Arnold Jason W, Simpson Joshua B, Roach Jeffrey, Kwintkiewicz Jakub, Azcarate-Peril M Andrea
Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, United States.
Department of Chemistry, College of Arts and Sciences, University of North Carolina, Chapel Hill, NC, United States.
Front Microbiol. 2018 Feb 20;9:242. doi: 10.3389/fmicb.2018.00242. eCollection 2018.
Large-scale microbiome studies have established that most of the diversity contained in the gastrointestinal tract is represented at the strain level; however, exhaustive genomic and physiological characterization of human isolates is still lacking. With increased use of probiotics as interventions for gastrointestinal disorders, genomic and functional characterization of novel microorganisms becomes essential. In this study, we explored the impact of strain-level genomic variability on bacterial physiology of two novel human strains (AMC143 and AMC010) of probiotic potential in relation to stress resistance. The strains showed differences with known probiotic strains ( GG, Lc705, and HN001) at the genomic level, including nucleotide polymorphisms, mutations in non-coding regulatory regions, and rearrangements of genomic architecture. Transcriptomics analysis revealed that gene expression profiles differed between strains when exposed to simulated gastrointestinal stresses, suggesting the presence of unique regulatory systems in each strain. physiological assays to test resistance to conditions mimicking the gut environment (acid, alkali, and bile stress) showed that growth of AMC143 was inhibited upon exposure to alkaline pH, while AMC010 and control strain LGG were unaffected. AMC143 also showed a significant survival advantage compared to the other strains upon bile exposure. Reverse transcription qPCR targeting the bile salt hydrolase gene () revealed that AMC143 expressed poorly (a consequence of a deletion in the promoter and truncation of gene in AMC143), while AMC010 had significantly higher expression levels than AMC143 or LGG. Insertional inactivation of the gene in AMC010 suggested that could be detrimental to bacterial survival during bile stress. Together, these findings show that coupling of classical microbiology with functional genomics methods for the characterization of bacterial strains is critical for the development of novel probiotics, as variability between strains can dramatically alter bacterial physiology and functionality.
大规模微生物组研究已经证实，胃肠道中包含的大部分多样性体现在菌株水平；然而，对人类分离株进行详尽的基因组和生理学特征描述仍然缺乏。随着益生菌作为胃肠道疾病干预手段的使用增加，新型微生物的基因组和功能特征描述变得至关重要。在本研究中，我们探讨了菌株水平的基因组变异性对两种具有益生菌潜力的新型人类菌株（AMC143和AMC010）抗逆性相关细菌生理学的影响。这些菌株在基因组水平上与已知的益生菌菌株（GG、Lc705和HN001）存在差异，包括核苷酸多态性、非编码调控区域的突变以及基因组结构重排。转录组学分析表明，当暴露于模拟胃肠道应激时，菌株之间的基因表达谱不同，这表明每个菌株中存在独特的调控系统。测试对模拟肠道环境条件（酸、碱和胆汁应激）抗性的生理学试验表明，AMC143暴露于碱性pH时生长受到抑制，而AMC010和对照菌株LGG不受影响。与其他菌株相比，AMC143在胆汁暴露后也表现出显著的生存优势。针对胆汁盐水解酶基因（）的逆转录qPCR显示，AMC143表达水平较低（这是AMC143中启动子缺失和基因截短的结果），而AMC010的表达水平明显高于AMC143或LGG。AMC010中该基因的插入失活表明，该基因在胆汁应激期间可能对细菌存活有害。总之，这些发现表明，将经典微生物学与功能基因组学方法相结合来表征细菌菌株对于新型益生菌的开发至关重要，因为菌株之间的变异性可以显著改变细菌的生理学和功能。
