Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
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DOI：
10.1128/msystems.00149-20
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发表时间：
2019-05
期刊：
影响因子：
6.4
通讯作者：
Brittany A. Niccum;E. Kastman;Nicole Kfoury;A. Robbat;B. Wolfe
中科院分区：
文献类型：
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作者：
Brittany A. Niccum;E. Kastman;Nicole Kfoury;A. Robbat;B. Wolfe
我们的工作表明，用于构建微生物组的特定微生物菌株可以影响该系统的物种组成、扰动响应和功能输出。这些发现表明，单靠16S rRNA基因分类图谱预测微生物群落动态的潜力可能有限，因为它们通常不能捕捉菌株水平的多样性。来自我们人工合成社区的观察还表明，菌株水平的多样性有可能推动表面成熟奶酪的美学和质量的变异性。摘要多样性可以在微生物物种中产生基因组和表型菌株水平的多样性。这种微多样性在种群中得到了广泛的认可，但微生物菌株水平多样性在社区一级的后果特征很差。使用奶酪皮模型系统，我们测试了来自不同地理区域的微生物群的菌株多样性是否影响组装动力学和功能输出。我们首先从美国和欧洲不同地区生产的九种干酪中分离出相同的三种细菌(金黄色葡萄球菌、橙色短杆菌和营养短杆菌)，以构建由相同三种细菌的不同菌株组成的九个合成微生物群落。比较基因组学确定了不同的系统发育集群和基因组内容在九个合成群落中的显著差异。当我们用最初相同的成分组装每个合成群落时，群落结构随着时间的推移而分化，导致群落具有不同的优势类群。分类上相同的群落对非生物(高盐)和生物(真菌青霉)扰动表现出不同的反应，一些群落没有反应，而另一些群落的组成发生了很大的变化。还观察到9个群落的功能差异，色素产生(从淡黄色到橙色)和从果皮释放出的挥发性有机化合物组成(从坚果到硫磺)有显著差异。重要性我们的工作表明，用于构建微生物组的特定微生物菌株可以影响该系统的物种组成、扰动响应和功能输出。这些发现表明，单靠16S rRNA基因分类图谱预测微生物群落动态的潜力可能有限，因为它们通常不能捕捉菌株水平的多样性。来自我们人工合成社区的观察还表明，菌株水平的多样性有可能推动表面成熟奶酪的美学和质量的变异性。
Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses. ABSTRACT Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system, we tested whether strain diversity across microbiomes from distinct geographic regions impacts assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe to construct nine synthetic microbial communities consisting of distinct strains of the same three bacterial species. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine synthetic communities. When we assembled each synthetic community with initially identical compositions, community structure diverged over time, resulting in communities with different dominant taxa. The taxonomically identical communities showed differing responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine communities, with significant variation in pigment production (light yellow to orange) and in composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury). IMPORTANCE Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses.