Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA.
ISME J. 2020 Jun;14(6):1359-1368. doi: 10.1038/s41396-020-0613-7. Epub 2020 Feb 19.
Understanding when and why new species are recruited into microbial communities is a formidable problem with implications for managing microbial systems, for instance by helping us better understand whether a probiotic or pathogen would be expected to colonize a human microbiome. Much theory in microbial temporal dynamics is focused on how phylogenetic relationships between microbes impact the order in which those microbes are recruited; for example, species that are closely related may competitively exclude each other. However, several recent human microbiome studies have observed closely related bacteria being recruited into microbial communities in short succession, suggesting that microbial community assembly is historically contingent, but competitive exclusion of close relatives may not be important. To address this, we developed a mathematical model that describes the order in which new species are detected in microbial communities over time within a phylogenetic framework. We use our model to test three hypothetical assembly modes: underdispersion (species recruitment is more likely if a close relative was previously detected), overdispersion (recruitment is more likely if a close relative has not been previously detected), and the neutral model (recruitment likelihood is not related to phylogenetic relationships among species). We applied our model to longitudinal human microbiome data, and found that for the individuals we analyzed, the human microbiome generally follows the underdispersion (i.e., nepotism) hypothesis. Exceptions were oral communities and the fecal communities of two infants that had undergone heavy antibiotic treatment. None of the datasets we analyzed showed statistically significant phylogenetic overdispersion.
了解新物种何时以及为何被招募到微生物群落中是一个艰巨的问题，这对管理微生物系统具有重要意义，例如，帮助我们更好地理解益生菌或病原体是否有可能定植人类微生物组。微生物时间动态学的许多理论都集中在微生物之间的系统发育关系如何影响这些微生物被招募的顺序上；例如，密切相关的物种可能会相互竞争排斥。然而，最近的几项人类微生物组研究观察到密切相关的细菌在短时间内被招募到微生物群落中，这表明微生物群落的组装是历史偶然的，但密切相关的近亲的竞争排斥可能并不重要。为了解决这个问题，我们开发了一个数学模型，该模型在系统发育框架内描述了新物种在微生物群落中随时间被检测到的顺序。我们使用我们的模型来测试三种假设的组装模式：过分散（如果最近检测到近亲，则物种的招募更有可能）、过分散（如果最近没有检测到近亲，则招募更有可能）和中性模型（招募的可能性与物种之间的系统发育关系无关）。我们将我们的模型应用于纵向人类微生物组数据，发现对于我们分析的个体，人类微生物组通常遵循过分散（即裙带关系）假设。例外是口腔群落和两个接受过大量抗生素治疗的婴儿的粪便群落。我们分析的任何数据集都没有显示出统计学上显著的系统发育过度分散。
