Aspergillus niger, one of the most common and important fungal species, is ubiquitous in various environments. A. niger isolates possess a large number of cryptic biosynthetic gene clusters (BGCs) and produce various biomolecules as secondary metabolites with a broad spectrum of application fields covering agriculture, food, and pharmaceutical industry. By extensive literature search, this review with a comprehensive summary on biological and chemical aspects of A. niger strains including their sources, BGCs, and secondary metabolites as well as biological properties and biosynthetic pathways is presented. Future perspectives on the discovery of more A. niger-derived functional biomolecules are also provided in this review.

Fusarium, one of the most common fungal genera, has received considerable attention because of its biosynthetic exuberance, the result of many unique gene clusters involved in the production of secondary metabolites.

Chemical investigation of a co-culture of two endophytic fungi Aspergillus fumigatus D and Fusarium oxysporum R1 from two traditional medicinal plants, Edgeworthia chrysantha Lindl. and Rumex madaio Makino, led to isolation of a new amide 1 and six known compounds, including neovasinin (2), neovasifuranone B (3), N-(2-phenylethyl)acetamide (4), α-linolenic acid (5), α-elaeostearic acid (6), palmitoleic acid (7). On the basis of extensive spectroscopic analysis including 1D and 2D NMR, HR-ESI-MS and optical rotation measurement as well as comparison of literature data, chemical structure of 1 was unambiguous elucidated as (S, E)-methyl-2-(2,4-dimethylhex-2-enamido)acetate. Bioassay results indicated that none of these compounds exhibited strong inhibitory effect on three human pathogens Escherichia coli, Staphyloccocus aureus and Candida albicans with MIC values of ≥25 μM.

In order to search more antimicrobial natural products for new drug discovery, bioassay and chemical investigation of endophytic strains from Rumex madaio were carried out. Six fungal strains (numbered as L1, L6, L9, L10, R1, R2) were successfully isolated and their antimicrobial effects on three human pathogens, Escherichia coli, Staphyloccocus aureus and Candida albicans, were evaluated. The results indicated that ethyl acetate extracts of fermentation broth of these strains had no potent antimicorbial activity against E. coli and C. albicans while strains L1 and R1 had stronger inhibitory effects on S. aureus. On basis of morphological characteristics and 18S rRNA sequence analysis, strains L1 and R1 were respectively classified as Colletotrichum and Fusarium geni. The chemical study of strain R1 led to isolation of two known antimicrobial agents, dibutyl phthalate (1) and beauvericin (2).

A chemical investigation into endozoic fungus Aspergillus niger L14 derived from the marine sponge of Reniera japonica collected off Xinghai Bay (China) resulted in the isolation of two dimeric naphtho-γ-pyrones, fonsecinone A (1) and isoaurasperone A (2). Through a combination of ECD spectra and X-ray diffraction analysis, the chiral axes of compounds 1 and 2 were unambiguously determined as Rα-configurations. Bioassay results indicated that these substances exhibited remarkably inhibitory effects on human pathogens Helicobacter pylori G27 and 159 with MIC values of ≤4 μg/mL, which are similar to those of the positive control, ampicillin sodium. To the best of our knowledge, this is the first report on absolute configuration of 1 and crystallographic data of 2, as well as their potent anti-H. pylori activities.