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Journal of Integrative Agriculture  2026, Vol. 25 Issue (4): 0-    DOI: 10.1016/j.jia.2024.05.011
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High-fidelity gut metagenome: A new insight of identification of functional probiotics
Yuhui Wang1†, Peiwen Gao2†, Chenying Li3, Yuxi Lu4, 5, Yubo Zhang2, 6*, Yu Zhou1*, Siyuan Kong2*

1College of Computer Science and Technology, Taiyuan University of Technology, Taiyuan 030024, China

2Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China

3College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China

4School of Life Sciences, Henan University, Kaifeng 475004, China

5Shenzhen Research Institute of Henan University, Shenzhen 518000, China

6Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528225, China

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摘要  益生菌通过调节宿主肠道微生物群落的结构与代谢功能发挥其益处,被认为对人类和动物具有益处。因此,功能性益生菌的鉴定及其特性与适用性的深入探索,对于开发更有效的益生菌产品和制定人类健康与畜牧业领域个性化益生菌治疗策略具有至关重要的意义。然而,受当前测序技术的限制,尤其是在处理具有密切亲缘关系谱系的微生物群落时,使得宏基因组的组装变得复杂,完整的宏基因组组装基因组(cMAGs)的生成受到阻碍。这一限制制约了我们在益生菌菌株水平上的全面解析。因此,本文首先阐述了益生菌通过调节肠道微生物群落的结构和功能对宿主产生的益处,并强调功能性益生菌鉴定的重要性。接着本文按时间顺序详细介绍了益生菌研究中的技术进展,总结了这些技术在益生菌研究中的应用和研究意义,揭示了这些技术如何促进益生菌对肠道微生物群和宿主健康的影响,并阐述了这些技术的优点和缺点。由于这些技术的局限性,研究人员希望通过宏基因组组装获得完整的宏基因组数据。所以,本文深入探讨了基于不同测序技术的宏基因组组装方法和组装软件回顾了这组装方法在鉴定功能性益生菌中的应用和意义,并详细介绍了各种组装技术和软件的优势、局限性、原理以及它们在特定研究场景下的适用性。逐步揭示了随着测序技术与组装软件的不断进步,组装质量如何得以提升。最后我们依据不同的数据类型及各项测序技术和组装软件的特点创新性地总结了高保真度肠道宏基因组组装的程,从而为鉴定功能性益生菌提供了清晰和详细的指导

Abstract  Probiotics are considered to exert beneficial effects in humans and animals by modulating the structure and metabolic functions of the gut microbiota. Therefore, the identification of functional probiotics and in-depth exploration of the characteristics and applicability of probiotics are of paramount significance for the development of more effective probiotic products and the formulation of personalized probiotic treatment strategies in the fields of human health and livestock farming. However, due to current limitations in sequencing technologies and considering that microbial communities may encompass closely related lineages, rendering metagenome assembly complex, the generation of complete metagenome-assembled genomes (cMAGs) is hindered. This limitation constrains our comprehensive resolution at the probiotic strain level. In this review, we summarized the effects of probiotics on gut microbiota balance and host health from a functional perspective. The technical methods of functional probiotics identification were summarized from the technical point of view. Furthermore, we introduced methods for microbial metagenome assembly to elucidate the associated progress and advantages and disadvantages of these approaches. Finally, we highlight more advanced metagenomic assembly techniques that may help us assemble high-fidelity intestinal metagenomes, providing powerful tools for the identification of functional probiotics.
Keywords:  host health       gut microbiota              probiotics              gut metagenome              metagenomic assembly  
Online: 29 May 2024  
Fund: This work was supported by the Guangdong Basic and Applied Basic Research Foundation (No. 2022A1515010766); the Shenzhen Science and Technology Program (Grant No. RCBS20210609104512021 and KCXFZ20201221173205015); the National Natural Science Foundation of China (No. 32202653); the Project Funded by the China Postdoctoral Science Foundation (No. BX2021367 and 2021M703543). .
About author:  #Correspondence Yubo Zhang, E-mail: ribon_001@163.com; Yu Zhou, E-mail: zhouyu@tyut.edu.cn; Siyuan Kong, E-mail: kongsiyuan@caas.cn *These authors contributed equally to this work.

Cite this article: 

Yuhui Wang, Peiwen Gao, Chenying Li, Yuxi Lu, Yubo Zhang, Yu Zhou, Siyuan Kong. 2026. High-fidelity gut metagenome: A new insight of identification of functional probiotics. Journal of Integrative Agriculture, 25(4): 0-.

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