[Functional state of mast cells in microbial eczema].
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Adult↗
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[Current trends in the study of urinary infections].
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Anti-Bacterial Agents↗
Spatially resolved multi-omics analysis of indigenous Bacillus-fortified high-temperature Daqu.
Layer-dependent patterns associated with indigenous Bacillus fortification on high-temperature Daqu remain unclear. Here, six indigenous functional Bacillus strains were combined to fortify Daqu at three inoculation levels (QH4, QH5, QH6), with non-fortified as the control (CK). Upper, middle, and lower shelf-layer samples were profiled by physicochemical measurements, volatilomics, organic acid analysis, untargeted metabolomics, 16S/ITS amplicon sequencing, and metagenomics. PERMANOVA showed significant effects of treatment, spatial layer, and their interaction on physicochemical, volatile, bacterial, and fungal profiles (P = 0.001). Among the three inoculation levels, QH5 showed the most balanced performance: QH5_M exhibited the highest observed mean peak temperature (63.3 °C; +4.5 °C relative to CK_M), and its group-mean temperature remained ≥ 60 °C for seven consecutive days. Multi-omics analyses indicated coordinated, non-linear, and layer-dependent differences associated with indigenous Bacillus fortification, with QH5_M showing the most pronounced combined thermal, pyrazine, substrate, microbial, and predicted functional profile. These findings indicate that moderate indigenous Bacillus fortification was associated with distinct layer-dependent thermal and flavor profiles and coordinated microbial, metabolic, and predicted functional differences.
Bacillus↗
Spiramycin fermentation residue-derived biochar regulates soil nutrient cycling, microbial communities, and antibiotic resistance gene dynamics.
Spiramycin fermentation residues (SFR) are hazardous wastes enriched with residual antibiotics, yet they can serve as potential feedstocks for resource recovery after appropriate treatment. In this study, SFR-derived biochar (SFR-BC) was produced by pyrolysis and applied to agricultural soil to evaluate its effects on soil properties, microbial communities, potential pathogenic bacteria, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A 60-day soil incubation experiment was conducted with one control and three SFR-BC application rates of 0.5%, 1.0%, and 2.0%. SFR-BC improved soil physicochemical properties, nutrient status, enzyme activities, and microbial alpha diversity. Metagenomic analysis showed that SFR-BC altered the abundance of functional genes associated with carbon and nitrogen cycling, indicating shifts in microbial functional potential. SFR-BC also changed bacterial co-occurrence patterns, with the high-dose treatment showing a more complex and highly connected network structure during incubation. In addition, high-dose SFR-BC reduced several potential pathogenic bacteria, including major plant pathogenic taxa. SFR-BC decreased soil ARG abundance by 9.38%-33.67% and MGE abundance by 6.49%-27.89% relative to the control, showing a dose-dependent reduction in antibiotic resistance-related genetic elements. Network and PLS-PM analyses further indicated that ARG variation was statistically associated with soil physicochemical properties, microbial diversity, potential bacterial hosts, and MGEs. Overall, these results suggest that SFR-BC can improve short-term soil nutrient status and reduce ARGs, MGEs, and several potential pathogenic taxa under controlled incubation conditions, providing useful evidence for the potential valorization of antibiotic fermentation residues through pyrolysis.
Charcoal↗
Nitric oxide dioxygenase function and mechanism of flavohemoglobin, hemoglobin, myoglobin and their associated reductases.
Microbial flavohemoglobins (flavoHbs) and hemoglobins (Hbs) show large *NO dioxygenation rate constants ranging from 745 to 2900 microM(-1) s(-1) suggesting a primal *NO dioxygenase (NOD) (EC 1.14.12.17) function for the ancient Hb superfamily. Indeed, modern O2-transporting and storing mammalian red blood cell Hb and related muscle myoglobin (Mb) show vestigial *NO dioxygenation activity with rate constants of 34-89 microM(-1) s(-1). In support of a NOD function, microbial flavoHbs and Hbs catalyze O2-dependent cellular *NO metabolism, protect cells from *NO poisoning, and are induced by *NO exposures. Red blood cell Hb, myocyte Mb, and flavoHb-like activities metabolize *NO in the vascular lumen, muscle, and other mammalian cells, respectively, decreasing *NO signalling and toxicity. HbFe(III)-OO*, HbFe(III)-OONO and protein-caged [HbFe(III)-O**NO2] are proposed intermediates in a reaction mechanism that combines both O-atoms of O2 with *NO to form nitrate and HbFe(III). A conserved Hb heme pocket structure facilitates the dioxygenation reaction and efficient turnover is achieved through the univalent reduction of HbFe(III) by associated reductases. High affinity flavoHb and Hb heme ligands, and other inhibitors, may find application as antibiotics and antitumor agents that enhance the toxicity of immune cell-derived *NO or as vasorelaxants that increase *NO signalling.
Amino Acid Sequence↗
16S rRNA and Metagenomic Datasets of Gastrointestinal Microbiota in Fetal and 7-Day-Old Goat Kids.
The perinatal period (from late gestation to the neonatal stage) in ruminants is a critical phase for fetal organ maturation, where ecological succession of gastrointestinal microbial communities significantly impacts livestock production efficiency. However, research remains insufficient regarding the distribution patterns and functional annotation of microbial communities across different gastrointestinal compartments during this period. This study characterized early microbiota dynamics in Hutianshi Goats using 16S rRNA sequencing (4 fetal goats at 90 ± 10 gestational days) and metagenomics (3 7-day-old goat kids). The fetal goat group generated 852,694 valid reads, yielding 688,277 high-quality reads after chimera removal for downstream analysis. The 7-day-old goat kids group produced 1,081,588,182 final valid reads, after data processing and assembly, 8,561,345 contigs were generated. Gene prediction identified 6,095,352 genes. Multi-database annotations (NR, KEGG, CAZy, etc.) revealed functional potential and antimicrobial resistance traits. The public release of this dataset facilitates academic understanding of microbial community dynamics and host-microbe interactions during this developmental stage, providing both theoretical foundations and data resources for ruminant developmental biology and precision breeding regulation.
Animals↗
Mammalian hormones in microbial cells.
Hormones and hormone-binding proteins resembling those of vertebrates are widespread in fungi, yeast and bacteria. Functional responses of microbial cells to mammalian hormones have also been found. The evolutionary roots of the vertebrate endocrine system may, therefore, be far more ancient than is generally believed.
Animals↗
Genome-Resolved Metagenomics Revealed the Functional Potential of Core Novel and Known Genera Key to Processes in Full-Scale Aerobic Granular Sludge Plants.
Microbial communities are critical for nutrient removal in aerobic granular sludge (AGS) wastewater treatment plants (WWTPs). Despite the stable long-term operation of full-scale AGS WWTPs, the microbial populations and functional traits sustaining stable long-term performance remain poorly resolved. To address this gap, the recovered MAG catalog from nine full-scale AGS WWTPs across five countries was analyzed. From this catalog, 74 high-quality core MAGs were identified and used for downstream taxonomic characterization and functional analyses. These high-quality core MAGs spanned 48 established and 7 novel genera, representing 31 known and 43 novel species. Functional analysis linked core MAGs to key WWTP processes: polyphosphate accumulation (9), glycogen accumulation (12), denitrification (62), and nitrification (1). These included four novel MAGs with glycogen-accumulating (3) and polyphosphate-accumulating (1) potential and 11 capable of nitrous oxide reduction, critical for mitigating greenhouse gas emissions. Ca. Phosphoribacter was the most abundant genus, highlighting its underestimated role caused by misclassification as Tetrasphaera in 16S rRNA surveys. Specifically, Ca. P. hodrii was the dominant species, exhibiting enhanced sugar uptake and amino acid synthesis as likely drivers of its enrichment in the AGS WWTPs. Overall, this study resolves for the first time the taxa and functional traits consistently enriched in full-scale AGS systems, enabling a shift from an empirical performance assessment toward biologically informed process interpretation.
Sewage↗
Collectins and their role in lung immunity.
The collectins are a small family of secreted glycoproteins that contain C-type lectin domains and collagenous regions. They have an important function in innate immunity, recognizing and binding to microorganisms via sugar arrays on the microbial surface. Their function is to enhance adhesion and phagocytosis of microorganisms by agglutination and opsonization. In the lung, two members of the collectin family, surfactant proteins A and D, are major protein constituents of surfactant. Another collectin, mannan-binding lectin, is also present in the upper airways and buccal cavity and may protect against respiratory infections. Recent work has shown that collectins have roles in resistance to allergy and in the control of apoptosis and clearance of apoptotic macrophage in the lung.
Cell Adhesion↗
Building biofilms for saline hydrogenotrophic denitrification from contrasting origins: Convergent acclimation, divergent performance.
Hydrogenotrophic denitrification is promising for deep nitrogen removal from saline, low-C/N wastewaters, but rapid establishment of stable biofilms at high salinity remains challenging. Here, two saline-adapted inocula from two representative, functionally contrasting habitats-a functionally-diversified inoculum from mangrove sediment and a functionally-focused inoculum from seabed sediment-were acclimated in parallel H2-based membrane biofilm reactors at constant 3.5% salinity. The Diverse-derived biofilm required 80 d to reach steady state and achieved only partial denitrification with 61.1% nitrate removal and considerable nitrite accumulation. In contrast, the Focus-derived biofilm rapidly established complete denitrification within ∼40 d, which was maintained for >50 d, with effluent NOx- below 1 mg-N·L-1 and 98.7% nitrate removal. Microbiome analyses showed that identical operation promoted convergence in community structure and enriched similar community-level functional potentials. However, genome-resolved analysis revealed distinct source-dependent functional organization among dominant microbial populations. Complete denitrifiers co-encoding denitrifying, hydrogenotrophic, and autotrophic functions were preferentially enriched in the Focus-derived biofilm, whereas these functions remained partitioned among different dominant populations in the Diverse-derived biofilm, coinciding with less complete denitrification. These findings indicate that saline hydrogenotrophic denitrification performance depends not only on which functions are enriched at the community level, but also on how key functions become organized among microbial populations, providing a previously overlooked criterion for inoculum selection in saline biological nitrogen control.
Complete denitrification↗
Succession of aquatic microbial communities as a result of the water quality variations in continuous water.
The changes of structural and functional parameters of aquatic microbial communities in continuous water on campus of Tsinghua University, China are investigated, by polyurethane foam unit (PFU) method. The measured compositions of the communities include alga, protozoa, and some metazoa (such as rotifers). The measured indicators of water quality include water temperature, pH value, dissolved oxygen (DO), potassium permanganate index (COD(Mn)), total nitrogen (TN), total phosphorus (TP) and chlorophyll-a (Chla). The trophic level, expressed by the trophic level indices (TLIc), is assessed with analytic hierarchy process and principal component analysis (AHP-PCA) method. The changing trends of the structural and functional parameters of aquatic microbial communities, such as Margalef index of diversity (D), Shannon-weaver index of diversity (H), Heterotropy index (HI), number of species when the colonization gets equilibrium (S(eq)), colonizing speed constant (G) and time spent when 90 percent of S(eq) colonized in PFU (T(80%)), are also analyzed. The experimental results showed the succession of aquatic microbial communities along the water flow is consistent with the water quality changes, so the parameters of microbial community can reflect the changes of water quality from the ecological view.
Animals↗
An industrial application of multiparameter flow cytometry: assessment of cell physiological state and its application to the study of microbial fermentations.
BACKGROUND: When using traditional microbiological techniques to monitor cell proliferation and viability, stressed, sublethally injured, or otherwise "viable but nonculturable" cells often go undetected. Because of this, such cells often are not considered by mathematical models used to predict bioprocess performance on scale-up and inaccuracies result. Therefore, analytical techniques, decoupled from postsampling growth, are desirable to rapidly monitor individual cell physiologic states during microbial fermentations. METHODS: Microbial cells, including Escherichia coli, Rhodococus sp., and Sacharomyces cerevisiae, were taken at various stages from a range of fermentation processes and stained with one of three mixtures of fluorescent stains: rhodamine 123/propidium iodide, bis-oxonol/propidium iodide, or bis-oxonol/ethidium bromide/propidium iodide. An individual cell's physiologic state was assessed with a Coulter Epics Elite analyzer based on the differential uptakes of these fluorescent stains. RESULTS: It was possible to resolve an individual cell's physiologic state beyond culturability based on the functionality of dye extrusion pumps and the presence or absence of an intact polarized cytoplasmic membrane, enabling assessment of population heterogeneity. This approach allows the simultaneous differentiation of at least four functional subpopulations in microbial populations. CONCLUSIONS: Fluorescent staining methods used in our laboratories have led to a functional classification of the physiological state of individual microbial cells based on reproductive activity, metabolic activity, and membrane integrity. We have used these techniques extensively for monitoring the stress responses of microorganisms in such diverse areas as bioremediation, biotransformation, food processing, and microbial fermentation; microbial fermentation is discussed in this article.
Cell Physiological Phenomena↗
Functional and Structural Responses of a Degradative Microbial Community to Substrates with Varying Degrees of Complexity in Chemical Structure.
Abstract The objective of the present study was to determine whether cultivation of a degradative community on substrates with varying degrees of chlorination and complexity in chemical structure, as well as cultivation in batch and flow cell culture, would alter the community's functional capability. The community was isolated from oil-contaminated soil and maintained in the laboratory on 2,4,6-trichlorobenzoic acid for 5 months before its ability to grow on 15 different chemicals as sole carbon source was evaluated in batch and flow cell systems. While the community could grow and develop biofilms in flow cells on all the substrates, only 11 of the 15 substrates could support growth in batch culture. Although biofilm development was less extensive on chemicals such as pentachlorophenol (2.09% average area covered by biofilm; average biofilm depth = 3 µm) than on 2,4,6-trichlorobenzoic acid (50.84% area covered; biofilm depth = 6.4 µm), no correlation was observed between the degree of chlorination, or number of rings, and the number of planktonic cells or biofilm biomass. In contrast, physicochemical characteristics such as the octanol/water partition coefficient had a significant effect on the development of biofilm biomass. In the case of planktonic communities, the degree of chlorination and ring number also had no effect on the BIOLOG carbon utilization profiles of the resulting communities. Although the sessile communities generally clustered separately from their planktonic counterparts, principal component analysis of carbon utilization profiles of the sessile communities showed different grouping between growth on chlorinated and nonchlorinated substrates. Analysis of the degradative community maintained on 2,4,6-trichlorobenzoic acid over an extended period further showed that adaptation to a new chemical environment is a rather slow process, since the substrate utilization profiles did not stabilize even after 12 months. These results demonstrate the flexibility in metabolic ability and community structure found in microbial communities.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p215.html</hea
Journal Article↗
Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.
BACKGROUND: The rumen functions as an anaerobic fermentation chamber, housing microorganisms with cellulolytic and proteolytic capabilities that facilitate feed utilization. Fiber-degrading bacteria possess the capability to enhance the productivity of cellulolytic feed. The application of omics technologies has greatly improved our understanding of the rumen microbiome. Determining microbial composition and functional patterns in the rumen does not equate to a comprehensive exploration of rumen microbial resources and their mechanisms of action. This study seeks to integrate high throughput 16S rRNA data with information on culturomics, cellulolytic activities, nutrition, and synthetic microbial communities (SynCom) engineering. The objective is to evaluate the relationship between rumen microbial activity and fiber utilization efficiency in cattle, ultimately aiming to develop a more powerful intervention strategy for the ruminant industry. RESULTS: The enrichment culture with various carbon sources led to significant alterations in the composition and structure of rumen microbiota, particularly enhancing those associated with carbohydrate metabolism. Employing the culturomics methodology, 896 strains from 78 species (including 8 novel species) were isolated, resulting in a 10.1% isolation rate relative to the rumen bacterial community. Among them, 35 strains demonstrated boosted cellulose-degrading capability on plates, while 25 exhibited the ability to degrade hemicellulose as well. SynComs of these candidates were prepared based on the ratio observed in rumen microbiota exhibiting high cellulolytic performance. SynCom 3 improved the neutral detergent fiber degradation (NDFD) by 20.39% averagely. Additionally, both in vitro and in situ assessments indicated that the optimization of dose/strain in SynCom 3 significantly improved the in vitro NDFD by 20.56% and increased the in situ NDFD by 7.81%, along with the acidic detergent fiber (ADF, + 11.47%). Genomic analysis revealed that the SynCom 3 functioned well in fiber degradation through the synergistic action of key carbohydrate-active enzymes. CONCLUSIONS: This study strengthens rumen microbiome research by integrating omics and SynCom engineering within a microbiota-bacteria-enzymes-genes framework, revealing the significance of enzymatic synergy in carbohydrate metabolism. The findings establish a framework for utilizing low-abundance microbes and engineering functional consortia, which are crucial for improving ruminant feed utilization and biomass conversion. Future research should investigate the transcriptomic profiles and the metabolic cross-feeding mechanisms of fiber-degrading strains in the rumen. Video Abstract.
Animals↗
[Comparative evaluation of methods of intracellular ATP extraction from different types of microorganisms for bioluminescent determinationof microbial cells].
The efficiency of dimethyl sulfoxide (DMSO), trichloroacetic acid (TCA), and cetyltrimethylammonium bromide (CTAB) as extractants of intracellular ATP from various microorganisms was compared in bioluminescent measurements of microbial cell concentrations. Extraction with CTAB was found to provide an approximately ten times higher sensitivity of the bioluninescent assay of microbial cells than extraction with DMSO or TCA. In Gram-positive bacteria and yeasts, the ATP concentration in the extract was a linear function of the microbial suspension density only within a cell concentration range of D600 0.02-3.5 in the three types of tested extracts. In Gram-negative bacteria, a significant deviation from the linear dependence between ATP concentration and microbial suspension density was observed in CTAB extracts at D600 > 1.
Adenosine Triphosphate↗
Functional genomics-based studies of the microbial ecology of hyperthermophilic micro-organisms.
Although much attention has been paid to the genetic, biochemical and physiological aspects of individual hyperthermophiles, how these unique micro-organisms relate to each other and to their natural habitats must be addressed in order to develop a comprehensive understanding of life at high temperatures. Phylogenetic 16 S rRNA-based profiling of samples from various geothermal sites has provided insights into community structure, but this must be complemented with efforts to relate metabolic strategies to biotic and abiotic characteristics in high-temperature habitats. Described here are functional genomics-based approaches, using cDNA microarrays, to gain insight into how ecological features such as biofilm formation, species interaction, and possibly even gene transfer may occur in native environments, as well as to determine what genes or sets of genes may be tied to environmental functionality.
Biofilms↗
Abundance-transcription decoupling reveals functional partitioning in bioelectrochemical denitrification biofilms.
Bioelectrochemical denitrification (BED) is often attributed to electroactive microorganisms that access electrode-derived electrons, yet the relative functional contribution of electroactive taxa and denitrifying populations within complex BED biofilms remain unclear. Here, we integrated reactor measurements with genome-resolved metagenomics and metatranscriptomics to examine microbial community structure, functional potential, and gene transcription across contrasting BED operational regimes differing in dissolved oxygen (DO), hydraulic retention time (HRT)/loading, and poised potential. Nitrate removal exceeded 90% across all tested conditions, but nitrogen intermediate accumulation, current generation, and theoretical electron balance differed substantially. Electroactive taxa such as Geobacter dominated (>80% abundance) under longer HRT and stronger poised potential, but contributed minimally to the transcription of canonical denitrification genes. Weaker cathodic potential enriched transcriptionally active denitrifying taxa such as Stutzerimonas, Acidovorax, and MR-S7, while oxygen exposure induced redox-stress responses and reshaped nitrogen metabolism beyond being a competing electron acceptor. Together, these results reveal a decoupling between taxonomic abundance, genomic functional potential, and transcriptional contribution in BED biofilms, indicating that nitrate-removal performance cannot be inferred from current generation or electroactive-taxon abundance alone.
Bioelectrochemical system↗
Effects of Fecal Microbiota Transplantation on Intestinal Microbial Characteristics and Clinical Phenotypes in Patients with Parkinson's Disease.
Alterations in the gut microbiota have been associated with Parkinson's disease (PD), but longitudinal microbial changes after fecal microbiota transplantation (FMT) and their clinical associations remain poorly understood. This single-center retrospective observational study included 6 patients with PD, stratified into high- and low-severity subgroups based on disease duration (>6 years vs ≤6 years). Thirty-six fecal samples were collected before FMT and monthly for five months afterward. Microbial diversity, community structure, taxonomic composition, and predicted functional profiles were assessed using 16S ribosomal RNA gene sequencing. Analyses included alpha and beta diversity, taxonomic abundance, linear discriminant analysis effect size, Tax4Fun2-based functional prediction, and Spearman rank correlations between microbial features and clinical indicators. Descriptive analyses indicated differences in microbial richness, diversity, community structure, and predicted functions between severity subgroups and across post-FMT time points. At baseline, the low-severity subgroup had greater microbial richness and diversity than the high-severity subgroup, with relatively higher abundances of taxa including Bifidobacterium and Lactobacillus. One month after FMT, richness and diversity increased from baseline in the high-severity subgroup, accompanied by changes in taxonomic composition. Both subgroups showed time-associated variation in microbial diversity and predicted Kyoto Encyclopedia of Genes and Genomes pathway enrichment after FMT. Predicted functions included carbohydrate and amino acid metabolism, secondary metabolite biosynthesis, membrane transport, and signal transduction. Several operational taxonomic units correlated with indicators of motor impairment, constipation, sleep quality, functional status, and neuropsychiatric symptoms. FMT was therefore associated with longitudinal changes in gut microbial diversity, composition, and predicted functions, and specific microbial features were associated with motor and non-motor indicators. Given the small retrospective cohort, these findings are preliminary and warrant confirmation in larger controlled studies. Future studies should determine whether these microbial alterations are reproducible, persist beyond five months, reflect donor engraftment, and correspond to measurable clinical improvement after transplantation in PD.
Humans↗