Department of Microbiology, College of Basic Medical Sciences, Dalian Medical Universitygrid.411971.b, Dalian, China.
Puensum Genetech Institute, Wuhan, China.
Microbiol Spectr. 2022 Oct 26;10(5):e0034822. doi: 10.1128/spectrum.00348-22. Epub 2022 Aug 30.
Rheumatoid arthritis (RA) is influenced by oral and gut bacteria; however, much less is known about the relationship between oral or gut viromes and RA. Here, we performed whole-oral- and whole-gut-virome analyses based on shotgun sequencing of 497 samples. A comparative analysis of the oral and gut viromes in healthy controls and untreated and treated RA patients was performed, and system interaction networks among viruses, bacteria, and RA-associated clinical indices were constructed to address the potential relationship between the virome and RA by principal-coordinate analysis, distance-based redundancy analysis, permutational multivariate analysis, Spearman correlation coefficient analysis, and random-forest model analysis. The results showed that the viromes could be profiled in dental plaque, saliva, and fecal samples, among which saliva had the highest within-sample diversity. Importantly, significantly different diversities and compositions of the oral (i.e., dental plaque and saliva) viromes were observed not only between RA patients and healthy controls but also between untreated and treated RA patients, yet there were relatively minor differences in the gut viromes. Furthermore, to understand how these viruses affected the bacteriome, a virus-bacterium interaction network was constructed from dental plaque, saliva, and fecal samples of RA patients. Additionally, some RA-associated oral taxa, including phage (vOTU70), Bacteroides vulgatus, Lactococcus lactis, Escherichia coli, and Neisseria elongata, were correlated with the RA-related clinical indices. Whole-virome analysis illustrated the potential role of the oral and gut viromes in affecting our body either directly or via bacteria, which characterized neglected and new candidates contributing to the development of RA. Our results demonstrated community variation among dental plaque, saliva, and fecal viromes. In oral and gut samples from untreated and treated RA patients, the perturbance of viral composition and the correlation network of microbes and RA-associated clinical indices might be involved in the pathogenicity of RA. The findings in this study expand the knowledge of the potential role of oral and gut viral communities in the development of RA and may contribute to research on correlations between viruses and other diseases.
类风湿关节炎（RA）受口腔和肠道细菌的影响；然而，关于口腔或肠道病毒组与 RA 之间的关系知之甚少。在这里，我们基于 497 个样本的测序进行了全口腔和全肠道病毒组分析。对健康对照者以及未经治疗和治疗的 RA 患者的口腔和肠道病毒组进行了比较分析，并构建了病毒、细菌和 RA 相关临床指标之间的系统相互作用网络，通过主坐标分析、基于距离的冗余分析、置换多元分析、Spearman 相关系数分析和随机森林模型分析来解决病毒组与 RA 之间的潜在关系。结果表明，病毒组可以在牙菌斑、唾液和粪便样本中进行分析，其中唾液的样本内多样性最高。重要的是，不仅在 RA 患者和健康对照者之间，而且在未经治疗和治疗的 RA 患者之间，口腔（即牙菌斑和唾液）病毒组的多样性和组成存在显著差异，而肠道病毒组的差异相对较小。此外，为了了解这些病毒如何影响细菌组，我们从 RA 患者的牙菌斑、唾液和粪便样本中构建了一个病毒-细菌相互作用网络。此外，一些与 RA 相关的口腔分类群，包括噬菌体（vOTU70）、脆弱拟杆菌、乳酸乳球菌、大肠杆菌和奈瑟菌 elongata，与 RA 相关的临床指标相关。全病毒组分析说明了口腔和肠道病毒组在直接或通过细菌影响我们身体的潜在作用，这突出了一些被忽视的和新的候选者在 RA 发展中的作用。我们的研究结果表明牙菌斑、唾液和粪便病毒组之间存在群落差异。在未经治疗和治疗的 RA 患者的口腔和肠道样本中，病毒组成的扰动以及微生物与 RA 相关临床指标的相关网络可能与 RA 的发病机制有关。本研究的结果扩展了口腔和肠道病毒群落在 RA 发展中的潜在作用的知识，并可能有助于研究病毒与其他疾病之间的关系。
