Table 1.

Microbiome-specific bacteria implicated in or modified during viral infections. IV: Influenza virus; MPV: Metapneumovirus; RV: Rhinovirus; RSV: Respiratory Syncytial Virus. The main viruses responsible for respiratory infections (IV, RSV and RV) are also the most studied. It is interesting to note that the increase in considered bacteria exists independently of the observed virus (Lactobacillus rhamnosus, Escherichia coli and Staphylococcus aureus are protective whatever the viral model; the presence of Streptococcus pneumoniae is associated with an increase of the complication rate or seroconversion). Outcome “complication”: disease worsening; outcome “Protection”: indicate a limitation of the disease complications.

Virus	Model	Sample Site	Bacteria	Consequences	Outcome	Reference
IV	Human clinical samples	Induced sputum	Acinetobacter baumanii	Bacteria species increasing during A(H1N1) infection	No modification	Leung et al. [18]
			Bacillus spp.
			Pseudomonas aeruginosa
	Human clinical samples	Induced sputum	Neisseria spp.	Bacteria species decreasing during A(H1N1) infection	No modification	Leung et al. [18]
			Prevotella spp.
	Mouse model	Lung homogenates	Streptococcus pneumoniae	Increased severity	Complication	McCullers et al. [10]
	Human clinical samples	Nasopharyngeal samples	Streptobacillus spp.	Predict a severe form of influenza in children	Complication	Langevin et al. [13]
			Porphyromonas spp.
			Granulicatella spp.
			Fusobacterium spp.
			Lachnospiracea spp.
			Haemophilus spp.
	Human clinical samples	Nasopharyngeal samples	Staphylococcus aureus	Predict a benign form of influenza in children	Protection	Langevin et al. [13]
	Human clinical samples	Nasal swabs	Lactobacillus helveticus	Correlated with higher H1 IgA antibody response	Protection	Salk et al. [19]
			Bacteroides ovatus
	Human clinical samples	Nasopharyngeal samples Nasal swabs	Veillonella dispar	Predict a severe form of influenza in children Correlated with lower H1 IgA antibody response	Protection	Langevin et al. [13] Salk et al. [19]
	Human clinical samples	Nasopharyngeal samples Nasal swabs	Prevotella melaninogenica	Predict a severe form of influenza in children Correlated with Higher H1 IgA antibody response	Complication—Protection	Langevin et al. [13] Salk et al. [19]
	Human clinical samples	Nasal swabs	Streptococcus infantis	Correlated with Higher H1 IgA antibody response	Complication	Salk et al. [19]
MPV	Cellular model	Cellular model	Streptococcus pneumoniae	Increased seroconversion rate during challenge	Protection	Verkaik et al. [20]
RSV	Human clinical samples	Nasopharyngeal samples	Haemophilus influenzae Streptococcus spp.	Increased hospitalization rate	Complication	De Steenhuijsen Piters et al. [21]
	Mice model—Human clinical samples	Nasopharyngeal samples	Moraxella catarrhalis	Increased severity	Complication	Teo et al. [22] Beura et al. [23] Furusawa et al. [24]
	Mice model Human clinical samples	Nasopharyngeal samples Lung homogenates	Staphylococcus aureus	Decreased complications	Protection	De Steenhuijsen Piters et al. [21] Wang et al. [11]
	Cellular model	Cellular model	Escherichia coli	Increased protection against infection	Protection	Cagno et al. [25]
RV	Cellular model	Cellular model	Haemophilus influenzae	Entry point production via ICAM-1 and TLR-3 production	Complication	Sajjan et al. [26]