Search Results (40)

Sant’Agostino green table olives, traditionally processed in Apulia and flavoured with Foeniculum vulgare, represent a niche product whose microbial ecology remains largely unexplored. This study aimed to characterise the microbiota of the final product (both brine and fruit) after six months of storage with wild fennel. Four production batches were analysed using a combined culture-dependent and culture-independent approach. Microbiological counts revealed variable levels of aerobic mesophilic microorganisms, yeasts, lactic acid bacteria (LAB), and staphylococci, with yeasts and LAB being predominant. Ten LAB strains were identified, including Enterococcus faecium, Leuconostoc mesenteroides subsp. jonggajibkimchii, Leuconostoc mesenteroides subsp. cremoris, Leuconostoc pseudomesenteroides, Lactiplantibacillus plantarum, and Lactiplantibacillus pentosus. Yeast isolates belonged to Candida tropicalis, Torulaspora delbrueckii, and Saccharomyces cerevisiae. Amplicon sequencing (MiSeq Illumina) revealed distinct bacterial profiles between fruit and brine samples, with taxa from Actinobacteria, Bacteroidetes, Enterococcus, Lactobacillus, Leuconostoc, Alphaproteobacteria, Enterobacteriaceae, and other Gammaproteobacteria. Enterococcus and Leuconostoc were consistently detected, while Lactobacillus sensu lato appeared only in one fruit and one brine sample. These findings provide new insights into the microbial diversity of Sant’Agostino olives and contribute to the understanding of their fermentation ecology and potential for quality and safety enhancement. Full article

Soil contamination in industrial areas often involves complex mixtures of contaminants, making remediation a significant challenge. Microbe-assisted phytoremediation offers a promising solution, yet its success depends on understanding interaction between plants, microorganisms, and contaminants in rhizosphere. This study examined the effects of organic (oil sludge) and inorganic (Zn) contaminants, applied individually and in combination, on the rhizosphere bacterial community of Miscanthus × giganteus Greef et Deu (M×g), with emphasis on strains exhibiting plant growth-promoting, hydrocarbon-degrading, and metal-tolerant traits. A one-season greenhouse experiment included soils spiked with Zn (1650 mg kg⁻¹) and/or oil sludge (15 mL kg⁻¹). Oil sludge exerted a stronger influence on the taxonomic structure of rhizobacterial communities than Zn, largely shaping the patterns observed under co-contamination. Zn exposure increased the relative abundance of Actinobacteriota, whereas oil sludge favoured Proteobacteriota. Both contaminants, individually and together, enhanced the proportion of Sphingomonadaceae. Across all treatments, taxa with potential plant-growth-promoting traits were present, while co-contaminated soil harboured microorganisms capable of hydrocarbon degradation, heavy metal tolerance, and plant growth promotion. These findings highlight the adaptive capacity of the M×g rhizobiome and support its application in phytoremediation. The isolation and characterisation of rhizosphere-associated strains provide basis for developing microbial bioagents to enhance biomass production and remediation efficiency in multi-contaminated environments. Full article

Microbial enzymes, due to their efficiency, specificity, and sustainability, are central to innovative biotechnological strategies aimed at optimizing industrial processes such as winemaking. In this study, the potential of Aureobasidium pullulans m11-2, a native dimorphic fungus from the wine ecosystem, was evaluated as a source of hydrolytic enzymes capable of degrading grape cell wall polysaccharides. The strain was identified at the molecular level and characterised in terms of its morphology. To maximise enzyme production, various culture media were tested. Among the concentrations tested, the optimal levels of glucose and pectin were 1 g L⁻¹ and 10 g L⁻¹, respectively. The partially constitutive and inducible nature of the various polysaccharidase activities (pectinases, cellulases, and xylanases) was confirmed. The effect of grape skins (a winemaking by-product) on microbial growth and enzyme synthesis was evaluated, achieving a pectinase activity of 0.622 U mL⁻¹ when combined with 1 g L⁻¹ of glucose. Maximum enzyme yields were detected during the exponential growth phase in both citrus pectin and grape skin media, suggesting favorable conditions for continuous bioprocessing. These results confirm that A. pullulans m11-2 is an interesting microbial option for producing polysaccharidases that can be adapted to sustainable production systems. Full article

The precipitation of minerals, in particular carbonates, is a widespread phenomenon in all ecosystems, where it assumes a high relevance both from a geological and biogeochemical standpoint. Most carbonate rocks are of biological origin and made in an aquatic environment. In particular, bioprecipitation of carbonates is believed to have started in the Mesoproterozoic Era, thanks to a process often driven by photosynthetic microorganisms. Nevertheless, an important contribution to carbonate precipitation is also due to the metabolic activity of heterotrophic bacteria, which is not restricted to specific taxonomic groups or to specific environments, making this process a ubiquitous phenomenon. In this framework, the relationship between carbonatogenic microorganisms and other living organisms assumes a particular interest. This study aims to isolate and identify the culturable heterotrophic bacterial component associated with the coenosarc of Corallium rubrum in order to evaluate the occurrence of strains able to precipitate carbonates. In particular, the study was focused on the identification and characterisation of bacterial strains isolated from a coral coenosarc showing a high carbonatogenic capacity under laboratory conditions. Samples of C. rubrum were taken in the coastal waters of three Italian regions. The concentration of the aerobic heterotrophic microflora colonising C. rubrum coenosarc samples spanned from 3 to 6∙10⁶ CFU/cm². This variation in microbial populations colonising the C. rubrum coenosarc, spanning over 6 orders of magnitude, is not mirrored by a corresponding variability in the colony morphotypes recorded, with the mean being 5.1 (±2.1 sd). Among these bacteria, the carbonatogenic predominant species was Staphylococcus equorum (93% of the isolates), whereas Staphylococcus xylosus and Shewanella sp. accounted only for 3% of isolates each. All these strains showed a remarkable capacity of precipitating calcium carbonate, in the form of calcite crystals organised radially as well crystalised spherulites (S. equorum) or coalescing spherulites (Shewanella sp.). S. xylosus only produced amorphous precipitates of calcium carbonate. All bacterial strains identified were positive both for the production of urease and carbon anhydrase in vitro at 30 °C. It seems that they potentially possess the major biochemical abilities conducive to Ca²⁺ precipitation, as they showed in vitro. In addition, all our carbonatogenic isolates were able to hydrolyse the phytic acid calcium salt and then were potentially able to induce precipitation of calcium phosphates also through such a mechanism. Full article

Ischaemic stroke is the most prevalent stroke subtype, accounting for 80–90% of all cases worldwide, and remains a leading cause of morbidity and mortality. Its pathophysiology involves complex molecular cascades, with oxidative stress playing a central role. During cerebral ischaemia, reduced blood flow deprives neurons of essential oxygen and nutrients, triggering excitotoxicity, mitochondrial dysfunction, and excessive production of reactive oxygen and nitrogen species (RONS). Not only do these species damage cellular components, but they also activate inflammatory pathways, particularly those mediated by the transcription factor nuclear factor kappa-B (NF-κB). The pro-inflammatory milieu intensifies neuronal damage, compromises blood–brain barrier integrity, and exacerbates reperfusion-induced damage. Recent findings highlight the importance of the gut microbiota in modulating stroke outcomes, primarily through metabolic and immunological interactions along the gut–brain axis. Dysbiosis, characterised by reduced microbial diversity and an imbalance between beneficial and harmful strains, has been linked to increased systemic inflammation, oxidative stress, and worse prognoses. Specific gut-derived metabolites, including short-chain fatty acids (SCFAs) and trimethylamine N-oxide (TMAO), appear to either mitigate or intensify neuronal injury. SCFAs may strengthen the blood–brain barrier and temper inflammatory responses, whereas elevated TMAO levels may increase thrombotic risk. This narrative review consolidates both experimental and clinical data demonstrating the central role of oxidative stress in ischaemic stroke pathophysiology and explores the gut microbiota’s ability to modulate these damaging processes. Therapeutic strategies targeting oxidative pathways or rebalancing gut microbial composition, such as antioxidant supplementation, dietary modulation, probiotics, and faecal microbiota transplantation, present promising paradigms for stroke intervention. However, their widespread clinical implementation is hindered by a lack of large-scale, randomised trials. Future efforts should employ a multidisciplinary approach to elucidate the intricate mechanisms linking oxidative stress and gut dysbiosis to ischaemic stroke, thereby paving the way for novel, mechanism-based therapies for improved patient outcomes. Full article

This research aimed to characterise hydrocarbonoclastic bacteria isolated from naturally hydrocarbon-contaminated springs and the surrounding soils in the Agri Valley (Southern Italy) and to assess the effectiveness of bioaugmentation using a four-strain microbial consortium for removing hydrocarbons from artificially diesel-contaminated lake waters in mesocosm experiments. Four novel bacterial strains were selected for the experimentation: Gordonia amicalis S2S5, Rhodococcus erythropolis S2W2, Acinetobacter tibetensis S2S8, and Acinetobacter puyangensis S1W1. The four isolates can use diesel oil as their sole carbon source, and some exhibited a relatively high emulsifying capacity and ability to adhere to hydrocarbons. Furthermore, genome analyses revealed the presence of genes associated with the degradation, detoxification, and transport of various contaminants. Mesocosm experiments demonstrated that the bioaugmentation enhanced the capacities of the native lake microbial communities to remove hydrocarbons, although drastic changes in their composition (analysed through Next-Generation Sequencing—NGS) were observed. Taken together, these results suggest that naturally contaminated environments can serve as a valuable reservoir of microorganisms with significant biotechnological potential, particularly in the field of bioremediation. However, a complete understanding of the ability of the isolated bacterial strains to efficiently degrade contaminants requires further research to fully assess their capabilities and limitations across different settings. Full article

Beneficial bacteria are recognised for their antimicrobial compounds, making them valuable for disease control in agriculture. Bacillus species stand out for their stability, versatility, and selectivity as biocontrol agents. This study aimed to identify potential antagonists within the rhizosphere microorganisms by isolating bacterial strains from grapevine roots and rhizosphere soil in Moroccan vineyards. The antimicrobial activities of these isolates against Allorhizobium vitis, the causative agent of grapevine crown gall, were evaluated in vitro using a disc diffusion assay, followed by in planta assessments under preventive and simulated inoculation conditions. Screening led to the isolation of 123 strains, with six showing strong antagonistic properties, achieving inhibition percentages up to 39.6%. 16S rRNA sequencing led to identifying five Bacillus species: B. amyloliquefaciens, B. velezensis, B. halotolerans, B. subtilis, and B. anthracis. These strains were further characterised by their biochemical traits and plant growth-promoting abilities. Compatibility assays identified optimal combinations for microbial consortia, demonstrating pathogen inhibition up to 37.4%. In planta bioassays confirmed the effectiveness of the isolates and consortia, reducing tumour size. These findings highlight the potential of these Bacillus strains as biocontrol agents and underscore the value of microbial consortia as a sustainable approach to managing grapevine crown gall. Full article

Phosphonates such as ethylenediaminetetra (methylenephosphonic acid) (EDTMP) and aminotris (methylenephosphonic acid) (ATMP) are used every day in water treatment processes or in household products. Their consumption is still increasing, regardless of the debates on their environmental impact. Here, the microbial characterisation and determination of the biodegradation potential of selected industrially relevant phosphonates for the isolate Delftia sp. UMB14 is reported. The opportunistic strain was isolated from a biofilm that was derived from a conventional washing machine using conventional detergents containing phosphonates. In antimicrobial susceptibility testing, the strain was only susceptible to sulfonamide, tetracycline, and chloramphenicol. Physiological and biochemical characteristics were determined using the BIOLOG EcoPlate assay. Most importantly, the strain was shown to convert D-malic acid and D-mannitol, as confirmed for strains of Delftia lacustris, and thus the new isolate could be closely related. Biodegradation tests with different phosphonates showed that the strain preferentially degrades ATMP and EDTMP but does not degrade glyphosate (GS) and amino (methylphosphonic acid) (AMPA). A specific gene amplification confirmed the presence of phnX (phosphonoacetaldehyde hydrolase) and the absence of PhnJ (the gene for the core component of C–P lyase). The presence of PhnCDE is strongly suggested for the strain, as it is common in Delftia lacustris species. Full article

In response to the steady increase in antimicrobial-resistant strains, the World Health Organisation has emphasised the need to investigate new antimicrobial agents and alternative therapies that improve the spectrum of activity and reduce the dose required, thus improving safety. This study focused on the characterisation of Acanthospermum australe essential oil and green-synthesis silver nanoparticles (AgNP), evaluating their cytotoxicity in human cells, antimicrobial activity and synergistic effect against pathogens causing skin infections. The main components of the essential oil were germacrene A (24.07%), γ-cadinene (21.47%) and trans-caryophyllene (14.97%). Spherical AgNP with a diameter of 15 ± 3 nm were synthesised. The essential oil showed antimicrobial activity against dermatophytes and Malassezia globosa, while AgNP were found to be active against bacteria, yeasts and dermatophytes. Both compounds were found to be primarily non-cytotoxic at the concentrations required to inhibit microbial growth. Furthermore, the combined use of essential oil and AgNP showed a synergistic antimicrobial effect against dermatophytes and M. globosa. In conclusion, the results suggest that the combined use of bioactive compounds from natural sources, such as essential oil and biogenic AgNP, has the potential to improve antimicrobial efficacy against specific skin pathogens, particularly Microsporum canis, Nannizzia gypsea and M. globosa. Full article

Complex gut microbiota increases chickens’ resistance to enteric pathogens. However, the principles of this phenomenon are not understood in detail. One of the possibilities for how to decipher the role of gut microbiota in chickens’ resistance to enteric pathogens is to systematically characterise the gene expression of individual gut microbiota members colonising the chicken caecum. To reach this aim, newly hatched chicks were inoculated with bacterial species whose whole genomic sequence was known. Total protein purified from the chicken caecum was analysed by mass spectrometry, and the obtained spectra were searched against strain-specific protein databases generated from known genomic sequences. Campylobacter jejuni, Phascolarctobacterium sp. and Sutterella massiliensis did not utilise carbohydrates when colonising the chicken caecum. On the other hand, Bacteroides, Mediterranea, Marseilla, Megamonas, Megasphaera, Bifidobacterium, Blautia, Escherichia coli and Succinatimonas fermented carbohydrates. C. jejuni was the only motile bacterium, and Bacteroides mediterraneensis expressed the type VI secretion system. Classification of in vivo expression is key for understanding the role of individual species in complex microbial populations colonising the intestinal tract. Knowledge of the expression of motility, the type VI secretion system, and preference for carbohydrate or amino acid fermentation is important for the selection of bacteria for defined competitive exclusion products. Full article

Petroleum hydrocarbon pollution (PHP) poses a significant environmental threat and affects both marine and terrestrial ecosystems. This study focused on the isolation and screening of indigenous petroleum-degrading microorganisms from Mile 2 Lagoon, Lagos, Nigeria. This study aimed to investigate the biodegradability of crude oil and analyse the petroleum–hydrocarbon degradation characteristics of microbial consortia on a laboratory scale. Physicochemical analysis of the lagoon water revealed a neutral pH and high nitrate and phosphate concentrations, indicating minimal prior oil pollution. A continuous enrichment method was employed to cultivate microorganisms, using Ecravos light crude oil as the sole carbon and energy source. The enumeration of total heterotrophic microorganisms and hydrocarbon-utilising microorganisms, along with microbial characterisation, was conducted. This study identified three hydrocarbon-utilising bacteria (THUB-1-3) and two fungal strains (THUF-1-2) and demonstrated their ability to degrade crude oil. The growth profile of these isolates showed exponential growth, with the bacterial consortium achieving a maximum concentration of 9.9 × 10⁶ cfu/ml on day 28. Petroleum degradation kinetics showed that the microbial consortium degraded 93% of the crude oil over 42 days, with variations observed in different hydrocarbon fractions. This study provides valuable insights into the potential of indigenous microbial strains to mitigate the ecological impact of oil spills on aquatic environments. Full article

Tanning, crucial for leather production, relies heavily on chromium yet poses risks due to chromium’s oxidative conversion, leading to significant wastewater and solid waste generation. Physico-chemical methods are typically used for heavy metal removal, but they have drawbacks, prompting interest in eco-friendly biological remediation techniques like biosorption, bioaccumulation, and biotransformation. The EU Directive (2018/850) mandates alternatives to landfilling or incineration for industrial textile waste management, highlighting the importance of environmentally conscious practices for leather products’ end-of-life management, with composting being the most researched and viable option. This study aimed to isolate microorganisms from tannery wastewater and identify those responsible for different types of tanned leather biodegradation. Bacterial shifts during leather biodegradation were observed using a leather biodegradation assay (ISO 20136) with tannery and municipal wastewater as the inoculum. Over 10,000 bacterial species were identified in all analysed samples, with 7 bacterial strains isolated from tannery wastewaters. Identification of bacterial genera like Acinetobacter, Brevundimonas, and Mycolicibacterium provides insights into potential microbial candidates for enhancing leather biodegradability, wastewater treatment, and heavy metal bioremediation in industrial applications. Full article

Gut microbes thrive by utilising host energy and, in return, provide valuable benefits, akin to a symbiotic relationship. Here, metagenomic sequencing was performed to characterise and compare the community composition, diversity and antibiotic resistance of the gut microbiota of Relict gull (Larus relictus) and Anatidae species. Alpha diversity analysis revealed that the intestinal microbial richness of L. relictus was significantly lower than that of Anatidae, with distinct differences observed in microbial composition. Notably, the intestines of L. relictus harboured more pathogenic bacteria such as clostridium, which may contribute to the decline in their population and endangered status. A total of 117 strains of Escherichia coli were isolated, with 90.60% exhibiting full susceptibility to 21 antibiotics, while 25.3% exhibited significant biofilm formation. Comprehensive Antibiotic Resistance Database data indicated that glycopeptide resistance genes were the most prevalent type carried by migratory birds, alongside quinolone, tetracycline and lincosamide resistance genes. The abundance of resistance genes carried by migratory birds decreased over time. This metagenomic analysis provides valuable insights into the intestinal microbial composition of these wild bird species, offering important guidance for their conservation efforts, particularly for L. relictus, and contributing to our understanding of pathogen spread and antibiotic-resistant bacteria. Full article

Representatives of the genus Bifidobacterium are widely used as probiotics to modulate the gut microbiome and alleviate various health conditions. The action mechanisms of probiotics rely on their direct effect on the gut microbiota and the local and systemic effect of its metabolites. The main purpose of this animal experiment was to assess the biosafety of the Bifidobacterium longum strain BIOCC1719. Additional aims were to characterise the influence of the strain on the intestinal microbiota and the effect on several health parameters of the host during 15- and 30-day oral administration of the strain to mice. The strain altered the gut microbial community, thereby altering luminal short-chain fatty acid metabolism, resulting in a shift in the proportions of acetic, butyric, and propionic acids in the faeces and serum of the test group mice. Targeted metabolic profiling of serum revealed the possible ability of the strain to positively affect the hosts’ amino acids and bile acids metabolism, as the cholic acid, deoxycholic acid, aspartate, and glutamate concentration were significantly higher in the test group. The tendency to increase anti-inflammatory polyamines (spermidine, putrescine) and neuroprotective 3-indolepropionic acid metabolism and to lower uremic toxins (P-cresol-SO₄, indoxyl-SO₄) was registered. Thus, B. longum BIOCC1719 may exert health-promoting effects on the host through modulation of the gut microbiome and the host metabolome via inducing the production of health-promoting bioactive compounds. The health effects of the strain need to be confirmed in clinical trials with human volunteers. Full article

Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease. Full article