Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut

Jicheng Wang,Wenjun Liu,Heping Zhang,Zhihong Sun,Jiachao Zhang

doi:10.1038/s41522-021-00227-2

Abstract

Little is known about the replication and dynamic transcription of probiotics during their “passenger” journey in the human GI tract, which has therefore limited the understanding of their probiotic mechanisms. Here, metagenomic and metatranscriptomic sequencing was used to expose the in vivo expression patterns of the probiotic Lactobacillus casei Zhang (LcZ), which was compared with its in vitro growth transcriptomes, as well as the dynamics of the indigenous microbiome response to probiotic consumption. Extraction of the strain-specific reads revealed that replication and transcripts from the ingested LcZ were increased, while those from the resident L. casei strains remained unchanged. Mapping of all sequencing reads to LcZ genome showed that gene expression in vitro and in vivo differed dramatically. Approximately 39% of mRNAs and 45% of sRNAs of LcZ well-expressed were repressed after ingestion into human gut. The expression of ABC transporter genes and amino acid metabolism genes was induced at day 14 of ingestion, and genes for sugar and SCFA metabolism were activated at day 28 of ingestion. Expression of rli28c sRNA with peaked expression during the in vitro stationary phase was also activated in the human gut; this sRNA repressed LcZ growth and lactic acid production in vitro. However, the response of the human gut microbiome to LcZ was limited and heterogeneous. These findings implicate the ingested probiotic has to change its transcription patterns to survive and adapt in the human gut, and the time-dependent activation patterns indicate highly dynamic cross-talk between the probiotic and human gut microbes.

Highlights

Probiotics are defined as live microorganisms that confer health benefits to the host when present in adequate amounts[1], which are one of the most commonly consumed dietary supplements.The concept of probiotic consumption, referring to dietary live bacteria supplementation, has sustained the continuous growth of the market[2,3]
The transcription pattern of Lactobacillus in vitro and in the murine gut has been investigated[32,33], exploring the fate of ingested probiotics thoroughly at the transcriptional level remains a challenge in the human gut
To the best of our knowledge, this study presented the first effort to profile the replication and transcription of mRNAs and small RNA (sRNA) of probiotic and resident Lactobacillus in the human gut by extracting the transcripts of probiotic bacteria from metatranscriptomic sequencing reads

Summary

Introduction

Probiotics are defined as live microorganisms that confer health benefits to the host when present in adequate amounts[1], which are one of the most commonly consumed dietary supplements.The concept of probiotic consumption, referring to dietary live bacteria supplementation, has sustained the continuous growth of the market[2,3]. Another study mapped meta-transcriptomic reads obtained from fecal samples from elderly volunteers onto the probiotic L. rhamnosus GG, showing high expression of LGG at 28 days of ingestion in some elders[23]. We took advantage of the high-throughput metagenomic and metatranscriptomic sequencing reads obtained from fecal samples of healthy young volunteers before and during probiotic ingestion and extracted strain-specific reads to explore the in vivo colonization, replication, and transcription of ingested Lactobacillus casei Zhang (LcZ), a koumiss-derived probiotic lactic acid bacterium, has been demonstrated to improve gut health[24,25].

Results

Conclusion