Search Results (154)

The fungal component of microbiota, known as the mycobiome, inhabits different body niches such as the skin and the gastrointestinal, respiratory, and genitourinary tracts. Much information has been gained on the bacterial component of the human microbiota, but the mycobiome has remained somewhat elusive due to its sparsity, variability, susceptibility to environmental factors (e.g., early life colonization, diet, or pharmacological treatments), and the specific in vitro culture challenges. Functionally, the mycobiome is known to play a role in modulating innate and adaptive immune responses by interacting with microorganisms and immune cells. The latter elicits anti-fungal responses via the recognition of specific fungal cell-wall components (e.g., β-1,3-glucan, mannan, and chitin) by immune system receptors. These receptors then regulate the activation and differentiation of many innate and adaptive immune cells including mucocutaneous cell barriers, macrophages, neutrophils, dendritic cells, natural killer cells, innate-like lymphoid cells, and T and B lymphocytes. Mycobiome disruptions have been correlated with various diseases affecting mostly the brain, lungs, liver and pancreas. This work reviews our current knowledge on the mycobiome, focusing on its composition, research challenges, conditioning factors, interactions with the bacteriome and the immune system, and the known mycobiome alterations associated with disease. Full article

Downy mildew, caused by Plasmopara viticola, is a major threat to grapevine (Vitis vinifera) cultivation in humid climates. Restrictions on synthetic pesticides and inconsistent efficacy of current biocontrol agents, especially under rainy conditions, complicate disease management. This study evaluated the potential of compost tea to suppress downy mildew in a two-year field experiment (2023 and 2024), combined with reduced synthetic fungicide applications. The study design compared two phytosanitary management strategies on a commercial vineyard: a conventional fungicide against a compost tea strategy supplemented with two cymoxanil applications. The experiment set up had three replicated blocks, each consisting of 100 plants for a total of 600 plants. Mechanistic insights were provided through controlled laboratory experiments involving pre- and post-infection leaf assays, vineyard bacteriome profiling, via 16S rRNA gene sequencing for bacterial communities, across vineyard compartments, i.e., bulk soil, rhizosphere, and phyllosphere, and grapevine metabolomic analysis by GC-MS analysis. Field trials demonstrated that compost tea combined with two fungicide applications effectively reduced disease severity, notably outperforming the fungicide alone in the particularly rainy year of 2023. Bacteriome analysis revealed that compost tea treatment enriched beneficial bacterial genera, including Pseudomonas, Sphingomonas, Enterobacter, Massilia, and Bacillus, known for their growth-promoting and biocontrol activity in the rhizosphere and phyllosphere. Laboratory assays on detached leaves further showed that compost tea alone could suppress both infection and sporulation of P. viticola. Metabolomic analysis highlighted the accumulation of compounds such as tartaric and shikimic acids in compost tea treated leaves, suggesting a potential role in induced resistance. The findings indicate that applying compost tea with reduced fungicide treatments represents a promising and sustainable strategy for managing grapevine downy mildew, even in challenging climates. Full article

Improved antiretroviral therapy (ART) has significantly increased the life expectancy of people living with HIV (PLWH). At the same time, other complications like metabolic syndrome (MetS) are coming up as new challenges to handle. This review aims to explore the emerging evidence of gut microbiome and virome alterations in human immunodeficiency virus-1 (HIV-1) infection and associated metabolic disorders, such as type-2 diabetes (T2DM) and cardiovascular disease (CVD), with a focus on their interplay, contribution to immune dysfunction, and potential as therapeutic targets. We conducted a comprehensive review of the current literature on gut bacteriome and virome changes in HIV-1-infected individuals and those with metabolic comorbidities emphasizing their complex interplay and potential as biomarkers or therapeutic targets. HIV-1 infection disrupts gut microbial homeostasis, promoting bacterial translocation, systemic inflammation, and metabolic dysregulation. Similarly, metabolic disorders are marked by reduced beneficial short-chain fatty acid-producing bacteria and an increase in pro-inflammatory taxa. Alterations in the gut virome, particularly involving bacteriophages, may exacerbate bacterial dysbiosis and immune dysfunction. Conversely, some viral populations have been associated with immune restoration post-ART. These findings point toward a dynamic and bidirectional relationship between the gut virome, bacteriome, and host immunity. Targeted interventions such as microbiome modulation and fecal virome transplantation (FVT) offer promising avenues for restoring gut homeostasis and improving long-term outcomes in PLWH. Full article

Petroleum-derived contaminants pose a significant threat to the soil microbiome. Therefore, it is essential to explore materials and techniques that can restore homeostasis in disturbed environments. The aim of the study was to assess the response of the soil microbiome to contamination with diesel oil (DO) and gasoline (G) and to determine the capacity of sorbents, vermiculite (V), dolomite (D), perlite (P) and agrobasalt (A), to enhance the activity of microorganisms under Zea mays cultivation conditions in pot experiments. The restoration and activity of the soil microbiome were evaluated based on the abundance and diversity of bacteria and fungi, using both classical microbiological methods and Next Generation Sequencing (NGS). Bioinformatic tools were employed to calculate the physicochemical properties of proteins. DO increased the abundance of cultured microorganisms, whereas G significantly reduced it. Both DO and G increased the number of ASVs of Proteobacteria and decreased the relative abundance of Gemmatimonadetes, Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, and fungal OTUs. These contaminants stimulated the growth of bacteria from the genera Rhodanobacter, Sphingomonas, Burkholderia, Sphingobium, and Mycobacterium, as well as fungi belonging to the Penicillium genus. Conversely, they had a negative effect on Kaistobacter, Rhodoplanes, and Ralstonia, as well as the fungi Chaetomium, Pseudaleuria, and Mortierella. DO caused greater changes in microbial alpha diversity than G. The stability of microbial proteins was higher at 17 °C than at −1 °C. The most stable proteins were found in bacteria and fungi identified within the core soil microbiome. These organisms exhibited greater diversity and more compact RNA secondary structures. The application of sorbents to contaminated soil altered the composition of bacterial and fungal communities. All sorbents enhanced the growth of organotrophic bacteria (Org) and fungi (Fun) in DO-contaminated soils, and actinobacteria (Act) and fungi in G-contaminated soils. V and A had the most beneficial effects on cultured microorganisms. In DO-contaminated soils, all sorbents inhibited the growth of Rhodanobacter, Parvibaculum, Sphingomonas, and Burkholderia, while stimulating Salinibacterium and Penicillium. In G-contaminated but otherwise unamended soils, all sorbents negatively affected the growth of Burkholderia, Sphingomonas, Kaistobacter, Rhodoplanes, Pseudonocardia, and Ralstonia and increased the abundance of Gymnostellatospora. The results of this study provide a valuable foundation for developing effective strategies to remediate soils contaminated with petroleum-derived compounds. Full article

Background: Diet is known to influence the composition of the gut microbiome. For patients who require enteral feeding, there has been a growing popularity of using blenderized tube feeds (BTFs) as an alternative to standard enteral formula (SEF). There is limited literature exploring the impact of BTFs on the gut microbiome. Methods: Twenty-eight patients 1 to 22 years of age who received their nutrition via gastrostomy tube for over 4 weeks were included and participants were divided into BTF and SEF groups. Demographics and clinical information were collected from the medical records, and all legal guardians completed a semi-structured interview using a questionnaire. 16SrRNA sequencing was used for bacteriome analysis. Results: Eleven patients in the BTF group and seventeen in the SEF group were included. No significant differences in the demographics were noted. Patients on BTFs had no emesis compared to seven (41%) in the SEF group, p = 0.02. There were no significant differences in other clinical characteristics and comorbidities. No significant differences in the gut microbiome between the groups were noted for alpha and beta diversities, richness, and evenness (at both genus and species levels). Differential abundance analysis showed only a few significant differences between the groups at all reported taxonomic levels. Conclusions: Patients on BTFs had a significantly decreased prevalence of emesis compared to the SEF group. No significant differences in the microbiome between the groups were noted for alpha and beta diversities, richness, and evenness. Prospective studies are recommended to verify our preliminary data and further evaluate the implications of our study results. Full article

The COVID-19 pandemic has highlighted the complex interplay between the gut microbiota and systemic immune responses, particularly through the gut–lung axis. Disruptions in gut microbial diversity and function—commonly referred to as dysbiosis—have been increasingly implicated in the pathogenesis of SARS-CoV-2 infection. In this study, we assessed the gut bacteriome and permeability in SARS-CoV-2-infected patients using 16S sequencing and ELISA assays, respectively. We also measured blood inflammatory cytokines and fecal secretory IgA to evaluate systemic and mucosal immune responses. Significant alterations in both alpha and beta diversity metrics were observed in patients with COVID-19 (n = 79) and those with post-COVID-19 condition (n = 141) compared to the controls (n = 97). Differential abundance and taxonomic analyses revealed distinct microbial profiles in the infected groups. Increased plasma levels of IL-2, IL-6, IL-17A, IFN-γ, and zonulin were detected in patient samples. Some genera were elevated during acute infection, which was positively correlated with C-reactive protein, while Enterobacteriaceae and Escherichia-Shigella were associated with increased zonulin levels, indicating compromised intestinal barrier function. These findings suggest that gut dysbiosis may contribute to bacterial translocation and systemic inflammation. Overall, our results highlight the importance of the gut–lung axis and suggest that modulating the gut microbiota could support immune regulation in SARS-CoV-2 infection. Full article

Androgenetic alopecia (AGA) is the most common form of patterned hair loss, exhibiting gender-specific clinical features. Recent studies highlight the importance of the skin microbiome in maintaining skin health, but the relationship between the hair follicle microbiome and hair loss, particularly AGA, remains understudied. Hair follicle layer samples were collected directly from the crown region of female pattern hair loss (FPHL), male pattern hair loss (MPHL), and healthy adult women (control) groups. Microbial DNA was extracted and analyzed using Illumina 16S rRNA V3–V4 gene amplicon sequencing. Alpha-diversity and beta-diversity analyses and taxonomic and functional profiling were conducted through relative abundance, LEfSe, and PICRUSt2 analyses. The alpha-diversity analysis showed a significant decrease in microbial richness in the hair loss groups. Unweighted UniFrac-based beta-diversity analysis revealed significant clustering between the control group and the FPHL group. Taxonomic profiling and LEfSe analysis identified differences in microbial composition and biomarkers. PICRUSt2 analysis further revealed altered pathways related to porphyrin metabolism, fatty acid biosynthesis, and steroid hormone metabolism. Additionally, differences in microbiome composition and potential functions were found between the FPHL and MPHL groups. This study provides comprehensive insights into the hair follicle microbiome, revealing unique microbial patterns and functional alterations associated with FPHL. Understanding these microbiome characteristics may contribute to targeted approaches for addressing AGA. Further research is warranted. Full article

Allergic rhinitis and asthma are common chronic airway diseases that present significant public health challenges. Previous research has shown how the nasal and oral mycobiomes influence the onset, progression and severity of these two conditions, but no study so far has directly compared those mycobiomes within the same cohort during health and disease. To address this gap, I analyzed next-generation fungal ITS sequence data from 349 participants, including individuals with allergic rhinitis, asthma, and healthy controls. The nasal and oral mycobiomes showed a great overlap in composition but differed significantly (p < 0.04) in the relative abundance of several dominant genera. Moreover, only 18.6% of the fungal amplicon variants were shared among cavities. Microbial alpha-diversity was significantly higher (p < 0.05) in the nasal cavity, while beta-diversity varied significantly (p < 0.045) across all indices and clinical groups. Fungal networks were largely fragmented and showed relatively low ecological niche specialization, which contrasts with a previous study of bacteriomes from the same cohort. These networks also differed in structure, complexity and keystone nodes across clinical phenotypes. Overall, these findings highlight that the nasal and oral mycobiomes play distinct yet interconnected roles in allergic rhinitis and asthma. Full article

The Rio Bravo/Grande River is a binational water resource between Mexico and the United States and supports diverse anthropogenic activities. However, limited studies on its microbiological composition focus on molecular techniques. Therefore, the aim of this study was to characterize the bacteriome and identify potentially pathogenic bacteria in surface waters of the Rio Bravo/Grande in northeastern Tamaulipas, Mexico, using the 16S rRNA gene metabarcoding technique. Surface water samples were collected from the localities of Diaz Ordaz, Reynosa, and Matamoros between 2016 and 2017. DNA extraction and sequencing were performed, focusing on the V3–V4 region of the 16S rRNA gene. A taxonomic analysis revealed the presence of 13 bacterial phyla, with Proteobacteria (40%), Firmicutes (28%), and Actinobacteria (10.2%) being the most abundant. At the genus level, Bacillus, Pseudomonas, and Acinetobacter were predominant, while 16 potentially pathogenic species, including Acinetobacter baumannii and Vibrio vulnificus, were identified. Alpha and beta diversity analyses highlighted significant differences in the bacterial diversity among the sampling sites, indicating that the river has some capacity to recover from anthropogenic and environmental disturbances. This study underscores the need for the continuous monitoring of the Rio Bravo/Grande to protect public health and maintain the water quality in the face of increasing anthropogenic pressures. Full article

Microbial transplantation represents a sustainable strategy to address productivity gaps in agricultural soils by transferring microbiomes that enhance nutrient cycling, pathogen suppression, and stress tolerance. This study evaluates whether probiotic consortia from high-yield soybean soils (donor soil) could improve crop performance in less productive fields (recipient soil). We developed a host-adapted inoculant from soybean rhizospheres grown in donor soil and applied it to seeds at five concentrations (0.25–10 g/kg seed) in recipient soil, with untreated controls for comparison. To assess crop-specific microbial recruitment, we prepared a parallel bean-derived inoculant under identical conditions. Through 16S rRNA sequencing and growth/yield analysis, we found the following: (1) Distinct bacteriome assemblies between soybean- and bean-derived inoculants, confirming host specificity; (2) Successful enrichment of beneficial taxa (Enterobacteriaceae increased by 15–22%, Rhizobiaceae by 7–12%) despite native community resilience; and (3) Consistent yield improvement trends (4.8–6.2%), demonstrating potential to bridge productivity gaps. These results show that transplanted microbiomes can effectively modulate rhizosphere communities while maintaining ecological balance. This work establishes a scalable approach to address soil productivity limitations through microbiome transplantation. Future research should optimize (a) inoculant composition for specific productivity gaps; (b) delivery systems; and (c) compatibility with resident microbiomes, particularly in systems where niche-specific processes govern microbial establishment. Full article

Allergic rhinitis and asthma are significant public health concerns worldwide. While previous studies have explored how nasal and buccal bacteriotas influence these conditions, few have directly compared their bacteriomes within the same cohort. To bridge this gap, I analyzed 16S rRNA next-generation sequencing data from 347 individuals, including participants with allergic rhinitis, asthma and healthy controls. The nasal and buccal bacteriomes shared all dominant bacterial taxa but differed significantly in their phylum- and genus-level relative abundances. Alpha-diversity was significantly higher in the buccal cavity, while beta-diversity varied significantly across all indices and clinical groups. Over 80% of the predicted metabolic pathways were differentially regulated between the two cavities, yet these functional differences remained fairly consistent across clinical groups. Naso-buccal bacterial networks exhibited striking differences in structure, complexity and hub nodes. Notably, the network of healthy controls showed a clear segregation between nasal and buccal bacteria, with 93.5% of the interactions occurring within each respective cavity, and contained few pathogenic keystone taxa. In contrast, bacterial networks from diseased individuals exhibited reduced ecological specialization and more pathogenic keystone taxa linked to airway disease. These findings, thus, demonstrate that the naso-buccal bacteriome plays distinct yet interconnected roles in allergic rhinitis and asthma. Full article

The study of interactions between gut microbiota and the well-being of the host has become increasingly popular in the last decades. Growing interest in gut microbiota–host interactions has brought attention to faecal microbiota transplantation (FMT) as a clinically effective, though still debated, therapeutic approach. This review discusses how limitations in the characterisation of gut bacteriomes—particularly interindividual variation and methodological inconsistencies—may influence the outcomes of FMT. The concept of enterotypes is considered as a framework that could support more refined stratification of donors and recipients, offering a possible route toward greater precision in microbiota-based interventions. Further on, the review touches on the subject of interactions among the host, the bacteriome, and the phageome—the community of bacteriophages—with specific focus on the presence and intriguing distribution patterns of crAssviruses. The final chapters are dedicated to discussing the current state of the FMT procedure and its variations, as well as the possibility of performing faecal virome transplants (FVTs) as a potentially safer and equally efficient alternative. Full article

Pediatric asthma is the most common chronic childhood disease in the US and a major public health concern. It is considered to comprise multiple clinical variants or phenotypes with different etiologies and pathophysiologies. Former research has shown that airway bacteriomes vary in composition and structure across pediatric asthma phenotypes, but their functional diversity and bacterial interactions have hardly been investigated. A previous study of 163 children from Washington DC identified three statistically different asthma phenotypes, each with a unique nasopharyngeal bacterial composition and diversity. Here, I reanalyze 16S rRNA high-throughput sequences from the same cohort to characterize their bacterial metabolism and interactions. I detect 61 to 102 metabolic pathways (PICRUSt2; q ≤ 0.05) differentially expressed across the three asthma phenotypes. Most of those pathways are related to biosynthesis and degradation processes and statistically (p ≤ 0.0012) separated the three clinical groups. Co-occurrence networks also differ in connectivity across phenotypes, suggesting unique bacterial interactions in each group. Five to eight keystone taxa are detected across phenotypes. Insights from this and previous studies, hence, confirm the airway bacteriome heterogeneity across pediatric asthma, increasing our understanding of its etiology and pathophysiology, and provide new taxonomic and functional biomarkers of disease for targeted interventions and therapies. Full article

(1) Background: The Guarapiranga reservoir, located in the metropolitan region of São Paulo (RMSP), plays an important role in supplying water to the population. However, the growing urbanization in the region, which has occurred in a disorderly manner and lacks basic sanitation infrastructure, has had a detrimental impact on the reservoir’s conditions. The aim of this study was to evaluate the physicochemical parameters and detect coliforms to determine the water quality of the Guarapiranga reservoir, as well as to characterize the microbial diversity and antimicrobial-resistance genes (ARGs) present in the reservoir water. (2) Methods: Four sampling campaigns of the Guarapiranga reservoir were carried out between October 2020 and July 2022. Physicochemical analyses, and selective microbiological culture for coliforms, as well as the extraction of bacterial DNA for subsequent sequencing and search for ARGs were carried out. (3) Results: Analysis of the physicochemical results showed a progressive reduction in the quality of the reservoir’s water, and the microbiological tests consistently showed the presence of Escherichia coli, Salmonella spp., Shigella spp. and Klebisiella spp. in the water samples collected from the reservoir. Analyses of the sequencing data showed the predominant presence of the phyla Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, and 12 ARGs were detected in the reservoir. (4) Conclusions: The increase in sewage discharge, mainly due to the growth of irregular housing, has affected the quality of the water, as indicated by the physicochemical analysis and detection of coliforms and ARGs. Full article

Background: According to the One Health concept, the physical proximity between pets and their owners facilitates the interspecies spread of bacteria including those that may harbor numerous antimicrobial resistance genes (ARGs). Methods: A shotgun sequencing metagenomic data-based bacteriome and resistome study of 1830 canine saliva samples was conducted considering the subsets of ARGs with higher public health risk, ESKAPE pathogen relatedness (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), and survey results on the physical and behavioral characteristics of the participating dogs. Results: A total of 318 ARG types achieved sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes through various resistance mechanisms. ARGs against tetracyclines, cephalosporins, and, interestingly, peptides appeared in the highest number of samples. Other Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the drug classes most frequently affected by ARGs of higher public health risk and ESKAPE pathogen-related ARGs of higher public health risk. Several characteristics, including coat color, sterilization status, size, activity, or aggressiveness, were associated with statistically significant differences in ARG occurrence rates (p < 0.0500). Conclusions: Although the oral microbiome of pet owners is unknown, the One Health and public health implications of the close human–pet bonds and the factors potentially underlying the increase in salivary ARG numbers should be considered, particularly in light of the presence of ARGs affecting critically important drugs for human medicine. Full article