Microbiota Modulation of the Gut-Lung Axis in COVID-19

Microbiota, probiotics and respiratory infections: the three musketeers can tip off potential management of COVID-19

Rapid infectivity of SARS-CoV2 with recent viral variants is posing a challenge in the development of robust therapeutic strategies. On the other hand, microbiota is debated for its involvement in SARS-CoV2 infection with varied opinions. Although ample data about the role of microbiota and probiotics in respiratory viral infections are available, their role in COVID-19 is limited albeit emerging rapidly. The utilization of probiotics for the management of COVID-19 is still under investigation in many clinical trials. Existing information coupled with recent COVID-19 related studies can suggest various ways to use microbiota modulation and probiotics for managing this pandemic. Present article indicates the role of microbiota modulation and probiotics in respiratory infections. In addition, scattered evidence was gathered to understand the potential of microbiota and probiotics in the management of SARS-CoV2. Gut-airway microbiota connection is already apparent in respiratory tract viral infections, including SARS-CoV2. Though few clinical trials are evaluating microbiota and probiotics for COVID-19 management, the safety evaluation must be given more serious consideration because of the possibility of opportunistic infections among COVID-19 patients. Nevertheless, the information about microbiota modulation using probiotics and prebiotics can be helpful to manage this outbreak and this review presents different aspects of this idea.

COVID-19 Infection Alters the Microbiome: Elite Athletes and Sedentary Patients Have Similar Bacterial Flora

Regular exercise can upgrade the efficiency of the immune system and beneficially alter the composition of the gastro-intestinal microbiome. We tested the hypothesis that active athletes have a more diverse microbiome than sedentary subjects, which could provide better protection against COVID-19 during infection. Twenty active competing athletes (CA) (16 male and 4 females of the national first and second leagues), aged 24.15 ± 4.7 years, and 20 sedentary subjects (SED) (15 male and 5 females), aged 27.75 ± 7.5 years, who had been diagnosed as positive for COVID-19 by a PCR test, served as subjects for the study. Fecal samples collected five to eight days after diagnosis and three weeks after a negative COVID-19 PCR test were used for microbiome analysis. Except for two individuals, all subjects reported very mild and/or mild symptoms of COVID-19 and stayed at home under quarantine. Significant differences were not found in the bacterial flora of trained and untrained subjects. On the other hand, during COVID-19 infection, at the phylum level, the relative abundance of Bacteroidetes was elevated during COVID-19 compared to the level measured three weeks after a negative PCR test (p < 0.05) when all subjects were included in the statistical analysis. Since it is known that Bacteroidetes can suppress toll-like receptor 4 and ACE2-dependent signaling, thus enhancing resistance against pro-inflammatory cytokines, it is suggested that Bacteroidetes provide protection against severe COVID-19 infection. There is no difference in the microbiome bacterial flora of trained and untrained subjects during and after a mild level of COVID-19 infection.

Patient Nutrition and Probiotic Therapy in COVID-19: What Do We Know in 2021?

BACKGROUND

The main nutritional consequences of COVID-19 include reduced food intake, hypercatabolism, and rapid muscle wasting. Some studies showed that malnutrition is a significant problem among patients hospitalized due to COVID-19 infection, and the outcome of patients with SARS-CoV-2 is strongly associated with their nutritional status. The purpose of this study was to collect useful information about the possible elements of nutritional and probiotic therapy in patients infected with the SARS-CoV-2 virus.

METHODS

A narrative review of the literature, including studies published up to 13 September 2021.

RESULTS

Probiotics may support patients by inhibiting the ACE2 receptor, i.e., the passage of the virus into the cell, and may also be effective in suppressing the immune response caused by the proinflammatory cytokine cascade. In patients' diet, it is crucial to ensure an adequate intake of micronutrients, such as omega-3 fatty acids (at 2-4 g/d), selenium (300-450 μg/d) and zinc (30-50 mg/d), and vitamins A (900-700 µg/d), E (135 mg/d), D (20,000-50,000 IU), C (1-2 g/d), B6, and B12. Moreover, the daily calorie intake should amount to ≥1500-2000 with 75-100 g of protein.

CONCLUSION

In conclusion, the treatment of gut dysbiosis involving an adequate intake of prebiotic dietary fiber and probiotics could turn out to be an immensely helpful instrument for immunomodulation, both in COVID-19 patients and prophylactically in individuals with no history of infection.

Gut Microbiota Modulation as a Potential Target for the Treatment of Lung Infections

The gastrointestinal and respiratory systems are colonized by a complex ecosystem of microorganisms called the microbiota. These microorganisms co-evolved over millions of years with the host, creating a symbiotic relationship that is fundamental for promoting host homeostasis by producing bioactive metabolites and antimicrobial molecules, and regulating the immune and inflammatory responses. Imbalance in the abundance, diversity, and function of the gut microbiota (known as dysbiosis) have been shown to increase host susceptibility to infections in the lungs, suggesting crosstalk between these organs. This crosstalk is now referred to as the gut-lung axis. Hence, the use of probiotics, prebiotics, and synbiotics for modulation of gut microbiota has been studied based on their effectiveness in reducing the duration and severity of respiratory tract infections, mainly owing to their effects on preventing pathogen colonization and modulating the immune system. This review discusses the role and responses of probiotics, prebiotics, and synbiotics in the gut-lung axis in the face of lung infections.

Vitamin K in COVID-19—Potential Anti-COVID-19 Properties of Fermented Milk Fortified with Bee Honey as a Natural Source of Vitamin K and Probiotics

Vitamin K deficiency is evident in severe and fatal COVID-19 patients. It is associated with the cytokine storm, thrombotic complications, multiple organ damage, and high mortality, suggesting a key role of vitamin K in the pathology of COVID-19. To support this view, we summarized findings reported from machine learning studies, molecular simulation, and human studies on the association between vitamin K and SARS-CoV-2. We also investigated the literature for the association between vitamin K antagonists (VKA) and the prognosis of COVID-19. In addition, we speculated that fermented milk fortified with bee honey as a natural source of vitamin K and probiotics may protect against COVID-19 and its severity. The results reported by several studies emphasize vitamin K deficiency in COVID-19 and related complications. However, the literature on the role of VKA and other oral anticoagulants in COVID-19 is controversial: some studies report reductions in (intensive care unit admission, mechanical ventilation, and mortality), others report no effect on mortality, while some studies report higher mortality among patients on chronic oral anticoagulants, including VKA. Supplementing fermented milk with honey increases milk peptides, bacterial vitamin K production, and compounds that act as potent antioxidants: phenols, sulforaphane, and metabolites of lactobacilli. Lactobacilli are probiotic bacteria that are suggested to interfere with various aspects of COVID-19 infection ranging from receptor binding to metabolic pathways involved in disease prognosis. Thus, fermented milk that contains natural honey may be a dietary manipulation capable of correcting nutritional and immune deficiencies that predispose to and aggravate COVID-19. Empirical studies are warranted to investigate the benefits of these compounds.

The Gut-Lung Axis in Cystic Fibrosis

Cystic fibrosis (CF) is a heritable, multiorgan disease that impacts all tissues that normally express cystic fibrosis transmembrane conductance regulator (CFTR) protein. While the importance of the airway microbiota has long been recognized, the intestinal microbiota has only recently been recognized as an important player in both intestinal and lung health outcomes for persons with CF (pwCF). Here, we summarize current literature related to the gut-lung axis in CF, with a particular focus on three key ideas: (i) mechanisms through which microbes influence the gut-lung axis, (ii) drivers of microbiota alterations, and (iii) the potential for intestinal microbiota remediation.

Neither inflammatory bowel disease nor immunosuppressants are associated with an increased risk of severe COVID-19: an observational Dutch cohort study

Conflicting data about inflammatory bowel disease [IBD] and immunosuppressants are risk factors for severe COVID-19 confuse patients and healthcare providers. Clinical reports with longer follow-up are lacking. A retrospective search was performed for severe COVID-19 (hospital admission and/or mortality) one year after the SARS-CoV-2 outbreak in an IBD cohort from one of the most affected Dutch regions. Cohort characteristics were explored by value-based healthcare data, including immunotherapy. COVID-19 cases were detected by ICD-10 codes and further examined for IBD determinants (including medication) and COVID-19 characteristics (intensive care admission, respiratory support, treatment, mortality). The national mortality register was consulted, ensuring detection of patients that died without admission. Results were compared with regional and national general population registries. The IBD cohort consisted of 1453 patients (51% Crohn’s disease, 54% women, 39.9% using immunotherapy), including children. Biologics use increased during the study. Eight cases (0.55%) had severe COVID-19: seven were hospitalized (0.48%, 95% confidence interval [CI] 0.21–1.04), and two died (0.14%, CI 0.002–0.55). Six patients had comorbidity, one used immunotherapy, and four had no medication. Both deceased patients were older than 80 years, had severe comorbidity, but used no immunotherapy. Hospitalization occurred significantly more in the IBD cohort than regionally (0.18%, CI 0.17–0.19, p = 0.015), but not significantly more than nationally (0.28%, CI 0.279–0.284). Mortality was equal in IBD patients, regionally (0.11%, CI 0.10–0.12) and nationally (0.13%, CI 0.125–0.128). Neither IBD nor immunosuppressants are associated with increased risks of severe COVID-19 in an observational study with one-year follow-up.

Applications of laboratory findings in the prevention, diagnosis, treatment, and monitoring of COVID-19

The worldwide pandemic of coronavirus disease 2019 (COVID-19) presents us with a serious public health crisis. To combat the virus and slow its spread, wider testing is essential. There is a need for more sensitive, specific, and convenient detection methods of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Advanced detection can greatly improve the ability and accuracy of the clinical diagnosis of COVID-19, which is conducive to the early suitable treatment and supports precise prophylaxis. In this article, we combine and present the latest laboratory diagnostic technologies and methods for SARS-CoV-2 to identify the technical characteristics, considerations, biosafety requirements, common problems with testing and interpretation of results, and coping strategies of commonly used testing methods. We highlight the gaps in current diagnostic capacity and propose potential solutions to provide cutting-edge technical support to achieve a more precise diagnosis, treatment, and prevention of COVID-19 and to overcome the difficulties with the normalization of epidemic prevention and control.

Investigation of SARS-CoV-2 faecal shedding in the community: a prospective household cohort study (COVID-LIV) in the UK

BACKGROUND

SARS-CoV-2 is frequently shed in the stool of patients hospitalised with COVID-19. The extent of faecal shedding of SARS-CoV-2 among individuals in the community, and its potential to contribute to spread of disease, is unknown.

METHODS

In this prospective, observational cohort study among households in Liverpool, UK, participants underwent weekly nasal/throat swabbing to detect SARS-CoV-2 virus, over a 12-week period from enrolment starting July 2020. Participants that tested positive for SARS-CoV-2 were asked to provide a stool sample three and 14 days later. In addition, in October and November 2020, during a period of high community transmission, stool sampling was undertaken to determine the prevalence of SARS-CoV-2 faecal shedding among all study participants. SARS-CoV-2 RNA was detected using Real-Time PCR.

RESULTS

A total of 434 participants from 176 households were enrolled. Eighteen participants (4.2%: 95% confidence interval [CI] 2.5-6.5%) tested positive for SARS-CoV-2 virus on nasal/throat swabs and of these, 3/17 (18%: 95% CI 4-43%) had SARS-CoV-2 detected in stool. Two of three participants demonstrated ongoing faecal shedding of SARS-CoV-2, without gastrointestinal symptoms, after testing negative for SARS-CoV-2 in respiratory samples. Among 165/434 participants without SARS-CoV-2 infection and who took part in the prevalence study, none had SARS-CoV-2 in stool. There was no demonstrable household transmission of SARS-CoV-2 among households containing a participant with faecal shedding.

CONCLUSIONS

Faecal shedding of SARS-CoV-2 occurred among community participants with confirmed SARS-CoV-2 infection. However, during a period of high community transmission, faecal shedding of SARS-CoV-2 was not detected among participants without SARS-CoV-2 infection. It is unlikely that the faecal-oral route plays a significant role in household and community transmission of SARS-CoV-2.

Melinacidin-Producing Acrostalagmus luteoalbus, a Major Constituent of Mixed Mycobiota Contaminating Insulation Material in an Outdoor Wall

Occupants may complain about indoor air quality in closed spaces where the officially approved standard methods for indoor air quality risk assessment fail to reveal the cause of the problem. This study describes a rare genus not previously detected in Finnish buildings, Acrostalagmus, and its species A. luteoalbus as the major constituents of the mixed microbiota in the wet cork liner from an outdoor wall. Representatives of the genus were also present in the settled dust in offices where occupants suffered from symptoms related to the indoor air. One strain, POB8, was identified as A. luteoalbus by ITS sequencing. The strain produced the immunosuppressive and cytotoxic melinacidins II, III, and IV, as evidenced by mass spectrometry analysis. In addition, the classical toxigenic species indicating water damage, mycoparasitic Trichoderma, Aspergillus section Versicolores, Aspergillus section Circumdati, Aspergillus section Nigri, and Chaetomium spp., were detected in the wet outdoor wall and settled dust from the problematic rooms. The offices exhibited no visible signs of microbial growth, and the airborne load of microbial conidia was too low to explain the reported symptoms. In conclusion, we suggest the possible migration of microbial bioactive metabolites from the wet outdoor wall into indoor spaces as a plausible explanation for the reported complaints.

Interplays between human microbiota and microRNAs in COVID-19 pathogenesis: a literature review

[Purpose]

Recent studies have shown that COVID-19 is often associated with altered gut microbiota composition and reflects disease severity. Furthermore, various reports suggest that the interaction between COVID-19 and host-microbiota homeostasis is mediated through the modulation of microRNAs (miRNAs). Thus, in this review, we aim to summarize the association between human microbiota and miRNAs in COVID-19 pathogenesis.

[Methods]

We searched for the existing literature using the keywords such “COVID-19 or microbiota,” “microbiota or microRNA,” and “COVID-19 or probiotics” in PubMed until March 31, 2021. Subsequently, we thoroughly reviewed the articles related to microbiota and miRNAs in COVID-19 to generate a comprehensive picture depicting the association between human microbiota and microRNAs in the pathogenesis of COVID-19.

[Results]

There exists strong experimental evidence suggesting that the composition and diversity of human microbiota are altered in COVID-19 patients, implicating a bidirectional association between the respiratory and gastrointestinal tracts. In addition, SARS-CoV-2 encoded miRNAs and host cellular microRNAs modulated by human microbiota can interfere with viral replication and regulate host gene expression involved in the initiation and progression of COVID-19. These findings suggest that the manipulation of human microbiota with probiotics may play a significant role against SARS-CoV-2 infection by enhancing the host immune system and lowering the inflammatory status.

[Conclusion]

The human microbiota-miRNA axis can be used as a therapeutic approach for COVID-19. Hence, further studies are needed to investigate the exact molecular mechanisms underlying the regulation of miRNA expression in human microbiota and how these miRNA profiles mediate viral infection through host-microbe interactions.

Oral Microbiome Dysbiosis Is Associated With Symptoms Severity and Local Immune/Inflammatory Response in COVID-19 Patients: A Cross-Sectional Study

The human oral microbiome (HOM) is the second largest microbial community after the gut and can impact the onset and progression of several localized and systemic diseases, including those of viral origin, especially for viruses entering the body via the oropharynx. However, this important aspect has not been clarified for the new pandemic human coronavirus SARS-CoV-2, causing COVID-19 disease, despite it being one of the many respiratory viruses having the oropharynx as the primary site of replication. In particular, no data are available about the non-bacterial components of the HOM (fungi, viruses), which instead has been shown to be crucial for other diseases. Consistent with this, this study aimed to define the HOM in COVID-19 patients, to evidence any association between its profile and the clinical disease. Seventy-five oral rinse samples were analyzed by Whole Genome Sequencing (WGS) to simultaneously identify oral bacteria, fungi, and viruses. To correlate the HOM profile with local virus replication, the SARS-CoV-2 amount in the oral cavity was quantified by digital droplet PCR. Moreover, local inflammation and secretory immune response were also assessed, respectively by measuring the local release of pro-inflammatory cytokines (L-6, IL-17, TNFα, and GM-CSF) and the production of secretory immunoglobulins A (sIgA). The results showed the presence of oral dysbiosis in COVID-19 patients compared to matched controls, with significantly decreased alpha-diversity value and lower species richness in COVID-19 subjects. Notably, oral dysbiosis correlated with symptom severity (p = 0.006), and increased local inflammation (p < 0.01). In parallel, a decreased mucosal sIgA response was observed in more severely symptomatic patients (p = 0.02), suggesting that local immune response is important in the early control of virus infection and that its correct development is influenced by the HOM profile. In conclusion, the data presented here suggest that the HOM profile may be important in defining the individual susceptibility to SARS-CoV-2 infection, facilitating inflammation and virus replication, or rather, inducing a protective IgA response. Although it is not possible to determine whether the alteration in the microbial community is the cause or effect of the SARS-CoV-2 replication, these parameters may be considered as markers for personalized therapy and vaccine development.

Probiotics as Adjunctive Treatment for Patients Contracted COVID-19: Current Understanding and Future Needs

The coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which rages all over the world and seriously threatens human life and health. Currently, there is no optimal treatment for COVID-19, and emerging evidence found that COVID-19 infection results in gut microbiota dysbiosis. The intestinal microbial richness of patients of COVID-19 does not return to normal levels even six months after recovery, but probiotic adjunctive treatment has been found to restore gut homeostasis. An updated PubMed search returned four finished clinical trials that supported the use of probiotics as adjunctive treatment for COVID-19, while at least six clinical trials aiming to investigate beneficial effects of probiotic intake in managing COVID-19 are currently in progress worldwide. Here in we tentatively summarized the understanding of the actions and potential mechanisms of probiotics in the management of COVID-19. We also highlighted some future needs for probiotic researchers in the field. The success in using probiotics as adjunctive treatment for COVID-19 has expanded the scope of application of probiotics, meanwhile deepening our knowledge in the physiological function of probiotics in modulating the gut-lung axis.

Probiotics for the Prevention of Acute Respiratory-Tract Infections in Older People: Systematic Review

The aim of this systematic review was to present the indirect influence of probiotics on the incidence and duration of acute upper respiratory-tract infections in older people, by regulating the immune system. Eight randomized, placebo-controlled clinical trials met the inclusion criteria, considering the threshold of older people being 60 years and over. Single strain probiotics were used in all studies, including three probiotic strains used in fermented foods: Lactobacillus delbrueckii subsp. bulgaricus OLL1073R-1, Lacticaseibacillus paracasei subsp. paracasei CNCM I-1518 and Lacticaseibacillusparacasei Shirota, and three probiotic strains used as food supplements: Loigolactobacillus coryniformis K8 CECT5711, Bacillus subtilis CU1 and Lacticaseibacillus rhamnosus GG. Current evidence showed that certain probiotic strains were better than a placebo in lowering the incidence or number of older people experiencing acute upper respiratory tract infections; however, not all probiotic strains were efficient, and not all studies reported statistically significant outcomes. More high quality large-scale properly controlled clinical studies focusing on older people are warranted.

Diabetes and coronavirus (SARS-CoV-2): Molecular mechanism of Metformin intervention and the scientific basis of drug repurposing

Coronavirus Disease 2019 (COVID-19), caused by a new strain of coronavirus called Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), was declared a pandemic by WHO on March 11, 2020. Soon after its emergence in late December 2019, it was noticed that diabetic individuals were at an increased risk of COVID-19-associated complications, ICU admissions, and mortality. Maintaining proper blood glucose levels using insulin and/or other oral antidiabetic drugs (such as Metformin) reduced the detrimental effects of COVID-19. Interestingly, in diabetic COVID-19 patients, while insulin administration was associated with adverse outcomes, Metformin treatment was correlated with a significant reduction in disease severity and mortality rates among affected individuals. Metformin was extensively studied for its antioxidant, anti-inflammatory, immunomodulatory, and antiviral capabilities that would explain its ability to confer cardiopulmonary and vascular protection in COVID-19. Here, we describe the various possible molecular mechanisms that contribute to Metformin therapy's beneficial effects and lay out the scientific basis of repurposing Metformin for use in COVID-19 patients.

Nutritional Status and the Critically Ill Patient: Gut Microbiota and Immuno-Nutrition in I.C.U. at the Time of SARS-COV 2 Pandemic

Background: Gut microbiota is a complex ecosystem of bacteria, viruses, archaea, protozoa and yeasts in our intestine. It has several functions, including maintaining human body equilibrium. Microbial “dysbiosis” can be responsible for outbreak of local and systemic infections, especially in critically ill patients. Methods: to build a narrative review, we performed a Pubmed, Medline and EMBASE search for English language papers, reviews, meta-analyses, case series and randomized controlled trials (RCTs) by keywords and their associations: critically ill patient; nutrition; gut microbiota; probiotics; gut virome; SARS-COV 2. Results: Over the antibiotic-based “selective decontamination”, potentially responsible for drug-resistant microorganisms development, there is growing interest of scientists and the pharmaceutical industry for pre-, probiotics and their associations as safe and reliable remedies restoring gut microbial “eubiosis”. Very first encouraging evidences link different gut microbiota profiles with SARS-COV 2 disease stage and gravity. Thus, there is frame for a probiotic therapeutic approach of COVID-19. Conclusions: gut microbiota remodulation seems to be a promising and safe therapeutic approach to prevent local and systemic multi-resistant bug infections in the intensive care unit (ICU) patients. This approach deserves more and more attention at the time of SARS-COV 2 pandemic.

Fecal Microbiota Transplantation during and Post-COVID-19 Pandemic

COVID-19 is a major pandemic facing the world today, which has implications on current microbiome-based treatments such as fecal microbiota transplantation (FMT) used for recurrent Clostridioides difficile infections. The bidirectional relationship between the inhabitants of our gut, the gut microbiota, and COVID-19 pathogenesis, as well as the underlying mechanism involved, must be elucidated in order to increase FMT safety and efficacy. In this perspective, we discuss the crucial cross-talk between the gut microbiota and the lungs, known as the gut-lung axis, during COVID-19 infection, as well as the putative effect of these microorganisms and their functional activity (i.e., short chain fatty acids and bile acids) on FMT treatment. In addition, we highlight the urgent need to investigate the possible impact of COVID-19 on FMT safety and efficacy, as well as instilling stringent screening protocols of donors and recipients during COVID-19 and post-COVID-19 pandemic to produce a cohesive and optimized FMT treatment plan across all centers and in all countries across the globe.