Bacteria, Volume 4, Issue 1 (March 2025) – 12 articles

In the recent past, microbiome manipulation has emerged as a promising approach to improve plant growth performance by exploring the deep insight of plant–microbe interactions. The exploration of a plant microbiome either present on an ectosphere or endosphere can provide a far better understanding about the potential application of plant-associated microbes for the improvement of plant growth, protection from pathogen invasion, and tolerance to environmental stresses of a diverse nature. In this context, next-generation sequencing methods, omics approaches, and synthetic biology have made significant progress in plant microbiome research and are being frequently used to explore the intriguing role of plant-associated microorganisms. Despite the successfulness of conventional approaches, the incorporation of CRISPR/Cas9, RNA interference technology, rhizosphere engineering, microbiome engineering, and other manipulation techniques appear to be a promising approach to enhancing plant performance, and tolerance against biotic and abiotic stress factors. The present review presents the significance of plant microbe interaction, vital functional aspects, collaborative action, potential constraints, and finally the latest developments in bioengineering approaches destined for microbiome modulation with an objective to improve the performance of a host plant challenged with environmental stressors. Full article

The microbiome plays a crucial role in cancer development, influencing fundamental processes such as cell proliferation, apoptosis, immune system regulation, and host metabolism. Recent studies have highlighted a possible relationship between esophageal cancer and the oral microbiota, making oral microflora a possible risk factor. The bacteria Prevotella intermedia, Tannerella forsythia, Streptococcus sanguinis, and Streptococcus mutans, implicated in various oral pathologies, were of interest in this study, which was initiated to examine their potential role in the etiology of esophageal squamous cell carcinoma (ESCC). To achieve this, a case-control design was used, with whole saliva samples collected from 24 healthy controls and 24 patients with esophageal squamous cell carcinoma. DNA was then extracted, and real-time PCR was performed to quantify the presence of the targeted bacteria in both groups. The results showed that all the bacteria studied were present in the saliva of both patients with ESCC and healthy controls. However, expression levels were significantly higher in patients with ESCC. Specifically, a marked increase in the presence of P. intermedia, T. forsythia, S. sanguinis, and S. mutans was observed in the patients with cancer compared to the healthy controls. In short, this study highlights a significant imbalance in the microbial flora, with an increased abundance of selected bacteria in patients with ESCC. The monitoring of these bacteria could thus be exploited to track patients who are at risk. Their integration into diagnostic and therapeutic strategies would offer new prospects for the early diagnosis and improved prognosis of patients at risk of ESCC. Full article

This study explores the prevalence and antibiotic resistance of urinary tract infections (UTIs) in pregnant women in central Portugal. A retrospective observational study was conducted on 201 positive urine cultures from pregnant women at a hospital center between January 2018 and December 2022. The data collected included age, hospital admission source, history of antibiotic therapy, catheterization status, identity of bacterial isolates, and their antibiotic profile. The most common bacterial strains were Escherichia coli (52.4%) and Streptococcus agalactiae (16.9%). In terms of antibiotic resistance, Escherichia coli demonstrated complete sensitivity to ertapenem, while Streptococcus agalactiae showed sensitivity to four antibiotics, including trimethoprim/sulfamethoxazole. Notably, most infections occurred in the third trimester, underscoring the need for continuous monitoring throughout pregnancy. This study emphasizes the importance of tailored treatment strategies to manage UTIs in pregnancy effectively, reducing the potential maternal and fetal complications. These findings contribute to regional data on UTI management in pregnant populations and aim to support improved healthcare practices. These regional data provide a solid foundation for optimizing healthcare practices in pregnant women, suggesting targeted approaches to combat antibiotic resistance and improve maternal–fetal safety during UTI treatment. Full article

Background: Purple urine discoloration, known as purple urine bag syndrome (PUBS), has various etiologies ranging from benign to serious conditions. We present a case of cefiderocol-induced PUBS and review the literature. Methods: A 56-year-old bedridden patient developed purplish urine discoloration three days after initiating cefiderocol treatment for severe sepsis caused by carbapenem-resistant Acinetobacter baumannii/nosocomialis isolated from an infected sacral pressure ulcer. A comprehensive literature review of PubMed and Google Scholar was performed, with articles screened by two independent reviewers. Results: Our patient’s urine color cleared one day after cefiderocol discontinuation. Eight additional cases of cefiderocol-induced PUBS were identified in the literature. In all reported cases, urine discoloration resolved spontaneously within 1 to 3 days of cefiderocol cessation. Conclusions: Cefiderocol-induced PUBS is being increasingly recognized. While generally benign and self-limiting, it is crucial to exclude other potentially life-threatening diagnoses before attributing PUBS to cefiderocol. Full article

Members of the Dolichocephalovirinae subfamily are giant viruses with an elongated head and a flexible tail that is used to infect Caulobacter strains. In this paper, we describe the isolation and characterization of nine newly isolated phages and present evidence that seven of these phages represent a new Dolichocephalovirinae genus that has significant differences from the four previously described Dolichocephalovirinae genera. In addition, since these new phages were isolated from a single sampling site over the course of three years, a comparison of their genome sequences reveals a low level of within-population diversity resulting from both single-nucleotide polymorphisms and insertions or deletions. A comparison of the host ranges of these phages suggests that differences in host susceptibility may be an important factor in maintaining this diversity. Full article

Background: Aeromonas hydrophila is a key pathogen affecting freshwater fish, including Labeo rohita (rohu), causing significant aquaculture losses. This study explores the role of intimin and invasin, known virulence factors, in A. hydrophila pathogenesis using in silico methods. Methods: We analyzed the distribution of invasin and intimin across 53 A. hydrophila genomes and examined their physicochemical properties, secondary structures, and 3D models. Since crystal structures were unavailable, homology-based modeling was employed to study the structure of rohu β-integrins. In silico docking was performed to explore the interactions between intimin/invasin and β-integrins. Results: Our findings revealed that intimin and invasin were present in only 6 out of the 53 A. hydrophila strains examined, which were designated as hypervirulent strains. The transmembrane regions of intimin and invasin were modeled as β-barrels, a common feature of porins. The in silico docking experiments indicated the significant binding affinity of invasin and intimin with all the β-integrins of rohu fish, suggesting a critical role in host attachment and cellular internalization. Conclusions: This in silico study highlights the pivotal role of invasin and intimin in host tissue’s binding efficacy, offering valuable insights into the binding potential of A. hydrophila across various organs in rohu fish. Full article

Biofilms, formed by microbial communities that increase resistance to antibiotics, are responsible for chronic infections, making their combat a therapeutic priority. Taking this into account, the fruit Caryocar coriaceum stands out for its potential in the treatment of infectious diseases. The different parts of this plant can be used, and the fixed oil extracted from its fruit, rich in fatty acids, is indicated as responsible for its biological activities. Thus, the objective of this study was to evaluate the chemical composition of the fixed oil extracted from the fruits of C. coriaceum (FOCC), in addition to analyzing its action in the inhibition and pre-formed biofilm disruption of bacteria. The fixed oil was extracted from the internal mesocarp through exhaustive extraction with n-hexane, resulting in a yield of 38.29%. For antibiofilm evaluation, multidrug-resistant bacterial strains were exposed to the oil, and the antibiofilm activity was verified through biofilm formation and pre-formed biofilm disruption assays. The chemical analysis of the fixed oil of C. coriaceum (FOCC) identified eight fatty acids, representing 98.2% of the total composition, with a predominance of oleic acid (60.1%) and palmitic acid (33.5%). FOCC demonstrated approximately 70% inhibition of Streptococcus mutans biofilm formation at a concentration of 10 mg/mL and approximately 60% inhibition against Staphylococcus aureus and Pseudomonas aeruginosa. In pre-formed biofilm disruption, FOCC showed low efficacy against S. mutans and P. aeruginosa but showed greater activity against Enterococcus faecalis and S. aureus. These results indicate that FOCC has the potential to prevent biofilms, but its pre-formed biofilm disruption capacity is still limited. Full article

Phosphorus is a macronutrient crucially important for plant growth and development; its limited amount in soil and water poses bewildering concerns amongst agronomists. Externally applied phosphorus fertilizers can fulfil crops’ phosphorus needs throughout essential growth stages; however, the overapplication of phosphorus fertilizers leads to diminished phosphorus acquisition efficiency (PAE), disrupts the delicate balance of nutrients in soil and water, leads to deficiencies in other essential elements, poses significant environmental risks, and accelerates the loss of phosphorus mineral supplies. Moreover, much of the applied phosphorus may become fixed as insoluble phosphates by combining with calcium, iron, aluminum, manganese, etc., present in soil, making it unavailable for the plants. Phosphate solubilizing bacteria (PSB) can render insoluble phosphate accessible to plants by solubilization and mineralization, hence enhancing crop yields while ensuring environmental sustainability. Earthworms are vital soil invertebrates that interact continuously with soil and soil microorganisms and play an essential role in maintaining soil fertility. The present study aims to screen and identify potential phosphate solubilizing bacteria from the intestinal tract of the earthworm Aporrectodea rosea. The experimental results indicate that the strain PSEG-1 was effective in phosphate solubilization, with a solubilization index of 1.6 in Pikovskaya (PVK)’s medium. The strain produced organic acid in the National Botanical Research Institute (NBRIP)’s medium. Phenotypic and genotypic studies of the isolate showed that the strain PSEG-1 belongs to Klebsiella variicola. Our results suggest that the vermi-bacterial strain Klebsiella variicola PSEG-1 possesses intrinsic abilities to solubilize phosphate, which could be exploited for formulating potential microbial biofertilizers to enhance crop production. Full article

This study aimed at systematically exploring the seasonalities of bacterial identifications from 1 February 2014 to 31 January 2020 in hospitalized patients, considering the infectious site and the community-acquired or hospital-associated origin. Bacterial identifications were extracted from the data warehouse of the Institut Hospitalo-Universitaire Mediterranée Infection surveillance system, along with their epidemiological characteristics. Each species’ series was processed using a scientific workflow based on the TBATS time series model. Possible co-seasonalities were researched using seasonal peak clustering and series cross-correlations. In this study, only the 15 most frequent species were described in detail. The three most frequent species were Escherichia coli, Staphylococcus aureus, and Staphylococcus epidermidis, with median weekly incidences of 145, 74, and 39 cases, respectively. Samplings of S. aureus and E. coli follow the same seasonal dynamics. S. aureus hospital-associated infections exhibited a significant association with temperature, humidity, and pressure change, whereas community-acquired infections were only associated with precipitations. More seasonal peaks were observed during the winter season. Among the 15 peaks of this seasonal maximum, 6.7% came from blood (Klebsiellia oxytoca) and 13.3% from respiratory specimens (E. coli and S aureus). Our results showed significant associations of periodicity between pathogens, origin of infection, type of sampling, and weather drivers. Full article

This research is focused on assessing the antibacterial properties of Pogostemon benghalensis stem bark and inflorescence extracts, as well as their inhibitory effects on xanthine oxidase, antioxidant potential, overall phenolic content, and flavonoid concentration. The cold maceration technique was used to obtain extracts using water, methanol, and ethyl acetate solvents. The disk diffusion method demonstrated the significant antibacterial efficacy of the methanol stem bark extract against Staphylococcus epidermidis, with a zone of inhibition (ZOI) of 13 mm, and the inflorescence methanol extract against Klebsiella pneumonia (ZOI: 12.9 mm). Moreover, the methanol stem bark extract exhibited the minimum bactericidal concentration (MBC) at 1.56 mg/mL and the minimum inhibitory concentration (MIC) at 0.78 mg/mL against S. epidermidis. The ethyl acetate inflorescence extract displayed noteworthy xanthine oxidase inhibition (IC₅₀: 29.1 µg/mL) comparable to allopurinol (IC₅₀: 12.7 µg/mL). Furthermore, the methanol stem bark extract exhibited a remarkable DPPH free radical inhibitory effect, showing an IC₅₀ value of 42.5 µg/mL. The total polyphenol content ranged from 29.9 μg to 161.3 µg GAE per mg of dried extract weight in the methanol inflorescence extract, while the total flavonoid content ranged from 38.4 μg to 96.8 μg QE per mg of dried extract weight within the water-derived extract. Overall, these findings demonstrate the potent antibacterial properties, xanthine oxidase inhibition, and antioxidant activity of P. benghalensis extracts. Full article

To safeguard against microbial diseases and maintain optimal silk yields, the sericulture industry relies on antibiotics to promote the health, well-being, and vitality of silkworms (Bombyx mori). Antibiotics are commonly incorporated into synthetic diets for rearing silkworms or included as key components in bed disinfectant formulations. The silkworm-rearing industry’s reliance on antibiotics has led to concerns about the development of antibiotic-resistant bacteria. Previous research has uncovered a dual role for antibiotics: not only do they prevent disease, but they also promote silkworm growth by reshaping the gut microbiome and enhancing nutrient absorption, highlighting the need for judicious use. Therefore, there is a critical need for prudent management and further exploration of alternative growth-promoting strategies to minimize resistance risks. This study investigates the relationship between antibiotic administration and silkworm growth, shedding light on the mechanisms underlying antibiotic-induced effects and assessing the risk of antimicrobial resistance (AMR) emergence and dissemination. Full article

The cat oral microbiome plays an important role in maintaining host health, yet little is known about how to apply microbial data in a clinical setting. One such use of microbiome signatures is in cases of feline chronic gingivostomatitis (FCGS), a severe debilitating complex disease of the oral cavity. FCGS-afflicted cats have limited treatment options, and individual patient responses to treatment are needed. In this work, we used deep sequencing of total RNA of the oral microbiome to chronicle microbial changes that accompanied an FCGS-afflicted cat’s change from treatment-non-responsive to treatment-responsive within a 17-month span. The oral microbiome composition of the two treatment-non-responsive time points differed from that of the treatment-responsive point, with notable shifts in the abundance of Myscoplasmopsis, Aspergillus, and Capnocytophaga species. Intriguingly, the presence of the fungal groups Aspergillus and Candida primarily differentiated the two non-responsive microbiomes. Associated with responder status were multiple Capnocytophaga species, including Capnocytophaga sp. H2931, Capnocytophaga gingivalis, and Capnocytophaga canimorsus. The observation that the oral microbiome shifts in tandem by response to treatment in FCGS suggests a potential use for microbiome evaluations in a clinical setting. This work contributes to developing improved molecular diagnostics for enhanced efficacy of individualized treatment plans to improve oral disease. Full article