Nutrition Strategies Pre-infection, during, and Post-infection with Coronavirus Disease

Coronavirus disease is a serious viral infection that is characterized by severe inflammation and lymphopenia. The virus attacks many organs causing acute respiratory distress and malfunctioning of the organs leading to death. Through strengthening of the innate immune system, a balanced diet plays a critical role in defense against bacterial and viral diseases. A healthy diet before, during and after an infection can lessen the severity of the symptoms and speed up the recovery of damaged cells. Due to the Mediterranean diet's high concentration of bioactive polyphenols, which have antioxidant, anti-inflammatory, and antithrombic properties, numerous studies have suggested that it is a preventative dietary strategy against many diseases including coronavirus disease. Nutrition and herbal plants play a key role to enhance the immunity of people to protect and fight against coronavirus. Diet rich in antioxidants and phytochemicals represents perfect barrier to the virus through elevation of the innate immunity of the body. In addition, gut microbiota including prebiotics, probiotics, and synbiotics were found to enhance immunity to reduce the symptoms of the disease during infection. Protein-rich foods and honey bee products reported significant role during and post-coronavirus infection. This review presents updated information from original pre-clinical and clinical researches, and review articles as well to expose the nutritive strategies including breastfeeding benefits to infants pre-infection, during, and post-infection with coronavirus.Copyright © 2023, Scientific Foundation SPIROSKI. All rights reserved.

Gut Microbiota in Coronavirus Disease 2019

Coronavirus disease 2019 (COVID-19) pandemic has changed the globe ever since its first appearance in December 2019. It is an acute respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and over 540 million people have contracted COVID-19 as of mid-2022. For COVID-19 patients, gastrointestinal symptoms including anorexia and diarrhoea are frequently occurred, implicating the involvement of gut microbiota in the pathogenesis of COVID-19. Indeed, accumulating evidence has reported the association of altered microbiota with SARS-CoV-2 infection, disease severity, and post-acute COVID-19 syndrome. In this chapter, the roles of gut microbiota in COVID-19 as well as its mechanistic interplays with host after SARS-CoV-2 infection are explored. Given its importance to this disease, approaches to restore the altered microbiota may be utilised as potential treatments of COVID-19. Hence, different strategies to modulate the microbiota including dietary intervention, prebiotics, and probiotics against SARS-CoV-2 infection are also discussed. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023.

Study of the Relationship between Mucosal Immunity and Commensal Microbiota: A Bibliometric Analysis.

This study presents the first bibliometric evaluation and systematic analysis of publications related to mucosal immunity and commensal microbiota over the last two decades and summarizes the contribution of countries, institutions, and scholars in the study of this field. A total of 1423 articles related to mucosal immunity and commensal microbiota in vivo published in 532 journals by 7774 authors from 1771 institutions in 74 countries/regions were analyzed. The interaction between commensal microbiota in vivo and mucosal immunity is essential in regulating the immune response of the body, maintaining communication between different kinds of commensal microbiota and the host, and so on. Several hot spots in this field have been found to have received extensive attention in recent years, especially the effects of metabolites of key strains on mucosal immunity, the physiopathological phenomena of commensal microbiota in various sites including the intestine, and the relationship between COVID-19, mucosal immunity and microbiota. We hope that the full picture of the last 20 years in this research area provided in this study will serve to deliver necessary cutting-edge information to relevant researchers.

Revitalizing myocarditis treatment through gut microbiota modulation: unveiling a promising therapeutic avenue.

Numerous studies have demonstrated that gut microbiota plays an important role in the development and treatment of different cardiovascular diseases, including hypertension, heart failure, myocardial infarction, arrhythmia, and atherosclerosis. Furthermore, evidence from recent studies has shown that gut microbiota contributes to the development of myocarditis. Myocarditis is an inflammatory disease that often results in myocardial damage. Myocarditis is a common cause of sudden cardiac death in young adults. The incidence of myocarditis and its associated dilated cardiomyopathy has been increasing yearly. Myocarditis has gained significant attention on social media due to its association with both COVID-19 and COVID-19 vaccinations. However, the current therapeutic options for myocarditis are limited. In addition, little is known about the potential therapeutic targets of myocarditis. In this study, we review (1) the evidence on the gut-heart axis, (2) the crosslink between gut microbiota and the immune system, (3) the association between myocarditis and the immune system, (4) the impact of gut microbiota and its metabolites on myocarditis, (5) current strategies for modulating gut microbiota, (6) challenges and future directions for targeted gut microbiota in the treatment of myocarditis. The approach of targeting the gut microbiota in myocarditis is still in its infancy, and this is the study to explore the gut microbiota-immune system-myocarditis axis. Our findings are expected to pave the way for the use of gut microbiota as a potential therapeutic target in the treatment of myocarditis.

Coccidioidomycosis and Host Microbiome Interactions: What We Know and What We Can Infer from Other Respiratory Infections.

Between 70 and 80% of Valley fever patients receive one or more rounds of antibiotic treatment prior to accurate diagnosis with coccidioidomycosis. Antibiotic treatment and infection (bacterial, viral, fungal, parasitic) often have negative implications on host microbial dysbiosis, immunological responses, and disease outcome. These perturbations have focused on the impact of gut dysbiosis on pulmonary disease instead of the implications of direct lung dysbiosis. However, recent work highlights a need to establish the direct effects of the lung microbiota on infection outcome. Cystic fibrosis, chronic obstructive pulmonary disease, COVID-19, and M. tuberculosis studies suggest that surveying the lung microbiota composition can serve as a predictive factor of disease severity and could inform treatment options. In addition to traditional treatment options, probiotics can reverse perturbation-induced repercussions on disease outcomes. The purpose of this review is to speculate on the effects perturbations of the host microbiome can have on coccidioidomycosis progression. To do this, parallels are drawn to aa compilation of other host microbiome infection studies.

Oral microbial taxa associated with risk for SARS-CoV-2 infection.

Hypothesis and objective: The oral and digestive tract microbial ecosystem has sparked interest because of its impact on various systemic diseases and conditions. The oral cavity serves not only as a reservoir for many potentially virulent microbiota but also as an important entry point and portal to the human body system. This is especially significant in the transmissibility of the virulent current pandemic virus SARS-CoV-2. The oral and digestive microbiome influences the inflammatory burden and effectiveness of the immune system and serves as a marker of activity of these host processes. The host immune response plays a role in infection susceptibility, including SARS-CoV-2. The purpose of this study is to investigate the role of specific salivary oral microbiome in susceptibility to SARS-CoV-2 infection. Methods and results: One hundred six subjects of known medical and dental history who consented to provide saliva samples between January 2017 and December 2019 were included in this study. Sixteen had become COVID-19 positive based on the PCR test by 3/01/2021. A comparison of oral microbiome bacteria taxa profiles based on 16S rRNA sequencing revealed differences between the two groups in this pilot study. Conclusions: These bacteria taxa may be markers of increased susceptibility to SARS-CoV-2 infection in the unvaccinated population.

Difference analysis of intestinal microbiota and metabolites in piglets of different breeds exposed to porcine epidemic diarrhea virus infection.

The gut microbial composition of the Luchuan (LC) piglet, one of China's native breeds, has rarely been studied, especially when compared to other breeds. This study developed a porcine epidemic diarrhea virus (PEDV) infection model in LC and Largewhite (LW) piglets, and analyzed the patterns and differences of intestinal microbial communities and metabolites in piglets of these two breeds after infection. The diarrhea score, survival time, and distribution of viral antigens in the intestine of piglets infected with PEDV differed among breeds, with the jejunal immunohistochemistry score of LW piglets being significantly higher than that of LC piglets (P < 0.001). The results of 16S rRNA sequencing showed differences in microbial diversity and community composition in the intestine of piglets with different breeds between PEDV infection piglets and the healthy controls. There were differences in the species and number of dominant phyla and dominant genera in the same intestinal segment. The relative abundance of Shigella in the jejunum of LC piglets after PEDV infection was significantly lower than that of LW piglets (P < 0.05). The key microorganisms differed in the microbiota were Streptococcus alactolyticus, Roseburia faecis, Lactobacillus iners, Streptococcus equi, and Lactobacillus mucosae (P < 0.05). The non-targeted metabolite analysis revealed that intestinal metabolites showed great differences among the different breeds related to infection. Spearman correlation analysis was conducted to examine any links between the microbiota and metabolites. The metabolites in the intestine of different breeds related to infection were mainly involved in arginine biosynthesis, synaptic vesicle cycle, nicotinic acid and nicotinamide metabolism and mTOR signaling pathway, with significantly positive or negative correlations (P < 0.05) between the various microorganisms. This study provides a theoretical foundation for investigating the application of core microorganisms in the gut of piglets of different breeds in the digestive tracts of those infected with PEDV, and helps to tackle the antimicrobial resistance problem further.

Modulation of innate immunity in airway epithelium for host-directed therapy.

Innate immunity of the mucosal surfaces provides the first-line defense from invading pathogens and pollutants conferring protection from the external environment. Innate immune system of the airway epithelium consists of several components including the mucus layer, mucociliary clearance of beating cilia, production of host defense peptides, epithelial barrier integrity provided by tight and adherens junctions, pathogen recognition receptors, receptors for chemokines and cytokines, production of reactive oxygen species, and autophagy. Therefore, multiple components interplay with each other for efficient protection from pathogens that still can subvert host innate immune defenses. Hence, the modulation of innate immune responses with different inducers to boost host endogenous front-line defenses in the lung epithelium to fend off pathogens and to enhance epithelial innate immune responses in the immunocompromised individuals is of interest for host-directed therapy. Herein, we reviewed possibilities of modulation innate immune responses in the airway epithelium for host-directed therapy presenting an alternative approach to standard antibiotics.

Hyaluronan with Different Molecular Weights Can Affect the Gut Microbiota and Pathogenetic Progression of Post-Intensive Care Syndrome Mice in Different Ways.

Post-intensive care syndrome (PICS) poses a serious threat to the health of intensive care unit (ICU) survivors, and effective treatment options are currently lacking. With increasing survival rates of ICU patients worldwide, there is a rising interest in developing methods to alleviate PICS symptoms. This study aimed to explore the potential of using Hyaluronan (HA) with different molecular weights as potential drugs for treating PICS in mice. Cecal ligation and puncture (CLP) were used to establish a PICS mice model, and high molecular weight HA (HMW-HA) or oligo-HA were used as therapeutic agents. Pathological and physiological changes of PICS mice in each group were monitored. 16S rRNA sequencing was performed to dissect gut microbiota discrepancies. The results showed that both molecular weights of HA could increase the survival rate of PICS mice at the experimental endpoint. Specifically, 1600 kDa-HA can alleviate PICS in a short time. In contrast, 3 kDa-HA treatment decreased PICS model survivability in the early stages of the experiment. Further, via 16S rRNA sequence analysis, we observed the changes in the gut microbiota in PICS mice, thereby impairing intestinal structure and increasing inflammation. Additionally, both types of HA can reverse this change. Moreover, compared to 1600 kDa-HA, 3 kDa-HA can significantly elevate the proportion of probiotics and reduce the abundance of pathogenic bacteria (Desulfovibrionaceae and Enterobacteriaceae). In conclusion, HA holds the advantage of being a potential therapeutic drug for PICS, but different molecular weights can lead to varying effects. Moreover, 1600 kDa-HA showed promise as a protective agent in PICS mice, and caution should be taken to its timing when considering using 3 kDa-HA.

Diversity, composition, and networking of saliva microbiota distinguish the severity of COVID-19 episodes as revealed by an analysis of 16S rRNA variable V1-V3 region sequences.

Studies on the role of the oral microbiome in SARS-CoV-2 infection and severity of the disease are limited. We aimed to characterize the bacterial communities present in the saliva of patients with varied COVID-19 severity to learn if there are differences in the characteristics of the microbiome among the clinical groups. We included 31 asymptomatic subjects with no previous COVID-19 infection or vaccination; 176 patients with mild respiratory symptoms, positive or negative for SARS-CoV-2 infection; 57 patients that required hospitalization because of severe COVID-19 with oxygen saturation below 92%, and 18 fatal cases of COVID-19. Saliva samples collected before any treatment were tested for SARS-CoV-2 by PCR. Oral microbiota in saliva was studied by amplification and sequencing of the V1-V3 variable regions of 16S gene using an Illumina MiSeq platform. We found significant changes in diversity, composition, and networking in saliva microbiota of patients with COVID-19, as well as patterns associated with severity of disease. The presence or abundance of several commensal species and opportunistic pathogens were associated with each clinical stage. Patterns of networking were also found associated with severity of disease: a highly regulated bacterial community (normonetting) was found in healthy people whereas poorly regulated populations (disnetting) were characteristic of severe cases. Characterization of microbiota in saliva may offer important clues in the pathogenesis of COVID-19 and may also identify potential markers for prognosis in the severity of the disease. IMPORTANCE SARS-CoV-2 infection is the most severe pandemic of humankind in the last hundred years. The outcome of the infection ranges from asymptomatic or mild to severe and even fatal cases, but reasons for this remain unknown. Microbes normally colonizing the respiratory tract form communities that may mitigate the transmission, symptoms, and severity of viral infections, but very little is known on the role of these microbial communities in the severity of COVID-19. We aimed to characterize the bacterial communities in saliva of patients with different severity of COVID-19 disease, from mild to fatal cases. Our results revealed clear differences in the composition and in the nature of interactions (networking) of the bacterial species present in the different clinical groups and show community-patterns associated with disease severity. Characterization of the microbial communities in saliva may offer important clues to learn ways COVID-19 patients may suffer from different disease severities.

Functional Foods: A Promising Strategy for Restoring Gut Microbiota Diversity Impacted by SARS-CoV-2 Variants.

Natural herbs and functional foods contain bioactive molecules capable of augmenting the immune system and mediating anti-viral functions. Functional foods, such as prebiotics, probiotics, and dietary fibers, have been shown to have positive effects on gut microbiota diversity and immune function. The use of functional foods has been linked to enhanced immunity, regeneration, improved cognitive function, maintenance of gut microbiota, and significant improvement in overall health. The gut microbiota plays a critical role in maintaining overall health and immune function, and disruptions to its balance have been linked to various health problems. SARS-CoV-2 infection has been shown to affect gut microbiota diversity, and the emergence of variants poses new challenges to combat the virus. SARS-CoV-2 recognizes and infects human cells through ACE2 receptors prevalent in lung and gut epithelial cells. Humans are prone to SARS-CoV-2 infection because their respiratory and gastrointestinal tracts are rich in microbial diversity and contain high levels of ACE2 and TMPRSS2. This review article explores the potential use of functional foods in mitigating the impact of SARS-CoV-2 variants on gut microbiota diversity, and the potential use of functional foods as a strategy to combat these effects.

Bifidobacterium: a probiotic for the prevention and treatment of depression.

Depression is a common psychological disease, which has become one of the main factors affecting human health. It has a serious impact on individuals, families, and society. With the prevalence of COVID-19, the incidence of depression has further increased worldwide. It has been confirmed that probiotics play a role in preventing and treating depression. Especially, Bifidobacterium is the most widely used probiotic and has positive effects on the treatment of depression. The mechanisms underlying its antidepressant effects might include anti-inflammation and regulation of tryptophan metabolism, 5-hydroxytryptamine synthesis, and the hypothalamus-pituitary-adrenal axis. In this mini-review, the relationship between Bifidobacterium and depression was summarized. It is hoped that Bifidobacterium-related preparations would play a positive role in the prevention and treatment of depression in the future.

Intestinal microbiota, pain, dementia

The review is dedicated the interconnection between neurodegenerative diseases, chronic pain and gut microbiota's structure and function. The gut microbiota's role in gut-brain axis, neuroimmune interaction is considered. The modern data about gut dysbiosis in Alzheimer disease, Parkinson disease, osteoarthrosis, neuropathic pain in COVID infection, muscular-skeletal pain in fibromyalgia, irritable bowel syndrome et cetera are provided. The gut microbiota's modification by means of pre and probiotics in combination with medicines and diet modification can be used for the treatment of chronic pain and dementia.Copyright © T.M. MANEVICH.

Effect of synbiotics on inflammatory markers and white blood cell count in COVID-19 patients: a randomized, double-blind, placebo-controlled clinical trial

PurposeToday, coronavirus disease-19 (COVID-19) treatment is an evolving process, and synbiotic administration has been suggested as a new therapeutic strategy. This study aims to investigate the effect of synbiotic supplementation in COVID-19 patients.Design/methodology/approachIn this placebo-controlled trial, 80 patients were randomized to receive oral synbiotic capsule (containing fructooligosaccharide and seven bacterial strains;Lactobacillus (L) casei, L. rhamnosus, Streptococcus thermophilus, Bifidobacterium breve, L. acidophilus, Bifidobacterium longum, L. bulgaricus, each one 109 colony-forming units) or placebo for two months. Inflammatory markers (Interleukin-6 [IL-6], C-reactive protein [CRP], erythrocyte sedimentation rate [ESR]) and white blood cell (WBC) count were evaluated at two timepoints (baseline, two months later). The measured variables were adjusted for confounders and analyzed by SPSS v21.0.FindingsAll 80 enrolled patients completed the study. The study adherence was good (approximately 70%). The mean changes for IL-6 were not significant (Δ = −0.6 ± 10.4 pg/mL vs Δ = +11.2 ± 50.3 pg/mL, p > 0.05). There were no significant improvements for CRP, ESR and WBC.Originality/valueAdministration of synbiotics for two months did not improve inflammatory markers in COVID-19 patients.

Clostridium Difficillae Infection in Post-Covid Patients

Intro: The ongoing pandemic caused by the SARS-CoV-2 virus has brought many new insights into medicine. During the first months of the pandemic, when there were no comprehensive guidelines for precise antimicrobial therapy, empirical overuse of broad-spectrum antibiotics was observed. Which resulted in the development of clostidium infection in certain cases. In our report, we address 83 cases of clostridial colitis in post-covid patients from 3/2020 to 3/2021 and their specific therapy. Method(s): Retrospective analysis of risk factors for clostridial infection and therapy of clostridial colitis. Finding(s): In the period 3/2020-3/2021, 9617 patients were diagnosed with SARS-CoV-2 virus infection in our hospital, of which 1247 were hospitalized. In 83 cases, clostridial colitis occurred during or after the covid infection had resolved. Mortality in this group was 17%, which corresponds to 14 patients. Previous empirical administered antiobiotics in COVID-19 infection contributed to the development of clostridial colitis in case of 22 patients (27%) by clarithromycin, in 14 pacients (17%) by penicillins and by 3rd generation cephalosporins in 9 patients (11%). The average duration of therapy with broad-spectrum antibiotics was 15.63 days (+-8.99). Other risk factors we observed are: PPI use (25%), active malignant disease (10%), previous glucocorticoid therapy (22%). Vancomycin was used in clostridial infection therapy in 47% (39), metronidazole in 31% (25) and fidaxonicin in 7% (6). In the group, we observed recurrence of clostridium difficile infection in 14% of patients and FMT was performed in 6 patients. Conclusion(s): This study shows a higher percentage of clostridial infection in cases of long-term therapy with broad-spectrum antibiotics. It also points to the effect of specific antimicrobial therapy for infection caused by the bacterium Clostridium difficile and the possibility of using fecal bacteriotherapy.Copyright © 2023

Delineating Health and Health System: Mechanistic Insights into Covid 19 Complications

This book discusses the organ-specific systemic manifestations of COVID-19. The initial chapters of the book review the origin and evolution of the coronaviruses, followed by pathogenesis and immune response during COVID-19 infection. The book also provides insight into the role of angiotensin-converting enzyme 2 in the onset of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis. It summarizes the neurological aspects of SARS-CoV2, including transmission pathways, mechanisms of invasion into the nervous system, and mechanisms of neurological disease. It also delineates the association of severe disease with high blood plasma levels of inflammatory cytokines and inflammatory markers in SARS-CoV-2 infection. Lastly, it discusses the perturbation of gut microbiota by SARS-CoV-2 and uncovers the potential risk of virus infection on reproductive health. © The Editor(s) (if applicable) and The Author(s), under exclusive licence to Springer Nature Singapore Pte Ltd. 2021.

COVID-19 Pandemic and Mental Illness: Impact of Gut Microbiota

The world is currently facing a global pandemic caused by SARS-CoV-2. Although COVID-19 is primarily a respiratory illness, various studies have demonstrated the ability of this virus in spreading to extrapulmonary sites, thereby leading to multiorgan failure and eventually death in highly susceptible individuals. The scourge of the virus world over has led to a severe impact (direct and indirect) on the mental health of individuals belonging to all age groups. In this context, the role of gut microbiota in influencing mental health via the gut-brain axis holds immense significance. Recent evidences have highlighted the possible link between COVID-19 infection, gut dysbiosis, and various psychological and neurological abnormalities. Thus, maintenance of a healthy gut microbiome becomes imperative given the absence of a definite cure to such a dangerous illness as COVID-19. Various strategies such as regular intake of a healthy diet and personalized nutrition, co-supplemented with probiotics, prebiotics, and psychobiotics, should be adopted wherein gut microbiota profile can be manipulated for providing multiple benefits to the host. Religiously following such practices will not only enrich the gut with beneficial microbes and boost host immunity but also prove to be a strong prophylactic measure in reducing the incidence/severity of diseases such as COVID-19 virulence and result in improved prognosis of infected individuals. © The Author(s), under exclusive licence to Springer Nature Singapore Pte Ltd. 2021.

Emerging applications of phage therapy and fecal virome transplantation for treatment of Clostridioides difficile infection: challenges and perspectives.

Clostridioides difficile, which causes life-threatening diarrheal disease, is considered an urgent threat to healthcare setting worldwide. The current standards of care solely rely on conventional antibiotic treatment, however, there is a risk of promoting recurrent C. difficile infection (rCDI) because of the emergence of antibiotic-resistant strains. Globally, the alarming spread of antibiotic-resistant strains of C. difficile has resulted in a quest for alternative therapeutics. The use of fecal microbiota transplantation (FMT), which involves direct infusion of fecal suspension from a healthy donor into a diseased recipient, has been approved as a highly efficient therapeutic option for patients with rCDI. Bacteriophages or phages are a group of viruses that can infect and destroy bacterial hosts, and are recognized as the dominant viral component of the human gut microbiome. Accumulating data has demonstrated that phages play a vital role in microbial balance of the human gut microbiome. Recently, phage therapy and fecal virome transplantation (FVT) have been introduced as promising alternatives for the treatment of C. difficile -related infections, in particular drug-resistant CDI. Herein, we review the latest updates on C. difficile- specific phages, and phage-mediated treatments, and highlight the current and future prospects of phage therapy in the management of CDI.

Gut microbiota profile of COVID-19 patients: Prognosis and risk stratification (MicroCOVID-19 study).

Background: Gut microbiota is intrinsically associated with the immune system and can promote or suppress infectious diseases, especially viral infections. This study aims to characterize and compare the microbiota profile of infected patients with SARS-CoV-2 (milder or severe symptoms), non-infected people, and recovered patients. This is a national, transversal, observational, multicenter, and case-control study that analyzed the microbiota of COVID-19 patients with mild or severe symptoms at home, at the hospital, or in the intensive care unit, patients already recovered, and healthy volunteers cohabiting with COVID-19 patients. DNA was isolated from stool samples and sequenced in a NGS platform. A demographic questionnaire was also applied. Statistical analysis was performed in SPSS. Results: Firmicutes/Bacteroidetes ratios were found to be significantly lower in infected patients (1.61 and 2.57) compared to healthy volunteers (3.23) and recovered patients (3.89). Furthermore, the microbiota composition differed significantly between healthy volunteers, mild and severe COVID-19 patients, and recovered patients. Furthermore, Escherichia coli, Actinomyces naeslundii, and Dorea longicatena were shown to be more frequent in severe cases. The most common COVID-19 symptoms were linked to certain microbiome groups. Conclusion: We can conclude that microbiota composition is significantly affected by SARS-CoV-2 infection and may be used to predict COVID-19 clinical evolution. Therefore, it will be possible to better allocate healthcare resources and better tackle future pandemics.

The causal links between gut microbiota and COVID-19: A Mendelian randomization study.

Several studies have shown a possible correlation between gut microbiota and COVID-19. However, the cause-and-effect relationship between the two has not been investigated. We conducted a two-sample Mendelian randomization study (MR) study using publicly available GWAS data. Inverse variance weighted (IVW) analysis was the main MR analysis technique and was supplemented with other sensitivity analyses. Forty-two bacterial genera were associated with COVID-19 susceptibility, hospitalization, and severity in the IVW method. Among these gut microbiota, five gut microbiota (genus unknowngenus [id.1000005472], family unknownfamily [id.1000005471], genus Tyzzerella3, order MollicutesRF9.id.11579, and phylum Actinobacteria) were significantly associated with COVID-19 hospitalization and severity. Three gut microbiota (class Negativicutes, order Selenomonadales, and class Actinobacteria) were significantly associated with COVID-19 hospitalization and susceptibility, while two microbiota (class Negativicutes and order Selenomonadales) were significantly associated with COVID-19 hospitalization and severity, and susceptibility. Sensitivity analysis did not detect any heterogeneity and horizontal pleiotropy. Our findings demonstrated that several microorganisms were causally linked to COVID-19, and improved our understanding of the relationship between gut microbiota and COVID-19 pathology.