Intensive aquaculture has significantly boosted aquatic product yields, but it often compromises sensory quality and remains constrained by reliance on unsustainable fishmeal. The Mulberry-dyke and Fish-pond system, used in China for millennia, suggests a circular approach, yet the underlying mechanism remains poorly understood. In this study, silkworm excrement (SE) from traditional sericulture (TSE) and modern insect factories (ISE) was evaluated as a functional aquafeed. Body weight, gut histology, and immunohistochemistry were employed to assess host health. Gut microbiome, electronic tongue analysis, and muscle metabolomics were conducted to assess fish flavor and identify flavor-related microorganisms. A single-strain feeding experiment further validated the microbiome-gut-muscle axis using electronic tongue analysis, gut transcriptomics, and determination of free amino acids and nucleotides. SE supplementation maintained fish yield while improving intestinal structure. Compared with commercial feed (CF), both SE treatments increased gut microbial diversity and community stability, and more than half of the significantly different ASVs were shared between the TSE and ISE groups, mainly involving immune regulation, nutrient metabolism, and flavor formation. SE, particularly TSE, enhanced antioxidant capacity and reduced lipid peroxidation, possibly through microbial regulation of lysophosphatidylcholines. As consistently indicated by electronic tongue and muscle metabolomics analyses, SE significantly improved fish flavor, with increased umami and reduced bitterness. Network analysis and single-strain feeding further suggested that Methylorubrum populi, Gemmobacter aquatilis, and Rhodobacter sphaeroides contributed to flavor improvement by regulating host amino acid and nucleotide metabolism along the microbiome-gut-muscle axis. These findings highlight SE as a promising sustainable bioresource for aquaculture.

The silkworm (Bombyx mori) has emerged as a powerful invertebrate model for gut microbiome research due to its simple yet representative gut microbiota, cost-effective rearing, and established germ-free systems. This review synthesizes current knowledge on the ecological drivers and functional roles of silkworm gut microbiota, emphasizing its interaction with host health, environmental adaptation, and biotechnological applications. The microbial community of silkworms is highly plastic, shaped by various intrinsic (developmental stage, sex) and extrinsic (diet, environmental conditions) factors. Key microbial taxa, including Enterococcus, Bacillus, Acinetobacter, Pseudomonas, and Staphylococcus, form a dynamic core community with demonstrated probiotic attributes. These microbes contribute to nutrient metabolism (such as cellulose digestion and amino acid synthesis), immune modulation (through the production of antimicrobial peptides), and detoxification (by degrading xenobiotics). Meanwhile, their dysbiosis correlates with reduced growth, silk yield, and pathogen resistance. Notably, several gut symbionts produce or stimulate natural antimicrobial proteins, including bacteriocins (such as enterococcin LX) and host-derived antimicrobial peptides, which exhibit activity against microbial pathogens. Understanding these microbial associations is crucial for developing microbe-based probiotic formulations, antimicrobial therapies, and enzyme-driven bioprocesses to enhance sericultural productivity and sustainability. Despite progress, significant gaps remain in our understanding of host-microbe coevolution, immune-microbiota crosstalk, and the genetic basis of microbial resilience. Future research integrating multi-omics approaches and gnotobiotic models will unravel mechanistic insights, enabling targeted manipulation of the silkworm microbiota for agricultural, environmental, and medical innovations.

The gut microbiota forms a competitive biological barrier against enteric pathogens and may also modulate antiviral immunity and disease prevention. This review presents recent advances demonstrating the tripartite model of the gut microbiome-immunity-virus axis in lepidopteran insects. Emerging evidence indicates that their gut microbiota regulates antiviral immunity through context-dependent mechanisms shaped by host species identity, microbial community composition, and strain-specific differences in viral resistance. Rather than acting as a uniformly protective factor, gut microbes fine-tune the local immune environment chiefly through antimicrobial peptide induction, modulation of prophenoloxidase/melanization, Duox/reactive oxygen species regulation, and maintenance of epithelial homeostasis. Although RNA interference, stimulator of interferon gene-related, and Janus kinase/signal transducer and activator of transcription signaling are established antiviral pathways in Lepidoptera, their direct regulation by gut microorganisms during viral infection remains elusive. These microbiota-conditioned immune states can either restrict viral replication and maintain gut barrier integrity or, conversely, favor virus pathogenesis when infection disrupts gut homeostasis, drives dysbiosis, or suppresses key antiviral effectors. Furthermore, strain-specific microbiome signatures correlate with differential viral resistance in susceptible and resistant hosts. By positioning the gut microbiome as a crucial immunological interface, this review integrates symbiosis biology into insect antiviral immunity and highlights microbiome-informed opportunities for sustainable pest management and the protection of beneficial insects.

Microplastics (MPs) are ubiquitous in terrestrial and aquatic ecosystems, where they rapidly acquire organic coatings and biofilms (the plastisphere) and interact with co-occurring chemical pollutants. However, the conditions under which MPs become ecologically relevant in increasing disease risk remain underexplored. A key controversy is that microbial detection or enrichment on MPs is often treated as evidence of pathogen “vectoring,” yet most studies do not quantify viability/infectivity, detachment, or delivered dose to hosts under environmentally realistic conditions. This review synthesizes evidence on MP-pathogen interactions and dispersal across ecosystems and reframes “MPs as vectors” through a vectorial-capacity lens that distinguishes association from transmission relevance and links MP-mediated risk to measurable dose delivery at host-relevant interfaces. Across ecosystems, evidence supports biofilm-driven persistence and enrichment of opportunistic taxa, but direct demonstrations of MP-mediated infection remain limited. We further highlight an unresolved issue, whether MPs confer unique transmission advantages compared with size-matched natural particulates that also sorb microbes and contaminants but are rarely used as comparators. We examine host susceptibility as a risk multiplier: MP exposure can compromise epithelial barriers via oxidative stress, modulate innate immunity, and disrupt microbiome-mediated colonization resistance. Plastisphere biofilms may also function as eco-evolutionary microhabitats that enrich antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), with plausible enhancement of horizontal gene transfer, although field-scale attribution is still scarce. Finally, we outline priorities for standardized evidence grading, comparator-based study designs, and quantitative metrics (loading, viability decay, detachment kinetics) to enable risk attribution and guide monitoring and mitigation.

Purpose This review aims to promote the broader application of insect protein by summarizing its nutritional and functional properties, with the ultimate goal of mitigating food security challenges exacerbated by global population growth. Design/methodology/approach This study employs a narrative review to evaluate the potential of insect protein for food applications. The analysis encompasses its nutritional profile, functional properties, innovative processing technologies, and food safety risk management. Findings This review demonstrates that insect protein is a high-quality nutritional source, characterized by high protein content, a balanced amino acid profile, a favorable lipid composition rich in essential fatty acids, and an abundance of vitamins and minerals. Its inherent advantages in resource efficiency and low environmental impact have led to its endorsement by the FAO as a strategic alternative protein source to support sustainable food systems. Originality/value In the context of rising global protein demand and the environmental limitations of conventional agriculture, this study consolidates evidence that edible insect protein represents a viable and sustainable alternative. Its integration into the food supply chain holds significant potential to alleviate pressure on traditional livestock and plant protein systems, thereby contributing to global food security.

Whether Lepidoptera harbor a conserved core gut microbiome has long remained contentious. Through large-scale microbiome profiling of folivorous larvae, their host plants, and associated soils across three climatically distinct regions of China, we identify two soil-derived generalist bacteria, Ralstonia insidiosa and Delftia sp., that colonize 97.92% of larval species examined, attaining mean relative abundances exceeding 47%, with the soil microbial reservoir as their principal source. Strikingly, these two taxa exhibit strong mutual exclusion within the larval gut yet govern host development through diametrically opposed metabolic strategies: R. insidiosa promotes larval weight gain, whereas Delftia sp. suppresses growth. This functional bifurcation, in which two widespread generalists exert opposite phenotypic effects, represents a previously undescribed phenomenon in insect-microbe symbiosis. Our findings provide broad evidence that soil microbial reservoirs can shape aboveground herbivore fitness via horizontally acquired bacteria, offering mechanistic insights for microbiome-based ecological management.

Industrial insect farming generates large quantities of manure, yet the fate and transmission risk of antibiotic resistance genes (ARGs) during insect-manure composting are largely unknown. Here, we compared ARG risks during the composting of silkworm excrement from traditional (TSE) and industrialized (ISE) sericulture. Specifically, in TSE, enriched ARGs were closely linked to pathogens, whereas in ISE, antibiotic-use practices drove ARG enrichment. Through metagenomic binning analysis, we identified 119 ARG-hosting taxa (TSE: 71, ISE: 48). In the TSE group, Pseudomonadota was the primary high-risk MAG, carrying an average of 20 ARGs per genome, while Bacillota dominated in the ISE group, with only five ARGs per genome. Furthermore, 52.1% of high-risk MAGs in the TSE group were considered potential pathogens, whereas the proportion was 33.3% in the ISE group. We then quantified ARG transmission risk using the ARGs-Mobile Genetic Elements (MGEs) distance index and further validated it through a compost-soil microcosm experiment, which indicated a higher risk of ARG transmission in the TSE group. Furthermore, the ARG transmission risk increased in the TSE group but decreased in the ISE group during composting. Notably, over 50% of ARGs formed stable combinations with specific MGEs, highlighting potential targets for reduction strategies. Finally, structural equation modeling revealed that biotic factors (MGEs and bacterial composition) had direct effects on ARGs, while abiotic factors (temperature and compost properties) influenced them indirectly. Overall, this study provides the first ecotechnological insights into ARG risks in insect manure compost, paving the way for sustainable insect bioresource production.

Nano(micro)plastics (NMPs) and agrochemicals are ubiquitous pollutants. The small size and physicochemical properties of NMPs make them potential carriers for pollutants, affecting their bioavailability and impact on living organisms. However, little is known about their interactions in terrestrial ecosystems. This study investigates the adsorption of Fenpropathrin (FPP) onto two different sizes of polystyrene NMPs and examines their impacts on an insect model, silkworm Bombyx mori. We analyzed the systemic effects of acute exposure to NMPs and FPP, individually and combined, at organismal, tissue, cellular, and gut microbiome levels. Our results showed that NMPs can adsorb FPP, with smaller particles having higher adsorption capacity, leading to size-dependent increases in the bioaccumulation and toxicity of FPP. These effects led to higher mortality, reduced body weight, delayed development, and decreased cocoon production in silkworms. Additionally, the pollutants caused physical and oxidative damage to the midgut and altered gene expression related to juvenile hormone (JH) and silk protein synthesis. The gut microbiome analysis revealed significant changes and reduced abundance of potentially beneficial bacteria. Thus, the aggravated toxicity induced by NMPs was size-dependent, with smaller particles (NPs) having a greater impact. This study demonstrates the role of NMPs as carriers for contaminants, increasing their bioavailability and toxicity in terrestrial ecosystems. These findings have significant implications for ecosystem health and biodiversity.

A newly emerged foot rot disease of sweet potato (Ipomoea batatas) has been observed in the warm, humid, and low-lying areas of southeast Zhejiang Province, causing significant yield losses. The disease is characterized by dark brown lesions encircling the basal stem, wilting, and chlorotic leaves. Infected tubers develop deep, irregular, dark brown lesions, reducing crop quality and yield. This study aimed to identify the causal pathogen. Symptomatic samples were collected, and potential pathogens were isolated, purified, and tested for pathogenicity following Koch's postulates. Morphological characterization and phylogenetic analysis of rDNA-ITS, EF1-alpha, and CAL genes confirmed Phomopsis destruens as the causal agent. These findings provide crucial insights into the etiology of this emerging disease and offer a foundation for developing effective management strategies to mitigate its impact on sweet potato production in Zhejiang Province.

While conventional sericulture has developed effective disinfection methods, the increasing demand for silk and pupae is driving mechanization, potentially altering or introducing silkworm pathogens. New disinfection strategies are essential for sustainable sericulture production. This study first investigated the bacterial community differences between conventional and mechanized silkworm-rearing environments. Then, under the mechanized environment, we evaluated three commercially available disinfectants with different mechanisms: hypochlorous acid (HClO), nano platinum-polyhexamethylene guanide (Pt-PHMG), and medium-chain fatty acids (MCFA). Our results indicated significant bacterial differences between the two environments, with potential pathogenic bacteria present in both environments. Moreover, the bacterial communities remained relatively stable, while conventional disinfection methods were less effective in mechanized conditions. In contrast, regardless of whether they were applied before or after silkworm rearing, all three disinfectants demonstrated significant efficacy, with the total environmental bacterial load reduced by approximately 0.5 to 1 order of magnitude after application. Among them, Pt-PHMG exhibited the best performance by inhibiting pathogens such as Staphylococcus, Enterococcus, and Bacillus, followed by MCFA and HClO. The results also suggested a need for stronger disinfection strategies after silkworm rearing. These findings not only provide important hygiene practices to ensure mechanized silkworm rearing, but also offer valuable insights for the future development of disinfection strategies in modern sericulture.

The midgut and fat body of insects control key physiological processes, including growth, digestion, metabolism, and stress response. Single-nucleus RNA sequencing (snRNA-seq) is a promising way to reveal organ complexity at the cellular level, yet data for lepidopteran insects are lacking. We utilized snRNA-seq to assess cellular diversity in the midgut and fat body of Spodoptera frugiperda. Our study identified 20 distinct clusters in the midgut, including enterocytes, enteroendocrine, stem-like cells, and muscle cells, and 27 clusters in the fat body, including adipocytes, hemocytes, and epithelial cells. This dataset, containing all identified cell types in midgut and fat body, is valuable for characterizing the cellular composition of these organs and uncovering new cell-specific biomarkers. This cellular atlas enhances our understanding of cellular heterogeneity of fat and midgut, serving as a basis for future functional and comparative analyses. As the first snRNA-seq study on the midgut and fat body of S. frugiperda, it will also support future research, contribute to lepidopteran studies, and aid in developing targeted pest control strategies.

With the vigorous development of sericulture, the traditional labor-intensive small-scale silkworm rearing has been progressively transformed into a large-scale mechanized system. Consequently, silkworm factories can produce cocoons continuously throughout the year. However, this intensive production pattern generates a substantial amount of silkworm excrement. If not managed properly or disposed indiscriminately, silkworm excrement can lead to severe environmental pollution. In recent years, increasing attention has been paid to the comprehensive utilization of this bioresource. Numerous studies have explored its potential in a wide range of applications. This review systematically summarizes current research on silkworm excrement utilization, particularly focusing on its fundamental characteristics, key technologies, and application areas. Future efforts should aim to promote efficient resource recycling and support the development of sericulture.

Ecosystems are interconnected networks of diverse habitat types, rather than isolated patches. However, the role of the multi-habitat landscape in influencing microbial diversity remains poorly understood. This study investigates bacterial and fungal communities within a 2500-year agricultural heritage system, the Mulberry-dyke and Fish-pond (MF), which integrates various terrestrial and aquatic habitats. Using amplicon sequencing, metagenomics, metatranscriptomics, and genomic analyses, these findings reveal a significant proportion of unclassified microbial taxa, underscoring the importance of MF systems as an untapped reservoir of microbial genetic resources. Moreover, single-nucleotide-level analyses demonstrate that a multi-habitat landscape enhances microbial diversity through ecosystem-wide assembly, facilitated by cross-habitat microbial dispersal. Taxa found across multiple habitats exhibit convergence in microdiversity and adaptive genetic traits, indicating both ecological and functional mechanisms underlying their adaptability. A global analysis of public microbiome datasets furthermore confirms that regions with higher habitat heterogeneity support significantly higher taxonomic and functional diversity of microbiomes. Overall, this study sheds new light on the overlooked microbial diversity in traditional agricultural heritages and emphasizes the value of ancestral ecological wisdom underlying multi-habitat integration for ecosystem management. These insights offer valuable guidance for developing sustainable agricultural strategies, enhancing microbial diversity, and reinforcing ecosystem resilience in the face of global change.

Plastic pollution, particularly the widespread presence of microplastics, has emerged as a global environmental threat. Conventional plastics are highly resistant to degradation and can persist in ecosystems for decades, posing a serious long-term risk to wildlife, habitats, and human health. Increasing evidence suggests that insects and their gut microbiota may play a significant role in the degradation of these plastics. This review examines the mechanisms by which insects and their associated microorganisms contribute to microplastic biodegradation. Plastivorous insect larvae such as Spodoptera frugiperda, Galleria mellonella, Tenebrio molitor and Zophobas atratus have demonstrated the ability to ingest and partially degrade diverse polymers. The initial mechanical breakdown caused by insect mandibles increases the surface area, which allows gut microbes to colonize the material. Once these microbes are established, they form biofilms that help with adhesion, create localized redox environments, and concentrate degradative enzymes at the polymer interface. The enzymatic machinery of insect-associated microbes plays a crucial role in breaking down polymers. Oxidative enzymes, including DyP-type peroxidases, multicopper oxidases, alkane monooxygenases, and laccases, initiate the oxidation of polymers, while hydrolases and esterases further break down the resulting fragments. Co-metabolic processes and microbial consortia improve degradation efficiency by primary degraders by producing oxidized intermediates, which are then consumed and mineralized by secondary fermenters. Despite significant progress, the complete biochemical pathways of microplastic mineralization remain unclear. Degradation rates are slow, and scalability challenges hinder practical applications, with incomplete mineralization in insect biodegradation potentially causing secondary microplastics. Understanding these mechanisms will lay the groundwork for developing insect-microbe systems as potential biotechnological solutions to mitigate plastic pollution in terrestrial environments.

In the context of a rapidly expanding global population, mulberry leaf protein emerges as an emerging source of plant protein, with most applications currently at Technology Readiness Level (TRL), presenting substantial potential for application in functional foods and nutraceuticals. This paper analyzes three key advantages of mulberry leaf protein. Firstly, the abundant and inexpensive production of mulberry leaves establishes a solid foundation for large-scale protein extraction. Secondly, advancements in the preparation processes and production technology for mulberry leaf protein have further enhanced its viability. Thirdly, mulberry leaf protein boasts excellent nutritional value and outstanding functional properties, along with multiple biological activities, including antioxidant effects, aging delay, and blood-pressure-lowering activity. These superior qualities considerably broaden its range of applications. Furthermore, this paper evaluates existing research (before 30 June 2025) while exploring prospective avenues for future investigation. The findings of this review are important for enhancing the understanding of the potential applications of mulberry leaf protein in food science and nutrition. The aim is to provide new ideas for the efficient utilization of mulberry leaf protein resources and the establishment of a global food security system.

The Anthropocene presents unprecedented challenges to global biodiversity and ecosystems. The silkworm Bombyx mori, which is the cornerstone of the sericulture industry, faces numerous challenges in this rapidly changing world due to various anthropogenic factors, including environmental pollution, climate change, diseases and pathogens, habitat degradation, declining genetic diversity, and economic instability. This review explores the effects of these multifaceted challenges on silkworms and their implications for the sericulture industry. Environmental pollution, particularly from pesticides, micro- and nanoplastics, and air and water pollution, stands out as one of the major concerns for silkworm health and quality. Additionally, temperature extremes, drought, flooding, unpredictable weather patterns, land use changes, disease outbreaks, antibiotic resistance, labor shortages, and market volatility have threatened the sustainability of silkworm-rearing practices and the sericulture industry. Here, we propose integrated mitigation strategies that span genetic (resilient strains), environmental (pollution control), and biotechnological approaches. Additionally, we have proposed strategies to mitigate the negative impacts of these factors and enhance the resilience of sericulture in the face of the Anthropocene. By detailing the specific challenges faced by sericulture today, this review raises awareness among stakeholders and underscores the urgency of utilizing integrated strategies to address these challenges and ensure the sustainability of silk production.

Acclimation to abiotic stress is crucial for insect adaptation, particularly under extreme climatic conditions. The model organism silkworm Bombyx mori serves a valuable system for studying thermal stress responses. Here we reveal that heat hardening (30 °C for 2 h) significantly enhances larval survival under subsequent heat shock (45.2 °C), increasing survival rates from 20 % to 70 %. Transcriptomic analysis indicated the head displaying a greater number of upregulated genes compared to the gut. Functional annotation identified critical pathways for heat stress adaptation, including protein processing in the endoplasmic reticulum, longevity regulation, and ATP-dependent chaperone activity. Notably, key heat shock proteins (Hsps), such as Hsp90, Hsp70, Hsp20.4, and Hsp19.9, were significantly upregulated in both tissues during heat hardening (HH) and heat hardening following heat shock (HHHS), highlighting their pivotal role in thermotolerance. RNA interference further confirmed the essential roles of Hsp90 and Hsp19.9 in enhancing survival under heat stress, while silencing Hsp70 and Hsp20.4 had no significant effects, suggesting gene-specific contribution. These findings not only provide comprehensive insights into the molecular mechanisms of heat stress adaptation in B. mori, but also identify key pathways and genes that may enhance thermotolerance in widespread lepidopteran insects in the context of global climate change.

Antibiotic resistance genes (ARGs) are emerging environmental contaminants that pose increasing risks to ecosystems and human health. However, the distribution and drivers of ARGs associated with woody plants remain underexplored. In this study, we leverage large-scale sampling and metagenomics to provide a comprehensive survey of ARGs in both mulberry (Morus) field soil and rhizosphere across China. Our findings revealed significant regional differences in ARG diversity and composition, exhibiting a distance-decay pattern. The most abundant ARG types identified were multidrug, novobiocin, and macrolide-lincosamide-streptogramin, with the dominant resistance mechanisms being efflux pumps, antibiotic target alteration, and enzymatic inactivation. Structural equation modelling further showed that ARG profiles were primarily influenced by mobile genetic elements (MGEs) and annual mean temperature, with high-risk ARGs increasing significantly. We also observed notable regional and compartmental differences in MGEs, with both richness and abundance being higher in the rhizosphere compared to bulk soil. Moreover, co-occurrence network analysis revealed that ARG-MGE associations in the rhizosphere were stronger and more complex, likely promoting ARG dissemination. Our results not only provide the first overview of ARG profiles in widely planted mulberry but also characterize the factors shaping the antibiotic resistome, paving the way for managing ARG risks in woody plants.

This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submitted to the journal. At Microbiome, we are seeking studies that provide either new mechanistic insights into the role of microbiomes in health and environmental systems or substantial conceptual or technical advances. Manuscripts need to meet high standards of language accuracy, quality of microbiome analyses, and data and protocol availability, including detailed reporting of wet-lab and in silico protocols, all of which can critically enhance transparency and reproducibility. We think that such efforts are essential to push the boundaries of our knowledge on microbiomes in a concerted, international effort.