Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C., Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs China, Inner Mongolia Agricultural University, Hohhot, China.
School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, Hainan, China.
NPJ Biofilms Microbiomes. 2021 Jul 1;7(1):55. doi: 10.1038/s41522-021-00227-2.
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.
目前对于益生菌在人类胃肠道“乘客”旅程中的复制和动态转录知之甚少，这限制了人们对其益生菌机制的理解。在这里，我们使用宏基因组学和宏转录组学测序来揭示益生菌干酪乳杆菌 Zhang（LcZ）的体内表达模式，将其与体外生长转录组进行比较，并研究了内源性微生物组对益生菌消耗的动态响应。提取菌株特异性读数表明，摄入的 LcZ 复制和转录物增加，而驻留的干酪乳杆菌菌株的转录物保持不变。将所有测序读数映射到 LcZ 基因组上表明，体外和体内的基因表达有很大的不同。大约 39%的 LcZ 高表达的 mRNA 和 45%的 sRNA 在摄入人体肠道后受到抑制。摄入后第 14 天，ABC 转运基因和氨基酸代谢基因的表达被诱导，而摄入后第 28 天，糖和 SCFA 代谢基因被激活。在体外静止期表达峰值最高的 rli28c sRNA 的表达也在人体肠道中被激活；这种 sRNA 抑制了 LcZ 的体外生长和乳酸产生。然而，人体肠道微生物组对 LcZ 的反应是有限的和异质的。这些发现表明，摄入的益生菌必须改变其转录模式才能在人类肠道中生存和适应，并且时间依赖性激活模式表明益生菌和人类肠道微生物之间存在高度动态的相互作用。
