Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria

Each species of intestinal bacteria requires a nutritional source to maintain its population in the intestine. Dietary factors are considered to be major nutrients; however, evidence directly explaining the in situ utilization of dietary factors is limited. Microscale bacterial distribution would provide clues to understand bacterial lifestyle and nutrient utilization. However, the detailed bacterial localization around dietary factors in the intestine remains uninvestigated. Therefore, we explored microscale habitats in the murine intestine by using histology and fluorescent in situ hybridization, focusing on dietary factors. This approach successfully revealed several types of bacterial colonization. In particular, bifidobacterial colonization and adhesion on granular starch was frequently and commonly observed in the jejunum and distal colon. To identify the bacterial composition of areas around starch granules and areas without starch, laser microdissection and next-generation sequencing-based 16S rRNA microbial profiling was performed. It was found that Bifidobacteriaceae were significantly enriched by 4.7 fold in peri-starch areas compared to ex-starch areas. This family solely consisted of Bifidobacterium pseudolongum. In contrast, there was no significant enrichment among the other major families. This murine intestinal B. pseudolongum had starch-degrading activity, confirmed by isolation from the mouse feces and in vitro analysis. Collectively, our results demonstrate the significance of starch granules as a major habitat and potential nutritional niche for murine intestinal B. pseudolongum. Moreover, our results suggest that colonizing bifidobacteria effectively utilize starch from the closest location and maintain the location. This may be a bacterial strategy to monopolize solid dietary nutrients. We believe that our analytical approach could possibly be applied to other nutritional factors, and can be a powerful tool to investigate in vivo relationships between bacteria and environmental factors in the intestine.肠道内的每一种细菌都需要营养源以维持其在肠道中的种群规模。膳食因素被认为是主要的营养来源；然而，直接阐释细菌在肠道原位利用膳食因素的相关证据仍较为匮乏。细菌的微观分布特征可为解析细菌的生活方式与营养利用策略提供线索，但目前学界对肠道内膳食因素周边的细菌精细定位情况仍缺乏研究。为此，本研究以膳食因素为研究重点，采用组织学技术与荧光原位杂交（fluorescent in situ hybridization）方法，探究小鼠肠道内的微观栖息环境。该方法成功揭示了多种细菌定植模式；其中，双歧杆菌在颗粒状淀粉上的定植与黏附现象在空肠与结肠远端中均频繁且普遍地被观测到。为明确淀粉颗粒周边区域与无淀粉区域的细菌组成，研究人员采用激光显微切割（laser microdissection）与基于二代测序（next-generation sequencing）的16S rRNA微生物谱分析（16S rRNA microbial profiling）技术开展实验。结果显示，与无淀粉区域相比，淀粉周边区域的双歧杆菌科（Bifidobacteriaceae）丰度显著提升4.7倍，且该科仅由假长双歧杆菌（Bifidobacterium pseudolongum）构成。与之相对，其余主要细菌科类未出现显著的丰度富集现象。从小鼠粪便中分离得到的该小鼠肠道假长双歧杆菌经体外实验验证，具备淀粉降解活性。综上，本研究结果证实了颗粒状淀粉作为小鼠肠道假长双歧杆菌主要栖息环境与潜在营养生态位的重要意义。此外，研究结果表明定植的双歧杆菌可通过紧邻淀粉颗粒的位置高效利用淀粉并维持该栖息位置，这可能是细菌垄断固体膳食营养的一种生存策略。我们认为本研究采用的分析方法可推广应用于其他膳食营养因素的相关研究，同时亦可作为探究肠道内细菌与环境因子体内互作关系的有力工具。