Alterations of the gut microbiota in coronavirus disease 2019 and its therapeutic potential

Table 1 Alterations of the gut microbiota composition in coronavirus disease 2019 patients

Study	Method	Increased abundance of gut microbiota	Decreased abundance of gut microbiota	Main conclusion
Gu et al[15], 2020	16S rrna	Streptococcus, Rothia, Veillonella, Actinomyces, Erysipelatoclostridium	Ruminococcaceae family, Lachnospiraceae family, Agathobacter, Fusicatenibacter, Roseburia	Gut microbiota has potential value as a diagnostic biomarker and therapeutic target for COVID-19
Zuo et al[10], 2020	Shotgun	Clostridium hathewayi, Actinomyces viscosus, Bacteroides nordii	Eubacterium, Faecalibacterium prausnitzii, Roseburia, Lachnospiraceae	Fecal microbiota alterations are associated with fecal virus levels and COVID-19 severity; symbionts were depletion and opportunistic pathogens were enrichment in COVID-19 patients; gut dysbiosis persists in COVID-19 patients after virus clearance
Tao et al[16], 2020	16S rrna	Streptococcus, Clostridium, Lactobacillus, Bifidobacterium	Bacteroidetes, Roseburia, Faecalibacterium, Coprococcus, Parabacteroides	IL-18 level was higher in the fecal samples from COVID-19 patients; dysbiosis may contribute to SARS-CoV-2-induced production of inflammatory cytokines and cytokine storm in the gut
Tang et al[17], 2020	Q-PCR	Enterococcus, Enterobacteriaceae	Faecalibacterium prausnitzii, Clostridium butyricum, Clostridium leptum, Eubacterium rectale	Specific gut microbiota can be considered diagnostic biomarkers for COVID-19; the Ec/E ratio can be used to predict death in critically ill patients
Zuo et al[18], 2020	Shotgun	Candida albicans, Candida auris, Aspergillus flavus	-	The guts of COVID-19 patients are accompanied by massive fungal blooms
Yeoh et al[12], 2021	Shotgun	Actinobacteria, Ruminococcus gnavus, Ruminococcus torques, Bacteroides dorei	Bifidobacterium adolescentis, Faecalibacterium prausnitzii, Eubacterium rectale	Immunomodulatory gut bacteria were depleted in COVID-19 patients; gut dysbiosis persists in COVID-19 patients after virus clearance; gut microbiota composition was associated with disease severity
Wu et al[19], 2021	16S rrna	Streptococcus, Weissella, Enterococcus, Rothia, Lactobacillus, Actinomyces, Granulicatella	Blautia, Coprococcus, Collinsella	Personalized microbiome affects disease outcomes in COVID-19 patients; targeting the gut microbiota has potential to prevent and treat COVID-19
Zuo et al[20], 2021	Shotgun	Collinsella aerofaciens, Collinsella tanakaei, Streptococcus infantis, Morganella morganii	Parabacteroides merdae, Bacteroides stercoris,Alistipes onderdonkii, Lachnospiraceae bacterium 1_1_57FAA	Elimination of gut SARS-CoV-2 activity and modulation of gut microbiome composition should be considered new treatments for COVID-19; the 3’ end of SARS-CoV-2 genome was highly covered than the 5’ end
Lv et al[21], 2021	ITS sequencing	-	Ascomycota (Aspergillaceae, Candida parapsilosis, Talaromyces wortmannii); Basidiomycota (Malassezia yamatoensis, Rhodotorula mucilaginosa, Moesziomyces aphidis, Trechispora sp. and Wallemia sebi)	Total gut fungal burden was significantly elevated in patients infected with SARS- CoV-2; altered gut fungi and microbiota are closely related to patient clinical characteristics
Suskun et al[22], 2022	16S rrna	Bifidobacterium adolescentis, Dorea formicigenerasus, Eubacterium dolichum, Eggerthella lenta	Faecalibacterium prausnitzii	First evaluate the microbiota composition in multisystem inflammatory syndrome in children cases

COVID-19: Coronavirus disease 2019; SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; IL: Interleukin.