Table 2. Gut microbiome in patients with a respiratory tract infection compared to healthy participants.

First author and year	RTI pathogen	Variation abundance	Gut taxa reported in RTI patients compared to healthy participants
			Phylum	Family	Genus	Species
Ren Z., et al., 2021	SARS-CoV-2	Increase			Enterococcus, Streptococcus
		Decrease		Ruminococcaceae Lachnospiraceae	Bacteroides, Bifidobacterium, Blautia, Faecalibacterium, Pseudobutyrivibrio
		No change			Akkermansia
Newsome et al., 2021	SARS-CoV-2				Corynebacterium, Campylobacter, Finegoldia
Yeoh et al., 2021	SARS-CoV-2	Increase	Bacteroidetes			Akkermansia muciniphila Bacteroides dorei Bacteroides ovatus Bacteroides vulgatus Bacteroides caccce Ruminococcus gnavus Ruminococcus torques
		Decrease	Actinobacteria			Bifidobacterium adolescentis Bifidobacterium pseudocatenulatum Collinsella aerofaciens Coprococcus comes Dorea longicatena Eubacterium rectale Faecalibacterium prausnitzii Ruminococcus bromii Ruminococcus obeum Subdoligranulum sp.
Gu et al., 2020	SARS-CoV-2	Increase		Actinomycetaceae Micrococcaceae Streptococcaceae	Streptococcus
		Decrease	Actinobacteria Firmicutes	Bifidobacteriaceae Coriobacteriaceae Erysipelotrichaceae Lachnospiraceae Peptostreptococcaceae Ruminococcaceae	Agathobacter Anaerostipes Bifidobacterium Blautia Collinsella Dorea Erysipelotoclostrium Faecalibacterium Fusicatenibacter Intestinibacter Romboutsia Ruminococcus	Clostridium stricto 1 Eubacterium hallii Ruminococcus torques
		No change			Rothia
Gu et al., 2020	Influenza H1N1	Increase		Actinomycetaceae Micrococcaceae
		Decrease	Actinobacteria Firmicutes	Bifidobacteriaceae Coriobacteriaceae Erysipelotrichaceae Lachnospiraceae Peptostreptococcaceae Ruminococcaceae	Agathobacter Anaerostipes Bifidobacterium Blautia Collinsella Dorea Erysipelotoclostrium Faecalibacterium Fusicatenibacter Intestinibacter Romboutsia Ruminococcus Streptococcus Rothia	Clostridium stricto 1 Eubacterium hallii Ruminococcus torques
		No change		Streptococcaceae
Zuo et al., 2020	SARS-CoV-2	Increase	Actinobacteria Firmicutes Verrucomicrobia	Erysipelotrichaceae	Coprobacillus Coprococcus Enterobacter Parabacteroides	Actinomyces odontolyticus Actinomyces viscosus Alistipes indistinctus Bacteroides nordii Clostridium hathewayi Clostridium ramosum Enterobacter cloacae
		Decrease	Bacteroidetes	Lachnospiraceae	Alloiococcus Dorea Faecalibacterium Roseburia	Alistipes onderdonkii Anaerovorax odorimutans Bacteroides ovatus Dorea longicatena Eubacterium ventriosum Faecalibacterium prausnitzii
Zuo et al., 2020	CAP	Decrease			Coprobacillus	Clostridium ramosum Erysipelotoclostrium ramosum Eubacterium ventriosum Enterococcus faecium Lachnospiraceae sp.
Ren et al., 2020	CAP	Increase	Actinobacteria Proteobacteria	Actinomycetaceae Bifidobacteriaceae Enterobacteriaceae Enterococcaceae Leuconostocaceae Moraxellaceae Prevotellaceae Streptococcaceae	Acetivibrio Acinetobacter Actinomyces Bacillus Bifidobacterium Enterococcus Escherichia Lactococcus Psychrobacter Scardovia Streptococcus Shigella	Actinomyces viscosus Subdoligranulum sp.
		Decrease	Bacteroidetes Firmicutes Verrucomicrobia	Christensenellaceae Lachnospiraceae Ruminococcaceae Bacteroidaceae	Bacteroides Clostridium Dorea Lachnospira Faecalibacterium Ruminococcus	Anaerostipes hadras
Li L., et al., 2019	rRTIs	Increase	Bacteroidetes Proteobacteria	Streptococcaceae	Bacteroides Enterococcus Escherichia Parabacteroides Shigella	Lachnoclostridium sp. Ruminococcus gnavus
		Decrease	Actinobacteria Firmicutes Tenericutes Verrucomicrobia	Ruminococcaceae	Actinomyces Blautia Butyricoccus Clostridium Corynebaterium Faecalibacterium Klebsiella Lactobacillus Prevotella Ruminococcus Veillonella Verrucomicrobiae	Erysipelotoclostrium ramosum Eubacterium rectale Subdoligranulum sp.
Hu et al., 2019	TB	Increase	Actinobacteria Bacteroidetes Fusobacteria		Actinomyces Bacteroides Bifidobacterium Blautia Oscillibacter Parabacteroides Paraprevotella Phascolarctobacterium Prevotella Scardovia Veillonella Verrucomicrobiae	Parascardovia sp.
		Decrease	Firmicutes Proteobacteria Verrucomicrobia		Alistipes Atopobium Collinsella Eubacterium Gardnerella Klebsiella Megamonas Roseburia Ruminococcus	Subdoligranulum sp.
		No change		Coriobacteriaceae	Adlercreutzia Agathobacter Clostridium Enterobacter Rothia
Li W., et al., 2019	TB	Increase	Bacteroidetes Proteobacteria	Enterococcaceae Prevotellaceae	Enterococcus Prevotella
		Decrease	Actinobacteria Firmicutes	Bifidobacteriaceae Lachnospiraceae Rikenellaceae Ruminococcaceae	Bacteroides Bifidobacterium Dorea Faecalibacterium Ruminococcus	Faecalibacterium prausnitzii
Luo et al., 2017	New TB	Increase	Firmicutes Proteobacteria Verrucomicrobia		Akkermansia Faecalibacterium Fusobacterium Parabacteroides Streptococcus
		Decrease	Bacteroidetes		Prevotella
		No change			Bacteroides Succinivibrio Veillonella Verrucomicrobiae
Luo et al., 2017	Recurrent TB	Increase	Actinobacteria Proteobacteria		Akkermansia Streptococcus Veillonella Verrucomicrobiae
		Decrease	Bacteroidetes Firmicutes		Faecalibacterium Parabacteroides Prevotella Succinivibrio
		No change			Bacteroides Fusobacterium
Qin et al., 2015	Influenza H7N9	Increase	Firmicutes Proteobacteria		Clostridium Enterococcus Escherichia Lactobacillus Parabacteroides Prevotella Shigella Streptococcus Veillonella	Enterococcus faecium
		Decrease	Bacteroidetes		Bacteroides Blautia Eubacterium Roseburia Ruminococcus
		No change	Actinobacteria		Coprococcus Dorea Faecalibacterium

Taxa abundance variation was reported as increased (green), decreased (yellow), or no change (colourless). Abbreviations: Respiratory Tract Infection (RTI), Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Tuberculosis (TB), Community-Acquired Pneumonia (CAP), Recurrent-RTI (rRTI), Influenza A virus subtype H1N1, Influenza A virus subtype H7N9.