COVID-19 and the gut microbiome: connection between viral infection and microbial balance

During the study, sequencing analysis was performed on stool samples from 65 patients with confirmed COVID-19 (by RT-PCR). The data obtained were compared with those from 65 healthy individuals used as controls. The median age of the COVID-19 patients was 55 years (range: 29–70 years), and 28 (43.07%) were women. Nasopharyngeal swabs from these patients were tested for COVID-19 using the RT-PCR-based Allplex 2019-nCoV assay (Arrow Diagnostics S.r.l., Genoa, Italy). Stool samples from both COVID-19 patients and healthy individuals were collected in sterile containers and stored at -80°C within a few hours of collection until analysis. DNA extraction from stool samples was performed first using a lysis buffer with additional homogenization steps, as per protocol, and then using the MagPurix® Magnetic Bead-Based Bacterial DNA Extraction Kit and the MagPurix Automated Extraction System (Resnova, Rome, Italy), following the manufacturer's instructions. DNA purity was measured using a NanoDrop 1000 spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA), and DNA concentrations were measured with a Qubit® dsDNA High Sensitivity (HS) Assay Kit (ThermoFisher Scientific, Waltham, MA, USA). Library preparation was performed using Microbiota Solution A, B, and Myco (Arrow Diagnostics) to analyze the V1–V2-V3–V4-V6 hypervariable regions of bacterial 16S rRNA. Library quality controls were performed using both the Qubit dsDNA HS kit and the High Sensitivity D1000 ScreenTape assay for TapeStation (Agilent Technologies, Santa Clara, CA, USA) to assess concentration, profile, and size. Next-generation sequencing was performed in paired-end (2x151bp) on a Mid Output v2 platform for the Illumina NextSeq® 550 (Illumina, San Diego, CA, USA). Sequencing data (Fastq files) were analyzed using the MicrobAT Suite—SmartSeq (Novara, Italy) to identify operational taxonomic units (OTUs). Statistical analyses were performed using the MicrobiomeAnalyst program (https://www.microbiomeanalyst.ca/). Coronavirus disease (COVID-19) is an infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can be asymptomatic or present with multiple organ dysfunctions. Although the virus primarily affects the respiratory system, it can also target the gastrointestinal tract (GIT). Clinical studies have reported an increasing number of GI symptoms in patients with COVID-19, with an incidence rate between 2% and 50%. SARS-CoV-2 enters host cells via the angiotensin-converting enzyme 2 (ACE2) receptor, which is highly expressed in both the respiratory and GI tracts. ACE2 plays a crucial role in controlling intestinal inflammation and gut microbial ecology, and its interaction with the virus could lead to changes in the intestinal microbiota. Patients with COVID-19 exhibited decreased bacterial diversity in their fecal microbiome, particularly a reduction in short-chain fatty acid (SCFA)-producing bacteria from the Lachnospiraceae, Ruminococcaceae, and Eubacteriaceae families, along with an increase in opportunistic pathogens from the Enterobacteriaceae family. Beneficial species such as Faecalibacterium prausnitzii, which is involved in maintaining gut immune homeostasis, were also reduced in abundance, indicating the influence of the disease on microbiota structure. Gut dysbiosis, along with increased gut permeability, may contribute to the risk of bloodstream infections in COVID-19. The translocation of bacteria, leukocytes, and inflammatory mediators through the gut-lung axis may contribute to organ deterioration in COVID-19. Therapeutic strategies such as prebiotics, probiotics, and fecal microbiota transplantation (FMT) may help reestablish eubiosis and improve COVID-19 outcomes.