Bacteria

For years, the Bacillus genus has encompassed a heterogeneous group of individuals whose main common trait was their ability to sporulate in the presence of oxygen. This criterion has been revised, resulting in the reclassification of several species into new genera and to a redefinition of the characteristics of the members of this taxon. Currently, the species of the genus are grouped into the Subtilis clade and the Cereus clade. The former, called Bacillus sensu stricto, initially composed of B. subtilis, B. licheniformis, B. pumilus, and B. amyloliquefaciens, has subsequently incorporated new species related to these. The Cereus clade, Bacillus cereus sensu lato, consists of pathogenic species (B. anthracis, B. cereus, and B. thuringiensis) as well as others of significance in agriculture and industry. Furthermore, identifying these individuals remains complex, requiring alternatives to 16S rRNA sequencing. The ability to form spores resistant to stressful conditions provides a significant advantage over other genera, with observable differences in sporulation rates and spore structure among different species. Additionally, Bacillus spp. are known for their capacity to produce antimicrobial substances, lytic enzymes, and volatile organic compounds, each with diverse applications. Some species are even used as probiotics. This review delves into aspects related to the taxonomy and identification of microorganisms belonging to the genus Bacillus, which often present challenges. The aim is to provide a comprehensive overview of the topic. In addition, it highlights the characteristics and applications of the genus, emphasizing its importance in biotechnology and microbiology. Full article

The Lactobacillales (LB) stand apart among bacterial orders, using manganese (Mn) instead of iron to support their growth and swiftly ferment complex foods while acidifying their environment. The present work investigates whether a shift in the use of Mn could mark the origin of LB. Transmembrane carriers of the ubiquitous Slc11 family play key roles in LB physiology by catalyzing proton-dependent Mn import. In prior studies, the Slc11 clade found in LB (MntH Cb, MCb) showed both remarkable structural plasticity and highly efficient Mn uptake, and another Slc11 clade, MCg1, demonstrated divergent evolution coinciding with emergence of bacterial genera (e.g., Bordetella, Achromobacter). Herein, the Slc11 clade MCb is subdivided in sister groups: MCb_ie and MCb_gut. MCb_ie derives directly from the Slc11 clade MCa, pointing an intermediate stage in the evolution of MCb_gut. MCb_ie predominates in marine Bacillaceae, is more conserved than MCb_gut, lacks the structural plasticity that typify MCb_gut carriers, and responds differently to identical mutagenesis. Exchanging MCb_ie/MCb_gut amino acid residues at sites that distinguish these clades showed conformation-dependent effects with both MCb_ie and MCb_gut templates, and the 3D location of the targeted sites in the carrier structure together suggests that the mechanism to open the inner gate, and release Mn into the cytoplasm, differs between MCb_ie and MCb_gut. Building on the established phylogeny for Enterococcus revealed that a pair of genes encoding MCb_gut was present in the common ancestor of LB, as MCb_gu1 and MCb_gu2 templates exhibited distinct structural dynamics properties. These data are discussed when examining whether MCb_gut⁺ LB could emerge in the upper gut of early vertebrates (ca. 540 mya), through genome contraction and evolution toward Mn-centrism, as they specialized as gastric aids favoring stomach establishment in jawed vertebrates through bi-directional communication with host nervous, endocrine and immune systems. Full article

Oral health remains one of the most taken for granted parts of human body health, even though poor oral health has now been linked to various diseases, such as cancers, diabetes, autoimmune complications, neurological disorders, and cardiovascular disease, just to name a few. As we review in this paper, substance use or abuse, including alcohol, smoking, recreational drugs, and pharmaceutical drugs can have significant implications on oral health, which in turn can lead to more systemic diseases. In this paper, we show that oral microbiome dysbiosis and inflammatory cytokine pathways are two of the most significant mechanisms contributing to oral health complications from substance use. When substance use decreases beneficial oral species and increases periodontopathogenic strains, a subsequent cascade of oncogenic and inflammatory cytokines is triggered. In this review, we explore these mechanisms and others to determine the consequences of substance use on oral health. The findings are of significance clinically and in research fields as the substance-use-induced deterioration of oral health significantly reduces quality of life and daily functions. Overall, the studies in this review may provide valuable information for future personalized medicine and safer alternatives to legal and pharmaceutical substances. Furthermore, they can lead towards better rehabilitation or preventative initiatives and policies, as it is critical for healthcare and addiction aid specialists to have proper tools at their disposal. Full article

According to the World Health Organization (WHO), tuberculosis (TB) remains a significant global health challenge, with approximately 10 million new cases and 1.4 million deaths reported in 2020. TB disproportionately affects low- and middle-income countries, where factors such as migrant population, malnutrition, type 2 diabetes, human immunodeficiency virus (HIV) co-infection, and COVID-19 exacerbate its impact. TB also leads to substantial economic losses due to decreased productivity and high healthcare costs. Despite advances in treatments, TB remains a major public health issue, particularly in poorer regions. In Mexico, TB is considered a moderate-incidence disease, with higher prevalence in border states, mainly due to population displacements. Effective TB control requires collaboration between Mexico and the United States of America given the high cross-border human movement, like in the Baja California State that reported predominantly pulmonary TB cases. Effective management of TB involves rapid diagnosis and identification of antibiotic resistance. Techniques such as PCR, high-resolution computed tomography (HRCT), and/or Xpert MTB/RIF have enhanced diagnostic accuracy. Future perspectives about TB management focus on developing new drugs and vaccines to combat drug-resistant strains, and the comorbidities associated, which must be addressed to reinforce of health public programs. Full article

This paper explores the intriguing parallels between bacterial behavior and human actions, specifically the tendency of bacteria to adhere to surfaces, construct bacterial “houses” known as a biofilm matrix, nurture growth and reproduction within the biofilm matrix, and disperse upon maturity. Termed as the bacterial “houses”, biofilm matrices exert significant influence on various aspects of human life. A well-structured biofilm matrix serves as the foundation for establishing biofilm reactors capable of efficiently removing heavy metal pollutants from water. Conversely, a dysfunctional biofilm matrix can lead to infections and subsequent illnesses in the human body. Therefore, the study of the biofilm matrix emerges as pivotal. Employing a bibliographic study methodology, this paper analyzes 1000 web of science articles in the field, investigating key keywords, influential countries/regions, organizations, and their interconnections. The findings illuminate the primary themes in biofilm matrix research and offer insights into future directions for this critical field of study. Full article

Antimicrobial resistance is a significant public health issue. The unprecedented spread of antimicrobial-resistant organisms has been identified by the World Health Organization as one of the leading healthcare threats. Projections for annual worldwide deaths attributed to antimicrobial resistance approach 10 million by 2050, with an associated economic burden of USD 100 trillion. This paper reviews the mechanisms known to contribute to antimicrobial resistance and provides insight into potential available alternatives to conventional antibiotics. Antimicrobial approaches addressed include dual antibiotic therapy, antimicrobial peptides, monoclonal antibodies, bacteriophages, probiotics, nanomaterials, and cannabinoids. Key pathogens in need of antimicrobials referred to as the ESKAPE pathogens are discussed. Full article

Background: Several Acinetobacter species live in different ecosystems, such as soil, freshwater, wastewater, and solid wastes, which has attracted considerable research interests in public health and agriculture. Methods: We assessed the distribution of Acinetobacter baumannii and Acinetobacter nosocomialis in three freshwater resources (Great Fish, Keiskemma, and Tyhume rivers) in South Africa between April 2017–March 2018. Molecular identification of Acinetobacter species was performed using Acinetobacter-specific primers targeting the recA gene, whilst confirmed species were further delineated into A. baumannii and A. nosocomialis. Similarly, virulence genes; afa/draBC, epsA, fimH, OmpA, PAI, sfa/focDE, and traT in the two Acinetobacter species were assessed. Results: Our finding revealed that 410 (48.58%) and 23 (2.7%) of the isolates were confirmed as A. baumannii and A. nosocomalis, respectively. Additionally, three hundred and eight (75.12%) A. baumannii and three (13.04%) A. nosocomialis exhibited one or more of the virulence genes among the seven tested. OmpA was the most prevalent virulence gene in A. baumannii in freshwater sources. Conclusions: The distribution of clinically important Acinetobacter species in the freshwater sources studied suggests possible contamination such as the release of hospital wastewater and other clinical wastes into the environment thereby posing a risk to public health. Full article

It is imperative to say that we are immersed in a sea of microorganisms due to their ubiquitous presence on the planet, from soil to water and air. Human bodies harbor a vast array of microorganisms from both the inside and out called the human microbiome. It is composed of single-celled organisms, including archaea, fungi, viruses, and bacteria, including bacteriophages, where bacteria are the biggest players, and this is collectively referred to as the human microbiome. These organisms have a symbiotic relationship with humans and impact human physiology where they colonize various sites on and in the human body, adapting to specific features of each niche. However, dysbiosis, or the deviation from normal microbial composition, is associated with adverse health effects, disrupted ecosystems, and eco-imbalance in nature. In this review, we delve into the comprehensive oversight of bacteria, their cosmopolitan presence, and their additional applications affecting human lives. Full article

Biofilms are accumulations of microorganisms in an extracellular polymeric substance matrix which are composed of polysaccharides, proteins, lipids, and nucleic acids. Many bacteria can switch between a planktonic form and a biofilm form. The planktonic bacteria have relatively high cell growth and reproduction rates and have a reduced likelihood of survival but can adapt to occupy new habitats. The biofilm state appears to be a natural and predominant state of bacteria. The need for the formation of bacterial biofilm is that it enhances the tolerance of bacteria to harsh environmental conditions, thereby allowing bacteria to avoid being washed away by water flow or the bloodstream by simply attaching to a surface or tissue, and the EPS matrix protects bacteria cells, in deeper layers, against antimicrobial agents, probably by limiting the diffusion of these agents. Biofilm formation steps are initial contact/attachment to the surface, followed by micro-colony formation, maturation and formation of the architecture of the biofilm, and finally detachment/dispersion of the biofilm. Once formed, biofilm restricts bacterial mobility and increases cell density. Secretions of autoinducers into the environment are critical for cross-signaling between bacteria. This cross-talk is called quorum sensing (QS). Quorum sensing is a cell–cell communication mechanism between bacteria that allows specific processes to be controlled, such as biofilm formation and virulence factor expression. Bacterial quorum sensing signaling mainly consists of acyl-homoserine lactones (produced by Gram-negatives), autoinducing peptides (produced by Gram-positives), and autoinducer-2 (produced by both Gram-negatives and Gram-positives). Therefore, this review is aimed at how bacterial biofilms work and are formed. Full article

Corynebacterium rouxii is one of the recently described species of the Corynebacterium diphtheriae complex. As this species can potentially infect different hosts and harbor the tox gene, producing diphtheria toxin, we present its first pangenomic analysis in this work. A total of fifteen genomes deposited in online databases were included. After confirming the taxonomic position of the isolates by genomic taxonomy, the genomes were submitted to genomic plasticity, gene synteny, and pangenome prediction analyses. In addition, virulence and antimicrobial resistance genes were investigated. Finally, epidemiological data were obtained through molecular typing, clustering, and phylogenetic analysis. Our data demonstrated genetic diversity within the species with low synteny. However, the gene content is extensively conserved, and the pangenome is composed of 2606 gene families, of which 1916 are in the core genome and 80 are related to unique genes. Prophages, insertion sequences, and genomic islands were found. A type I-E CRISPR-Cas system was also detected. Besides the tox gene, determinants involved in adhesion and iron acquisition and two putative antimicrobial resistance genes were predicted. These findings provide valuable insight about this species’ pathogenicity, evolution, and diversity. In the future, our data can contribute to different areas, including vaccinology and epidemiology. Full article

The current healthcare environment is at risk due to the facilitated transmission and empowerment of the ESKAPE pathogens, comprising of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species. These pathogens have posed significant challenges to global public health and the threat has only amplified over time. These multidrug-resistant bacteria have become adept at escaping the effects of conventional antibiotics utilized, leading to severe healthcare-associated infections and compromising immunocompromised patient outcomes to a greater extent. The impact of ESKAPE pathogens is evident in the rapidly rising rates of treatment failures, increased mortality, and elevated healthcare costs. To combat this looming crisis, diverse strategies have been adopted, ranging from the development of novel antimicrobial agents and combination therapies to the implementation of stringent infection control measures. Additionally, there has been a growing emphasis on promoting antimicrobial stewardship programs to optimize the use of existing antibiotics and reduce the selective pressure driving the evolution of resistance. While progress has been made to some extent, the rapid adaptability of these pathogens and the enhancement of antimicrobial resistance mechanisms proves to be a major hurdle yet to be crossed by healthcare professionals. In this viewpoint, the impending threat heralded by the proliferation of ESKAPE pathogens, and the need for a concerted global effort via international collaborations for the assurance of effective and sustainable solutions, are explored. To curb the possibility of outbreaks in the future and to safeguard public health, better preparation via global awareness and defense mechanisms should be given paramount importance. Full article

The rhizosphere of a plant is home to helpful microorganisms called plant growth-promoting rhizobacteria (PGPR), which play a crucial role in promoting plant growth and development. The significance of PGPR for long-term agricultural viability is outlined in this review. Plant growth processes such as nitrogen fixation, phosphate solubilization, and hormone secretion are discussed. Increased plant tolerance to biotic and abiotic stress, reduced use of chemical fertilizers and pesticides, and enhanced nutrient availability, soil fertility, and absorption are all mentioned as potential benefits of PGPR. PGPR has multiple ecological and practical functions in the soil’s rhizosphere. One of PGPR’s various roles in agroecosystems is to increase the synthesis of phytohormones and other metabolites, which have a direct impact on plant growth. Phytopathogens can be stopped in their tracks, a plant’s natural defenses can be bolstered, and so on. PGPR also helps clean up the soil through a process called bioremediation. The PGPR’s many functions include indole acetic acid (IAA) production, ammonia (NH₃) production, hydrogen cyanide (HCN) production, catalase production, and more. In addition to aiding in nutrient uptake, PGPR controls the production of a hormone that increases root size and strength. Improving crop yield, decreasing environmental pollution, and guaranteeing food security are only some of the ecological and economic benefits of employing PGPR for sustainable agriculture. Full article

Carao (Cassia grandis) contains numerous bioactive substances that contribute to gastrointestinal well-being. The present study assessed the potential impacts of carao on the viability and performance of Streptococcus thermophilus and Lactobacillus bulgaricus under various adverse conditions. These conditions included bile, acid, gastric juice, and lysozyme exposure, simulating the digestive process from the mouth to the intestines. The activity of proteases from cultures was monitored to examine their proteolytic capabilities. To achieve this, the cultures were cultivated in a solution containing plant material, and the results were compared against a control sample after an incubation period. Subsequently, the total phenolic content, total carotenoid content, antioxidant activity, sugar profile, and acid profile of the plant materials were analyzed. These analyses were conducted to explore these compounds’ influence on cultures’ survival. Seeds contained the highest total phenols (766.87 ± 11.56 µg GAE/mL), total carotenoid content (7.43 ± 0.31 mg Q/mL), and antioxidant activity (40.76 ± 1.87%). Pulp contained the highest moisture (12.55 ± 0.44%), ash (6.45 ± 0.15%), lipid (0.66 ± 0.07%), protein (16.56 ± 0.21%), sucrose (9.07 ± 0.78 g/100 g), and fructose (3.76 ± 0.06 g/ 100 g). The crust had the highest content of ash (85.14 ± 0.27%) and succinic acid (2.01 ± 0.06 g/100 g). Results indicated that seeds negatively affected cultures’ survival in the bile tolerance test and had positive effects on Lactobacillus bulgaricus in the protease activity test. Otherwise, the other carao tissues could not change the results significantly (p > 0.05) compared to the control in different tests. The carao crust positively affected cultures’ against protease activity, especially in Lactobacillus bulgaricus, and had a negative effect on the growth of S. thermophilus in the lysozyme and gastric acid resistance test. Full article

Nipple fruit (Solanum mammosum), teosinte (Dioon mejiae), Caesar mushroom (Amanita caesarea), and weevil (Rhynchophorus palmarum) powders have shown great nutritional content with meaningful dietary applications. This study aspired to investigate the impact of nipple fruit, teosinte, Caesar mushroom, and weevil powders on the bile tolerance, acid tolerance, lysozyme tolerance, gastric juice resistance, and protease activity of Lactobacillus casei. Nipple fruit, teosinte, Caesar mushroom, and weevil powders were combined at 2% (wt/vol), whereas the control samples did not include the ingredients. The bile and acid tolerances were analyzed in Difco De Man–Rogosa–Sharpe broth incubated under aerobic conditions at 37 °C. The bile tolerance was investigated by adding 0.3% oxgall, whereas the acid tolerance was studied by modifying the pH to 2.0. The lysozyme tolerance was studied in electrolyte solution containing lysozyme (100 mg/L), while the gastric juice tolerance was analyzed at pH levels of 2, 3, 4, 5, and 7. The protease activity was studied spectrophotometrically at 340 nm in skim milk incubated under aerobic conditions at 37 °C. The results show that nipple fruit increased the counts, whereas Caesar mushroom and weevil powders resulted in lower counts for bile tolerance, acid tolerance, lysozyme resistance, and simulated gastric juice tolerance characteristics. Furthermore, the protease activity increased by adding nipple fruit to skim milk. According to the results, nipple fruit may improve the characteristics of L. casei in cultured dairy by-products. Full article

A variety of agrochemicals, especially fertilizers, are applied indiscriminately by farmers across trapezoidal landscapes to increase productivity and satisfy the rising food demand. Around one-third of the populace in developing nations is susceptible to zinc (Zn) deficiency as a result of their direct reliance on cereals as a source of calories. Zinc, an essential micronutrient for plants, performs several critical functions throughout the life cycle of a plant. Zinc is frequently disregarded, due to its indirect contribution to the enhancement of yield. Soil Zn deficiency is one of the most prevalent micronutrient deficiencies that reduces crop yield. A deficiency of Zn in both plants and soils results from the presence of Zn in fixed forms that are inaccessible to plants, which characterizes the majority of agricultural soils. As a result, alternative and environmentally sustainable methods are required to satisfy the demand for food. It appears that the application of zinc-solubilizing bacteria (ZSB) for sustainable agriculture is feasible. Inoculating plants with ZSB is likely a more efficacious strategy for augmenting Zn translocation in diverse edible plant components. ZSB possessing plant growth-promoting characteristics can serve as bio-elicitors to promote sustainable plant growth, through various methods that are vital to the health and productivity of plants. This review provides an analysis of the efficacy of ZSB, the functional characteristics of ZSB-mediated Zn localization, the mechanism underlying Zn solubilization, and the implementation of ZSB to increase crop yield. Full article

Bakanae is one of the important diseases of rice in Bangladesh that causes substantial yield loss every year. We collected thirty isolates of Fusarium spp. from bakanae-infected rice plants from different agroecological zones of Bangladesh and investigated the variations in cultural and morphological characteristics and pathogenicity. Diversity was found in cultural characteristics, viz., colony features, phialide, chlamydospore formation, shape, and size of macro- and microconidia. Three variants of Fusarium species such as F. moniliforme, F. fujikuroi, and F. proliferatum were identified on PDA media based on their cultural and morphological characteristics. Isolate FM10 (F. moniliforme) exhibited the highest disease aggressiveness in developing elongated plants (26.50 cm), the highest number of chlorotic leaves (5.75), and a lower germination percentage. We evaluated different bioagents against the virulent isolate of F. moniliforme to develop a rice bakanae disease management approach. Four bioagents, viz., Trichoderma spp., Bacillus subtilis, Pseudomonas fluorescens, and Achromobacter spp., were evaluated for growth suppression of F. moniliforme. Among the bioagents, Achromobacter spp. and B. subtilis (BS21) showed 73.54% and 71.61% growth suppression, respectively. The investigation revealed that the application of Achromobacter spp. and B. subtilis (BS21) would be a potential candidate for effective and eco-friendly management of the bakanae disease of rice. Full article

(1) Background: Given the widespread use of Alkalihalobacillus clausii (A. clausii) as a probiotic in recent decades and the detection of bacteremia cases in a group of patients, we sought to analyze cases of A. clausii bacteremia following oral probiotic use (2) Methods: A retrospective observational study was conducted at a private hospital in San Jose, Costa Rica. Cases of bacteremia caused by A. clausii confirmed by the microbiology laboratory were analyzed in patients who received oral treatment with this probiotic between January 2020 and January 2022. In addition, an isolate (HCB-AC2) was compared through whole genome sequencing to demonstrate the correlation of bacteremia and A. clausii. Possible vulnerability factors related to the development of this condition were determined. (3) Results: Four cases were identified in this hospital over 2 years. Genomic analysis of isolate HCB-AC2, using two different methods, showed identical results. This indicates that HCB-AC2 is genomically identical to ENTpro and the Enterogermina^® reference genome. The median age was 71 years, and all patients had some degree of immunosuppression. All patients met at least three sepsis criteria at the time of bacterial identification. Most patients were treated with vancomycin and levofloxacin. Three of the identified patients died. (4) Conclusion: A. clausii can be used as a probiotic, but caution is advised when used in immunosuppressed and elderly patients. These findings align with those reported in similar case studies. Full article

The presence of nontuberculous mycobacteria in biofilms on the surface of medical devices may affect the opportunistic pathogens that are common inhabitants of such biofilms. This study assessed the effect of Mycolicibacterium iranicum cell-free supernatants on biofilm formation and antibiotic susceptibility of Escherichia coli and Staphylococcus epidermidis differing in the anti-hemoglobin activity level. The cell-free supernatants have been shown to stimulate biofilm formation and also help reduce susceptibility of opportunistic pathogens to a number of antibiotics. Full article