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Aspergilli sp. are ubiquitous in nature. They are geographically widely distributed and have been observed in a broad range of habitats, because they can colonize a wide variety of substrates.
There are conflicting opinions about whether A. oryzae can be isolated in nature. Although the details of the genetic relationship between A. oryzae and A. flavus remain unclear, the two species are so closely related that all strains of A. oryzae are regarded by some as natural variants of A. flavus modified through years of selection for fermenting of foods. A. oryzae is regarded as not being pathogenic for plants or animals, though there are a handful of reports of isolation of A. oryzae from patients.