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Subjects aged 1\u201369\u2005years who were clinically stable provided sputum (n=200) or bronchoalveolar lavage (n=55). 18 anaerobic and 39 aerobic genera were cultured from 59% and 95% of samples, respectively; 16 out of 57 genera had a \u22655% prevalence across centres.<\/jats:p><jats:p>Analyses of microbial communities using co-occurrence networks in sputum samples showed groupings of oral, including anaerobic, bacteria, whereas typical CF pathogens formed distinct entities.<jats:italic>Pseudomonas<\/jats:italic>was associated with worse nutrition and F508del genotype, whereas anaerobe prevalence was positively associated with pancreatic sufficiency, better nutrition and better lung function. A higher total anaerobe\/total aerobe CFU ratio was associated with pancreatic sufficiency and better nutrition. Subjects grouped by factor analysis who had relative dominance of anaerobes over aerobes had milder disease compared with a<jats:italic>Pseudomonas<\/jats:italic>-dominated group with similar proportions of subjects that were homozygous for F508del.<\/jats:p><jats:p>In summary, anaerobic bacteria occurred at an early age. 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