Dai Lin, Kou Hedan, Xia Yao, Wen Xiujun, Gao Jianpeng, Ma Zhanshan Sam
Faculty of Science, Kunming University of Science and Technology, Kunming, China.
Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China.
PeerJ. 2017 Jun 28;5:e3383. doi: 10.7717/peerj.3383. eCollection 2017.
Colorectal cancer (CRC) is the third commonest malignant tumor. Previous studies have revealed that the composition change of the human gut microbiome, measured by community diversity, is associated with the progression of CRC. However, a further question, whether or not the mechanism of community assembly and diversity maintenance of the gut microbiome is influenced by CRC has not been addressed. To address this question, we applied Hubbell's neutral theory for biodiversity to reanalyze the dataset from Wang et al.'s (2012) study of the gut microbiome sampled from CRC patients and healthy individuals. Our reanalysis presents two important findings. Firstly, our analysis demonstrated that only around 4% () samples (in total of both the CRC and control groups) have their species abundance distribution (SAD) satisfied the prediction of the neutral theory null model. No significant difference in the number of the samples satisfying the neutral null model was detected between the healthy individuals and CRC patients, suggesting that the nature or mechanism of community assembly and diversity maintenance of the gut microbiome is not significantly influenced by CRC. That is, the stochasticity of survival, reproduction and migration of gut microbes, as implied by the neutral theory model, does not play a significant role in shaping the community assembly and diversity maintenance. We further infer that the alternative hypothesis to the neutral null model, i.e., the deterministic should be the driving forces that shape the assembly and diversity maintenance of the gut microbiome in both the healthy individuals and CRC patients. Secondly, although CRC does not seem to influence the nature of community assembly, we postulate that it may indirectly influence the outcome (i.e., the community composition as measured by community diversity) of the community assembly, possibly by influencing niche differentiations. This postulation is supported by our second finding: the diversity of the gut microbiome in CRC patients is significantly lower than that in the healthy individuals as demonstrated by the fundamental diversity parameter () of the neutral theory model. This second finding offers an independent confirmation of the relationship between the CRC disease and diversity of the gut microbiome, about which existing studies have presented conflicting evidences. Finally, we suggest that hybrid modeling which integrates both the neutral and niche theories should be explored in future studies to further understanding of the CRC influence on the human gut microbiome.
结直肠癌（CRC）是第三大常见恶性肿瘤。先前的研究表明，通过群落多样性衡量的人类肠道微生物组组成变化与CRC的进展相关。然而，一个进一步的问题，即肠道微生物群落组装和多样性维持机制是否受CRC影响尚未得到解决。为了解决这个问题，我们应用Hubbell的生物多样性中性理论重新分析了Wang等人（2012年）对从CRC患者和健康个体中采集的肠道微生物组的研究数据集。我们的重新分析得出了两个重要发现。首先，我们的分析表明，只有约4%（）的样本（CRC组和对照组总计）其物种丰度分布（SAD）符合中性理论零模型的预测。在健康个体和CRC患者之间，满足中性零模型的样本数量未检测到显著差异，这表明肠道微生物群落组装和多样性维持的本质或机制不受CRC的显著影响。也就是说，中性理论模型所暗示的肠道微生物生存、繁殖和迁移的随机性在塑造群落组装和多样性维持方面不起重要作用。我们进一步推断，中性零模型的替代假设，即确定性因素应该是塑造健康个体和CRC患者肠道微生物群落组装和多样性维持的驱动力。其次，虽然CRC似乎不影响群落组装的本质，但我们推测它可能间接影响群落组装的结果（即通过群落多样性衡量的群落组成），可能是通过影响生态位分化。我们的第二个发现支持了这一推测：如中性理论模型的基本多样性参数（）所示，CRC患者肠道微生物组的多样性显著低于健康个体。这第二个发现为CRC疾病与肠道微生物组多样性之间的关系提供了独立的证实，现有研究对此关系给出了相互矛盾的证据。最后，我们建议在未来的研究中探索整合中性和生态位理论的混合建模，以进一步了解CRC对人类肠道微生物组的影响。
