Data_Sheet_1_Dysbiosis of Oral and Gut Microbiomes in SARS-CoV-2 Infected Patients in Bangladesh: Elucidating the Role of Opportunistic Gut Microbes.docx

Coronavirus disease-2019 (COVID-19) is an infectious disease caused by SARS-CoV-2 virus. The microbes inhabiting the oral cavity and gut might play crucial roles in maintaining a favorable gut environment, and their relationship with SARS-CoV-2 infection susceptibility and severity is yet to be fully explored. This study investigates the diversity and species richness of gut and oral microbiota of patients with COVID-19, and their possible implications toward the severity of the patient's illness and clinical outcomes. Seventy-four (n = 74) clinical samples (gut and oral) were collected from 22 hospitalized patients with COVID-19 with various clinical conditions and 15 apparently healthy people (served as controls). This amplicon-based metagenomic sequencing study yielded 1,866,306 paired-end reads that were mapped to 21 phyla and 231 classified genera of bacteria. Alpha and beta diversity analyses revealed a distinct dysbiosis of the gut and oral microbial communities in patients with COVID-19, compared to healthy controls. We report that SARS-CoV-2 infection significantly reduced richness and evenness in the gut and oral microbiomes despite showing higher unique operational taxonomic units in the gut. The gut samples of the patients with COVID-19 included 46 opportunistic bacterial genera. Escherichia, Shigella, and Bacteroides were detected as the signature genera in the gut of patients with COVID-19 with diarrhea, whereas a relatively higher abundance of Streptococcus was found in patients with COVID-19 having breathing difficulties and sore throat (BDST). The patients with COVID-19 had a significantly lower abundance of Prevotella in the oral cavity, compared to healthy controls and patients with COVID-19 without diabetes, respectively. The altered metabolic pathways, including a reduction in biosynthesis capabilities of the gut and oral microbial consortia after SARS-CoV-2 infection, were also observed. The present study may, therefore, shed light on interactions of SARS-CoV-2 with resilient oral and gut microbes which might contribute toward developing microbiome-based diagnostics and therapeutics for this deadly pandemic disease.

新型冠状病毒肺炎2019（COVID-19）是由SARS-CoV-2病毒引起的一种传染性疾病。口腔和肠道中的微生物可能在对维持有利的肠道环境方面发挥关键作用，而它们与SARS-CoV-2感染易感性和严重程度的关系尚待充分探讨。本研究旨在探究COVID-19患者肠道和口腔微生物群的多样性和物种丰富度，及其对疾病严重程度和临床结果的可能影响。研究者从22名患有COVID-19且病情各异的住院患者（包括肠道和口腔样本）以及15名看似健康的人（作为对照组）中收集了74（n = 74）个临床样本。基于扩增子技术的宏基因组测序研究产生了1,866,306对端序列读数，这些读数被映射到21个门和231个已分类的细菌属。α-和β-多样性分析显示，与健康对照组相比，COVID-19患者的肠道和口腔微生物群表现出明显的失调。研究发现，尽管肠道中显示出更高的独特操作分类单元，SARS-CoV-2感染显著降低了肠道和口腔微生物群的丰富度和均匀度。COVID-19患者的肠道样本中包含46个条件致病菌属。在患有腹泻的COVID-19患者肠道中检测到埃希菌、志贺菌和拟杆菌为标志性属，而在呼吸困难及咽喉痛（BDST）的COVID-19患者中，发现相对较高的链球菌丰度。与健康对照组以及无糖尿病的COVID-19患者相比，COVID-19患者的口腔中普雷沃菌丰度显著降低。此外，还观察到SARS-CoV-2感染后肠道和口腔微生物群落生物合成能力的降低等代谢途径的改变。因此，本研究可能有助于揭示SARS-CoV-2与具有弹性的口腔和肠道微生物之间的相互作用，这可能有助于开发基于微生物组的COVID-19这种致命流行病的诊断和治疗方法。