Extended Data Fig. 4: Co-occurrence networks and prevalence of observed keystone taxa identified in the low (LEF) and high (HEF) exacerbation frequency clusters.

The interaction profiles of key taxa with other microbes within their network is illustrated for the (a–d) low-exacerbation frequency and (e–h) high-exacerbation frequency clusters respectively. Bacteria and fungi with established pathogenic potential including Streptococcus, Haemophilus, Candida and Cryptococcus are illustrated. Though common to both clusters, these ‘busy’, ‘critical’ and ‘influential’ microbes exhibited marked differences in their interaction networks when assessed individually thereby suggesting that microbial interactions, rather than mere presence or absence of a given microbe, may have a direct bearing on the clinical status of patients observed in the high frequency exacerbation cluster. Positive and negative interactions (expressed as edge weights) are colour-coded for illustration as indicated in the figure legend. The prevalence of microbial taxa (detected at >1% relative abundance) among each group is represented by horizontal bars for LEF (Blue) and HEF (purple) clusters. (i), Bacteria, (j) Fungi, (k) Viruses.