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At least 19 recordsLinked to original sources

PubMed2026

Elucidation of microbial community structure, small-molecule metabolic and flavor profile characteristics in Xuanwei ham under different processing techniques.

This study systematically compared the impacts of traditional (TH) and modern (MH) processing techniques on the physicochemical properties, microbial community structure, metabolome, and volatile aroma compounds of Xuanwei ham. The results showed that the TH group had higher moisture content and water activity, along with a more tender texture, whereas the MH group exhibited greater hardness and chewiness. Microbiological analysis revealed that the interior of the MH group had higher species richness of both fungi and bacteria, while the TH group maintained higher fungal diversity. Metabolomic analysis identified 112 differential metabolites, with sweet amino acids and certain lipids being more enriched in modern ham, whereas traditional ham contained higher levels of umami amino acids, polyunsaturated fatty acids, and flavor compounds such as carnosine. KEGG pathway enrichment indicated that the differences were primarily concentrated in amino acid biosynthesis and metabolism-related pathways. Volatile flavoromics analysis identified 45 odor-active compounds and screened 15 key aroma-active substances. Among them, modern processed ham was significantly enriched in fatty aldehydes such as (E)-2-nonenal, hexanal, nonanal, and octanal, whereas traditional processed ham was characterized by 1-octen-3-ol, (E,E)-2,4-decadienal, methional, acetoin, and benzeneacetaldehyde. Correlation analysis confirmed that dominant microbes in Xuanwei ham were significantly associated with differential metabolites and characteristic aroma compounds, respectively. This study provides a scientific basis for standardizing production processes, enabling precise quality control, and promoting high-quality industrial development of Xuanwei ham.

Animals↗

PubMed2026

Comparative profiling of microbial community structure, enzyme potential, metabolic features, and volatile composition in craft and Jiafan Huangjiu processes.

Craft Huangjiu and Jiafan Huangjiu represent two distinct industrial Huangjiu product outcomes with contrasting volatile profiles. This study compared craft Huangjiu (L70) and Jiafan Huangjiu (L79) to characterize their physicochemical, microbial, gene-level functional, metabolic, and volatile features. Because L70 involved mid-fermentation addition of finished Huangjiu, this comparison was not intended to isolate the sole effect of fermentation interruption versus continued fermentation. L79 showed more extensive carbon and nitrogen utilization, with lower residual substrates and higher ethanol and acetic acid contents than L70, whereas L70 retained a less complete fermentation state. At the volatile level, GC-MS and volatile metabolomics consistently showed an ester-enriched profile in L79 and a more alcohol-dominant profile in L70. FlavorDB-based putative annotation and threshold-based OAV analysis further indicated distinct database-assigned descriptor distributions and potential odor-active compounds, with more OAV > 1 ester-related compounds in L79. Metagenomic analysis showed that L70 was dominated by Lactobacillus acetotolerans, whereas L79 contained higher relative abundances of Saccharomyces cerevisiae, Aspergillus oryzae, Aspergillus flavus, and Fructilactobacillus fructivorans. Metagenomic functional annotation showed higher representation of hydrolysis-related CAZy genes and ester-related enzyme annotations in L79. KEGG-based pathway mapping further indicated greater gene-level potential for ethanol-, acetate-, and acetyl-CoA-related metabolism in L79. Accordingly, the L70 profile should be interpreted as the integrated final-product outcome of process intervention, exogenous input, and subsequent fermentation. The findings provide a comparative basis for future flavor regulation and process optimization in Huangjiu and other fermented alcoholic beverages.

Volatile Organic Compounds↗

PubMed2025

Comparative analysis of antibiotic resistance genes between fresh pig manure and composted pig manure in winter, China.

Antibiotic resistance is a critical global public health issue. The gut microbiome acts as a reservoir for numerous antibiotic resistance genes (ARGs), which influence both existing and future microbial populations within a community or ecosystem. However, the differences in ARG expression between fresh and composted feces remain poorly understood. In this study, we collected eight samples from a farm in Kaifeng City, China, comprising both fresh and composted pig manure. Using a high-throughput quantitative PCR array, we analyzed differences in ARG expression between these two types of manure. Our findings revealed significant differences in ARG profiles, as demonstrated by principal coordinate analysis (PCoA). Further analysis identified 39 ARGs (log2FC > 1, p < 0.05) in composted pig manure, with 25 genes downregulated and 14 upregulated. Notably, tetB-01, blaOCH, and blaOXY were the most abundant in composted pig manure compared to fresh manure. Additionally, 16S rRNA species profiling revealed that the composting process significantly altered the microbial community structure, with an increased abundance of Firmicutes and a decreased abundance of Bacteroidetes in composted pig manure. In summary, composting substantially transforms both the microbial community structure and the ARG profile in pig manure, underscoring its potential role in modulating the dynamics of ARGs in agricultural environments.

Animals↗

PubMed2026

DURABLE: A Workflow for Determining Corrosion-Driving and Protective Microbial Mechanisms.

Microbiologically influenced corrosion (MIC) threatens global infrastructure, causing billions of dollars in annual losses. Its persistence stems from unresolved mechanisms─particularly the metabolites produced by microorganisms that drive or inhibit corrosion─and the microbial community structures. Progress has been hindered by the absence of systematic workflows to rapidly and accurately identify MIC-relevant microorganisms and their functions. Here, we present DURABLE (Detection of Unique Corrosion Resistant or Accelerating Biologics in a Laboratory Environment), a pipeline that couples high-throughput microbial screening with genomic and metabolic workflows. We applied the DURABLE workflow to six diesel tank samples and revealed fuel-dependent microbial community structures, which showed greater diversity and evenness in bacterial communities than their fungal counterparts. The workflow used carbon steel beads to rapidly screen over 80 bacterial isolates for corrosive activity, reducing assay time to approximately 2 days compared with the conventional 30-day metal coupon test. More than 40 isolates were identified as corrosive. Further testing using mass spectrometry analysis revealed corrosion-associated metabolites, which were further validated using electrochemical assays. Thus, DURABLE achieved a ∼15-fold increase in screening speed and provided a scalable and mechanistic framework for dissecting MIC dynamics. We expect this advance will enable the development of precision mitigation strategies in hydrocarbon fuel infrastructure.

Bacteria↗

PubMed2025

Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.

The precise microbial determinants driving clinical outcomes in severe pneumonia are unknown. Competing ecological forces produce dynamic microbiota states in health and disease, and a more thorough understanding of these states has the potential to improve pneumonia therapy. Here, we leverage a large collection of bronchoscopic samples from patients with suspected pneumonia to determine lung microbial ecosystem dynamics throughout the course of pneumonia. We combine 16S rRNA gene, metagenomic, and metatranscriptomic sequencing with bacterial-load quantification to reveal clinically relevant drivers of pneumonia progression. Microbiota states are predictive of pneumonia subtypes and exhibit differential stability and pneumonia therapy response. Disruptive forces, such as aspiration, are associated with cohesive changes in gene expression and microbial community structure. In summary, we show that host and microbiota landscapes change in unison with clinical phenotypes and that microbiota state dynamics reflect pneumonia progression. We suggest that distinct pathways of lung microbial community succession mediate pneumonia progression.

Humans↗

PubMed2026

Adaptive Evolution Reveals Metabolic Plasticity and Functional Redundancy in an Anaerobic Microbiome under Extreme Ammonia Stress.

Ammonia toxicity represents a primary biochemical bottleneck governing microbial community structure and performance during the anaerobic digestion of the organic fraction of municipal solid waste. However, the mechanistic basis of microbial adaptation to chronic ammonia levels remains poorly characterized. In this study, a long-term sequential enrichment strategy under progressively increasing ammonia concentrations (350-1500 mgN L-1), integrated with genome-centric metagenomics and metatranscriptomics, was employed to resolve the response of an organic waste-degrading microbiome over a 240 day period. Increasing ammonia pressure induced a progressive decline in methanogenesis and accumulation of volatile fatty acids, particularly acetate. Despite these inhibitory pressures, methane production was only halved relative to the initial baseline reflecting a resilient methanogenic community. This stability was driven by a restructuring of the microbiome, where functional redundancy across divergent taxa preserved core metabolic functions. Key adaptive responses included the reconfiguration of carbon fixation pathways, specifically via a variant of the Wood-Ljungdahl pathway coupled with the glycine cleavage system acting as an alternative acetate oxidation route, as well as sustained osmoprotectant biosynthesis. Cellular homeostasis was preserved through H+ replenishment via multiple energy-converting complexes and K+ influx to maintain cation-proton balance. Collectively, these findings demonstrate that metabolic plasticity and the preservation of core metabolic functions are the primary determinants of ammonia resilience, sustaining methane production under inhibitory conditions.

Ammonia↗

PubMed2026

Metagenomic insights into the mechanisms of heteroatom-doped, iron-loaded biochar in enhancing anaerobic digestion of waste activated sludge.

Anaerobic digestion is a crucial technology for resource recovery from waste activated sludge. Enhancing its methane production efficiency using conductive materials is a key research objective. This study aimed to elucidate the mechanisms by which conductive materials promote this process. Three types of biochar(FeS@BC300, FeP@BC600, and FeP@BC900) were prepared by doping bamboo powder with N, P, S and iron salts under pyrolysis conditions at 300-900 °C, and their physical and chemical properties were characterized, including surface functional groups, specific surface area, capacitance, electrical resistance, electron-accepting capacity (EAC), and electron-donating capacity (EDC). These analyses assessed the influence of synthesis parameters. These materials were subsequently introduced into the anaerobic digestion of thermally hydrolyzed sludge to evaluate their impacts on methanogenic performance, microbial community structure, and metabolic pathways. The results show that the FeP@BC600 material, which exhibited the highest EDC, substantially increased microbial cytochrome c production (by 29.2 % compared to the control). This enhancement improved interspecies electron transfer, stimulated ATP synthesis (increased by 41.5 %), and reinforced both hydrogenotrophic and acetoclastic methanogenic pathways, ultimately elevating methane production by 55 %. Integrated analysis of metagenomic data, material properties, and performance metrics revealed that the key mechanism by which FeP@BC600 promotes methanogenesis is through the enrichment of cytochrome c-encoding genes, thereby facilitating direct interspecies electron transfer (DIET) and augmenting ATP synthesis. This study provides a foundation for the subsequent application of conductive materials to enhance anaerobic digestion and offers guidance for the optimized design of such materials.

Sewage↗

PubMed2026

Integrative machine learning models to unravel gut microbial dysbiosis and functional disruption in polycystic ovary syndrome.

OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared with healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models. DESIGN: Case-controlled metagenomic data analysis SUBJECTS: Gut metagenomic data from women diagnosed with PCOS and age-matched healthy female controls EXPOSURE: Presence of PCOS MAIN OUTCOME MEASURES: The primary outcome measures will include gut microbial alpha and beta diversity indices, microbial taxon abundance, functional pathway profiles, predicted metabolite levels, microbe-functional pathway-metabolite interaction networks, and the diagnostic accuracy of microbiome-based machine learning models. RESULTS: Alpha and beta diversity analyses revealed marked gut microbial dysbiosis in women with PCOS, despite comparable species richness to healthy controls. Differential abundance analysis identified 41 significantly altered microbial species, including enrichment of proinflammatory taxa, such as Bacteroides vulgatus and Ruminococcus gnavus, and depletion of beneficial commensals, including Roseburia hominis and Prevotella copri. These compositional shifts indicate a proinflammatory microbial community structure in PCOS. Functional profiling demonstrated the upregulation of pathways involved in nucleotide turnover, lipid and carbohydrate metabolism, and neurotransmitter synthesis, potentially contributing to metabolic and neuroendocrine disruption. Network analysis revealed fragmented and unstable microbial-metabolite associations in PCOS compared with cohesive networks in controls. Microbiome-based machine learning models achieved a diagnostic accuracy of 84.25% (area under the curve 0.93), underscoring their predictive potential. CONCLUSION: The gut microbiome in PCOS is characterized by a proinflammatory community structure and disrupted metabolic pathways. These findings demonstrate the diagnostic potential of microbiome-based models and underscore the gut microbiome as a promising target for therapeutic interventions in the management of PCOS.

Polycystic Ovary Syndrome↗

PubMed2026

Comparative analysis of gut microbiota in yaks under different feeding management strategies during cold seasons.

Yaks (Bos grunniens) are crucial for the livelihoods of pastoral communities in cold regions, where feed scarcity during the cold season poses challenges to their health and productivity, underscoring the necessity of understanding how dietary management influences the gut microbiota. In this study, 24 yak steers matched for body weight and health status were randomly allocated to four groups: natural grazing or indoor feeding with roughage-to-concentrate ratios of 50:50, 70:30, or 90:10. Fecal samples were collected for 16S rDNA sequencing and subsequent functional prediction of the microbiota. The results showed that Firmicutes and Bacteroidetes were the dominant phyla across all groups, and UCG-005 and Rikenellaceae_RC9_gut_group were the predominant genera. Concentrate supplementation during the cold season significantly enhanced microbial richness and diversity, with the 70:30 ratio exerting the most pronounced beneficial effects on microbiota structure and key taxa enrichment. These findings highlight the critical role of dietary management in shaping the yak gut microbiota during cold seasons and suggest that the 70:30 ratio optimally improves microbial community structure, thereby promoting yak health and productivity under harsh climatic conditions. Future research should explore the long-term implications of such dietary strategies.

Animals↗

PubMed2026

Elevated water levels drive greenhouse gas mitigation in the riparian zone profile.

Wetlands are critical for climate regulation, with their hyporheic zone serving as sensitive interfaces for groundwater-soil-atmosphere exchange. These zones are active hotspots for carbon-nitrogen cycling and greenhouse gas (GHG) emissions (CO2, CH4, N2O), yet the impact of water level fluctuations on these emissions and their microbial drivers in freshwater wetlands remains poorly understood. This study investigated the spatiotemporal dynamics of GHG emissions and carbon-nitrogen coupling processes along riparian soil profiles of Baiyangdian Lake during water level fluctuations. Employing static chamber measurements, microcosms, quantitative PCR, Metagenome-Assembled genome (MAG) analyses, and Structural Equation Modeling (SEM), we observed that GHG emissions were significantly affected by water level fluctuations. Specifically, CO2 and N2O fluxes, as well as CO2 production potential were significantly lower at high-water-level conditions. Water level also emerged as a key driver of microbial community structure, with Methylococcaceae and Methanosarcinaceae as key regulators of CH4 emission, and Anaeromyxobacteraceae as central to N2O dynamics. A high-quality Methylomirabilales-like MAG, possessing the complete pathway for coupled nitrate reduction and methane oxidation, was identified. Its abundance negatively correlated with water level, suggesting that these C-N coupling bacteria contribute to reducing GHG emissions. This study provides crucial theoretical insights and identifies microbial targets for mitigating wetland GHG emission through hydrological management.

Greenhouse Gases↗

PubMed2026

Functional convergence of rTCA-related carbon-fixation potential and biochemical residue accumulation in seagrass sediments.

Seagrass meadows are globally significant blue carbon ecosystems, yet the microbial and biochemical mechanisms driving sediment organic carbon (SOC) accumulation remain poorly understood. To address this, we employed an integrated approach combining metagenomic sequencing, biochemical assays, and structural equation modeling to investigate carbon cycling in the seagrass and adjacent unvegetated sediments of Swan Lake, China. A total of 115,179 carbon fixation genes and 119,615 decomposition genes were identified, revealing distinct microbial community structures among the habitats. Seagrass sediments harbored more diverse carbon-fixing (CFMs) and decomposing microorganisms (CDMs), with 83 medium-to high-quality metagenome-assembled genomes (MAGs) recovered. While neutral community model analysis indicated that stochastic processes predominantly governed community assembly, functional analyses highlighted specific drivers of sequestration. The reductive tricarboxylic acid (rTCA) cycle emerged as the dominant carbon fixation pathway, with key genes (e.g., aclA, korA) showing strong positive correlations with SOC. Conversely, decomposition pathways for starch and lignin were negatively associated with SOC. Furthermore, seagrass sediments exhibited elevated concentrations of total amino sugars (TAS) and lignin phenols (TLP), which linked significantly to carbon fixation rather than decomposition. PLS-SEM revealed statistically significant associations among seagrass traits, environmental variables, microbial carbon-fixation potential, biochemical residue pools, and SOC, supporting a mechanistic pathway in which enhanced microbial functional potential drives the accumulation of recalcitrant biochemical residues, thereby facilitating long-term carbon retention in sediments. These findings emphasize the pivotal role of microbial anabolism and the accumulation of biosynthetic residues in sediment carbon storage, suggesting a functional convergence in seagrass-driven carbon sinks.

Metagenomics↗

PubMed2025

Bacterial immune systems as causes and consequences of microbiome structure.

Attacks from molecular parasites such as mobile genetic elements (MGEs) have driven the evolution of defense systems in bacterial genomes. Yet, despite significant advances in understanding the molecular mechanisms of these bacterial immune systems, we have only a rudimentary understanding of their ecology and evolution. Bacteria exist as part of complex microbiomes, but community ecology and microbiome research has yet to characterize the impacts of interactions between MGEs and defense mechanisms upon the structure, dynamics and evolution of microbiomes. This Essay introduces and discusses the interplay between bacterial community dynamics and bacterial immune systems, speculating about how these reciprocal interactions may shape microbial community structure and function.

Bacteria↗

PubMed2026

Comparative metagenomic analysis of microbial communities: unravelling microbial communities from the great Rann of Kachchh and coastal saltpans, Gujarat, India.

Hypersaline environments exhibit extreme physiochemical conditions yet support diverse microbial communities. These communities are not only ecologically important but also possess substantial potential for biotechnological exploitation. In this study, we employed a comparative metagenomic approach to assess microbial diversity using two distinct methodologies: (1) direct DNA extraction from raw sediment, and (2) DNA extraction following halophilic enrichment in selective media. Sediment samples were collected from multiple sites and pooled together within the Rann of Kachchh and close-by saltpans and were analysed using 16S rRNA sequencing coupled with bioinformatics pipelines. The results revealed pronounced differences in microbial community composition between the two approaches. Raw sediment samples exhibited significantly higher alpha diversity, with dominant taxa including Halobacterota, Cyanobacteria, and Desulfobacterota, with a substantial proportion of unclassified genera. In contrast, enriched samples were dominated by fast-growing, culturable genera such as Halobacterium, Alkalibacillus, and Candidatus haloredivivus. Principal Coordinate Analysis (PCoA) of beta diversity demonstrated distinct clustering between raw and enriched communities, even within samples from the same sites, underscoring the selective bias introduced by enrichment procedures. These findings emphasise that the methodological choice strongly influences the observed microbial diversity. The aim of this study was to compare microbial community composition in raw hypersaline sediments and enrichment cultures using metagenomic sequencing, to evaluate how enrichment selectively favours specific halophilic taxa. This comparative approach allows identification of the microbial groups that rapidly proliferate under controlled hypersaline conditions, thereby complementing direct environmental sequencing. By integrating both direct and enrichment-based metagenomic approaches, a more comprehensive understanding of microbial community structure in hypersaline environments can be achieved.

India↗

PubMed2026

Pilot metaproteomic profiling reveals bacterial diversity and potential medical and veterinary relevance of tick microbiomes in northern Algeria.

Ticks are major ectoparasites and vectors of pathogens affecting humans, livestock, and wildlife. They harbor diverse microbial communities that may influence tick biology and interactions with microorganisms; however, functional information on tick-associated microbiomes remains limited, particularly in North Africa. In this pilot study, we applied a metaproteomic approach based on high-resolution tandem mass spectrometry to characterize bacterial communities associated with three tick species collected in Algeria: Rhipicephalus sanguineus sensu lato, Hyalomma aegyptium, and Hyalomma dromedarii. Peptide spectra were assigned to taxa using a two-step database search strategy based on NCBInr, and bacterial composition and relative abundance were compared across tick species and sampling locations. A total of 40 bacterial genera belonging to 32 families and four phyla were identified. Microbiome composition differed significantly between tick genera and collection locations, suggesting an influence of species-specific and geographical factors on microbial community structure. Dominant genera included Streptomyces, Bacillus, Clostridium, Escherichia, Flavobacterium, Paenibacillus, and Providencia. Peptides related to Coxiella spp. were frequently detected, consistent with previous reports of Coxiella-like endosymbionts in ticks. This pilot study provides a first metaproteomic characterization of tick-associated communities in Algeria. The results reveal species- and location-associated differences in microbial composition and highlight the potential of metaproteomics for exploring tick-associated microbiomes in North Africa.

Animals↗

PubMed2025

Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.

Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.

Wetlands↗

PubMed2026

Brucellar spondylitis is associated with disturbance in gut microbiota and histamine metabolism associated inflammation.

BACKGROUND: The pathogenesis of brucellar spondylitis (BLS) has traditionally been considered to be primarily limited to local osteoarticular lesions. With the proposal of the "gut-spine axis" concept, the role of intestinal microecological dysbiosis in inflammatory spinal diseases has attracted in an increase of attention. The overactivated inflammatory cytokine network not only mediates bone destruction and intervertebral disc damage, but also forms a bidirectional interaction with gut microbiota dysbiosis through the "gut-spine axis," collectively driving disease progression. However, the inflammatory mechanism by which gut microbiota participates in the pathological process of BLS remains largely unclear. METHODS: This study recruited 20 BLS patients and 20 healthy donors. Multi-omics analysis including metagenomics, untargeted metabolomics, and targeted short-chain fatty acids (SCFAs) analysis, were used to compare the structural differences in gut microbiota between the two groups and screen for signature differential bacterial species. Plasma levels of histamine and histidine decarboxylase were measured by ELISA to clarify the role of differential histidine metabolic pathway in the disease. Additionally, plasma levels of lipopolysaccharide (LPS) and inflammatory cytokines (IL-1β, IL-6, IL-10, IL-17A, TNF-α) were detected by ELISA. The correlation between gut microbiota and inflammatory indicators was further analyzed. RESULTS: Compared to the healthy control group, the α-diversity of the gut microbiota in BLS patients was significantly reduced, with the microbial community structure exhibiting increased homogeneity. Beta diversity analysis revealed significant differences, suggesting that disease progression is associated with an overall imbalance in the gut microbiota and the deterioration of its specific structural composition. At the phylum level, the abundances of Actinomycetota, unclassified_d_Viruses, and Fusobacteriota were significantly increased in the gut microbiota of BLS patients compared to the control group, while the abundances of Bacillota and Pseudomonadota were significantly decreased. Further analysis revealed that, compared to the control group, the generic abundance of Enterococcus was significantly increased, while the proportions of Blautia, Faecalibacterium, Ruminococcus, Agathobacter, Roseburia, Clostridium, Eubacterium, Alistipes and Anaerobutyricum were significantly decreased. At the species level, the abundances of Enterococcus sp and Enterococcus-faecium were increased, whereas Blautia sp, Ruminococcus sp, Faecalibacterium sp, Faecalibacterium prausnitzii, Agathobacter rectalis, Eubacterium sp, Agathobacter sp, and Roseburia sp were decreased. Furthermore, untargeted metabolomics revealed that metabolites were enriched in the histidine metabolic pathway, and the levels of SCFAs including butyrate, isobutyrate, valerate, and 4-methylvalerate in the intestinal contents were reduced in BLS. Functional KEGG profiling revealed that key KOs involved in butyrate synthesis (e.g., K00074, K00172, K01640) and transport were globally downregulated in the patient group, whereas histidine decarboxylase KOs (K01693, K11755, K19787) that convert histidine to pro-inflammatory histamine were significantly enriched. The loss of butyrate-producing symbionts led to SCFAs deficiency and mucosal barrier disruption, creating ecological niches for facultatively anaerobic Enterococcus, which further exacerbated local inflammation via proteolytic fermentation and histamine production. Compared with the control group, BLS patients showed decreased plasma levels of IL-10, while levels of IL-1β, IL-6, IL-17A, and TNF-α were increased, and LPS levels were elevated. In addition, significantly elevated plasma pro-inflammatory LPS levels in patients with BLS suggest disruption of intestinal integrity and permeability. Correlation analysis indicated a close relationship between gut microbiota and inflammation. CONCLUSION: BLS is associated with gut microbiota dysbiosis and alterations in microbial metabolites, which may be linked to inflammatory responses and histamine metabolism. The differential microbial taxa identified in this study could be developed into a stool-based non-invasive diagnostic panel to facilitate early differentiation of BLS from other spinal disorders. Furthermore, restoring gut microbial balance through probiotic supplementation or dietary modulation may represent a promising adjunctive strategy to enhance the efficacy of standard antibiotic therapy and reduce disease recurrence.

Humans↗

PubMed1992

Expression and transfer of engineered catabolic pathways harbored by Pseudomonas spp. introduced into activated sludge microcosms.

Two genetically engineered microorganisms (GEMs), Pseudomonas sp. strain B13 FR1(pFRC20P) (FR120) and Pseudomonas putida KT2440(pWWO-EB62) (EB62), were introduced into activated sludge microcosms that had the level of aeration, nutrient makeup, and microbial community structure of activated sludge reactors. FR120 contains an experimentally assembled ortho cleavage route for simultaneous degradation of 3-chlorobenzoate (3CB) and 4-methyl benzoate (4MB); EB62 contains a derivative TOL plasmid-encoded degradative pathway for toluene experimentally evolved so that it additionally processes 4-ethyl benzoate (4EB). Experiments assessed survival of the GEMs, their ability to degrade target substrates, and lateral transfer of plasmid-encoded recombinant DNA. GEMs added at initial densities of 10(6) to 10(7) bacteria per ml of activated sludge declined to stable population densities of 10(4) to 10(5) bacteria per ml. FR120 degraded combinations of 3CB and 4MB (1 mM each) following 3 days of adaptation in the microcosms. Indigenous microorganisms required an 8-day adaptation period before degradation of 4MB was observed; 3CB was degraded only after the concentration of 4MB was much reduced. The indigenous microbial community was killed when both compounds were present at concentrations of 4.0 mM. However, in parallel microcosms containing FR120, the microbial community maintained a normal density of viable cells. Indigenous microbes readily degraded 4EB (2 mM), and EB62 did not significantly increase the observed rate of degradation. In filter matings, transfer of pFRC20P, which specifies mobilization but not transfer functions, from FR120 to P. putida UWC1 was not detectable (< 10(-7) transconjugants per donor cell).(ABSTRACT TRUNCATED AT 250 WORDS)

Benzoates↗

PubMed2025

New insights into soil amendment: Impact of humic acid on typical antibiotic resistance in agricultural soil.

Humic acid (HA) addition can improve agricultural soil, but little is known about how it affects the soil resistome. In this study, we used selective agar plate combined with quantitative PCR (qPCR) and 16S rRNA gene sequencing to investigate how HA influences antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in soil contaminated with erythromycin and kanamycin. 0.1 % HA reduced the abundance of culturable erythromycin-resistant bacteria (ERB), while promoting the growth of kanamycin-resistant bacteria (KRB). Lysinibacillus and Paenibacillus were the dominant genera in ERB and KRB, respectively, governing the changes in their abundances. At this concentration, the Lysinibacillus abundance in ERB decreased from 96.74 % to 70.57 %. Meanwhile, that of Paenibacillus in KRB increased from 33.40 % to 77.44 %. The copy number of ermF decreased after HA addition, while that of ermB increased. Furthermore, 0.1 % HA significantly reduced the copy number and relative abundance of aadA1 and aac(6')-Ib (aka aacA4)-03 in the soil. Changes in these two types of ARB and ARGs were primarily driven by shifts in the microbial community structure. Soil physicochemical properties, particularly increased organic matter (OM), altered the absolute abundance of ermB. Meanwhile, changes in intI1 abundance determined the risk associated with aadA1 and aac(6')-Ib (aka aacA4)-03. These findings emphasize the dual role of HA in the dissemination of antibiotic resistance in agricultural soils and highlight the necessity of considering dose-dependent effects when applying HA as a soil amendment.

Soil Microbiology↗