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Background   Aspergillus fumigatus  is the main causative agent of aspergillosis. Infections rarely occur in immunocompetent individuals, indicating efficient clearance of conidia by pulmonary defense mechanisms. Other aspergilli like  Aspergillus niger  also cause infections but to a much lesser extent. Our previous studies showed that  A. fumigatus  and  A. niger  have different behavior in the presence of type II alveolar A549 epithelial cells.  A. fumigatus  conidia are more efficiently internalized by these cells and germination is delayed when compared to  A. niger . In addition, hyphae that have escaped the epithelial cells grow parallel to the epithelium, while  A. niger  grows away from this cell layer .Results  Here it is shown that global gene expression of  A. fumigatus  and  A. niger  is markedly different upon contact with A549 cells. A total of 545 and 473 genes of  A. fumigatus  and  A. niger , respectively, were differentially expressed when compared to growth in the absence of A549 cells. Notably, only 53 genes (approximately 10%) were shared in these gene sets. The different response was also illustrated by the fact that only 4 out of 75 GO terms were shared that were enriched in the differentially expressed gene sets. The orthologues of  A. fumigatus  genes involved in hypoxia regulation and heat shock were also up-regulated in  A. niger,  whereas thioredoxin reductase and allergen genes were found up-regulated in  A. fumigatus  but down-regulated in  A. niger . Infection with  A. fumigatus  resulted in only 62 up and 47 down-regulated genes in A549. These numbers were 17 and 34 in the case of  A. niger.  GO terms related with immune response were down-regulated upon exposure to  A. fumigatus  but not in the case of  A. niger.  This indicates that  A. fumigatus  reprograms A549 to be less immunologically alert.    Conclusions  Our dual transcriptomic analysis supports earlier observations of a marked difference in life style between  A. fumigatus  and  A. niger  when grown in the presence of type II epithelial cells. The results indicate important differences in gene expression, amongst others down regulation of immune response genes in lung epithelial cells by  A. fumigatus  but not by  A niger.Electronic supplementary material  The online version of this article (10.1186/s12864-018-4895-3) contains supplementary material, which is available to authorized users.

Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert