Gut Microbiome Alterations in COVID-19

Abstract

Since the outset of the coronavirus disease 2019 (COVID-19) pandemic, the gut microbiome in COVID-19 has garnered substantial interest, given its significant roles in human health and pathophysiology. Accumulating evidence is unveiling that the gut microbiome is broadly altered in COVID-19, including the bacterial microbiome, mycobiome, and virome. Overall, the gut microbial ecological network is significantly weakened and becomes sparse in patients with COVID-19, together with a decrease in gut microbiome diversity. Beyond the existence of severe acute respiratory syndrome coronavirus type 2 ( SARS-CoV-2 ), the gut microbiome of patients with COVID-19 is also characterized by enrichment of opportunistic bacteria, fungi, and eukaryotic viruses, which are also associated with disease severity and presentation. Meanwhile, a multitude of symbiotic bacteria and bacteriophages are decreased in abundance in patients with COVID-19. Such gut microbiome features persist in a significant subset of patients with COVID-19 even after disease resolution, coinciding with ‘long COVID’ (also known as post-acute sequelae of COVID-19). The broadly-altered gut microbiome is largely a consequence of SARS-CoV-2 infection and its downstream detrimental effects on the systemic host immunity and the gut milieu. The impaired host immunity and distorted gut microbial ecology, particularly loss of low-abundance beneficial bacteria and blooms of opportunistic fungi including Candida , may hinder the re-assembly of the gut microbiome post COVID-19. Future investigation is necessary to fully understand the role of the gut microbiome in host immunity against SARS-CoV-2 infection, as well as the long-term effect of COVID-19 on the gut microbiome in relation to the host health after the pandemic.

RETRACTED: Microbiome-Based Hypothesis on Ivermectin’s Mechanism in COVID-19: Ivermectin Feeds Bifidobacteria to Boost Immunity

“…belong to the same phylum as a critically important constituent of the gut microbiome and common ingredient of probiotics, Bifidobacterium . Bifidobacterium abundance is known to decrease in SARS-CoV-2-infected subjects, as seen in ours and other studies ( Tao et al, 2020 ; Xu et al, 2020 ; Reinold et al, 2021 ; Yeoh et al, 2021 ; Zuo et al, 2021 ; Hazan et al, 2022b ). We have anecdotally observed, through our clinical experiences pre and post Fecal Microbiota Transplant, that certain bacteria in the same phylum may be able to replace each other’s function.…”

“…Ours and other data also support a protective role of Bifidobacterium in SARS-CoV-2 infection, possibly through these immune functions of Bifidobacterium . Our study and others ( Tao et al, 2020 ; Xu et al, 2020 ; Reinold et al, 2021 ; Yeoh et al, 2021 ; Zuo et al, 2021 ; Hazan et al, 2022b ) show that the gut microbiome, particularly Bifidobacterium levels, relates to positivity and severity of SARS-CoV-2 infection. Tao et al (2020) showed that changes in gut microbiota composition might contribute to SARS-CoV-2-induced production of inflammatory cytokines in the intestine, which may lead to the cytokine storm onset.…”

The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications

“…Increased stress-, inflammation-, and virulence-associated gene expression was observed, suggesting that these viruses play a role in the host immune response to SARS-CoV-2 infection [29]. Moreover, after disease resolution, delayed SARS-CoV-2 viral shedding and persistent gut virome dysbiosis were noted [74]. Immune dysregulation driven by SARS-CoV-2 infection may also promote imbalance of the microbial and viral ecosystems of the human body that could result in long COVID or post-acute sequelae of COVID-19 [70].…”

Effects of the Lipid Profile, Type 2 Diabetes and Medication on the Metabolic Syndrome—Associated Gut Microbiome

“…One limitation of the study was the relatively small sample used but we plan to extend our research to bigger cohorts. Importantly, we excluded from our analysis patients who had a history of COVID-19, considering that SARS-CoV-2 infection significantly alters the gut microbiome [ 81 ]. Given the heterogeneity in the overall microbial composition observed in the participants, further recruitment would enable the detection of additional correlations between gut microbiota and MetSyn and T2DM pathogenesis.…”