Adding CAyman paper (10.1101/2024.01.08.574624) manually

papers/_posts/2023-01-08-ducarmon-large-scale-computational.md

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+---
+layout: paper
+title: "Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman"
+nickname: 2023-01-08-ducarmon-large-scale-computational
+authors: Ducarmon QR, Karcher N, Tytgat HLP, Delannoy-Bruno O, Pekel S, Springer F, Schudoma C, Zeller G
+year: "2024"
+journal: "biorxiv"
+volume:
+issue:
+pages:
+is_published: true
+image:
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid:
+preprint:
+supplement:
+
+# Links
+doi: "10.1101/2024.01.08.574624"
+pmid:
+
+# Data and code
+github: []
+neurovault: []
+openneuro: []
+osf:
+figshare: []
+---
+{% include JB/setup %}
+
+# Abstract
+
+Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but bioinformatics tools for CAZyme profiling and interpretation of substrate preferences in microbial community data are lacking. To address this, we developed a CAZyme profiler (Cayman) and a hierarchical substrate annotation scheme. Leveraging these, we genomically survey CAZymes in human gut microbes (n=107,683 genomes), which suggests novel mucin-foraging species. In a subsequent meta-analysis of CAZyme repertoires in Western versus non-Western gut metagenomes (n=4,281) we find that non-Western metagenomes are richer in fibre-degrading CAZymes despite lower overall CAZyme richness. We additionally pinpoint the taxonomic drivers underlying these CAZyme community shifts. A second meta-analysis comparing colorectal cancer patients (CRC) to controls (n=1,998) shows that CRC metagenomes are deprived of dietary fibre-targeting, but enriched in glycosaminoglycan-targeting CAZymes. A genomic analysis of co-localizing CAZyme domains predicts novel substrates for CRC-enriched CAZymes. Cayman is broadly applicable across microbial communities and freely available from https://github.com/zellerlab/cayman.