Genome Analysis of a Newly Sequenced B. subtilis SRCM117797 and Multiple Public B. subtilis Genomes Unveils Insights into Strain Diversification and Biased Core Gene Distribution.

The bacterium Bacillus subtilis is a widely used study model and industrial workhorse organism that belongs to the group of gram-positive bacteria. In this study, we report the analysis of a newly sequenced complete genome of B. subtilis strain SRCM117797 along with a comparative genomics of a large collection of B. subtilis strain genomes. B. subtilis strain SRCM117797 has 4,255,638 bp long chromosome with 43.4% GC content and high coding sequence association with macromolecules, metabolism, and phage genes. Genomic diversity analysis of 232 B. subtilis strains resulted in the identification of eight clusters and three singletons. Of 147 B. subtilis strains included, 89.12% had strain-specific genes, of which 6.75% encoded strain-specific insertion sequence family transposases. Our analysis showed a potential role of strain-specific insertion sequence family transposases in intra-cellular accumulation of strain-specific genes. Furthermore, the chromosomal layout of the core genes was biased: overrepresented on the upper half (closer to the origin of replication) of the chromosome, which may explain the fast-growing characteristics of B. subtilis. Overall, the study provides a complete genome sequence of B. subtilis strain SRCM117797, show an extensive genomic diversity of B. subtilis strains and insights into strain diversification mechanism and non-random chromosomal layout of core genes.

Purine nucleosidase (PNase) activity, probiotics potential, and food applicability of a newly-isolated Levilactobacillus brevis LAB42.

Hyperuricemia, a condition characterized by elevated levels of uric acid in the blood, is known as a risk factor for gout disease. In this study, we isolated a total of 72 MRS-grown colonies and evaluated their purine nucleosidase (PNase) activity. Among the isolated bacteria, Levilactobacillus (L.) brevis LAB42 displayed the highest PNase activity. Our findings also indicate that PNase activity can vary among lactic acid bacterial strains and during different growth phases. Based on the kinetics study, LAB42 consistently exhibits the highest PNase activity. Due to its ability to attach to Caco-2 cells and its resistance to acidic environments and bile exposure, L. brevis LAB42 was chosen for further studies and showed that with the right combination of additives, it has the potential to be an appropriate starter for milk fermentation.

Complete genome sequence analysis, morphology and structural protein identification of two Bacillus subtilis phages, BSTP4 and BSTP6, which may form a new species in the genus Salasvirus.

In the present study, two new Bacillus subtilis phages, BSTP4 and BSTP6, were isolated and studied further. Morphologically, BSTP4 and BSTP6 are podoviruses with complete genome of 19,145 (39.9% G + C content) and 19,367 bp (39.8% G + C content), respectively, which became among the smallest Bacillus phages. Three most prominent structural proteins were separated and identified as pre-neck appendage, major head, and head fiber proteins using LC-MS/MS. Both phages encode putative terminal proteins (TP) and contain short inverted terminal repeats (ITRs) which may be important for their replication. In addition, non-coding RNA (pRNA) and parS sites were identified which may be required for DNA packaging and their maintenance inside the host, respectively. Furthermore, the phage genome sequences show significant similarity to B. subtilis group species genome sequences. Finally, phylogenomic and phylogenetic analyses suggest that BSTP4 and BSTP6 may form a new species in the genus Salasvirus, subfamily Picovirinae of family Salasmaviridae. Considering the small numbers of ICTV-accepted B. subtilis phages and the importance of the host in the food industry and biotechnology, the current study helps to improve our understanding of the diversity of B. subtilis phages and shed light on the phage-host relationships.

Genomic diversity and comprehensive taxonomical classification of 61 Bacillus subtilis group member infecting bacteriophages, and the identification of ortholog taxonomic signature genes.

BACKGROUND: Despite the applications of Bacillus subtilis group species in various sectors, limited information is available regarding their phages. Here, 61 B. subtilis group species-infecting phages (BSPs) were studied for their taxonomic classification considering the genome-size, genomic diversity, and the host, followed by the identification of orthologs taxonomic signature genes. RESULTS: BSPs have widely ranging genome sizes that can be bunched into groups to demonstrate correlations to family and subfamily classifications. Comparative analysis re-confirmed the existing, BSPs-containing 14 genera and 21 species and displayed inter-genera similarities within existing subfamilies. Importantly, it also revealed the need for the creation of new taxonomic classifications, including 28 species, nine genera, and two subfamilies (New subfamily1 and New subfamily2) to accommodate inter-genera relatedness. Following pangenome analysis, no ortholog shared by all BSPs was identified, while orthologs, namely, the tail fibers/spike proteins and poly-gamma-glutamate hydrolase, that are shared by more than two-thirds of the BSPs were identified. More importantly, major capsid protein (MCP) type I, MCP type II, MCP type III and peptidoglycan binding proteins that are distinctive orthologs for Herelleviridae, Salasmaviridae, New subfamily1, and New subfamily2, respectively, were identified and analyzed which could serve as signatures to distinguish BSP members of the respective taxon. CONCLUSIONS: In this study, we show the genomic diversity and propose a comprehensive classification of 61 BSPs, including the proposition for the creation of two new subfamilies, followed by the identification of orthologs taxonomic signature genes, potentially contributing to phage taxonomy.

Prevalence, Diversity and UV-Light Inducibility Potential of Prophages in Bacillus subtilis and Their Possible Roles in Host Properties.

Bacillus subtilis is an important bacterial species due to its various industrial, medicinal, and agricultural applications. Prophages are known to play vital roles in host properties. Nevertheless, studies on the prophages and temperate phages of B. subtilis are relatively limited. In the present study, an in silico analysis was carried out in sequenced B. subtilis strains to investigate their prevalence, diversity, insertion sites, and potential roles. In addition, the potential for UV induction and prevalence was investigated. The in silico prophage analysis of 164 genomes of B. subtilis strains revealed that 75.00% of them contained intact prophages that exist as integrated and/or plasmid forms. Comparative genomics revealed the rich diversity of the prophages distributed in 13 main clusters and four distinct singletons. The analysis of the putative prophage proteins indicated the involvement of prophages in encoding the proteins linked to the immunity, bacteriocin production, sporulation, arsenate, and arsenite resistance of the host, enhancing its adaptability to diverse environments. An induction study in 91 B. subtilis collections demonstrated that UV-light treatment was instrumental in producing infective phages in 18.68% of them, showing a wide range of host specificity. The high prevalence and inducibility potential of the prophages observed in this study implies that prophages may play vital roles in the B. subtilis host.

Rice leaf diseases prediction using deep neural networks with transfer learning.

Rice (Oryza sativa) is a principal cereal crop in the world. It is consumed by greater than half of the world's population as a staple food for energy source. The yield production quantity and quality of the rice grain is affecting by abiotic and biotic factors such as precipitation, soil fertility, temperature, pests, bacteria, virus, etc. For disease management, farmers spending lot of time and resources and they detect the diseases through their penniless naked eye approach which leads to unhealthy farming. The advancement of technical support in agriculture greatly assists for automatic identification of infectious organisms in the rice plants leaves. The convolutional neural network algorithm (CNN) is one of the algorithms in deep learning has been triumphantly invoked for solving computer vision problems like image classification, object segmentation, image analysis, etc. In our work, InceptionResNetV2 is a type of CNN model utilized with transfer learning approach for recognizing diseases in rice leaf images. The parameters of the proposed model is optimized for the classification task and obtained a good accuracy of 95.67%.

Hair Washing Formulations from Aloe elegans Todaro Gel: The Potential for Making Hair Shampoo.

This study aimed to describe the gross phytochemical constituents of Aloe elegans Todaro gel and evaluate the characteristics and quality of lab-made hair washing formulations prepared from the gel to show its potential in formulating hair washing shampoos. A. elegans gel mass was prepared from mature, healthy leaves collected from natural stand. Samples of 100% methanol extract of the gel were subjected to standard phytochemical screening and gas chromatography-mass spectroscopy (GC-MS) analysis. Five hair washing formulations (Fs) were, likewise, prepared by mixing 4.0-10.0 mL of gel with one (0.05 mL) to two (0.10 mL) drops of six synthetic and natural ingredients, namely, coconut oil, jojoba oil, olive oil, pure glycerin oil, lemon juice, and vitamin E. The gel to the total ingredient ratios (v/v) of the five formulations were 93 : 7 (F1), 94.5 : 5.5 (F2), 96.4 : 3.6 (F3), and 96.6 : 3.4 (F4 and F5). The formulations were evaluated using sensory inspection and common physicochemical methods. The phytochemical screening and GC-MS analysis revealed that A. elegans gel is the source of important chemical constituents used in the formulation of shampoos and similar products including saponins, capric acid, lauric acid, myristic acid, palmitic acid, linoleic acid, stearic acid, and phytol. Lab-made A. elegans hair washing formulations, especially those with 96.4-96.6% gel, were found to have similar characteristics and qualities with a common marketed shampoo. All the formulations were turbid with characteristic odor as the marketed shampoo. The pH values of the hair washing formulations (6.4-4.6) were comparable to those of the marketed shampoo (6.7). Formulations with higher proportion of gel had better foam stability, higher solid content (26-29%), higher surface tension (33-38 dynes/cm), shorter wetting time (150-160 sec), equivalent viscosities (26.45-26.73 poise), and conditioning performance than the marketed shampoo. These findings demonstrate that A. elegans gel mass can be used in the formulation of good-quality hair washing shampoos. We recommend future studies that aim to develop the phytochemical profile of the plant and a refined protocol of hair washing shampoo formulation.

In Vitro Micropropagation of Industrially and Medicinally Useful Plant Aloe trichosantha Berger Using Offshoot Cuttings.

This study was aimed to develop in vitro micropropagation protocol of Aloe trichosantha Berger using offshoots as explants. MS media supplemented with plant growth regulators helped explants develop shoots within about 14 to 17 days. The mean number of days to shooting has decreased from 16.8 ± 0.8 with 0.5/0.5 mg/L BAP/NAA supplement to 15.5 ± 0.5 with 2.0/0.5 mg/L BAP/NAA. While the mean shoot number has increased with increasing the concentration of BAP supplements, the reverse was true with mean shoot lengths, whereas supplement of 2.0/0.5 mg/L BAP/NAA has generated significantly more shoots (17 ± 3.8), and longer shoots were produced with the addition of 0.5/0.5 and 1.0/0.5 mg/L BAP/NAA. In regard to rooting, though higher concentrations of NAA have resulted in quick rooting, the rooting performance in terms of mean number and length of roots was better with low concentrations. All the plantlets subjected to greenhouse acclimatization in cocopeat have survived. Secondary acclimatization in composted and manured soil media has also resulted in 93 to 95% survival rate. Lighting conditions (nursery shade or direct sunlight) of secondary acclimatization did not lead to any difference in the survival rate of the plantlets.

In Vitro Micropropagation of Aloe adigratana Reynolds Using Offshoot Cuttings.

This study aimed at developing a suitable and reproducible protocol for in vitro micropropagation of Aloe adigratana Reynolds using explants from offshoots with the help of the most commonly used plant growth regulators (PGRs). Explants were initiated in full-strength Murashige and Skoog (MS) media enriched with 0.2 mg/L benzylaminopurine (BAP) + 0.2 mg/L naphthaleneacetic acid (NAA). Shooting experiment was conducted in full-strength MS media enriched with 0/0, 0.5/0.5, 1.0/0.5, 1.5/0.5, and 2.0/0.5 mg/L BAP/NAA. Likewise, rooting experiment was carried out in half-strength MS media enriched with NAA at 0.5, 1.0, and 1.5 mg/L and indol-3-butyric acid (IBA) at 0.5, 1.0, and 1.5 mg/L. Finally, acclimatization study was conducted in greenhouse, nursery, and open field. The shooting response of the plant was best in MS media enriched with 1.0 mg/L BAP + 0.5 mg/L NAA. This media formulation resulted in the shortest mean number of days to shooting (14.00 ± 2.30 days), the highest mean shoot number (4.00 ± 3.40), and the second highest mean shoot length (8.60 ± 2.10 cm). IBA enhanced rooting at higher concentrations (1.0 and 1.5 mg/L), but NAA did the same at lower concentrations (0.5 and 1.0 mg/L). All plantlets (n = 62) survived primary acclimatization. Secondary acclimatization in composted and matured soil media under nursery and open field (sun light) condition produced 88 to 93% survival rate. The death of plantlets in the secondary acclimatization is accounted to mechanical damage. This study demonstrated that the tested PGRs were useful in enhancing the in vitro micropropagation of the plant. Future studies need to focus on optimizing the protocol for large-scale, commercial micropropagation.

Formulation and Physicochemical Evaluation of Lab-Based Aloe adigratana Reynolds Shampoos.

Aloe L. species (Aloaceae) are ethnobotanically very valuable plants in many communities and civilizations. Nonetheless, very few species are extensively studied to explore their applications in the pharmaceutical and medical, cosmetic and personal care, food and beverage, and detergent industries. This study evaluated the characteristics and quality of lab-based shampoos formulated from the gel of Aloe adigratana Reynolds. Five shampoo formulations, 20 mL each, were prepared from A. adigratana gel in combination with one to two drops of coconut oil, jojoba oil, olive oil, pure glycerin oil, lemon juice, and vitamin E. Gel mass is prepared from mature, healthy leaves collected from the natural stand. The phytochemistry of the gel of the plant was also studied using phytochemical screening, proximate composition, and GC-MS analysis studies. Shampoo formulations with higher proportion (40 to 50% v/v) of A. adigratana gel were found to have comparable characteristics and qualities with a marketed shampoo. They fall within the range of acceptable quality parameters of commercial shampoos. The phytochemical studies of A. adigratana gel showed that the plant is the source of highly valued compounds for the preparation of shampoos. The gel was found to be rich in saponins as well as dodecanoic acid, hexadecanoic acid, and phytol. Future works should focus in the development of refined protocol towards formulating A. adigratana-based shampoos.

Preliminary Antimicrobial Profile of Solanum incanum L.: A Common Medicinal Plant.

Medicinal plants and plant remedies have been in use in Ethiopia for centuries. Studies on ethnobotany, ethnomedicine, and ethnoveterinary estimate that nearly 80% of Ethiopians use some type of medicinal plants and plant remedies. Medicinal plants are regarded as the most important and sometimes the only source of therapeutics in the country. Some 800 plant species are used as sources of medicine to treat about 300 physical and mental disorders. However, because these plant species are not adequately studied, there is a big limitation in their documentation, profiling, and management. Moreover, there is a continuous loss of knowledge about medicinal plants because the communities and people are adopting new lifestyles. Hence, this article reports the finding of a study aimed at providing the gross phytochemical characteristics and antimicrobial activities of ethanol and aqueous extracts of fruit, leaf, and stem of Solanum incanum L. against two Gram-negative (Escherichia coli and Salmonella typhi) and two Gram-positive (Bacillus subtilis and Staphylococcus aureus) bacteria for developing gross antimicrobial profile of the plant. Phytochemical screening of fruit, leaf, and stem extracts of S. incanum has shown that it is the source of alkaloids, saponins, flavonoids, glycosides, terpenoids, and steroids. According to agar disc-diffusion tests, 100 mg/mL extracts of the plant produced bacterial growth inhibition zones of 0.00 to 16.06 mm. Ethanol and aqueous leaf extracts produced inhibition zones ranging from 11.34 to 16.06 mm against all bacterial species. The greatest inhibition zone of 16.06 mm was recorded in E. coli subjected to ethanol leaf extract. The same extract resulted in a growth inhibition zone of 16.04 mm in S. aureus. The greatest growth inhibition zones in B. subtilis (13.34 mm) and S. typhi (11.56 mm) were observed with ethanol leaf and fruit extracts, respectively. Aqueous leaf extracts produced growth inhibition zones ranging from 10.45 mm (for S. typhi) to 14.02 mm (for E. coli). Ethanol leaf extracts resulted in the lowest Minimum Inhibition Concentration (MIC) of 1.56 mg/mL in E. coli and S. aureus. Therefore, fruits, leaves, and stems of S. incanum can be regarded as good sources of some bioactive compounds. The findings are important for taking measures for conservation and sustainable use of the plant as well as for further elucidation of its phytochemistry and antimicrobial efficacy of its constituents.