Genome Center, University of California , Davis, CA , USA.
Genome Center, Evolution and Ecology, Medical Microbiology and Immunology, University of California , Davis, CA , USA.
PeerJ. 2014 Dec 9;2:e659. doi: 10.7717/peerj.659. eCollection 2014.
Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some "probiotic" health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 10(9) CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 10(6) and 1.4 × 10(6) CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked. Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbes, beyond probiotics taken as supplements-i.e., ingested with food-are important contributors to the composition, inter-individual variation, and function of our gut microbiota.
人们对粪便中的微生物给予了更多的关注，而对食物中的微生物关注较少。历史上，致力于研究我们所吃的微生物的研究工作主要集中在相当狭窄的范围内，即那些引起疾病的微生物和那些被认为具有某些“益生菌”健康益处的微生物。人们对存在于典型美国饮食中的摄入微生物群落的影响知之甚少，甚至基本问题，如哪些微生物、它们有多少、它们在饮食和每餐之间有多大差异，都没有得到回答。为了估计通过食物和饮料摄入的微生物的平均总量及其在三种不同饮食模式下的每日膳食计划中的组成，我们对三种不同饮食模式的微生物群进行了特征描述。分析的三种饮食模式为：（1）普通美国人（AMERICAN）：专注于方便食品，（2）美国农业部推荐（USDA）：强调水果和蔬菜、瘦肉、奶制品和全谷物，以及（3）纯素（VEGAN）：不包括所有动物产品。膳食在家中厨房准备或在餐厅购买并混合，然后进行微生物分析，包括有氧、厌氧、酵母和霉菌平板计数以及 16S rRNA PCR 调查分析。基于平板计数，USDA 膳食计划的微生物总量最高，每天为 1.3×10(9)CFU，其次是 VEGAN 膳食计划和 AMERICAN 膳食计划，每天分别为 6×10(6)和 1.4×10(6)CFU。三种饮食模式之间的多样性没有显著差异。个体膳食根据与饮食模式无关的分类组成聚类。例如，富含乳酸菌的膳食来自三种饮食模式。一些分类群与膳食的营养含量相关。使用 PICRUSt 进行预测代谢组学分析表明，三种饮食模式之间以及基于生熟分类的膳食之间，一些功能 KEGG 类别存在差异。需要进一步研究以确定摄入的微生物对肠道微生物群的影响、食物、膳食和饮食之间的变化程度，以及饮食微生物对人类健康的影响程度。这些问题的答案将揭示摄入的微生物是否除了作为补充剂摄入的益生菌（即随食物摄入）之外，是否是肠道微生物群组成、个体间变异性和功能的重要贡献者。
