Search Results (25)

Microbiome data analysis is essential for understanding the role of microbial communities in human health. However, limited data availability often hinders research progress, and synthetic data generation could offer a promising solution to this problem. This study aims to explore the use of machine learning (ML) to enrich an unbalanced dataset consisting of microbial operational taxonomic unit (OTU) counts of 148 samples, belonging to 61 patients. In detail, 34 samples are from 16 adenomatous polyps (AP) patients, while 114 samples are from 46 colorectal cancer (CRC) patients. Synthesis of AP and CRC samples was conducted using the Synthetic Data Vault Python library, employing a Gaussian Copula synthesiser. Subsequently, the synthesised data quality was evaluated using a logistic regression model in parallel with an optimised support vector machine algorithm (polynomial kernel). The data quality is considered good when neither of the two algorithms can discriminate between real and synthetic data, showing low accuracy, F1 score, and precision values. Furthermore, additional statistical tests were employed to confirm the similarity between real and synthetic data. After data validation, layer-wise relevance propagation (LRP) was performed on a deep learning classifier to extract important OTU features from the generated dataset, to discriminate between CRC patients and those affected by AP. Exploiting the acquired features, which correspond to unique bacterial taxa, ML classifiers were trained and tested to estimate the validity of such microorganisms in recognising AP and CRC samples. The simplified version of the original OTU table opens up opportunities for further investigations, especially in the realm of extensive data synthesis. This involves a deeper exploration and augmentation of the condensed data to uncover new insights and patterns that might not be readily apparent in the original, more complex form. Digging deeper into the simplified data may help us better grasp the biological or ecological processes reflected in the OTU data. Transitioning from this exploration, the synergy of ML and synthetic data enrichment holds promise for advancing microbiome research. This approach enhances classification accuracy and reveals hidden microbial markers that could prove valuable in clinical practice as a diagnostic and prognostic tool. Full article

The microbiota in forage silage plays a pivotal role in determining the fermentation quality. Identifying effective microbial additives is essential to help forage producers refine their search for functional inoculants and to support farmers in adopting them for practical ensiling. This study investigated microbial and metabolomic dynamics in king grass silages treated with six commercial inoculants dominated by Enterococcus faecium-like species, Bacillus velezensis, and Lactobacillus paraplantarum. The fermentation characteristics, viable microbial diversity, and metabolite profiles were compared between treated and untreated silages using 16S rDNA sequencing and metabolic profiling via LC-QTOF-MS, integrated with multi-omics correlation analyses. Additive-treated silages showed improved fermentation quality, simplified bacterial correlation networks, and distinct microbial successions and interactions. A total of 1523 metabolites were detected, with 56–84 significantly altered in each treated group compared to the control. Metabolites with antimicrobial, antioxidant, and cholesterol-lowering activities were more abundant in treated silages, especially organic acids, amino acids, and short-chain fatty acids. Inoculants distinctly influenced amino acid, energy, nucleotide, and vitamin metabolism during ensiling. This study advances our understanding of how commercial microbial additives reshape the bacterial community structure and function in silages and highlights promising lactic acid bacteria species contributing to silage quality through the production of bio-functional metabolites. Full article

Straw application (SP) is a promising strategy for the improvement of soil fertility, but the biological effects and the mechanisms of its effects on microorganisms remain unclear. The investigation into the tea plantations (CK/S) in southern Henan, China, without/with straw amendment was carried out to assess the effects of SP on the soil bacterial communities using high-throughput sequencing. SP induced the community restructuring of the dominant phyla, e.g., Acidobacteriota, Pseudomonadota, Chloroflexota, with significantly increasing Nitrospirota, Vicinamibacterales and Anaerolineaceae (p < 0.05), while reducing Terriglobales (p < 0.05). These transitions correlated with significantly enhanced α-diversity and β-diversity divergence (p < 0.05). The linear discriminant analysis effect size (LEfSe) results confirmed the significant selective enrichment of nitrogen-cycling taxa (Nitrospira), copiotrophs (Chryseotalea), and anaerobic degraders (Anaerolineaceae), along with the suppression of the oligotrophic lineage (Ellin6067) by SP (p < 0.05). The co-occurrence networks of S had lower topological properties and negative cohesion (p < 0.05), which exhibited intensified simplified complexity and competition. The soil water content (WC) and pH were the main drivers of β-diversity variation and the keystone taxa assembly, as calculated out by distance-based redundancy analysis (dbRDA). This study demonstrates that SP can enhance bacterial network stability and functional redundancy by resource-driven niche partitioning between copiotrophic taxa and nitrogen-cycling guilds through a competition–cooperation equilibrium. Full article

Environmental DNA from bulk materials can be analyzed to gain an understanding of the bacterial, fungal, plant, and/or arthropod communities present. DNA metabarcoding is widely used to characterize these biological communities, by amplifying “barcode” regions and sequencing these amplicons via next-generation sequencing. The Earth Microbiome Project (EMP) adopted the use of indexed primers, PCR primers containing Illumina^® adapter sequences and a unique 12-nucleotide Golay barcode to simplify the identification of bacterial taxa via the 16S barcode. We sought to develop a wet laboratory workflow utilizing indexed primers that could cost-effectively reduce bench time while simultaneously targeting multiple DNA barcode regions to characterize bacterial (16S), fungal (ITS1), plant (ITS2, trnL p6 loop), and arthropod (COI) communities. The EMP primer constructs for 16S were modified to accommodate our DNA barcode regions of interest while also permitting successful demultiplexing following sequencing. A single indexed primer pair was designed for ITS1 and trnL p6 loop, and two primer pairs were developed for ITS2 and COI. To test the workflow, a total of 648 soil and 336 dust samples were processed, with key steps including DNA isolation, total DNA quantification, amplification with indexed primers, library purification and quantification, and Illumina MiSeq sequencing. Based on raw read counts and analysis of positive controls, the trnL p6 loop and ITS2 a primer pairs performed comparably to the originally designed 16S primers. Both COI primers pairs, ITS1 and ITS2 b primers, had lower raw reads compared to the other three primer pairs. The combination of the three plant targets successfully recovered all plant taxa in the positive controls except for Nephrolepis exaltata [Nephrolepidaceae] and the COI primers recovered all arthropod taxa except for the beetle. Notably, none of the taxa in the fungal positive control were recovered using ITS1. For environmental samples, sequencing was successful for all primers except COI c, and primer biases were observed for all three plant primers, in which a small number of families were uniquely amplified for each primer pair. This workflow can be applied to many disciplines that utilize DNA metabarcoding given its customizability and flexibility with Illumina sequencing chemistry. Full article

The summer-sowing short-season cotton cultivation model is an important method for simplified and mechanized cotton planting in the Yangtze River Basin. However, the effects of microbial fertilizers on cotton growth and soil under this model remain unclear. In 2023, we conducted a systematic analysis on the application of microbial fertilizers (compost) at varying levels (CK, MF1, MF2, and MF3) during different growth stages of cotton (bud, flowering, bolling, and boll opening). Results showed that appropriate microbial fertilizer application (MF2 and MF3) enhanced soil bacterial and fungal diversity, enriched beneficial microorganisms (e.g., Acidobacteriota and Candidatus Udaeobacter), improved soil nutrient availability, and increased antioxidant enzyme activity (POD, SOD), while reducing membrane lipid peroxidation (MDA). These effects led to significant improvements in yield traits, such as cotton plant height, number of fruiting branches and bolls, boll weight, and coat weight. The highest microbial fertilizer application level (MF3) resulted in a 54.35% increase in seed yield and a 75.37% increase in lint yield compared to CK. PLS-DA (Partial Least Squares Discriminant Analysis) and multivariate statistical analyses revealed that microbial fertilizer application fine-tuned soil microbial community composition, emphasizing the dynamic balance of the microbial ecosystem. This study provides scientific support for optimizing microbial fertilizer strategies to enhance the yield and quality of summer-sown short-season cotton and promote sustainable agriculture. Full article

Antibiotic resistance, in particular the dissemination of carbapenemase-producing organisms, poses a significant threat to global healthcare. This study introduces the qPCR CarbaScan LyoBead assay, a robust, accurate, and efficient tool for detecting key carbapenemase genes, including blaKPC, blaNDM, blaOXA-48, and blaVIM. The assay utilizes lyophilized beads, a technological advancement that enhances stability, simplifies handling, and eliminates the need for refrigeration. This feature renders it particularly well-suited for point-of-care diagnostics and resource-limited settings. The assay’s capacity to detect carbapenemase genes directly from bacterial colonies without the need for extensive sample preparation has been demonstrated to streamline workflows and enable rapid diagnostic results. The assay demonstrated 100% specificity and sensitivity across a diverse range of bacterial strains, including multiple allelic variants of target genes, facilitating precise identification of resistance mechanisms. Bacterial strains of the species Acinetobacter baumannii, Citrobacter freundii, Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae and Pseudomonas aeruginosa were utilized as reference material for assay development (n = 9) and validation (n = 28). It is notable that the assay’s long shelf life and minimal operational complexity further enhance its utility for large-scale implementation in healthcare, food safety, and environmental monitoring. The findings emphasize the necessity of continuous surveillance and the implementation of rapid diagnostic methods for the effective detection of resistance genes. Furthermore, the assay’s potential applications in other fields, such as toxin-antitoxin system research and monitoring of resistant bacteria in the community, highlight its versatility. In conclusion, the qPCR CarbaScan LyoBead assay is a valuable tool that can contribute to the urgent need to combat antibiotic resistance and improve global public health outcomes. Full article

Grazing intensity is one of the crucial anthropogenic activities on alpine grasslands. However, how grazing intensity affects soil microorganism diversities and their co-occurrence networks in alpine steppe remains uncertain. We carried out a controlled grazing experiment (null grazing, CK; moderate grazing, MG; and heavy grazing, HG) on a typical alpine steppe in the Lhasa River Basin, Central Tibet, China. We used high-throughput sequencing to find the sequences of bacterial 16S rRNA and fungal ITS gene amplicons. Then, we analyzed their alpha and beta diversities and set up co-occurrence networks that show how often they occur together. MG significantly increased the bacterial Shannon index and changed the bacterial community structure. In contrast, HG decreased the fungal ACE and Chao1 indices and also changed the fungal community structure (p < 0.05). Linear mixed-effect model revealed that available phosphorus in soil significantly impacted on soil bacterial Shannon, ACE, and Chao1 indices across grazing intensities, while total carbon in subsoil significantly affected these indicators of soil fungi. Moreover, MG increased the complexity of the co-occurrence network in the bacterial community, while HG simplified it. However, both MG and HG made the co-occurrence networks in the fungal community less complicated. This shows that the intensity of grazing has different impacts on how microbes interact with each other. Therefore, sustainable grazing intensity necessitates a deeper understanding of biodiversity conservation in alpine grasslands. Full article

Reasonably using reclaimed water (RW) for irrigation can help to alleviate water scarcity, while also providing both environmental and economic benefits. However, there is limited information regarding the potential impact of RW irrigation on the nutrients of saline–alkali soils and their microbial communities. This study investigates the effects of RW irrigation on saline–alkali soil properties and microbial communities using a 16S rRNA sequence analysis. The results show that the pH and electrical conductivity (EC) are significantly lower in RW treatment (p < 0.05). Compared to the saline–alkali soil that was not irrigated with RW (CK), the EC value decreased by 42.15–45.76%, in both 0–20 cm and 40–60 cm depth. RW exhibited a significant increase in the abundance of Actinobacteria (32.32–33.42%), Chloroflexi (7.63–15.79%), Firmicutes (9.27–10.42%), and Ascomycota (89.85–95.95%). Bacterial richness and diversity were significantly enhanced after RW irrigation (p < 0.05). At the genus level, the dominant bacterial genera included Bacillus, Penicillium, Aspergillus, and Talaromyces. Differences in the microbial community were observed between the two treatments and among soil depths within each treatment (p < 0.05). A network analysis indicated that the internal relationships among bacterial communities become more complex following RW irrigation, whereas the internal connections within fungal communities tend to become more simplified. A redundancy analysis (RDA) showed that soil microbial communities were directly influenced by EC, total nitrogen (TN), and available potassium (AK). Partial least squares path modeling (PLS-PM) results indicated that soil salinity and available nutrients were the most significant factors influencing the microbial community structure. Together, these results indicate that RW irrigation has a positive impact on ameliorating soil salinity and enhancing microbial community diversity in saline–alkali soils. These findings provide valuable insights for the future agricultural utilization of saline–alkali land. Full article

Soil microbial communities are particularly sensitive to selenium contamination, which has seriously affected the stability of soil ecological environment and function. In this study, we applied high-throughput 16S rRNA gene sequencing to examine the effects of low and high doses of sodium selenite and the selenite-degrading bacterium, Rhodococcus qingshengii PM1, on soil bacterial community composition, diversity, and assembly processes under controlled laboratory conditions. Our results indicated that sodium selenite and strain PM1 were key predictors of bacterial community structure in selenium-contaminated soils. Exposure to sodium selenite initially led to reductions in microbial diversity and a shift in dominant bacterial groups, particularly an increase in Actinobacteria and a decrease in Acidobacteria. Sodium selenite significantly reduced microbial diversity and simplified co-occurrence networks, whereas inoculation with strain PM1 partially reversed these effects by enhancing community complexity. Ecological modeling, including the normalized stochasticity ratio (NST) and Sloan’s neutral community model (NCM), suggested that stochastic processes predominated in the assembly of bacterial communities under selenium stress. Null model analysis further revealed that heterogeneous selection and drift were primary drivers of community turnover, with PM1 inoculation promoting species dispersal and buffering against the negative impacts of selenium. These findings shed light on microbial community assembly mechanisms under selenium contamination and highlight the potential of strain PM1 for the bioremediation of selenium-affected soils. Full article

The effects of balanced fertilization with nitrogen, phosphorus, and potassium (NPK) on foxtail millet productivity and the soil environment under the same conditions of total nutrients have received limited research attention. Therefore, in this study, three balanced fertilization patterns of 27-14-10 (T1), 27-17-7 (T2), and 30-10-11 (T3), and one no fertilization treatment (CK), a total of four treatments, were set up through a two-year field experiment to study the effects of balanced fertilization patterns on foxtail millet yield and soil environment. Mantel analysis was conducted to reveal the correlation between soil environmental factors and the community and their contribution to productivity. The results showed that: (1) all balanced fertilization treatments significantly increased foxtail millet yield, with the highest yield in the T1 treatment. (2) The contents of EC, available K, available P, and alkaline-hydrolyzable nitrogen in the soil of the two-year TI treatments were higher than those of the other treatments and increased by 7.20–9.36%, 24.87–52.35%, 55.83–56.38%, and 21.05–43.95%, respectively, compared with CK. (3) Soil urease activity in the T1 treatment increased significantly by 26.67% and 9.00% compared with the control over the two years. Sucrase activity increased by 36.27% and 23.88% in the T1 treatment compared to CK, and glutaminase activity increased by 33.33% and 19.23% in the T1 treatment compared to CK. (4) T1 treatment significantly increased the OUT number and diversity index of the soil bacterial community. (5) Mantel analysis and principal component analysis showed that available soil nutrients and soil enzymes were positively correlated, and soil enzymes and soil nutrients contributed more to foxtail millet productivity. In this study, the 27-14-10 balanced fertilization pattern was more effective, providing a theoretical basis for the research and development of special fertilizers for foxtail millet and offering technical guidance for realizing the light simplified cultivation of foxtail millet and sustainable development of cost–saving and increased efficiency. Full article

Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici has severely threatened sustainable greenhouse tomato production. However, the effects of nutrient enrichment due to excessive fertilization on Fusarium wilt remain unclear. This study aimed to investigate the relationships among soil nutrient enrichment, microbial community structure, and the occurrence of Fusarium wilt under greenhouse conditions. This study used chemical analysis and microbiological techniques to analyze rhizosphere soil samples from greenhouse tomato production areas with varying degrees of Fusarium wilt. The results showed that, as compared with the Health group, the rhizosphere soil of Disease group has a significant nutrient enrichment, which significantly influences bacterial diversity and structure. Particularly when soil NO₃⁻–N content exceeds 170.43 mg kg⁻¹, there was a significant reduction in the relative abundance of key biocontrol bacteria such as Bacillus and Lysinibacillus. This reduction indirectly contributes to an increase in Fusarium oxysporum abundance, subsequently elevating the likelihood of pathogen infection. Furthermore, the Disease group also exhibited a simplified co-occurrence network with a 22.37% reduction in competitive interactions between bacteria and fungi. These changes might collectively increase the risk of tomato Fusarium wilt infection. Meanwhile, the relative abundance of bacteria carrying antibiotic resistance genes significantly increased in the Disease group, which also reduced soil resistance. Together, the results presented here not only uncover the effect of long-term excessive fertilization on the occurrence of Fusarium wilt but also advance our understanding of the interactions among soil nutrient management and microbial communities in the tomato rhizosphere, which provides a scientific basis for formulating strategies to prevent soil-borne diseases in greenhouse tomatoes. Full article

The search for new biodegradable fertilizers to increase the productivity of agricultural plants is an urgent task. In this study, a complex microfertilizer was developed based on a chelating agent—glutamic-N,N-diacetic acid (GLDA). The evaluation encompassed assessments of biodegradability and effectiveness in fostering lettuce plant growth in hydroponic and conventional soil settings. The impact on endospheric bacteria, a sensitive indicator, was also examined. Results indicated a 59.8% degradation rate of the GLDA complex on the 28th day. The most notable positive effects were observed in above-ground plant biomass, with a 4.6-fold increase for hydroponics and 1.5 to 1.8-fold increases for root and foliar treatments in soil. In hydroponics, GLDA-treated plants showed 24 and 45 operational taxonomic units (OTUs) for leaves and 272 and 258 for roots (GLDA-treated and control plants). In soil, the OTU counts were 270 and 101, 221 and 111, and 198 and 116 in the leaves and roots of GLDA-treated and control plants (under root and foliar treatments), respectively. Non-metric multidimensional scaling (NMDS) and Indicator Species Analysis (ISA) demonstrated significant distinctions in endospheric communities between substrates (hydroponics and soil) in the presence of GLDA. Importantly, GLDA use simplified the composition of endospheric bacterial communities. Full article

The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included Gibberella, Alternaria, Filobasidium, Naganishia, Ascochyta, Apiotrichum, Comoclathris, and Aureobasidium, and the dominant bacterial genera mainly contained Sediminibacterium, Ralstonia, Pantoea, Bradyrhizobium, Brevundimonas, Mesorhizobium, Planococcus, and Planomicrobium. In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry. Full article

Microbial scale-up cultivation is the first step to bioremediating cadmium (Cd)-contaminated soils at the industrial scale. However, the changes in the microbial community as the bioreactor volume expands and their associations with soil Cd removal remain unclear. Herein, a six-stage scale-up cultivation process of mixotrophic acidophiles was conducted, scaling from 0.1 L to 10 m³, to remediate Cd-contaminated soils. The findings showed that bioreactor expansion led to a delay in sulfur and glucose oxidations, resulting in a reduced decline in solution pH and cell density. There were minimal differences observed in bacterial alpha-diversity and community structure as the bioreactor volume increased, except for the 10 m³ scale. However, bioreactor expansion decreased fungal alpha-diversity, changed the community structure, and simplified fungal community compositions. At the family level, Acidithiobacillaceae and Debaryomycetaceae dominated the bacterial and fungal communities throughout the scale-up process, respectively. Correlation analysis indicated that the indirect effect of mixotrophic acidophiles played a significant role in soil Cd removal. Bacterial community shifts, driven by changes in bioreactor volume, decreased the pH value through sulfur oxidation, thereby indirectly enhancing Cd removal efficiency. This study will contribute to the potential industrial application of mixotrophic acidophiles in bioremediating Cd-contaminated soils. Full article

The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the microbial community entailed an assessment of taxa abundance and diversity using Kraken version 2.1.2. The study delineated the prevalence of dominant bacterial phyla, including Proteobacteria, with varying abundance of Firmicutes, Bacteroidota, and Actinobacteria, and notable occurrence of Tenericutes. Furthermore, the presence of the fungal phylum Ascomycota was also detected. Among the identified barcodes, Barcode04 emerged as the most abundant and diverse, while Barcode06 exhibited greater evenness. Barcode03, 05, and 07 displayed moderate richness and diversity. Through an analysis of the relative abundance, a spectrum of viruses within Ae. aegypti populations was unveiled, with Negarnaviricota constituting the most prevalent phylum, followed by Nucleocytoviricota, Uroviricota, Artverviricota, Kitrinoviricota, Peploviricota, Phixviricota, and Cossaviricota. The presence of Negarnaviricota viruses raises pertinent public health concerns. The presence of other viral phyla underscores the intricate nature of virus–mosquito interactions. The analysis of viral diversity provides valuable insights into the range of viruses carried by Ae. aegypti. The community exhibits low biodiversity, with a few dominant species significantly influencing its composition. This has implications for healthcare and ecological management, potentially simplifying control measures but also posing risks if the dominant species are harmful. This study enriches our comprehension of the microbiome and virome associated with Ae. aegypti mosquitoes, emphasizing the importance of further research to fully comprehend their ecological significance and impact on public health. The findings shed light on the microbial ecology of Ae. aegypti, offering potential insights into mosquito biology, disease transmission, and strategies for vector control. Future studies should endeavor to establish specific associations with Ae. aegypti, elucidate the functional roles of the identified microbial and viral species, and investigate their ecological implications. Full article