Gut Microbiota Interplay With COVID-19 Reveals Links to Host Lipid Metabolism Among Middle Eastern Populations

Mohammad Tahseen Al Bataineh,Abdulmajeed Alkhajeh,Hussein Kannout,Habiba S Alsafar,Nawal Alkaabi,Guan K Tay,Marianne Daou,Maimunah Uddin,Ahmed F Yousef,Mariam Khalili,Mohd Azzam Kayasseh,Fathimathuz Waasia,Andreas Henschel,Samuel F Feng,Mira Mousa

doi:10.3389/fmicb.2021.761067

Abstract

The interplay between the compositional changes in the gastrointestinal microbiome, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) susceptibility and severity, and host functions is complex and yet to be fully understood. This study performed 16S rRNA gene-based microbial profiling of 143 subjects. We observed structural and compositional alterations in the gut microbiota of the SARS-CoV-2-infected group in comparison to non-infected controls. The gut microbiota composition of the SARS-CoV-2-infected individuals showed an increase in anti-inflammatory bacteria such as Faecalibacterium (p-value = 1.72 × 10–6) and Bacteroides (p-value = 5.67 × 10–8). We also revealed a higher relative abundance of the highly beneficial butyrate producers such as Anaerostipes (p-value = 1.75 × 10–230), Lachnospiraceae (p-value = 7.14 × 10–65), and Blautia (p-value = 9.22 × 10–18) in the SARS-CoV-2-infected group in comparison to the control group. Moreover, phylogenetic investigation of communities by reconstructing unobserved state (PICRUSt) functional prediction analysis of the 16S rRNA gene abundance data showed substantial differences in the enrichment of metabolic pathways such as lipid, amino acid, carbohydrate, and xenobiotic metabolism, in comparison between both groups. We discovered an enrichment of linoleic acid, ether lipid, glycerolipid, and glycerophospholipid metabolism in the SARS-CoV-2-infected group, suggesting a link to SARS-CoV-2 entry and replication in host cells. We estimate the major contributing genera to the four pathways to be Parabacteroides, Streptococcus, Dorea, and Blautia, respectively. The identified differences provide a new insight to enrich our understanding of SARS-CoV-2-related changes in gut microbiota, their metabolic capabilities, and potential screening biomarkers linked to COVID-19 disease severity.

Highlights

The newly emerged β-coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of the respiratory illness coronavirus disease-2019 or COVID-19
We subsequently describe the analysis pipeline for microbial communities based on QIIME 2, which underwent a paradigm shift from operational taxonomic units (OTUs) to amplicon sequence variants (ASVs), as the latter exhibit several advantages over the former (Langille et al, 2013; Callahan et al, 2017)
We explored the compositional variation of the gut microbiome among 86 COVID-19-positive and 57 COVID-19-non-infected individuals from the United Arab Emirates

Summary

Introduction

The newly emerged β-coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of the respiratory illness coronavirus disease-2019 or COVID-19. It was first reported in Wuhan, China, in late 2019, after which it spread rapidly worldwide, with an alarmingly high transmission rate. Severe acute respiratory syndrome coronavirus 2 invades human cells through the interaction of its surface spike protein with angiotensin-converting enzyme 2 (ACE2) receptors expressed on the surface of several human cell types (Li et al, 2020). The presence of ACE2 receptors in gut epithelia and the gastrointestinal symptoms of COVID-19-infected individuals suggest that the gastrointestinal tract is an extrapulmonary site for SARS-CoV-2 activity and infection (Hoffmann et al, 2020; Zuo et al, 2020b)

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