The dynamic balance between the preservation and distribution of microbial patent strains, the “gene chips” of biotechnology, has become a crucial benchmark for assessing a country’s competitiveness in the bioeconomy. By comparing the global data on the preservation and distribution of patent strains from 2001 to 2023, this paper systematically analyzes the gaps between China, the United States, and other countries in terms of resource reserves and circulation efficiency. The results revealed that while China was a global leader in preservation volume, its strain distribution rate lagged far behind the international level, which restricted technological innovation and industrial transformation. This study proposes comprehensive strategies such as optimizing the preservation systems, enhancing policy coordination, promoting industry-education-research collaborative innovation, strengthening international cooperation, and applying artificial intelligence and blockchain technologies throughout the entire chain. These strategies are designed to enhance the utilization rate of microbial strains, activate the value of China’s patent microbial resources, and position China at the forefront of the global bioeconomy.

China’s national food security faces rigid constraints due to land scarcity, a large population, and heavy reliance on imported feed proteins. In this context, the initiative to seek calories and proteins from microbes has become a strategic priority for building a diversified food supply system. Microbial alternative proteins represent a quintessential new quality productive force in agriculture. They offer distinct advantages, most notably high industrial efficiency and the ability to decouple protein production from food crops and arable land. This paper reviews China’s progress in this sector based on global biomanufacturing trends. The discussion focuses on synthetic biology-driven strain engineering, gas fermentation, and industrial-scale production. Furthermore, the article critically analyzes current bottlenecks, including intellectual property barriers for elite strains, high production costs, and lagging safety evaluation standards. Finally, we propose targeted recommendations to address these challenges. These include strengthening organized basic research, establishing an intelligent manufacturing system that integrates education, technology, and talents, and reforming regulatory frameworks. These insights aim to provide a strategic reference for China to secure a commanding position in the global bio-agriculture landscape.

The dark matter of microbes, encompassing uncultivated microbial taxa and unknown biological features, has been widely accepted by microbiologists. With the advancement of microbial investigation methods, a series of dark matter concepts related to microbes have been successively proposed, and numerous research advances in this field have been well-documented. However, these concepts exhibit complex and overlapping connotations, and their inherent connections and distinctions have not yet been clearly clarified. This review work systematically summarizes the current conceptual frameworks of different dark matter types of microbes and analyzes the relevant investigation methodologies and their development trends. This article will help researchers in the microbial resource field gain a clearer understanding of the conceptual connotation and current research status of microbe-associated dark matter and promote the in-depth development of dark matter resource mining.

The application of natural microbiomes is limited by their complex composition and uncontrollable functions, which makes synthetic microbiomes a core direction in microbiome engineering. Early binary synthetic microbiomes can achieve functional synergy under controlled conditions, whereas they exhibit poor stability and limited functional persistence in real complex environments due to their simple metabolic pathways and insufficient ecological redundancy. In recent years, the research on synthetic microbiomes has shifted from an empirically driven approach to rational design, achieving significant progress in strain resource acquisition, construction strategies (top-down, bottom-up, and their hybrid paradigms), and computational tools (e.g., genome-scale metabolic models). However, current design frameworks still focus primarily on functional realization, with insufficient attention paid to the long-term stability, system robustness, and multi-level ecological interactions of communities in complex environments. This paper systematically sorts out the evolutionary trajectory of synthetic microbiome construction paradigms and reviews the key elements for enhancing community stability. By establishing a multi-level metabolic network, this paradigm significantly improves the functional persistence and ecological robustness of synthetic microbiomes in complex and fluctuating environments. The future research on synthetic microbiomes needs to further integrate multidisciplinary technologies to improve the predictability and long-term stability of engineered microbiomes, providing a systematic theoretical framework and research directions for constructing highly robust synthetic microbiomes.

Microorganisms, as the oldest and most diverse life forms on Earth, possess significant development value due to their differentiated metabolic potential and biosynthetic capabilities, serving as core resources for the development of novel drugs and natural active products. Currently, the deep integration of artificial intelligence (AI) with microbial strain development is driving a paradigm shift in life sciences from “empirical screening” to “rational design”. This shift is driven both by the limitations of conventional research methods in addressing the complexity of microbial resources and by the unique advantages of AI in multi-omics data analysis, model prediction, and experimental process optimization. This article systematically reviews the roles of AI in the development and application of microbial strains, covering four aspects: strain breeding, metabolite development, disease diagnosis and treatment, and xenobiotic synthesis. Additionally, it discusses the core advantages and existing limitations of AI in the strain development process. In summary, through automated modeling and scientific prediction, AI not only accelerates the efficiency of microbial strain development but also provides multi-dimensional optimization strategies, serving as a core driver for technological innovation. The integration of AI is expected to break through traditional industrial bottlenecks and promote the sustainable development of the microbial industry.

Heavy ion radiation (HIR) is effective for generating new germplasm in plants and microorganisms due to its high mutation induction rate, broad mutagenesis spectrum, and excellent stability of mutants. However, the random mutagenesis induced by radiation limits the efficiency and quality of HIR-based mutation breeding, which has become a key problem to be tackled. According to the process of heavy ion radiation-based mutation breeding, this review proposes a set of tandem strategies to enable efficient and high-quality HIR-based mutation breeding practices. These strategies include adjusting the radiation parameters from multiple dimensions, regulating cellular sensitivity to radiation damage and damage repair capacity, combining heavy ion radiation with adaptive laboratory evolution, integrating heavy ion radiation with other mutagenic agents, adopting progressive radiation, formulating high-throughput screening schemes for mutants, and efficiently identifying, verifying, and integrating positive mutations. These strategies aim to improve the mutagenesis rate, screening efficiency, and utilization of positive mutations. Meanwhile, we envision a mutation breeding workstation that integrates a series of strategies to form a complete cycle for heavy-ion radiation-based mutation breeding. This study is expected to provide valuable insights for creating high-quality microbial resources through heavy-ion radiation.

Microorganisms in high-salt environments (including halophilic and halotolerant bacteria) are widely distributed in extreme habitats such as salt lakes, oceans, and saline soils. Due to their unique metabolic adaptation mechanisms, they have become an important source of structurally novel natural products. This article outlines their taxonomic status and ecological distribution, with a focus on summarizing the chemical structures of compatible solutes such as ectoine and glycine betaine among primary metabolites, and their core roles in osmotic pressure regulation and biomacromolecule protection. The structural types of secondary metabolites, including alkaloids, terpenoids, steroids, and polyketides, are systematically reviewed. Furthermore, this article summarizes the biological activities such as antibacterial, antitumor, antioxidant, enzyme inhibitory, and photoprotective effects and discusses the structure-activity relationships of secondary metabolites. Considering the unique properties of these metabolites, this article analyzes their application prospects in fields such as medicine and health, biomaterials, and environmental remediation. This review aims to provide a theoretical reference for the in-depth development of microbial resources in high-salt environments and the discovery of novel bioactive molecules.

Quorum sensing (QS) is a communication mechanism through which microorganisms secrete and sense signal molecules to regulate mircobial population behaviors. QS plays important roles in biofilm formation and gut colonization of probiotics. In recent years, interfering with the QS of probiotics has become a trending research field of synthetic biology. In this review, we summarize the distribution of QS systems in probiotics and highlights interfering strategies designed to regulate probiotic functions. We summary currently identified QS systems in probiotics and their detection methods, such as photoelectrochemical assays and chromatography-mass spectrometry techniques. Meanwhile, this review outlines the QS interfering approaches for probiotics, including the use of QS agonists and the optimization of related metabolic pathways. Finally, the probiotic intervention strategy targeting QS is proposed in this paper, providing a novel approach for regulating the efficacy of engineered probiotics, which is of great significance for the development and improvement of probiotic functional foods.

Objective To elucidate the diversity and community composition of endophytic and rhizospheric bacteria associated with Apocynum venetum in northern Xinjiang and to screen the strains with efficient and specific degumming potential. Methods Samples of A. venetum were collected from four regions: Karamay, Fukang, Urumqi, and Turpan. The bacterial community structure was analyzed by 16S rRNA gene high-throughput sequencing. Pure-culture techniques were employed for strain isolation, and functional strains exhibiting xylanase and pectinase activities but lacking cellulase activity were screened by Congo red staining and enzyme activity assays. Results High-throughput sequencing identified 872 genera of bacteria belonging to 345 families of 38 phyla, among which Pseudomonadota and Actinomycetota were the dominant phyla. Bacterial abundance and diversity followed the order: rhizospheric soil>root>leaf>stem. Microbial abundance and diversity at the Turpan site were lower than those at the other sampling sites. A total of 361 bacterial strains were isolated in pure culture, belonging to 86 genera, 47 families of 4 phyla. Nine specific degumming strains were screened out, of which seven (77.78%) strains were endophytes derived from stems and leaves. The optimal functional strain, Bacillus rugosus (VFS.M1.04), showed xylanase and pectinase activities of 2 237 U/mL and 1 002 U/mL, respectively. Conclusion The community structures of endophytic and rhizospheric bacteria associated with A. venetum are significantly influenced by habitats and plant parts. Bacillus is the dominant functional genus, and the homologous screening strategy effectively enables the acquisition of elite strains with strong degumming capacity and no cellulose degradation from stem and leaf endophytes. This study provides valuable microbial resources and a theoretical basis for developing a green biological degumming process for A. venetum. These findings support the targeted exploitation of plant-associated microbial strains for sustainable fiber processing.

Objective To systematically investigate the diversity of culturable yeasts in extreme environments (glaciers, salt lakes, deserts, etc.) of western China and explore yeast resources with special stress resistance traits. Methods Multiple substrate samples were collected from representative extreme environments. Eight media with different nutrient gradients were employed in combination with direct dilution plating and enrichment culture methods for yeast isolation. Strains were identified by 26S rDNA D1/D2 region sequence analysis. Multivariate statistical analysis was carried out to assess species diversity and community structure differences across habitats and culture methods. Results A total of 904 yeast strains were isolated, representing 77 species, 29 genera, 17 orders, 10 classes, 5 subphyla, and 2 phyla, including 11 potential new species. Basidiomycota was the dominant phylum (90.5%), and Naganishia, Rhodotorula, and Cystobasidium were the dominant genera. Distinct dominant species were observed among different habitats. Naganishia adeliensis and Naganishia albida were widely distributed across all investigated extreme environments, indicating strong broad-spectrum environmental adaptability. Rhodotorula mucilaginosa and Cystobasidium slooffiae were dominant species in glaciers and salt lakes. In addition, enrichment culture and oligotrophic media significantly improved the isolation efficiency of rare species. Conclusion Extreme environments in western China harbor remarkably rich yeast resources. While different extreme environments select for unique dominant groups, certain broadly adaptable polyextremophilic species are shared across environments. Extreme environments serve not only as a reservoir of new species but also potentially as an environmental reservoir for opportunistic pathogenic yeasts.