Coronavirus disease-19 (COVID-19), a global pandemic caused by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses unprecedented challenges to both the world economy and healthcare services (1). Contrary to initial public optimism, COVID-19 appears to be accompanied by influenza for an extended period of time. COVID-19 patients generally manifest with fever, cough, dyspnea and gastrointestinal symptoms (2). Research has demonstrated that symptoms of the gastrointestinal tract may precede respiratory symptoms (3, 4). However, the underlying pathogenic mechanisms and factors influencing COVID-19 remain unclear. Furthermore, understanding the similarities and differences between influenza and COVID-19 is crucial as they may interact or coexist. Several factors have been identified to affect the severity and mortality rate of COVID-19 patients (5, 6), with the microbiome emerging as a significant environmental factor requiring urgent investigation.

The human microbiome represents a complex microecosystem that plays a vital role in maintaining health. Various microbes interact and grow together in healthy individuals, forming a strict symbiotic relationship (7, 8). Owing to the specificity of microbial niches, the composition and function of microorganisms vary according to different parts of the human body, such as the gastrointestinal tract, skin, and airway (9). Microorganisms are currently considered to be associated with the development and progression of various diseases.

While severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily targets the respiratory tract. However, through several pathways characterized by enhanced intestinal epithelial-expressed angiotensin-converting enzyme 2 (ACE2) receptor, transmembrane protease serine 2 (TMPRSS2), and TMPRSS4, the gastrointestinal tract can also be infected with SARS-COV-2 (10, 11). Extensive research has demonstrated a dysbiotic microbiome in COVID-19 patients compared to no COVID-19 controls/influenza. Through 16S ribosomal RNA (rRNA) sequencing of the gut microbiome, Gu et al. found that COVID-19 patients were characterized by decreased α diversity compared to healthy controls, whereas showed increased Shannon index when compared with H1N1 patients (12). Moreover, metagenomic sequencing results revealed that several pharyngeal microbiomes were positively related to severe COVID-19 patients and elevated systemic inflammation markers, including Klebsiella spp. and Acinetobacter spp. (13). Meanwhile, COVID-19 patients, especially severe patients, exhibited a lower Shannon index compared with influenza B patients (13). A recent study reported a partially restored gut and throat swab microbiome of COVID-19 patients during hospitalization, although at a slower rate (14). Nevertheless, consistent robust findings have not been reported thus far. Moreover, the differences and similarities between influenza, a common respiratory infectious disease that currently breaks out frequently, and COVID-19 remain incompletely understood. Therefore, a systematic review of existing reports on the microbial change in COVID-19/influenza is critical.

This study focused on investigating the gut and respiratory tract microbiome of patients with COVID-19 and influenza. Additionally, a comprehensive analysis was conducted to explore the variations in microbiome among COVID-19 patients with different disease severities. The key findings of this study were as follows: (1) The Shannon index was more likely to decrease in patients with COVID-19/influenza versus no COVID-19/influenza controls. Meanwhile, The Shannon index of the gut and respiratory tract samples was also more likely to decrease in COVID-19 patients with more severe symptoms. (2) Most studies reporting β-diversity showed altered β-diversity in COVID-19/influenza patients. (3) In terms of specific microbial abundance changes, the intestinal microbiome of COVID-19 patients was characterized by elevated opportunistic pathogens along with reduced short-chain fatty acid (SCFAs)-producing microbiota. Similarly, both COVID-19 and influenza patients showed increased levels of Lactobacillus while experiencing reduced levels of Haemophilus and Neisseria within their respiratory tracts.

In this meta-analysis, the Shannon index of COVID-19/influenza patients was reduced versus no COVID-19/influenza controls, which is consistent with the results of previous researches (17, 18). Furthermore, when comparing COVID-19 patients with non-COVID-19 patients primarily presenting other respiratory symptoms such as flu and pneumonia, the Shannon index showed no significant difference. Meanwhile, the microbial abundance changes in COVID-19 and influenza were partially similar. The above evidence indicates that the microbial structure of COVID-19 is more likely to be similar to influenza. Several articles have described the microbial structures in COVID-19 patients compared to influenza patients, however, there were no consistent changes in these studies. Rattanaburi et al. employed 16S sequencing to conduct a comparative analysis of the upper respiratory tract microbiota in patients afflicted with influenza and COVID-19, the Shannon diversity index in influenza A and B groups exhibited a significantly lower level compared to that observed in non-influenza and COVID-19 groups (19). Opposite findings were obtained from another study employing metagenomic sequencing, the species-level alpha-diversity of the oropharyngeal microbiota is significantly reduced in COVID-19 patients compared to influenza patients, particularly among critically ill individuals with COVID-19 (13). Notably, both diseases share similarities including targeting respiratory epithelium cells and exhibiting similar symptoms (20, 21). Given their global impact as mainstream respiratory diseases affecting billions of people worldwide (22), it is crucial to enhance our understanding of differential diagnosis and distinctions between COVID-19 and influenza. However, the current understanding of SARS-CoV-2 and influenza remains inadequate. In the future, researchers need to further explore the underlying mechanisms. For example, whether consider microbial regulation methods such as fecal transplantation to treat influenza, COVID-19 and the long-term symptoms they cause in the future treatment strategy.

In this study, the respiratory and intestinal microbiomes of COVID-19 patients displayed distinct changes in microbial abundance. The intestinal microbiome is characterized by rising opportunistic pathogens (Enterococcus, Escherichia, Eggerthella, Fusobacterium) (23–25) and relatively diminished short-chain fatty acid (SCFAs) -producing microbiota (Anaerostipes, Coprococcus, Faecalibacterium, Roseburia) (26, 27). Interestingly, three studies reported increased Flavonifractor in recovered COVID-19 patients versus no COVID-19 controls. Flavonifractor is generally considered a butyrate-producing microbiota (27), suggesting potential improvement in the gut microbiome during recovery from COVID-19. Pseudomonas, as an opportunistic pathogen with drug resistance (28), was found to be enriched in the respiratory tract of patients with influenza.

It is worth noting that Enterobacteriaceae (including Escherichia and Enterococcus), as opportunistic pathogens, were not only enriched in the gut and respiratory tract of COVID-19 patients, but also in the gut of severe COVID-19 patients. Enterococcus is one of the most important pathogens causing healthcare associated infections (29). Recent research has revealed the gene expression of platelet aggregation and neutrophil degranulation was positively related to Enterococcus faecalis (30), especially in patients with severe COVID-19, suggesting potential involvement of the microbiome in COVID-19 progression. Furthermore, Enterococcus exhibits resistance to several commonly used antimicrobials (31), which may impede the recovery process of COVID-19 patients. Several SCFAs-producing microbiota were reduced in the gut of COVID-19 patients. Meanwhile, research has demonstrated that even after recovery from COVID-19, the depletion of SCFA-producing microbiota remains sustained (32). Depletion of SCFA-producing microbiota has been associated with various diseases including inflammatory bowel disease, depression, and rheumatoid arthritis (33–35). SCFAs are microbial metabolites with anti-inflammatory effects. The infection of SARS-CoV-2 may lead to disturbances in the intestinal environment, and eventually destroy the living environment of other symbiotic bacteria (27). Haemophilus is a common pathogen in human (36), although several studies have reported reduced Haemophilus in the respiratory tract of patients with COVID-19 and influenza. However, Haemophilus influenzae, a resident microbiome within the upper respiratory tract capable of causing secondary respiratory infections, is more likely to be increased in the respiratory tract of COVID-19 patients (37). The future necessitates further investigation into the underlying factors of changes in Haemophilus by researchers.

The upper respiratory tract and lower respiratory tract demonstrated similar microbial structures; one hypothesis is that the pathogenic microorganisms in oropharyngeal secretions may “micro aspirate” into the lungs (38, 39). Disturbances in the balance between migration and elimination of the lung microbiome during lung disease can lead to alterations in its composition, with bacteria possessing a competitive advantage becoming dominant. The epithelial barrier of the gut prevents the invasion of pathogenic microorganisms and helps maintain tolerance to food antigens; it may also be involved in systemic and pulmonary immune functions. Once compromised, microbes can migrate to the bloodstream or lungs, triggering sepsis or acute respiratory distress syndrome (40, 41). Meanwhile, some metabolites of gut microbiota in digestion, including SCFAs, can affect the human immune system, which in turn can control inflammation in the lungs. Accumulating evidence underscores the interplay and connection between the gut and lungs known as the gut-lung axis (42–44).

The composition and functional homeostasis of the human microbiota play a crucial role in maintaining and regulating normal immune function as well as combating infections (45, 46). The microbiome between the respiratory tract and gut exists in complex interactions. First, SARS-CoV-2 infection can induce lung tissue damage and trigger cytokine storms by promoting pro-inflammatory pathways such as NF-κB and TNF pathways (47–49). On the other hand, intestinal infection can lead to direct damage to the intestinal structure, further causing inflammation, and eventually leading to the disorder of gut and respiratory microbiota (50). In the gut and respiratory tract of COVID-19 patients, the absence of beneficial bacteria or the overgrowth of opportunistic pathogens may exacerbate the inflammatory response in the body, leading to the exacerbation of symptoms.

This study has several limitations. First, the lack of data on microbial diversity and abundance changes in numerous studies hinders the acquisition of robust conclusions. Additionally, there is currently no consistent standard for defining severe and mild COVID-19 patients in each articles. However, considering the necessity of investigating the microbial differences in COVID-19 patients with different severity, we extracted microbiome data from people with more severe symptoms (for example, Severe group, ICU group, and deceased group) versus patients with milder symptoms (for example., mild group, no ICU group, and live group). In future research endeavors, it is imperative to explore microbial changes across different levels of COVID-19 severity. Long-term cohorts are also in urgent need of investigating microbial changes and potential influencing mechanisms during recovery, particularly given the growing attention to the issue of ‘long COVID-19.’ Moreover, the meta-analysis exhibits a high degree of heterogeneity, which may impact the robustness of the conclusions. High heterogeneity is a common problem in current microbiome-related meta-analyses, not only in COVID-19, but also in other diseases (16). The elevated heterogeneity could be attributed to various factors such as variations in sequencing methods employed across studies and unavailability of raw data within any included studies. Despite employing multiple approaches to explore the sources of heterogeneity, satisfactory results were not obtained. Finally, we are not clear about the potential impact of drugs (antibiotics and proton pump inhibitors) and other demographic factors on the microbiome throughout the entire process of onset and recovery.

In this comprehensive review and meta-analysis, our results demonstrated the microbial composition of COVID-19 patients may be similar with influenza patients, manifested as declining Shannon index and similar microbial abundance change. After clearing the disease state, some SCFA-producing microbiota may be partially restored after clearance of SARS-CoV-2. Moreover, COVID-19 with different severity exhibits distinct microbial construction.

The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.

X-JC: Data curation, Methodology, Writing – original draft. D-DS: Data curation, Methodology, Writing – original draft. M-HZ: Data curation, Methodology, Writing – original draft. X-ZC: Formal analysis, Validation, Writing – original draft. NC: Formal analysis, Data curation, Writing – original draft. ML: Formal analysis, Project administration, Writing – original draft. B-ZL: Conceptualization, Investigation, Writing – review & editing. S-HL: Software, Writing – original draft. SH: Software, Writing – review & editing. J-BW: Formal analysis, Writing – review & editing. LG: Investigation, Writing – review & editing.