Microbial Diversity Research Articles

Background: The relationship between aging, gut microbiota, and cardiac repair after myocardial infarction (MI) remains unclear. Understanding this interaction may provide novel strategies for improving cardiovascular outcomes in the elderly. Methods: Aged mice were treated with antibiotics followed by fecal microbiota transplantation (FMT) from young or aged donors prior to MI. Cardiac function, gut integrity, immune signaling, and metabolism were evaluated. Gut microbiota and plasma metabolites were also profiled in ST-elevation myocardial infarction (STEMI) patients across age groups. Results: Young FMT improved post-MI cardiac function and reduced infarct size in aged mice. It preserved intestinal barrier integrity, reduced IL-17A–positive immune cells, and attenuated age-related intestinal shortening. Aging was associated with decreased microbial diversity, loss of beneficial taxa such as Akkermansia , and enrichment of inflammatory pathways. Cardiac metabolomics revealed reduced oxidative metabolism and increased lipid reliance in aged mice. In STEMI patients, aging correlated with lower microbiota diversity, altered taxonomic profiles, and shifts in lipid and amino acid metabolism. Conclusions: This study highlights the role of gut microbiota in cardiovascular health and aging. Microbiota transplantation improved cardiac recovery, suggesting its therapeutic potential and offering new insights into the gut–heart axis for future treatments in age-related cardiovascular disease.

Soil microbial genomic functional potential refers to the community's collective genetic capacity to mediate nutrient cycling processes involving carbon (C), nitrogen (N), and phosphorus (P). While the drivers of microbial community composition have been extensively studied, particularly in forest ecosystems, the effects of tree species identity, mycorrhizal type, and their mixture along tree diversity gradients on microbial genomic potential remain poorly understood. We predicted microbial genomic functional potential for carbon (C), nitrogen (N), and phosphorus (P) cycling genes, along with their ratios (C:N, C:P, N:P), using fungal ITS2 and bacterial 16S rRNA metabarcoding data from the rooting zone soil samples of eight tree species growing in the MyDiv experiment. We assessed the effects of a tree species identity, plot mycorrhizal type (mono: AM or ECM and mixed: AE = AM + EcM), and tree diversity levels (one, two, four) on the microbial C, N, and P cycling genomic potential and their ratios. We also tested the relationship of microbial diversity, microbial beta-diversity, and soil C:N:P stoichiometry with microbial C, N, and P cycling genomic potential and their ratios. Two-way ANOVAs showed that mycorrhizal type mixture consistently influenced the fungal and bacterial C, N, and P cycling genomic potential and their ratios, while tree diversity significantly affected fungal C and P genomic potential, as well as bacterial C and C:P ratio genomic potentials. Tree species identity impacted fungal genomic potential, particularly in AM and AE types, whereas bacterial functional potentials were significantly linked to tree diversity across AM, AE, and EcM plots. Fungal richness decreased significantly with C and P genomic potential in EcM plots but increased with N genomic potential in AM plots, showing contrasting effects on genomic potential ratios, while bacterial richness showed no significant relationship. Fungal and bacterial beta-diversity were both positively associated with C and P cycling genomic potentials in EcM and AE plots. The C:N and C:P genomic potential ratios increased, and N:P ratios decreased with increasing fungal beta-diversity in EcM and AE plots. Similar patterns were observed for bacterial genomic potential across all AM, EcM, and AE plots. Overall, soil C:N:P stoichiometry showed weak and non-significant correlations with microbial C, N, and P cycling genomic potential. Our findings highlight that plot mycorrhizal type mixture, tree species identity, and tree diversity shape the microbial C, N, and P cycling genomic functional potential. These results also underscore that community turnover, taxonomic replacement, and compositional restructuring of taxa, rather than merely overall richness, are the primary drivers of functional diversification in carbon, nitrogen, and phosphorus cycling among microbial communities.IMPORTANCEOur study suggests that forest management strategies fostering microbial community diversity through mixing tree species with different mycorrhiza types and increasing tree diversity could enhance soil microbial functions, increase nutrient cycling, and improve forest ecosystem resilience and productivity.

Abstract Microplastics and various other contaminants are frequently present in soil. Here we investigated the long-term integrated responses of changes in the microbial community, metabolomics, heavy metal availability, and nutritional properties of the cadmium-cuprum-zinc-contaminated coastal saline soil to the three different microplastics. Various categories of microplastics had notable impacts on the available potassium, organic matter, availability of cadmium and cuprum, as well as the enzymatic activity in soil. Microplastics contamination caused diverse changes in microbial diversity and the composition of bacterial and fungal communities, resulting in the enrichment of Mortierella and a decrease of Bacillus abundance. The metabolites in soil primarily affected by microplastics contamination were the pathways involved organic acids and their derivatives, organoheterocyclic compounds, as well as lipids and lipid-like substances. Therefore, the addition of microplastics to soil may influence soil fertility, metal mobility, and alter the structure and metabolic processes of the microbial community in soil.

Soil microbial biomass and microbial entropy are used as important indicators of soil quality. However, the effects of forest-stand types remain poorly understood. This study focused on three stands of Cryptomeria japonica var. sinensis (CJ), Liquidambar formosana (LF), and their mixed forests (CL) in Guizhou Province, China. Soil samples were collected from three depths to investigate variations in soil microbial biomass C, N, P (MBC, MBN, MBP), as well as microbial entropy C, N, P (qMBC, qMBN, qMBP) among different forest stands. Additionally, the influence of soil organic C (SOC), total N (TN), total P (TP), and their stoichiometry, along with soil microbial C:N:P stoichiometry and soil-microbial stoichiometric imbalances on soil microbial biomass and microbial entropy are analyzed. The variance analysis revealed, compared to pure stands, the mixed forest exhibited significantly higher MBC (38.84%), MBC stocks (46.72%), MBC/MBN (52.23%), MBC/MBP (52.23%), and qMBC (23.49%; p < 0.05). Pure stand LF showed approximately 30% higher soil microbial stoichiometric imbalances (C/N imb , C/P imb , and N/P imb ) than the other two stand types ( p < 0.05). While the pure CJ stand exhibited significantly higher qMBN and qMBP (19.62% and 17.26%, respectively; p < 0.05). MBC, MBN, MBP, and their storage decreased significantly with increasing soil depth ( p < 0.05), no significant effect on microbial stoichiometric ratios or microbial entropy. Correlation and redundancy analyses demonstrated that MBC, MBN, and MBP were highly significantly positively correlated with SOC, TN, and TP contents ( p < 0.01), whereas qMBC and qMBN exhibited highly significant negative correlations with SOC, TP, SOC/TP, TN/TP, C/P imb , and N/P imb ( p < 0.01). Soil TP and MBC/MBP were identified as the primary factors influencing soil microbial biomass variation, with explanatory rates of 42.8% and 14.8%, respectively. Furthermore, C/N imb and C/P imb emerged as key determinants affecting microbial entropy dynamics, accounting for 31.5% and 14.2% of the observed variation, respectively. This study provided valuable data and insights for developing mixed forest management strategies in karst areas.

Introduction This study elucidated how different plantation types in limestone mountains shape the community structure and co-occurrence networks of soil fungal habitatspecialization groups, offering a habitat-adaptation perspective on the assembly mechanisms of soil microbial diversity during ecological restoration. Methods In this study, we grouped soil fungi from plantations of coniferous forests (CF), mixed forests (MF) and broad-leaved forests (BF) into habitat-generalists, specialists and opportunists based on niche breadth, and examined how forest type shapes their diversity, community structure and co-occurrence networks along a habitat-specialization gradient. Results We found that: (1) The number and abundance of habitat-specialists significantly exceeded those of generalists. Habitat-generalists exhibited the highest abundance and ecological niche width in BF, whereas habitat-specialists were most abundant in CF. (2) The diversity index was the highest in BF across all habitat specialization groups. Differences in community structure among forest types increased with habitat specialization, and the composition of dominant tree species significantly influenced the community structure of each group. Soil properties primarily affected the community structure of habitat generalists and opportunists between BF and other forest types. (3) The network structure of habitat specialists exhibited high modularity, while habitat generalists formed independent subnetworks with more fragile structures. CF and BF exhibited strong intra-module connections and high modularity, whereas MF displayed high intermodule connectivity, which reduced their modularity. Both within-module (Zi) and between-module connectivity (Pi) of increased with habitat specialization and the proportion of broadleaved tree species. Discussion We concluded that broad-leaved plantations, by increasing soil environmental heterogeneity, promoted the diversity of habitat-specialists and enhancing their network hub roles, representing the optimal strategy for optimizing below-ground biodiversity and stability in limestone mountain forest restoration.

Primary sclerosing cholangitis (PSC) is a chronic, immune-mediated cholestatic liver disease characterized by progressive bile duct inflammation and fibrosis. Its strong association with inflammatory bowel disease (IBD) highlights the possible role of the gut–liver axis in disease pathogenesis. Here, we review the mechanisms that may contribute to the disruption of the gut–liver axis, leading to liver injury and the development of PSC. In particular, disruption of the intestinal barrier allows microbial products to enter the portal circulation, stimulating hepatic immune cells and triggering biliary inflammation. Concurrently, gut-primed lymphocytes expressing mucosal homing receptors migrate aberrantly to the liver, where they may contribute to biliary epithelial cell injury. Dysbiosis, characterized by reduced microbial diversity and the expansion of bile-tolerant and pro-inflammatory taxa, amplifies this immune activation and disturbs gut–liver homeostasis. Moreover, bile acids act as signaling molecules, regulating metabolism and immune responses through receptors such as FXR and TGR5. Dysregulation of these pathways may promote cholestasis, inflammation, and fibrosis. By understanding these interactions, we may identify novel therapeutic targets for PSC.

Metabolic dysfunction-associated steatohepatitis (MASH) is an advanced stage of fatty liver disease with no approved pharmacotherapies. The Quzhi Formula (QZF), a traditional Chinese medicine utilized clinically for nearly two decades, has shown promising efficacy against MASH; however, its mechanisms of action remain largely unexplored. To elucidate these mechanisms, we conducted a multi-omics investigation integrating 16S rRNA sequencing, untargeted metabolomics, and transcriptomics in a MASH mouse model, with findings validated by histology. QZF treatment significantly alleviated hepatic steatosis, restored gut microbial diversity, and suppressed the proliferation of Enterococcus , a genus implicated in MASH pathogenesis. Transcriptomic and metabolomic analyses demonstrated that QZF’s therapeutic effects were mediated through the regulation of lipid metabolic pathways and the activation of autophagy. Furthermore, we identified fraxin as a pivotal bioactive metabolite contributing to QZF-induced autophagy. Our study demonstrates that QZF ameliorates MASH in a concerted manner by remodeling the gut microbiota, reprogramming hepatic metabolism, and promoting autophagy via fraxin. These results provide a comprehensive mechanistic foundation for QZF as a multi-targeted therapeutic candidate for MASH.

To investigate the effect of adding microbial agents in the fermentation stage on the quality of tobacco leaves prepared by imitating black tea method. Using Yunyan 87 middle leaves as materials, two microbial agents of Schwanniomyces occidentalis and Bacillus subtilis were sprayed onto the leaves before fermentation, and the effects of different microbial treatments on the main chemical composition, sensory quality, microbial diversity of tobacco leaves were analyzed. The starch content in tobacco leaves treated with S. occidentalis and B. subtilis decreased by 25.00 and 47.64%, and the total pigment content decreased by 46.15 and 30.77%, respectively. Tobacco leaves treated with two microbial agents can increase the characteristic aroma of burnt sweet and sour sweet respectively. The treatment of the two agents can improve the community richness and species diversity of tobacco leaves, and effectively improve the abundance of dominant bacteria such as Firmicutes and Candida. Both exogenous microorganisms can effectively reduce the starch and pigment contents in tobacco leaves, improve the sensory quality of tobacco leaves, improve the diversity of microbial community, and then improve the quality of tobacco leaves prepared by imitating black tea method. Bangladesh J. Bot. 54(3): 783-790, 2025 (September) Special

High-throughput sequencing technology was used to systematically analyze the composition, diversity, and dynamic changes of soil microbial communities during the wheat growing season in Lintong, Shaanxi Province. The abundance of bacterial communities significantly increases after the complete planting cycle of wheat, while the fungal community structure was relatively stable. At the phylum level, Proteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria constitute the dominant bacterial communities. The fungal community was Ascomycota and Zygomycota. The growth process of wheat significantly changes the structural composition of bacterial communities, enhances enzyme activity and biological regulatory functions of bacterial communities, while inhibiting cellular processes and environmental information processing functions. This study revealed the succession pattern of soil microbial communities during the wheat growing season, identified key microbial groups that maintain soil ecosystem functions, and provided an important theoretical basis and practical guidance for the sustainable management of the surface substrate layer in the study area. Bangladesh J. Bot. 54(3): 741-748, 2025 (September) Special

Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD) that can lead to intestinal complications and systemic risks, significantly increasing the likelihood of colorectal cancer in individuals with long-term illness. Fucoidan has shown potential in alleviating UC; however, the structure–activity relationship remains challenging. The present study aims to compare fucoidan (CF) and its degraded derivatives (DF) in the prevention and treatment of UC. Structural analysis demonstrated that CF and DF possess similar monosaccharide compositions and sulfation content; however, they differ significantly in molecular weight, with CF measuring 582 kDa and DF 2.3 kDa. Additionally, DF display a lower degree of branching compared to CF. Results from the mouse model demonstrated that both CF and DF can effectively alleviate clinical symptoms of UC; however, the underlying mechanisms of action are likely to differ. Both CF and DF produced comparable improvements in the disease activity index. CF demonstrated superior efficacy in alleviating weight loss and maintaining colon length, whereas DF showed greater benefits in protecting the colonic mucosa and reducing inflammatory infiltration. The gut microbiota analysis indicated that DF was more effective in restoring microbial diversity in UC mice. Both CF and DF were capable of modulating microbial imbalances at the phylum and genus levels, although the specific taxa exhibited differences.

Alcoholic liver disease (ALD) remains a major global health burden, with over 283million individuals affected by alcohol use disorder (AUD). Early-stage ALD is characterized by gut microbiota dysbiosis, intestinal barrier dysfunction, and endotoxemia. Traditional therapies focusing solely hepatoprotection or lipid reduction often show limited efficacy due to their inability to restore the gut-liver axis balance. This study aimed to evaluate the adjuvant efficacy of a multi-strain probiotic formulation (including Weizmannia coagulans BC99, Lacticaseibacillus rhamnosus LRa05, Bifidobacterium animalis subsp. lactis BLa80, and Weizmannia coagulans BC179) combined with polyene phosphatidylcholine (Essentale®) in improving liver function and metabolic profiles in ALD patients.A randomized, single-blind, placebo-controlled clinical trial was conducted in 42 ALD patients. Participants received either Essentale® plus probiotics or Essentale® plus placebo for 30 days. Liver function tests, serum lipids, fecal microbiota (16S rRNA sequencing), and fecal metabolites (GC-MS) were assessed at baseline, day 15, and day 30.Compared to placebo, the probiotic group showed significant reductions in ALT, AST, GGT, and TG, along with increased HDL-C levels. Probiotics promoted the enrichment of Bifidobacterium, Faecalibacterium, and Akkermansia, and improved microbial diversity. Metabolomic profiling revealed upregulation of anti-inflammatory and antioxidant metabolites (e.g., EGCG, S-methylglutathione) and downregulation of pro-inflammatory lipotoxic intermediates. Spearman analysis confirmed correlations between key bacterial genera and liver/metabolic biomarkers.Multi-strain probiotics effectively modulate the gut-liver axis by reshaping gut microbiota and metabolic networks, thereby enhancing the therapeutic efficacy of conventional hepatoprotective drugs in ALD. These findings support their clinical potential as a safe and complementary strategy for managing ALD.

This study evaluated the effects of combining antibiotics with probiotics on the health and the gastrointestinal microbial communities of pigs in pre-fattening stage. Forty-two piglets in pre-fattening stage were divided into two groups: one received commercial feed with antibiotics and probiotics (Diet D1), and the other received commercial feed with only probiotics (Diet D2). Fecal microbiota and 23 blood health parameters were analyzed weekly. DNA sequencing and bioinformatics were used to study microbial community composition. An increased Firmicutes/Bacteroidetes ratio was observed. The D2 group exhibited lower microbial diversity, indicating an effective modulation of the microbiota caused by probiotics, regardless of whether they were combined with antibiotics or not. Potential pathogens were only found in D1, suggesting that antibiotics might introduce antibiotic-resistant pathogens and reduce probiotics' effects. The study shows that diets including probiotics, whether mixed with antibiotics or not, can effectively modulate pig microbiota without health compromises, promoting safer and sustainable farming practices by potentially replacing antibiotics with probiotics.

Vertical distributions of microplastics in long-term mulched soils and their potential impacts on soil properties and microbial diversity.

ABSTRACT The microbiome inhabiting the surface of leaves is essential for supporting forest health and productivity. Yet, the relevance of host selection and neighbourhood conditions in supporting phyllosphere microbial diversity remains poorly understood. Here, we used a large‐scale forest biodiversity experiment in subtropical China to elucidate the mechanisms driving phyllosphere microbial diversity. Our results showed that bacterial diversity depends more on plant traits associated with resource‐acquisitive strategy, while fungal diversity was more closely related to the trade‐off between plant productivity and defence. Additionally, bacterial diversity was highly structured by neighbourhood tree competition, whereas fungal diversity was mainly shaped by host plant functional traits. Furthermore, the relationship between microbial diversity and host traits was enhanced as tree species diversity increased. Together, our work provides novel evidence that tree competition plays crucial roles in promoting microbial diversity in the phyllosphere and highlights the importance of plant–microbe interaction in supporting ecosystem sustainability.

Long-term impacts of straw and biochar applications on microbial diversity and soil functions in paddy soils.

The role of the rhizosphere microbiome in naturally suppressing soilborne diseases remains a critical unknown in sustainable agriculture. We investigated this by challenging three genotypes of tomato plants grown in pre-sterilized and natural soils with three major soil-borne pathogens: Ralstonia solanacearum, Fusarium oxysporum f. sp. lycopersici, and Meloidogyne incognita. The results showed that all tomato genotypes grown in pre-sterilized soils exhibited significantly higher disease severity with all pathogens. This protective effect was linked to higher microbial diversity and the abundance of beneficial taxa like Sphingomonas and Mortierella in natural soil as a significant reduction was recorded in microbial diversity and these microbial taxa in pre-sterilized soil. Pre-sterilization shifted community assembly from deterministic processes to stochastic processes, reducing functional stability. Functional predictions further demonstrated an enrichment of growth-promoting and disease-suppressive traits in natural soils, while sterilized soils favored pathogen-associated functions. Co-occurrence network analysis confirmed that the natural microbiome formed a more complex and robust microbial network, likely increasing its resistance to pathogen invasion. Notably, the reintroduction of soil microbiota from healthy plants partially restored tomato resistance to the three pathogens. These findings highlight the key role of stable rhizosphere microbial communities in suppressing soil-borne diseases and emphasize the importance of conserving microbial diversity and functional stability for plant health and sustainable agriculture.

A deep metagenomic atlas of Qinghai-Xizang Plateau lakes reveals their microbial diversity and salinity adaptation mechanisms.

Advancing Myopia Management: The Therapeutic Potential of Microbiota-Targeted Interventions.

Experimental study of hydrochemical and microbial community characteristics during CO2-water-mineral interactions.

Dissecting the microbial, physicochemical, and flavor dynamics of core and peel layers in Houhuo Daqu: Insights into quality regulation.