Search Results (115)

Pasteurella multocida serotype B:2 is a primary agent of hemorrhagic septicemia (HS) in livestock, and the strain NQ01 isolated from yaks highlights its cross-species impact. In this study, a murine intranasal infection model was established using P. multocida NQ01 to assess how acute respiratory infection perturbs gut homeostasis. Mice were intranasally inoculated with NQ01, and at 36 h post-infection, ileal tissues and cecal contents were collected for histopathological examination, 16S rRNA gene sequencing, and untargeted metabolomic analysis. Histopathology revealed obvious acute bronchopneumonia but no overt ileal damage. However, 16S rRNA sequencing of cecal microbiota showed significant dysbiosis: microbial diversity was reduced and community composition shifted, including decreased short-chain fatty-acid-producing taxa and increased opportunistic genera. Metabolomic profiling detected 1444 significantly altered cecal metabolites, and pathway analysis indicated marked disruption of amino acid metabolism, notably the tyrosine metabolism pathway. Key tyrosine pathway metabolites were dysregulated (e.g., elevated L-tyrosine and dopamine with reduced L-DOPA), indicating a breakdown of this metabolic pathway. These findings demonstrate that acute respiratory P. multocida infection profoundly disturbs gut microbiota and metabolism, underscoring disruption of the gut–lung axis. This study provides new insight into the systemic consequences of HS-associated P. multocida infection and offers a basis for exploring the gut–lung interaction in hemorrhagic septicemia pathogenesis. Full article

The oral cavity acts as the anatomical gateway to the respiratory tract, sharing both microbiological and pathophysiological links with the lower airways. Although radiotherapy is a cornerstone treatment for lung cancer, reliable oral microbiome biomarkers for predicting patient outcomes remain lacking. We analyzed the oral microbiome of 136 lung cancer patients and 199 healthy controls across discovery and two validation cohorts via 16S rRNA sequencing. Healthy controls exhibited a significantly higher abundance of Streptococcus compared to patients (p = 0.049, p < 0.001, p < 0.001, respectively). The structure of the microbial community exhibited substantial dynamic changes during treatment. Responders showed enrichment of Rothia aeria (p = 0.027) and Prevotella salivae (p = 0.043), associated with prolonged overall survival (OS) and progression-free survival (PFS), whereas non-responders exhibited elevated Porphyromonas endodontalis (p = 0.037) correlating with shorter OS and PFS. According to Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2) analysis, Akkermansia and Alistipes were nearly absent in non-responders, while Desulfovibrio and Moraxella were virtually absent in responders. A diagnostic model based on Streptococcus achieved area under the curve (AUC) values of 0.85 (95% CI: 0.78–0.91) and 0.99 (95% CI: 0.98–1) in the validation cohorts, and a response prediction model incorporating Prevotella salivae and Neisseria oralis yielded an AUC of 0.74 (95% CI: 0.58–0.90). Furthermore, in small cell lung cancer, microbiota richness and diversity were inversely correlated with Eastern Cooperative Oncology Group (ECOG) performance status (p = 0.008, p < 0.001, respectively) and pro-gastrin-releasing peptide (ProGRP) levels (p = 0.065, p = 0.084, respectively). These results demonstrate that lung cancer-associated oral microbiota signatures dynamically reflect therapeutic response and survival outcomes, supporting their potential role as non-invasive biomarkers for diagnosis and prognosis. Full article

In vitro-cultured plant calli are colonized by diverse endophytes. As these endophytes are inherited from the maternal plant and appear to be highly dependent on the eco-niche of the host cells, they have been termed host-dependent endophytes (HDEs). HDEs occupy the most intimate microbial environment of plant cells. Nevertheless, our understanding of HDEs and their microenvironmental effects on host plants remains limited due to their cultivation-recalcitrant nature. In this study, grapevine (Vitis vinifera L. × V. labrusca L.) callus was subjected to long-term cultivation in media containing different antibiotics (Q: penicillin; L: streptomycin; Z: nystatin) with the intention of creating grapevine calli with different HDEs. The treated calli were then transferred to an antibiotic-free medium for continuous cultivation. After three cycles of subculture over a total period of 45 days, the endophytic microbiota of the grapevine calli were profiled and their physiological parameters were analyzed. Our results revealed that antibiotic treatments can effectively shape HDEs and create distinct bacterial and fungal HDE microbiota in grapevine calli. Compared to treatment without antibiotics (CK), the Q-treated callus contained more Gram-positive bacterial HDEs but fewer Gram-negative and stress-resistant bacterial HDEs, whereas the Z-treated callus had fewer Gram-positive bacterial HDEs and more Gram-negative, stress-resistant and potentially pathogenic bacterial HDEs. More importantly, grapevine calli with different HDE communities showed varying physiological traits such as respiratory rate, peroxidase activity and total sugar content. Correlative analyses further revealed the functional associations between HDE taxa and callus traits. This work provides an example for studying and utilizing plant HDEs. Full article

Background: Nontuberculous mycobacterial pulmonary disease (NTM-PD) is a chronic respiratory infection primarily caused by Mycobacterium avium complex (MAC) and Mycobacterium abscessus. These species differ markedly in antibiotic susceptibility and treatment response, yet the contribution of the respiratory microbiome to this clinical variability remains unclear. To date, however, comparative analyses of microbiome differences between MAC-PD and M. abscessus-PD and their associations with disease severity are limited. Methods: We conducted microbiome analysis of sputum from 37 patients with NTM-PD. Patients were antibiotic-naïve and classified into MAC-PD (n = 29) and M. abscessus-PD (n = 8) groups. Disease severity was determined using radiologic extent on chest computed tomography. Bacterial communities were profiled by 16S rRNA gene sequencing, and differential taxa and predicted functional pathways were analyzed using LEfSe and KEGG orthology databases. Results: Distinct microbiome profiles were observed between MAC-PD and M. abscessus-PD. Three anaerobic species—Porphyromonas pasteri, Fusobacterium periodonticum, and Prevotella nanceiensis—were significantly enriched in M. abscessus-PD (LDA effect size > 3, p < 0.05). Functional biomarker analysis revealed significant enrichment of the cobalamin (vitamin B12) biosynthesis pathway in patients with severe disease, while the C19/C18 steroid hormone biosynthesis pathway was enriched in those with mild disease (p < 0.05). Conclusions: In conclusion, our study demonstrates distinct differences in the respiratory microbiome between MAC-PD and M. abscessus-PD and identifies specific functional pathways associated with disease severity in NTM-PD. These findings highlight the potential value of microbial metabolic signatures as biomarkers for disease assessment. Full article

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants recognized for their toxicological significance. Increasing evidence suggests that chronic exposure to low-molecular-weight PAHs (LMW-PAHs) contributes to heightened disease vulnerability and immune dysregulation, particularly among rural female populations. Recent studies have further linked a significant association between PAH exposure and gut microbiome (GM) modifications. Considering the common embryonic origin of the intestinal and respiratory systems, cross-organ communication under conditions of PAH exposure warrants deeper exploration. Although current gut–lung axis research largely emphasizes microbial metabolites such as short-chain fatty acids and bile acids, the contribution of arachidonic acid (AA) metabolites in LMW-PAH-induced pulmonary inflammation via this axis remains poorly defined. To address this knowledge gap, we developed an animal model employing integrated 16S rRNA sequencing and metabolomics approaches to systematically examine phenanthrene (Phe) and fluorene (Flu) induced GM compositional shifts and associated metabolic reprogramming. Through comprehensive profiling, we identified candidate microorganisms and metabolites potentially involved in dysbiosis-mediated pulmonary inflammation, thereby elucidating the mechanistic basis of Phe and Flu-associated health risks. Full article

Rhizosphere microbiota, serving as pivotal drivers of multifunctionality in grassland ecosystems, are jointly shaped by the dual influences of biotic and abiotic factors. Among biotic components, plant functional types selectively modulate microbial communities through root exudate specificity, while soil fauna (e.g., nematodes and earthworms) drive microbial interaction networks via biophysical disturbances and trophic cascades. However, excessive nematode grazing suppresses the hyphal extension of arbuscular mycorrhizal fungi (AMF). Moderate grazing facilitates the proliferation of ammonia-oxidizing bacteria through fecal input, whereas intensive grazing induces topsoil compaction, leading to a dramatic 40–60% reduction in lipopolysaccharide content in Gram-negative bacteria. Long-term chemical fertilization significantly decreases the fungal-to-bacterial ratio, while organic amendments enhance microbial carbon use efficiency by activating extracellular enzymatic activities. Regarding abiotic factors, the stoichiometric characteristics of soil carbon, nitrogen, and phosphorus directly regulate microbial metabolic strategies. Hydrological dynamics influence microbial respiratory pathways through oxygen partial pressure shifts—drought stress inhibits mycelial network development. Future research should focus on predicting the emissions of gases such as N₂O (ozone monomer) and optimizing nitrogen fertilizer management to significantly reduce greenhouse gas emissions at the source. The soil organic carbon storage in grassland ecosystems is extremely large. Effective prediction and management can make these soils become important carbon “sinks”, offsetting the carbon dioxide in the atmosphere. At the same time, transcriptomics and metabolic flux analysis should be combined with multi-omics technologies and in situ labeling methods to provide theoretical basis and technical support for developing mechanism-based and predictable grassland restoration and adaptive management strategies from both macroscopic and microscopic perspectives. Full article

Ammonia is a key water quality factor limiting shrimp aquaculture. Intestinal health is closely associated with the nutrition, metabolism and immunity of shrimp. However, the response characteristics of the shrimp intestine to ammonia stress under seawater and low-salinity environments remain unclear. In this study, the shrimp Litopenaeus vannamei reared in seawater (salinity 30) or low-salinity (salinity 3) water were subjected to ammonia stress for 14 days, respectively. The changes in intestinal morphology, antioxidant capacity, immune response, energy metabolism, and microbial community were systematically investigated. The results showed that ammonia stress induced intestinal tissue damage in both seawater and low-salinity cultured shrimp, characterized by epithelial cell detachment and mucosal structural disruption. At the molecular level, ammonia stress triggered intestinal stress responses by interfering with key physiological processes such as antioxidant defense and endoplasmic reticulum stress. This process further led to varying degrees of disorders in physiological functions, including immune regulation, inflammatory response, and autophagic activity. In addition, ammonia stress disrupted the homeostatic balance of intestinal energy metabolism by affecting the expression of genes related to glucose metabolism, the tricarboxylic acid (TCA) cycle, and mitochondrial respiratory chain. In addition, ammonia stress increased the diversity of intestinal microbiota and caused microbial dysbiosis by increasing harmful bacteria (e.g., Vibrio) and decreasing beneficial bacterial groups (e.g., Bacillus). Ammonia stress generally enhanced intestinal microbiota chemotaxis. Specifically, predicted functions of microbiota in seawater-cultured shrimp showed increased carbohydrate, linoleic acid, and cofactor/vitamin metabolism; in low-salinity-cultured shrimp, functions including protein digestion/absorption, flavonoid/steroid hormone biosynthesis, and glycosaminoglycan degradation were reduced. These results revealed that ammonia stress compromised shrimp intestinal health by disrupting mucosal structure, triggering stress responses, and disturbing immune function, energy metabolism, and microbial homeostasis. Notably, low-salinity cultured shrimp exhibited more pronounced intestinal stress responses and greater physiological vulnerability than seawater-cultured counterparts. Full article

Airborne fungal exposure in confined indoor environments is a growing public health concern, however the microbial composition of air inside private vehicles remains underexplored. This study aimed to characterize culturable airborne fungi in vehicle cabins and evaluate their association with environmental and behavioral variables. Air samples (100 L) were collected from 69 vehicles using a standardized culture-based method. Simultaneously, a detailed survey was administered to vehicle owners to document usage patterns, maintenance habits, and odor perception. Results revealed a total culturable fungal load of 31,901 CFU/m³, with Cladosporium, Aspergillus, and Penicillium as the most frequently isolated genera. Statistical analysis showed that fungal abundance and community composition were significantly associated with vehicle usage factors such as air disturbance, parking environment, air filter maintenance, and perception of musty odors. Vehicles parked outdoors had significantly higher Bipolaris levels, while lack of regular filter replacement was strongly associated with elevated Alternaria abundance. The presence of musty or moldy odors correlated with a 2.5-fold increase in Aspergillus levels. Redundancy analysis confirmed that odor perception and parking behavior were the strongest predictors of fungal community structure, with specific genera displaying distinct ecological preferences across usage conditions. Usage patterns and maintenance habits significantly influence in-cabin fungal communities, with implications for respiratory health, particularly due to the presence of allergenic and opportunistic genera like Aspergillus, Alternaria, and Bipolaris. Regular air filter maintenance and attention to odor cues may help reduce fungal load and associated health risks. Full article

Bovine respiratory disease complex (BRDC) is a leading cause of morbidity and mortality in pre-weaned calves, yet the role of commensal nasal microbiota in outbreak severity remains poorly understood. This study characterized nasal bacterial communities during two BRDC outbreaks of differing severity (moderate vs. severe) and at ~30 days post-treatment. Nasal swabs were collected from calves and analyzed using 16S rRNA gene sequencing (V1–V3 regions, Illumina MiSeq) and quantitative PCR targeting three major BRDC pathogens. Microbial community profiles differed between outbreak groups and across timepoints. Calves in the severe outbreak group exhibited lower microbial diversity compared to those in the moderate outbreak. In both groups, diversity significantly increased from outbreak to post-treatment. At the time of disease, nasal communities were dominated by the genera Mycoplasmopsis, Mesomycoplasma, and Caviibacter, with qPCR confirming Mycoplasma bovirhinis as the predominant species. These findings indicate that BRDC outbreaks in pre-weaned calves are associated with reduced microbial diversity and the dominance of pathogenic Mycoplasma species, with recovery characterized by greater bacterial diversity. Shifts in nasal microbiome composition between outbreak and post-treatment may reflect pathogen-driven disruption during disease and subsequent microbial community rebalancing. Full article

Even with significant advances in therapeutic interventions and monitoring protocols, cystic fibrosis (CF) remains a critical pediatric health challenge affecting respiratory function and long-term patient outcomes. CF, caused by mutations in the CFTR gene, disrupts normal mucociliary clearance and creates conditions for chronic respiratory infections. The disorder affects individuals globally, with pediatric patients facing particularly complex microbial challenges that evolve throughout childhood growth. CF poses significant risks with progressive lung function decline and increased mortality, leading to potential short- and long-term respiratory complications. There is a growing concern among clinicians about the dynamic nature of airway microbial communities, with classical pathogens like Pseudomonas aeruginosa and Staphylococcus aureus showing sequential emergence patterns that complicate treatment strategies, highlighting an urgent need for microbiome-informed therapeutic approaches. Our review aims to provide a comprehensive overview of airway microbiome evolution in pediatric CF patients. We outline the molecular and ecological mechanisms involved in microbial community progression, as well as the age-related trajectories leading to pathogen-dominated ecosystems and the subsequent complications associated with microbial dysbiosis. Given the widespread implications of disrupted microbial balance on disease progression, our review also presents the temporal landscape of airway microbiome changes, including age-related microbial succession patterns, and explores the underlying mechanisms driving these ecological shifts. The progressive nature of microbial simplification frequently leads to treatment challenges, emphasizing the importance of investigating microbiome-targeted therapeutic interventions. Therefore, in this review, we also explore established therapeutic strategies, including CFTR modulators and probiotics, which could offer promising approaches to maintaining microbial balance and improving outcomes in pediatric CF patients. Full article

Background: Athletes’ skin is exposed to increased microbial challenges due to rigorous physical activity, perspiration, constant “skin-to-skin” contact, frequent showering, use of hygiene products, and environmental factors present in training settings. This study aims to characterize the skin microbiome communities of young wrestlers and kickboxers in comparison with their non-athlete age-peers. Methods: A total of 56 combat sport athletes (30 males and 26 females, mean age ± SD = 18.2 ± 1.5 years) and 25 non-athlete youths (control group: 13 males and 12 females, mean age ± SD = 19.8 ± 1.2 years) voluntarily consented to participate in the study conducted by our research team in 2023 and 2024. The skin microbiome analysis involved standardized sampling, DNA isolation, molecular sequencing, and bioinformatic analysis, thus enabling detailed characterization and comparison of the skin microbial community in contact sports athletes and the control group. Results: Our results revealed notable sexual dimorphism in the skin microbiome composition of youth. Males showed a higher relative abundance of bacterial genera associated with nosocomial infections and respiratory diseases, while females had more skin inflammation- and infection-related genera (relative abundances in males vs. in females: Corynebacterium—12.0 vs. 7.2; Luteimonas—4.4. vs. 1.4; Paracoccus—8.8 vs. 5.0; Psychrobacter—6.3 vs. 4.4; Cutibacterium—6.4 vs. 11.4; Kocuria—1.6 vs. 3.9; Micrococcus—5.8 vs. 8.5; Pseudomonas—1.2 vs. 3.4; Streptococcus 3.3 vs. 6.2). We also found skin microbiome differences between athletes and non-athletes in both sexes: wrestlers, who experience frequent skin-to-skin contact and wear less covering sportswear, had microbiome profiles distinct from both kickboxers and non-athletes (relative abundances in athletes vs. in non-athletes: Psychrobacter—7.3 vs. 0.4; Staphylococcus 9.5 vs. 18.5; predominance of genera by sports type: relative abundance of Cutibacterium and Streptococcus was higher in kickboxers, and relative abundance of Acinetobacter, Enhydrobacter, Micrococcus, and Enhydrobacter was higher in wrestlers). Bacteria linked to skin infections (e.g., Aliterella, Arthrobacter, and Empedobacter) were present in around 30% of wrestlers and kickboxers but were absent in the control group. Conclusions: These results underscore the heightened risk of skin infections in contact sports and highlight the importance of regular microbiome monitoring and hygiene protocols among young athletes. Full article

Background: Oral antiseptic formulations are widely used as adjuncts in oral hygiene to reduce pathogenic microorganisms and prevent oral diseases. While these agents are effective in controlling biofilm, their broader effects may disrupt the oral microbiota’s balance, potentially contributing to systemic health implications. The complex relationship between antiseptic use, microbial composition, and systemic outcomes remains insufficiently mapped. Objective: This scoping review aimed to explore and map the current evidence regarding the impact of antiseptic formulations on oral microbiota composition and to examine their potential associations with systemic diseases. Methods: A comprehensive literature search was performed using PubMed, Scopus, and Web of Science up to June 2025. Studies were included if they investigated antiseptic formulations commonly used in oral healthcare—such as chlorhexidine, essential oils, and cetylpyridinium chloride—and reported effects on oral microbiota and/or systemic health. Eligible study types included human clinical trials, observational studies, in vitro, and animal studies. Two reviewers independently screened and selected studies, with disagreements resolved by consensus. Data extraction focused on study design, antiseptic agents, microbial outcomes, and systemic implications. A total of 12 studies were included and charted. Results: The included studies demonstrated that oral antiseptics effectively reduce pathogenic microorganisms and improve clinical outcomes in oral diseases such as gingivitis and periodontitis. However, several studies also reported alterations in commensal microbial communities, suggesting a potential for dysbiosis. Some studies indicated possible links between antiseptic-induced microbial changes and systemic conditions, including cardiovascular and respiratory diseases. Conclusions: The evidence highlights a dual effect of antiseptic formulations: while beneficial in controlling oral pathogens, they may disrupt microbial homeostasis with possible systemic consequences. Further research is needed to evaluate long-term effects and develop targeted, microbiota-preserving oral hygiene strategies. Full article

The Mycoplasmataceae are a family of bacteria that typically cause respiratory, arthritic, and genitourinary disease in humans. Mycoplasma spp. of animal origin are also the causative agents of porcine wheezing disease, chronic respiratory disease and arthritis in chickens and other conditions. These diseases have a significant impact on public health and the economic development of livestock breeding. Clinical prevention and treatment of mycoplasma infections is primarily dependent on the use of antibiotics. However, inappropriate and excessive use of antimicrobials has enabled resistance development that has become a significant clinical concern. Mycoplasma are also robust biofilm producers, and this process is a major factor for the persistence of these infections, especially in conjunction with common antibiotic resistance mechanisms, including target gene mutations and the action of efflux pumps. A mycoplasma biofilm refers to a structured and stable microbial community formed by Mycoplasma spp. adhering to biological or non-biological surfaces under suitable conditions and secreting extracellular polymers (EPS) such as polysaccharides. This process allows the microorganisms to adapt to their surrounding environment and survive during the growth process. These biofilms render bacteria more resistant to antimicrobials than planktonic bacteria, resulting in biofilm-associated infections that are more challenging to eradicate and more likely to recur. The current study reviews progress from the fields of biofilm formation, structure and identification, correlations between biofilms and drug resistance and virulence as well as methods of biofilm prevention and control. Our aim was to provide a reference basis for the subsequent in-depth understanding of the research of mycoplasma biofilms. Full article

Mycoplasmal pneumonia of sheep (MPS), caused by Mesomycoplasma (Mycoplasma) ovipneumoniae, profoundly impacts ovine productivity and survival. Although gut–lung microbiota interactions are increasingly recognized in respiratory diseases, whether similar crosstalk occurs between the lung and rumen microbiota in MPS-affected sheep remains unknown. To investigate alterations in the lung and rumen microbiota of sheep with MPS, the crosstalk between these microbial communities, and their impacts on growth phenotypes. From a cohort of 414 naturally infected six-month-old male Hu sheep, we selected 10 individuals with severe pulmonary pathology and 10 healthy controls for detailed phenotypic and microbiome analyses. Assessment of 359 phenotypic traits revealed that MPS significantly impairs feed efficiency and growth rate (p < 0.05). Through 16S rRNA gene sequencing, we found that MPS significantly altered the pulmonary microbiota community structure (p < 0.01), with a noticeable impact on the rumen microbiota composition (p = 0.059). Succinivibrionaceae_UCG-001 was significantly depleted in both the rumen and lungs of diseased sheep (p < 0.05) and strongly associated with reduced average daily feed intake (p < 0.05). In addition, pulmonary Pasteurella and ruminal Succinivibrionaceae_UCG-002 were significantly enriched in MPS-affected sheep, showed a strong positive correlation (p < 0.05), and were both negatively associated with feed efficiency (p < 0.05). Notably, Pasteurella multocida subsp. gallicida may act as a keystone species influencing feed efficiency. These findings point to a previously unrecognized rumen-lung microbial axis that may modulate host productivity in sheep affected by MPS. This work provides new insights into the pathogenesis of MPS and offers potential targets for therapeutic intervention and management. Full article

Streptococcus pyogenes is a bacterial pathogen known to be the causative agent in many different illnesses, with Group A Streptococcus (GAS) pharyngitis (strep throat), being one of the more prevalent. The spread and severity of GAS pharyngitis can grow exponentially if individuals are not taking the proper precautions. Wastewater surveillance has been used to test for numerous different pathogens that humans spread throughout a community and in this study, we utilized wastewater surveillance to monitor GAS pharyngitis in a small city. Over a year, 57 wastewater influent samples were tested for S. pyogenes and three commonly tested respiratory viruses (Respiratory Syncytial Virus (RSV), SARS-CoV-2, Influenza A). Three microbial indicators and population normalizers (CrAssphage, Pepper mild mottle virus (PMMoV), and Mycobacterium) were tested as well to compare and contrast each indicator’s value and range over time. Wastewater data was then compared to publicly available search term data as clinical data was not readily available. There was a high correlation between the collected molecular data and the publicly available search term data for Streptococcus pyogenes. Additionally, this study provided more information about the seasonal trend of S. pyogenes throughout the year through molecular data and allowed for the ability to track peak infection months in this small city. Overall, these results highlight the substantial benefits of using wastewater surveillance for the monitoring of GAS pharyngitis. This study also provides helpful insights into future studies about the prevalence of respiratory bacteria and their seasonal trends in wastewater, allowing for public health systems to provide mitigation strategies. Full article