The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. (RNA-Seq). The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. (RNA-Seq)

Understanding how the human gut microbiota and host are impacted by probiotic bacterial strains requires carefully controlled studies in humans, and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks prior to, 7 weeks during, and 4 weeks following consumption of a commercially-available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were studied prior to and after gavage with all five sequenced FMP strains. Overall design: 73 samples total. Evaluation of changes in a model community's metatranscriptome over time after exposure to a consortium of 5 fermented milk product (FMP) strains (40 samples); evaluation of the gene expression of the FMP strains in other in vitro conditions, including MRS medium (B. animalis subsp. lactis only, 4 samples) and a commercial FMP fermentation (all 5 strains, 6 samples); evaluation of the gene expression of native human microbiomes before and after the consumption of a commercial FMP (23 samples).

探究益生菌菌株对人类肠道菌群 (gut microbiota) 及其宿主 (host) 的影响，需开展严格受控的人体研究，同时辅以肠道生态系统小鼠模型研究——后者可规避人类研究中难以控制的混杂变量 (confounding variables)。因此，本研究通过重复采样，对成年女性同卵双胞胎对的粪便宏基因组 (fecal microbiomes) 与宏转录组 (metatranscriptomes) 进行表征：采样时间点分别为商用发酵乳饮品 (FMP) 摄入前4周、摄入期间7周以及摄入后4周。该商用发酵乳饮品 (FMP) 含有由动物双歧杆菌乳亚种 (Bifidobacterium animalis subsp. lactis)、两株德氏乳杆菌保加利亚亚种 (Lactobacillus delbrueckii subsp. bulgaricus)、乳酸乳球菌乳脂亚种 (Lactococcus lactis subsp. cremoris) 以及嗜热链球菌 (Streptococcus thermophilus) 组成的复合菌株。此外，本研究还针对携带由15种物种组成的人类肠道菌群模型的悉生小鼠 (gnotobiotic mice) 展开研究：该模型菌群的基因组共包含58399个已知或预测的蛋白编码基因 (protein-coding genes)，分别在以全部5株已测序FMP菌株灌胃前后进行分析。整体实验设计：总计73份样本。具体包括：① 暴露于由5株FMP菌株组成的复合菌株后，模型菌群宏转录组随时间的变化分析 (40份样本)；② FMP菌株在其他体外 (in vitro) 培养条件下的基因表达分析，包括MRS培养基 (仅针对动物双歧杆菌乳亚种，4份样本) 与商用FMP发酵体系 (全部5株菌株，6份样本)；③ 健康人类原生肠道菌群在商用FMP摄入前后的基因表达分析 (23份样本)。