Gut and oral microbiota associations with viral mitigation behaviors during the COVID-19 pandemic

Imposition of social and health behavior mitigations are important control measures in response to the coronavirus disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Although postulated that these measures may impact the human microbiota including losses in diversity from heightened hygiene and social distancing measures, this hypothesis remains to be tested. Other impacts on the microbiota and host mental and physical health status associations from these measures are also not well-studied. Here we examine changes in stool and oral microbiota by analyzing 16S rRNA gene sequence taxonomic profiles from the same individuals during pre-pandemic (before March 2020) and early pandemic (May-November 2020) phases. During the early pandemic phase, individuals were also surveyed using questionnaires to report health histories, anxiety, depression, sleep and other lifestyle behaviors in a cohort of predominantly Caucasian adults (mean age = 61.5 years) with the majority reporting at least one underlying co-morbidity. We identified changes in microbiota (stool n = 288; oral n = 89) between pre-pandemic and early pandemic time points from the same subject and associated these differences with questionnaire responses using linear statistical models and hierarchical clustering of microbiota composition coupled to logistic regression. While a trend in loss of diversity was identified between pre-pandemic and early pandemic time points it was not statistically significant. Paired difference analyses between individuals identified fewer significant changes between pre-pandemic and early pandemic microbiota in those who reported fewer comorbidities. Cluster transition analyses of stool and saliva microbiota determined most individuals remained in the same cluster assignments from the pre-pandemic to early pandemic period. Individuals with microbiota that shifted in composition, causing them to depart a pre-pandemic cluster, reported more health issues and pandemic-associated worries. Collectively, our study identified that stool and saliva microbiota from the pre-pandemic to early pandemic periods largely exhibited ecological stability (especially stool microbiota) with most associations in loss of diversity or changes in composition related to more reported health issues and pandemic-associated worries. Longitudinal observational cohorts are necessary to monitor the microbiome in response to pandemics and changes in public health measures.

针对由严重急性呼吸综合征冠状病毒2型（Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2）引发的新型冠状病毒肺炎（coronavirus disease 2019, COVID-19）大流行，实施社交与健康行为干预措施是重要的防控手段。尽管有假说提出，强化卫生措施与社交距离等干预手段可能会对人类微生物群（human microbiota）造成影响，例如降低其多样性，但该假说仍有待验证。此外，此类干预措施对微生物群的其他影响，以及其与宿主身心健康状况的关联，目前也尚未得到充分研究。本研究通过分析同一批受试者在大流行前（2020年3月前）与大流行早期（2020年5月至11月）两个阶段的16S rRNA基因序列分类学特征（16S rRNA gene sequence taxonomic profiles），探究粪便与口腔微生物群的变化情况。在大流行早期阶段，研究团队还通过问卷对该队列受试者进行了调查，收集其健康史、焦虑、抑郁、睡眠及其他生活方式行为相关信息；该队列以白人成年人群为主，平均年龄为61.5岁，且多数受试者报告存在至少1种基础合并症。研究人员在同一受试者的大流行前与大流行早期两个时间点的样本中，发现了微生物群的变化（粪便样本n=288；口腔样本n=89），并通过线性统计模型（linear statistical models）、微生物群组成层级聚类（hierarchical clustering）结合逻辑回归（logistic regression）分析，将这些差异与问卷应答结果进行关联。尽管研究观察到大流行前与大流行早期两个时间点之间存在微生物群多样性降低的趋势，但该结果未达到统计学显著性（statistically significant）。配对差异分析（paired difference analyses）显示，在报告合并症更少的受试者中，大流行前与大流行早期的微生物群之间的显著差异更少。粪便与唾液微生物群的聚类转换分析（cluster transition analyses）表明，多数受试者在大流行前至大流行早期的阶段中，其微生物群的聚类归属未发生改变。那些微生物群组成发生偏移、脱离原有大流行前聚类的受试者，报告了更多健康问题以及与大流行相关的焦虑情绪。综合来看，本研究发现，从大流行前至大流行早期阶段，受试者的粪便与唾液微生物群整体上呈现生态稳定性（ecological stability，尤以粪便微生物群为甚）；多数与微生物群多样性降低或组成变化相关的关联，均与受试者报告的更多健康问题及大流行相关焦虑情绪有关。后续仍需开展纵向观察队列（longitudinal observational cohorts）研究，以监测微生物群对大流行及公共卫生措施变化的响应情况。