Microbiome analysis revealing microbial interactions and secondary bacterial infections in COVID‐19 patients comorbidly affected by Type 2 diabetes

Abstract

The mortality of coronavirus disease 2019 (COVID‐19) disease is very high among the elderly or individuals having comorbidities such as obesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes the metagenomic features in severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2)‐infected patients with or without type 2 diabetes, to identify the microbial interactions associated with its fatal consequences.This study compared the baseline nasopharyngeal microbiome of SARS‐CoV‐2‐infected diabetic and nondiabetic patients with controls adjusted for age and gender. The metagenomics based on next‐generation sequencing was performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan‐package in R. All three groups possessed significant bacterial diversity and dissimilarity indexes (p < 0.05). Spearman's correlation coefficient network analysis illustrated 183 significant positive correlations and 13 negative correlations of pathogenic bacteria (r = 0.6–1.0, p < 0.05), and 109 positive correlations between normal flora and probiotic bacteria (r > 0.6, p < 0.05). The SARS‐CoV‐2 diabetic group exhibited a significant increase in pathogens and secondary infection‐causing bacteria (p < 0.05) with a simultaneous decrease of normal flora (p < 0.05). The dysbiosis of the bacterial community might be linked with severe consequences of COVID‐19‐infected diabetic patients, although a few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal flora and probiotics through dietary supplementation and excessive inflammation reduction by preventing secondary infections might lead to a better outcome for those comorbid patients.

SARS‐CoV‐2 infection alters the gut microbiome in diabetes patients: A cross‐sectional study from Bangladesh

“…Loss of these commensal bacteria (e.g., Prevotella) from gut microbiomes indicates that Prevotella can act as a local probiotic and counteract SARS-CoV-2 to defend it in patients with COVID-19. 6 In a recent study, the genera Rothia and Shigella were found at elevated levels in the gut microbiomes of SARS-CoV-2 and H1N1 influenza patients, corroborating with the present study's findings. 46 Loss of pathogenic bacterial genera like Porphyromonas and Haemophilus in the gut microbiomes of the COVID-19 diabetes group raises the possibility that other cohabiting bacterial communities may also have adverse effects, such as the loss and deficiency of vital dietary nutrients like minerals and vitamins.…”

“…The bacterial genus Prevotella remained considerably lower in abundance in the gut microbiomes of CD compared to HC, possibly suggesting a decrease in commensal bacteria and counteraction against SARS‐CoV‐2 infections. Loss of these commensal bacteria (e.g., Prevotella ) from gut microbiomes indicates that Prevotella can act as a local probiotic and counteract SARS‐CoV‐2 to defend it in patients with COVID‐19 6 . In a recent study, the genera Rothia and Shigella were found at elevated levels in the gut microbiomes of SARS‐CoV‐2 and H1N1 influenza patients, corroborating with the present study's findings 46 .…”

“…4,5 Recently, a bidirectional relationship has been reported between COVID-19 and diabetes. 6 Several COVID-19 incidences were found with new onset of diabetes and severe metabolic complications of pre-existing diabetes, like diabetic ketoacidosis and hyperosmolar hyperglycemic state. 7,8 The pathophysiology of COVID-19-related diabetes seems to be quite complicated and makes it challenging for clinical management.…”

Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment

“…This is due to the ability of the gut microbiota to modulate their composition leading to preventive and therapeutic benefits, including the regulation of immune responses [ 217 , 218 , 219 ]. Furthermore, a recent study reported that the dysbiosis of the respiratory microbiome might be linked to the severe effects of COVID-19 diabetic patients [ 220 ].…”

Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern

“…SARS-CoV-2 Variant-wise detection result and percentages. services provided for routine COVID-19 surveillance at the Genome Center, Jashore University of Science and Technology (JUST) authorized by the Directorate General of Health Services (DGHS), Bangladesh26 .…”