Bacteria change their metabolic states to increase survival by forming aggregates. Ammonia-oxidizing bacteria also form aggregates in response to environmental stresses. Nitrosomonas mobilis, an ammonia-oxidizing bacterium with high stress tolerance, often forms aggregates mainly in wastewater treatment systems. Despite the high frequency of aggregate formation by N. mobilis, its relationship with survival currently remains unclear. In the present study, aggregates were formed in the late stage of culture with the accumulation of nitrite as a growth inhibitor. To clarify the significance of aggregate formation in N. mobilis Ms1, a transcriptome analysis was performed. Comparisons of the early and late stages of culture revealed that the expression of stress response genes (chaperones and proteases) increased in the early stage. Aggregate formation may lead to stress avoidance because stress response genes were not up-regulated in the late stage of culture during which aggregates formed. Furthermore, comparisons of free-living cells with aggregates in the early stage of culture showed differences in gene expression related to biosynthesis (ATP synthase and ribosomal proteins) and motility and adhesion (flagella, pilus, and chemotaxis). Biosynthesis genes for growth were up-regulated in free-living cells, while motility and adhesion genes for adaptation were up-regulated in aggregates. These results indicate that N. mobilis Ms1 cells adapt to an unfavorable environment and grow through the division of labor between aggregates and free-living cells.

Bacterial persisters are phenotypic variants that survive the treatment of lethal doses of growth-targeting antibiotics without mutations. Although the mechanism underlying persister formation has been studied for decades, how the persister phenotype is switched on and protects itself from antibiotics has been elusive. In this study, we focused on the lactate dehydrogenase gene (ldhA) that was upregulated in an Escherichia coli persister-enriched population. A survival rate assay using an ldhA-overexpressing strain showed that ldhA expression induced persister formation. To identify ldhA-mediated persister formation at the single-cell level, time-lapse microscopy with a microfluidic device was used. Stochastic ldhA expression was found to induce dormancy and tolerance against high-dose ampicillin treatment (500 μg/ml). To better understand the underlying mechanism, we investigated the relationship between ldhA-mediated persister formation and previously reported persister formation through aerobic metabolism repression. As a result, ldhA expression enhanced the proton motive force (PMF) and ATP synthesis. These findings suggest that ldhA-mediated persister formation pathway is different from previously reported persister formation via repression of aerobic metabolism.

本研究では，RNA分解酵素を病原菌に導入するシステムを構築し，新規抗菌薬の開発を目指す。病原菌への導入には，バクテリオファージを用いる。バクテリオファージは，外来遺伝子の導入効率が高く，効率的に外来のRNA分解酵素を病原菌に導入することが可能である。また，宿主認識特異性が高く，従来の抗菌スペクトルが広範な抗菌薬とは異なり，腸内細菌叢破綻の恐れが少ない。本研究では，バクテリオファージを遺伝子組換えしRNA分解酵素を搭載することに成功した。また，バクテリオファージ感染により細胞毒性が見られることを確認した。

細菌感染症医療現場で薬剤耐性菌が問題視されている一方で，製薬業界では多くの企業が抗菌薬の開発から撤退し始めている。本研究では，薬剤耐性菌に適用可能な新規抗菌薬の開発を目指し，RNA分解酵素に注目した。RNA分解酵素は細菌が持つストレス応答機構で，細菌種によりRNA分解酵素の特徴も様々である。特に，RNA分解酵素が認識して切断するRNA配列が異なることや，その切断活性が種により異なることが知られている。本研究では，切断配列や切断活性の異なるRNA分解酵素を大腸菌細胞内でそれぞれ人工的に発現する系を確立し，その毒性を比較した。その結果，大腸菌に最も強い毒性を発揮するRNA分解酵素を特定した。

近年，単一菌種の微生物でも，個々の細胞レベルで異なる表現型を持つことが明らかになってきた。表現型の不均一性に関する研究は，大腸菌のような易培養微生物ばかりで進んでおり，難培養微生物ではほとんど何もわかっていない。そこで，本研究では，難培養微生物である硝化細菌を用いて，表現型の不均一性を評価した。評価方法として，まず，多数のフラスコにおける増殖活性のばらつきの数値化を実施した。さらに本研究では，硝化細菌の中でも培養のしやすい株としにくい株を比較して，培養の難易度と不均一性の大きさの相関について解析をした。その結果，培養のしやすい株よりもしにくい株で不均一性が大きいことが明らかになった。