Search Results (425)

The gut microbiota plays a crucial role in early childhood development. Dysbiosis in this community has been linked to risk of disease. The transition from an exclusive milk-based diet to complementary feeding and eventual weaning is crucial for the development and maturation of the gut microbiota. However, the impact of breastfeeding duration during the complementary feeding period (typically 6 to 24 months of age) on microbial development trajectories remains incompletely characterized. Here, we investigated whether prolonged breastfeeding during the complementary feeding window influences gut microbiota succession by comparing children who continued breastfeeding with those who were fully weaned at the same ages. We analyzed 16S rRNA gene sequencing profiles of fecal samples collected from a cohort of Peruvian children at 6, 12, 18, and 24 months of age. Samples were categorized into two groups: a complementary feeding group (BF), which received both complementary foods and breast milk, and a post-weaning group (NBF), which had stopped receiving breast milk for over 7 days. We conducted both alpha and beta diversity to assess within- and between-sample microbial variation. Relative abundances of microbial taxa at the phylum and genus levels were also quantified. The results showed a clear age-related increase in both species richness and species evenness across early childhood, while BF had more gradual changes relative to NBF. Marked differences in community composition were observed between BF and NBF children at 12, 18, and 24 months, respectively. Children who continued breastfeeding maintained a Bifidobacterium-rich, lower-diversity microbiota for a longer period, whereas weaned children at the same age exhibited accelerated microbiota development toward an adult-like profile enriched in Bacteroidota and Bacillota (formerly Firmicutes). These findings suggest that breastfeeding during the complementary feeding period exerts a significant influence on gut microbiota development through the first two years of life, which is most likely independent of complementary food. The study provides potential implications for children’s health and nutrition guidelines from a perspective of gut microbiota succession. Full article

Understanding the spatiotemporal dynamics of water quality parameters and microbial communities in drinking water distribution systems (DWDS) and their interrelationships is critical for ensuring the safety of tap water supply. This study investigated the diurnal, monthly, and annual variation patterns of water quality and the stage-specific succession behaviors of microbial communities in a DWDS located in southeastern China. Results indicated that hydraulic shear stress during peak usage periods drove biofilm detachment and particle resuspension. This process led to significant diurnal fluctuations in total cell counts (TCC) and metal ions, with coefficients of variation ranging from 0.44 to 1.89. Monthly analyses revealed the synergistic risks of disinfection by-products (e.g., 24.5 μg/L of trichloromethane) under conditions of low chlorine residual (<0.2 mg/L) and high organic loading. Annual trends suggested seasonal coupling: winter pH reductions correlated with organic acid accumulation, while summer microbial blooms associated with chlorine decay and temperature increase. Nonlinear interactions indicated weakened metal–organic complexation but enhanced turbidity–sulfate adsorption, suggesting altered contaminant mobility in pipe scales. Microbial analysis demonstrated persistent dominance of oligotrophic Phreatobacter and prevalence of Pseudomonas in biofilms, highlighting hydrodynamic conditions, nutrient availability, and disinfection pressure as key drivers of community succession. These findings reveal DWDS complexity and inform targeted operational and microbial risk control strategies. Full article

Dictyophora indusiata cultivation is severely impeded by premature hyphal regression. This study elucidates the spatiotemporal dynamics of mycelial regression and associated microbial succession in both substrate and soil matrices across progressive regression stages (CK: normal growth; S1: initial recession; S2: advanced recession; S3: complete recession). Microscopic analysis revealed preferential mycelial regression in the substrate, preceding soil regression by 1–2 stages. High-throughput sequencing demonstrated significant fungal community restructuring, characterized by a sharp decline in Phallus abundance (substrate: 99.7% → 7.0%; soil: 78.3% → 5.5%) and concomitant explosive proliferation of Trichoderma (substrate: 0% → 45.2%; soil: 0.1% → 55.3%). Soil fungal communities exhibited a higher richness (Chao1, p < 0.05) and stability, attributed to functional redundancy (e.g., Aspergillus, Conocybe) and physical protection by organic–mineral complexes. Conversely, substrate bacterial diversity dominated, driven by organic matter availability (e.g., the Burkholderia–Caballeronia–Paraburkholderia complex surged to 59%) and optimized porosity. Niche analysis confirmed intensified competition in post-regression soil (niche differentiation) versus substrate niche contraction under Trichoderma dominance. Critically, Trichoderma overgrowing was mechanistically linked to (1) nutrient competition via activated hydrolases (e.g., Chit42) and (2) pathogenic activity (e.g., T. koningii causing rot). We propose ecological control strategies: application of antagonistic Bacillus subtilis (reducing Trichoderma by 63%), substrate C/N ratio modulation via soybean meal amendment, and Sphingomonas–biochar soil remediation. This work provides the first integrated microbial niche model for D. indusiata regression, establishing a foundation for sustainable cultivation. Full article

Microbial communities, as critical functional components of riverine ecosystems, play a pivotal role in biogeochemical cycles and water quality regulation. The South-to-North Water Diversion Middle Route Project (SNWD-MRP) is a major cross-basin water transfer initiative, and bacteria are essential for the stability of water quality in the project. This study employed environmental DNA (eDNA) metabarcoding targeting the 16S rRNA gene to investigate spatiotemporal variations in water quality and bacterial communities along the SNWD-MRP during summer and winter. Integrated analyses, including redundancy analysis (RDA), Mantel tests, and ecological network modeling, were applied to unravel the driving mechanisms of microbial succession. The water quality along the SNWD-MRP is generally classified as Grade I, with significant seasonal variations in water quality parameters and microbial community composition. In the summer, higher temperatures lead to an increased abundance of cyanobacteria. In contrast, during the winter, lower water temperatures and higher dissolved oxygen levels result in the dominance of Pseudomonas and Bacillota species. RDA identified the permanganate index as the primary driver of microbial composition across seasons, with total phosphorus and total nitrogen having a greater influence in winter. Mantel tests highlighted significant correlations between Cyanobacteria and total phosphorus during winter. Ecological network analysis revealed that the complexity and connectivity of the winter network increased, likely due to suitable nutrient levels rendering the microbial network more complex and stable. These findings underscore the synergistic effects of temperature and nutrient availability on microbial succession, providing actionable insights for optimizing water quality management and ecological stability in large-scale water diversion systems. Full article

Using meta-analysis of 479 sites across Chinese forests from 136 publications, we quantified changes in soil microbial diversity across forest successional stages and compared patterns between plantation and natural secondary forests. Our systematic review included 136 publications (92 in Chinese, 44 in English), spanning tropical to cold temperate climate zones from 1995–2025. Microbial $\alpha$-diversity exhibited a significant U-shaped pattern across successional stages: early succession (0–15 years) and mature forests (>50 years) had higher Shannon diversity (4.56 ± 0.34 and 4.72 ± 0.41, respectively) than middle-aged forests (16–50 years, 4.18 ± 0.27; standardized mean difference = 0.54, 95% CI: 0.39–0.69, p < 0.01). Response patterns differed significantly among microbial groups (Q = 8.74, p = 0.013), with fungi showing the strongest successional responses (SMD = 0.61, 95% CI: 0.43–0.79), followed by bacteria (SMD = 0.49, 95% CI: 0.32–0.66) and actinomycetes (SMD = 0.42, 95% CI: 0.24–0.60). Natural secondary forests consistently supported higher microbial diversity than plantations (SMD = 0.42, 95% CI: 0.28–0.56), particularly for fungal communities (SMD = 0.47, 95% CI: 0.31–0.63). The climate zone significantly moderated diversity–succession relationships, with subtropical regions showing the largest changes ($\Delta$Shannon = 0.68 ± 0.07) compared to temperate ($\Delta$Shannon = 0.42 ± 0.05) and tropical regions ($\Delta$Shannon = 0.54 ± 0.06). Meta-analytic structural equation modeling revealed that soil organic carbon (path coefficient $\beta$ = 0.68, p < 0.001), total nitrogen ($\beta$ = 0.43, p < 0.001), and pH ($\beta$ = −0.35, p < 0.01) were key mediators connecting succession stage with microbial diversity. Despite substantial between-study heterogeneity (I² = 83.6%), a publication bias was not detected (Egger’s test, p = 0.347). These findings provide the first comprehensive quantification of microbial diversity patterns during forest succession in China, with important implications for forest management and ecological restoration strategies targeting microbial conservation. Full article

This study aimed to elucidate stage-specific dynamics, assembly mechanisms, and functional roles of bacterial communities during Macrobrachium rosenbergii larval development through high-resolution microbiota profiling. A high-frequency sampling strategy (126 samples across 11 zoeal stages and 1 post-larval stage within 21 days) and 16S rRNA absolute quantification sequencing were employed. Bacterial succession, persistent taxa, and ecological processes were analyzed using abundance-occupancy modeling, neutral community modeling, and PICRUSt2-based functional prediction. Absolute bacterial abundance exhibited a triphasic abundance trajectory. Initial accumulation: Linear increase (Dph 1–5, peak Δlog10 = +1.7). Mid-stage expansion: Peak abundance (log10 = 7.5 copies/g, Dph 7–8). Late-stage remodeling: Secondary peak (log10 = 7.1 copies/g, Dph 19). Eighty dominant amplicon sequence variants (ASVs) (dominant taxa: Herminiimonas, Maritalea, and Enterobacteriaceae) comprised > 95% of the total abundance and coexisted via niche partitioning. Community construction was dominated by ecological drift/dispersal limitation (neutral model R² = 0.16, p < 0.01). Metabolic pathways (e.g., nutrient metabolism) shifted with dietary transition. “Phylogenetic replacement” underpinned microbiota resilience against environmental perturbations. Optimizing aquaculture environments offers a viable antibiotic-free strategy for microbial management, advancing our understanding of host microbe interactions and ecological niche differentiation in aquatic animals. Full article

Fermentation plays a pivotal role in shaping the flavor and overall quality of Pu-erh tea, a microbially fermented dark tea. Here, we monitored physicochemical properties, chemical constituents, and microbial succession at 15 fermentation time points. Amplicon sequencing identified Staphylococcus, Bacillus, Kocuria, Aspergillus, Blastobotrys, Thermomyces, and Rasamsonia as dominant genera, with prokaryotic communities showing greater richness and diversity than eukaryotic ones. Beta diversity and clustering analyses revealed stable microbial structures during late fermentation stages. Non-targeted metabolomics detected 347 metabolites, including 56 significantly differential compounds enriched in caffeine metabolism and unsaturated fatty acid biosynthesis. Fermentation phases exhibited distinct metabolic patterns, with volatile aroma compounds (2-acetyl-1-pyrroline, 2,5-dimethylpyrazine) and health-beneficial fatty acids (linoleic acid, arachidonic acid) accumulating in later stages. OPLS-DA and KEGG PATHWAY analyses confirmed significant shifts in metabolite profiles relevant to flavor and biofunctionality. RDA revealed strong correlations between microbial taxa, environmental parameters, and representative metabolites. To functionally verify microbial contributions, 17 bacterial and 10 fungal strains were isolated. Six representative strains, mainly Bacillus and Aspergillus, exhibited high enzymatic activity on macromolecules, confirming their roles in polysaccharide and protein degradation. This integrative multi-omics investigation provides mechanistic insights into Pu-erh tea fermentation and offers a scientific basis for microbial community optimization in tea processing. Full article

The growth potential of Crinum bulbispermum was evaluated on gold mine tailings. The primary objectives were to model the species’ climatic niche in relation to gold mining regions, assess its germination success on tailings, and compare seedling survival and growth on tailings versus other soil types. Species distribution modelling identified the South African Grassland Biome on the Highveld (1000+ m above sea level), where the majority of gold mines are located, as highly suitable for the species. Pot trials demonstrated above 85% germination success across all soil treatments, including gold mine tailings, indicating its potential for restoration through direct seeding. An initial seedling establishment rate of 100% further demonstrated the species’ resilience to mine tailings, which are often seasonally dry, nutrient-poor, and may contain potentially toxic metals. However, while C. bulbispermum was able to germinate and establish in mine tailings, long-term growth potential (over 12 months) was constrained by low organic carbon content (0.11%) and high salinity (194.50 mS/m). These findings underscore the critical role of soil chemistry and organic matter in supporting long-term plant establishment and growth on gold tailings. Building on previous research, this study confirms the ability of this thick-rooted geophyte to tolerate chemically extreme soil conditions. Crinum bulbispermum shows promise for phytostabilization and as a potential medicinal plant crop on tailings. However, future research on microbial community interactions and soil amendment strategies is essential to ensure its long-term sustainability. Full article

Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition of the substrate and the gut of E. fetida at three time points (weeks 0, 6, and 12). The V3–V4 region of the 16S rRNA gene was sequenced, and microbial diversity was characterized using QIIME2. Significant differences in alpha diversity (observed features, Shannon index, and phylogenetic diversity) and beta diversity indicated active microbial succession. Proteobacteria, Bacteroidota, and Actinobacteriota were the dominant phyla, with abundances varying across habitats and over time. A significant enrichment of Proteobacteria, Bacteroidota, and the genera Chryseolinea, Flavobacterium, and Sphingomonas was observed in the manure treatments. In contrast, Actinobacteriota, Firmicutes, and the genera Methylobacter, Brevibacillus, Enhygromyxa, and Bacillus, among others, were distinctive of the gut samples and contributed to their dissimilarity from the manure treatments. Simultaneously, the physicochemical parameters indicated progressive substrate stabilization and nutrient enrichment. Notably, the organic matter and total organic carbon contents decreased (from 79.47% to 47.80% and from 46.10% to 27.73%, respectively), whereas the total nitrogen content increased (from 1.70% to 2.23%); these effects reduced the C/N ratio, which is a recognized indicator of maturity, from 27.13 to 12.40. The macronutrient contents also increased, with final values of 1.41% for phosphorus, 1.50% for potassium, 0.89% for magnesium, and 2.81% for calcium. These results demonstrate that vermicomposting modifies microbial communities and enhances substrate quality, supporting its use as a biofertilizer for sustainable agriculture, soil restoration, and agrochemical reduction. Full article

Landslides are a common geological hazard in mountainous areas, causing significant damage to ecosystems and production activities. Near-natural ecological restoration is considered an effective strategy for post-landslide recovery. To investigate the impact of near-natural restoration strategies on the recovery of plant communities and soil in landslide-affected areas, we selected landslide plots in Lantian County at 1, 6, and 11 years post-landslide as study sites, surveyed plots undergoing near-natural restoration and adjacent undisturbed control plots (CK), and collected and analyzed data on plant communities and soil properties. The results indicate that vegetation succession followed a path from “human intervention to natural competition”: species richness peaked at 1 year post-landslide (D_m = 4.2). By 11 years, dominant species prevailed, with tree species decreasing to 4.1 ± 0.3, while herbaceous diversity increased by 200% (from 4 to 12 species). Soil recovery showed significant temporal effects: total nitrogen (TN) and dehydrogenase activity (DHA) exhibited the greatest increases after 1 year post-landslide (132% and 232%, respectively), and by 11 years, the available nitrogen (AN) in restored plots recovered to 98% of the CK levels. Correlations between plant and soil characteristics strengthened over time: at 1 year, only 6–9 pairs showed significant correlations (p < 0.05), increasing to 21–23 pairs at 11 years. Near-natural restoration drives system recovery through the “selection of native species via competition and activation of microbial functional groups”. The 6–11-year period post-landslide is a critical window for structural optimization, and we recommend phased dynamic regulation to balance biodiversity and ecological functions. Full article

The growing environmental concerns associated with petroleum-based plastics require the development of sustainable, biodegradable alternatives. Polyhydroxyalkanoates (PHAs), a family of biodegradable bioplastics, offer a promising potential as eco-friendly substitutes due to their renewable origin and favorable degradation properties. This research investigates the use of synthetic condensate, mimicking the liquid fraction from drying and shredding of household food waste, as a viable substrate for PHA production using mixed microbial cultures. Two draw-fill reactors (DFRs) were operated under different feed organic concentrations (2.0 ± 0.5 and 3.8 ± 0.6 g COD/L), maintaining a consistent carbon-to-nitrogen ratio to selectively enrich microorganisms capable of accumulating PHAs through alternating nutrient availability and deficiency. Both reactors achieved efficient organic pollutant removal (>95% soluble COD removal), stable biomass growth, and optimal pH levels. Notably, the reactor with the higher organic load (DFR-2) demonstrated a modest increase in PHA accumulation (19.05 ± 7.18%) compared to the lower-loaded reactor (DFR-1; 15.19 ± 6.00%), alongside significantly enhanced biomass productivity. Polymer characterization revealed the formation of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), influenced by the substrate composition. Microbial community analysis showed an adaptive shift towards Proteobacteria dominance, signifying successful enrichment of effective PHA producers. Full article

Background/Objectives: Inflammatory bowel disease (IBD) is characterized by chronic relapsing and remitting inflammation of the gastrointestinal tract. Fecal microbiota transplantation (FMT) has emerged as an FDA-approved treatment for recurrent Clostridioides difficile infections (CDIs), with promising potential in patients with IBD. This manuscript aimed to provide a comprehensive and updated review of the available literature on fecal microbiota transplantation, its clinical use in IBD in general, as well as in patients with IBD and CDI. Methods: An extensive literature search was performed from October 2024 to March 2025. All publications available within PubMed, Medline, Embase, Google Scholar, and Cochrane databases were reviewed. All original articles, case reports, review articles, systematic reviews, and meta-analyses were included. Qualitative and quantitative data were both extracted. Discussion: Intestinal microbiota is an integral part of the human body, and dysbiosis (an imbalance in the gut’s microbial community) has been linked with several pathologies. Dysbiosis in IBD is marked by reduced beneficial bacteria and increased pro-inflammatory pathogens, contributing to mucosal damage and immune dysregulation. FMT has emerged as a solution to dysbiosis, with the first case recorded in 1917. FMT has been successful in treating patients with CDI. The diagnostic value of the gut microbiome is currently being explored as a possible therapeutic approach to IBD. Several studies have assessed FMT in patients with IBD and CDI with promising results in both ulcerative colitis (UC) and Crohn’s disease (CD) but varying efficacy based on administration routes, donor selection, and processing methods. In the context of recurrent CDI in patients with IBD, FMT demonstrates a high cure rate and potential benefit in concurrently improving IBD activity. However, risks such as IBD flare-ups post-FMT remain a concern. Conclusions: FMT holds promising potential in the management of CDI in patients with IBD. By restoring microbial diversity and correcting dysbiosis, FMT offers a novel, microbiota-targeted alternative to conventional therapies. While data support its efficacy in improving disease remission, variability in outcomes underscores the need for standardized protocols and additional large-scale, controlled studies. Continued research efforts into donor selection, treatment regimens, and long-term safety will be critical to optimizing FMT’s role in IBD and CDI care as well as improving patient outcomes. Full article

Triticale (Triticosecale Wittmack) is a versatile forage crop valued for its high yield, balanced nutrition, and environmental adaptability. However, the dough-stage triricale has higher dry matter and starch content but lower water-soluble carbohydrate levels than earlier stages, posing fermentation challenges that may impair silage quality. This study aimed to investigate the effects of lactic acid bacteria inoculation on the fermentation quality, bacterial community, and metabolome of whole-plant triticale silage at the dough stage. Fresh triticale was ensiled for 30 days without or with an inoculant containing Lactiplantibacillus plantarum and Streptococcus bovis. Fermentation quality, bacterial succession, and metabolic profiles were analyzed at multiple time points. Inoculation significantly improved fermentation quality, characterized by a rapid pH drop, increased lactic acid production, and better preservation of fiber components. Microbial analysis revealed that inoculation successfully established Lactobacillus as the dominant genus while suppressing spoilage bacteria like Enterobacter and Clostridium. Metabolomic analysis on day 30 identified numerous differential metabolites, indicating that inoculation primarily altered pathways related to amino acid and purine metabolism. In conclusion, inoculating dough-stage triticale with this LAB combination effectively directs the fermentation trajectory. It enhances silage quality not only by optimizing organic acid profiles and microbial succession but also by modulating key metabolic pathways, ultimately leading to improved nutrient preservation. Full article

Forensic entomotoxicology is a subdiscipline that utilizes necrophagous insects as bioindicators for detecting drugs and toxicants in decomposed remains, particularly in cases where conventional biological matrices are no longer available. Toxic substances can profoundly alter insect development, physiology, and community succession, potentially impacting the accuracy of postmortem interval (PMI) estimation. This review systematically summarizes the effects of various xenobiotics, including pesticides, illicit drugs, sedatives, heavy metals, and antibiotics on larval growth, physiological traits, and gut microbial composition in forensically relevant flies. However, most studies to date have relied primarily on phenotypic observations, with limited insight into underlying molecular mechanisms. Significant interspecies and dose-dependent variability also exists in the absorption, metabolism, and physiological responses to xenobiotics. We highlight recent advances in multi-omics technologies that facilitate the identification of molecular biomarkers associated with xenobiotic exposure, particularly within the insect detoxification system. Key components such as cytochrome P450 monooxygenases (P450s), glutathione S-transferases (GSTs), and ATP-binding cassette (ABC) transporters play essential roles in xenobiotic metabolism and insecticide resistance. Additionally, the insect fat body serves as a central hub for detoxification, hormonal regulation, and energy metabolism. It integrates signals related to xenobiotic exposure and modulates larval development, making it a promising model for future mechanistic studies in insect toxicology. Altogether, this review offers a comprehensive and reliable framework for understanding the complex interactions between toxic substance exposure, insect ecology, and decomposition in forensic investigations. Full article

Soil microbes play a crucial role in driving biogeochemical cycles and are closely linked with aboveground plants during forest succession. Moso bamboo (Phyllostachys edulis) encroachment into adjacent forests of varying composition is known to alter plant diversity in subtropical and tropical regions. However, how soil microbial communities respond to this vegetation type transformation has not fully explored. To address this knowledge gap, a time-alternative spatial method was employed in the present study, and we investigated the effect of Moso bamboo expansion into subtropical broad-leaved forest and coniferous forest on soil microbial phospholipid fatty acids (PLFAs). We also measured the dynamics of key soil properties during the Moso bamboo expansion processes. Our results showed that Moso bamboo encroachment into subtropical broad-leaved forest induced an elevation in soil bacterial PLFAs (24.78%) and total microbial PLFAs (22.70%), while decreasing the fungal-to-bacterial (F:B) ratio. This trend was attributed to declines in soil NO₃⁻-N (18.63%) and soil organic carbon (SOC) concentrations (28.83%). Conversely, expansion into coniferous forests promoted soil fungal PLFAs (40.41%) and F:B ratio, primarily driven by increases in soil pH (4.83%) and decreases in SOC (36.18%). These results provide mechanistic insights into how contrasting expansion trajectories of Moso bamboo restructure soil microbial communities and highlight the need to consider vegetation context-dependency when evaluating the ecological consequences of Moso bamboo expansion. Full article