Connections and interactions have been found between the microbiome of the gut and oral-pharynx in the context of SARS-CoV-2


Researchers from Capital Medical University-China, Hong Kong University of Science and Technology-Hong Kong SAR, Tsinghua University-China and Peking University-China have in a new study found that altered microbiomes in SARS-CoV-2 infection pose threat of antibiotic resistance.

Microbiome plays a critical role in modulating the human host metabolism and immune system. Connections and interactions have been found between the microbiome of the gut and oral-pharynx in the context of SARS-CoV-2 and other viral infections, hence, to broaden the understanding of host-viral responses in general and to deepen the knowledge of COVID-19, the study team performed a large-scale, systematic evaluation of the effect of SARS-CoV-2 infection on human microbiota in patients with varying disease severity.

The study findings were published on a preprint server and are currently being peer reviewed.

We systematically evaluated the microbiota in diverse sample types of COVID-19 patients. There are alterations directly associated with disease severity in the URT, represented mainly by pharyngeal swab samples, and also in the gut microbiome. Moreover, the URT and gut microbiota show different patterns of alterations.

There is reduced microbial diversity in both pharyngeal swabs and sputum samples, which may be due to loss of normal flora and expansion of Streptococcus.

This echoes a previous study that discovered Streptococcus to be dominant in the URT of recovered COVID-19 patients, and S. parasanguinis to be correlated with prognosis in non-severe subjects [28].

In gut samples, we saw depletion of beneficial microbes, including Roseburia, Bifidobacterium, Parabacteroides and Faecalibacterium in patients, which are well-known SCFA-generating groups [52,53]. SCFAs are a subset of fatty acids produced by the gut microbiota through fermentation of partially-digestible or nondigestible polysaccharides, and play important roles in maintaining mucosal integrity, modulating metabolism, as well as regulating local and distal immune homeostasis [20,72–74].

Compared to the URT, gut microbiomes showed more dispersion and heterogeneity among patients, as well as greater distance to corresponding healthy controls, indicating a wider range of perturbed states in patient gut microbiota composition.

The human microbiome and its dynamics are important in modulating the host immune system; the recovery of microbiome homeostasis is also critical for the recovery of COVID-19 patients [75,76]. SARS-CoV-2 infection can affect multiple organs; moreover, multi-faceted long-term symptoms have been reported for patients infected with SARS-CoV-2, with around 70–80% of patients showing at least one symptom 6 months after their discharge from hospital [77].

The main symptoms were fatigue, muscle weakness, sleep disturbance, dyspnea, anxiety/depression, hair loss, loss of taste/smell, chest pain and diarrhea [78]. Incidentally, studies have shown that alteration of the gut microbiota persist in a significant subset of patients with COVID-19 even after disease resolution and clearance of SARS-CoV-2 [22,27].

One study found that gut microbiota richness was not restored to normal levels even up to 6 months after hospital discharge [79]; another recently revealed the association of gut microbiota with post-acute COVID-19 syndrome [80]. Thus far, there is accumulating evidence of respiratory tract and gut microbiota alterations as a result of SARS-CoV-2 infection, leading to depletion of normal flora and enrichment of pathogenic species along with overall reduced microbiome diversity [23,24,81].

One study with small sample size reported synchronous transition of both URT and gut microbiome from early dysbiosis towards late more diverse status in mild COVID-19 patients during hospitalization [81].

In our study cohort, both URT and gut microbiota remained relatively stable during the study period, and no obvious trend of restoration was observed. Host- or environment-specific patterns of microbiome disruption, as well as impaired host immunity at different body sites could pose varying challenges to restoring microbiome and immunological homeostasis when recovering from COVID-19.

Further investigation is needed to fully understand the role of the microbiome in host immunity against SARS-CoV-2 infection, as well as its relationship to the long-term effects post-COVID-19.

Along with changes in microbiome composition, different gene expression profiles that suggest functional changes were also observed in microbial communities of the URT and gut. An abundance of bacterial stress-response and toxin genes were detected in patients’ pharyngeal swabs and sputum.

Genes related to transport of diverse molecules were also enriched in patients’ microbiota, including components of antibiotic resistance-associated multi-drug efflux systems. Together with the discovery of reduced microbial diversity and expansion of a single microbe in the URT, this raises concerns regarding secondary infections and antimicrobial resistance in COVID-19 patients.

In the gut microbiota of patients, there was loss of genes related to fatty acid and carbohydrate metabolism, especially the depletion of SFCA-generation pathways, which is also consistent with the microbial compositional changes.

Like the URT, patients’ gut microbiota also displayed elevated molecule transport and stress-response gene expression, further highlighting the stressful microenvironment associated with SARS-CoV-2 infection.

In summary, we revealed different types of respiratory tract and gut microbiota alterations in COVID-19 patients, in terms of both microbial composition and function. We also did not observe any obvious trend of microbiome restoration during the study period, for both body sites sampled.

Moreover, the compositional and functional profiling results further raises concerns of antibiotic resistance associated with the disease, which may further hinder the recovery of normal microbiota and leave long-term effects post-COVID-19. As such, more attention to potential antibiotic resistance and microbial homeostasis during clinical care of COVID-19 patients could offer additional insights for improving outcomes.

There are some limitations to this study. Due to the urgency and special situation of this disease, and pressures on clinical resources, sampling timepoints and recordings of detailed clinical procedures were sometimes sacrificed to prioritize clinical care, resulting in missing samples at certain timepoints, or lack of sampling at baseline.

Longer follow-up after patients’ recovery would also be more helpful for evaluating the relationship between alteration patterns and the restoration of microbiota in different body sites.

Additional faecal samples from more symptomatically severe patients would also be beneficial to further elucidate the association of the gut microbiota and disease status; currently this sample type is lacking due to sampling difficulties in the clinic. Since sputum samples may contain flora from both upper and lower respiratory tract, they are therefore not a classical URT sample type.

As such, we have used them mainly to supplement our findings from the pharyngeal swab samples. It is also extremely difficult to experimentally validate the findings of potential antibiotic resistance, stress-response and toxin related microbial pathways since the original samples are of limited quantity.

We would like thank Dr. Tursi and Dr. Papa for their interest and positive comments on our study. Their comments reinforced the crucial role of gut-lung axis in the pathogenesis of SARS-CoV-2 infection and provided further evidence to support modulation of the gut microbiota as an adjunctive therapy for COVID-191.

A recent study that have analysed the stool samples of over 100 COVID-19 patients reported that individuals with lower levels of beneficial bacteria species had higher levels of inflammatory cytokines suggesting a link between an individual’s gut microbiome composition and severity of SARS-CoV-2 infection2.

It has also been found that altered gut microbiome composition persisted after recovery and may contribute to lingering symptoms, known as “long COVID”3. These data are a strong impetus for consideration of microbiota modulation to facilitate timely recovery and reduce the burden of post-acute COVID-19 syndrome.

While it is not yet fully understood how the gut microbiome influences the health of its host, one mechanism is thought to be through substances known as metabolites that bacteria release. These metabolites themselves can reach other organs and tissues and appear to have a significant influence on the immune system.

A recent study reported that patients with COVID-19 displayed impaired capacity for short-chain fatty acid (SCFA) and L-isoleucine biosynthesis in their gut microbiome that persisted after recovery and correlated with disease severity and host immune responses.

These findings suggest that strategies to supplement SCFA or L-isoleucine could be developed to improve disease outcome4.
The authors highlighted the role of high dose probiotic in improving outcomes in hospitalised patients with COVID-19 patients. Our recent data5 supported this concept.

In an open-label pilot study, we recently tested the efficacy of a newly developed probiotic formula (SIM01) which is an oral encapsulated formulation of 3 lysophilised Bifidobacteria and 3 prebiotics as an adjuvant therapy on immunologic response and gut microbiota among patients hospitalised for COVID-19.

Interestingly, we found that COVID-19 subjects who had SIM01 had hastened antibody formation against SARS-CoV-2, reduced plasma pro-inflammatory markers and showed reduction in nasopharyngeal viral load, compared with a control group. Using metagenomic sequencing, we demonstrated colonisation of the bacterial species in SIM01 which was associated with restoration of gut dysbiosis associated with SARS-CoV-25.

Recent evidence suggests that the gut microbiota is involved in the humoral immune response and could shape the B cell repertoire following vaccination6. It has been reported that differential baseline bacterial species were associated with higher vaccine response.

Specifically, the presence of an immunomodulatory bacteria, Bifidobacterium adolescentis, was associated with higher neutralising antibodies to CoronaVac suggesting that this bacteria may serve as an adjuvant to potentially overcome waning immunity of inactivated vaccine.

Although BNT162b2 vaccine induced over 90% neutralising antibody response, waning of spike-antibody levels has been reported in infection- naïve individuals over a period of 3-10 weeks after second vaccine dose 8.

Further investigation on the longitudinal assessment of the gut microbiota profile and anti-body response in the longer term will have significant implications in delineating how microbiota influences immunogenicity and long-term durability of vaccine response.

In summary, the therapeutic rationale of the modulation of the intestinal microbiota as adjunctive therapy for COVID-19 is likely to be applicable not only to improved outcome in patients with COVID- 19 but also to improve vaccine response and reduce vaccine-related side effects.

Well-design clinical trials will be important to advance our knowledge on the potential of gut microbiota manipulation as an adjuvant therapy for SARS-CoV-2 infection and/or immunization schedule.


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