Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities.

IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Francesca De Filippis, Vincenzo Valentino, Min Yap, Raul Cabrera-Rubio, Coral Barcenilla, Niccolò Carlino, José F Cobo-Díaz, Narciso Martín Quijada, Inés Calvete-Torre, Patricia Ruas-Madiedo, Carlos Sabater, Giuseppina Sequino, Edoardo Pasolli, Martin Wagner, Abelardo Margolles, Nicola Segata, Avelino Álvarez-Ordóñez, Paul D Cotter, Danilo Ercolini
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Abstract

The resident microbiome in food industries may impact on food quality and safety. In particular, microbes residing on surfaces in dairy industries may actively participate in cheese fermentation and ripening and contribute to the typical flavor and texture. In this work, we carried out an extensive microbiome mapping in 73 cheese-making industries producing different types of cheeses (fresh, medium and long ripened) and located in 4 European countries. We sequenced and analyzed metagenomes from cheese samples, raw materials and environmental swabs collected from both food contact and non-food contact surfaces, as well as operators' hands and aprons. Dairy plants were shown to harbor a very complex microbiome, characterized by high prevalence of genes potentially involved in flavor development, probiotic activities, and resistance to gastro-intestinal transit, suggesting that these microbes may potentially be transferred to the human gut microbiome. More than 6100 high-quality Metagenome Assembled Genomes (MAGs) were reconstructed, including MAGs from several Lactic Acid Bacteria species and putative new species. Although microbial pathogens were not prevalent, we found several MAGs harboring genes related to antibiotic resistance, highlighting that dairy industry surfaces represent a potential hotspot for antimicrobial resistance (AR) spreading along the food chain. Finally, we identified facility-specific strains that can represent clear microbial signatures of different cheesemaking facilities, suggesting an interesting potential of microbiome tracking for the traceability of cheese origin.

Abstract Image

乳业微生物组图谱揭示了具有益生菌和生物保护活性的新物种和新基因。
食品工业中的常驻微生物群可能会影响食品质量和安全。特别是,乳制品工业表面的微生物可能会积极参与奶酪的发酵和成熟过程,并对奶酪的典型风味和口感做出贡献。在这项工作中,我们对欧洲 4 个国家生产不同类型奶酪(新鲜奶酪、中熟奶酪和长熟奶酪)的 73 家奶酪生产企业进行了广泛的微生物组图谱绘制。我们对奶酪样品、原材料和从食品接触面和非食品接触面以及操作人员的手和围裙上采集的环境拭子中的元基因组进行了测序和分析。结果表明,乳制品厂蕴藏着非常复杂的微生物群,其特点是可能参与风味开发、益生菌活性和抗胃肠道转运的基因的高流行率,这表明这些微生物有可能转移到人类肠道微生物群中。研究人员重建了 6100 多个高质量的元基因组组装基因组(MAGs),包括几个乳酸菌物种和推测的新物种的 MAGs。虽然微生物病原体并不普遍,但我们发现了几个携带抗生素耐药性相关基因的 MAGs,这表明乳制品工业表面是抗菌素耐药性(AR)沿食物链传播的潜在热点。最后,我们还发现了不同设施的特异性菌株,它们可以代表不同奶酪制作设施的明显微生物特征,这表明微生物组追踪在奶酪来源追溯方面具有有趣的潜力。
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来源期刊
npj Biofilms and Microbiomes
npj Biofilms and Microbiomes Immunology and Microbiology-Microbiology
CiteScore
12.10
自引率
3.30%
发文量
91
审稿时长
9 weeks
期刊介绍: npj Biofilms and Microbiomes is a comprehensive platform that promotes research on biofilms and microbiomes across various scientific disciplines. The journal facilitates cross-disciplinary discussions to enhance our understanding of the biology, ecology, and communal functions of biofilms, populations, and communities. It also focuses on applications in the medical, environmental, and engineering domains. The scope of the journal encompasses all aspects of the field, ranging from cell-cell communication and single cell interactions to the microbiomes of humans, animals, plants, and natural and built environments. The journal also welcomes research on the virome, phageome, mycome, and fungome. It publishes both applied science and theoretical work. As an open access and interdisciplinary journal, its primary goal is to publish significant scientific advancements in microbial biofilms and microbiomes. The journal enables discussions that span multiple disciplines and contributes to our understanding of the social behavior of microbial biofilm populations and communities, and their impact on life, human health, and the environment.
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