BMC Microbiology最新文献

Background: Enterohemorrhagic Escherichia coli (EHEC) O157 is implicated in serious food and water-borne diseases as hemorrhagic colitis (HC), and the potentially fatal hemolytic uremic syndrome (HUS). However, new players of non-O157 EHEC have been implicated in serious infections worldwide. This work aims at analyzing serotype and genotypic-based virulence profile of EHEC local isolates.

Methods: A total of 335 samples were collected from different sources in Egypt. E. coli was isolated and subjected to serotyping. Non-O157 EHEC isolates were tested for virulence genes using PCR, phenotypic examination, phylogenetic typing, and molecular investigation by ERIC typing and MLST to disclose genetic relatedness of isolates. A heat map was used to identify potential associations between the origin of the isolates, their phenotypic and genotypic characteristics.

Results: A total of 105 out of 335 isolates were identified as E. coli. Surprisingly, 49.5% of these isolates were EHEC, where O111, O91, O26 and O55 were the most prevalent serotypes including 38.46% from stool, 21.15% urine, 23.1% cheese, 9.62% meat products, 3.85% from both yogurt and sewage water. Screening 15 different virulence genes revealed that sheA, stx2 and eae were the most prevalent with abundance rates of 85%, 75% and 36%, respectively. Fifteen profiles of virulence gene association were identified, where the most abundant one was stx2/sheA (19%) followed by stx2/stx2g/sheA/eae (11.5%). Both stx2/sheA/eae and stx2/stx2g/sheA were equally distributed in 9.6% of total isolates. Phylogenetic typing revealed that pathogenic phylogroups B2 and D were detected among clinical isolates only. Forty-six different patterns were detected by ERIC genotyping. MLST resolved three sequence types of ST70, ST120 and ST394. The heat map showed that 21 isolates were of 70% similarity, 9 groups were of 100% clonality.

Conclusions: The prevalence of non-O157 EHEC pathotype was marginally higher among the food isolates compared to the clinical ones. The endemic ST120 was detected in cheese, necessitating crucial measures to prevent the spread of this clone. Clinical EHEC isolates exhibited a higher score, and combination of virulence genes compared to food and sewage water isolates, thereby posing a significant public health concern.

Background: Previous studies have identified structurally diverse N-acyl amino acid methyl esters (NAMEs) in culture extracts of Roseovarius tolerans EL-164 (Roseobacteraceae). NAMEs are structural analogues of the common signaling compounds N-acyl homoserine lactones (AHLs), but do not participate in AHL-mediated signaling. NAMEs show minor antialgal and antimicrobial activity, but whether this activity serves as the primary ecological role remains unclear.

Results: To enable dose-dependent bioactivity-testing, we have established a chromatographic method for quantification of NAMEs in bacterial culture extracts. The concentrations determined for the two major NAMEs produced by EL-164, C16:1-NAME and C17:1-NAME, ranged between 0.685 and 5.731 mg L^- 1 (2.0-16.9 µM) and 5.3-86.4 µg L^- 1 (15.0-244.3 nM), respectively. Co-quantification of the C14:1-AHL showed concentrations ranging between 17.5 and 58.7 mg L^- 1 (56.6-189.7 µM). We observed distinct production patterns for NAMEs and AHLs, with a continuous NAME production during the entire incubation period. We conducted a spike-in experiment, using the determined metabolite concentrations. By comparing the transcriptomes of pre- and post-metabolite-spikes, we identified three clusters of differentially expressed genes with distinct temporal expression patterns. Expression levels of stress response genes differed between NAME- and AHL-spiked EL-164 cultures in the stationary phase.

Conclusions: Our findings support previous studies suggesting an ecological role for C16:1-NAME as antibiotic, by proving that NAME concentrations in batch cultures were higher than the minimal inhibitory concentrations against Maribacter sp. 62 - 1 (Flavobacteriia) and Skeletonema costatum CCMP 1332 (Coscinodiscophyceae) reported in the literature. Our study further exemplified the broad application range of dose-dependent testing and highlighted the different biological activities of NAMEs and AHLs.

Background: Advances in metagenome sequencing data continue to enable new methods for analyzing biological systems. When handling microbial profile data, metagenome sequencing has proven to be far more comprehensive than traditional methods such as 16s rRNA data, which rely on partial sequences. Microbial community profiling can be used to obtain key biological insights that pave the way for more accurate understanding of complex systems that are critical for advancing biomedical research and healthcare. However, such attempts have mostly used partial or incomplete data to accurately capture those associations.

Methods: This study introduces a novel computational approach for the identification of co-occurring microbial communities using the abundance and functional roles of species-level microbiome data. The proposed approach is then used to identify signature pathways associated with inflammatory bowel disease (IBD). Furthermore, we developed a computational pipeline to identify microbial species co-occurrences from metagenome data at various granularity levels.

Results: When comparing the IBD group to a control group, we show that certain co-occurring communities of species are enriched for potential pathways. We also show that the identified co-occurring microbial species operate as a community to facilitate pathway enrichment.

Conclusions: The obtained findings suggest that the proposed network model, along with the computational pipeline, provide a valuable analytical tool to analyze complex biological systems and extract pathway signatures that can be used to diagnose certain health conditions.

The lactic acid bacteria are one of the sustainable ways of food production. As the native lactic acid bacteria (LAB) easily manipulate the substrate, helps in production of health essential probiotics with enhancing the bioavailability of the substrate. Here also, in present study, the native LAB isolates isolated from the millets and characterize them for the functional analysis for the human health association. In the present study, fermented millet-associated lactic acid bacteria were screened and characterized for their probiotic potential, safety evaluation and antimicrobial activity. A total of 33 isolates were purified as lactic acid bacteria based on colony shape and biochemical assays. However, only 13 isolates were found to be catalase-negative. Among the 13 isolates, 5 isolates exhibited optimum growth at 6.5% and 9.5% of salt concentrations, pH of 4.5 to 8.5 and 17 °C to 40 °C of the temperature. The probiotic properties of the five isolates exhibited that the survival rates in acid and bile salt concentration ranged from 56.2 to 73.7% and 55.3 to 70.3%, respectively. Similarly, the surface hydrophobicity of the isolates was 41-75%. Antibiotic assay revealed that all five isolates were resistant to Amoxicillin, Cloxacillin, and Penicillin-V. Interestingly, all the isolates except ME26 displayed susceptibility towards Penicillin (2 units) and Tetracycline (10 µg). Further, the four isolates (ME25, ME26, ME9, and ME2) had more antifungal activity against Aspergillus flavus. However, only three, except ME1 and ME2, showed maximum antibacterial activity and produced more antimicrobial compounds compared to reference strain L. plantarum Pb3. The potential probiotic isolates were identified as Weisella cibaria ME9, Weisella cibaria ME26, and Weisella confusa ME25.

Background: Although antibiotics have significantly improved human and animal health, their intensive use leads to the accumulation of antimicrobial resistance (AMR) in the environment. Moreover, certain waste management practices create the ideal conditions for AMR development while providing predictable resources for wildlife. Here, we investigated the role of landfills in the potentiation of New World vultures to disseminate environmental AMR. We collected 107 samples (soil, water, and feces) between 2023 and 2024, in different bird use sites (roosts, landfills and boneyards).

Results: We isolated enterococci (EN), Escherichia coli (EC), and Salmonella spp. (SM), performed antibiotic susceptibility tests, and quantified the presence of antibiotic resistance genes (ARGs) within all samples. We identified EN, EC, and SM, in 50, 37, and 26 samples, from the three vulture use areas, respectively. AMR was mainly to aminoglycoside, cephalosporin, and tetracycline, and the prevalence of multidrug resistance (MDR) was 5.3% (EC), 78.2% (EN), and 17.6% (SM). Variations in bacterial abundance and AMR/MDR profiles were found based on the season, use site, and sample types, which was corroborated by ARG analyses.

Conclusions: Our study suggests that landfills constitute a source of zoonotic pathogens and AMR for wildlife, due to readily available refuse input. Using non-invasive molecular methods, we highlight an often-ignored ecosystem within the One Health paradigm.

In this study, we describe Pseudomegasporoporia margallensis as a novel species and report Microporellus subadustus as a new record from Pakistan based on morphology and phylogeny. Both genera are firstly reported in the country. Pseudomegasporoporia margallensis sp. nov. is characterized by light brownish gray poroid hymenphore, grayish brown subiculum surface, frequent generative hyphae in the subiculum with abundant clamp connections, and arboriform-branched skeletal hyphae in subiculum and tubes, and it forms a sister lineage of P. nerricola in the phylogeny. This novel taxon, showing 37 nucleotide differences in ITS nrDNA and 10 in LSU nrLSU sequences from P. nerricola, has GenBank accession numbers PP702233, PP702234, PP702235, PP702236, and PP70223, and is registered under MycoBank no. MB853645. This higlights the genetic distinction and importance of molecular identification in fungal taxonomy. The new species and the new record are described with detail illustrations.

Background: Premature infants are more prone to brain injuries owing to incomplete nervous system development and poor adaptation outside the mother's body. Without timely intervention, premature infants with brain injuries often develop intellectual disabilities, causing significant burdens on families and the society. Multiple studies have shown that gut dysbiosis can affect the nervous system, and vice versa. This study aimed to explore the changes in gut microbiota of typical premature infants and those with brain injuries on the third and seventh days after birth using 16 S rRNA technology.

Methods: Fecal samples from typical premature infants (non-brain injury group, n = 17) and those with brain injuries (brain injury group, n = 21) were collected on days 1, 3, and 7 after birth for 16 S rRNA sequencing. Alpha diversity analysis was used to evaluate the diversity of gut microbiome. LEfSe and DESeq2 were used to analyze of the microorganisms' characteristics and differentiate the microorganisms between the two groups.

Results: At the phylum level, Firmicutes, Proteobacteria, and Actinobacteria were the dominant flora in both groups. At the genus level, the proportion of Enterococcus in fecal samples of the brain injury group was higher than that of the non-brain injury group on day three after birth; however, the opposite was observed on day seven. Rothia and Lactobacillales were characteristic bacteria of the non-brain injury group on days three and seven after birth, whereas Enterococcus and Bifidobacteria were characteristic bacteria of the brain injury group on days three and seven after birth, respectively. Three days after birth, the Shannon and Simpson indices of the non-brain injury group were significantly higher than those of the brain injury group.

Conclusion: Premature infants with brain injuries have a unique gut microbiota that is different from that of typical premature infants, indicating correlation between brain injuries and gut microbiota.

Background: Xanthomonas vasicola pv. musacearum is responsible for the widespread Banana Xanthomonas Wilt in banana cultivation regions across the globe. Biocontrol measures for disease management remain limited amidst increasing antimicrobial resistance and unsustainable conventional agricultural practices. The purpose of this study is to explore a viable alternative or adjunct strategy through the use of bacteriophages for disease management.

Results: Kintu was isolated from sewage and displayed clear and circular plaques measuring 3 mm. Based on transmission electron microscopy, Kintu displays siphovirus characteristics, including an icosahedral head and a non-contractile tail. Kintu infects 78% (22 out of 28) Ugandan Xvm strains, has an optimal multiplicity of infection of 1, a 10 min adsorption and latent period, a 35 min burst period, and a burst size of 15 particles per bacterium. Phage titers remain stable for two and half months (75 days) in SM buffer at -20 ^oC and - 40 ^oC but decrease significantly (p ≤ 0.0001) at 4 ^oC. Kintu is active at pH 3 and 11, maintains viability at temperatures between 25 ^oC and 120 ^oC and tolerates UV irradiation for up to 2 min and 20 s. Kintu inhibits Xvm growth at MOI ratios of 0.1, 1 and 10. The genome is a double stranded DNA molecule that consists of 48,985 base pairs and a G + C content of 51.71%. Antibiotic resistance genes or genes associated with a lysogenic life cycle are absent. There is limited sequence similarity of Kintu with other phages, making it a novel phage belonging to an unclassified genus of the class Caudoviricetes.

Conclusion: Kintu is a novel bacteriophage that infects and lyses Xanthomonas vasicola pv. musacearum, the causative agent for Banana Xanthomonas Wilt. Its stability across diverse temperatures and pH conditions highlights its potential as a biocontrol agent for managing the disease.

Background: SepIVA has been reported to be an essential septation factor in Mycolicibacterium smegmatis and Mycobacterium tuberculosis. It is a coiled-coil protein with similarity to DivIVA, a protein necessary for polar growth in members of the phylum Actinomycetota. Orthologues of SepIVA are broadly distributed among actinomycetes, including in Streptomyces spp.

Results: To clarify the role of SepIVA and its potential involvement in cell division in streptomycetes, we generated sepIVA deletion mutants in Streptomyces venezuelae and found that sepIVA is dispensable for growth, cell division and sporulation. Further, mNeonGreen-SepIVA fusion protein did not localize at division septa, and we found no evidence of involvement of SepIVA in cell division. Instead, mNeonGreen-SepIVA was accumulated at the tips of growing vegetative hyphae in ways reminiscent of the apical localization of polarisome components like DivIVA. Bacterial two-hybrid system analyses revealed an interaction between SepIVA and DivIVA. The results indicate that SepIVA is associated with polar growth. However, no phenotypic effects of sepIVA deletion could be detected, and no evidence was observed of redundancy with the other DivIVA-like coiled-coil proteins Scy and FilP that are also associated with apical growth in streptomycetes.

Conclusions: We conclude that S. venezuelae SepIVA, in contrast to the situation in mycobacteria, is dispensable for growth and viability. The results suggest that it is associated with polar growth rather than septum formation.