Gut microbiota
It is proven that the angiotensin-converting enzyme 2 (ACE2) is the main receptor for COVID-19 which is expressed in many organs inside the human body including the lungs, small intestine, kidneys, and skin epithelium [83]. Thus, all these organs could be a possible target for SARS-CoV-2. In addition, GI symptoms including nausea, vomiting, and diarrhea have a high prevalence among COVID-19 patients, and these patients have been shown to have more severe conditions compared to patients lacking GI symptoms [84, 85]. On the other hand, it has been shown that acute respiratory disease syndrome (ARDS)-which is the major cause of mortality among COVID-19 patients-is an outcome of a deregulated inflammatory cascade and uncontrolled cytokine production and increased interleukin (IL), tumor necrosis factor (TNF), and C-reactive protein (CRP) levels [86]. Recent research has unraveled the possible role of gut microbiota in regulating of the immune system. Gut bacteria impact the lungs' microbiota by producing a wide variety of substances including endotoxins, metabolites, and intestinal hormones which are also known as the gut–lung axis [87]. Therefore, the presence of the virulent microbiome in the gut-lung axis can cause a pro-inflammatory reaction and cytokine release which is called gut dysbiosis [88, 89]. Additionally, it is proven that gut dysbiosis has a role in the pathogenesis of several diseases including; inflammatory bowel disease, Parkinson’s disease, celiac disease, diabetes, colorectal cancer, and chronic respiratory diseases like COPD, and Asthma [90–95]. Similarly, there is evidence that altered gut microbiota composition has a crucial role in the severity and virulence of bacterial and viral infections [96]. Many studies have reported gut dysbiosis among COVID-19 patients and noted that it would be a major contributor to poor outcomes [97].
Dysbiosis
The majority of human gut bacteria comprises the following microbial phyla; Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobiac with Firmicutes and Bacteroidetes making up over 90% of the total gut microbiota [98–100]. These bacteria can regulate and control the immune response and defense system via a variety of mechanisms, and any imbalance in their composition can lead to immune dysfunction and pathogenesis [101, 102]. This imbalance which is also called gut dysbiosis has been reported in almost all included studies in our systematic review, in total 25 studies, investigated the two-way dynamics between COVID-19 and gut microbiota mostly via fecal/colon sampling.
In general, the main alternations in the gut microbiome of COVID-19 infected individuals were the higher abundance of; Bacteroides, Streptococcus, Fusobacterium, Campylobacter, Lactobacillus, Proteobacteria, Enterococcaceae, Enterococcus, Rothia, Pseudomonas, Veillonella, Clostridium, and Staphylococcaceae, and lower presence of; Coprococcus, Faecalibacterium, Eubacterium, Roseburia, Bifidobacterium, and Blautia. In our review, five studies reported an increase in Bacteroides in COVID-19 patients [51, 61, 78–80] while only one reported a decrease in them [42]. These studies observed a rise in Bacteroides stercoris, Bacteroides dorei, Bacteroides vulgatus, Bacteroides massiliensis, Bacteroides oleiciplenus, and Bacteroides ovatus as main species in fecal samples of COVID-19 patients. Additionally, one study reported an increase in Bacteroides fragilis in afebrile COVID-19 patients. Bacteroides have a crucial role in the gut microbiome and their alterations have been linked to several diseases [103–105]. Additionally, It can be interpreted that the increasing levels of the Bacteroides family in COVID-19 patients’ gut microbiome may assist with the clearance of the virus, as it is shown that Bacteroides may be able to downregulate ACE-2 receptor expression[106];thus, they can limit SARs-CoV-2 replication in the gut. On the other hand, the overuse of antibiotics among COVID-19 cases can cause an increase in Bacteroides caccae; while, in patients who have not received antibiotics, Bacteroides nordii is more common [106]. Bacteroides dorei is a controversial bacterium because of the available evidence regarding its increase and decrease among COVID-19 patients and the fact that they also can downregulate the ACE-2 receptor but they are also linked to some pro-inflammatory cytokines [107].
Blautia spp. was another common genus mentioned by four articles in our review. One study reported a decrease in the levels of this bacterium [75], while another study reported increasing patterns of this bacteria [42]; in addition, its presence in the gut microbiome of CRC patients has been linked to more severe disease[44] and increased levels of this bacterium have been reported after COVID-19 recovery [46]. In a similar study investigating the alterations of gut microbial composition among COVID-19 patients, the authors reported declining beneficial species and increasing opportunistic pathogens such asBlautia sp. That its abundance is associated with more severe illnesses [108]. Additionally, another study concluded the same and identified the abundance of Blautiaobeumas a predictor of disease severity [109].
Two studies investigated Clostridium spp. among COVID-19 patients. One reported decreasing levels of Clostridium nexile [61], and the other article reported an association between Clostridium ramosum and Clostridium hatheway with severe forms of COVID-19 disease and noted that they may predispose patients to portal vein thrombosis [20]. In similar studies, it has been shown that Clostridium leptum is positively correlated to neutrophil counts in COVID-19 patients; while Clostridium butyricum is negatively correlated [38]. Additionally, it is proven that NK activity is negatively associated with Clostridium ramosum, and Clostridium symbiosum [110]. Some studies have reported that increasing levels of Clostridium difficile can worsen COVID-19 patients' condition [111, 112].
Five studies reported alterations in Streptococcus spp., in fecal samples of COVID-19 patients. Four studies reported increasing levels of this bacterium [29, 42, 61, 73] and two articles specified Streptococcus thermophilus [61], and Streptococcus infantis [29] as the main increasing bacteriain COVID-19 patients’ gut. On the other hand, two studies reported a decrease in this bacterium level[61, 69]; Li et al. specified Streptococcus salivarius as the main decreasing species [61]. Some studies have noted the increase in Streptococcus spp. would be an indicator of opportunistic pathogens abundance [113, 114]. One study has indicated that Streptococcus salivarius colonization can limit the incidence of some viral respiratory tract infections among COVID-19 patients [115]. In other studies, Streptococcus increase has been linked to the excessive expressions of pro-inflammatory cytokines including; IL-18, TNF-α, and IFN-γ that can exacerbate the clinical outcomes among COVID-19 patients [114, 116]. Streptococcus thermophilusis was also reported to positively correlate with the severity of COVID-19[61]. It is also proven that Streptococcus spp. can impact the lung microbiome and direct it into a more inflammatory condition [117].
Regarding Lachnospira, two studies noted alterations of this bacteria in the gut microbiome of COVID-19 patients, one reported an increase [61] while the other study reported a decline in its levels [27]. Lachnospira is a short-chain fatty acids (SCFAs) producing bacteriathat assist with gut homeostasis. Several studies have reported similar findings among COVID-19 patients [105, 110, 118, 119].
Coprococcus genus changes were reported by two articles, and both articles reported a declining pattern of this bacteria in the gut microflora of COVID-19 patients [61, 75]. One specified the Coprococcuscatus as the main decreasing species [61]. A similar studyby Cao et al. showed that Coprococcuscatuscould decrease among antibiotic-receiving COVID-19 patients [110]. In addition, one study found lower relative levels of Coprococcus, in COVID-19 patients compared to both flu patients and healthy cases [120]. Coprococcus comes was also reported to be positively correlated with CD3+/CD4+/CD8 + lymphocyte counts [109].
Two studies reported decreasing trends of Eubacterium bacterium among COVID-19 patients’ gut microflora [61, 78]. Eubacterium hallii and Eubacterium rectale were the main species that declined. Many other studies have also noted the decreasing levels of this bacterium that can be linked to antibiotic overuse among COVI-19 patients [106, 121]. On the other hand, Some species of this genus including Eubacterium ventriosum have been shown to have anti-inflammatory effects in CD4 + and CD8 + T cells, and produce butyrate and modulate the immune system response; thus, its decline can worsen the conditions of COVID-19 patients [110].
Fusobacterium ulcerans was unique bacteria found in COVID-19 patients’ microflora [61]. It has been found that the abundance of Fusobacterium among hepatits B-positive patients would result in increasing levels of pro-inflammatory factors including IL-6 and IL-1β [122]. One study has reported 4 cases of Fusobacterium nucleatum septicemia as a possible complication of COVID-19 which can be due to the dysbiosis caused by SARS-CoV-2[123].
Three studies investigated the alterations of Campylobacter genus in the gut microbiome of COVID-19 patients. Two studies reported increasing levels of this bacteria [67, 75], and one study associated this genus with a more severe disease [24]. One Similar study has reported the abundance of Campylobacter gracilis among severe cases of COVID-19[110]. Also, one study has mentioned Campylobacter among the top three abundant opportunistic pathogens [124].
Corynebacterium genus variations in the gut microbiome of COVID-19 patients had an oscillating pattern. One study reported an increase in its levels [67], while one other study reported a decrease of this bacteria [75]. In a similar study, Corynebacterium durum was reported to be increased among severe COVID-19 cases [110].
Four studies stated a decrease in Bifidobacterium genus in COVID-19 patients’ gut microbiome[42, 69, 78, 79] while only one study reported an increase in this genus [61]. Although Bifidobacterium longum was reported as the main increasing species [61], Bifidobacterium adolescentis was reported by another study as the decreasing bacteria [79]. In addition, one study linked Bifidobacterium to COVID-19 viral load [75]. Many species of these genera including; Bifidobacterium animalis, B. longum and B. bifidum reduce the levels of inflammatory cytokines like tumor necrosis factor-α (TNF-α), and enhance the anti-inflammatory cytokine IL-10 thus in general have anti-inflammatory effects [125]. In addition, the scientific society has a particular interest in this bacterium as a probiotic with anti-inflammatory properties for the treatment of many conditions ranging from IBD to Clostridioides difficile infection [126, 127]. Also, Bifidobacterium spp. possess immunomodulatory effects via affecting Th17 pathway and in the improvement of the inflammatory response [128–130]. In general, Bifidobacterum reduces cell injury by inhibiting TNF-α and macrophages by enhancing Treg response [131]. Similar studies also reported a decline in Bifidobacterium of COVID-19 patients’ gut microbiome and concluded that this decline would cause a reduced immune function, thus will result in a symptomatic SARS-Cov-2 infection [132]. All this information emphasizes the vital effects of this genus in regulating the immune system and outlines that its decline among COVID-19 patients would have detrimental impacts on the prognosis and severity of the disease.
Increasing levels of Lactobacillus genus in the COVID-19 patients’ gut microbiome were reported by two studies [50, 79]. While one study reported a decline in Lactobacillus spp. in the samples of COVID-19 patients [133]. One similar study conducted in China noted gut dysbiosis among COVID-19 patients with decreased levels of Lactobacillus [134]. It has been shown that gut commensals including lactobacillus release SCFA such as butyrate, propionate, and acetate which attach to dendritic cells and macrophages and regulate the immune system. It has been demonstrated that Lactobacillus casei enhances the phagocytic activity of macrophages and would cause the excessive expression of IgA, IFN-γ, and TNF-α and possess protective features against flu virus infections. Also Lactobacillus paracasei, and Lactobacillus rhamnosus improve the efficacy of H1N1, H5N1, and H3N2 vaccines response [135]. These studies signify the important effects of this bacterium in the gut microbiome of COVID-19 patients as an anti-inflammatory genus [136], additionally, its decline has been associated with prolonged use of doxycycline and hydroxychloroquine [137].
A decrease in Roseburia genus (butyrate-producing) was reported and linked to severe COVID-19 infection [27]. Similar findingsindicating a decline of this genus in COVID-19 patients and other upper respiratory tract viral infections including influenza were documented in other studies [20, 88, 110, 138]. Roseburia, also has been shown to be reduced in patients with IBS, metabolic syndrome, and obesity. Roseburia is an anaerobic SCFA-producing bacterium. SCFA is a crucial substance in the prevention and reduction of inflammation via regulation of anti-inflammatory cytokines like IL-10 and it maintains mucosal integrity, also SCFAs limit the opportunistic pathogens' overgrowth, and improve antiviral immunity [139, 140]. Thus, its possible decrease in COVID-19 patients would predispose them to a more severe disease course.
Alterations in Proteobacteriagenus were indicated in three studies, two of them reported increasing patterns among COVID-19 patients [27, 77], while only one reported a decline [51]. This bacterium’s increase has also been reported by Khan et al. among COVID-19 patients [118], and one study reported an abundance of Proteobacteria genus in the blood microbiome [133]. A higher presence of Proteobacteria has been demonstrated also in influenza virus infection [141].
Faecalibacterium genus alterations were reported by only two studies. One study has reported a decline in Faecalibacteriumprausnitzii in COVID-19 patient gut microflora samples [78], while the other included study reported an increase in this genus [42]. Similarly, a significantly lower abundance of Faecalibacterium among COVID-19 patients was reported by Hazan et al., who also reported that the increase of Faecalibacterium genus and F. prausnitzii species was inversely associated with SARS-CoV-2 positivity and COVID-19 severity [132]. In addition, many studies have linked Faecalibacterium decrease to COVID-19 severity [38, 117]. Faecalibacterium produces butyrate and this substance would eventually affect intestinal mucosa and enhance its integrity[142]. Similarly, one study has reported the effects of Faecalibacteriumprausnitzii in the gut microbiota and reported that it negatively correlates with inflammatory bowel disease relapse, which also proposes the fact that this species would modulate auto-inflammatory reactions similar to those that occur in COVID-19 [143].
Firmicutes genus had an alternating pattern of changes in the gut microbiome of COVID-19 patients. One study reported that Firmicutes was observed more among negative or recovered COVID-19 patients [46] and two studies reported declining patterns of this genus [50, 55] while, two other studies indicated that this genus was increased in COVID-19 patients’ gut flora[59, 77]. In addition, one study has shown that the Firmicutes to Bacteroidetes had increased among acute COVID-19 patients[59]. Conversely, another study reported the opposite and stated that this ratio had declined among them [61]. Khan et al. also reported that the abundance of Firmicutes in the COVID-19 patients has decreased significantly, and also indicated a gradual decline in Firmicutes to Bacteroidetes ratio from mild to severe COVID-19 infected groups [118], similarly this decline has been reported in conditions such as follows; systemic inflammation, cognitive disorders, Crohn’s disease, depression, and diabetes mellitus type 2 [144, 145]. Some similar studies investigated Systemic Lupus erythematosus (SLE) and reported a low Firmicutes/Bacteroidetes ratio among SLE patients [146, 147]. All these studies, highlight the possible effects of Firmicutes and Firmicutes to Bacteroidetes ratio, on inflammatory and autoimmune reactions in a variety of diseases such as COVID-19.
Three studies demonstrated Enterococcaceae and Enterococcus changes and reported their abundance in COVID-19 patients’ gut samples [50, 75, 80]. Zou et al. specified Enterococcus faecalis as the main increasing species among COVID-19 patients that had fever [80]. Tang et al. also stated that Enterococcus to Enterobacteriaceae ratio could change in severe/critical COVID-19 cases, and it significantly rose in deceased patients compared to survivors, thus this index can have a predictive value for ill COVID-19 patients [148]. In one study among ALL patients,Enterococcaceae gut abundance had a predictive value for febrile neutropenia and diarrhea after chemotherapy [149]. Therefore, Enterococcus abundance would play an important role in the severity and poor outcomes of COVID-19 patients.
Rothia genus increase in the gut flora of COVID-19 patients was reported by two studies [73, 75]. Similarly, other studies have reported increasing levels of opportunistic bacteria including Rothia spp. among COVID-19 patients[88, 150]. Some studies have previously reported possible associations of this bacterium with lung injuries [13, 106]. One study reported that Rothia was higher even among recovered patients compared to the control group, which would be indicative of COVID-19 long-term effects on gut microbiota. Rothia is also found to be correlated with Th17-induced inflammation in the lungs and pneumonia among immunosuppressed individuals [151, 152], its abundance in gut flora would indicate the migration of bacteria from the respiratory tract to the intestines.
Pseudomonas genus changes in gut flora were reported by only two articles, one reported a decrease in the gut microbiome of COVID-19 patients [75];whileanother study reported an increase in this genus levels [77]. Prasad et al. also reported an abundance of Pseudomonas spp. in blood samples of COVID-19 patients[133]. Pseudomonas was among the most predominant genera in the lung microbiome of COVD-19 patients [153, 154].
Collinsella was reported by three included studies in our review, one study reported an increase in Collinsellaaerofaciens species [29], while other studies stated that this genus’ levels had decreasing patterns in the gut microflora of COVID-19 patients [69, 75]. Collinsella, is reported by some studies in the gut microbiome of severe cases of COVID-19 patients. One study reported that this genus has shown to produce ursodeoxycholate which is a substance that has the following effects: limits SARS-CoV-2 attachment to ACE-2, suppresses inflammatory cytokines including TNF-α, IL-1β, IL-2, IL-4, and IL-6, and has anti-apoptotic and antioxidant features, the same study concluded that lower presence of Collinsella was associated with high COVID-19 mortality while its normal presence was significantly correlated to lower mortality rates among COVID-19 patients [155].
In regards to Ruminococcus genus, one study reported increasing levels of this bacteria in the gut flora of CRC patients that would predispose them to more severe COVID-19 disease [44], and another study found a negative association between this bacteria and COVID-19 viral load [75]. Similar studies have reported a high abundance of Ruminococcusgnavus, and Ruminococcus torques species among COVID-19 patients[156]. In addition, some studies have indicated the co-occurring and possible detrimental effects of Ruminococcusgnavus and Ruminococcus torques in the pathogenesis of inflammatory bowel disease and also demonstrated that these species result in higher proinflammatory cytokine release [157, 158]. On the other hand, some studies have reported decreasing levels of Ruminococcusbromii, and Ruminococcusobeum in the gut flora of COVID-19 patients [20, 159]. One study reported that declining levels of Ruminococcusobeum could be a subsequent result of antibiotics overuse in COVID-19 patients [160].
One study had reported increasing levels of fungal microorganisms including; Aspergillus flavus, Aspergillus niger, and Candida Albicans in the gut microbiome of COVID-19 patients [82]. On the other hand, the study by Lv et al. reported a decrease in Aspergillus rugulosus, Aspergillus tritici, and Aspergillus penicillioidein COVID-19 patients’ gut microbiome [159].
Veillonella genus increase among COVID-19 patients was reported by three articles [50, 73, 75]. Similarstudies have reported the abundance of this bacterium in the gut microbiome composition of COVID-19 patients, and one specified Veillonellaparvula as the main increasing species [88, 110, 161]. One study also indicated that Veillonella may be associated with the severity of COVID-19 [161].
Staphylococcaceae genus changes in the gut microbiota of COVID-19 patients were reported by two articles [24, 50]. One study associated Staphylococcus epidermis with a more severe course of diseases [24], and the other study reported increasing levels of this bacteria in the gut microbiome among COVID-19 patients[50]. Similarly, one study reported the abundance of Staphylococcaceae spp. in serums samples of COVID-19 patients [133].
Severity
Five articles included in our study reported that gut microbiota composition can be a predictive factor in the severity of COVID-19 disease [24, 27, 61, 71, 78], and only one study reported no such association [67]. It has been shown that normal gut microbiota can decrease the severity of the COVID-19 course [20, 24, 42, 43]. Babszky et al reported that Bacteroidetes spp. in the feces has an anti-inflammatory effect and possess protective features against severe COVID-19 infection [43]. Similarly, Dereschuk et al. reported that Less severe COVID infection can be associated with the presence of Bacillus subtilis spp. In blood microbiotas [24]. Also, Zuo et al. reported that Faecalibacteriumprausnitzii has a negative correlation with the severity of the disease.
On the other hand, nine studies reported possible associations of some gut bacteria genera with more severe forms of COVID-19 [20, 24, 27, 28, 44, 50, 69, 78, 79]. In a study by Dereschuk et al., COVID-19 infection was severe among patients with blood microbiota as follows: E. coli, Bacillus, Campylobacter hominis, Pseudomonas, Thermoanaerobacterpseudethanolicus, Thermoanaerobacteriumthermosaccharolyticum, and Staphylococcus epidermis [24]. Also, loss of beneficial microorganisms was reported to increase potential pathogens for instance Enterococcus, especially among ICU patients [50]. Moreira-Rosário et al. reported a decrease in butyrate-producing bacteria including; Roseburia spp., Lachnospira spp., and an increase in Proteobacteria spp. among moderate and severe COVID-19 patients’ gut microbiota [27]. Similarly, Reinold et al. found that a reduction in butyrate-producing bacteria could be linked to more severe disease [69]. Zhang et al. mentioned that the alterations in the gut microbiota of COVID-19 patients can reduce the levels of L-Isoleucine, SCFA (Short-Chain Fatty Acid), and L-Isoleucine even one month after recovery and this would result in more severe diseases [79]. Finally, it was reported by Zuo et al. that Coprobacilum spp., Clostridium Ramosum, and Clostridium hathewayi were associated with more severe diseases [20]. One similar systematic review stated that Bifidobacterium, Bacteroides, Corynebacterium, Ruminococcus, Parabacteroides, Campylobacter, Clostridium, Ruminococcus, Rothia, Enterococcus, Megasphaera, Enterococcus, and Aspergillus had high abundance among severe COVID-19 patients while, Lachnospira, Roseburia, Faecalibacterium, Eubacterium, and Firmicutes/Bacteroidetes ratio had declined among severe COVID-19 cases [97]. Other similar studies also have noted the higher abundancy of opportunistic pathogens including; Veilonella, Streptococcus, Rothia, and Actinomyces [20, 88], and declining levels of beneficial commensal bacteria such asRoseburia, Agathobacter, Fusicatenibacter, and Ruminococcaceae among moderate to severe COVID-19 patients [20].
Diversity and Richness
Some articles noted alterations in microbiome diversity and richness among COVID-19 patients; two articles reported an increase in gut microbial diversity [42, 59], while four noted a decrease in general microbiome diversity, alpha diversity, and Shannon index among COVID-19 patients [28, 46, 50, 55]. Additionally, two articles only mentioned alterations in Chao, Simpson, Alpha, and Beta diversity indices of the gastrointestinal microbiome and did not specify the trends [73, 75]. In addition, three studies reported a rise in opportunistic bacteria in the gut microflora and a significant loss of beneficial gut microbial barrier among COVID-19 cases [20, 29, 81].
Viral Load
Only two articles investigated the relations between gut microbiota and COVID-19 viral load, one reported no relation between COVID-19 viral load and gastrointestinal microbiome [42], while the other one noted that in the gut microbiota, Prevotellacopri, and Eubacterium dolichum were associated positively with SARS-CoV-2 viral load, and Streptococcus anginosus spp., Dialister spp., Alistipes spp., Ruminococcus spp., C. citroniae spp., Bifidobacterium spp., Haemophilus spp., and Haemophilusparainfluenza were linked negatively to this load [75].
Upper respiratory tract microbiota
The relation between the microbiota of the upper respiratory tract (URT), including nasopharyngeal, oropharyngeal, and respiratory tract, and COVID-19 as a viral respiratory disease is an intricate, two-sided, and dynamic association. In the current review, 24 studies discussed the role of URT microbiota in the pathogenesis of COVID-19 infection. The impact of URT microbiota on the preservation of the lung immune system is one of the important aspects as it correlates with respiratory infections [45, 74, 162]. Unusual changes in URT microbiota in COVID-19 patients, especially moderate and severe patients, were reported in comparison to healthy individuals [21, 45]. The richness of microbiota was higher in COVID-19 patients [57, 72] and most of them were opportunistic bacteria [56]. COVID-19 infection may induce URT microbiota to multiply the inflammatory bacteria like Haemophilusinfluenzeae and parainfluenzae which are associated with acute respiratory diseases like pneumonia [45]. Also, it may increase Neisseria subflava; which is less abundant of it in COVID-19 patients are significantly related to a high rate of mortality [21, 45]. The high level of Klebsiella and Serratia were also associated with more severe diseases [25].
We found that the duration of hospitalization in ICU and the type of oxygen therapy have a higher impact on the composition of microbiota compared to SARS-CoV-2 viral load [22, 54]. Certainly, microbiome dysbiosis (Bacteria, viruses, and archaea) can cause an abnormal inflammatory response that could lead to a poor outcome of COVID infection [56]. A notable association between URT and inflammatory Cytokines levels (like IL-6, TNF-α, and IL-1b) was observed and it can explain the significant link between URT microbiota and COVID-19 severity and mortality rate [70, 72]. These statements are consistent with the findings of some studies about the higher reduction of anti-inflammatory metabolic factors in long COVID-19 patients treated with antibiotics, invasive mechanical ventilation, and ICU admission compared to mild patients [22, 45, 54, 62]. In addition, a quick return of dysbiosis level to normal values during recovery in mild COVID-19 cases was reported [47, 53]. Jing Liu at al. found that the microbiota level of COVID-19 patients after recovery becomes near similar to that of healthy individuals [62].
Some studies showed that the abundance and diversity of URT microbiota in severe and moderate COVID-19 patients had no significant difference in comparison with mild COVID-19 patients and healthy individuals [47]. Also, the same diversity was reported in the analysis of specific kinds of microbiota; in microbial alpha-diversity [48, 57, 65, 76] and beta-diversity [65, 76]. In contrast, changes in microbial indices were reported byMaria Paz Ventero et al. as lower microbial alpha-diversity and higher beta-diversity among deceased COVID-19 patients [74]. Another study showed a significant reduction of taxonomic features richness in beta-diversity in COVID-19 patients [48]. The findings of a study by the alpha-diversity analysis for microbiome richness suggested that recovered patients had a higher diversity of microbiota than healthy individuals, and the healthy individuals had a higher diversity of microbiota compared with acute COVID-19 patients [56]. Accordingly, a more diverse URT microbiota seems to be an early biomarker of clinical improvement in COVID-19 patients [74].
Genus Streptococcus increases in COVID-19 patients [21, 48, 54, 63, 70, 72, 75]. The Streptococcus abundance is representative of opportunistic bacterial invasion extent [163]. The abundance of Streptococcus is associated with higher expression of IFN-ƴ, IL-18, IL-6, and TNF-α and further inflammatory cytokines which worsens the clinical outcome of infection [72, 163, 164].
The genusRothiais widely found in the URT of patients with COVID-19 infection [21, 48, 54, 60, 75]. It seems that this genus is associated with lung injuries due to inflammatory activities [54, 165].
The opportunistic pathogenic genus, Corynebacterium, is reported in COVID-19 patients [21, 57]. Corynebacterium is one of the microbiotas in URT whose alternation is associated with the severity of COVID-19 and poor prognosis [53, 57].
There are dominancy of genus Prevotella and Veillonella in COVID-19 patients which could influence the progression of pneumonia [21, 58, 63, 72]. These species could be associated with an increased risk of mortality in older and severe COVID-19 patients due to pneumonia [25, 54, 65, 75].
Other opportunistic pathogenesis of the upper respiratory tract like Haemophilus, Stenotrophomonas, Acinetobacter, Moraxella, Corynebacterium, Gemella, Ralstonia, Pseudomonas [53], Granulicatella[52], Megasphaera [25] were increased in COVID-19 patients which are associated with serious clinical outcomes. Also, in Severe COVID-19 patients, an increase of Megasphaera, and infatal COVID-19 patients increase Rothiadentocariosa, Streptococcus infantis, Veillonelladispar [21] were seen which may be associated with secondary pneumonia due to mechanical ventilation.
Probiotic implementation
Thirteen studies included in our review assessed the effects of probiotic implementations on symptoms, morbidity, and mortality rates among COVID-19 patients [23, 30–41]. Probiotics are live microorganisms whose administration in sufficient quantities has been demonstrated to ameliorate immune response, participate in metabolism, and balance the host microbiome[166, 167]. Probiotics can be used as a complementary choice for the prevention and treatment of viral and bacterial infections[168]. Many studies have proven that probiotics possess anti-viral effects via a variety of mechanisms including; innate and adaptive immune system immunomodulation, mucosal protection maintenance, and pathogens inhibition through binding them [169]. Among all probiotics mainly two genera of Lactobacillus and Bifidobacterium have been shown to be the two most common probiotics in use for the treatment of viral respiratory tract infections including; influenza virus, adenovirus, pneumovirus and respiratory syncytial virus[170–172]. On the other hand, many studies have reported that COVID-19 infection can cause major alterations and imbalance to the host’s gut-lung axis microbiome composition (Dysbiosis) and this may be one of the key factors in COVID-19 pathogenesis [173], in addition, the gut microbiota diversity is significantly decreased among the elderly and this may justify higher COVID-19 mortality rates among them [174]. Thus, although RCT studies that investigate probiotics efficacy among COVID-19 patients in the literature are scarce, some retrospective studies have assessed the therapeutic, preventive, and beneficial effects of probiotics among COVID-19 patients [175].
In our study, the most common probiotics used were Lactobacillus and Bifidobacterium as well and nine studies investigated the efficacy of these two genera among COVID-19 patients [23, 30, 31, 33, 36–38, 40, 41]. In addition, few studies had utilized other less common probiotics as follows; Bos taurus, Morone, Leuconostoc, Lachesana, Limulus, Oryctolagus, Pentadiplandra, Rhamnosus, and Enterococcus [30, 33, 40]. Moreover, two studies utilized distinguished methods for balancing patients’ altered microbiome including; Fecal microbiota transplantation (FMT)[35] and washed microbiota transplantation (WMT) [39], and two studies didn’t specify the exact type of studied probiotic [32, 34]. Almost all these studies reported a diverse variety of probiotics’ beneficial effects in combat against COVID-19 symptoms, prognosis, and outcome.
Two studies included in this review reported that Lactobacillus plantarum metabolites have a high affinity for binding to ACE2 molecules, and Lactobacillus plantarum and Lactococcus lactis particles can bind with high affinity to SARS-COV-2 virus molecules thus they can be used against COVID-19 infection [23, 30]. In one RCT conducted to assess the possible effects of probiotics among COVID-19 patients using Lactiplantibacillus plantarum, plus Pediococcusacidilactici strains, 53.1% of the probiotic-receiving group achieved total remission while this number was significantly lower in the control group at 28.1%. in this study Probiotic treatment was associated with reduced nasopharyngeal viral load, pulmonary infiltrations, and duration of symptoms, compared to the control group, also, probiotic treatment significantly increased anti-SARS-CoV-2 IgM and IgG antibodies compared to the placebo group [176]. In addition, taking Lactobacillus rhamnosus GG was mentioned to be protective against COVID-19 and capable of reducing the severity of the disease[38]. Another study reported that taking probiotic Lactobacillus and Bifidobacterium could produce organic acids, ethanol, and exopolysaccharides molecules that possess anti-viral effects and may be useful in combating COVID-19 [37]. One RCT study reported that prophylactic use of probiotic Loigolactobacilluscoryniformis was associated with significantly higher levels of IgG antibodies post-vaccination and it could be associated with a better immune response against COVID-19 infection and after inoculation [177].
Two studies reported the beneficial effects of Bifidobacterium in decreasing mortality rates and hospital admission duration of moderate/severe COVID-19 patients, increasing blood antibody levels, and lowering inflammatory cytokines [31, 41]. Similarly, one study reported that the use of Probiotics was associated with a shorter duration of COVID-19 illness and hospitalization and improved the conditions of COVID-19 patients [40]. A similar study assessed the effects of bacteriotherapy via the administration of Streptococcus, Lactobacillus, and Bifidobacterium strains. The authors reported that the risk of respiratory failure was 8 times lower in the bacteriotherapy group; additionally, the prevalence of ICU admissions and mortality rates were higher among the non-bacteriotherapy patients [121]. In addition, three studies included in our review, noted the effectiveness of probiotics in treating diarrhea among COVID-19 patients [33, 34, 36]. Similar studies have reported consistent results with our study that probiotics can treat gut dysbiosis and thus mitigate the GI symptoms arising from it [178, 179]. One RCT conducted in China reported that the use of probiotics comprising of combined Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus tablets was associated with a better immune function and reduced secondary bacterial or fungal infection [180]. Finally, Fecal microbiota transplantation (FMT) was reported to be a novel therapy with beneficial effects as follows; increasing microbial richness, restoring gut microbiota through decreasing Proteobacteria, and increasing Bifidobacterium, Faecalibacterium, and Actinobacteria, and alleviating GI symptoms [35]. Similarly, washed microbiota transplantation (WMT) was reported to be effective and safe for COVID-19 patients [39]. Therefore, Lactobacilli and Bifidobacteria can be considered the main probiotics that can assist the most with balancing gut microbiome and possibly correct the dysbiosis caused by COVID-19.