Search Results (37)

Daqu is the core saccharifying and fermenting starter for strong-flavor Baijiu, and its quality is strongly shaped by the workshop microenvironment. Here, mature Daqu from a newly built workshop and a long-established workshop within the same distillery were compared under identical raw materials and process conditions. Physicochemical properties, volatile flavor compounds (HS-SPME-GC–MS), bacterial and fungal communities (16S/ITS sequencing), and Tax4Fun-predicted functions were jointly analyzed. The quality indicators of the Daqu in the new workshop are qualified, but the acidity (and moisture) is higher, and the fermentation, saccharification and liquefaction abilities are lower. The Daqu in the old workshop is rich in esters, the aroma is more mature, and the total ester content is about twice that of the new workshop. Both Daqu types shared similar core taxa, but the new workshop was dominated by a simpler Weissella–Thermomyces consortium, while the old workshop was enriched in Bacillus, lactic acid bacteria, Rhizomucor, Saccharomycopsis, and Wickerhamomyces. Correlation and network analyses linked these old-workshop core genera to key ethyl esters, higher alcohols and pyrazines, and Tax4Fun indicated a stronger bias toward amino acid/carbohydrate metabolism and membrane transport in the old workshop. These results show that workshop age reshapes Daqu quality by co-modulating physicochemical traits, microbial consortia and functional potential, and suggest microbial and functional targets for accelerating the “maturation” of new workshops. Full article

Arid and semi-arid soils represent extreme habitats where microbial life is constrained by high temperature, low water availability, salinity, and nutrient limitation, yet these ecosystems harbor unique bacterial communities that sustain key ecological processes. To explore the diversity and functional potential of prokaryotic assemblages in Algerian drylands, we compared soils from three contrasting sites: The Oasis of Djanet (RM1), the hyper-arid Tassili of Djanet desert (RM2), and the semi-arid El Ouricia forest in Sétif (RM3). Physicochemical analyses revealed strong environmental gradients: RM2 exhibited the highest pH (8.66), electrical conductivity (11.7 dS/m), and sand fraction (56%), whereas RM3 displayed the greatest moisture (10.9%), organic matter (7.6%), and calcium carbonate (20.7%) content, with RM1 generally showing intermediate levels. High-throughput 16S rRNA gene sequencing generated >60,000 effective reads per sample with sufficient coverage (>0.99). Alpha diversity indices indicated the highest bacterial richness and diversity in RM2 (Chao1 = 3144, Shannon = 10.0), while RM3 showed lower evenness and the dominance of a few taxa. Across sites, 66 phyla and 551 genera were detected, dominated by Actinobacteriota (38–45%) and Chloroflexi (13–44%), with Proteobacteria declining from RM1 (17.5%) to RM3 (3.3%). Venn analysis revealed limited overlap, with only 58 operational taxonomic units shared among all sites, suggesting highly habitat-specific communities. Predictive functional profiling (PICRUSt2, Tax4Fun, FAPROTAX) indicated metabolism as the dominant functional category (≈50% of KEGG Level-1), with carbohydrate and amino acid metabolism forming the metabolic backbone. Notably, transport functions (ABC transporters), lipid metabolism, and amino acid degradation pathways were enriched in RM2–RM3, consistent with adaptation to osmotic stress, nutrient limitation, and energy conservation under aridity. Collectively, these findings demonstrate that Algerian arid and semi-arid soils host diverse, site-specific bacterial communities whose functional repertoires are strongly shaped by soil chemistry and climate, highlighting their ecological and biotechnological potential. Full article

Raccoon dog fur is a commercially valuable animal product. As the scale of raccoon dog breeding continues to expand, ensuring the health of these animals has become an urgent priority. The gut microbiota plays a central role in regulating animal health; however, current research on the composition of raccoon dog gut microbiota remains limited. This study aimed to characterize changes in the gut microbiota of suckling raccoon dogs across different stages, providing a foundation for future scientific feeding practices. Fecal samples of eight lactating raccoon dogs were collected and tested for microbiota on days 14, 21, and 45. Our results showed that the richness and diversity of microbiota increased with age in suckling raccoon dogs, peaking on the 45th day. Significant separation between groups was observed in both PCoA and NMDS analyses. UPGMA analysis indicated temporal fluctuations in gut microbiota composition. At the phylum level, Firmicutes and Bacteroidetes were the dominant taxa across all stages. LEfSe analysis at the genus level showed that Bacteroides was the most enriched taxon on the 14th day, Fusobacterium on the 21st day, and Prevotella_9 on the 45th day. Tax4Fun and PICRUSt analyses identified metabolism and genetic information processing as the primary functional roles of the gut microbiota. Further investigation suggested that the microbiota may benefit raccoon dogs through membrane transport, carbohydrate metabolism, amino acid metabolism, and energy metabolism. These findings establish a theoretical basis for improving the survival rate of suckling raccoon dogs and developing scientifically informed feeding and management protocols. Full article

The monitoring and surveillance of antimicrobial resistance (AMR) is an important procedure in clinical patient management and epidemiological public health. Conventionally, culture-based tools such as disk diffusion methods or broth dilution methods for antibiotic susceptibility tests are used. While culture-independent approaches, such as PICRUSt2, Tax4Fun, or MicFunPred, have recently been tried based on predictive functional profiling using the 16S rRNA marker gene, evaluations of AMR tools are scarce. A total of 20 E. coli strains (Carbapenem-resistant (CRE) positive: 10, CRE negative: 10) were used. The AMR phenotype was based on Vitek2 (bioMerieux). DNA was extracted from the 20 strains, and 16S rRNA (V3-V4 region) and shotgun sequencing was carried out. The bioinformatic pipelines were QIIM2 for 16S rRNA and MetaPhlAn4 for shotgun. The functional prediction tools were PICRUSt2, Tax4Fun, and MicFunPred for 16S rRNA and AMRFinderPlus for shotgun. The presence/absence of 23 KEGG numbers regarding AMR in PICRUSt2, Tax4Fun, and MicFunPred were compared to shotgun AMR profiles. The F1 scores were calculated according to each 16S marker gene-based prediction tool using a confusion matrix. A total of 12 classes of antibiotics, including carbapenem, were analyzed. The F1 scores of 16S predictive functional profilers regarding AMR were 0.22 for Tax4Fun, 0.12 for PICRUSt2, and 0.08 for MicFunPred. While Tax4Fun showed the highest F1 score of the three 16S predictive functional profilers, the F1 scores were generally low. Our study highlights the necessity of integrating specialized AMR databases and improving algorithmic approaches to achieve meaningful accuracy in resistance prediction. Full article

Biodegradation is a green and efficient method for lignin depolymerization and conversion. In order to screen potential bacterial strains for efficient lignin degradation, composts of cow dung and wheat straw were prepared, and the dynamic changes in the predicted bacterial community structure and function in different periods of the composts were investigated. Then, bacteria with an efficient lignin degradation ability were finally screened out from the compost samples. Based on the monitoring results of the physicochemical indexes of the composting process, it was found that the temperature and pH of the compost firstly increased and then decreased with the extension of time, and the water content and C/N gradually decreased. High-throughput sequencing of compost samples from the initial (DA), high-temperature (DB), and cooling (DC) periods revealed that the number of OTUs increased sharply then stabilized around 2000, and the alpha diversity of the bacterial community decreased firstly and then increased. The predominant phyla identified included Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes, determined by the relative abundance of beta-diversity-associated species. Functional gene analysis conducted using Tax4Fun revealed that the genes were primarily categorized into Metabolism, Genetic Information Processing, Environmental Information Processing, and Cellular Processes. Based on the decolorization of aniline blue and the degradation efficiency of alkali lignin, eight bacterial strains were isolated from compost samples at the three stages. Cupriavidus sp. F1 showed the highest degradation of alkali lignin with 66.01%. Cupriavidus sp. D8 showed the highest lignin degradation potential with all three enzyme activities significantly higher than the other strains. The results provide a strategy for the lignin degradation and utilization of biomass resources. Full article

The Hainan gibbon (Nomascus hainanus) is one of the most endangered primates globally, threatened by habitat destruction, genetic diversity loss, and ecological competition. In this study, given the critical role of the gut microbiota in host immune regulation and nutrient metabolism, we investigated the composition of and age-related variations in the gut microbiota in Hainan gibbons. Using 16S rRNA sequencing, we systematically investigated the gut microbial diversity of Hainan gibbons. We collected 41 fecal samples from Hainan Tropical Rainforest National Park, covering three age groups: juveniles (4–6 years), subadults (7–10 years), and elderly animals (≥13 years). This study found that microbiota composition changed significantly with age. Juveniles had higher microbial diversity and complexity, while subadults showed an increased abundance of Fibrobacter and Prevotella in their microbial communities, along with a Tax4Fun-predicted enrichment of functional genes related to energy metabolism, cell motility, and nervous system functions. LEfSe analysis identified statistically significant microbial taxa among different age groups, with Bacteroidota and Firmicutes being the dominant phyla across all groups with varying proportions. These results highlight the critical role of the gut microbiota in the health and adaptability of Hainan gibbons, offering insights for conservation strategies. The findings of this study are significant for understanding the changes in gut microbiota and their ecological functions across different life stages of endangered primates. Full article

Effects of heavy metals on soil microbial communities have been extensively studied due to their persistence in the environment and imposed threats to living organisms; however, there is a lack of in-depth studies of the impacts of heavy metals on plant endophyte communities. Therefore, the responses of plant endophyte communities to different concentrations of heavy metals were investigated in this study. The endophyte communities of plants existing in severely (W1, Pb, 110.49 mg/kg, Cd, 1.11 mg/kg), moderately (W2, Pb, 55.06 mg/kg, Cd, 0.48 mg/kg), and mildly (W3, Pb, 39.06 mg/kg, Cd, 0.20 mg/kg) contaminated soils were analyzed by 16s rRNA high-throughput Illumina sequencing. Furthermore, networks were constructed to illustrate the relationships between microorganisms and environmental factors. High-quality sequences were clustered at a 97% similarity level. Results revealed that the diversity of the community and relative abundance of Cyanobacteria phylum increased with decreasing levels of pollution. Cyanobacteria and Proteobacteria were found to be the dominant phylum, while Methylobacterium and Sphingomonas were observed as the dominant genus. Tukey’s HSD test showed that the relative abundances of Cyanobacteria and Proteobacteria phyla and Methylobacterium and Sphingomonas genera differed significantly (p < 0.01) among the plants of the three sample sites. Environmental factor analysis revealed a significant negative correlation (p < 0.01) of Cyanobacteria and a significant positive correlation (p < 0.01) of Methylobacterium with the heavy metal content in the environment. These findings suggest that Cyanobacteria and Methylobacterium may be phylum and genus indicators, respectively, of heavy metal toxicity. Tax4Fun analysis showed the effect of heavy metal toxicity on the abundance of genes involved in plant metabolism. In addition, culturable endophytic strains were isolated to study their resistance to heavy metal stress and their ability to promote plant growth. The potting tests showed that the JG1 strain was tolerant to heavy metals, and it could significantly promote the growth of the host plant under stress caused by multiple heavy metals. Compared to the control, the JG1-treated plants showed a 23.14% increase in height and a 12.84% increase in biomass. Moreover, AP, AK, and HN contents in JG1-treated plants were 20.87%, 12.55%, and 9.03% higher, respectively, under heavy metal stress. The results of this study provide a scientific basis for the construction of an efficient plant endophyte restoration system. Full article

Massive labile carbon and nitrogen inputs into lakes change greenhouse gas emissions. However, the rapid driving mechanism from eutrophic and swampy lakes is not fully understood and is usually contradictory. Thus, we launched a short-term and anaerobic incubation experiment to explore the response of greenhouse gas emissions and microbial communities to glucose and nitrate nitrogen (NO₃⁻-N) inputs. Glucose addition significantly increased CH₄ and CO₂ emissions and decreased N₂O emissions, but there were no significant differences. NO₃⁻-N addition significantly promoted N₂O emissions but reduced CH₄ accumulative amounts, similar to the results of the Tax4Fun prediction. Bacterial relative abundance changed after glucose addition and coupled with the abundance of denitrification genes (nirS and nirK) decreased while maintaining a negative impact on N₂O emissions, considerably increasing methanogenic bacteria (mcrA1) while maintaining a positive impact on CH₄ emissions. Structural equation modeling showed that glucose and NO₃⁻-N addition directly affected MBC content and greenhouse gas emissions. Further, MBC content was significantly negative with nirS and nirK, and positive with mcrA1. These results significantly deepen the current understanding of the relationships between labial carbon, nitrogen, and greenhouse emissions, further highlighting that labile carbon input is the primary factor driving greenhouse gas emissions from eutrophic shallow lakes. Full article

The Asian dung beetle (Catharsius molossus L.; Coleoptera: Scarabeidae) has been shown to positively affect soil bacterial diversity and the agronomic features of crop plants. In this study, we used bioinformatic tools to investigate the differences in bacterial functional phenotypes and ecological functions between control soil, cow dung-amended soil (CD), and cow dung-amended soil composted by dung beetles (DB). The soil bacterial metagenomes were sequenced and analyzed with the bioinformatic packages BugBase, PICRUSt2, Tax4Fun, and FAPROTAX to evaluate the effects of dung beetle-mediated composting on bacterial functions such as human and plant pathogenicity, trophic strategies, and soil nutrient transformation. BugBase proved useful for the determination of differences in major functional phenotypes, whereas FAPROTAX was effective at identifying differences in bacterial ecological functions between the treatments. Both tools suggested a relative decrease in human pathogens in the DB soil. This was corroborated by the pairwise comparison of abundances in bacterial species, which showed a significant reduction in the abundance of the broad-host-range pathogen Pseudomonas aeruginosa in the DB soil. In addition, FAPROTAX suggested a decrease in plant pathogens and an increase in chitinolytic bacteria, meaning that the DB treatment might be beneficial to the plant-growth-promoting bacteria involved in biological control. Finally, FAPROTAX revealed an array of ecological functions related to trophic strategies and macro- and micronutrient metabolism. According to these results, the activity of C. molossus beetles enhanced methanotrophy, ammonification, nitrification, sulfate reduction, and manganese oxidation, whereas iron respiration was decreased in the DB-treated soil. Our results represent a collection of general insights into the effects of C. molossus beetles on soil bacterial functions, which also reflect on the nutrient composition of dung beetle-composted soil. Full article

Soil is the basis of bamboo growth and quality formation of bamboo shoots and has an important contribution to the sustainable development of agriculture. To this end, We studied the soil properties and microbial communities of Dendrocalamus brandisii by collecting twenty-one soil samples from its seven typical geographic provenances in Yunnan Province, China. Bacterial 16S rRNA gene amplicons were used to detect soil bacteria and predict bacterial functions using Tax4Fun. The results indicated that the soil bacterial diversity indices (ACE, Chao1, Simpson, and Shannon) were significantly different among different geographical provenances. The dominant bacterial groups at the phylum level in all seven regions were Proteobacteria (19.78~29.06%), Actinobacteria (13.53~30.01%), Chloroflexi (8.03~31.47%), and Acidobacteria (7.12~19.17%), with markedly different constitution proportions. Total phosphorus, available potassium, and pH were the main environmental factors affecting soil bacterial communities. There were significant differences in the secondary metabolic pathways and phenotypes of soil bacterial functions, exhibiting a diversity of functions. The geographical variables of the soil bacterial community in D. brandisii varied with spatial scales. Environmental factors such as available potassium (AK), pH, and total nitrogen (TN) have an impact on soil bacterial communities. Full article

With the continuous rise of the sea cucumber aquaculture industry in China, the tropical sea cucumber aquaculture industry is also improving. However, research on the gut microorganisms of tropical sea cucumbers in captivity is scarce. In this study, high-throughput sequencing methods were used to analyze the gut microbial composition of Stichopus monotuberculatus and Holothuria scabra in the dry season and wet season of artificial environments. The results showed that 66 phyla were obtained in all samples, of which 59 phyla were obtained in the dry season, and 45 phyla were obtained in the wet season. The Tax4Fun analysis showed that certain gut bacterial communities affect the daily metabolism of two sea cucumber species and are involved in maintaining gut microecological balance in the gut of two sea cucumber species. In addition, compared with differences between species, PCoA and UPGMA clustering analysis showed the gut prokaryotes of the same sea cucumber species varied more in different seasons, indicating that the influence of environment was higher than the feeding choices of sea cucumbers under relatively closed conditions. These results revealed the gut bacterial community composition of S. monotuberculatus and H. scabra and the differences in gut bacterial structure between two sea cucumber species in different seasons were compared, which would provide the foundation for tropical sea cucumber aquaculture in the future. Full article

The type and composition of food strongly affect the variation and enrichment of the gut microbiota. The gut–microbiota–spleen axis has been developed, incorporating the spleen’s function and maturation. However, how short-chain fatty-acid-producing gut microbiota can be considered to recover spleen function, particularly in spleens damaged by changed gut microbiota, is unknown in geese. Therefore, the gut microbial composition of the caecal chyme of geese was assessed by 16S rRNA microbial genes, and a Tax4Fun analysis identified the enrichment of KEGG orthologues involved in lipopolysaccharide production. The concentrations of LPS, reactive oxygen species, antioxidant/oxidant enzymes, and immunoglobulins were measured from serum samples and spleen tissues using ELISA kits. Quantitative reverse transcription PCR was employed to detect the Kelch-like-ECH-associated protein 1–Nuclear factor erythroid 2-related factor 2 (Keap1-Nrf2), B cell and T cell targeting markers, and anti-inflammatory/inflammatory cytokines from the spleen tissues of geese. The SCFAs were determined from the caecal chyme of geese by using gas chromatography. In this study, ryegrass-enriched gut microbiota such as Eggerthellaceae, Oscillospiraceae, Rikenellaceae, and Lachnospiraceae attenuated commercial diet-induced gut microbial alterations and spleen dysfunctions in geese. Ryegrass significantly improved the SCFAs (acetic, butyric, propionic, isovaleric, and valeric acids), AMPK pathway-activated Nrf2 redox signaling cascades, B cells (B220, CD19, and IgD), and T cells (CD3, CD4, CD8, and IL-2, with an exception of IL-17 and TGF-β) to activate anti-inflammatory cytokines (IL-4 and IL-10) and immunoglobulins (IgA, IgG, and IgM) in geese. In conclusion, ryegrass-improved reprogramming of the gut microbiota restored the spleen functions by attenuating LPS-induced oxidative stress and systemic inflammation through the gut–microbiota–spleen axis in geese. Full article

The addition of organic materials is pivotal for the efficacy of reductive soil disinfestation (RSD). However, data on the influence of varying amounts of organic matter during RSD on soil-borne disease mitigation, yield increase, and rhizosphere microecological health in the current flue-cured tobacco season remain limited. This study analyzed various organic material addition rates (CK, G0.8, G1.0, and G1.2) at two experimental sites (K and Y). The results indicated that increasing the application of organic material improved the soil physicochemical properties (pH, AN, AP, AK, OM, and C/N), mitigated the severity of black shank and Fusarium root rot, and amplified the tobacco yield. The K/YG1.2 treatment significantly reduced the Shannon and Sobs fungal indices across both sites, and enhanced the relative abundance of the bacteria Actinobacteria, Chloroflexi, Firmicutes, and Acidobacteriota, while decreasing the relative abundance of Ascomycota. The bacterial genera were predominantly represented by Sphingomonas and Bacillus, whereas the fungal genera were represented by Saitozyma, Mortierella, and Fusarium. The addition of organic materials during RSD substantially decreased the relative abundance of Mortierella and Fusarium. Using FUNGGuild and Tax4Fun to evaluate the application of adding organic matter during the RSD process, we identified that rhizosphere fungi in high application rates of flue-cured tobacco were primarily saprophytic or pathogenic saprophytes, which were mainly involved in the metabolism, environmental information processing, genetic information processing, and cellular processes. The results of the two experimental sites indicate that applying 15 t·ha⁻¹ (K/YG1.2) of solid residues such as vegetables during RSD emerges as the optimal choice. This strategy is highly effective in guaranteeing the sterilization and pest control effect of the RSD process, facilitating the reconstruction of microbial community diversity, lowering pathogen abundance, managing soil-borne diseases that are prevalent in the current flue-cured tobacco season, and leading to an increase in tobacco yield. Full article

Long-term coal mining has created unique microbial communities in deep coal mines. Revealing the microbial community structure and metabolic functions in the underground environment can contribute to a better understanding of the coal mine ecosystem. In this study, we collected underground sediment samples from producing mines in eastern China at mining depths of −400 to −1100 m and performed high-throughput sequencing. Results showed that most of the genera in the underground sediment can degrade organic matter, such as polycyclic aromatic hydrocarbons (PAHs), benzene, toluene, and xylene, etc. The dominant genera in the underground sediment were Hydrogenophaga, Thauera, Pseudomonas, Rhodobacter, and Dietzia. Samples were divided into coal roadway (CR) and rock roadway (RR) groups according to the sampling location. The microbial community structure differed significantly (p < 0.05) between these two groups of samples, with the distribution of main genera in the CR group samples showing a negative correlation with Cu and a positive correlation with temperature. The samples from the CR and RR groups were significantly different (p < 0.05) in their metabolic functions, including membrane transport, metabolism of other amino acids, folding, sorting, and degradation. Microorganisms in the RR group samples showed high resistance to heavy metals, while microorganisms in the CR group had higher degradation functions of organic pollutants. Bugbase phenotypic predictions indicated a high potential pathogenicity of microorganisms in coal mine sediment, which was mainly contributed by the genera Hydrogenophaga, Pseudomonas, Geothermobacter, and Methylophaga, etc. This study deepens the understanding of microbial communities in deep coal mine environments; however, the organic contamination and biological health risks of underground environments require extensive attention. Full article

Intestinal microflora is correlated with obesity, metabolic diseases and digestive tract dysfunctions that are closely related to human health. Nobiletin (NOB) is a dietary polymethoxylated flavonoid with protective effects and activities against oxidative stress, inflammation and cardiovascular disorders. However, the effect and molecular mechanism of NOB in regulating white fat deposition have not been explored. In this study, we reported that NOB administration attenuates weight gain and glucose tolerance in mice fed a high−fat diet (HFD). Additionally, NOB administration substantially restored lipid metabolic disorder and repressed the level of genes related to lipid metabolism in HFD−induced obese mice. The sequencing of 16S rRNA genes in fecal samples unveiled that NOB administration reversed HFD−induced intestinal microbiota composition, particularly in the relative abundances of Bacteroidetes and Firmicutes at the phylum and genus level. Furthermore, NOB supplementation significantly improved the indexes of Chao1 and Simpson and implied NOB can improve intestinal flora diversity in HFD−fed mice. Next, we used LEfSe analysis to explore biomarkers presented as a taxon in different groups. Compared to the HFD group, NOB treatment significantly diminished the proportion of Ruminococcaceae, Ruminiclostridium, Intesinimonas, Oscillibacter and Desulfovibrio. Enriched metabolic pathways were predicted by Tax4Fun analysis and demonstrated that the lipid metabolic pathway is higher in the HFD + NOB group. More importantly, the correlation analysis demonstrated that Parabacteroides was significantly positive and Lactobacillus was negatively related to both body weight and inguinal adipose tissue weight. Collectively, our data emphasized that NOB has the potential to attenuate obesity and confirmed a mechanism for gut microbiota that mediated the beneficial effect of NOB. Full article