerable potential as a promising producer of biologically active compounds.
Topics: Bacillus subtilis; Biotechnology
PubMed: 32163397
DOI: 10.31857/S0026898420010085 -
Chembiochem : a European Journal of... Dec 2022The biosynthesis of dopamine (DA) from L-tyrosine as starting material is an excellent yet challenging strategy. Here we developed a versatile, multi-enzymatic platform...
The biosynthesis of dopamine (DA) from L-tyrosine as starting material is an excellent yet challenging strategy. Here we developed a versatile, multi-enzymatic platform for the biocatalytic preparation of DA in a continuous mode with excellent conversion (90 %) and reaction time (45 min). The system exploits the immobilization of a decarboxylase from Bacillus pumilis (Fdc) and a tyrosinase from Agaricus bisporus (Tyr), which were combined to mimic the in-vivo synthesis of DA (both primary and secondary metabolisms) giving rise to an efficient strategy with a considerable reduction of process associated costs and environmental impact. To enhance the system automation, an in-line purification via catch-and-release procedure was added.
Topics: Dopamine; Agaricus; Monophenol Monooxygenase; Biocatalysis; Tyrosine; Bacillus
PubMed: 36315165
DOI: 10.1002/cbic.202200462 -
Molecules (Basel, Switzerland) Oct 2020Since the discovery of penicillin, bacteria are known to be major sources of secondary metabolites that can function as drugs or pesticides. Scientists worldwide... (Review)
Review
Since the discovery of penicillin, bacteria are known to be major sources of secondary metabolites that can function as drugs or pesticides. Scientists worldwide attempted to isolate novel compounds from microorganisms; however, only less than 1% of all existing microorganisms have been successfully identified or characterized till now. Despite the limitations and gaps in knowledge, in recent years, many isolates were identified to harbor a large number of biosynthetic gene clusters encoding gene products for the production of secondary metabolites. These chemically diverse bioactive metabolites could serve as a repository for novel drug discovery. More specifically, current projects on whole-genome sequencing of identified a large number of biosynthetic gene clusters that encode enzymes for the synthesis of numerous antimicrobial compounds, including lipopeptides and polyketides; nevertheless, their biological applications are yet to be identified or established. In this review, we discuss the recent research on synthesis of bioactive compounds by and related species, their chemical structures, bioactive gene clusters of interest, as well as their biological applications for effective plant disease management.
Topics: Agriculture; Anti-Infective Agents; Bacillus; Lipopeptides; Polyketides
PubMed: 33121115
DOI: 10.3390/molecules25214973 -
Molecular Biology and Evolution Jan 2021Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed...
Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
Topics: Bacillus subtilis; Biofilms; Biological Evolution
PubMed: 32871001
DOI: 10.1093/molbev/msaa217