Microbiome Profiling Using Shotgun Metagenomic Sequencing Identified Unique Microorganisms in COVID-19 Patients With Altered Gut Microbiota

Abstract

COVID-19 is mainly associated with respiratory distress syndrome, but a subset of patients often present gastrointestinal (GI) symptoms. Imbalances of gut microbiota have been previously linked to respiratory virus infection. Understanding how the gut–lung axis affects the progression of COVID-19 can provide a novel framework for therapies and management. In this study, we examined the gut microbiota of patients with COVID-19 (n = 47) and compared it to healthy controls (n = 19). Using shotgun metagenomic sequencing, we have identified four microorganisms unique in COVID-19 patients, namely Streptococcus thermophilus, Bacteroides oleiciplenus, Fusobacterium ulcerans, and Prevotella bivia. The abundances of Bacteroides stercoris, B. vulgatus, B. massiliensis, Bifidobacterium longum, Streptococcus thermophilus, Lachnospiraceae bacterium 5163FAA, Prevotella bivia, Erysipelotrichaceae bacterium 6145, and Erysipelotrichaceae bacterium 2244A were enriched in COVID-19 patients, whereas the abundances of Clostridium nexile, Streptococcus salivarius, Coprococcus catus, Eubacterium hallii, Enterobacter aerogenes, and Adlercreutzia equolifaciens were decreased (p < 0.05). The relative abundance of butyrate-producing Roseburia inulinivorans is evidently depleted in COVID-19 patients, while the relative abundances of Paraprevotella sp. and the probiotic Streptococcus thermophilus were increased. We further identified 30 KEGG orthology (KO) modules overrepresented, with 7 increasing and 23 decreasing modules. Notably, 15 optimal microbial markers were identified using the random forest model to have strong diagnostic potential in distinguishing COVID-19. Based on Spearman’s correlation, eight species were associated with eight clinical indices. Moreover, the increased abundance of Bacteroidetes and decreased abundance of Firmicutes were also found across clinical types of COVID-19. Our findings suggest that the alterations of gut microbiota in patients with COVID-19 may influence disease severity. Our COVID-19 classifier, which was cross-regionally verified, provides a proof of concept that a set of microbial species markers can distinguish the presence of COVID-19.

Results from EDIFICE : A French pilot study on COVID-19 and the gut microbiome in a hospital environment

“…The reduced diversity in the patient group is consistent with previous reports indicating an overall lower alpha diversity in COVID-19 patients compared to controls ( (Gu et al 2020;Chen et al 2022;Mazzarelli et al 2021;Reinold et al 2021;Tao et al 2020;Moreira-Rosário et al 2021;Li et al 2021)), note that some authors reported on the Chao index instead of Shannon. Many environmental factors can contribute to a reduced alpha diversity such as urban life styles (Filippo et al 2010), disease state (in particular metabolic syndrome (Le Chatelier et al 2013) and IBD (Pascal et al 2017)) and drugs (in particular antibiotics and PPIs) (Vich Vila et al 2020) but not so much to age (Badal et al 2020).…”

“…Roseburia and Faecalibacterium) are all butyrate producers. The significant decrease in butyrate producers (such as Faecalibacterium, Roseburia, Eubacterium or Ruminococcus) has consistently been reported by others on COVID-19 patients (Gu et al 2020;Tang et al 2020;Zuo et al 2020;Mazzarelli et al 2021;Yeoh et al 2021;Reinold et al 2021;Tao et al 2020;Moreira-Rosário et al 2021;Li et al 2021) although not butyrivibrio specifically. Butyrate producers are well documented beneficial bacteria and are decreased in multiple diseases.…”

“…The significant decrease in alpha diversity observed in elderly COVID-19 patients with significant co-morbidities was therefore expected and cannot, here, be attributed to COVID-19 status given the unmatched design of the trial. Previous reports indicate, however, that the decrease in alpha diversity is unlikely to be attributed to age or to antibiotics alone given that similar conclusions were reached in trials with matched designs or excluding previous antibiotics use (Gu et al 2020;Reinold et al 2021;Li et al 2021) and that alpha diversity correlates to disease severity (Moreira-Rosário et al 2021;Mazzarelli et al 2021). In any case, evaluation within each group remains highly informative.…”

“…Indeed, 16S based analysis does not allow accurate species level classification. Two other reports that used a shotgun metagenomic approach also reported Erysipelotrichaceae_noname as enriched in COVID-19 patients (Li et al 2021) or associated with disease severity (Zuo et al 2020). It could thus be interesting to perform de novo assembly of this bacteria in COVID19 patients to better characterize it.…”

Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes

“…Although 16S 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 16 . Other studies, based on whole-metagenome shotgun (WMS) sequencing, explored the links between the human microbiome and SARS-CoV-2 infection by mapping short metagenomic reads to reference genome databases [17][18][19][20][21] . Despite the fact that the analysis of WMS sequencing data provides more information than 16S rRNA gene sequencing data analysis, existing studies based on reference genome databases are subject to the limitations and biases of those databases and unable to characterize microbes that do not have closely related culture representatives.…”