Jarvis Karen G, Daquigan Ninalynn, White James R, Morin Paul M, Howard Laura M, Manetas Julia E, Ottesen Andrea, Ramachandran Padmini, Grim Christopher J
Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, United States.
Resphera Biosciences, Baltimore, MD, United States.
Front Microbiol. 2018 Oct 23;9:2540. doi: 10.3389/fmicb.2018.02540. eCollection 2018.
Food microbiome composition impacts food safety and quality. The resident microbiota of many food products is influenced throughout the farm to fork continuum by farming practices, environmental factors, and food manufacturing and processing procedures. Currently, most food microbiology studies rely on culture-dependent methods to identify bacteria. However, advances in high-throughput DNA sequencing technologies have enabled the use of targeted 16S rRNA gene sequencing to profile complex microbial communities including non-culturable members. In this study we used 16S rRNA gene sequencing to assess the microbiome profiles of plant and animal derived foods collected at two points in the manufacturing process; post-harvest/pre-retail (cilantro) and retail (cilantro, masala spice mixes, cucumbers, mung bean sprouts, and smoked salmon). Our findings revealed microbiome profiles, unique to each food, that were influenced by the moisture content (dry spices, fresh produce), packaging methods, such as modified atmospheric packaging (mung bean sprouts and smoked salmon), and manufacturing stage (cilantro prior to retail and at retail). The masala spice mixes and cucumbers were comprised mainly of , , and . Cilantro microbiome profiles consisted mainly of , followed by , and low levels of and . The two brands of mung bean sprouts and the three smoked salmon samples differed from one another in their microbiome composition, each predominated by either by or . These data demonstrate diverse and highly variable resident microbial communities across food products, which is informative in the context of food safety, and spoilage where indigenous bacteria could hamper pathogen detection, and limit shelf life.
食品微生物群组成会影响食品安全和质量。许多食品的固有微生物群在从农场到餐桌的整个连续过程中受到养殖方式、环境因素以及食品制造和加工过程的影响。目前，大多数食品微生物学研究依赖于基于培养的方法来鉴定细菌。然而，高通量DNA测序技术的进步使得利用靶向16S rRNA基因测序来分析复杂的微生物群落成为可能，包括不可培养的成员。在本研究中，我们使用16S rRNA基因测序来评估在制造过程中的两个时间点采集的植物源和动物源食品的微生物群概况；收获后/零售前（香菜）和零售时（香菜、马萨拉香料混合物、黄瓜、绿豆芽和烟熏三文鱼）。我们的研究结果揭示了每种食品独特的微生物群概况，这些概况受到水分含量（干香料、新鲜农产品）、包装方法（如气调包装，用于绿豆芽和烟熏三文鱼）以及制造阶段（零售前和零售时的香菜）的影响。马萨拉香料混合物和黄瓜主要由 、 和 组成。香菜的微生物群概况主要由 组成，其次是 ，以及少量的 和 。两个品牌的绿豆芽和三个烟熏三文鱼样本在微生物群组成上彼此不同，每个样本主要由 或 主导。这些数据表明不同食品中存在多样且高度可变的固有微生物群落，这在食品安全以及腐败方面具有参考价值，因为本土细菌可能会妨碍病原体检测并限制保质期。
