Improved gut microbiota features after the resolution of SARS‑CoV‑2 infection

Several studies to date have analyzed the gut microbiota of patients with severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infection both during and after disease resolution [1, 2]. However, information on long-term follow-up is lacking. Therefore, we evaluated changes to the gut microbiome six months after SARS-CoV-2 infection resolution in 30 Italian patients hospitalized for pneumonia in our center during the first wave of the pandemic.

Faecal samples of 31 SARS-CoV-2-positive patients were harvested within 48 h from admission and prior to transfer to the intensive care unit (ICU), in order to minimize any impact of the pharmaceutical treatment on the gut microbiome, and again six months after discharge. During this , patients were regularly interviewed and none of them reported any infection/antibiotic treatment or symptoms of new onset. Eighteen patients hospitalized in the same period for SARS-CoV-2-unerlated pneumonia served as control group. Following hospital admission, at the time of fecal specimen collection, both control group (94.7%) and patients showing SARS-CoV-2 related pneumonia (71%) were receiving the same antibiotic treatment schedule, as per Hospital protocol. Faecal samples analysis was conducted as described in the Additional file 4. Characteristics of the study population are shown in Table 1. Gut microbiota alpha-diversity was similar between patients affected by either SARS-CoV-2 or non-SARS-CoV-2 pneumonia; it showed a slight enhanced trend after SARS-CoV-2 negativization, increasing significantly after the resolution of SARS-CoV-2 infection when compared with the control group (p  =  0.346, p  =  0.043 and p  =  0.048, Kruskal–Wallis Test, for Shannon index, inverse Simpson index and Pielou’s Evenness, respectively). In particular, equitability among bacterial species increased and appeared to be driven by microbial changes ensuing SARS-CoV-2 infection resolution (Fig. 1A). The PCoA of inter-individual variation based on weighted UniFrac distance showed a slender split among the study groups, although it was not statistically significant (p  =  0.114, PERMANOVA; Additional file 1: Figure S1). As shown in Fig. 1B, Bacteroidetes relative abundance was higher (≈ 36.8%) in SARS-CoV-2 positive patients than in those with SARS-CoV-2 negative pneumonia (≈13.6%), and declined to 18.7% when SARS-CoV-2 infection resolved (p  =  0.004, Kruskal–Wallis Test). Conversely, Firmicutes were prevalent (≈ 75%) in controls and in samples collected after SARS-CoV-2 infection resolution, while the relative abundance was lower (≈ 50%) in SARS-CoV-2 positive pneumonia group (p  =  0.001, Kruskal–Wallis Test).

Focusing on the twenty most represented bacterial genera, we observed specific patterns of Bacteroides, Blautia and Enterococcus variations among groups (Fig. 1C). Particularly, Bacteroides and Enterococcus genera appeared to correlate inversely, with the former genus being increased in SARS-CoV-2 positive patients compared to the other groups (p  =  0.003), whereas the latter genus showed a decreasing trend (p  =  0.082). Finally, Blautia increased after SARS-CoV-2 infection resolution, rebalancing the gut microbiota composition (p  =  0.029). As expected, linear discriminant analysis (LDA) showed that bacterial elements belonging to Bacteroidetes (i. e., Oscillibacter, Ruminococcaceae DTU089, Bacteroidaceae, Bacteroidia, Parabacteroides and Tannerellaceae) were enriched in SARS-CoV-2 positive patients, whereas Lactobacillales, Streptococcus, Staphylococcus and Acidoaminococcus were increased in those with SARS-CoV-2-unrelated pneumonia (p  <  0.05, Kruskal–Wallis Test; Fig. 1D). Conversely, Lachnospiraceae (i. e., NK4A136 group, Fusicantibacter and Roseburia) and Ruminococcaceae UCG-013 were increased after SARS-CoV-2 infection resolution. DESeq2 analysis reported substantially the same results (Additional file 2: Table S1, Additional file 3: Table S2).

Our study conducted in a Western population confirms that gut microbiota alpha diversity is similar in patients with SARS-CoV-2 related or unrelated pneumonia. Nevertheless, we observed an increase in alpha-diversity after the resolution of SARS-CoV-2 acute infection. This may be related to the effects of SARS-CoV-2 on the gut microbiota, but the contribution of drugs (e.g., antibiotics) administered before hospitalization or during its initial phase may not be negligible. Nevertheless, alpha-diversity modification may be not sufficient to assess recovery of the healthy status.

Previous Chinese studies [3‐5] compared the gut microbiota of patients with SARS-CoV-2-related and community-acquired pneumonia, confirming a surge of opportunistic pathogens and a reduction in commensals elements. Our data confirm Bacteroidetes enrichment in patients with COVID-19 [3]. Conversely, Firmicutes appeared to decline, whereas no significant variation was observed for Actinobacteria [3]. During SARS-CoV-2 infection, inflammation is a key determinant of disease severity [6‐8]. Interestingly, cytokine storm is positively associated with Bacteroides relative abundance [3]. Conversely, Blautia with its anti-inflammatory properties may play an important role in the recovery from COVID-19 [9]. Indeed, interleukin-10 (IL-10) serum levels significantly decrease with the reduction of Ruminococcus obeum (otherwise Blautia) abundance [3], and this correlates with the failure in controlling host’s inflammatory response. This study suffers of the limitations of the small sample size, but our results corroborate those achieved on populations with different ethnicity. Even though many factors can affect the gut microbiota, our findings support the hypothesis of a specific impact of SARS-CoV-2 infection on the gut microbiota.

This study supports the previous evidence that SARS-CoV-2 infection is associated with changes in the gut microbiome. However, many gut microbiome-related factors could influence the course of COVID-19, calling for more studies in the next future.