Mordant Angie, Blakeley-Ruiz J Alfredo, Kleiner Manuel
Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC.
bioRxiv. 2024 Dec 11:2024.12.10.627769. doi: 10.1101/2024.12.10.627769.
Diet has strong impacts on the composition and function of the gut microbiota with implications for host health. Therefore, it is critical to identify the dietary components that support growth of specific microorganisms . We used protein-based stable isotope fingerprinting (Protein-SIF) to link microbial species in gut microbiota to their carbon sources by measuring each microbe's natural C content (δC) and matching it to the C content of available substrates. We fed gnotobiotic mice, inoculated with a 13 member microbiota, diets in which the C content of all components was known. We varied the source of protein, fiber or fat to observe C signature changes in microbial consumers of these substrates. We observed significant changes in the δC values and abundances of specific microbiota species, as well as host proteins, in response to changes in C signature or type of protein, fiber, and fat sources. Using this approach we were able to show that upon switching dietary source of protein, fiber, or fat (1) some microbial species continued to obtain their carbon from the same dietary component (e.g., protein); (2) some species switched their main substrate type (e.g., from protein to carbohydrates); and (3) some species might derive their carbon through foraging on host compounds. Our results demonstrate that Protein-SIF can be used to identify the dietary-derived substrates assimilated into proteins by microbes in the intestinal tract; this approach holds promise for the analysis of microbiome substrate usage in humans without the need of substrate labeling.
The gut microbiota plays a critical role in the health of animals including humans, influencing metabolism, the immune system, and even behavior. Diet is one of the most significant factors in determining the function and composition of the gut microbiota, but our understanding of how specific dietary components directly impact individual microbes remains limited. We present the application of an approach that measures the carbon isotope "fingerprint" of proteins in biological samples. This fingerprint is similar to the fingerprint of the substrate used to make the proteins. We describe how we used this approach in mice to determine which dietary components specific intestinal microbes use as carbon sources to make their proteins. This approach can directly identify components of an animal's diet that are consumed by gut microbes.
饮食对肠道微生物群的组成和功能有重大影响，进而影响宿主健康。因此，确定支持特定微生物生长的饮食成分至关重要。我们使用基于蛋白质的稳定同位素指纹分析（Protein-SIF），通过测量每种微生物的天然碳含量（δC）并将其与可用底物的碳含量相匹配，将肠道微生物群中的微生物物种与其碳源联系起来。我们给接种了由13种微生物组成的微生物群的无菌小鼠喂食所有成分碳含量已知的饮食。我们改变蛋白质、纤维或脂肪的来源，以观察这些底物的微生物消费者的碳特征变化。我们观察到，随着碳特征或蛋白质、纤维和脂肪来源类型的变化，特定微生物群物种以及宿主蛋白质的δC值和丰度发生了显著变化。使用这种方法，我们能够证明，在改变蛋白质、纤维或脂肪的饮食来源时：（1）一些微生物物种继续从相同的饮食成分（如蛋白质）中获取碳；（2）一些物种改变了其主要底物类型（如从蛋白质变为碳水化合物）；（3）一些物种可能通过摄取宿主化合物来获取碳。我们的结果表明，Protein-SIF可用于识别肠道微生物在蛋白质中同化的饮食衍生底物；这种方法有望用于分析人类微生物群的底物利用情况，而无需进行底物标记。
肠道微生物群在包括人类在内的动物健康中起着关键作用，影响新陈代谢、免疫系统甚至行为。饮食是决定肠道微生物群功能和组成的最重要因素之一，但我们对特定饮食成分如何直接影响个体微生物的理解仍然有限。我们展示了一种测量生物样品中蛋白质碳同位素“指纹”的方法的应用。这个指纹类似于用于制造蛋白质的底物的指纹。我们描述了我们如何在小鼠中使用这种方法来确定特定肠道微生物用作碳源来制造其蛋白质的饮食成分。这种方法可以直接识别肠道微生物消耗的动物饮食成分。
