Molecular Phylogenetic Analysis of 16S rRNA Sequences Identified Two Lineages of Helicobacter pylori Strains Detected from Different Regions in Sudan Suggestive of Differential Evolution

Phenotypic, genotypic, and resistome of mesophilic spore-forming bacteria isolated from pasteurized liquid whole egg

The production of whole-liquid eggs is of significant economic and nutritional importance. This study aimed to assess the phenotypic and genotypic diversity of mesophilic aerobic spore-forming bacteria (n = 200) isolated from pasteurized whole liquid egg and liquid egg yolk. The majority of the isolates were identified as belonging to the genera Bacillus (86 %), followed by Brevibacillus (10 %) and Lysinibacillus (4 %). For the phenotypic characterization, isolates were subjected to various heat shocks, with the most significant reductions observed at 80 °C/30 min and 90 °C/10 min for isolates recovered from raw materials. On the other hand, the decrease was similar for isolates recovered from raw material and final product at 100 °C/5 min and 110 °C/5 min. Genotypic genes related to heat resistance (cdnL, spoVAD, dacB, clpC, dnaK, and yitF/Tn1546) were examined for genotypic characterization. The dnaK gene showed a positive correlation with the highest thermal condition tested (110 °C/5 min), while 100 °C/5 min had the highest number of positively correlated genes (clpC, cdnL, yitF/Tn1546, and spoVAD). Whole Genome Sequencing of four strains revealed genes related to sporulation, structure formation, initiation and regulation, stress response, and DNA repair in vegetative cells. The findings of this study indicate that these mesophilic aerobic spore-forming bacteria may adopt several strategies to persist through the process and reach the final product. As the inactivation of these microorganisms during egg processing is challenging, preventing raw materials contamination and their establishment in processing premises must be reinforced.

A Review of Helicobacter pylori Diagnostics in Africa : From the Bedside to the Laboratory

Helicobacter pylori (H. pylori) is endemic in Africa with a prevalence estimate of 79.1%. In addition, there is a significant community burden of dyspepsia in Africa, similar to other western countries. However, the majority of infected persons do not manifest the disease. In Africa, for instance, peptic ulcer disease is prevalent, whereas gastric cancer has reportedly low incidence. Therefore, it is important that testing is focused, targeting individuals most likely to benefit from treatment. In Africa, there are currently no guidelines for H. pylori testing and treatment. Empirical treatment is common due to variable access to diagnostics and health care. To assess the spectrum of H. pylori testing in Africa, we performed a literature search in PubMed over the past 10 years, 2013 to 2023. Histology was the most widely used modality in 16 out of 18 countries. Capacity for culture was shown in 11 studies, importantly across regions of Africa. H. pylori serology was demonstrated in 8 countries, although it has limited sensitivity in identifying active infection. H. pylori test-and-treat strategy has been shown to be cost-effective. Particularly in a region with high antibiotic resistance, adopting this strategy ensures that only confirmed positive patients are treated. Furthermore, test-of-cure ought to be mandatory to guide future therapies. Health authorities can leverage polymerase chain reaction facilities, left behind by the coronavirus disease 2019 pandemic, to make molecular susceptibility testing available in the near future. A systematic approach to testing incorporating indication for endoscopy and medication use is recommended.

Lupin, a Unique Legume That Is Nodulated by Multiple Microsymbionts: The Role of Horizontal Gene Transfer

Lupin is a high-protein legume crop that grows in a wide range of edaphoclimatic conditions where other crops are not viable. Its unique seed nutrient profile can promote health benefits, and it has been proposed as a phytoremediation plant. Most rhizobia nodulating Lupinus species belong to the genus Bradyrhizobium, comprising strains that are phylogenetically related to B. cytisi, B. hipponenese, B. rifense, B. iriomotense/B. stylosanthis, B. diazoefficiens, B. japonicum, B. canariense/B. lupini, and B. retamae/B. valentinum. Lupins are also nodulated by fast-growing bacteria within the genera Microvirga, Ochrobactrum, Devosia, Phyllobacterium, Agrobacterium, Rhizobium, and Neorhizobium. Phylogenetic analyses of the nod and nif genes, involved in microbial colonization and symbiotic nitrogen fixation, respectively, suggest that fast-growing lupin-nodulating bacteria have acquired their symbiotic genes from rhizobial genera other than Bradyrhizobium. Horizontal transfer represents a key mechanism allowing lupin to form symbioses with bacteria that were previously considered as non-symbiotic or unable to nodulate lupin, which might favor lupin’s adaptation to specific habitats. The characterization of yet-unstudied Lupinus species, including microsymbiont whole genome analyses, will most likely expand and modify the current lupin microsymbiont taxonomy, and provide additional knowledge that might help to further increase lupin’s adaptability to marginal soils and climates.

Characterization of symbiotic and nitrogen fixing bacteria

Symbiotic nitrogen fixing bacteria comprise of diverse species associated with the root nodules of leguminous plants. Using an appropriate taxonomic method to confirm the identity of superior and elite strains to fix nitrogen in legume crops can improve sustainable global food and nutrition security. The current review describes taxonomic methods preferred and commonly used to characterize symbiotic bacteria in the rhizosphere. Peer reviewed, published and unpublished articles on techniques used for detection, classification and identification of symbiotic bacteria were evaluated by exploring their advantages and limitations. The findings showed that phenotypic and cultural techniques are still affordable and remain the primary basis of species classification despite their challenges. Development of new, robust and informative taxonomic techniques has really improved characterization and identification of symbiotic bacteria and discovery of novel and new species that are effective in biological nitrogen fixation (BNF) in diverse conditions and environments.

First insights into molecular basis identification of 16 s ribosomal RNA gene of Staphylococcus aureus isolated from Sudan

Objective

In this study, we analyzed the molecular evolution of Staphylococcus aureus isolates using 16S rRNA gene and phylogenetic analysis to detect the prevalence of S. aureus infections in Sudan.

Results

Molecular detection of S. aureus has shown that 20 (43.47%) of patients were positive for S. aureus. The phylogenetic tree of 16S rRNA sequences was divided into three lineages of S. aureus isolates detected from wound infections in Sudan. Nucleotides base-pair substitution was appeared at position 249. This mutation do not linked with Macrolides, Lincosamides and Streptogramines b resistant phenotype. Further studies should investigate the effect of that mutation on resistance to other antibiotics.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05569-w.

Green Synthesis of Silver Nanoparticles by Cytobacillus firmus Isolated from the Stem Bark of Terminalia arjuna and Their Antimicrobial Activity

This work reports an eco-friendly synthesis of silver nanoparticles (AgNPs) using endophytic bacteria, Cytobacillus firmus isolated from the stem bark of Terminalia arjuna. The synthesis of AgNPs was confirmed by visual observation as a change in color of the bacterial solution impregnated with silver. Further, the morphology of the AgNPs, average size, and presence of elemental silver were characterized by UV-Visible spectroscopy, scanning electron microscopy, and dynamic light scattering spectroscopy. The roles of endophytic secondary metabolites in the metal reduction, stabilization, and capping of silver nanoparticles were studied by qualitative FTIR spectral peaks. The antimicrobial ability of AgNPs was evaluated against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria and pearl millet blast disease-causing fungi (Magnoporthe grisea). The biosynthesized AgNPs showed good antibacterial and antifungal activities. AgNPs effectively inhibited the bacterial growth in a dose-dependent manner and presented as good antifungal agents towards the growth of Magnoporthe grisea.

First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach

BACKGROUND

Helicobacter pylori (H. pylori) infects nearly half of the world's population with a variation in incidence among different geographic regions. Genetic variants in the promoter regions of the IL1B gene can affect cytokine expression and creates a condition of hypoacidity which favors the survival and colonization of H. pylori. Therefore, the aim of this study was to characterize the polymorphic sites in the 5'- region [-687_ + 297] of IL1B in H. pylori infection using in silico tools.

RESULTS

A total of five nucleotide variations were detected in the 5'-regulatory region [-687_ + 297] of IL1B which led to the addition or alteration of transcription factor binding sites (TFBSs) or composite regulatory elements (CEs). Genotyping of IL1B - 31 C > T revealed a significant association between -31 T and susceptibility to H. pylori infection in the studied population (P = 0.0363). Comparative analysis showed conservation rates of IL1B upstream [-368_ + 10] region above 70% in chimpanzee, rhesus monkey, a domesticated dog, cow and rat.

CONCLUSIONS

In H. pylori-infected patients, three detected SNPs (- 338, - 155 and - 31) located in the IL1B promoter were predicted to alter TFBSs and CE, which might affect the gene expression. These in silico predictions provide insight for further experimental in vitro and in vivo studies of the regulation of IL1B expression and its relationship to H. pylori infection. However, the recognition of regulatory motifs by computer algorithms is fundamental for understanding gene expression patterns.