研究人员在顽固的益生菌上抬起面纱
For Immediate Release
北卡州立大学的新研究显示progress in gathering information on an important – yet difficult to characterize – human gut bacterium calledBifidobacterium, which is used in many probiotics that help maintain healthy microbiomes. The findings hold promise to help make so-called “good bacteria” even better.
“随着我们的实验室扩展和多样化我们使用的好细菌的类型，我们转向更挑剔的细菌，例如Bifidobacterium,” said Rodolphe Barrangou, the Todd R. Klaenhammer Distinguished Professor of Food, Bioprocessing and Nutrition Sciences at NC State and corresponding author of apaper describing the research published inProceedings of the National Academy of Sciences。“这种细菌比其他细菌更难生长，更难与其他细菌一起工作，但是我们能够做出一些重要的发现，并更多地了解该细菌的健康促进功能的遗传基础。”
“Bifidobacteriumis one of the two main players in the probiotic industry along withLactobacillusNC State Ph.D. Meichen（Echo）Pan说：“在婴儿的结肠中尤其重要。”该论文的学生和第一作者。“但是与Lactobacillus。”
NC State researchers used both the bacterium’s internal CRISPR-Cas system as well as a portable engineered CRISPR effector to make their findings. CRISPR-Cas systems are adaptive immune systems that allow bacteria to withstand attacks from enemies like viruses. These systems have been adapted by scientists to remove or cut and replace specific genetic code sequences.
Bifidobacterium事实证明，有大量的本地CRISPR-CAS系统，其中之一是相对研究的I型I-G系统。
In separate experiments, the researchers used this internal system and a portable Cas effector called a cytosine base editor to resensitize aBifidobacteriumstrain to a common antibiotic – tetracycline. Many bacteria carry natural resistance to antibiotics.
“Restoring antibiotic sensitivity is conceptually and practically important because bacteria can potentially transfer antibacterial resistance to other bacteria in the gut,” Pan said.
研究人员还发现，不同细菌菌株，所谓的单核苷酸多态性或SNP的微小变化似乎反映了菌株表型或特征的巨大差异。
“This was a surprising lesson: One letter difference in strains with genetic codes that are over 99% similar can make huge differences,” Barrangou said. “What genes turn on and how they behave due to their environment can make a huge difference and will require researchers to customize the CRISPR tool to adapt the editing strategy accordingly.”
NC State and the North Carolina Agricultural Foundation supported the work, in a collaborative effort with IFF. Co-authors of the paper include former NC State post-doctoral researcher Claudio Hidalgo-Cantabrana, NC State graduate student Avery Roberts, and former NC State staff scientist Yong Jun Goh, Wesley Morovic of IFF Health and Biosciences, and Kimberly K.O. Walden at the University of Illinois Urbana Champaign.
-Kulikowski-
Note to editors: An abstract of the paper follows.
“Genomic and Epigenetic Landscapes Drive CRISPR-based Genome Editing inBifidobacterium”
作者: Meichen Pan, Claudio Hidalgo-Cantabrana, Avery Roberts, Yong Jun Goh, Rodolphe Barrangou, NC State University; Wesley Morovic, IFF Health and Biosciences; Kimberly K.O. Walden, University of Illinois
Published: July 18, 2022 inProceedings of the National Academy of Sciences
DOI: 10.1073/pnas.2205068119
Abstract:Bifidobacteriumis a commensal bacterial genus ubiquitous in the human gastrointestinal tract, which is associated with a range of health benefits. The advent of CRISPR-based genome editing technologies provides opportunities to investigate the genetics of important bacteria, and transcend the lack of genetic tools in bifidobacteria to study the basis for their health-promoting attributes. Here, we repurpose the endogenous type I-G CRISPR-Cas system and adopt an exogenous CRISPR base editor for genome engineering inB. Animalis亚种。乳酸，证明基因组和表观遗传环境都可以驱动跨菌株的编辑结果。我们对内源性I-G系统进行了重新编程，以筛选自然发生的大量删除，最大27 kb，并在TETW中产生500 bp的删除，以消除四环素的耐药性。优化了CRISPR-Cytosine基础编辑器以安装C•G-TO-T•琥珀色突变以重新敏感多重B. lactisstrains to tetracycline. Remarkably, we uncovered new epigenetic patterns that are distributed unevenly amongB. lactisstrains, despite their genomic homogeneity, that may contribute to editing efficiency variability. Insights were also expanded toBifidobacterium longum subsp. infantisto emphasize the broad relevance of these findings. This study highlights the need to develop individualized CRISPR-based genome engineering approaches for distinct bacterial strains and opens new avenues for engineering of next generation probiotics.
