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

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

doi:10.1186/s40168-021-01102-0

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

Microbiome. 2021 Jun 30;9(1):151. doi: 10.1186/s40168-021-01102-0.

Authors

Shi Huang^#^{1

2

3}, Shuaiming Jiang^#¹, Dongxue Huo^#¹, Celeste Allaband⁴, Mehrbod Estaki², Victor Cantu⁵, Pedro Belda-Ferre^{2

3}, Yoshiki Vázquez-Baeza^{2

3}, Qiyun Zhu^{2

3}, Chenchen Ma¹, Congfa Li^{1

6}, Amir Zarrinpar^{3

7

8}, Yang-Yu Liu⁹, Rob Knight^{10

11

12

13}, Jiachao Zhang^{14

15

16}

Affiliations

¹ School of Food Science and Engineering, Hainan University, Haikou, China.
² UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
³ Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
⁴ Biomedical Sciences Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
⁵ Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
⁶ Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, 570228, China.
⁷ UCSD Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
⁸ VA San Diego Healthcare, 3350 La Jolla Village Dr, San Diego, CA, 92161, USA.
⁹ Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
¹⁰ UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. robknight@ucsd.edu.
¹¹ Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. robknight@ucsd.edu.
¹² Biomedical Sciences Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. robknight@ucsd.edu.
¹³ Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. robknight@ucsd.edu.
¹⁴ School of Food Science and Engineering, Hainan University, Haikou, China. zhjch321123@163.com.
¹⁵ UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. zhjch321123@163.com.
¹⁶ Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, 570228, China. zhjch321123@163.com.

^# Contributed equally.

Abstract

Background: Improving 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.

Results: We 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.

Conclusions: Collectively, 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. Video abstract.

Keywords: Adaptive evolution; Lactiplantibacillus plantarum; Probiotic; Universal strategy.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Video-Audio Media

MeSH terms

Animals
Bifidobacterium
Gastrointestinal Microbiome*
Humans
Mice
Microbiota*
Probiotics*
Zebrafish

Abstract

Publication types

MeSH terms

Grants and funding