Plasma Microbiome in COVID-19 Subjects: An Indicator of Gut Barrier Defects and Dysbiosis

Abstract

The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) complications. We aimed to investigate whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n = 146) and healthy individuals (n = 47) were collected during hospitalization and routine visits. Plasma microbiome was analyzed using 16S rRNA sequencing and gut permeability markers including fatty acid binding protein 2 (FABP2), peptidoglycan (PGN), and lipopolysaccharide (LPS) in both patient cohorts. Plasma samples of both cohorts contained predominately Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria. COVID-19 subjects exhibit significant dysbiosis (p = 0.001) of the plasma microbiome with increased abundance of Actinobacteria spp. (p = 0.0332), decreased abundance of Bacteroides spp. (p = 0.0003), and an increased Firmicutes:Bacteroidetes ratio (p = 0.0003) compared to healthy subjects. The concentration of the plasma gut permeability marker FABP2 (p = 0.0013) and the gut microbial antigens PGN (p < 0.0001) and LPS (p = 0.0049) were significantly elevated in COVID-19 patients compared to healthy subjects. These findings support the notion that the intestine may represent a source for bacteremia and contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.

Keywords: COVID-19; circulating microbiome; dysbiosis; gut barrier permeability.

Figure 1

16S rRNA analyses in the plasma of COVID-19 patients. (A) Total read counts and measures of alpha diversity—(B) Faith’s Phylogenetic Diversity, (C) Observed OTUs, (D) Pielou’s Evenness, and (E) Shannon’s Dysbiosis Index—were calculated and indicate no aggregate changes in alpha diversity. Data are presented as mean ± S.E.M. Each dot represents a sample in the cohorts. Student’s t-test p-values are indicated where applicable (ns, p > 0.05). (F) Unsupervised 2D principal coordinates analysis (PCoA) of weighted UniFrac distance revealed significant alterations in beta-diversity in COVID-19 subjects (PERMANOVA p-value). Each dot indicates one patient plasma sample.

Figure 2

COVID-19-positive subjects exhibit significant dysbiosis of the plasma microbiome at the phylum level. (A) Pie charts representing dominant phyla that constitute the circulating microbiome in COVID-19-positive subjects. Individual phyla (B–E) which were found to be differentially abundant in the plasma of COVID-19-positive subjects including increased Actinobacteria and decreased Bacteroidota. (F) The Firmicutes:Bacteroidetes (F:B) ratio indicates a significant increase in dysbiosis of the dominant phyla. Data are presented as mean ± S.E.M. Each dot represents a sample in the cohorts. Student’s t-test p-values are indicated where applicable (ns, p > 0.05).

Figure 3

COVID-19-positive subjects exhibit significant dysbiosis of the plasma microbiome at the genus/species level. Linear discriminant analysis (LDA) of CPM normalized counts of Metaphlan displaying differential abundances of several prominent genera in the COVID-19 plasma samples including Bifidobacterium, Pantoea, Streptococcus, and Brevibacterium spp.

Figure 4

SARS-CoV-2 infection induces increased gut permeability and endotoxemia. ELISA results of plasma (A) fatty acid binding protein 2 (FABP2) and the gut microbial antigens (B) peptidoglycan (PGN) and (C) lipopolysaccharide (LPS) which indicate increased gut barrier integrity and increased endotoxemia in COVID-19-infected subjects. Data are presented as mean ± S.E.M. Each dot represents a sample in the cohorts. Student’s t-test p-values are indicated where applicable.

Figure 5

Schematic diagram representing the hypothesis of COVID-19 infection promoting gut barrier defects and translocation of the gut microbiome into the systemic circulation, resulting in worsened outcomes. This figure was generated via Biorender.com.