Search Results (2,669)

Background/Objectives: Asthma affects millions of patients worldwide and impacts their quality of life, particularly among children. Colonisation or an imbalance within natural resident microbiota may drive inflammatory responses in asthma; antibiotic resistance genes (ARGs) have also been investigated in asthma microbiome studies. However, research on the association between airway microbiota and ARGs remains limited. Therefore, we elucidated functional-level characterisation at the level of ARGs, virulence factors, and active pathways among a paediatric asthma cohort relative to a healthy control. Methods: Overall, 29 children with asthma and 20 control subjects were enrolled, and 3 swabs (2 nasal and 1 oropharyngeal) were obtained from each participant. Genomic DNA was extracted and sent for shotgun sequencing, after which bioinformatic analysis was conducted to remove human reads and analyse the microbiota pattern in the samples. The abundance of antibiotic resistance genes was evaluated along with the distribution of virulence genetic markers. Functional investigation of the most prevalent metabolic pathways was also performed. Results: Upper airway microbiome functional capacity varied by anatomical location, with oropharyngeal communities exhibiting greater metabolic breadth than nasal communities, suggesting the sample source to be the dominant factor shaping gene content, pathway profiles, and community structure. Asthma-related functional differences were modest, and no biological pathways remained significant following false discovery rate correction. Enrichment of antimicrobial resistance genes was observed, particularly those conferring resistance to β-lactams, macrolides, and tetracyclines. Conclusions: Different anatomical niches exhibit differential activities, and further exploration in this direction could aid in the development of diagnostic and therapeutic biomarkers for asthma. Full article

Background/Objectives: Breastfeeding represents a critical developmental window during which maternal biology, environmental exposures, and nutrition converge to influence infant gastrointestinal health and long-term developmental trajectories. From a One Health perspective, breastfeeding can be conceptualized not as a static nutritional act, but as a dynamic and modifiable biological system in which maternal factors shape early-life microbiota assembly and immune programming. This narrative review explores how microbiota-oriented strategies during breastfeeding may foster a favorable trajectory of infant health, potentially extending to transgenerational outcomes. Methods: This narrative review is structured around a ten-point decalogue addressing interconnected domains relevant to the maternal–milk–infant microbiota axis, including maternal diet, microbial diversity, environmental exposures, psychological stress and probiotic use. Current mechanistic and clinical evidence was examined to evaluate how these domains may modulate microbiota composition and function during breastfeeding. Attention was given to probiotic supplementation, including strain specificity, timing of administration, and clinical context, as well as to the broader implications of a One Health framework. Results: Available evidence suggests that maternal nutritional patterns, environmental and psychosocial exposures, and targeted microbiota-modulation strategies may influence the composition and functional properties of human milk and the developing infant microbiota. Probiotic use during breastfeeding appears to have strain-specific and context-dependent effects, with potential benefits in selected clinical scenarios. However, findings remain heterogeneous, and uncertainties persist regarding optimal strains, timing, and long-term outcomes. Conclusions: Breastfeeding can be understood as a dynamic biological interface shaped by maternal and environmental factors. Integrating microbiota-oriented strategies within a One Health framework may support infant gastrointestinal health and possibly contribute to longer-term developmental trajectories. Nevertheless, careful interpretation of the current evidence is warranted to avoid reductionist, supplement-centered approaches and to prevent maternal overmedicalization or blame. Full article

Antibiotic therapy represents one of the strongest ecological perturbations of the human gut microbiota, inducing rapid and often prolonged alterations in community structure, metabolic activity, and functional resilience. While the use of probiotics to mitigate antibiotic-associated dysbiosis is widely adopted in clinical practice, probiotic selection is still largely empirical and insufficiently grounded in biological compatibility with specific antibiotic pressures. In this conceptual review, antibiotics are reframed not merely as antimicrobial agents, but as ecological forces that shape microbial survival, quiescence, and recolonization dynamics. We propose a biologically informed framework that distinguishes genetic antibiotic resistance from functional or ecological insensitivity, highlighting how microbial traits, such as the absence or inaccessibility of the antibiotic target, metabolic state, sporulation, and cellular architecture, influence the persistence of probiotics during antibiotic exposure. By integrating the mechanisms of action of antibiotics with key physiological and structural features of probiotic microorganisms, we develop a conceptual framework aimed at rationalizing the compatibility of probiotics and antibiotics. This framework does not imply clinical efficacy but provides an interpretative tool to guide hypothesis generation, experimental validation, and the design of future targeted probiotic strategies. A more ecologically grounded approach to probiotic selection may ultimately improve microbiota support during antibiotic therapy and advance personalized microbiome modulation. Full article

When using traditional approaches, such as pharmacokinetics and pharmacodynamics, the entire cellular or molecular response to drugs in the body cannot be fully ascertained or established. The oral medication process involves pharmacokinetics, followed by oral microbiomics and then gut microbiomics and pharmacodynamics. Recently, there has been increasing interest in the role of genetics (pharmacogenetics and pharmacogenomics) in both humans and microbiomes, as well as omics alterations (e.g., epigenetic, transcriptomic, proteomic, and metabolomic alterations as a consequence of drug exposure), which can help to ascertain the cellular responses to medications. Both the efficacy and toxicity of a drug are influenced by these factors. To assess these at an individual level, an integrative Personalized Medicine Model may be needed to help with medication management. Two example application cases for SSRIs and statins demonstrate the clinical usefulness of such a model, which can guide clinicians during drug selection and dosing to reduce reliance on trial-and-error, thus potentially improving patient outcomes and safety. Integrating this framework into practical clinical workflows requires the capture, analysis, and translation of multi-omics data in order to realize decision support protocols and actionable drug recommendations. This review also discusses IT requirements and different stakeholder roles. Although the proposed model can guide the treatment of diseases at the individual patient level, further research is still needed before it can be implemented as part of drug development research, clinical care, and healthcare delivery systems. Full article

The cervicovaginal microbiome (CVMB) is pivotal in maintaining the homeostasis of the lower female genital tract and has emerged as a significant modulator of cervical carcinogenesis. Although persistent infection with high-risk human papillomavirus (HR-HPV) is a prerequisite for the development of cervical intraepithelial neoplasia (CIN) and subsequent cervical carcinoma, it remains insufficient alone to drive oncogenesis. Accumulating evidence suggests that alterations in the CVMB composition profoundly impact HPV persistence, local immune responses, and disease progression. A vaginal microbiota dominated by Lactobacillus species, most notably Lactobacillus crispatus, correlates with low microbial diversity, robust immune regulation, and facilitated HPV clearance. Conversely, microbial dysbiosis—characterized by Lactobacillus depletion and a concomitant proliferation of anaerobic taxa, typical of Community State Type (CST) IV and Lactobacillus iners-dominated profiles—is strongly associated with chronic inflammation, oxidative stress, epithelial barrier compromise, and an elevated risk of CIN progression. This review synthesizes current evidence regarding the multifaceted interactions among the cervicovaginal microbiome, HPV pathogenesis, immune dysregulation, and oxidative stress in the etiology of CIN. Elucidating these intricate host–microbiome dynamics may precipitate the discovery of novel microbiome-derived biomarkers, ultimately informing innovative prophylactic and therapeutic interventions for cervical cancer. Full article

Advances in sequencing technologies have transformed human microbiome research, yet most analyses still rely on species-level profiles. However, strains rather than species represent the true ecological and functional units of the microbiome. Individual strains can vary substantially in gene content, metabolic capacity, virulence factors, antimicrobial resistance, and host-interaction properties. These differences critically influence immune responses, epithelial barrier integrity, disease susceptibility, and therapeutic outcomes. Here, we synthesize recent human microbiome studies that provide robust strain-resolved evidence, focusing on three major themes: (i) the emergence and long-term persistence of personalized strain repertoires, (ii) strain-specific pathobiont traits that drive host pathology, and (iii) the implications of strain-level ecology for the development of next-generation microbiome therapeutics. We also highlight key methodological innovations including high-resolution amplicon profiling, advanced metagenomic and single-cell genomics, and culture-based functional approaches that collectively enable strain-level resolution and are reshaping the field. Full article

Early life represents a critical developmental programming window during which nutrition and microbial exposures shape long-term physiological function. Feeding mode is a major determinant of infant gut microbiota assembly and metabolic activity. This narrative review synthesizes current evidence comparing breastfeeding (BF) and formula feeding in relation to microbial composition, functional capacity, and immune programming during the preweaning and early postweaning periods. BF may support a relatively stable, bifidobacteria-dominated microbiota enriched in pathways involved in carbohydrate utilization, vitamin biosynthesis, and immune modulation. Human milk oligosaccharides, secretory IgA, lactoferrin, and milk-associated microbes collectively guide microbial succession, enhance barrier integrity, and support immune tolerance. In contrast, formula-fed infants typically exhibit greater microbial diversity, earlier transition toward adult-like profiles, and increased abundance of facultative anaerobes, alongside the enrichment of pathways related to bile acid and amino acid metabolism. Microbiota patterns in formula-fed infants are further influenced by formula composition, including protein load, lipid structure, and supplementation with prebiotics, probiotics, and human milk oligosaccharide analogues. Although advances in formula design have reduced compositional gaps, functional differences in microbial stability and immune programming persist. Recognizing early infancy as a sensitive programming window underscores the need for microbiome-informed nutritional strategies and longitudinal, multi-omics research to clarify causal mechanisms and optimize early-life interventions. Full article

Background: The skin microbiome plays a crucial role in maintaining barrier function and preventing inflammaging. Heat-treated probiotics offer stability advantages for topical formulations while potentially maintaining bioactive properties. Objective: To evaluate the safety, molecular mechanisms, and clinical efficacy of heat-treated Lactiplantibacillus plantarum Skinbac™ SB01 and Bifidobacterium animalis spp. lactis Skinbac™ SB05 in reducing visible signs of skin aging. Methods: In vitro studies assessed cytotoxicity (MTT/LDH assays), Aquaporin-3 (AQP3) expression, and reactive oxygen species (ROS) production in Normal Human Epidermal Keratinocytes (NHEK). A 30-day open-label clinical study (n = 20 females, 18–70 years) evaluated three formulations (face cream, serum, and eye contour) using instrumental measurements of hydration, elasticity, density, and roughness parameters. Results: In vitro testing showed a significant increase in AQP3 expression (+22% ± 3%, p = 0.03) and a non-significant reduction in ROS levels (−33% ± 9%, p = 0.06) at 10⁷ TFU/well, with no cytotoxicity observed. Clinical evaluation demonstrated statistically significant improvements: eye contour formulation achieved +10.5% deep skin hydration (p < 0.0001) and −11% average roughness (p < 0.0001); serum showed +28.7% immediate hydration (p < 0.0001); and face cream improved gross skin elasticity by +6.3% (p < 0.01). No adverse events were reported. An independent and methodologically distinct placebo-controlled study was included for contextual support and was not directly compared with the present trial; this study evaluated a related 1% postbiotic formulation and reported statistically significant improvements over placebo in roughness, wrinkle depth, hydration, and biomechanical parameters. Conclusions: This pilot study provides preliminary evidence that heat-treated L. plantarum SB01 and B. animalis spp. lactis SB05 formulations could safely improve skin hydration and reduce roughness parameters. While in vitro results show a significant increase in AQP3 expression and an exploratory (non-significant) reduction in ROS levels, larger controlled trials are warranted to confirm clinical efficacy. Full article

Glycosphingolipids are amphiphilic compounds that feature sugar or glycan moieties installed onto a ceramide lipid. The synthesis of glycosphingolipids by members of the human gut microbiome, and their known immune stimulating activity, have made them of interest for potential pharmaceutical roles. However, the known diversity of glycosphingolipid glycans in bacteria remains limited, highlighting the need to isolate novel glycosphingolipid-producing organisms as a source of these compounds. The order Sphingomonadales, one of the major clades of sphingolipid producing bacteria, conserves a serine palmitoyltransferase (SPT) enzyme needed for the initial biosynthetic step in sphingolipid production which can be targeted as part of isolation efforts. With these bacteria known to live in diverse environments such as soil microbiomes, soap scum biofilms, and cyanobacterial microbiomes, there are many environments to target for the isolation of these bacteria. In this work, we designed a set of polymerase chain reaction (PCR) primers for the isolation of diverse Sphingomonadales strains by targeting the SPT gene (spt), which we used to isolate strains from the genera Sphingomonas and Novosphingobium in soil, soap scum biofilms, and xenic cyanobacterial cultures. In these efforts, streptomycin improved the encounter rate, as represented by the SPT assay true-positive rate. Our isolates represent novel genomic space: with genomes from both genera that have low similarity to known genomes, suggestive of novel species, while several novel plasmids were also missing known marker sequences. Full article

Background: Psoriasis is a chronic immune-mediated inflammatory disease characterized by systemic inflammation and complex immune dysregulation that extends beyond the skin and may affect the oral environment. Increasing evidence suggests that saliva may serve as a non-invasive diagnostic medium reflecting both local and systemic pathological processes. This systematic review aimed to critically evaluate current evidence on salivary biomarkers in psoriasis, focusing on inflammatory mediators, oxidative stress parameters, immune-related factors, and oral microbiota alterations, and to assess their potential clinical and diagnostic relevance. Methods: A systematic literature search was performed according to PRISMA guidelines using PubMed, Scopus, and Web of Science databases, covering studies published between 1994 and October 2024. Original human studies evaluating salivary biomarkers in patients with psoriasis were included based on predefined PECOS criteria. Studies involving confounding inflammatory oral diseases without separate analysis were excluded. Eleven eligible studies were included in a qualitative synthesis. Results: The analyzed studies consistently demonstrated multidimensional alterations in salivary composition in psoriasis patients compared with healthy controls. Increased levels of pro-inflammatory cytokines (TNF-α, IFN-γ, IL-2) and reduced anti-inflammatory IL-10 indicated persistent immune activation. Elevated oxidative stress markers, including total oxidant status and oxidative stress index, supported the role of redox imbalance in disease pathogenesis. Alterations in innate immune components, such as salivary α-amylase, immunoglobulin A, and lysozyme, suggested impaired oral immune regulation. Moreover, emerging microbiome data revealed shifts toward pro-inflammatory bacterial taxa, including Prevotella and Porphyromonas. Some studies indicated that biologic therapy may modulate salivary biomarker profiles. Conclusions: Salivary biomarkers reflect systemic inflammatory and immunological alterations associated with psoriasis and represent promising non-invasive tools for disease monitoring and clinical assessment. Nevertheless, substantial methodological heterogeneity and limited sample sizes highlight the need for large-scale, standardized, and longitudinal studies to validate their diagnostic applicability. Full article

Diet is a key modulator of the gut microbiota, thereby influencing host physiology. Microbial colonization begins early in life, influenced by maternal sources, mode of birth, diet, and environmental exposures, and stabilizes into an adult-like microbiome during early childhood. This maturation yields a microbial ecosystem dominated by Firmicutes and Bacteroidetes that contributes to host physiological homeostasis. Gut microorganisms function as an integrated metabolic system that transforms dietary substrates into bioactive metabolites, including short-chain fatty acids (SCFAs), amino acid-derived compounds, and microbial lipids. These metabolites regulate glucose and lipid metabolism, intestinal barrier integrity, and immune modulation. Although many metabolic functions are conserved, their activity is shaped by diet, microbial cross-feeding, and local intestinal conditions, enabling functional specialization within the gut. Disruption of this system, known as dysbiosis, is associated with alterations in microbial diversity and metabolic output that have been linked to metabolic diseases, including obesity and related disorders. Evidence from experimental models and observational studies suggests that these associations may involve interconnected inflammatory and metabolic mechanisms, such as impaired intestinal barrier function, low-grade inflammation, and altered dietary energy harvest; however, causal relationships in humans remain incompletely understood. Beyond peripheral effects, the gut microbiome influences host metabolism via the gut–brain axis, a bidirectional network that integrates neural, endocrine, immune, and metabolic signaling. Microbiota-derived metabolites and gut hormone modulation contribute to appetite regulation, energy balance, and glucose homeostasis, while central neuroendocrine signaling can reciprocally shape the intestinal microbial niche. Collectively, these findings highlight the gut microbiome as a central regulator of host metabolism, whose disruption may contribute to the development of metabolic disease. Full article

Cryptosporidium spp. and Giardia duodenalis are globally important intestinal protozoa causing diarrheal disease in humans and animals, with significant zoonotic potential. This study aimed to investigate the prevalence, molecular diversity, and potential transmission dynamics of these parasites in humans, livestock, and environmental samples from a rural community in Türkiye using a One Health approach, and to assess their associations with gut microbiome composition. Faecal samples were collected from 124 humans, 305 livestock (cattle, sheep, and goats), and 40 environmental samples (water and mud). Parasites were detected using qPCR and nested PCR, with positive samples genotyped by sequencing. Microbiome profiling was performed using 16S rRNA gene amplicon sequencing. Giardia duodenalis was detected in 12.1% of humans, 17.5% of livestock, and 2.5% of environmental samples, with assemblages A, B, and E identified, including the first detection of assemblage E in a human in Türkiye. Cryptosporidium spp. were found in 8.9% of humans, 19.3% of livestock, and 55% of environmental samples, with C. parvum as the dominant zoonotic species. Microbiome analysis revealed no significant differences in overall diversity. This study provides the first One Health assessment of Cryptosporidium spp. and Giardia duodenalis in Türkiye, emphasizing zoonotic transmission risks linked to livestock and the environment. Full article

Background: Antimicrobial resistance (AMR) is a global healthcare threat. Traditional largely non-selective antibiotics produce side effects due to the natural host microbiome being modified creating a loss in homeostasis. In women, AMR is a cause of acute generational impact. For example, bacterial vaginosis (BV), the most common gynecological infection in reproductive-age women, is a serious public health concern due to its high rates of recurrence, secondary infections, and reproductive issues; and two currently prescribed antibiotics for BV do not fully resolve the symptoms. Objective: The strong need for innovative, potent, safe, and selective therapeutics has prompted a search for such bioactive molecules in milk. Resulting from 200 million years of evolutionary pressure, mammalian lactation not only nourishes infants, but it has also been under relentless Darwinian selective pressure to provide protection from a variety of infections. Methods: Computationally designed human-milk-inspired peptides (AMPs) were tested in standard microbicidal assays for activity against BV pathogens, and evaluated for stability and safety. Results: Several AMPs are bactericidal towards Gardnerella vaginalis, a major BV-associated pathogen, and other BV-associated pathogens. Some novel AMPs do not impact the viability of key lactobacilli linked to a healthy vaginal microbiome. These stable, membrane-acting cationic AMPs reduce inflammation during an infection assay and are safe in EpiVag organoid tissues. Conclusions: AMPs can address concerns like non-selectivity and antibiotic resistance—thereby addressing AMR. Lead AMPs from this study offer a promising solution for the development of novel therapeutics for the treatment of BV, which may reduce the burden of AMR. Full article

Tripartite interaction among arbuscular mycorrhizal fungi (AMF), small grain cereals—including wheat, barley, oats, and rye—and pathogenic organisms constitute a highly complex ecological system with major implications for plant health, productivity and resilience. AMF colonization increases nutrient acquisition, particularly phosphorus and nitrogen, while concurrently priming host defense mechanisms that increase resistance to a broad spectrum of pathogens. These benefits, however, are strongly context-dependent and modulated by AMF species composition, host genotype, soil characteristics, and environmental conditions. AMF activate resistance pathways and modulate the rhizosphere microbiome, underscoring their central role in shaping plant–pathogen dynamics. Importantly, the relevance of these interactions extend beyond crop protection and yield stability to encompass food security and sustainability goals aligned with the One Health framework, which recognizes the interconnectedness of plant, environmental, and human health. Field implementation of AMF-based strategies has the potential to reduce reliance on chemical fertilizers and pesticides, thereby promoting sustainable cereal production, restoring soil biodiversity, and enhancing ecosystem services, with downstream benefits for human nutrition and environmental safety. This review integrates current knowledge on AMF–cereal–pathogen interactions, synthesizing mechanistic advances and applied perspectives while identifying critical knowledge gaps that must be addressed to effectively deploy AMF in resilient and sustainable agroecosystems within a One Health context. Full article

Synanthropic cockroaches, especially Blattella germanica and Periplaneta americana, are persistent pests of human dwellings, healthcare facilities, food establishments, farms, and transport infrastructure. Accumulating field and laboratory studies indicate that synanthropic cockroaches carry clinically important bacteria, fungi, and parasites, including multidrug-resistant strains harbouring extended-spectrum β-lactamase, carbapenemase, and other antimicrobial-resistant determinants. Cockroaches acquire these organisms from sewage, waste, food residues, animal excreta, and contaminated clinical environments, and retain them on the cuticle and within a complex gut microbiota. Dissemination is predominantly mechanical, via contact transfer and deposition of regurgitate and faeces on food, equipment, and surfaces, but may be amplified by gut colonisation, microbial interactions, and horizontal gene transfer within the cockroach microbiome. In hospitals, cockroaches can connect high-burden reservoirs (drains, waste areas, kitchens) with vulnerable units, including intensive care units (ICUs), neonatal intensive care units (NICUs), burn units, and haemato-oncology wards. In food and livestock systems, they may contaminate housing, ingredients, and finished products, enabling spillover along supply chains and at ports. This review synthesises current evidence and highlights the following priorities: integrate cockroaches into infection prevention, food safety, and biosecurity; incorporate cockroach sampling into antimicrobial resistance (AMR) and genomic surveillance; and advance mechanistic research on cockroach–microbiota–pathogen interactions to improve pest management and safely explore cockroach-derived antimicrobial compounds. In this review, we distinguish external mechanical carriage (cuticular contamination) from internal gut carriage; we use “gut colonisation” only when persistence/replication or prolonged shedding is demonstrated. Full article