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BACKGROUND In commercial production of Cordyceps militaris (a famous Chinese medicine), cereal grains are usually utilized as cultivation substrates. This study aimed to evaluate the efficiency of agricultural wastes as substitute materials in the low-cost production of C. militaris. Cottonseed shells ( CS), corn cob particles ( CCP), Italian poplar sawdusts ( IPS) and substrates spent by Flammulina velutipes ( SS) were employed to cultivate C. militaris, using rice medium as control. RESULTS CS and CCP were suitable for fruit body formation of C. militaris, with yields of 22 and 20 g per bottle respectively. Fruit bodies grown on CCP showed the highest levels of cordycepin and adenosine, up to 9.45 and 5.86 mg g−1 respectively. The content of d-mannitol in fruit bodies obtained on CS was 120 mg g−1 (80% of the control group), followed by that on CCP, 100 mg g−1. Fruit bodies cultivated on CCP displayed a high crude polysaccharide level of 26.9 mg g−1, which was the closest to that of the control group (34.5 mg g−1). CONCLUSION CS and CCP are effective substrates for the production of fruit bodies and bioactive compounds by C. militaris. This study provides a new approach to decreasing the cost of C. militaris cultivation and dealing with these agricultural wastes. © 2016 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

[Display omitted] • C. militaris strain 147 displayed a strong xylose utilisation capability. • Xylose metabolism enhanced the cordycepin synthesis in the fungus. • The cordycepin yield reached 6.54 g/L by optimising medium components. • Xylose altered the expression of genes involving purine and amino acid metabolisms. Cordycepin is an important active metabolite of Cordyceps militaris. Xylose, an attractive feedstock for producing chemicals through microbial fermentation, cannot be effectively utilised by many reported C. militaris strains. Herein, a xylose-utilising C. militaris strain 147 produced the highest level of cordycepin (3.03 g/L) in xylose culture. Xylose, alanine, and ammonium citrate were determined as the main affecting factors on the cordycepin production using a Plackett-Burman design. The combination of these factors was optimised using response surface methodology, and the maximal 6.54 g/L of cordycepin was produced by the fungus in the optimal medium. Transcriptome analysis revealed that xylose utilisation upregulated the transcriptional levels of genes participating in purine and energy metabolisms in the fungus, which may facilitate the formation of precursors for cordycepin biosynthesis. This investigation provides new insights into the efficient production of cordycepin and is conducive to the valorisation of biomass rich in xylose. [ABSTRACT FROM AUTHOR]