Prevalence of Antimicrobial Resistance and Respective Genes among Bacillus spp., a Versatile Bio-Fungicide

The Resistance Abilities of Some Bacillus Species to Gastrointestinal Tract Conditions: Whole Genome Sequencing of the Novel Candidate Probiotic Strains Bacillus clausiiBA8 and Bacillus subtilisBA11

This study aims to investigate the resistance of potential probiotic Bacillus species to various conditions in the gastrointestinal (GI) tract and their safety characteristics. MALDI-TOF MS identified all tested strains with a good safety score of ≥ 2.0; the strains demonstrated the capacity to pass through the Gl tract, exhibiting a reduction of > 6 log/CFU live cells. Furthermore, they exhibited varying survival rates in an acidic environment (pH 2.0-3.0) and the presence of Ox-Bile (1% w/v) (p < 0.05). Following exposure to pH 3.0 and Ox-Bile, the survival rate of Bacillus spp. ranged between 85.94% and 91.24% and 87.30% and 91.54%, respectively. The results of the in vitro experiments showed that the six Bacillus strains had comparable characteristics (e.g., tolerance to GI track enzyme, auto-aggregation ability) to the reference probiotic strain Lactiplantibacillus plantarum LA15. The auto-aggregation results of the B. clausii BA8 strain, which has demonstrated resistance to GI tract conditions, were also noteworthy. This strain showed 72.32% after 2 h and 74.55% at the end of 5 h. Most suitable for use as probiotic strains B. clausii BA8 and B. subtilis BA11, sequenced via Illumina NovaSeq, showed average nucleotide identity (ANI) values of 98.1% and 97.8%, respectively. The genome annotation of B. clausii and B. subtilis with Prokka revealed 4,498,248-4,215,606 bp genome length, 44%-43% GC content, and 110-26 contigs, respectively. B. clausii BA8 has been comprehensively characterized, is of low risk for human consumption, and has been recommended as a potential probiotic strain. However, further in vivo experimentation is required to confirm these findings.

Influence of soil type on bacterial growth and tolerance to experimentally added human antibiotics

The human antibiotics cefuroxime (CXM) and azithromycin (AZI) are among the most commonly prescribed. A significant portion of both are excreted and has been detected in sewage treatment plant effluents. The increasing use of such effluents in crops for irrigation and as fertilisers poses a threat to soil microbiota because of the presence of antibiotics. The lack of studies on CXM and AZI in soils hinders our understanding of their potential toxic effects on soil bacterial communities and ecosystem services. This study significantly contributes to the literature by quantifying the toxicity of CXM and AZI at varying concentrations in 12 different crop soils and tracking their evolution over time. The study also examined whether antibiotic pressure led to the development of more tolerant bacterial communities. The results of this study are the values of the logarithm of the antibiotic concentration at which 50 % of bacterial growth is inhibited (Log IC50) and indicate that both antibiotics are toxic to soil bacteria. The direct toxicity of CXM (1 day after contamination) was higher (Log IC50: 0.9 = 7.9 mg kg-1) than that of AZI (Log IC50: 3.4 = 2362 mg kg-1). However, bacterial growth was less affected by CXM over time, whereas AZI remained toxic in some soils until day 42 (Log IC50: 3.2 = 1533 mg kg-1 and 3.4 = 2291 mg kg-1, respectively). The overall results indicate that selective pressure exerted by antibiotics generates antibiotic tolerance in soils, even at the lowest antibiotic concentration studied (7.8 mg kg-1). The general trend was to increase tolerance to higher antibiotic concentrations up to the highest concentration studied (2000 mg kg-1). However, the degree of tolerance developed was highly dependent on soil type. More studies should be conducted to quantitatively assess the toxic and tolerance-developing effects of antibiotics in soils. Such information will be valuable for identifying which antibiotics pose a threat to the soil microbiota and consequently to human health.

Dynamic interaction of antibiotic resistance between plant microbiome and organic fertilizers: sources, dissemination, and health risks

Antibiotic resistance is a global health problem driven by the irrational use of antibiotics in different areas (such as agriculture, animal farming, and human healthcare). Sub-lethal concentrations of antibiotic residues impose selective pressure on environmental, plant-associated, and human microbiome leading to the emergence of antibiotic-resistant bacteria (ARB). This review summarizes all sources of antibiotic resistance in agricultural soils (including manure, sewage sludge, wastewater, hospitals/pharmaceutical industry, and bioinoculants). The factors (such as the physicochemical properties of soil, root exudates, concentration of antibiotic exposure, and heavy metals) that facilitate the transmission of resistance in plant microbiomes are discussed. Potential solutions for effective measures and control of antibiotic resistance in the environment are also hypothesized. Manure exhibits the highest antibiotics load, followed by hospital and municipal WW. Chlortetracycline, tetracycline, and sulfadiazine have the highest concentrations in the manure. Antibiotic resistance from organic fertilizers is transmitted to the plant microbiome via horizontal gene transfer (HGT). Plant microbiomes serve as transmission routes of ARB and ARGS to humans. The ingestion of ARB leads to human health risks (such as ineffectiveness of medication, increased morbidity, and mortality).

Antibiotic resistance characterization, virulence factors and molecular characteristics of Bacillus species isolated from probiotic preparations in China

OBJECTIVES

The aim of this study was to determine the phenotypic and molecular characteristics of antibiotic-resistant Bacillus spp. isolated from probiotic preparations in China.

METHODS

Bacillus strains were isolated from probiotic preparations and then identified using 16S rDNA sequencing. Drug sensitivity tests were conducted to determine their susceptibility to seven antibiotics. Whole genome sequencing was performed on the most resistant strains, followed by analysis of their molecular characteristics, resistance genes, and virulence factors.

RESULTS

In total, we isolated 21 suspected Bacillus species from seven compound probiotics, which were identified by 16S rDNA as 12 Bacillus licheniformis, six Bacillus subtilis and three Bacillus cereus. The determination of antimicrobial susceptibility showed widespread resistance to chloramphenicol (95.2%), erythromycin (85.7%) and gentamicin (42.9%). Whole genome sequencing of seven resistant strains revealed that J-6-A (Bacillus subtilis) and J-7-A (Bacillus cereus) contained a plasmid. The resistance gene analysis revealed that each strain contained more than ten resistance genes, among which J-7-A was the most. The streptomycin resistance gene strA was detected in all strains. The chloramphenicol resistance genes ykkC and ykkD were found in J-1-A to J-5-A and were first reported in Bacillus subtilis. The erythrocin resistance gene ermD was detected in strains J-1-A to J-4-A. There were also more than 15 virulence factors and gene islands (GIs) involved in each strain.

CONCLUSIONS

These results confirm the potential safety risks of probiotics and remind us to carefully select probiotic preparations containing strains of Bacillus species, especially Bacillus cereus, to avoid the potential spread of resistance and pathogenicity.

Isolation and identification of a new Bacillus glycinifermentans strain from date palm rhizosphere and its effect on barley seeds under heavy metal stress

Soil contamination by heavy metals is one of the major problems that adversely decrease plant growth and biomass production. Inoculation with the plant growth-promoting rhizobacteria (PGPR) can attenuate the toxicity of heavy metals and enhancing the plant growth. In this study, we evaluated the potential of a novel extremotolerant strain (IS-2 T) isolated from date palm rhizosphere to improve barley seedling growth under heavy metal stress. The species-level identification was carried out using morphological and biochemical methods combined with whole genome sequencing. The bacterial strain was then used in vitro for inoculating Hordeum vulgare L. exposed to three different Cr, Zn, and Ni concentrations (0.5, 1, and 2 mM) in petri dishes and different morphological parameters were assessed. The strain was identified as Bacillus glycinifermentans species. This strain showed high tolerance to pH (6-11), salt stress (0.2-2 M), and heavy metals. Indeed, the minimum inhibitory concentrations at which bacterium was unable to grow were 4 mM for nickel, 3 mM for zinc, more than 8 mM for copper, and 40 mM for chromium, respectively. It was observed that inoculation of Hordeum vulgare L. under metal stress conditions with Bacillus glycinifermentans IS-2 T stain improved considerably the growth parameters. The capacity of the IS-2 T strain to withstand a range of abiotic stresses and improve barley seedling development under lab conditions makes it a promising candidate for use as a PGPR in zinc, nickel, copper, and chromium bioremediation.

Probiotic Potential of Bacillus sp. 62A Isolated from a Marine Extreme Environment

Antimicrobial resistance is an important health concern globally, and probiotics are considered an alternative to minimize it. The present study examined the in vitro probiotic characteristics and in vivo immunomodulatory potential of Bacillus sp. 62A - an extremophile bacterium. Bacillus sp. 62A was evaluated in vitro for its cytotoxicity, hemolytic activity, antibiotic susceptibility, and resistance to gastrointestinal conditions (bile salts, low pH, and intestinal adherence). Additionally, the immunomodulatory effect of Bacillus sp. 62A was studied in mice. The animals were supplemented daily with phosphate-buffered saline (control) and Bacillus sp. 62A at 1 × 108 colony forming units (CFU). Samples were taken on days 5 and 10. Isolated splenocytes were challenged with Escherichia coli for immunological analyses and immune-related gene expression. Serum and feces were collected for IgA and IgG determination. Bacillus sp. 62A did not show cytotoxicity, hemolytic activity, or resistance to antibiotics. Furthermore, the bacterium has autoaggregation and intestinal adhesion capacities and grows in the presence of bile salts and low pH. Bacillus supplementation in mice improved respiratory burst activity, nitric oxide production, and IL-1β and IL-6 gene expressions, mainly at 10 days. After E. coli challenge, Bacillus supplementation in mice induced an anti-inflammatory response through a decrease in immunological parameters and an increase in IL-10 gene expression. Moreover, serum IgA and IgG and fecal IgG augmented in supplemented mice. In conclusion, Bacillus sp. 62A has biosafe and immunomodulatory probiotic potential.

Editorial for Special Issue-''Research Progress and Applications of Natural Products"

This Special Issue (S [...].

Prevalence and Antibiotic Resistance of Bacillus sp. Isolated from Raw Milk

Milk, due to its diversity in terms of its nutritional content, is an important element of the human diet, as well as a good medium for the development of bacteria. The genus Bacillus contains ubiquitous aerobic, rod-shaped, endospore-producing gram-positive bacteria. Representatives of the Bacillus cereus group and the Bacillus subtilis group contribute to shortening the shelf life of milk and dairy products by degrading milk components and its additives. They also produce a number of heat-stable toxins and can cause a number of ailments, mainly in the digestive system. The aim of this research was to identify Bacillus sp. strains isolated from raw milk and to determine their antibiotic resistance. Strains isolated from raw milk samples (n = 45) were identified by MALDI-TOF MS. Ninety strains of Bacillus sp. were identified, for which the antibiotic resistance phenotype was determined. A total of 90 strains of Bacillus were classified in five groups (the Bacillus cereus group (n = 35), B. licheniformis (n = 7), the B. subtilis group (n = 29), B. pumilus (n = 16), and Bacillus sp. (n = 3). All isolates were susceptible to chloramphenicol and meropenem. The antibiotic resistance profiles of the tested groups of Bacillus spp. differed from each other, which is of particular concern in relation to multidrug-resistant representatives of the B. cereus group resistant to cefotaxime (94.29%), ampicillin (88.57%), rifampicin (80%), and norfloxacin (65.71%). Our study provides data on the prevalence and antibiotic sensitivity of Bacillus sp. In raw milk, suggesting a potential risk to health and the dairy industry.