Table 1.

Gut–lung axis in human chronic respiratory diseases.

Lung disease	Microbiota disorders in		Comments	References
	Lungs	Gut
Chronic obstructive pulmonary disease (COPD)	Decreased lung microbiota diversity, Proteobacteria expansion		Associated with both COPD severity and exacerbations	Garcia-Nuñez et al., 2014; Wang et al., 2016; Mayhew et al., 2018
		Increased gastro-intestinal permeability and level of circulating gut microbiota-dependent trimethylamine-N-oxide	Associated with long-term all-cause mortality in COPD patients	Ottiger et al., 2018
Asthma	Proteobacteria (Haemophilus, Neisseria, Pseudomonas, Rickettsia and Moraxella species) and Firmicutes (Lactobacillus)		Overrepresented in asthmatic patients and/or associated with an uncontrolled asthma	Hilty et al., 2010; Marri et al., 2013; Huang et al., 2015; Denner et al., 2016; Zhang et al., 2016; Durack et al., 2017; Sverrild et al., 2017
	Bacteroidetes and Fusobacteria Moraxella catarrhalis, Bacteroides, Haemophilus and Streptococcus		Reduced in asthmatic patients Associated with worse FEV1 and higher sputum neutrophil counts	Zhang et al., 2016 Green et al., 2014; Sverrild et al., 2017
	Malassezia		Overrepresented in asthmatic patients	van Woerden et al., 2013
	Aspergillus fumigatus		Associated with corticosteroid treatment	Fraczek et al., 2018
		Early-life perturbations - Low gut microbial diversity - Increased bacterial abundance of Clostridium, Streptococcus and Bacteroides fragilis - Decreased bacterial abundances of Lachnospira, Veillonella, Faecalibacterium, Rothia Bacteroides and Bifidobacterium - Increased fungal abundances of Saccharomyces and Pichia kudriavzevii - Decreased fungal abundances of Candida tropicalis and Debaryomyces hansenii	Increased risk of childhood asthma development	Björkstén et al., 2001; Penders et al., 2007; Vael et al., 2008; van Nimwegen et al., 2011; Abrahamsson et al., 2012; Arrieta et al., 2015, 2018; Stiemsma et al., 2016
Cystic fibrosis (CF)	Decreased lung microbiota diversity		Correlated with the disease evolution and associated with exacerbation	Zhao et al., 2012; Stokell et al., 2015; Frayman et al., 2017
	Streptococcus, Prevotella, Rothia, Veillonella, Acintomyces, Neisseria, Haemophilus, Gemella		Major bacterial taxa in CF pediatric patients	Worlitzsch et al., 2009; Madan et al., 2012; Renwick et al., 2014; Coburn et al., 2015; Frayman et al., 2017
	Streptococcus,Prevotella, Rothia, Veillonella,Acintomyces, Pseudomonas		Major bacterial taxa in CF adult patients	Cox et al., 2010; Hampton et al., 2014; Coburn et al., 2015; Frayman et al., 2017
	Candida albicans and Aspergillus fumigatus		Major fungi isolated in CF patient; C. albicans was more likely co-associated with P. aeruginosa	Delhaes et al., 2012; Willger et al., 2014; Kim et al., 2015; Nguyen et al., 2016
		Decrease of Parabacteroides	Predictive of an airway colonization with Pseudomonas aeruginosa Association	Hoen et al., 2015
		Increased abundances of Staphylococcus, Streptococcus, Escherichia coli and Veillonella dispar	Association with CF intestinal inflammation	Hoffman et al., 2014; Enaud et al., 2019 Enaud et al., 2019
		Decreased abundances of Bacteroides, Bifidobacterium adolescentis and Faecalibacterium prausnitzii	Association with with CF intestinal inflammation