Protein sequences originating from complete genomes and that can be assigned to CAZy families are listed in the links below. The only genomes that are consistently surveyed in the CAZy database are those released by the NCBI as regular entries in the daily releases of GenBank. In a very limited number of cases, we have included data from RefSeq genomes.

The collection of carbohydrate-active enzymes encoded by the genome of an organism ("CAZome") provides an insight into the nature and extent of the metabolism of complex carbohydrates of the species. The CAZomes of free living organisms typically correspond to 1-5% of the predicted coding sequences. Extremely reduced CAZomes are characteristic of species with a strict intracellular parasitic lifestyle. Because of the massive chemical, structural and functional variability of carbohydrates, CAZome analyses and comparisons highlight significant differences between species.

Although often useful, the simple assignment of a protein sequence to a CAZy family does not constitute a refined functional prediction for genomic annotation. For the later task, we are developping a CAZy-based annotation methodology, which takes into account protein modularity, family and subfamily assignment, relatedness to experimentally characterized enzymes and expertise in the varying substrate specificity of carbohydrate-active enzymes. This methodology, which results in coherent, expert and comparable sets of annotations, is applied to novel genomes and metagenomes on a collaborative basis.

Tables for Direct Genome Access by Kingdom


Our published work on CAZymes in genomes, metagenomes and transcriptomes

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[74] Ohm et al. (2012) Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathogens 8(12): e1003037 23236275].

[73] de Wit et al. (2012) The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genet. 8(11):e1003088 23209441].

[72] Morin et al. (2012) The genome sequence of the Button Mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc. Natl. Acad. Sci. USA 109, 17501-17506 23045686].

[71] Barry et al. (2012) Effects of dietary fiber on the feline gastrointestinal metagenome. J. Proteome Res. 11, 5924-5933 23075436].

[70] Bottacini et al. (2012) Bifidobacterium asteroides PRL2011 genome analysis reveals clues for colonization of the insect gut. PLoS One 7(9):e44229 23028506].

[69] Suzuki et al. (2012) Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. BMC Genomics 13, 444 22937793].

[68] O’Connell et al. (2012) Life-style transitions in plant pathogenic Colletotrichum fungi defined by genome and transcriptome analyses. Nature Genetics 44, 1060-1065 22885923].

[67] Dassa et al. (2012) Genome-wide analysis of Acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system. BMC Genomics 13, 210 22646801].

[66] Floudas et al. (2012) The Paleozoic origin of white rot wood decay reconstructed using 31 fungal genomes. Science 336, 1715-1719 22745431].

[65] Chen et al. (2012) Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nature Communications 3:913. doi: 10.1038/ncomms1923 22735441].

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[60] Ipcho et al. (2012) Transcriptome analysis of Stagonospora nodorum; gene models, effectors, metabolism and pantothenate dispensability. Molec. Plant Pathol. 13, 531–545 [PMID: 22145589].

[59] Zhang et al. (2012) Carbohydrate-active enzymes revealed in Coptotermes formosanus (Isoptera: Rhinotermitidae) transcriptome. Insect Mol Biol. 21, 235-245 [PMID: 22243654].

[58] Price et al. (2012) Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 335, 843-847 [PMID: 22344442].

[57] McNulty et al. (2011) The impact of a consortium of fermented milk strains on the human gut microbiome: a study involving monozygotic twins and gnotobiotic mice. Science Transl. Med. 3(106):106ra106 [PMID: 22030749].

[56] Berka et al. (2011) Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nature Biotechnol. 29, 922-927 [PMID: 21964414].

[55] De Luca et al. (2011) The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment. PLoS One 6: e23784 [PMID: 21912644].

[54] Manzo et al. (2011) Carbohydrate-active enzymes from pigmented Bacilli: a genomic approach to assess carbohydrate utilization and degradation. BMC Microbiol 11, 198 [PMID: 21892951].

[53] Amselem et al. (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics 7, e1002230 [PMID: 21876677].

[52] Klosterman et al. (2011) Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog. 7, e1002137 [PMID: 21829347].

[51] Eastwood et al. (2011) The plant cell wall decomposing machinery underlies the functional diversity of forest fungi. Science, 333, 762-765 [PMID: 21764756].

[50] Muegge et al. (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970-974 [PMID: 21596990].

[49] Duplessis et al. (2011) Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc. Natl. Acad. Sci. USA 108, 9166-9171 [PMID: 21536894].

[48] Goodwin et al. (2011) Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity and stealth pathogenesis. PLoS Genetics 7, e1002070. [PMID: 21695235].

[47] Kubicek et al. (2011) Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol. 12, R40 [PMID: 21501500].

[46] Dam et al. (2011) Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. Nucleic Acids Res. 39, 3240-3254 [PMID: 21227922].

[45] Sucgang et al. (2011) Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol. 12, R20 [PMID: 21356102].

[44] Diguistini et al. (2011) Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc. Natl. Acad. Sci. USA 108, 2504-2509 [PMID: 21262841].

[43] Swanson et al. (2011) Phylogenetic and gene-centric metagenomics of the canine gastrointestinal microbiome reveals similarities with human and mouse gut metagenomes. ISME J 5, 639-649 [PMID: 20962874].

[42] Battaglia et al. (2011) Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level. BMC Genomics 12, 38 [PMID: 21241472].

[41] Turroni et al. (2010) Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc. Natl. Acad. Sci. USA 107, 19514-19519 [PMID: 20974960].

[40] Hemme et al. (2010) Genome announcement: sequencing of multiple clostridia genomes related to biomass conversion and biofuels production. J. Bacteriol. 192, 6494-6496 [PMID: 20889752].

[39] Tasse et al. (2010) Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res. 20, 1605-1612 [PMID: 20841432].

[38] Ohm et al. (2010) Formation of mushrooms and lignocellulose degradation encoded in the genome sequence of Schizophyllum commune. Nature Biotechnol. 28, 957-963 [PMID: 20622885].

[37] Purushe et al. (2010) Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii; insights into their environmental niche. Microbial Ecology 60, 721-729 [PMID: 20585943].

[36] Rincon et al. (2010) Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1. (2010) PLoS One 5, e12476 [PMID: 20814577].

[35] Levesque et al. (2010) Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire. Genome Biology 11, R73 [PMID: 20626842].

[34] Turnbaugh et al. (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc. Natl. Acad. Sci USA 107, 7503-7508 [PMID: 20363958].

[33] Martin et al. (2010) Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464, 1033-1038 [PMID: 20348908].

[32] Ma et al. (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464, 367-373 [PMID: 20237561].

[31] Ventura et al. (2009) The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet 5(12) e1000785 [PMID: 20041198].

[30] Coleman et al. (2009) The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet 5, e1000618 [PMID: 19714214].

[29] Yang et al. (2009) The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PloS One 4, e6085 [PMID: 19568419].

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[27] Turnbaugh et al. (2009) A core gut microbiome in obese and lean twins. Nature 457, 480-484 [PMID: 19043404].

[26] McBride et al. (2009) Novel features of the polysaccharide digesting gliding bacterium Flavobacterium johnsoniae revealed by genome sequence analysis. Appl. Environm. Microbiol. 75, 6864-6875 [PMID: 19717629].

[25] Berg Miller et al. (2009) Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One 4, e6650. [PMID: 19680555].

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[23] Ward et al. (2009) Three genomes from the phylum Acidobacteria provide insight into their lifestyles in soils. Appl. Environ. Microbiol. 75, 2046-2056 [PMID: 19201974].

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[21] Martinez et al. (2009) Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc. Natl. Acad. Sci. USA 106, 1954-1959 [PMID: 19193860].

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[16] Abad et al. (2008) Genome sequence of the metazoan plant-specific nematode Meloidogyne incognita. Nature Biotechnol. 26, 909-915. [PMID: 18660804].

[15] Deboy et al. (2008) Insights into plant cell-wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J. Bacteriol. 190, 5455-5463 [PMID: 18556790].

[14] Weiner et al. (2008) Complete genome sequence of the complex carbohydrate-degrading marine bacterium Saccharophagus degradans strain 2-40T. PLoS Genet., 4(5):e1000087. [PMID: 18516288].

[13] Martinez et al. (2008) Genome sequence analysis of the cellulolytic fungus Trichoderma reesei (syn. Hypocrea jecorina) reveals a surprisingly limited inventory of carbohydrate-active enzymes. Nature Biotechnol. 26, 553-560. [PMID: 18454138].

[12] Espagne et al. (2008) The genome sequence of the model Ascomycete fungus Podospora anserina. Genome Biol. 9:R77 (doi:10.1186/gb-2008-9-5-r77) [PMID: 18460219].

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[8] Xie et al. (2007) Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Appl. Environm. Microbiol. 73, 3536-3546. [PMID: 17400776].

[7] Geisler-Lee et al (2006) Poplar Carbohydrate-Active Enzymes (CAZymes). Gene identification and expression analyses. Plant Physiol 140, 946-962. [PMID: 16415215].

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