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

Abstract

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.

Gut microbiota in COVID-19: key microbial changes, potential mechanisms and clinical applications

“…Amongst these studies, which originated from different populations in China, USA, Japan, Bangladesh, United Arab Emirates, Portugal, Germany and Hungary, the faecal microbiome of patients with COVID-19 showed decreased bacterial diversity 27 – 30 and reduced abundance of short-chain fatty acid (SCFA)-producing bacteria from the Lachnospiraceae, Ruminococcaceae and Eubacteriaceae families as well as increased opportunistic pathogens from Enterobacteriaceae families 27 – 29 , 31 – 37 compared with the faecal microbiome of healthy individuals. Specifically, the abundance of Faecalibacterium 27 , 28 , 31 , 33 – 35 , 37 , Eubacterium 28 , 34 , 37 , 38 , Coprococcus 27 , 35 , 36 , 38 , Ruminococcus 27 , 28 , 35 , Lachnospira 27 , 35 , 38 and Roseburia 27 , 35 was decreased, whereas that of Enterococcus 32 , 34 – 36 , Rothia 28 , 32 , 35 , 36 and Lactobacillus 27 , 35 , 36 was increased. Intriguingly, a number of studies with a modest sample size of typically ~30 patients have reported that patients with COVID-19 had a distinct gut microbiome composition compared with patients with community-acquired viral pneumonia 39 and influenza virus infection 28 , 35 .…”

Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes

“…Those microbes and their genes, collectively known as the human gut microbiome, modulate host immunity 10 . To date, several studies, based on 16 S rRNA gene sequencing, have demonstrated that the human upper respiratory and gut microbiome are broadly altered in patients with COVID-19 11 – 16 . Although 16 S rRNA gene sequencing provides valuable insights into the general characteristics of the human microbiota, it does not offer the taxonomic resolution needed to capture sufficient sequence variation to discriminate between closely related taxa 17 .…”

Chemotherapy-associated oral microbiome changes in breast cancer patients

“…An in-depth analyses of our results revealed a highly significant increase in the normalized counts of Escherichia/Shigella, Megasphaera, and Prevotella. Escherichia/Shigella is a common oral and intestinal pathogen ( 22 ) also associated with changes in the human microbiome after SARS-CoV-2 infections ( 43 ). Oral Megasphaera was associated with inflammatory illnesses like rheumatoid arthritis and periodontitis ( 44 , 45 ).…”