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Background  The use of inedible lignocellulosic biomasses for biomanufacturing provides important environmental and economic benefits for society. Efficient co-utilization of lignocellulosic biomass-derived sugars, primarily glucose and xylose, is critical for the viability of lignocellulosic biorefineries. However, the phenomenon of glucose repression prevents co-utilization of both glucose and xylose in cellulosic hydrolysates.    Results  To circumvent glucose repression, co-utilization of cellobiose and xylose by  Bacillus coagulans  NL01 was investigated. During co-fermentation of cellobiose and xylose,  B. coagulans  NL01 simultaneously consumed the sugar mixtures and exhibited an improved lactic acid yield compared with co-fermentation of glucose and xylose. Moreover, the cellobiose metabolism of  B. coagulans  NL01 was investigated for the first time. Based on comparative genomic analysis, two gene clusters that encode two different operons of the cellobiose-specific phosphoenolpyruvate-dependent phosphotransferase system (assigned as CELO1 and CELO2) were identified. For CELO1, five genes were arranged as  celA  (encoding EIIA cel ),  celB  (encoding EIIB cel ),  celC  (encoding EIIC cel ),  pbgl  (encoding 6-phospho-β-glucosidase), and  celR  (encoding a transcriptional regulator), and these genes were found to be ubiquitous in different  B. coagulans  strains. Based on gene knockout results, CELO1 was confirmed to be responsible for the transport and assimilation of cellobiose. For CELO2, the five genes were arranged as  celR ,  celB ,  celA ,  celX  (encoding DUF871 domain-containing protein), and  celC , and these genes were only found in some  B. coagulans  strains. However, through a comparison of cellobiose fermentation by NL01 and DSM1 that only possess CELO1, it was observed that CELO2 might also play an important role in the utilization of cellobiose in vivo despite the fact that no  pbgl  gene was found. When CELO1 or CELO2 was expressed in  Escherichia coli , the recombinant strain exhibited distinct cellobiose uptake and consumption.    Conclusions  This study demonstrated the cellobiose-assimilating pathway of  B. coagulans  and provided a new co-utilization strategy of cellobiose and xylose to overcome the obstacles that result from glucose repression in a biorefinery system.    Electronic supplementary material  The online version of this article (10.1186/s13068-018-1323-5) contains supplementary material, which is available to authorized users.

biotechnology for biofuels

Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons