NUS Silkworm Midgut Study Uncovers Key Cell Clusters Responding to Fungal and Viral Infections

Revolutionary Mapping of Silkworm Midgut Cells Reveals Infection Response Mechanisms

The National University of Singapore (NUS) has played a pivotal role in a groundbreaking study that maps the silkworm midgut at the single-cell level, identifying key cell clusters that respond to fungal and viral infections. Published in the Journal of Advanced Research on February 16, 2026, the research utilized single-nucleus RNA sequencing (snRNA-seq) to create the first comprehensive cell atlas of the Bombyx mori midgut, a critical organ for nutrient absorption and pathogen defense in this economically vital insect.

Silkworms, or Bombyx mori, are the cornerstone of sericulture, producing over 80% of the world's raw silk, an industry valued at billions globally. Pathogens like the fungus Nosema bombycis (causing pebrine disease) and the virus Bombyx mori nucleopolyhedrovirus (BmNPV, causing grasserie disease) inflict massive losses, with BmNPV alone accounting for over 60% of cocoon crop failures in affected areas. This NUS-collaborative effort uncovers how specific midgut cells orchestrate immune responses, paving the way for targeted disease resistance strategies.

Silkworm as a Model Organism in Lepidopteran Research

Bombyx mori serves as an ideal model for lepidopteran insects, which include major agricultural pests like moths and butterflies. Its fully sequenced genome and ease of rearing make it perfect for studying gut immunity, relevant to crop protection and biotechnology. The midgut, comprising over 50% enterocyte cells (ECs), goblet cells (GCs), enteroendocrine cells (EEs), intestinal stem cells (ISCs), and muscle cells (MCs), is the primary battleground against ingested pathogens.

In Singapore, while commercial sericulture is limited due to urban constraints, NUS researchers contribute to global silk innovation, including engineered spider silk hybrids for biomedical applications. This study extends NUS's expertise in virology and microbiology, led by Assoc Prof Justin Jang Hann Chu from the Yong Loo Lin School of Medicine.

Advanced Methods: Single-Nucleus RNA Sequencing Unlocks Cellular Secrets

snRNA-seq was employed to profile nuclei from healthy and infected midgut tissues at 24 hours (early infection) and 96 hours (late infection). This technique bypasses RNA degradation issues in fixed tissues, enabling high-resolution transcriptomics. Data from PRJNA1280782 yielded 20 distinct cell clusters (C0-C19), annotated via marker genes, KEGG, and GO pathways.

• ECs: 54.4% (nutrient absorption, primary immune responders)
• GCs: 25.9% (mucus production; new marker gene Cel identified)
• EEs: 10.6% (hormone secretion)
• ISCs: 2.17% (regeneration)
• MCs: 7.0% (peristalsis)

Infection experiments with N. bombycis and BmNPV revealed dynamic gene expression shifts, highlighting clusters like C2 and C16.

The Cell Atlas: 20 Clusters and a New Goblet Cell Marker

The atlas revealed unprecedented diversity, with EC-like clusters C0 and C12 expressing high levels of innate immune genes. A novel finding was the GC marker Cel, validated across datasets, aiding future studies on mucus barriers against pathogens. This granularity is crucial for lepidopteran biology, where gut cells vary regionally.

In Singapore's biotech ecosystem, such atlases support NUS's push in single-cell genomics, applicable to human gut microbiomes and disease models.

Key Cell Clusters: C4 and C13 as Common Susceptible Sites

C4 (ECs) and C13 (ISCs) emerged as vulnerable to both pathogens, showing high viral loads and fungal spore proliferation. Conversely, C2 and C16 (ECs) displayed low infectivity but upregulated immune genes, positioning them as resistance hubs. Genes in these clusters that inhibit both N.b and BmNPV were screened, offering targets for CRISPR editing or RNAi therapies.

For sericulture, engineering these clusters could reduce losses by 30-50%, mirroring successes in transgenic Bt crops.

Immune Dynamics: Early vs Late Infection Responses

At 24hpi, broad immune activation in ECs countered initial invasion. By 96hpi, susceptible clusters amplified pathogen replication, while resistant ones sustained defenses. This temporal map explains disease progression, from asymptomatic to lethal.

NUS virologist Assoc Prof Chu's expertise in RNA viruses like BmNPV bridges insect and human virology, enhancing Singapore's pandemic preparedness.

Implications for Sericulture and Pest Management

Pebrine and grasserie cause 20-60% cocoon losses annually, costing Asia billions. Targeting C2/C16 genes could breed resistant strains, boosting yields. As a lepidopteran model, findings apply to cotton bollworm control, vital for Singapore's food security imports.

• CRISPR knock-in of resistance genes in ISCs for self-renewing protection
• Probiotics enhancing GC mucus barriers
• RNAi sprays targeting viral replication in ECs

Singapore's NUS drives sustainable biotech, aligning with RIE2025 goals.

NUS's Contribution and Singapore's Biotech Landscape

Led primarily by Southwest University, the study benefited from NUS's Justin Chu, expert in viral entry and antivirals. His lab's work on flaviviruses complements insect virus research, fostering international ties.

NUS ranks top in Asia for life sciences, with facilities like the Centre for Bioimaging Sciences supporting such high-tech studies. Singapore invests S$25B in RIE2025 for biotech, positioning it as a hub.

Broader Applications in Biotechnology and Human Health

Insect gut models inform human IBD and microbiome therapies. Silkworm silk, already used in sutures, could incorporate antimicrobials from resistant cells. snRNA-seq advances accelerate drug discovery, as seen in NUS's COVID research.

Future Outlook: Engineering Resilient Silkworms

Next steps include functional validation of screened genes via CRISPR silkworms. Multi-omics integration could reveal microbiota roles. For Singapore, this bolsters food tech and biomaterials.

Photo by National Institute of Allergy and Infectious Diseases on Unsplash

Conclusion: Pioneering Insect Immunity at NUS

This NUS-involved study transforms our understanding of insect gut defenses, promising resilient sericulture and beyond. Researchers eyeing entomology or virology careers should check higher-ed-jobs, university-jobs, and rate-my-professor for NUS opportunities. Explore higher-ed-career-advice for tips.