Search Results (347)

Ongoing urbanization continuously reshapes water quality, habitat structure, and biological communities in river ecosystems; however, its impacts on host-associated microbial communities remain poorly documented. The fish gut microbiota, a critical interface between the aquatic environment and host physiology, is widely recognized as an integrative indicator of both environmental change and host ecological traits. This study established a continuous urbanization gradient along Shanghai’s Suzhou River, spanning from suburban areas through the outer and inner ring roads to the city center. Five common wild fish species (Coilia nasus, Hemiculter bleekeri, Culter alburnus, Acheilognathus macropterus, and Pseudorasbora parva) were collected, and their gut microbiota were characterized via high-throughput 16S rRNA gene sequencing. Significant variation in OTU richness, alpha diversity, and community structure was observed across urbanization gradients and among fish species. Principal coordinate analysis revealed that samples from suburban areas were structurally distinct from those collected in other zones, whereas inner-ring and urban-core areas exhibited substantial compositional overlap. Taxonomic analysis revealed that Firmicutes and Pseudomonadota dominated all samples; however, their relative abundances and genus-level composition varied considerably among fish species and across the urbanization gradient. PICRUSt-based functional prediction indicated that metabolic pathways predominated, particularly those involved in global and overview maps, carbohydrate metabolism, amino acid metabolism, energy metabolism, and metabolism of cofactors and vitamins. Collectively, these findings demonstrate that fish gut microbial communities exhibit spatial structuring along the urbanization gradient, with species-specific responses linked to ecological traits. This study provides valuable data on host-associated microbial communities in urban rivers and offers a reference for incorporating microbial indicators into urban water ecological assessments. Full article

To address ammonium nitrogen (NH₄⁺-N) and nitrite accumulation in intensive marine shrimp aquaculture, a marine recirculating aquaculture system (RAS) for Penaeus vannamei centered on a moving bed biofilm reactor (MBBR) was constructed to investigate the microbial basis of nitrogen removal. The results showed that the MBBR contributed most to NH₄⁺-N removal, demonstrating favorable nitrification potential under marine conditions (0.513 mg·L⁻¹·h⁻¹). The biofilm carrier formed a complete attached layer and developed a mature biofilm structure. Microbial community analysis revealed clear differentiation between the biofilm and sediment. The biofilm community was dominated by norank_f__Caldilineaceae (9.89%). Linear discriminant analysis effect size identified the nitrifying genus Nitrospira to be significantly enriched on the biofilm side (α = 0.05, linear discriminant analysis > 2.0). In addition, PICRUSt2-based functional prediction suggested a higher potential in biofilm than in sediment for ammonia oxidation and downstream nitrogen transformation, involving ammonia monooxygenase (EC:1.14.99.39), hydroxylamine dehydrogenase (EC:1.7.2.6), nitrate reductase (EC:1.7.99.4), and nitrite reductase (EC:1.7.2.1). Thus, this study provides a microbial basis and process strategy for P. vannamei RAS. Full article

Background: The nasopharyngeal microbiome is crucial for respiratory health in mammals, yet it remains poorly characterized in the endangered forest musk deer (Moschus berezovskii), particularly in the context of disease. Methods: We compared the bacterial (16S rRNA) and fungal (ITS2) communities in the nasopharynx of healthy (n = 6) and clinically diseased (n = 6) individuals. Results: Although alpha diversity did not differ significantly, beta diversity (PCoA) analysis revealed distinct bacterial (PERMANOVA, R² = 0.165, p = 0.014) and fungal (R² = 0.577, p = 0.003) community structures between groups. The diseased group exhibited a significant increase in the bacterial phylum Proteobacteria (70.97% vs. 46.27%), primarily driven by the genera Bibersteinia and Pseudomonas. Fungal communities in the diseased group were dominated by a higher relative abundance of Ascomycota and Basidiomycota, with significant enrichment of Wallemia and Aspergillus. LEfSe analysis identified Pseudomonas and multiple fungal taxa (e.g., Wallemia, Aspergillus) as biomarkers for the diseased group. PICRUSt2 prediction indicated enrichment of pathways related to carotenoid biosynthesis and sphingolipid metabolism in the diseased state, while FUNGuild analysis suggested a higher abundance of animal/plant pathogen-related fungi. Conclusions: Symptomatic respiratory infections in forest musk deer are associated with significant dysbiosis of the nasopharyngeal microbiome, characterized by the marked enrichment of potential bacterial opportunists (e.g., Pseudomonas) and specific fungal taxa (e.g., Wallemia, Aspergillus), alongside distinct functional shifts in the microbiome. These findings provide the first integrated bacterial–fungal profile of the nasopharyngeal microbiome in this endangered species, and highlight potential microbial biomarkers associated with respiratory disease. Full article

Anaerobic digestion (AD) of animal manures for biogas production faces challenges including nutritional imbalance, foaming, and process instability. This study evaluated bioaugmentation with surfactant-degrading microbial consortia and cell-free extracts derived from well-characterized oil-contaminated soils during cow and pig manure digestion. These previously analyzed soils contained distinct microbial communities dominated by Pseudomonas in acidic, high-PAH soils and Bacillus in neutral-pH soils with genetic potential for hydrocarbon degradation. Over 30 days, six treatments were assessed using the Automatic Methane Potential Test System (AMPTS II), with pH monitoring, foaming analysis, and 16S rRNA sequencing coupled with PICRUSt2 functional prediction. Supplementation with microbial consortia and extract markedly increased cumulative biogas outputs (cow manure: 407.76 to 603.28 mL/gVS and pig manure: 403.82 to 627.5 mL/gVS), biomethane by 30–50%, reduced digestion time by 5–6 days, and improved pH stability. Foaming reduction was substrate-specific: extracts reduced foam by up to 60% in pig manure, while consortia reduced it by up to 65% in cow manure. Microbial analysis revealed enrichment of fermentative and syntrophic taxa (Clostridium sensu stricto and Paludibacter) and upregulation of methanogenesis pathways (tetrahydromethanopterin S-methyltransferase). This study illustrates that tailored bioaugmentation utilizing consortia from hydrocarbon-contaminated soils provides an environmentally sustainable method to enhance methane yields, improve stability, and control foaming in manure AD, with outcomes significantly affected by the type of manure and amendment strategy employed. Full article

Seasonal dietary shifts are associated with significant alterations in the gut microbiome of herbivores, yet the specific impacts of these shifts on microbial metabolic functions have not been fully elucidated. To address this gap, we employed DNA metabarcoding of fecal samples and 16S rRNA gene sequencing to explore the relationship between seasonal diet and gut microbiome composition in a population of sika deer (Cervus nippon kopschi). Our findings indicate pronounced seasonal variations in both dietary composition and gut microbial community structure. Notably, during the winter months, the gut microbiome exhibited a significant enrichment of predicted pathways (predicted using PICRUSt2) related to fatty acid and lipid biosynthesis and degradation, amino acid degradation, and the TCA cycle. Conversely, the active growing seasons (spring and summer) were characterized by enhanced glycolysis and amino acid biosynthesis pathways. These functional shifts showed significant correlations with seasonal changes in dietary nutrients, such as crude protein and fiber, and climatic factors. Our results suggest that seasonal dietary changes are associated with a restructuring of the gut microbiome’s metabolic potential, which may assist sika deer in adapting to fluctuating physiological demands and environmental challenges across different seasons. Full article

Background/Objectives: This exploratory study (n = 6 per group) investigated the associations between supplementation with α-lipoic acid (AL), betaine (BT), and L-carnitine (LC) and gut microbiota composition in a high-fat diet (HFD)-induced obesity mouse model. Methods: Four-week-old male C57BL/6J mice were fed a control diet (10% fat), HFD (60% fat), or HFD supplemented with AL, BT, or LC (300 mg/kg BW/day) for nine weeks. Results: All three compounds were associated with shifts in microbial composition compared to the HFD-only group. While AL and BT supplementation moderately modulated specific Firmicutes and Bacteroidetes taxa, LC supplementation was linked to a more pronounced reduction in the Firmicutes/Bacteroidetes ratio and a decreased abundance of genera such as Christensenellaceae, Lachnospiraceae, and Coprococcus 3. These microbial changes were correlated with obesity-related metabolic and adiposity markers, including leptin and lipid parameters. Furthermore, functional profiling via PICRUSt suggested potential alterations in amino acid metabolism; however, these findings represent inferred metabolic potential rather than direct metagenomic measurements. Conclusions: Collectively, these results indicate differential associations between dietary supplementation and gut microbiota composition in HFD-fed mice. Although this study was conducted within an exploratory framework and utilized a modest sample size, the observed microbial shifts consistently paralleled metabolic alterations, supporting biologically plausible associations that warrant further mechanistic investigation. Full article

Idesia polycarpa ‘Yitong 2’ is a high-oil cultivar widely promoted in central China, yet field evidence on how soil bacterial communities respond during early plantation establishment remains limited. Here, we conducted fixed-site monitoring in a newly established ‘Yitong 2’ plantation in the Luohe River Basin (Henan, China). Bulk soil (0–30 cm) was collected before planting (March 2024) and at 3, 6 and 12 months after planting (June 2024, September 2024 and March 2025). Soil physicochemical properties were measured and bacterial communities were profiled by 16S rRNA gene (V3–V4) amplicon sequencing; functional potential was inferred using PICRUSt2. Available potassium increased significantly, whereas soil organic matter showed a decrease–recovery trajectory. Bacterial richness (Chao1) decreased after planting, while evenness increased; Shannon diversity remained stable. Community composition shifted directionally, with higher relative abundance of Pseudomonadota (formerly Proteobacteria) and reduced Acidobacteriota at later stages. PERMANOVA based on Bray–Curtis distances indicated significant temporal differences in community structure. RDA indicated that soil organic matter and bulk density were the primary drivers of community structural variation. Functionally, the overall metabolic framework remained stable, whereas pathways related to genetic information processing and metabolism exhibited significant differences (p < 0.05). By examining both intra-annual dynamics and inter-annual changes in soil bacteria and physicochemical properties following the planting of ‘Yitong 2’, this study clarifies patterns of soil property variation and trajectories of microbial community structure and functional potential, thereby providing a scientific basis for the establishment of high-quality I. polycarpa plantations and the sustainable development of soil ecosystems. Full article

Soil fungi are pivotal drivers of biogeochemical cycling, mediating nutrient transformation, plant–soil feedbacks, and ecosystem stability. Understanding their responses to vegetation succession is essential for predicting ecosystem recovery in fragile volcanic landscapes. We investigated soil fungal communities across five successional stages on the Jingpo Lake lava plateau—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—using high-throughput ITS sequencing and soil physicochemical analysis. Basidiomycota and Ascomycota dominated at the phylum level, with Sebacina, Cortinarius, and Mortierella as core genera. Alpha diversity (Shannon, Simpson, Chao1) was significantly higher in early-successional GL and SL than in DB (p < 0.05), while CB exhibited the lowest community evenness (Pielou-e). Co-occurrence networks revealed greater connectivity in GL, whereas forest types showed simplified topologies. LEfSe identified distinct fungal biomarkers for each vegetation type. PICRUSt2-based functional prediction indicated biosynthesis as the dominant pathway (>40%), with significant variation among vegetation types. Redundancy analysis (RDA) identified soil organic matter (SOM) as the primary predictor of fungal community composition. Our findings indicate that vegetation succession is associated with changes in fungal diversity and function primarily linked to variations in SOM, with moisture regimes as a secondary contextual factor. Notably, advanced forest stages exhibited reduced fungal diversity and simplified community structure—highlighting a trade-off between nutrient enrichment and microbial complexity in volcanic ecosystems. These insights advance our understanding of plant–soil–microbe coupling during ecosystem restoration on lava plateaus. Full article

The brewing of Traditional Hakka Huangjiu (THHJ) is usually divided into saccharification and post-fermentation. Microbial succession during saccharification is the major factor influencing the development of the volatile and non-volatile substances in THHJ during post-fermentation. This study systematically investigated the dynamic changes in microbial community, volatile substances and microbial metabolites by using absolute quantitative sequencing and multi-omics analysis. This study also reported that the correlation between microorganisms and substance biosynthesis was analyzed using PICRUSt. Absolute quantitative sequencing results showed that Pediococcus, Saccharomycopsis, Rhizopus, Weissella, and Limosilactobacillus were the dominant microbial genera during saccharification. 737 volatile compounds (170 esters, 94 hydrocarbons, 82 organoheterocyclic compounds) and 4370 metabolites (18 organic acids, 22 amino acids, 1124 peptides and 9 categories of functional compounds) were identified throughout the post-fermentation period. Sensory profiling revealed six main flavor attributes (Balsamic, sweet, rose, green, fruity, bitter) in THHJ and phenylethyl alcohol exerted the most prominent effect on the overall flavor of THHJ. Correlation analysis revealed that the biosynthesis of phenylethyl alcohol was potentially correlated with Saccharomyces, Cyberlindnera, Pichia, Pediococcus, Pseudomonas and Lactococcus. The biosynthesis of flavonoids was potentially correlated with Pediococcus, Lactococcus, and Lactiplantibacillus. These findings contribute to monitoring product quality and optimizing the processing techniques of THHJ. Full article

This study aimed to investigate the effects of dietary NFC/NDF ratio on nutrient apparent digestibility, fecal fermentation parameters, microbial diversity, and plasma metabolomics in Yili horses. Twenty-four healthy Yili horses with similar body weights (406 ± 22.73 kg) were divided into four groups, each with six replicates: the Control Group (CG), Low-NFC Group (LG), Medium-NFC Group (MG), and High-NFC Group (HG). The experiment lasted 52 d, comprising a 7-day adaptation period and a 45-day experimental period. Total fecal collection was conducted from days 41 to 45 to calculate nutrient apparent digestibility. On the final day, rectal fecal samples and blood samples were collected for full-length 16S rRNA gene sequencing and plasma metabolomics analysis. The results revealed the following findings: (1) The apparent digestibility of crude protein (CP) in the MG and HG groups was significantly higher than in the CG (p < 0.01), and significantly higher in the LG group compared to the CG (p < 0.05). (2) Significant differences were observed in fecal pH, propionate concentration, and the acetate-to-propionate ratio between the CG and the experimental groups (p < 0.05). (3) At the phylum level, Firmicutes, Bacteroidota, and Verrucomicrobiota were dominant in the fecal microbiota of all groups. PICRUSt2 prediction indicated that the MG and HG groups primarily enhanced energy conversion efficiency through amino acid metabolism and pantothenate and CoA biosynthesis metabolic pathways. (4) A total of 204 differential metabolites were identified between the CG and MG groups, with 98 upregulated and 106 downregulated in the MG group compared to the CG. These metabolites were mainly enriched in pantothenate and CoA biosynthesis, fructose and mannose metabolism, pyruvate metabolism, and starch and sucrose metabolism pathways. In summary, appropriately increasing NFC/NDF content influences the gut microbiota composition and energy metabolism of Yili horses, thereby effectively improving their digestion and absorption of dietary nutrients. Full article

Background: Dextran sodium sulfate (DSS)-induced colitis serves as a preclinical model for studying gut dysbiosis and inflammation relevant to inflammatory bowel disease (IBD) and its long-term complication of colorectal cancer (CRC). Beetroot (Beta vulgaris L.) extract, rich in betalains, polyphenols, and nitrates, exhibits antioxidant and anti-inflammatory properties. This study investigated beetroot extract’s effects on gut microbiota composition and predicted functional pathways in DSS-induced colitis. Methods: Male BALB/c mice were divided into four groups: control (water), DSS-only, beetroot 250 mg/kg + DSS, and beetroot 500 mg/kg + DSS. Beetroot extract was administered orally for 14 days prior to and during DSS exposure. Gut microbial profiles were analyzed using 16S rRNA sequencing, while microbial diversity, community structure, and predicted metabolic functions were evaluated using Shannon, Chao1, PCoA, PERMANOVA, and PICRUSt2 analyses. Results: DSS administration significantly reduced body weight, microbial diversity, and Bacteroidota abundance, while increasing Proteobacteria and Desulfobacterota—a classic colitis-associated dysbiosis signature. Beetroot supplementation restored body weight and microbial balance in a dose-dependent manner, with the 500 mg/kg group showing near-complete normalization of the microbiota. Functional predictions revealed the upregulation of short-chain fatty acid (SCFA) biosynthesis, glutathione metabolism, and amino acid pathways, and suppression of lipopolysaccharide biosynthesis. Identified phytochemicals, including betanin, ferulic acid, and rutin, were associated with antioxidant and prebiotic activities that support microbial restoration. Conclusions: Beetroot extract mitigates DSS-induced gut dysbiosis and inflammation by enhancing microbial diversity, restoring SCFA-associated taxa, and promoting anti-inflammatory and antioxidant pathways. These findings highlight beetroot as a promising natural dietary intervention for colitis and microbiome-associated intestinal disorders. Full article

Insects’ gut microbiota and their hosts share a mutually dependent symbiotic relationship. However, how insect dietary breadth relates to microbial diversity remains unclear. This study compared the gut bacterial communities of the polyphagous Aulacophora indica and the oligophagous Aulacophora lewisii. Using an integrated approach of cultivation, 16S rRNA high-throughput sequencing, and bioinformatic analyses, we assessed their composition, diversity, and functional potential. Using cultivation-based methods revealed that A. indica showed a greater abundance and diversity of culturable bacteria, dominated by Proteobacteria and Actinobacteria, compared to A. lewisii (Proteobacteria and Firmicutes). In contrast, high-throughput sequencing revealed the opposite pattern: A. lewisii exhibited significantly higher overall species richness and diversity. This apparent paradox highlights the methodological complementarity between cultivation and sequencing. Furthermore, the community composition differed notably at the genus level. Functional prediction via PICRUSt2 v2.2.0 indicated that core metabolic pathways, including carbohydrate metabolism, amino acid metabolism, and energy metabolism, were more enriched in A. indica. In summary, this study reveals systematic multi-dimensional differences in the gut microbiomes of these beetles, providing a theoretical foundation and microbial resources for understanding ecological adaptation and developing targeted control strategies based on gut microbiota. Full article

This study investigates whether fecal microbiota transplantation (FMT) can alleviate gut microbiota dysbiosis induced by a high-fat diet (HFD) through modulation of fatty acid metabolism, competition for nutrients, production of short-chain fatty acids (SCFAs), and restoration of mucus layer integrity. To elucidate the mechanisms by which FMT regulates colonic microbial function and host metabolic responses, 80 male Bal b/c mice were randomly assigned to four experimental groups (n = 20 per group): Normal Diet Group (NDG), High-Fat Diet Group (HDG), Restrictive Diet Group (RDG), and HDG recipients of NDG-derived fecal microbiota (FMT group). The intervention lasted for 12 weeks, during which body weight was monitored biweekly. At the end of the experiment, tissue and fecal samples were collected to assess digestive enzyme activities, intestinal histomorphology, gene expression related to gut barrier function, and gut microbiota composition via 16S rRNA gene sequencing. Results showed that mice in the HDG exhibited significantly higher final body weight and greater weight gain compared to those in the NDG and RDG (p < 0.05). Notably, FMT treatment markedly attenuated HFD-induced weight gain (p < 0.05), reducing it to levels comparable with the NDG (p > 0.05). While HFD significantly elevated the activities of α-amylase and trypsin (p < 0.05), FMT supplementation effectively suppressed these enzymatic activities (p < 0.05). Moreover, FMT ameliorated HFD-induced intestinal architectural damage, as evidenced by significant increases in villus height and the villus height-to-crypt depth ratio (V/C) (p < 0.05). At the molecular level, FMT significantly downregulated the expression of pro-inflammatory cytokines (IL-1β, IL-1α, TNF-α) and upregulated key tight junction proteins (Occludin, Claudin-1, ZO-1) and mucin-2 (MUC2) relative to the HDG (p < 0.05). 16S rRNA analysis demonstrated that FMT substantially increased the abundance of beneficial genera such as Lactobacillus and Bifidobacterium while reducing opportunistic pathogens including Romboutsia (p < 0.05). Furthermore, alpha diversity indices (Chao1 and ACE) were significantly higher in the FMT group than in all other groups (p < 0.05), indicating enhanced microbial richness and community stability. Functional prediction using PICRUSt2 revealed that FMT-enriched metabolic pathways (particularly those associated with SCFA production) and enhanced gut barrier-related functions. Collectively, this study deepens our understanding of host–microbe interactions under HFD-induced metabolic stress and provides mechanistic insights into how FMT restores gut homeostasis, highlighting its potential as a therapeutic strategy for diet-induced dysbiosis and associated metabolic disorders. Full article

Iron is an essential nutrient for piglets, but iron sources vary greatly in bioavailability, and their effects on intestinal health remain unclear. In this study, 21-day-old weaned piglets were used to compare the effects of different iron sources (ferrous sulfate (FeSO₄), ferric ammonium citrate (FAC), and ferrous glycinate (Fe-Gly)) on growth performance, intestinal inflammation, and gut microbiota. Compared to the FeSO₄ group, the Fe-Gly group significantly increased the body weight of piglets at 35 days (p < 0.05), promoted the average daily feed intake (ADFI) and average daily gain (ADG) of piglets from day 21 to 35 (p < 0.01), and also markedly reduced the diarrhea rate of piglets (p < 0.01). Meanwhile, although FAC increased growth performance-related indicators (ADG, ADFI) in piglets, there was no significant statistical difference compared with FeSO₄ (p > 0.10). Moreover, Fe-Gly supplementation significantly elevated serum iron levels and total iron-binding capacity (p < 0.01), while significantly reducing the iron content in colonic chyme (p < 0.0001). Both the Fe-Gly and FAC significantly improved the anti-inflammatory and antioxidant capacities of the piglets (p < 0.01). Interestingly, Fe-Gly primarily increased the abundance of Lactobacillus, thereby reducing the abundance of harmful bacteria such as Escherichia coli. Functional prediction using PICRUSt2 revealed that Fe-Gly supplementation tended to elevate the relative abundance of gut bacteria capable of carbohydrate metabolism and amino acid synthesis. In conclusion, this study demonstrated that dietary Fe-Gly supplementation improved systemic iron status, effectively reduce residual iron in the intestine, inhibit the proliferation of pathogenic bacteria in the gut, promote the growth performance and intestinal health of piglets, and reduce the diarrhea rate. Full article

Low ethyl caproate and high ethyl lactate contents pose a significant challenge in producing Chinese nong-xiang baijiu. The formation of these esters depends on the metabolism of their precursors—caproic acid and lactic acid—within the pit mud (PM) microbiome. However, the specific taxa driving the metabolic flux from lactate accumulation to caproate synthesis remain unclear. This study aimed to identify potential functional microbes capable of caproate biosynthesis and lactate utilization by systematically analyzing PM samples from the upper, middle, and lower layers of three different pit ages (0, 20, and 50 years). Results showed that 50-year-old PM exhibited significantly higher caproic acid and ammonium nitrogen levels, but lower lactic acid content, compared to the 0- and 20-year-old counterparts. Notably, Petrimonas, Caproiciproducens, and Sedimentibacter were significantly enriched in the 50-year-old PM. Their relative abundances correlated positively with caproic acid and negatively with lactic acid. Furthermore, PICRUSt2 analysis indicated higher abundances of genes associated with caproate synthesis and lactate utilization in the 50-year-old microenvironment. We propose that Petrimonas, Caproiciproducens, and Sedimentibacter are potential functional candidates for lactate degradation and caproate generation. These findings provide a scientific basis for modulating the microbiome for “increasing ethyl caproate and reducing ethyl lactate”, thereby enhancing baijiu quality. Full article