This genome-centric pipeline would categorize putative cellulolytic anaerobes into six genotype groups based on differential cellulose-hydrolyzing capacity and varying synergy mechanisms. In the interpretation of complete genomes of 2,768 microbe strains whose phenotypes have been well documented, with the incorporation of an automatic recognition of synergy among the carbohydrate active elements annotated, an explicit genotype–phenotype correlation was evidenced to be feasible for cellulolytic anaerobes, and a bioinformatic pipeline was developed accordingly. Recognition of the synergy machineries that include but not limited to the cellulosome gene clusters is equally important as the annotation of individual carbohydrate-active modules or genes. Regarding genome-centric interpretation on the specific functional niche of cellulose hydrolysis for anaerobes, often encountered in practice is a lack of confidence in predicting the anaerobes’ real cellulolytic competency based solely on abundances of the varying carbohydrate-active enzyme modules annotated or on their taxonomy affiliation.
In the era of high-throughput sequencing, genetic information that is inherently whispering hints of the microbes’ functional niches is becoming easily accessible however, properly identifying and characterizing these genetic hints to infer the microbes’ functional niches remains a challenge. 4Shenzhen Bay Laboratory, Shenzhen, China.3School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China.2School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China.1Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Pokfulam, China.Yubo Wang 1, Liguan Li 1, Yu Xia 1,2 and Tong Zhang 1,3,4*
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