Search Results (33)

Ecological restoration in the cold and high-altitude mining areas of the Qinghai–Tibet Plateau is faced with dual challenges of extreme environments and insufficient microbial adaptability. This study aimed to screen local microbial resources with both extreme environmental adaptability and plant-growth-promoting functions. Local fungi (DK; F18-3) and commercially available bacteria (B0) were used as materials to explore their regulatory mechanisms for plant growth, soil physicochemical factors, microbial communities, and metabolic profiles in the field. Compared to bacterial treatments, local fungi treatments exhibited stronger ecological restoration efficacy. In addition, the DK and F18-3 strains, respectively, increased shoot and root biomass by 23.43% and 195.58% and significantly enhanced soil nutrient content and enzyme activity. Microbiome analysis further implied that, compared with the CK, DK treatment could significantly improve the α-diversity of fungi in the rhizosphere soil (the Shannon index increased by 14.27%) and increased the amount of unique bacterial genera in the rhizosphere soil of plants, totaling fourteen genera. Meanwhile, this aggregated the most biomarkers and beneficial microorganisms and strengthened the interactions among beneficial microorganisms. After DK treatment, twenty of the positively accumulated differential metabolites (DMs) in the plant rhizosphere were highly positively associated with six plant traits such as shoot length and root length, as well as beneficial microorganisms (e.g., Apodus and Pseudogymnoascus), but two DMs were highly negatively related to plant pathogenic fungi (including Cistella and Alternaria). Specifically, DK mainly inhibited the growth of pathogenic fungi through regulating the accumulation of D-(+)-Malic acid and Gamma-Aminobutyric acid (Cistella and Alternaria decreased by 84.20% and 58.53%, respectively). In contrast, the F18-3 strain mainly exerted its antibacterial effect by enriching Acidovorax genus microorganisms. This study verified the core role of local fungi in the restoration of mining areas in the Qinghai–Tibet Plateau and provided a new direction for the development of microbial agents for ecological restoration in the Qinghai–Tibet Plateau. Full article

Ziziphus lotus (L.) Lam. (Rhamnaceae), a key shrub species native to North Africa, is commonly found in arid and semi-arid regions. Renowned for its resilience under harsh conditions, it forms vegetation clusters that influence the surrounding environment. These clusters create microhabitats that promote biodiversity, reduce soil erosion, and improve soil fertility. However, in agricultural fields, Z. lotus is often regarded as an undesirable species. This study investigated the bacterial diversity and community composition along spatial gradients around Z. lotus patches in barley-planted and non-planted fields. Using 16S rRNA gene sequencing, 84 soil samples were analyzed from distances of 0, 3, and 6 m from Z. lotus patches. MiSeq sequencing generated 143,424 reads, representing 505 bacterial ASVs across 22 phyla. Alpha-diversity was highest at intermediate distances (3 m), while beta-diversity analyses revealed significant differences in community composition across distances (p = 0.035). Pseudomonadota dominated close to the shrub (44% at 0 m) but decreased at greater distances, whereas Bacillota and Actinobacteriota displayed distinct spatial patterns. A core microbiome comprising 44 ASVs (8.7%) was shared across all distances, with the greatest number of unique ASVs identified at 3 m. Random forest analysis highlighted Skermanella and Rubrobacter as key discriminatory taxa. These findings emphasize the spatial structuring of bacterial communities around Z. lotus patches, demonstrating the shrub’s substantial influence on bacterial dynamics in arid ecosystems. Full article

Probiotics, as live microbial agents, play a pivotal role in modulating host microbiota balance, enhancing immunity, and improving gastrointestinal health. However, their application is hindered by critical challenges, such as inactivation during processing, storage, and gastrointestinal delivery, as well as low colonization efficiency. This article comprehensively reviews recent advances in probiotic delivery systems, focusing on innovative technologies, including hydrogels, nanocoatings, emulsions, and core–shell microgels. It provides an in-depth analysis of natural polyphenol-based nanocoatings and metal–phenolic network (MPN) single-cell encapsulation strategies for enhancing bacterial survival rates while highlighting the unique potential of microalgae-based bio-carriers in targeted delivery. Research demonstrates that well-designed edible delivery systems can effectively preserve probiotic viability and enable controlled intestinal release, offering novel strategies to reshape a healthy gut microbiome. While these systems show promise in maintaining probiotic activity and gut colonization, challenges remain in safety, scalable production, and clinical translation. Overcoming these barriers is crucial to fully harnessing probiotics for human health. Full article

Plants inhabiting environments with suboptimal growth conditions often have a more pronounced capacity to attract and sustain microbial communities that improve nutrient absorption and expand abiotic stress tolerance. Rhodiola rosea L. is a succulent plant of the Crassulaceae family adapted to survive in sandy or rocky soils or dry tundra. The aim of the present study was to investigate the diversity and plant growth-stimulating potential of R. rosea endophytic microbiota. Metataxonomic analysis of the bacterial diversity in the rhizome of R. rosea revealed 108 families. Among these, three families were found exclusively in the core microbiome of 1-year-old plants, while nine families were unique to the core microbiome of mature plants grown in the field for more than 4 years. Seventy-three endophytic bacteria isolates were obtained from the rhizome of R. rosea plants and were assigned into 14 distinct bacterial genera of Firmicutes (26%) or Proteobacteria (74%) phyla. Screening for functional genes related to the nitrogen cycle, phosphorus mineralisation or dissolution, and traits associated with nitrogen fixation (56% of isolates), siderophore production (40%), inorganic phosphorus solubilisation (30%), and production of indole-related compounds (51%) led to the classification of the isolates into 16 distinct clusters. Co-cultivation of 45 selected isolates with germinating Arabidopsis seedlings revealed 18 and 5 isolates that resulted in more than a 20% increase in root or shoot growth, respectively. The study results established the complexity of the succulent R. rosea endophytic microbiome and identified isolates for potential plant growth-stimulating applications. Full article

Background/Objectives: Faecal microbiota transplantation (FMT) is considered a safe and effective therapy for recurrent Clostridioides difficile infection. It is the only current clinical indication for this technique, although numerous clinical research studies and trials propose its potential usefulness for treating other pathologies. Donor selection is a very rigorous process, based on a personal lifestyle interview and the absence of known pathogens in faeces and serum, leading to only a few volunteers finally achieving the corresponding certification. However, despite the high amount of data generated from the ongoing research studies relating microbiota and health, there is not yet a consensus defining what is a “healthy” microbiota. To date, knowledge of the composition of the microbiota is not a requirement to be a faecal donor. The aim of this work was to evaluate whether the analysis of the composition of the microbiota by massive sequencing of 16S rDNA could be useful in the selection of the faecal donors. Methods: Samples from 10 certified donors from Mikrobiomik Healthcare Company were collected and sequenced using 16S rDNA in a MiSeq (Illumina) platform. Alpha (Chao1 and Shannon indices) and beta diversity (Bray–Curtis) were performed using the bioinformatic web server Microbiome Analyst. The differences in microbial composition at the genera and phyla levels among the donors were evaluated. Results: The microbial diversity metric by alpha diversity indexes showed that most donors exhibited a similar microbial diversity and richness, whereas beta diversity by 16S rDNA sequencing revealed significant inter-donor differences, with a more stable microbial composition over time in some donors. The phyla Bacillota and Bacteroidota were predominant in all donors, while the density of other phyla, such as Actinomycota and Pseudomonota, varied among individuals. Each donor exhibited a characteristic genera distribution pattern; however, it was possible to define a microbiome core consisting of the genera Agathobacter, Eubacterium, Bacteroides, Clostridia UCG-014 and Akkermansia. Conclusions: The results suggest that donor certification does not need to rely exclusively on their microbiota composition, as it is unique to each donor. While one donor showed greater microbial diversity and richness, clear criteria for microbial normality and health have yet to be established. Therefore, donor certification should focus more on clinical and lifestyle aspects. Full article

Grafting is a commonly employed technique for enhancing the yield and improving resistance to biotic and abiotic stress of cultivated plants. However, whether and how continuous cropping of grafted plants affects the composition, function, and stability of the soil fungal community remain poorly understood. In this study, we investigated the effects of planting years (including 0 years (Y0), 2 years (Y2), 10 years (Y10), and 18 years (Y18)) of grafted watermelon on the structure and functional composition of the soil fungal community under field conditions. Compared with the Y0 soil, the Y2, Y10, and Y18 soils exhibited a significant (p < 0.05) decrease in the richness, Shannon index, and evenness (56.8–65.7%, 22.4–46.3%, and 3.8–38.1%, respectively) in the alpha diversity of the fungal community, but a significant (p < 0.05) increase (0.4–1.3 times) in the fungal population. The structure, core and unique microbiomes, and functional composition of the soil fungal community differed significantly across different planting years. The Y2, Y10, and Y18 soils exhibited significant increases (p < 0.05) in relative abundances of Ascomycota and saprophytic fungi and the proportion of core OTUs, but significantly decreased abundances of Basidiomycota, Chytridiomycota, Rozellomycota, pathogenic and symbiotic fungi, and the proportion of unique OTUs when compared with the Y0 soil. The types of potential plant pathogens and their relative abundance were also significantly increased alongside the planting years (among Y2, Y10, and Y18 soils). Furthermore, the results indicated that the continuous cropping of grafted watermelon altered the co-occurrence networks, leading to a reduction in the complexity and stability of the fungal community networks. Overall, our findings suggest that continuous cropping of grafted watermelon may adversely affect the structure and functioning of soil microbial community, eventually decreasing the effectiveness of grafting technology disease control. Full article

Living in arid environments presents unique challenges to organisms, including limited food and water, extreme temperatures, and UV exposure. Reptiles, such as the South American leaf-toed gecko (Phyllodactylus gerrhopygus), have evolved remarkable adaptations to thrive in such harsh conditions. The gut microbiome plays a critical role in host adaptation and health, yet its composition remains poorly characterized in desert reptiles. This study aimed to characterize the composition and abundance of the gut microbiome in P. gerrhopygus inhabiting the hyperarid Atacama Desert, taking into account potential sex differences. Fecal samples from adult female and male geckos were analyzed by 16S rRNA gene amplicon sequencing. No significant differences in bacterial alpha diversity were observed between the sexes. However, the phylum Bacteroidota was more abundant in females, while males had a higher Firmicutes/Bacteroidota ratio. The core microbiome was dominated by the phyla Bacteroidota, Firmicutes, and Proteobacteria in both sexes. Analysis of bacterial composition revealed 481 amplicon sequence variants (ASVs) shared by female and male geckos. In addition, 108 unique ASVs were exclusive to females, while 244 ASVs were unique to males. Although the overall bacterial composition did not differ significantly between the sexes, certain taxa exhibited higher relative abundances in each sex group. This study provides insight into the taxonomic structure of the gut microbiome in a desert-adapted reptile and highlights potential sex-specific differences. Understanding these microbial communities is critical for elucidating the mechanisms underlying host resilience in Earth’s most arid environments, and for informing conservation efforts in the face of ongoing climate change. Full article

Knowledge regarding how abiotic and biotic environmental factors operate in soil microbiome reassembly remains rudimentary in coastal saline–alkaline soils amended by different organic ameliorants. In this study, field trials were conducted to investigate the impacts and underlying mechanisms of sewage sludge (S) and sludge-based vermicompost (V) at the application amounts of 0, 50, and 100 t ha⁻¹ on soil physicochemical characteristics, carbon source utilization pattern, and bacteriome in coastal saline–alkaline soils. Results revealed that impacts of the organic ameliorants on soil’s physicochemical and microbial attributes were highly dependent upon the carbon types and amounts applied. Unsurprisingly, applying sewage sludge and vermicompost significantly alleviated environmental constraints, such as saline–alkaline stress and nutrient deficiency, with lower pH, salinity, and higher soil organic carbon content observed in organics-amended soils. Specifically, higher microbial substrate metabolic activity, but lower diversity was observed in saline–alkaline soils amended by organic ameliorants. In addition, reassembled bacteriomes harboring distinguishable core and unique community profiles were observed in reclaimed soils as compared to unamended saline–alkaline soil. Procrustes analysis showed that the soil microbial utilization pattern of carbon sources was significantly related to the alterations in their physicochemical property and bacterial core microbiome. Additionally, Redundancy Analysis (RDA) revealed that soil core bacteriome reassembly was dominated by the integrated impacts of soil salinity, successively followed by carbohydrates, amino acids, polymers, pH, soil organic carbon (SOC), and available nitrogen (AN). Overall, this study provides a comprehensive understanding of soil abiotic and biotic determinants in bacteriome assembly in coastal saline–alkaline soil remediation mediated by organic ameliorants. Full article

Actinobacteria are important sources of antibiotics and have been found repeatedly in coral core microbiomes, suggesting this bacterial group plays important functional roles tied to coral survival. However, to unravel coral–actinobacteria ecological interactions and discover new antibiotics, the complex challenges that arise when isolating symbiotic actinobacteria must be overcome. Moreover, by isolating unknown actinobacteria from corals, novel biotechnological applications may be discovered. In this study, we compared actinobacteria recovery from coral samples between two widely known methods for isolating actinobacteria: dry stamping and heat shock. We found that dry stamping was at least three times better than heat shock. The assembly of isolated strains by dry stamping was unique for each species and consistent across same-species samples, highlighting that dry stamping can be reliably used to characterize coral actinobacteria communities. By analyzing the genomes of the closest related type strains, we were able to identify several functions commonly found among symbiotic organisms, such as transport and quorum sensing. This study provides a detailed methodology for isolating coral actinobacteria for ecological and biotechnological purposes. Full article

Understanding how the human virome, and which of its constituents, contributes to health or disease states is reliant on obtaining comprehensive virome profiles. By combining DNA viromes from isolated virus-like particles (VLPs) and whole metagenomes from the same faecal sample of a small cohort of healthy individuals and patients with severe myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), we have obtained a more inclusive profile of the human intestinal DNA virome. Key features are the identification of a core virome comprising tailed phages of the class Caudoviricetes, and a greater diversity of DNA viruses including extracellular phages and integrated prophages. Using an in silico approach, we predicted interactions between members of the Anaerotruncus genus and unique viruses present in ME/CFS microbiomes. This study therefore provides a framework and rationale for studies of larger cohorts of patients to further investigate disease-associated interactions between the intestinal virome and the bacteriome. Full article

Lentil (Lens culinaris Medik.) is an essential legume crop providing healthy and nutritious food for people in low- to middle-income countries, worldwide. Lentil roots support symbiotic interactions with soil rhizobia species fostering nitrogen fixation; however, assemblage and diversity of the complete microbial rhizosphere community and the effect of seed genotype and origin remain largely unexplored. In this study we examined, via metagenomic analysis, the effects of seed origin on the rhizosphere’s communities in samples of the famous Greek lentil landrace, Eglouvis, derived from different local farmers and farming systems (including a Gene Bank sample), in comparison to a commercial variety. The landrace exhibited higher rhizosphere microbiome diversity compared to the commercial variety for all indexes. A core microbiome comprised of 158 taxa was present in all samples, while a greater number of unique bacterial taxa was recorded in the landrace samples compared to the commercial cultivar. Notably, landrace samples originated from organic farming had more than double the number of unique taxa compared to conventional counterparts. The study revealed a higher diversity of N₂ fixers and archaea, Crenarchaeota and Thaumarchaeota, in landrace samples and particularly in those derived from organic farming, underpinning the distinct recruiting efficiency of beneficial soil microbes by the landrace. Full article

Endophytes are essential in plant succession and evolution, and essential for stress resistance. Coralloid root is a unique root structure found in cycads that has played a role in resisting adverse environments, yet the core taxa and microbial community of different Cycas species have not been thoroughly investigated. Using amplicon sequencing, we successfully elucidated the microbiomes present in coralloid roots of 10 Cycas species, representing all four sections of Cycas in China. We found that the endophytic bacteria in coralloid roots, i.e., Cyanobacteria, were mainly composed of Desmonostoc_PCC-7422, Nostoc_PCC-73102 and unclassified_f__Nostocaceae. Additionally, the Ascomycota fungi of Exophiala, Paraboeremia, Leptobacillium, Fusarium, Alternaria, and Diaporthe were identified as the core fungi taxa. The Ascomycota fungi of Nectriaceae, Herpotrichiellaceae, Cordycipitaceae, Helotiaceae, Diaporthaceae, Didymellaceae, Clavicipitaceae and Pleosporaceae were identified as the core family taxa in coralloid roots of four sections. High abundance but low diversity of bacterial community was detected in the coralloid roots, but no significant difference among species. The fungal community exhibited much higher complexity compared to bacteria, and diversity was noted among different species or sections. These core taxa, which were a subset of the microbiome that frequently occurred in all, or most, individuals of Cycas species, represent targets for the development of Cycas conservation. Full article

Reductive soil disinfestation (RSD) and chemical soil fumigation (CSF) comprise the most popular pre-planting soil management strategies. Their efficiency in suppressing several plant diseases in agricultural production systems has been compared. However, the disease-control effect of these methods on Fusarium wilt disease in Dioscorea batatas Decne (D. batatas) remains unclear. Importantly, dissimilarities in the impact of their bio-predictors on plant health have not been well characterized. Herein, four treatments, including no treatment (CK), RSD with gran chaff (GC-RSD) and molasses (MO-RSD), and CSF with dazomet (DA-CSF), were performed in a pot experiment using D. batatas-diseased soil. Compared with the CK treatment, the Fusarium oxysporum population significantly decreased by 88.89–97.78% following the DA-CSF, GC-RSD, and MO-RSD treatments. The bacterial community and functional composition of the soil were considerably altered by these treatments. However, the incidence of Fusarium wilt disease in D. batatas was significantly decreased in the two RSD-treated soils, rather than in DA-CSF-treated soils. Bacterial α-diversity and population as well as some key nitrogen-related functional gene expressions as bio-predictors were significantly lower in DA-CSF-treated soil than in RSD-treated soil. In particular, the core (e.g., Azotobacter, Phenylobacterium, Clostridium, Bradyrhizobium, Microvirga, and Caulobacter) and unique (e.g., Pseudomonas, Brevundimonas, Flavobacterium, Ochrobactrum, and Sphingobacterium) functional microbiomes in RSD-treated soil exerted a positive impact on soil functional composition of the soil and plant growth. Taken together, our results indicate that RSD outperformed CSF in promoting plant health by regulating the bacterial community and functional composition. Full article

It is known that alcoholic beverages alter the human gut microbiome. This study focused on the potential impact of non-ethanolic ingredients in whisky on the gut bacteriome. A pilot study was carried out on 15 whisky drinkers, 5 rice beer drinkers, and 9 non-drinkers to determine the effect of alcoholic beverages on the host microbiome and metabolome. Additionally, a mouse model was used to assess the differential impact of three whisky brands (each with an equal ethanol concentration). The results indicate that the non-ethanolic components have an impact on the gut microbiome, as well as on the metabolites in blood and feces. The amount of Prevotella copri, a typical core Indian gut bacterium, decreased in both the human and mouse groups of whisky type 1, but an increase in abundance of Helicobacteriaceae (p = 0.01) was noticed in both groups. Additionally, the alcohol-treated cohorts had lower levels of short-chain fatty acids (SCFAs), specifically butyric acid, and higher amounts of lipids and stress marker IL1-ß than the untreated groups (p = 0.04–0.01). Furthermore, two compounds, ethanal/acetaldehyde (found in all the whisky samples) and arabitol (unique to whisky type 1), were tested in the mice. Similar to the human subjects, the whisky type 1 treated mouse cohort and the arabitol-treated group showed decreased levels of Prevotella copri (p = 0.01) in their gut. The results showed that non-ethanolic compounds have a significant impact on host gut bacterial diversity and metabolite composition, which has a further vital impact on host health. Our work further emphasizes the need to study the impact of non-ethanolic ingredients of alcoholic beverages on host health. Full article

The ecology of infectious diseases involves wildlife, yet the wildlife interface is often neglected and understudied. Pathogens related to infectious diseases are often maintained within wildlife populations and can spread to livestock and humans. In this study, we explored the fecal microbiome of coyotes and wild hogs in the Texas panhandle using polymerase chain reactions and 16S sequencing methods. The fecal microbiota of coyotes was dominated by members of the phyla Bacteroidetes, Firmicutes, and Proteobacteria. At the genus taxonomic level, Odoribacter, Allobaculum, Coprobacillus, and Alloprevotella were the dominant genera of the core fecal microbiota of coyotes. While for wild hogs, the fecal microbiota was dominated by bacterial members of the phyla Bacteroidetes, Spirochaetes, Firmicutes, and Proteobacteria. Five genera, Treponema, Prevotella, Alloprevotella, Vampirovibrio, and Sphaerochaeta, constitute the most abundant genera of the core microbiota of wild hogs in this study. Functional profile of the microbiota of coyotes and wild hogs identified 13 and 17 human-related diseases that were statistically associated with the fecal microbiota, respectively (p < 0.05). Our study is a unique investigation of the microbiota using free-living wildlife in the Texas Panhandle and contributes to awareness of the role played by gastrointestinal microbiota of wild canids and hogs in infectious disease reservoir and transmission risk. This report will contribute to the lacking information on coyote and wild hog microbial communities by providing insights into their composition and ecology which may likely be different from those of captive species or domesticated animals. This study will contribute to baseline knowledge for future studies on wildlife gut microbiomes. Full article