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

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.

Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota

“…It suggested that there were strong antagonistic relationships between probiotics and indigenous gut microbes, which were more intense in mice. This is consistent with the results of the previous studies 22 . However, correlation analysis revealed that the number and magnitude of local adaptive SNVs were greatly related to the host environment, and which probiotic strain(s) have been supplemented.…”

“…To mitigate the potential effect of confounding factors, such as individuality in the gut microbiome, in our analyses, six probiotic studies were focused, including Bifidobacterium longum AH1206 ( B. longum AH1206) 7 , Supherb Bio-25 19 , L. rhamnosus GG 20 , Probio-Fit 21 , L. plantarum HNU082 22 and Lactobacillus casei Zhang ( L. casei Zhang) where host participants had paired/repeated microbiome measurements before and after the probiotic intervention. The correlation pattern between nSNVs and the beta diversity of gut microbiota was highly specific to what probiotic strains had been consumed (Fig.…”

“…Following the data curation process above (Supplementary Fig. 3 ), we finally pinpointed 11 probiotic studies, a total of 421 fecal samples, 224 probiotic-treatment individuals, and 197 placebo control that were included in our meta-analysis 7 , 8 , 10 , 18 – 20 , 22 , 36 – 38 (Tables 1 and 2 ). The study was approved by the Ethical Committee; for human participants, they provided informed consent before they enrolled in the study.…”

Gut microbe Lactiplantiballus plantarum undergoes different evolutionary trajectories between insects and mammals

“…Among these, four genes belong to the phosphotransferases system (PTS), a highly conserved bacterial phosphotransferase cascade whose components modulate many cellular functions in response to carbohydrate availability (Deutscher et al, 2006) and which has already been observed to be over-expressed or mutated in other mouse gut colonization experiments (Barreto et al, 2020; Marco et al, 2009; Zhang et al, 2013). This is in line with a recent study showing that L. plantarum convergently evolves across vertebrate animal hosts (i.e., human, mouse, zebrafish) by acquiring mutations primarily modulating carbohydrate utilization and acid tolerance (Huang et al, 2021).…”

Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes

“…LBTs face many challenges to survival in the luminal environment, both from the host (e.g., peristalsis, innate and adaptive immunity) and other native microorganisms (e.g., competition, niche availability) ( Walker and Owen, 1990 ). Probiotic strains not adapted to the luminal environment cannot easily compete with microbes that have adapted to their specific luminal niche over thousands of generations ( Huang et al, 2021 ). This phenomenon is apparent in most patients who have received fecal microbiota transplant, where the individual’s native microorganisms return and largely, or completely, displace the transplanted microbes ( Li et al, 2016 ).…”