Search Results (222)

Background: The human gut microbiome is highly complex, and its composition is strongly influenced by dietary patterns. Alterations in microbiome structure have been associated with a range of diseases, including type 2 diabetes mellitus. However, the underlying mechanisms for this remain poorly understood. In this study, a novel in vitro approach was utilized to investigate the interplay between gut bacteria, dietary metabolites, and metabolic dysfunction. Methods: Two representative gut bacterial species—Bacteroides thetaiotaomicron and Lactobacillus fermentum—were isolated from human faecal samples and subjected to controlled dietary manipulation to mimic eubiotic and dysbiotic conditions. Metabolites produced under these conditions were extracted, characterized, and quantified. To assess the functional impact of these metabolites, we utilized the INS-1 832/3 insulinoma cell line, evaluating insulin sensitivity through glucose-stimulated insulin secretion and ERK1/2 activation. Results: Our findings demonstrate that metabolites derived from high-carbohydrate/high-fat diets exacerbate metabolic dysfunction, whereas those generated under high-fibre conditions significantly enhance insulin secretion and glucose-dependent ERK1/2 activation in co-culture compared to monocultures. Conclusions: This work systematically disentangles the complex interactions between gut microbiota, diet, and disease, providing mechanistic insights into how microbial metabolites contribute to the onset of metabolic disorders. Full article

A rapid decline of coral reefs is taking place around the world, with climate warming being the biggest driver behind this deterioration. Efforts to increase coral climate resilience via bioengineering methods have thus become urgent, and there is hope that such interventions can help corals and coral reefs survive until a time when no further climate warming occurs and perhaps a future of climate cooling is imaginable. The manipulation of coral-associated bacterial communities is among the less advanced interventions currently being explored. Nevertheless, early findings provide confidence that some level of thermal enhancement can be achieved via the inoculation of corals with beneficial bacteria. The small number of studies available, however, is limited in terms of the traits used to select candidate bacteria and their ability to ascribe host enhancement to specific bacterial taxa and functions. Further, findings to date are unable to decipher whether candidate bacteria integrate stably within the coral microbiome. These shortcomings prevent assessment of the efficacy of bacterial manipulation to enhance the long-term thermal resilience of corals on the reef. Here we summarise the state-of-play of the field and provide recommendations to fast-track this approach via fine-tuning experimental designs and methods. Full article

Ruminant livestock production faces increasing pressure to reduce environmental impacts while maintaining productivity and food security. This comprehensive review examines current strategies and emerging technologies for enhancing environmental sustainability in ruminant systems. The review synthesizes recent advances across four interconnected domains: genetic and genomic approaches for breeding environmentally efficient animals, rumen microbiome manipulation, nutritional strategies for emission reduction, and precision management practices. Specifically, genetic and genomic strategies demonstrate significant potential for long-term sustainability improvements through selective breeding for feed efficiency, methane reduction, and enhanced longevity. Understanding host–microbe interactions and developing targeted interventions have also shown promising effects on optimizing fermentation efficiency and reducing methane production. Key nutritional interventions include dietary optimization strategies that improve feed efficiency, feed additives, and precision feeding systems that minimize nutrient waste. Furthermore, management approaches encompass precision livestock farming technologies including sensor-based monitoring systems, automated feeding platforms, and real-time emission measurement tools that enable data-driven decision making. Integration of these approaches through system-based frameworks offers the greatest potential for achieving substantial environmental improvements while maintaining economic viability. In addition, this review identifies key research gaps including the need for standardized measurement protocols, long-term sustainability assessments, and economic evaluation frameworks. Future directions emphasize the importance of interdisciplinary collaboration, policy support, and technology transfer to accelerate adoption of sustainable practices across diverse production systems. Full article

Continuous monoculture of Panax notoginseng leads to severe replant disease, yet the mechanisms by which root exudates mediate rhizosphere microbiome assembly and pathogen enrichment remain poorly understood. Here, we demonstrate that long-term root exudate accumulation acts as an ecological filter, driving the fungal community toward a phylogenetically impoverished, pathogen-dominated state. Specifically, exudates enriched the soil-borne pathogen Fusarium while reducing the abundance of potentially antagonistic fungi. In contrast, bacterial communities exhibited higher resilience, with exudates selectively enriching oligotrophic taxa such as Terrimonas and MND1, but suppressing nitrifying bacteria (e.g., Nitrospira) and plant-growth-promoting rhizobacteria (PGPR). Microbial functional profiling revealed a shift in nitrogen cycling, characterized by suppressed nitrification and enhanced nitrate reduction. Crucially, co-occurrence network analysis identified bacterial taxa strongly negatively correlated with Fusarium, providing a synthetic community blueprint for biocontrol strategies. Our study establishes a mechanistic link between root exudate accumulation and negative plant–soil feedback in monoculture systems, highlighting microbiome reprogramming as a key driver of replant disease. These insights offer novel avenues for manipulating rhizosphere microbiomes to sustain crop productivity in intensive agricultural systems. Full article

Changes in the soil microbial community for studies of different novel communities can be promoted by different methodologies, among which soil autoclaving stands out as a quick and readily available tool. However, this procedure may also directly or indirectly alter nitrogen (N) and phosphorus (P) dynamics. The purposes of this study were as follows: (i) to characterize microbial activity after soil autoclaving through microbial ¹⁴CO₂-respiration; and (ii) to evaluate the effect of microbial manipulation and autoclaving on soil N and ³³P dynamics. For this, two sets of soil samples from two areas (forest and cultivated area) were used in the laboratory. Firstly, ¹⁴C-glucose was added to the soils and after 24 h five soil microbiomes were generated: AS (autoclaved soil), and AS re-inoculated with serial dilutions (w/v) prepared by successive mixing of soil suspensions in sterile deionized water obtaining 10⁻¹, 10⁻³, and 10⁻⁶, which generated the treatments AS + 10⁻¹, AS + 10⁻³, and AS + 10⁻⁶; and the treatment NS (non-autoclaved control), all incubated for 28 d. ¹⁴CO₂ emission was used to characterize microbial activity; additionally, N dynamics were assessed at the end of incubation. In a second assay, ³³P was applied to the soil before autoclaving and re-inoculation. Following further incubation (14 d), a ³³P chemical fractionation was performed. The following are based on the results: (i) ¹⁴CO₂ emission: microbial activity in the autoclaved soil is null, but after a reinoculation of AS + 10⁻¹ and AS + 10⁻³ soil dilution suspension, the ¹⁴CO₂-respiration is higher than in an NS. (ii) regarding the N dynamics, in autoclaved soils, the microbial levels increased N-NH₄⁺ concentration, with an evident increase in the AS + 10⁻³ and AS + 10⁻¹, and a reduction in the N-NO₃⁻ concentration in comparison to the NS. For ³³P, the autoclaving procedure itself reduced the ³³P lability, regardless of the levels of microbial community reinoculated. Full article

Autologous stem cell transplantation (ASCT) is the standard frontline consolidation strategy in fit, eligible patients with chemosensitive multiple myeloma, and it also serves as salvage option in other haematological malignancies, such as diffuse large B cell lymphoma. Moreover, ASCT is known to disrupt the gut microbiome (GM), and the impact on clinical outcomes has been understudied. The aim of this review is to examine the associations between the GM and outcomes in patients undergoing ASCT. Using the PRISMA 2020 guidelines for systematic reviews and meta-analyses, a total of 11 articles were included in this review, comprising both observational studies (cohort studies, case–control studies) and interventional trials (randomised controlled trials). Consistent findings included a notable decrease in beneficial bacteria, including Bacteriodetes, Firmicutes and Faecalibacterium prausnitzii, which maintain gut homeostasis and modulate immune responses. Conversely, an increase in pathogenic bacteria, including Escherichia coli, Enterococcus spp. and Klebsiella spp., was observed post-transplantation. This review includes an overview of the GM following ASCT and the techniques commonly used to assess it, and highlights gaps, thereby identifying key areas for future research, although conclusions are limited by variation in sample size and reporting inconsistencies. Understanding the GM’s role in ASCT may lead to interventions that optimise patient outcomes through therapeutic manipulation of the GM. Full article

The intestinal microbiome plays a pivotal role in the physiology and health of terrestrial gastropods yet remains largely unexplored. This study aimed to characterize the gut microbial communities of the farmed snail Cornu aspersum maxima and to assess the effects of dietary supplementation with the probiotic Lactobacillus plantarum, the prebiotic inulin, and their combination (synbiotic) on microbial diversity, snail growth, and survival. In total, 300 sexually immature snails (~9.8 g average body mass, ~5 months old) were assigned to four dietary groups (Control, Probiotic, Prebiotic, Synbiotic), each comprising three replicates of 25 snails. Individuals of similar size were placed in each container within the treatment groups. The Probiotic group received 1.25 mg of L. plantarum (1010 CFU/g) per 5 g of feed, the Prebiotic group received 1 g of inulin per 5 g of feed, and the Synbiotic group received both supplements at the same dosages. Over the 60-day trial, the gut microbiota was analyzed via 16S rRNA amplicon sequencing using Oxford Nanopore technology. The results revealed significant treatment-dependent shifts (p < 0.05) in microbial composition at both the phylum and genus levels. The dominant bacterial phyla identified were Proteobacteria and Actinobacteria, while a notable increase in unclassified microbial taxa was observed, especially in the inulin-supplemented groups. Despite its known probiotic properties, L. plantarum was not detected post-administration, suggesting a transient effect. The synbiotic group exhibited significantly higher microbial diversity (Shannon index, p < 0.05) but also the highest mortality rate. All groups showed limited weight gain, with reductions observed after day 30. Potentially pathogenic genera (e.g., Klebsiella, Mycoplasma, Staphylococcus) were detected but showed reduced abundance in the probiotic- and prebiotic-treated groups, suggesting a protective effect. Overall, probiotic supplementation with L. plantarum enhanced the abundance of beneficial Actinobacteria and reduced potentially pathogenic taxa, while the prebiotic inulin promoted the growth of unclassified but potentially beneficial genera. However, synbiotic administration, despite increasing microbial diversity, was associated with adverse outcomes including 100% mortality at day 60. These findings highlight both the potential and the risks of dietary manipulation of the snail microbiome, underscoring the need for cautious application of synbiotics in snail farming. They also underscore the dynamic nature of the snail gut microbiome and its responsiveness to dietary interventions, providing valuable insights for sustainable snail farming and future probiotic applications in invertebrate species. Full article

Technological advancements in computational power and algorithm design have enabled artificial intelligence to become a transformative force in microbiome research. This paper presents a concise overview of recent applications of this computational paradigm in human and animal health, with a particular emphasis on aquaculture. International projects focused on the intestinal microbiome have allowed human research to consistently dominate in terms of application cases, offering insights into various pathological conditions. In contrast, animal research has leveraged artificial intelligence in microbiome analysis to promote sustainable productivity, addressing environmental and public health concerns linked to livestock husbandry. In aquaculture, on the other hand, artificial intelligence has mainly supported management practices, improving rearing conditions and feeding strategies. When considering microbiome manipulation, however, fish farms have often relied on traditional methods, without harnessing the immense potential of artificial intelligence, whose recent applications include biomonitoring and modeling interactions between microbial communities and environmental factors in farming systems. Given the paradigm shift currently underway in both human health and animal husbandry, we advocate for a transition in the aquaculture industry toward smart farming, whose interconnected infrastructure will allow to fully leverage artificial intelligence to seamlessly integrate both biological measurements and rearing parameters. Full article

The rhizosphere microbiome, a critical determinant of plant health and productivity, exhibits structure–activity relationships influenced by plant genotype. This study investigated how three tea varieties with distinct phenotypes—Zhongcha 108 (ZC, green leaves), Huangjinya (HJY, chlorophyll-deficient yellow leaves), and Zijuan (ZJ, anthocyanin-rich purple leaves)—modulate the rhizosphere microbiome by integrated metagenomic, transcriptomic, and metabolomic analysis. Results revealed significant differences in rhizosphere bacterial diversity and composition among varieties, driven by differential abundances of Actinobacteria and Proteobacteria. HJY and ZJ exhibited higher bacterial richness and diversity compared to ZC. Root transcriptome profiling identified phenylpropanoid biosynthesis as a central pathway, with differentially expressed genes involved in flavonoid and lignin biosynthesis. Metabolite profiling highlighted varietal differences in root and rhizosphere organic acids and phenylpropanoid derivatives (e.g., hydroxycinnamyl aldehydes, sinapic acid), strongly correlating with microbial community structure. Functional metagenomics indicated that the carbohydrate and amino acid metabolism pathways in rhizosphere bacteria were influenced by root metabolites, further establishing phenylpropanoid partitioning as a keystone driver for microbial niche differentiation. These findings demonstrate that tea varieties shape rhizosphere microbiomes via genotype-specific phenylpropanoid metabolism, offering insights into targeted manipulation of plant–microbe interactions for enhancing tea plant development and tea quality. Full article

Helicobacter pylori (H. pylori) represents a major healthcare problem, colonizing more than half of the population worldwide. Usually acquired during childhood, it has a significant impact on human health. After forty years of extensive research, there are aspects of the complex H. pylori–human organism interplay that require further investigation. A comprehensive review was conducted after an extensive literature search in the PubMed/Medline, Web of Science, and EMBASE databases concerning H. pylori and human microbiota reports. Although the exact nature of H. pylori’s relation with the human microbiome remains elusive, its presence as well as its eradication treatment are associated with the alteration of bacterial communities’ composition not only in the gastric microenvironment but also in all digestive tract levels, with particular changes in both children and adults. Understanding microbiota composition is a step towards personalized medicine. Although the current literature on pediatric patients related to this topic is scarce, the available positive results reported in adult studies encourage pediatric research on microbiota manipulation, promising beneficial outcomes. Full article

Colorectal cancer (CRC), a prevalent malignancy, is a significant global health concern. The intricate interplay of genetic mutations, inflammatory processes, and environmental factors underscores the complexity of CRC’s etiology. The human gut harbors a diverse microbial community that plays a key role in maintaining homeostasis and influencing various aspects of host physiology. Perturbations in the gut microbiome (GM) composition and function have been implicated in CRC carcinogenesis. This bidirectional relationship involves microbial contributions to inflammation, DNA damage, and immune modulation, shaping the tumor microenvironment (TME). Bacteriophages, viruses that infect bacteria, contribute to the microbiome’s diversity and function by influencing bacterial abundance and composition. These phages can impact host–microbiome interactions, potentially influencing CRC risk. Furthermore, they can be manipulated to transport targeted medication, without being metabolized. Antibiotics exert selective pressures on the gut microbiome, leading to shifts in bacterial populations and potential dysbiosis. Probiotics can modulate the composition and activity of the GM and could be considered adjunctive therapy in the treatment of CRC. Understanding the intricate balance between bacteriophages, antibiotics–probiotics, and the GM is essential for comprehending CRC etiology and progression. Full article

Disease caused by Plasmodiophora brassicae severely disrupts cruciferous crops by altering root physiology and rhizosphere ecology. While pathogen-induced shifts in rhizosphere microbiomes are documented, the mechanisms linking root exudate reprogramming to microbial community remodeling remain poorly understood. Here, we integrated untargeted metabolomics and 16S rRNA sequencing to investigate how root exudates reshape the rhizosphere microbiome of tumorous stem mustard (Brassica juncea var. tumida) through P. brassicae infection. Metabolomic profiling identified 1718 root exudate metabolites, with flavones (e.g., apigenin 7-O-β-D-rutinoside, VIP > 1.5) and phenolic derivatives (e.g., gastrodin) being selectively enriched in infected plants. P. brassicae infection significantly increased rhizobacterial richness (ACE index, p < 0.05) and restructured the community composition, marked by enrichment of Paenibacillus (LDA score > 3.0). Procrustes analysis revealed tight coupling between microbial community shifts and metabolic reprogramming (M² = 0.446, p = 0.005), while Spearman correlations implicated pathogen-induced metabolites like geniposidic acid in recruiting beneficial Paenibacillus. Our results reveal that plant hosts dynamically secrete defense-related root metabolites to remodel the rhizosphere microbiome in response to P. brassicae infection. This dual-omics approach elucidates a chemical dialogue mediating plant–microbe–pathogen interactions, offering novel insights for engineering disease-suppressive microbiomes through root exudate manipulation. Full article

Background/Objectives: Endometriosis is a chronic, estrogen-driven gynecological disorder affecting approximately 10% of reproductive-aged women worldwide, with significant physical, psychosocial, and socioeconomic impacts. Recent research suggests a possible involvement of the gut microbiome in endometriosis disease mechanisms through immune manipulation, estrogen metabolism, and inflammatory networks. This narrative review aims to summarize current evidence on gut microbiota changes in endometriosis patients, explore the mechanisms by which gut dysbiosis contributes to disease progression, and examine epidemiological links between gastrointestinal health and endometriosis risk. Methods: A narrative review was conducted to synthesize available literature on the compositional changes in gut microbiota associated with endometriosis. The review also evaluated studies investigating potential mechanisms and epidemiological patterns connecting gut health with endometriosis development and severity. Results: Alterations in gut microbiota composition were observed in endometriosis patients, suggesting roles in immune dysregulation, estrogen metabolism, and inflammation. Potential gut-oriented interventions, including dietary changes, probiotics, and lifestyle modifications, emerged as promising management options. However, methodological variability and research gaps remain barriers to clinical translation. Conclusions: Integrating gut microbiome research into endometriosis management holds potential for improving early diagnosis, patient outcomes, and healthcare system sustainability. The study emphasizes the need for further research to address existing challenges and to develop public health strategies that incorporate microbiome-based interventions in population-level endometriosis care. Full article

Recent advances in microbiome studies have deepened our understanding of endosymbionts and gut-associated microbiota in host biology. Of those, lepidopteran systems in particular harbor a complex and diverse microbiome with various microbial taxa that are stable and transmitted between larval and adult stages, and others that are transient and context-dependent. We highlight key microorganisms—including Bacillus, Lactobacillus, Escherichia coli, Pseudomonas, Rhizobium, Fusarium, Aspergillus, Saccharomyces, Bifidobacterium, and Wolbachia—that play critical roles in microbial ecology, biotechnology, and microbiome studies. The fitness implications of these microbial communities can be variable; some microbes improve host performance, while others neither positively nor negatively impact host fitness, or their impact is undetectable. This review examines the central position played by the gut microbiota in interactions of insects with plants, highlighting the functions of the microbiota in the manipulation of the behavior of herbivorous pests, modulating plant physiology, and regulating higher trophic levels in natural food webs. It also bridges microbiome ecology and applied pest management, emphasizing S. frugiperda as a model for symbiont-based intervention. As gut microbiota are central to the life history of herbivorous pests, we consider how these interactions can be exploited to drive the development of new, environmentally sound biocontrol strategies. Novel biotechnological strategies, including symbiont-based RNA interference (RNAi) and paratransgenesis, represent promising but still immature technologies with major obstacles to overcome in their practical application. However, microbiota-mediated pest control is an attractive strategy to move towards sustainable agriculture. Significantly, the gut microbiota of S. frugiperda is essential for S. frugiperda to adapt to a wide spectrum of host plants and different ecological niches. Studies have revealed that the microbiome of S. frugiperda has a close positive relationship with the fitness and susceptibility to entomopathogenic fungi; therefore, targeting the S. frugiperda microbiome may have good potential for innovative biocontrol strategies in the future. Full article

Chaetomium globosum is a widely distributed fungal species recognized for its ability to produce a range of secondary metabolites. This fungus plays a significant ecological role by degrading organic matter and contributing to nutrient cycling in diverse ecosystems. In recent years, C. globosum has attracted considerable scientific interest due to its potential as a biocontrol agent [BCA] against a wide array of diseases in numerous plant species. While the precise mechanisms of C. globosum as a BCA remain poorly understood, interference competition through antibiosis is one of the key mechanisms. Moreover, C. globosum can enhance plant health by promoting nutrient availability, manipulating the rhizosphere microbiome, and inducing plant defense responses. The formulation of C. globosum for agricultural applications has been reported, which can significantly improve stability and efficacy under field conditions. However, despite significant advancements in omics and molecular biology technologies, the biology of C. globosum is understudied. Enhanced research into the genetics and functional genomics of C. globosum could pave the way for its applications in sustainable agriculture. This review summarizes the role of C. globosum as a BCA, focusing on its underlying mechanisms such as genomics and transcriptomics, and the effects of C. globosum application on soil health and the rhizosphere microbiome. Full article