Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome

Shi Huang,Dongxue Huo,Pedro Belda-Ferre,Qiyun Zhu,Jiachao Zhang,Congfa Li,Shuaiming Jiang,Victor Cantu,Yang-Yu Liu,Chenchen Ma,Yoshiki Vázquez-Baeza,Celeste Allaband,Mehrbod Estaki,Amir Zarrinpar,Rob Knight

doi:10.1186/s40168-021-01102-0

Abstract

BackgroundImproving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods.ResultsWe combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10–70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice.ConclusionsCollectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans.1TYRt-mQpEqyYou2DA7bqRVideo abstract

Highlights

Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts
Here, Lactiplantibacillus plantarum HNU082 (Lp082) was used as a model strain to compare the adaptive evolution patterns of a probiotic under different host selection pressures
109 bacterial strains of Lp082 were isolated from feces or intestine content of three hosts, out of which 77 isolates were from humans, 25 from mice, and only 7 from zebrafish for the duration of the whole experiment (Fig. 1B, C, Table S1 and Table S2)

Summary

Introduction

Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. The gut-adaptive evolution of a probiotic genome can confer sufficient fitness advantages to engage in interactions with gut residents and host factors [6, 7], which eventually determine if and how long the probiotic can engraft for the intended therapeutic effect. The observed in vivo evolution of probiotics presented novel opportunities to understand or leverage these gut-selective forces for genetic engineering of probiotics for better engraftment outcomes, such as E. coli. Understanding the mechanism behind these adaptations may fundamentally update our knowledge of probiotic evolution and open venues for engineering desired traits of probiotics for humans by simulating evolutionary pressures such as passing them through the gut of an animal host or a similar artificial system. We can further ask if and how the fitness advantages of a probiotic gained from passing through the mouse gut can be stably transferred to a human host resulting in enhanced engraftment outcomes

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Conclusion