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The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples\u2019 microbiome was dominated by bacteria, where the classes <jats:italic>Gammaproteobacteria<\/jats:italic>, <jats:italic>Alphaproteobacteria<\/jats:italic>, and <jats:italic>Balneolia<\/jats:italic> stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited \u03b2-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic\/functional profiles of Portuguese compost samples.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Key points<\/jats:title>\n                <jats:p><jats:italic>\u2022 Sequence- and function-based metagenomics were used to find CAZymes in compost samples.<\/jats:italic><\/jats:p>\n                <jats:p><jats:italic>\u2022 Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes.<\/jats:italic><\/jats:p>\n                <jats:p><jats:italic>\u2022 Compost-derived fosmid libraries are enriched in clones with \u03b2-glucosidase activity.<\/jats:italic><\/jats:p>\n              <\/jats:sec>","DOI":"10.1007\/s00253-023-12627-9","type":"journal-article","created":{"date-parts":[[2023,7,7]],"date-time":"2023-07-07T09:02:06Z","timestamp":1688720526000},"page":"5379-5401","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples"],"prefix":"10.1007","volume":"107","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0919-7618","authenticated-orcid":false,"given":"C\u00e1tia","family":"Santos-Pereira","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9971-9140","authenticated-orcid":false,"given":"Joana","family":"Sousa","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9933-2176","authenticated-orcid":false,"given":"\u00c2ngela M. 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