Search Results (19)

The Protected Designation of Origin (PDO) “Oliva di Gaeta” is a type of Italian fermented table olive obtained through a spontaneous fermentative process (“Itrana” method) driven by the indigenous olives microbiota. Although the use of starter cultures may improve the fermentative process and the quality of the final product, this has been poorly investigated for PDO Gaeta olives. In this study, we evaluated the use of Lactiplantibacillus pentosus O17 as a starter culture for the production of Gaeta-like olives. Three fermentations were performed: a spontaneous process (according to PDO regulation, trial A), fermentation driven by Lpb. pentosus O17 (trial B), and O17-driven fermentation combined with different brine formulation (trial C). Physicochemical properties (i.e., pH, titratable acidity, salt, and total phenolic content) and microbial population (plate counting and metataxonomy) were monitored up to 180 days. Sensory and texture profiles were evaluated in the final product. Driven fermentations (trials B and C) led faster acidification and enhanced the microbial quality of table olives without altering the organoleptic features of Gaeta-like olives. Our study suggests that the use of a starter culture and a different brining method could improve the microbiological quality of Gaeta-like olives, while preserving the traditional identity and the sensory attributes related to this PDO product. Full article

Background/Objectives: Cold-smoked salmon (CSS) is a ready-to-eat product with minimal preservation hurdles and a microbiota shaped by raw-material contamination and processing environments. Short breaks in refrigeration commonly occur during shopping and transport, yet their microbiological impact remains unclear. Here, we used ASV-resolved 16S rRNA gene metataxonomics to characterize storage-driven microbiota dynamics in CSS—quantifying ASV-level genetic diversity and phylogeny-aware (UniFrac) community structure—and to evaluate the effect of a brief, consumer-mimicking 2 h room-temperature cold-chain disruption. Methods: Three CSS types (organic, conventional Norwegian, and conventional Scottish) were stored at 5 °C for 35 days. On day 16, half of each batch was exposed to 2 h at room temperature (RT) before analysis; paired controls remained refrigerated. Culture-based counts (total mesophiles, lactic acid bacteria, Photobacterium spp.; indicator/pathogen screens) were performed per ISO methods. Community profiling used 16S rRNA (V3–V4) amplicon sequencing with QIIME 2/DADA2 and SILVA taxonomy. Linear mixed effects modelled alpha diversity; beta diversity by PERMANOVA on UniFrac distances; differential abundance by ANCOM-BC. Results: ASV-resolved 16S rRNA gene profiles of CSS were dominated by Pseudomonadota and Bacillota, with storage-driven shifts and taxon-specific trajectories (e.g., increasing Latilactobacillus). Both time and product type significantly explained phylogeny-aware community structure (unweighted and weighted UniFrac), consistent with storage-driven phylogenetic convergence across products. At day 16, ASV-level genetic diversity (Shannon/Observed features) and genus-level composition did not differ between RT-disrupted and continuously refrigerated samples. Culture-dependent counts increased from baseline to day 16 and largely plateaued by day 35, with lactic acid bacteria in Norwegian CSS continuing to rise; no systematic effect of the 2 h RT exposure was observed in culture-based comparisons. Indicator/pathogen screens detected no unexpected pathogenic species throughout the study period. Conclusions: Refrigerated storage drives pronounced, phylogeny-aware microbiota shifts and cross-product convergence in cold-smoked salmon, whereas a single 2 h RT interruption at mid-storage did not measurably alter ASV-level genetic diversity or community structure under the tested conditions. Integrating culture-based enumeration with ASV-resolved 16S rRNA gene metataxonomics provides complementary insights for shelf-life evaluation and risk assessment in ready-to-eat seafood. Full article

Honey is a sugar-rich product produced by Apis mellifera bees, with significant variability in properties due to the influence of geographic and climatic conditions and the predominant flora in the production region. Economically, beekeeping is an activity that generates profit and fulfills environmental and social functions, reinforcing the pillars of sustainability. This study aimed to characterize samples of honey sold in southern Brazil, including physicochemical analyses, the detection of microbiological contaminants with potential impact on human health, and the detailed identification of bacterial composition through the Next-Generation Sequencing (NGS). The present study was divided into five main stages: (1) sample collection; (2) sample fractionation; (3) physicochemical analysis; (4) microbiological analysis; (5) 16S metataxonomy analysis. The physicochemical analyses agreed with the regulated values, indicating the good quality of the honey and the absence of adulteration. The microbiological analyses indicated the absence of Salmonella spp., in addition to a low count of total coliforms. The limits for molds and yeasts were exceeded in three samples, indicating non-compliance with current MERCOSUR legislation. Metabarcoding analysis identified a total of 15,736 OTUs divided into three different genera: Bacillus (41.54%), Lysinnibacillus, and Rossellomorea, all belonging to the Bacillaceae family. Some pathogenic species were identified, namely the Bacillus cereus group and Bacillus pumilus. Our results point to an increased need for surveillance, as honey contamination can lead to public health problems, requiring improvements in legislation and control parameters. Full article

Although climate warming-induced snow cover reduction, as well as the development of ski tourism in hot and dry countries, is shifting industries toward the use of technical snowmaking, its use raises hydrological, health-related, and environmental concerns. This study was aimed at enhancing our current understanding of the impact of technical snowmaking on the environment and human health. Culturable bacteriological indicators of water quality (Escherichia coli, fecal enterococci, Salmonella, and Staphylococcus), the presence and concentration of antimicrobials, genes determining bacterial antibiotic resistance (ARGs), and next-generation sequencing-based bacterial community composition and diversity were examined from river water, technological reservoirs, and technical snow from five ski resorts. The number of culturable bacteria and prevalence of most ARGs decreased during snowmaking. The concentration of antimicrobial agents changed irregularly, e.g., ofloxacin and erythromycin dropped in the snowmaking process, while cefoxitin was quantified only in technical snow. The bacterial community composition and diversity were altered through the technical snowmaking process, resulting in the survivability of freezing temperatures or the presence of antimicrobial agents. Water storage in reservoirs prior to snowmaking allows us to reduce bacterial and ARG contaminants. Frequent and thorough cleaning of snowmaking devices may aid in reducing the negative impact snowmaking can have on the environment by reducing contaminant input and limiting the disturbance of the ecological balance. Full article

Iron ore extraction can lead to significant environmental degradation, particularly due to the generation of tailings during the beneficiation process. This issue was highlighted by the B1 dam collapse in Brumadinho, Brazil, in 2019. Therefore, the study and monitoring of affected areas is essential to assess soil quality throughout the rehabilitation process, whether through natural recovery or active rehabilitation practices. Microbial indicators can serve as valuable tools to track the recovery of these areas, given their high sensitivity and rapid response to environmental changes. The aim of this study was to evaluate soil microbial indicators, such as enzyme activity, microbial biomass carbon, microbial basal respiration and microbial diversity, and to select microbial approaches for monitoring the area affected by mining tailings in Brumadinho. The results indicated that the reference area initially outperformed the affected area on all evaluated bioindicators, highlighting environmental stress in the affected zone. Over the course of the study, the two areas began to show greater similarity, suggesting a natural recovery of the soil together with the return of natural vegetation. Indicators such as microbial carbon biomass went from values close to 50 mg of C Kg of soil⁻¹ in the affected area, to around 200, statistically equal to the reference. qCO₂ also varied in the affected area to values statistically equal to those of the reference over time, variated in the first collection to 0.25 mg of C-CO₂ mg of C⁻¹ h⁻¹ in the affected area against 0.1 in the reference area; in the last collection, both areas presented values close to 0.2. Enzymatic activity had superior values in the reference area about the affected area, being urease, and arylsulfatase more sensitive to show differences between areas over time. The metataxonomic data again revealed indicator species for each environment, including genera such as Bacillus, Mycobacterium, Acidibacter, and Burkholderia representative of the reference, and the genera Ramlibacter, Sinomonas, Psedarthrobacter, and Knoellia indicators of the affected area. By the end of this study, the applicability of microbial indicators for monitoring soil microbiota and its ecosystem services was successfully demonstrated. In addition, specific microbial indicators were proposed for monitoring areas affected by iron mining tailings. Full article

Pneumonia caused by Pneumocystis jirovecii infection (PCP) is a potentially life-threatening illness, particularly affecting the immunocompromised. The past two decades have shown an increase in PCP incidence; however, the underlying factors that promote disease severity and fatality have yet to be fully elucidated. Recent evidence suggests that the microbiota of the respiratory tract may play a role in stimulating or repressing pulmonary inflammation, as well as the progression of both bacterial and viral pneumonia. Here, we employed 16S rRNA metataxonomic sequencing to profile the respiratory microbiota of patients with mild-moderate and severe PCP. Our results show that the upper and lower airways of PCP patients have bacterial profiles which have been associated with a pro-inflammatory response. Furthermore, we find that severe PCP is associated with lower bacterial diversity and an increase in Prevotella and a decrease in Neisseria. Functionally, severe PCP was associated with a decrease in metabolic pathways of molecules with anti-inflammatory and antimicrobial properties. To our knowledge, this is the first study showing an association of PCP severity with shifts in the respiratory microbiome and may provide some insight into which patients are more susceptible to the more severe manifestations of the disease. Full article

Clostridioides difficile infection (CDI) is generally treated with vancomycin, metronidazole or fidaxomicin, although fecal microbiota transplantation (FMT) represents a promising therapeutic option for antibiotic-resistant recurrent C. difficile infections (rCDIs) in adults. In pediatric cystic fibrosis (CF) patients, CDIs are generally asymptomatic and respond to treatment. Here, we present the case of an 8-year-old female, initially diagnosed as “CFTR-related metabolic syndrome/cystic fibrosis screen positive, inconclusive diagnosis” (CMRS/CFSPID), who then progressed to CF at 12 months. In the absence of CF-related symptoms, she presented multiple and disabling episodes of bloody diarrhoea with positive tests for C. difficile antigen and A/B toxin. After conventional treatments failed and several CDI relapses, FMT was proposed. Donor screening and GM donor–receiver matching identified her mother as a donor. Metataxonomy and targeted metabolomics provided, through a pre- and post-FMT time course, gut microbiota (GM) profiling to assess GM engraftment. At first, the GM map revealed severe dysbiosis, with a prevalence of Bacteroidetes and Proteobacteria (i.e., Klebsiella spp., Escherichia coli), a reduction in Firmicutes, a GM nearly entirely composed of Enterococcaceae (i.e., Enterococcus) and an almost complete depletion of Verrucomicrobia and Actinobacteria, mostly represented by Veillonella dispar. Post FMT, an increment in Bifidobacterium spp. and Collinsella spp. with a decrease in V. dispar restored intestinal eubiosis. Consistently, four weeks after FMT treatment, the child’s gut symptoms cleared, without CDI recurrence. Full article

Autism spectrum disorder (ASD) is a neurodevelopmental disorder. Investigations of gut microbiota (GM) play an important role in deciphering disease severity and symptoms. Overall, we stratified 70 ASD patients by neuropsychological assessment, based on Calibrated Severity Scores (CSSs) of the Autism Diagnostic Observation Schedule-Second edition (ADOS-2), Child Behavior Checklist (CBCL) and intelligent quotient/developmental quotient (IQ/DQ) parameters. Hence, metataxonomy and PICRUSt-based KEGG predictions of fecal GM were assessed for each clinical subset. Here, 60% of ASD patients showed mild to moderate autism, while the remaining 40% showed severe symptoms; 23% showed no clinical symptoms, 21% had a risk of behavior problems and 56% had clinical symptoms based on the CBCL, which assesses internalizing problems; further, 52% had no clinical symptoms, 21% showed risk, and 26% had clinical symptoms classified by CBCL externalizing problems. Considering the total CBCL index, 34% showed no clinical symptoms, 13% showed risk, and 52% had clinical symptoms. Here, 70% of ASD patients showed cognitive impairment/developmental delay (CI/DD). The GM of ASDs with severe autism was characterized by an increase in Veillonella, a decrease in Monoglobus pectinilyticus and a higher microbial dysbiosis index (MDI) when compared to mild-moderate ASDs. Patients at risk for behavior problems and showing clinical symptoms were characterized by a GM with an increase of Clostridium, Eggerthella, Blautia, Intestinibacter, Coprococcus, Ruminococcus, Onthenecus and Bariatricus, respectively. Peptidoglycan biosynthesis and biofilm formation KEGGs characterized patients with clinical symptoms, while potential microbiota-activated PPAR-γ-signaling was seen in CI/DD patients. This evidence derived from GM profiling may be used to further improve ASD understanding, leasing to a better comprehension of the neurological phenotype. Full article

Recent evidence indicates that the gut microbiota (GM) has a significant impact on the inflammatory bowel disease (IBD) progression. Our aim was to investigate the GM profiles, the Microbial Dysbiosis Index (MDI) and the intestinal microbiota-associated markers in relation to IBD clinical characteristics and disease state. We performed 16S rRNA metataxonomy on both stools and ileal biopsies, metabolic dysbiosis tests on urine and intestinal permeability and mucosal immunity activation tests on the stools of 35 IBD paediatric patients. On the GM profile, we assigned the MDI to each patient. In the statistical analyses, the MDI was correlated with clinical parameters and intestinal microbial-associated markers. In IBD patients with high MDI, Gemellaceae and Enterobacteriaceae were increased in stools, and Fusobacterium, Haemophilus and Veillonella were increased in ileal biopsies. Ruminococcaceae and WAL_1855D were enriched in active disease condition; the last one was also positively correlated to MDI. Furthermore, the MDI results correlated with PUCAI and Matts scores in ulcerative colitis patients (UC). Finally, in our patients, we detected metabolic dysbiosis, intestinal permeability and mucosal immunity activation. In conclusion, the MDI showed a strong association with both severity and activity of IBD and a positive correlation with clinical scores, especially in UC. Thus, this evidence could be a useful tool for the diagnosis and prognosis of IBD. Full article

Verticillium wilt is a devastating disease affecting many crops, including hops. This study aims to describe fungal and bacterial populations associated with bulk and rhizosphere soils in a hop field cultivated in Slovenia with the Celeia variety, which is highly susceptible to Verticillium nonalfalfae. As both healthy and diseased plants coexist in the same field, we focused this study on the detection of putative differences in the microbial communities associated with the two types of plants. Bacterial communities were characterized by sequencing the V4 region of the 16S rRNA gene, whereas sequencing of the ITS2 region was performed for fungal communities. The bacterial community was dominated by phyla Proteobacteria, Acidobacteriota, Bacteroidota, Actinobacteriota, Planctomycetota, Chloroflexi, Gemmatimonadota, and Verrucomicrobiota, which are typically found in crop soils throughout the world. At a fungal level, Fusarium sp. was the dominant taxon in both bulk and rhizosphere soils. Verticillium sp. levels were very low in all samples analyzed and could only be detected by qPCR in the rhizosphere of diseased plants. The rhizosphere of diseased plants underwent important changes with respect to the rhizosphere of healthy plants where significant increases in potentially beneficial fungi such as the basidiomycetes Ceratobasidium sp. and Mycena sp., the zygomycete Mortierella sp., and a member of Glomeralles were observed. However, the rhizosphere of diseased plants experienced a decrease in pathogenic basidiomycetes that can affect the root system, such as Thanatephorus cucumeris (the teleomorph of Rhizoctonia solani) and Calyptella sp. Full article

Propolis is a resinous material produced by honeybees from different plant sources and used in the hive as a building material and to protect the colony from parasites and pathogens. Despite its antimicrobial properties, recent studies showed that propolis hosts diverse microbial strains, some with great antimicrobial potential. In this study, the first description of the bacterial community of propolis produced by the gentle Africanized honeybee was reported. Propolis was sampled from hives of two different geographic areas of Puerto Rico (PR, USA), and the associated microbiota investigated by both cultivation and metataxonomic approaches. Metabarcoding analysis showed appreciable bacterial diversity in both areas and statistically significant dissimilarity in the taxa composition of the two areas, probably due to the different climatic conditions. Both metabarcoding and cultivation data revealed the presence of taxa already detected in other hive components and compatible with the bee’s foraging environment. Isolated bacteria and propolis extracts showed antimicrobial activity against Gram-positive and Gram-negative bacterial tester strains. These results support the hypothesis that the propolis microbiota could contribute to propolis’ antimicrobial properties. Full article

Birds are important hosts in the life cycle of some species of ticks. In Colombia, there are few eco-epidemiological studies of tick-borne diseases; the existing ones have been focused on areas where unusual outbreaks have occurred. This study describes the identification of ticks collected from birds and vegetation, and the detection of bacteria in those ticks and in blood samples from birds in an urban fragment of tropical dry forest in the department of Magdalena, Colombia. Bird sampling was carried out monthly in 2021, and 367 birds, distributed among 41 species, were captured. All collected ticks were identified as Amblyomma sp. or Amblyomma dissimile. The presence of rickettsiae in ticks collected from birds was evaluated by molecular analysis of the gltA, ompA and sca1 genes. 16S rRNA meta-taxonomy was used to evaluate rickettsiae in ticks collected from vegetation and in blood samples from birds. The presence of the species “Candidatus Rickettsia colombianensi” was detected in ticks from birds. Bacteria of the family Rickettsiacea was the most abundant in ticks collected from vegetation. Bacteria of the families Staphylococcaceae, Comamonadaceae and Pseudomonadaceae were prevalent in the samples of blood from birds. Rickettsia spp. was also detected in low abundance in some of the bird blood samples. Full article

The preparation of sourdough may include the use of starter microorganisms to address the fermentation process toward specific conditions. The aim of this work was to study the dynamics of the microbial ecosystem in three liquid sourdoughs (SD1, SD2 and SD3) triggered with the same microbial strains. Lactiplantibacillus plantarum (formerly known as Lactobacillus plantarum), Saccharomyces cerevisiae and Candida lambica strains were inoculated as starters, and sourdoughs were differentiated for the fermentation conditions and for the method of starter inoculation. The analyses were performed on the three sourdoughs propagated in the laboratory for 22 days and on the sample SD1, which was transferred to a bakery and refreshed over many months. The dynamics of microbial communities were studied by plate-count analysis and metataxonomic approach. The acidity of sourdough was evaluated over time. Metataxonomic analysis highlighted a large heterogeneity of fungi microbiota in all sourdough preparations, many of them probably originated from the flour, being pathogens of plants. Few yeast species were found, and S. cerevisiae was plentiful but did not predominate over the other species, whereas the C. lambica species decreased over time and then disappeared in all preparations. The bacterial microbiota was less heterogeneous than the fungi microbiota; the species L. plantarum, Leuconostoc citreum and Levilactobacillus brevis (formerly known as Lactobacillus brevis) were always present in all sourdoughs, whereas Fructilactobacillus sanfranciscensis (formerly known as Lactobacillus sanfranciscensis) became the dominant species in bakery-propagated SD1 and in SD2 at the end of the propagation period. Full article

The contamination of oats with Fusarium toxins poses a high risk for food safety. Among them, trichothecenes are the most frequently reported in European oats, especially in northern countries. The environmental conditions related to the climate change scenario might favour a distribution shift in Fusarium species and the presence of these toxins in Southern European countries. In this paper, we present an ambitious work to determine the species responsible for trichothecene contamination in Spanish oats and to compare the results in the United Kingdom (UK) using a metataxonomic approach applied to both oat grains and soil samples collected from both countries. Regarding T-2 and HT-2 toxin producers, F. langsethiae was detected in 38% and 25% of the oat samples from the UK and Spain, respectively, and to the best of our knowledge, this is the first report of the detection of this fungus in oats from Spain. The relevant type B trichothecene producer, F. poae, was the most frequently detected Fusarium species in oats from both origins. Other important trichothecene producers, such as the Fusarium tricinctum species complex or Fusarium cerealis, were also frequently detected in oat fields. Many Fusarium toxins, including T-2 and HT-2 toxins, deoxynivalenol, or nivalenol, were detected in oat samples. The results obtained in this work revealed a clear change in the distribution of trichothecene producers and the necessity to establish the potential of these species to colonize oats and their ability to produce mycotoxins. Full article

A prospective study was conducted to identify bacterial communities in the nasal and laryngeal cavities of pigs with or without clinical signs of respiratory disease in a longitudinal fashion, from weaning to the finishing phase. Nasal and laryngeal swabs were collected from asymptomatic pigs (n = 30), as well as from pigs with clinical signs of respiratory disease (n = 30) at the end of the weaning (T1—33 days) phase, end of the nursery phase (T2—71 days), and finishing (T3—173 days). Total DNA was extracted from each sample, and the V4 hypervariable region of the 16S rRNA gene was amplified and sequenced with the Illumina MiSeq platform. Principal coordinates analysis indicated no significant differences between the nasal and laryngeal bacterial communities. Nevertheless, the microbiota composition in the upper respiratory tract (URT) was clearly distinct between animals, with or without signs of respiratory disease, particularly at post-weaning and the end of nursery. In pigs with clinical signs of respiratory disease, Actinobacillus, Streptococcus Porphyromonas, Veillonella, and an unclassified genus of Pasteurellaceae were more abundant than in pigs with no signs. Metabolic prediction identified 28 differentially abundant pathways, mainly related to carbohydrate, energy, amino acid, anaerobic, and nucleotide metabolism in symptomatic pigs (especially in T2). These findings provide evidence that the composition of the URT bacterial microbiota differs significantly when comparing pigs with or without respiratory clinical signs after weaning, and this difference is maintained in the nursery phase; such differences, however, were not evident at the finishing phase. Full article