Search Results (290)

Estuarine ecosystems face intense anthropogenic pressures, yet systematic research on how domestic wastewater influences the dissolved organic carbon (DOC) pool via microbial community regulation remains limited. In this study, we conducted a microcosm experiment simulating wastewater input into the Qiantang River and integrated multi-omics (16S rRNA sequencing, metagenomics, metatranscriptomics, and FT-ICR MS) to elucidate the mechanism. Results showed that: (1) Wastewater input increased initial DOC and changed its degradation pattern: slower decay but higher removal. (2) Compared to the control, the wastewater-amended group exhibited a decreased fluorescence intensity contribution of carboxyl-rich alicyclic molecule (CRAM)-like compounds, indicating reduced chemical stability of recalcitrant DOC (RDOC). (3) Wastewater drove directional microbial succession from catabolic-dominant taxa (e.g., Comamonas, Citrobacter) to anabolic-dominant taxa (e.g., Reyranella), shifting metabolism from pollutant degradation to endogenous synthesis, thereby lowering the system’s efficiency in forming stable RDOC. (4) Multi-omics revealed a “stimulation-balance” functional response: early activation of xenobiotic degradation and signal transduction (day 2), followed by a shift to anabolic metabolism (day 28). This functional transition, driven by microbial succession, ultimately reduced RDOC stability. Our findings reveal that wastewater reshapes the microbial carbon pump, providing a theoretical basis for assessing estuarine carbon sink responses to pollution control measures. Full article

Salinity is a dominant ecological driver shaping microbial community structure and function in hypersaline environments. Here, we investigated transcriptional responses to rapid salinity fluctuations using metatranscriptomic analyses of an intermediate-salinity brine sample from the Santa Pola solar salterns (Alicante, Spain). To this end, two experimental conditions were applied: salinity increase (12.4% to 17%) and salinity dilution (12.4% to 7%). Differential gene expression, functional enrichment, and protein isoelectric point (pI) distributions were analyzed to characterize osmoadaptive mechanisms. Salinity increase triggered a stress-dominated response characterized by upregulation of compatible solute biosynthesis (e.g., glycine betaine and ectoine), protein turnover, and chaperone activity, alongside repression of translation, energy metabolism, and transport systems. In contrast, salinity dilution induced metabolic reactivation, including enhanced translation, energy production, and osmolyte degradation pathways, indicating recovery from osmotic stress. Functional shifts were accompanied by changes in proteome physicochemical properties, with increased salinity promoting a shift toward higher pI proteins, consistent with salt-out strategies. These findings reveal a highly dynamic and asymmetric transcriptional plasticity, where osmotic upshift imposes stronger constraints than downshift, driving coordinated metabolic reprogramming and proteome restructuring in intermediate-salinity microbial communities. Full article

Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) are persistent pollutants resistant to conventional treatment processes and pose significant environmental risks. The aim of this study was to comparatively evaluate the metatranscriptomic responses of activated sludge bacterial communities to PFOS and PFOA exposure at environmentally relevant (150 ng/L) and elevated (1050 ng/L) concentrations. Activated sludge from the Zeekoegat Wastewater Treatment Plant (Pretoria, South Africa) was used under aerobic conditions for 45 days. Taxonomic profiling revealed a Proteobacteria-dominated community with distinct pollutant-specific shifts. Under PFOA exposure, Pseudomonas dominated at low concentration, while Achromobacter and Burkholderia increased at higher levels. Under PFOS exposure, Kerstersia dominated at low concentration, whereas Comamonas, Sphingopyxis, and Polaromonas were enriched at higher concentration. Functional analysis revealed increased abundance of stress-response and metabolic pathways, including ABC transporters, chaperonins (GroEL), and β-oxidation. Overall, the results indicate a dose-dependent microbial adaptation, with pollutant type driving functional responses. These findings highlight pollutant-specific microbial responses and adaptation under PFAS exposure in activated sludge systems. These findings highlight pollutant-specific microbial strategies and the potential of activated sludge microbiomes in PFAS transformation processes. Full article

Rodents and shrews are important reservoir hosts due to their close association with human activities and their role in carrying various zoonotic pathogens. Recently, meta-transcriptomic sequencing has become a powerful tool for surveilling and screening novel pathogens from wild animals. However, many of these studies focused only on the diversity and genetic evolution of viruses from wildlife, while ignoring non-viral pathogens such as bacterial and eukaryotic microorganisms. Here, we performed a comprehensive infectome analysis of 227 tissue samples collected from 42 rodents and 16 shrews across six cities of Guangdong Province, China. We identified 34 viral families, including 23 mammalian viruses. Phylogenetic analysis revealed a henipavirus from the kidneys of shrews closely related to the Langya virus with potential infection risks to humans. Additionally, two potential pathogenic bacteria and 12 eukaryotic pathogens from six genera were found, showing clearer organ tropism than viruses. Interestingly, a moderate positive abundance correlation between Usmuvirus newyorkense and Trichinella suggested a potential virus–parasite association. We used machine learning models to evaluate the zoonotic potential of the obtained viruses, which indicated that 15 of 23 viral species were high risk for human infection. These findings provide important insight into the substantial zoonotic threat posed by pathogens circulating in wild small mammals in southern China and highlight the necessity for persistent wildlife pathogen surveillance. Full article

The consumption of wild rodents in certain regions of Southwest China creates a potential interface for zoonotic pathogen exposure, yet the virome composition of edible rodents remains insufficiently characterized. In this study, we performed multi-organ RNA metatranscriptomic analysis of three commonly consumed rodent species (Niviventer andersoni, Berylmys bowersi, and Rattus losea) collected from Guizhou Province, analyzing five visceral organs per species. A total of 1198 viral contigs spanning 37 viral families were identified, revealing diverse viral communities across host species and tissues, with host identity emerging as a key factor shaping virome structure. Sequences related to Seoul virus were detected in the lungs of R. losea, showing high similarity to previously reported strains, and sequences closely related to porcine Rotavirus A were identified in the lung samples of N. andersoni, indicating a close phylogenetic relationship with livestock-associated viruses. While these findings do not confirm active infection or transmission, they may reflect potential environmental exposure or ecological links at the wildlife–livestock interface. Overall, this study provides a baseline characterization of the multi-organ virome of edible rodents and highlights the importance of integrated surveillance and risk assessment within a One Health framework. Full article

The relationship between microorganisms and human health is inseparable. In today’s increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments. Full article

Traditional fermented foods and beverages (TFFB) rely on complex microbial communities that generate distinctive flavors, nutritional attributes, and cultural value, but spontaneous or empirically controlled fermentations often limit reproducibility. Defined microbial consortia (DMCs) provide a promising route for improving fermentation controllability and product consistency, although overly simplified starters may fail to reproduce the ecological robustness and sensory complexity of traditional systems. This review focuses on how multi-omics and culturomics can support rational DMC design in TFFB. We summarize how metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics reveal community structure, functional potential, active expression, metabolic output, and cultivable strain resources. Particular attention is given to translating multi-omics evidence into strain prioritization through the identification of keystone microorganisms that drive core fermentation functions and helper microorganisms that support ecological or metabolic stability. We further propose an Assembly-Assessment-Redesign (A-A-R) framework for iterative DMC optimization, linking strain selection, functional validation, performance evaluation, and consortium redesign. Finally, we discuss key challenges, including cross-omics integration, experimental verification of microbial functions, standardized validation criteria, and the transfer of laboratory-designed consortia to industrial fermentation systems. Full article

Microalgae-based wastewater treatment can support sustainable crop production. This study evaluated whether ethanol supplementation improves swine wastewater (SW) treatment by Dictyosphaerium sp. and enhances algal biofertilizer production. Across the ethanol levels tested, 500 mg/L ethanol significantly promoted algal growth and enhanced liquid-phase net removal of total salts, carbonate/bicarbonate, ammonium, phosphate, and calcium. Ethanol supplementation also reduced apparent nitrogen loss, and no residual ethanol was detected at the end of the culture. In the biofertilizer production experiment, peak algal biomass, algal nitrogen, and algal phosphorus increased by 320.0–407.4%, 122.7–158.1%, and 100.0–170.0%, respectively. Metatranscriptomic analysis showed active transcription of adh, aldh/aldB, and acs in Dictyosphaerium sp. and some bacterial taxa, mainly Flavobacterium, Chryseobacterium, Comamonas, and Brevundimonas. Community and transcriptomic results indicate enhanced photosynthetic activity and taxon-specific N- and P-related transcriptional responses, consistent with altered nitrate/nitrite transformation potential and increased nitrogen retention in the algal–bacterial system. Under the tested conditions, ethanol supplementation shows promise for SW treatment and algal biofertilizer production. Full article

The lower airways are a dynamic environment where physical, microbial, and molecular factors intersect to regulate respiratory health and disease. The muco-microbiotic (MuMi) layer, composed of mucus, resident microbes, and extracellular vesicles (EVs), is not just a passive barrier but also an active site for host–microbe communication. This layer integrates epithelial cell biology, microbial activity, and immune responses within the bronchial environment. New transcriptomic and metatranscriptomic technologies show that it is not only which microbes are present but also their gene activity that closely links to airway inflammation and disease. EV-associated RNAs from both host and microbial cells act as key messengers, influencing epithelial responses, immune activity, mucus properties, and microbial behaviour. This review highlights evidence that positions the MuMi layer as central to understanding lower airway disease, particularly asthma and chronic obstructive pulmonary disease (COPD). Distinct gene expression programs and biomarker profiles, such as exhaled nitric oxide, may reflect different disease mechanisms even in cases with similar clinical features, such as eosinophilia. Multi-omic approaches focused on the MuMi layer enable better disease classification, biomarker discovery, and therapy selection. By putting the MuMi interface at the core of precision pulmonology, we provide a framework for advancing personalised care in chronic respiratory diseases. Full article

Antimicrobial resistance (AMR) has become one of the top ten global public health threats. Many countries have recognized the societal and economic burden of AMR. AMR has reduced the effectiveness of antimicrobial therapies, and this results in high mortality, morbidity, and health care expenditure. Like all the other developing countries, South Africa (SA) falls under the same ambiguous management system of antimicrobials. A lot of research focused on the global public health threat “AMR”. However, studies on AMR in wastewater are not yet enough, even though they are beginning to gain momentum. This paper highlights the imperatives of surveying AMR pathogens in wastewater since wastewaters are consecrated as hotspots for the dissemination and propagation of AMR genes. RNA was extracted from the untreated wastewater samples collected from the Tshwane district in Gauteng province, SA. Metatranscriptomics analysis was proposed for the analysis and profiling of AMR genes present in the wastewater. A total of 39 AMR gene families and 39 AMR drug classes were detected across 17 samples. The Metatranscriptomics approach discussed in this paper demonstrates the importance of wastewater surveillance, as it can be used as an early detecting system for communicable diseases and for monitoring wastewater. Full article

Bats are reservoirs for many emerging viruses, yet broad-scale spatial patterns of bat viromes and their ecological determinants remain unclear, limiting spillover risk assessment. To address this, we conducted a standardized survey across central to southern China. During 2022–2023, fecal samples were collected from 527 bats representing 17 species at 21 caves in seven provinces. Using each cave as the analytical unit, samples from all species at a site were pooled to construct 21 fecal RNA virome libraries for metatranscriptomic sequencing; viral-like contigs were annotated, and viral alpha/beta diversity was quantified at the genus level. Sites were grouped by geographic distance and latitude to evaluate spatial differentiation and to relate virome patterns to host community attributes and environmental factors. We annotated 56 viral families, including 19 vertebrate-associated families, with multiple families and genera shared across geographic groupings. Vertebrate-associated viral diversity showed limited evidence of geographic isolation within the study region but suggested gradual turnover with latitude. Host species richness was the strongest correlate of virome diversity, exceeding the effects of evaluated environmental variables (e.g., climate and human activity). These results support prioritization of species-rich bat habitats for surveillance and risk assessment. Full article

Alzheimer’s disease (AD) is characterized by progressive cognitive decline and the accumulation of amyloid-β (Aβ) plaques and tau neurofibrillary tangles. Beyond genetic and proteostatic mechanisms, infection- and dysbiosis-based models of AD have gained renewed attention, including the antimicrobial protection hypothesis, in which Aβ may participate in innate immune defense. Here, we reanalyzed ribosomal depleted (Ribo-Zero) RNA-seq data from dorsolateral prefrontal cortex (DLPFC) samples from the Mount Sinai Brain Bank cohort (GSE53697) to screen for non-human transcripts. Reads underwent quality control and adapter trimming, taxonomic classification with Kraken2, abundance re-estimation with Bracken, and differential abundance testing with edgeR. Across 17 samples (9 advanced AD and 8 controls), we detected low-biomass microbial signals, with Acinetobacter radioresistens showing enrichment in the AD group (FDR = 0.018). Several additional taxa showed suggestive group differences but did not remain significant after multiple testing correction, including Lactobacillus iners (FDR = 0.051). We also performed an exploratory in silico analysis of an A. radioresistens biofilm-associated protein homolog, identifying predicted amyloidogenic motifs and surface-exposed regions that may be relevant to cross-seeding hypotheses, although no mechanistic inference can be drawn without experimental validation. Given the technical challenges of inferring microbial signals from post-mortem brain RNA-seq data, including contamination risk, low microbial biomass, and overwhelming host background, these findings should be interpreted as hypothesis-generating and warrant orthogonal validation in larger, microbiome-aware cohorts. Full article

The human microbiome influences health and disease through diverse biochemical and functional outputs (e.g., enzymes, structural proteins, metabolites, and other cellular components) that affect nearly every aspect of human physiology. Metatranscriptomics (MT), an unbiased RNA sequencing approach, is a high-throughput and high-content method that quantifies both gut microbial taxonomy and active biochemical functions. Because microbial community composition and gene expression are dynamic, understanding temporal variation in the gut metatranscriptome across multiple time scales is essential. Here, we report the temporal dynamics of gut microbiome species and functions using a large cohort (n = 6157) with a clinically validated stool MT test. We quantified microbiome stability from hours to years and assessed taxonomic and functional resilience to major luminal perturbations, such as colonoscopy bowel preparation. Longitudinal analyses of samples collected within the same day, and across days, weeks, months, and years, revealed consistently high stability in both composition and gene expression within a single day and, importantly, across an approximate six-month period. Among individuals reporting stable diets and no antibiotic exposure, taxonomic and functional profiles remained stable for up to three years. Following colonoscopy preparation, our preliminary study of the microbiome demonstrated strong resilience, returning to its pre-procedure state within one week. Overall, these findings demonstrate that the gut microbiome is generally stable over a six-month time frame, with longer-term changes occurring gradually. These findings support the robustness of stool-based MT profiling for species-level and pathway-resolved functional analysis in longitudinal research and health applications. Full article

Ticks serve as primary vectors for a wide array of RNA viruses, yet the diversity and distribution of tick-associated RNA viruses remain incompletely characterized in Hebei province. To address this gap, we conducted a systematic metatranscriptomic investigation of 986 ticks representing six species, collected from the diverse ecological landscapes of Hebei Province in northern China. Our analysis recovered 25 complete or near-complete viral genomes spanning 12 families, including Phenuiviridae, Flaviviridae, and Nairoviridae. Of critical public health significance, we identified Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in both Haemaphysalis longicornis and Dermacentor nuttalli. Phylogenetic reconstruction revealed marked geographic stratification where strains from the coastal plains clustered with the dominant Genotype F, while those from the mountainous north formed a characteristic and divergent lineage phylogenetically linked to isolates from Inner Mongolia. Furthermore, a novel viral agent provisionally named Zhangjiakou Hepacivirus was discovered in Haemaphysalis japonica. This virus shared less than 80% nucleotide identity with the rodent-associated Hepacivirus P, consistent with a rodent origin and possible cross-species transmission. Collectively, these findings reveal descriptive variation associated with vector identity, physiological status, and ecological context in shaping viral evolution and underscore the need for continuous metagenomic surveillance to mitigate emerging tick-borne disease risks within a One Health framework. Full article

This study investigated the ecological selection and enrichment of anaerobic ammonium-oxidizing bacteria (AnAOB) driven by endogenous carbon cycling in a low-oxygen SBR biofilm system without external carbon addition. The system was operated using dried biofilm inoculation, continuous low oxygen (DO < 0.1 mg/L), and complete drainage. After 117 days, AnAOB were enriched to 8.14% relative abundance and became the dominant functional group. At an influent total nitrogen (TN) of 25 mg/L, the average effluent TN and NH₄⁺-N were 6.37 and 3.75 mg/L, respectively, corresponding to a TN removal efficiency of 75% and meeting the Class A discharge standard. Metagenomic and metatranscriptomic analyses revealed that anammox was the primary nitrogen removal pathway, with nitrite supplied through partial nitrification and endogenous partial denitrification. Higher expression of nitrate reductase genes than of nitrite reductase genes favored nitrite accumulation through endogenous partial denitrification, thereby creating a self-sustaining internal cycle between nitrate reduction and anammox. Extracellular polymeric substances (EPS) served as the key internal carbon source driving this process. This ecological regulation strategy provides an energy-efficient and stable strategy for mainstream low C/N municipal wastewater treatment without external carbon addition. Full article