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BMC Microbiology Jun 2018Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions... (Comparative Study)
Comparative Study
BACKGROUND
Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis.
RESULTS
The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results.
CONCLUSIONS
It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism's resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group.
Topics: Bacillus; Bacillus pumilus; Bacterial Proteins; DNA Gyrase; Gene Order; Genome, Bacterial; Molecular Sequence Annotation; Open Reading Frames; Phylogeny; Sequence Analysis, DNA; Spacecraft; Spores, Bacterial
PubMed: 29884123
DOI: 10.1186/s12866-018-1191-y -
Animals : An Open Access Journal From... Sep 2020The importance of as feed additives in animals' production is well recognized. and are involved in promoting animal growth performance and immunological indicators....
The importance of as feed additives in animals' production is well recognized. and are involved in promoting animal growth performance and immunological indicators. However, their precise roles in the modulation of microbiota and immune response in goat rumen and intestines have not been investigated. The aim of the current work was to evaluate the impacts of fsznc-06 and fsznc-09 in the development of rumen and small intestinal and microbial communities in rumen and caecum of weanling Jintang black goats. Morphological alterations of rumen and small intestine (duodenum, jejunum, and ileum) were evaluated by histochemical staining, and ruminal contents and cecal feces were analyzed by 16S rRNA sequencing in an Illumina NovaSeq platform. Morphological analysis showed that feeding weanling goats with fsznc-06 or fsznc-09 enhanced ruminal papilla and small intestinal villus growth. In addition, 16S rRNA sequencing analysis indicated that microbial richness and diversity (Shannon, Simpson, Chao1, and ACE) and the relative richness of multiple or potential beneficial bacteria were higher in weaned black goats fed on fsznc-06 or fsznc-09, but that of multiple or potentially pathogenic bacteria were lower, as compared with the control group. Tax4Fun analysis predicting the functional profiling of microbial communities showed that microbial communities in rumen or caecum were highly influential on metabolism and organism systems after feeding weanling goats with fsznc-06 or fsznc-09. It was suggested that fsznc-06 and fsznc-09 might be an auspicious antibiotic alternative to improve black goat growth and health by changing rumen and gut microbiota positively.
PubMed: 32916846
DOI: 10.3390/ani10091604 -
Frontiers in Microbiology 2022Heterotrophic bacteria are assumed to play an important role in processing of phytoplankton-derived dissolved organic matter (DOM). Although the algae-derived organic...
Heterotrophic bacteria are assumed to play an important role in processing of phytoplankton-derived dissolved organic matter (DOM). Although the algae-derived organic matter is commonly studied, the transformation and processing of DOM by epiphytic bacteria for phytoplankton have rarely been investigated, especially under warming and acidification. In this study, is used to explore the ecologically important marine diatom -derived DOM under different conditions (temperature, 27°C and 31°C; CO, 400 and 1,000 ppm), utilizing fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (EEM-PARAFAC). Fluorescence regional integration and the peak selecting method are used to generate B, T, N, A, M, and C peaks in the EEM fluorescence spectroscopy. The main known fluorophores including that protein-like components (peaks B and T), unknown components (peak N), and humic-like component (peaks A, M, and C). Our experimental results showed that under higher temperature and pressure of CO (CO) conditions, -derived DOM fluorescence was dominated by a protein-like signal that slower waning throughout the experiment, becoming an increasingly humic-like substance, implying that processing by the epiphytic bacteria () produced more complex molecules. In addition, spectroscopic indices (e.g., fluorescence index, biological index, freshness index , and humification index) were changed in varying degrees. This study reveals and confirms the direct participation of heterotrophic bacteria in the transformation and generation of algae-derived DOM in the laboratory, underlining the influence of global warming and ocean acidification on this process.
PubMed: 35283861
DOI: 10.3389/fmicb.2022.833670 -
Microorganisms Jun 2023Due to their capacity to produce antimicrobial peptides that can prevent the growth of diseases, many spp. are beneficial to plants. In this study, we looked into the...
Due to their capacity to produce antimicrobial peptides that can prevent the growth of diseases, many spp. are beneficial to plants. In this study, we looked into the antagonistic activity of the 3-19 strain and its derivatives following targeted genome editing. Two peptide genes with antibacterial action, bacilysin () and bacteriocin (), and the F gene, which encodes the sigma factor of sporulation, were specifically inactivated using the CRISPR-Cas9 system in the genome of 3-19. Antibacterial activity against and decreased as a result of the inactivation of target genes in the 3-19 genome, with a noticeable effect against bacilysin. The growth dynamics of the culture changed when the , , and F genes were inactivated, and the altered strains had less proteolytic activity. An asporogenic mutant of 3-19 was obtained by inactivating the F gene. It has been proven that bacilysin plays a unique part in the development of 3-19's antagonistic action against soil microorganisms.
PubMed: 37375011
DOI: 10.3390/microorganisms11061508 -
PloS One 2016The soil-related Bacillus and Paenibacillus species have increasingly been implicated in various human diseases. Nevertheless, their identification still poses problems...
The soil-related Bacillus and Paenibacillus species have increasingly been implicated in various human diseases. Nevertheless, their identification still poses problems in the clinical microbiology laboratory and, with the exception of Bacillus anthracis and Bacillus cereus, little is known on their pathogenicity for humans. In this study, we evaluated the use of matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) in the identification of clinical isolates of these genera and conducted genotypic and phenotypic analyses to highlight specific virulence properties. Seventy-five clinical isolates were subjected to biochemical and MALDI-TOF MS identification. 16S rDNA sequencing and supplemental tests were used to solve any discrepancies or failures in the identification results. MALDI-TOF MS significantly outperformed classical biochemical testing for correct species identification and no misidentification was obtained. One third of the collected strains belonged to the B. cereus species, but also Bacillus pumilus and Bacillus subtilis were isolated at high rate. Antimicrobial susceptibility testing showed that all the B. cereus, B. licheniformis, B. simplex, B. mycoides, Paenibacillus glucanolyticus and Paenibacillus lautus isolates are resistant to penicillin. The evaluation of toxin/enzyme secretion, toxin-encoding genes, motility, and biofilm formation revealed that B. cereus displays the highest virulence potential. However, although generally considered nonpathogenic, most of the other species were shown to swim, swarm, produce biofilms, and secrete proteases that can have a role in bacterial virulence. In conclusion, MALDI-TOF MS appears useful for fast and accurate identification of Bacillus and Paenibacillus strains whose virulence properties make them of increasing clinical relevance.
Topics: Bacillus; Bacterial Typing Techniques; DNA, Bacterial; DNA, Ribosomal; Gram-Positive Bacterial Infections; Humans; Paenibacillus; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 27031639
DOI: 10.1371/journal.pone.0152831 -
Frontiers in Microbiology 2023Microbial consortia play a key role in human health, bioenergy, and food manufacturing due to their strong stability, robustness and versatility. One of the microbial...
Microbial consortia play a key role in human health, bioenergy, and food manufacturing due to their strong stability, robustness and versatility. One of the microbial consortia consisting of and for the production of the vitamin C precursor, 2-keto-L-gulonic acid (2-KLG), has been widely used for large-scale industrial production. To further investigate the cell-cell communication in microbial consortia, a microbial consortium consisting of and was constructed and the differences in protein expression at different fermentation time points (18 h and 40 h) were analyzed by iTRAQ-based proteomics. The results indicated that was subjected to acid shocks in the coculture fermentation system and responded to it. In addition, the quorum sensing system existed in the coculture fermentation system, and could secrete quorum-quenching lactonase (YtnP) to inhibit the signaling pathway of . This study offers valuable guidance for further studies of synthetic microbial consortia.
PubMed: 37025640
DOI: 10.3389/fmicb.2023.1131000 -
Molecular Plant-microbe Interactions :... Oct 2020Elucidation of the underlying mechanisms of plant growth promotion of rhizobacteria is very important. This study explored the mechanism by which LZP02 promotes growth...
Elucidation of the underlying mechanisms of plant growth promotion of rhizobacteria is very important. This study explored the mechanism by which LZP02 promotes growth in rice roots through proteomic, transcriptomic, and metabolomic techniques. The results showed that LZP02 promoted the absorption of phosphorous, calcium, and magnesium ions by colonization of rice roots and enhanced peroxidase, catalase, superoxide dismutase, and CaMg adenosine triphosphatase activities and chlorophyll contents in rice. The proteomic results showed that most of the differentially expressed proteins were involved in carbohydrate metabolism and that the biosynthesis of other secondary metabolites was also increased. According to RNA-seq and reverse transcription-quantitative PCR analyses, expression of some genes involved in carbohydrate metabolism and phenylpropanoid biosynthesis was upregulated in rice roots. Regarding metabolomics, phenylpropanoid biosynthesis, starch and sucrose metabolism, the pentose phosphate pathway, and glyoxylate and dicarboxylate metabolism were increased. The results indicated that LZP02 promoted the growth of rice roots by enhancing carbohydrate metabolism and phenylpropanoid biosynthesis.
Topics: Bacillus pumilus; Carbohydrate Metabolism; Gene Expression Regulation, Plant; Oryza; Phenylalanine; Plant Roots; Proteomics; Secondary Metabolism
PubMed: 32597697
DOI: 10.1094/MPMI-04-20-0106-R -
International Journal of Molecular... Oct 2022This study describes two novel bacteriophages infecting members of the group. Even though members of the group are not recognized as pathogenic, several strains...
This study describes two novel bacteriophages infecting members of the group. Even though members of the group are not recognized as pathogenic, several strains belonging to the group have been reported to cause infectious diseases in plants, animals and humans. group species are highly resistant to ultraviolet radiation and capable of forming biofilms, which complicates their eradication. Bacteriophages Novomoskovsk and Bolokhovo were isolated from soil samples. Genome sequencing and phylogenetic analysis revealed that the phages represent two new species of the genus (class ). The phages remained stable in a wide range of temperatures and pH values. A host range test showed that the phages specifically infect various strains of . The phages form clear plaques surrounded by halos. Both phages Novomoskovsk and Bolokhovo encode proteins with pectin lyase domains-Putative depolymerases. Obtained in a purified recombinant form, the proteins produced lysis zones on the lawn of a strain. This suggests that Novomoskovsk and Bolokhovo may be effective for the eradication of biofilms.
Topics: Humans; Bacillus pumilus; Phylogeny; Ultraviolet Rays; Bacteriophages; Bacillus
PubMed: 36361776
DOI: 10.3390/ijms232112988 -
Foods (Basel, Switzerland) May 2021Feruloyl esterase (FAE; EC 3.1.1.73) catalyzes the hydrolysis of the 4-hydroxy-3-methoxycinnamoyl group in an esterified sugar to assist in waste biomass degradation or...
Feruloyl esterase (FAE; EC 3.1.1.73) catalyzes the hydrolysis of the 4-hydroxy-3-methoxycinnamoyl group in an esterified sugar to assist in waste biomass degradation or to release ferulic acid (FA). An FAE-producing strain was isolated from humus soil samples and identified as SK52.001. The BpFAE gene from SK52.001 was speculated and heterogeneously expressed in WB800 for the first time. The enzyme exists as a monomer with 303 amino acids and a molecular mass of 33.6 kDa. Its specific activity was 377.9 ± 10.3 U/ (mg protein), using methyl ferulate as a substrate. It displays an optimal alkaline pH of 9.0, an optimal temperature of 50 °C, and half-lives of 1434, 327, 235, and 68 min at 50, 55, 60, and 65 °C, respectively. Moreover, the purified BpFAE released 4.98% FA of the alkali-acidic extractable FA from de-starched wheat bran (DSWB). When the DSWB was enzymatically degraded by the synergistic effect of the BpFAE and commercial xylanase, the FA amount reached 49.47%. It suggested that the alkaline BpFAE from SK52.001, which was heterologously expressed in WB800, possesses great potential for biomass degradation and achieving high-added value FA production from food by-products.
PubMed: 34071417
DOI: 10.3390/foods10061229 -
PloS One 2014Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) despite being increasingly used as a method for microbial identification,...
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) despite being increasingly used as a method for microbial identification, still present limitations in which concerns the differentiation of closely related species. Bacillus pumillus and Bacillus safensis, are species of biotechnological and pharmaceutical significance, difficult to differentiate by conventional methodologies. In this study, using a well-characterized collection of B. pumillus and B. safensis isolates, we demonstrated the suitability of MALDI-TOF-MS combined with chemometrics to accurately and rapidly identify them. Moreover, characteristic species-specific ion masses were tentatively assigned, using UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases and primary literature. Delineation of B. pumilus (ions at m/z 5271 and 6122) and B. safensis (ions at m/z 5288, 5568 and 6413) species were supported by a congruent characteristic protein pattern. Moreover, using a chemometric approach, the score plot created by partial least square discriminant analysis (PLSDA) of mass spectra demonstrated the presence of two individualized clusters, each one enclosing isolates belonging to a species-specific spectral group. The generated pool of species-specific proteins comprised mostly ribosomal and SASPs proteins. Therefore, in B. pumilus the specific ion at m/z 5271 was associated with a small acid-soluble spore protein (SASP O) or with 50S protein L35, whereas in B. safensis specific ions at m/z 5288 and 5568 were associated with SASP J and P, respectively, and an ion at m/z 6413 with 50S protein L32. Thus, the resulting unique protein profile combined with chemometric analysis, proved to be valuable tools for B. pumilus and B. safensis discrimination, allowing their reliable, reproducible and rapid identification.
Topics: Bacillus; Bacterial Proteins; Bacterial Typing Techniques; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 25314655
DOI: 10.1371/journal.pone.0110127