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

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 vi...

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Autores principales:	Jicheng Wang, Jiachao Zhang, Wenjun Liu, Heping Zhang, Zhihong Sun
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Microbial ecology QR100-130
Acceso en línea:	https://doaj.org/article/1b3100ecaa824b8f9ae0a67f5230177c
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spelling	oai:doaj.org-article:1b3100ecaa824b8f9ae0a67f5230177c2021-12-02T14:34:04ZMetagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut10.1038/s41522-021-00227-22055-5008https://doaj.org/article/1b3100ecaa824b8f9ae0a67f5230177c2021-07-01T00:00:00Zhttps://doi.org/10.1038/s41522-021-00227-2https://doaj.org/toc/2055-5008Abstract 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.Jicheng WangJiachao ZhangWenjun LiuHeping ZhangZhihong SunNature PortfolioarticleMicrobial ecologyQR100-130ENnpj Biofilms and Microbiomes, Vol 7, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbial ecology QR100-130
spellingShingle	Microbial ecology QR100-130 Jicheng Wang Jiachao Zhang Wenjun Liu Heping Zhang Zhihong Sun Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut
description	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.
format	article
author	Jicheng Wang Jiachao Zhang Wenjun Liu Heping Zhang Zhihong Sun
author_facet	Jicheng Wang Jiachao Zhang Wenjun Liu Heping Zhang Zhihong Sun
author_sort	Jicheng Wang
title	Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut
title_short	Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut
title_full	Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut
title_fullStr	Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut
title_full_unstemmed	Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut
title_sort	metagenomic and metatranscriptomic profiling of lactobacillus casei zhang in the human gut
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/1b3100ecaa824b8f9ae0a67f5230177c
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Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut

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