High-fidelity gut metagenome: A new insight of identification of functional probiotics

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.