<i>iMeta</i> Conference 2024: Building an innovative scientific research ecosystem for microbiome and One Health

Abstract

The iMeta Conference 2024 provides a platform to promote the development of an innovative scientific research ecosystem for microbiome and One Health. The four key components - Technology, Research (Biology), Academic journals, and Social media - form a synergistic ecosystem. Advanced technologies drive biological research, which generates novel insights that are disseminated through academic journals. Social media plays a crucial role in engaging the public and facilitating scientific communication, thus amplifying the impact of research. Together, these elements create a self-sustaining loop that fosters continuous innovation and collaboration in the field of bioinformatics, biotechnology and microbiome research. The iMeta Conference 2024, held from October 11 to 13, 2024, at the Nanshan District People's Hospital in Shenzhen, China, attracted over 400 leading scientists, researchers, and industry professionals from around the world (File S1). Organized by the editorial team of iMeta, a top-tier interdisciplinary journal in biotechnology, microbiome, and bioinformatics, this conference has been emerging as a premier platform for cutting-edge research in these fields. The iMeta journal, led by Chief Editors Prof. Shuangjiang Liu and Prof. Jingyuan Fu, has an impressive impact factor of 23.8, within the top 0.5% of journals worldwide (107 out of 21,848), and 11th in mainland China. Additionally, iMetaOmics, a subjournal co-edited by Prof. Fangqing Zhao and Prof. Jun Yu, is projected to have an impact factor of over 10, positioning it as a high-level interdisciplinary journal that welcomes submissions [1]. Since its inception in 2022, the iMeta journal has launched a series of conferences aimed at advancing research, fostering international collaboration, and promoting the development of the field [2]. Following successful events in Qingdao and Beijing [3], the 2024 edition marks the third event in this series that was co-organized by the Southern University of Science and Technology (Department of Biochemistry and Key University Laboratory of Metabolism and Health of Guangdong), Xianghu Laboratory, TreatGut, and HaploX. The conference covered a wide range of key topics (Figure 1), including Cutting-Edge Technologies, Gut Microbiota, Omics, Medicine, One Health, International Projects, and Journal Forum. These sessions highlighted the interdisciplinary nature of modern life sciences, with presentations covering microbial ecology, advancements in sequencing technologies, genome editing, and the broader implications of these innovations on human, animal, and environmental health. With the theme of “Building an Innovative Research Ecosystem,” the iMeta Conference 2024 provided an interdisciplinary forum where participants could share breakthroughs, explore collaborative opportunities, and discuss the future of biotechnology, microbiome, and bioinformatics research. The opening ceremony included addresses from prominent figures such as Tieying Hou, President of Nanshan District People's Hospital, Hua Yang, Executive Deputy Director of Xianghu Laboratory, and Shuang-Jiang Liu, Chief Editor of iMeta. They provided an overview of the major mission and development of Nanshan Hospital and Xianghu Laboratory and emphasized iMeta's mission to “serve readers and authors.” The hosts and organizers extended a warm welcome to all attendees and expressed their best wishes for the conference's success. In addition, the ceremony featured five keynote speeches, covering diverse topics such as the screening of antibiotic alternatives based on gut microbiota responses, research on microecology and cancer, in situ analysis techniques for microbiota–host interfaces, reflections in microbiome research on Koch's postulates, and the study of chemical molecule-driven mechanisms in microbiota–host interactions. These talks not only reviewed the history of microbial research and revisited the foundational “Koch's postulates” but also highlighted how emerging technologies and interdisciplinary approaches are propelling advancements in microbiology. Professor Yulong Yin delivered a report on swine ecology, focusing on four key areas: quorum sensing, approaches for screening antibiotic alternatives based on quorum sensing, methods for regulating quorum sensing and their effects, and the development of new antibiotic alternatives. He explained that high-density microbial communities in the gut secrete specific signaling molecules, allowing them to adapt to the complex gut environment and fulfill physiological roles [4]. Alternatives to antibiotics, such as plant extracts, organic acids, and probiotics, can inhibit pathogen colonization, enhance epithelial barrier function, and promote nutrient absorption through quorum sensing. Prof. Yin also discussed how synthetic biology enables the engineering of probiotics that neutralize pathogen defense mechanisms through quorum sensing, thereby improving feed conversion efficiency. His talk provided a comprehensive overview of the theoretical mechanisms, practical applications, and product development in swine ecology, offering new directions for reducing disease and promoting animal growth. Professor Jun Yu explored the connection between microecology and colorectal cancer, focusing on two major areas: the role of gut microbiota in digestive tumor mechanisms and its application in diagnosing and treating digestive system cancers. She first discussed the relationships between gut microbiota and digestive tumors, examining the interactions between tumor-associated bacteria and the host [5]. In the second part of her presentation, Prof. Yu highlighted four key aspects: the interplays between gut microbiota and drugs, fecal microbial markers for diagnosing digestive tumors, the use of anticancer bacteria in prevention and treatment, and the influence of bacteria and their metabolites on tumor immunotherapy [6]. Throughout the presentation, she referenced relevant research cases, emphasizing the potential of these findings to advance clinical diagnosis, prevention, and treatment strategies for digestive system cancers. Professor Fangqing Zhao focused on technological advancements for studying the interactions between microbiota and hosts. His research addresses host gene expressions and regulatory patterns, as well as in situ analysis techniques for understanding the complex interactions within biological systems [7]. He introduced new real-time transcriptomic sequencing technology based on programmable control, along with single-cell spatial omics technology. These technologies have significantly reduced batch effects, increased gene detection rates, improved resolution, and lowered analysis costs, paving the way for more precise studies of microbiota–host dynamics. Professor Shuang-Jiang Liu revisited the classical “Koch's postulates,” which serve as the gold standard for establishing causality between microbes and diseases. He explored the challenges of applying these postulates to microbiomes, especially regarding the isolation and cultivation of microbial strains and the issue of functional redundancy within microbial communities. Prof. Liu discussed key terminologies in microbiome research and reviewed the development of microbiology. He proposed a redefinition of Koch's postulates to address the complexities involved in studying microbiomes, highlighting the evolving nature of this foundational concept. Professor Hongwei Liu focused on the chemical molecule-driven mechanisms that shape interactions between microbiota and their hosts. He highlighted key challenges in gut microbiome research, such as identifying core functional strains, functional genes, metabolic pathways, and physiologically active substances. Prof. Liu reported on the effects of administering exogenous active molecules on gut bacterial growth, community structure, and host functions. For instance, compounds from Ganoderma (reishi mushroom) have been shown to promote the growth of Parabacteroides distasonis, which helps alleviate glucose and lipid metabolic disorders in the host. Prof. Liu also presented findings from metabolomic studies, which identified a novel secondary bile acid produced by Christensenella minuta that plays a role in improving host metabolism [8]. His talk demonstrated how a chemistry-based approach can open new avenues for understanding the microbiome and its implications for human health. This session featured eight speakers who presented on the intricate relationships between medicine, animals, plants, and microorganisms, as well as related advanced technologies. The medical field was represented by Prof. Hubing Shi from the West China School of Medicine at Sichuan University and Associate Professor Li Liang from the Southern University of Science and Technology. Prof. Shi presented on “Immune Surveillance and Evasion Mechanisms in Tumor Metastasis,” addressing three key questions: (1) Are CTCs subject to immune surveillance? (2) If so, which immune cells are responsible? (3) How do CTCs evade surveillance? He explored these questions using pancreatic cancer liver metastasis models, providing new insights into the immune system's role in tumor progression [9]. Associate Professor Li delivered a report on “Microbe-Host Interactions and Drug Development Using a Platform of Cultured Clinical Samples and Human Organoids.” He emphasized the growing significance of organoids as a host model for studying microbial infections and immunity mechanisms, highlighting their high potential for pharmaceutical research and drug development. In the section of animal immune and plant biotechnology studies, Professor Wenkai Ren from South China Agricultural University and Professor Shuangxia Jin from Huazhong Agricultural University gave compelling presentations. Professor Ren discussed “Amino Acid Metabolism and Immune Cell Fate in Piglets,” showing that amino acid metabolism plays a vital role in the immune characteristics, disease resistance, and fate of immune cells. His research sheds light on metabolic pathway reshaping, signaling pathways, epigenetic changes, and posttranslational modifications, which are critical for reducing high mortality rates in piglets. On the plant side, Prof. Jin focused on the “Development of Gene Editing Tools for Cotton and Their Application in Molecular Breeding.” He presented a detailed overview of the diversity of genome editing technologies, such as the delivery system for CRISPR/Cas components into plant cells, CRISPR/Cas9, Cas12a, Cas12b, base editors (CBE, ABE), dCas9-TV transcription activation systems, and Cas13 knockdown systems. He highlighted the wide applications of these genome editing systems in cotton molecular breeding for improving yield, quality, and stress tolerance [10, 11]. Additionally, the session featured presentations by Prof. Diwei Zheng from the Institute of Process Engineering at the Chinese Academy of Sciences, Assistant Professor Robert Schlaberg from Illumina, and Chief Technology Officer Bangzhou Zhang from TreatGut Biotechnology Co., Ltd. Prof. Zheng discussed advances in bacterial biomaterial technology, including the development of engineered strains with specialized functions such as drug delivery, fluorescent imaging, and light-controlled drug synthesis [12]. Assistant Professor Schlaberg presented on sequence-based solutions for identifying pathogens and antibiotic resistance, offering new tools for tackling antimicrobial resistance. Finally, CTO Bangzhou Zhang introduced a platform for microbiome medicine and translational research, which includes precise microbiota transplantation therapy platforms and live microbial drugs, providing promising new avenues for medical treatments. The Cutting-Edge Technology Session featured 13 speakers who shared insights into the latest experimental, analytical, and sequencing technologies. Presentations centered around the development of innovative methods and tools, such as metaRUpor for genome extraction of rare species, Tencent's medical AI model for assisted diagnosis, microbial analysis tools like metaProbiotics and MOBFinder [13], and CycloneSEQ nanopore sequencing technology. Topics covered systematic research on antibiotic resistance genes, analysis of gut microbial metabolism, studies on microbial interactions, single-cell transcriptomics, and the application of high-throughput data in environmental viromics and microecology. Professor Huizeng Sun from Zhejiang University delivered the keynote speech, systematically introducing advances in microbial single-cell transcription research, highlighting the principles of single-cell transcriptomics based on random primer microfluidics and microbial pan-genome mapping, with successful applications in the study of rumen microorganisms [14]. Professor Yan Ni from the National Clinical Research Center for Child Health offered an in-depth presentation on integrated analysis methods for gut microbiota and metabolism that have been recently introduced in the newest version MetOrigin 2.0 (http://metorigin.met-bioinformatics.cn), covering quick database search, covering correlation analysis, metabolic function analysis, origin analysis, gut microbial enzyme analysis, and microbe-metabolism mediation effect analysis. The session concluded with discussions on the growing need for more advanced and efficient methods to process and analyze target data in the context of high-throughput sequencing. The Biotechnology Session featured five presentations that emphasized cutting-edge technologies such as single-cell and spatial omics, single-bacterium RNA sequencing, and in situ targeted isolation of functional microorganisms, alongside their practical applications. Professor Yongcheng Wang from Zhejiang University developed a new generation of high-throughput single-cell whole-transcriptome sequencing platform based on random primers [15]. This platform not only processes eukaryotic cells but also achieves single-cell transcriptome sequencing for bacteria and other microorganisms. It has produced excellent results even with less active frozen and FFPE (Formalin-Fixed Paraffin-Embedded) samples. Prof. Shengguo Zhao from the Chinese Academy of Agricultural Sciences introduced two innovative targeted isolation technologies for functional microorganisms using magnetic nanoparticles and microbeads. These methods significantly reduce the nature of techniques and like high and of These technologies a in and microorganisms. The session also highlighted the of technologies in complex tackling challenges in microorganisms, and to human disease research and For instance, studies presented on using to study the gut role in metabolic the molecular mechanisms tumor and advances in microbiology. These presentations emphasized the critical role of emerging in addressing complex biological and The Session featured four presentations that explored such as to Acid Metabolism for Research and Clinical of Tumor and and and the connection between microorganisms and human and health. He from TreatGut Biotechnology Co., Ltd. demonstrated the clinical of precise microbiota Professor Wang from Zhejiang University presented findings on a which was shown to the of in the gut and enhance the of acid This to the of of bile acid and activation of the which inhibit and new for Assistant Professor from the Southern University of Science and Technology discussed the use of single-cell sequencing technology for tumor cells the mechanisms of tumor metastasis and its potential clinical applications. Associate Wang explained the and its implications for treating offering new for These presentations the potential of microorganisms through plant compounds the gut with precise microbiota transplantation to a critical role in future treatments. The Gut Session highlighted a range of cutting-edge research, how the gut microbiome disease mechanisms and innovative approaches (Figure The presentations covered topics from research to clinical applications, focusing on the complex relationships between gut microbiota and disease as well as One led by Prof. team and in was the first to that specific bacterial produced by gut strains can liver The team developed targeted the and opening new avenues for Professor Jin team the probiotics from the of in the The study that probiotics can disease by and acid The team developed novel strategies for the of from and reported by Associate Professor sequencing to the crucial role of gut microbiota in drug resistance The study that gut in These microbes and the in cells, promoting drug resistance and tumor This provides insights into how gut microbiota interactions drive drug resistance through metabolic These studies not only understanding of the intricate between gut microbiota and but also a crucial scientific for the development of more treatment The One Health Session featured presentations that emphasized the of human, animal, and environmental highlighting the of interdisciplinary collaboration to challenges (Figure Professor Wang the of antimicrobial in and how these have into major of resistance These resistance genes, which in the environment treatment and to the of a to human and public the of the in is critical for the development and of antibiotic resistance. 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Topics covered plant microbial ecology, and innovative applications in medicine and (Figure One presentation was delivered by Associate Professor Liu, who discussed with analysis to the mechanisms of plant gene functions He emphasized that high-throughput sequencing technologies have increased the of plant this data to gene function a this approach the for future and Associate Professor introduced novel strategies for microbial in Using innovative and techniques as and the team and a of microbial including with and This research not only the microbial diversity in but also highlighted their potential to and presentations included Associate Professor on the role of in cancer Professor research on the diversity and functions of and Associate Professor of bacterial epigenetic These studies the of omics research in advancing understanding of biological processes and new technologies. The session the of omics technologies, from research to practical applications, offering new and solutions in such as ecology, and The International Session featured three keynote focusing on advancements in scientific collaboration and technological innovation (Figure Li from the National Science Center presented on the International Human and the International These to collaboration and in research. Li emphasized the of team in scientific and research an she worldwide to more in international academic to advancements in the field of from the Institute of at the Chinese Academy of Agricultural Sciences provided an in-depth on international including and the These are to tools and methods to improving the and of microbiome for the of a to and promote omics technology for international collaboration to enhance and within the research community and CTO of a focused on sequencing and bioinformatics technologies. 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Following the the Chief Editor Shuangjiang Liu presented to the and Prof. Liu the discussions editorial the in the growth, identifying and an to the and The Journal featured five covering of journal and editorial Director of provided an overview of the journal, which on data research in life and in a wide of from to like imaging, and The journal also on data tools, and alongside research and highlighted and key to Professor Executive of the journal, discussed its role as a leading journal by the National Center for and the Chinese for by University in omics, bioinformatics, and related fields. provided insights into and as a key journal for Science and Technology Professor from presented on the of academic journals, including Advanced In her she a do three of the attendees that their was to share their This how the to share a major scientific research. 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