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Bernard Henrissat - One of the best experts on this subject based on the ideXlab platform.
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Classification of glycoside hydrolases and glycosyltransferases from hyperthermophiles
Methods in Enzymology, 2020Co-Authors: Bernard Henrissat, Pedro M. CoutinhoAbstract:Publisher Summary Glycoside hydrolases and glycosyltransferases are widespread groups of Carbohydrate-Active Enzymes present in virtually all organisms and are involved, respectively, in the hydrolysis and in the biosynthesis of glycosidic bonds between carbohydrates or between a carbohydrate and a noncarbohydrate moiety. The wide diversity of carbohydrate structures is accompanied by an equal diversity of the Enzymes responsible for both their synthesis and selective hydrolysis. Carbohydrate-Active Enzymes have long been classified according to their substrate specificity, which formed the basis of their Enzyme Commission (EC number) classification by the IUBMB. Classifications of these and other classes of Carbohydrate-Active Enzymes, like polysaccharide lyases and carbohydrate esterases, can be used to understand the carbohydrate flux in organisms made possible by the advent of genomics. This universal system can be used for the identification and classification of glycoside hydrolases and glycosyltransferases from hyperthermophiles.
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Poplar Carbohydrate-Active Enzymes: whole-genome annotation and functional analyses based on RNA expression data.
Plant Journal, 2019Co-Authors: Vikash Kumar, Bernard Henrissat, Matthieu Hainaut, Nicolas Delhomme, Chanaka Mannapperuma, Peter Immerzeel, Nathaniel R. Street, Ewa J. MellerowiczAbstract:Carbohydrate-Active Enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key Enzymes for the bi ...
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A metagenomics investigation of Carbohydrate-Active Enzymes along the goat and camel intestinal tract.
International Microbiology, 2019Co-Authors: Saad B. Almasaudi, Vincent Lombard, Elodie Drula, Abdessamad El Kaoutari, Elrashdy M. Redwan, Bernard HenrissatAbstract:Studies of the digestive microbiota of ruminant animals most often focus on the bacterial diversity in the rumen or the feces of the animals, but little is known about the diversity and functions of their distal intestine. Here, the bacterial microbiota of the distal intestinal tract of two goats and two camels was investigated by metagenomics techniques. The bacterial taxonomic diversity and Carbohydrate-Active enzyme profile were estimated for samples taken from the small intestine, the large intestine, and the rectum of each animal. The bacterial diversity and abundance in the small intestine were lower than in the rectal and large intestinal samples. Analysis of the Carbohydrate-Active enzyme profiles at each site revealed a comparatively low abundance of Enzymes targeting xylan and cellulose in all animals examined, similar to what has been reported earlier for sheep and therefore suggesting that plant cell wall digestion probably takes place elsewhere, such as in the rumen.
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A Metagenomics Investigation of Carbohydrate-Active Enzymes along the Gastrointestinal Tract of Saudi Sheep.
Frontiers in Microbiology, 2017Co-Authors: Saad B. Almasaudi, Vincent Lombard, Elodie Drula, Abdessamad El Kaoutari, Hussein A. Almehdar, Elrashdy M. Redwan, Bernard HenrissatAbstract:The digestive microbiota of humans and of a wide range of animals has recently become amenable to in-depth studies due to the emergence of DNA-based metagenomic techniques that do not require cultivation of gut microbes. These techniques are now commonly used to explore the feces of humans and animals under the assumption that such samples are faithful proxies for the intestinal microbiota. Sheep (Ovis aries) are ruminant animals particularly adapted to life in arid regions and in particular Najdi, Noaimi (Awassi) and Harrei (Harri) breeds that are raised in Saudi Arabia for milk and/or meat production. Here we report a metagenomics investigation of the distal digestive tract of one animal from each breed that (i) examines the microbiota at three intestinal subsites (small intestine, mid-colon and rectum), (ii) performs an in-depth analysis of the Carbohydrate-Active Enzymes genes encoded by the microbiota at the three subsites and (iii) compares the microbiota and Carbohydrate-Active enzyme profile at the three subsites across the different breeds. For all animals we found that the small intestine is characterized by a lower taxonomic diversity than that of the large intestine and of the rectal samples. Mirroring this observation, we also find that the spectrum of encoded Carbohydrate-Active Enzymes of the mid-colon and rectal sites is much richer than that of the small intestine. However, the number of encoded cellulases and xylanases in the various intestinal subsites was found to be surprisingly low, indicating that the bulk of the fiber digestion is performed upstream in the rumen, and that the carbon source for the intestinal flora is probably constituted of the rumen fungi and bacteria that pass in the intestines. In consequence we argue that ruminant feces, which are often analyzed for the search of microbial genes involved in plant cell wall degradation, are probably a poor proxy for the lignocellulolytic potential of the host.
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Comparative analysis of carbohydrate active Enzymes in Clostridium termitidis CT1112 reveals complex carbohydrate degradation ability.
PLOS ONE, 2014Co-Authors: Riffat Munir, Bernard Henrissat, John J. Schellenberg, Tobin J. Verbeke, Richard Sparling, David B. LevinAbstract:Clostridium termitidis strain CT1112 is an anaerobic, gram positive, mesophilic, cellulolytic bacillus isolated from the gut of the wood-feeding termite, Nasutitermes lujae. It produces biofuels such as hydrogen and ethanol from cellulose, cellobiose, xylan, xylose, glucose, and other sugars, and therefore could be used for biofuel production from biomass through consolidated bioprocessing. The first step in the production of biofuel from biomass by microorganisms is the hydrolysis of complex carbohydrates present in biomass. This is achieved through the presence of a repertoire of secreted or complexed carbohydrate active Enzymes (CAZymes), sometimes organized in an extracellular organelle called cellulosome. To assess the ability and understand the mechanism of polysaccharide hydrolysis in C. termitidis, the recently sequenced strain CT1112 of C. termitidis was analyzed for both CAZymes and cellulosomal components, and compared to other cellulolytic bacteria. A total of 355 CAZyme sequences were identified in C. termitidis, significantly higher than other Clostridial species. Of these, high numbers of glycoside hydrolases (199) and carbohydrate binding modules (95) were identified. The presence of a variety of CAZymes involved with polysaccharide utilization/degradation ability suggests hydrolysis potential for a wide range of polysaccharides. In addition, dockerin-bearing Enzymes, cohesion domains and a cellulosomal gene cluster were identified, indicating the presence of potential cellulosome assembly.
Paul Dupree - One of the best experts on this subject based on the ideXlab platform.
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Development and application of a high throughput carbohydrate profiling technique for analyzing plant cell wall polysaccharides and carbohydrate active Enzymes.
Biotechnology for Biofuels, 2013Co-Authors: Xiaofei Li, Denis V. Rubtsov, Katja S. Johansen, Nuno Faria-blanc, Kristian B. R. M. Krogh, Simon R. Turner, Peter Jackson, Jennifer C. Mortimer, Paul DupreeAbstract:Background: Plant cell wall polysaccharide composition varies substantially between species, organs and genotypes. Knowledge of the structure and composition of these polysaccharides, accompanied by a suite of well characterised glycosyl hydrolases will be important for the success of lignocellulosic biofuels. Current methods used to characterise enzymatically released plant oligosaccharides are relatively slow. Results: A method and software was developed allowing the use of a DNA sequencer to profile oligosaccharides derived from plant cell wall polysaccharides (DNA sequencer-Assisted Saccharide analysis in High throughput, DASH). An ABI 3730xl, which can analyse 96 samples simultaneously by capillary electrophoresis, was used to separate fluorophore derivatised reducing mono- and oligo-saccharides from plant cell walls. Using electrophoresis mobility markers, oligosaccharide mobilities were standardised between experiments to enable reproducible oligosaccharide identification. These mobility markers can be flexibly designed to span the mobilities of oligosaccharides under investigation, and they have a fluorescence emission that is distinct from that of the saccharide labelling. Methods for relative and absolute quantitation of oligosaccharides are described. Analysis of a large number of samples is facilitated by the DASHboard software which was developed in parallel. Use of this method was exemplified by comparing xylan structure and content in Arabidopsis thaliana mutants affected in xylan synthesis. The product profiles of specific xylanases were also compared in order to identify Enzymes with unusual oligosaccharide products. Conclusions: The DASH method and DASHboard software can be used to carry out large-scale analyses of the compositional variation of plant cell walls and biomass, to compare plants with mutations in plant cell wall synthesis pathways, and to characterise novel carbohydrate active Enzymes.
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Development and application of a high throughput carbohydrate profiling technique for analyzing plant cell wall polysaccharides and carbohydrate active Enzymes
Biotechnology for Biofuels, 2013Co-Authors: Xiaofei Li, Denis V. Rubtsov, Katja S. Johansen, Nuno Faria-blanc, Kristian B. R. M. Krogh, Simon R. Turner, Peter Jackson, Jennifer C. Mortimer, Paul DupreeAbstract:Background: Plant cell wall polysaccharide composition varies substantially between species, organs and genotypes. Knowledge of the structure and composition of these polysaccharides, accompanied by a suite of well characterised glycosyl hydrolases will be important for the success of lignocellulosic biofuels. Current methods used to characterise enzymatically released plant oligosaccharides are relatively slow. Results: A method and software was developed allowing the use of a DNA sequencer to profile oligosaccharides derived from plant cell wall polysaccharides (DNA sequencer-Assisted Saccharide analysis in High throughput, DASH). An ABI 3730xl, which can analyse 96 samples simultaneously by capillary electrophoresis, was used to separate fluorophore derivatised reducing mono- and oligo-saccharides from plant cell walls. Using electrophoresis mobility markers, oligosaccharide mobilities were standardised between experiments to enable reproducible oligosaccharide identification. These mobility markers can be flexibly designed to span the mobilities of oligosaccharides under investigation, and they have a fluorescence emission that is distinct from that of the saccharide labelling. Methods for relative and absolute quantitation of oligosaccharides are described. Analysis of a large number of samples is facilitated by the DASHboard software which was developed in parallel. Use of this method was exemplified by comparing xylan structure and content in Arabidopsis thaliana mutants affected in xylan synthesis. The product profiles of specific xylanases were also compared in order to identify Enzymes with unusual oligosaccharide products. Conclusions: The DASH method and DASHboard software can be used to carry out large-scale analyses of the compositional variation of plant cell walls and biomass, to compare plants with mutations in plant cell wall synthesis pathways, and to characterise novel carbohydrate active Enzymes. © 2013 Li et al.; licensee BioMed Central Ltd.
Pedro M. Coutinho - One of the best experts on this subject based on the ideXlab platform.
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Classification of glycoside hydrolases and glycosyltransferases from hyperthermophiles
Methods in Enzymology, 2020Co-Authors: Bernard Henrissat, Pedro M. CoutinhoAbstract:Publisher Summary Glycoside hydrolases and glycosyltransferases are widespread groups of Carbohydrate-Active Enzymes present in virtually all organisms and are involved, respectively, in the hydrolysis and in the biosynthesis of glycosidic bonds between carbohydrates or between a carbohydrate and a noncarbohydrate moiety. The wide diversity of carbohydrate structures is accompanied by an equal diversity of the Enzymes responsible for both their synthesis and selective hydrolysis. Carbohydrate-Active Enzymes have long been classified according to their substrate specificity, which formed the basis of their Enzyme Commission (EC number) classification by the IUBMB. Classifications of these and other classes of Carbohydrate-Active Enzymes, like polysaccharide lyases and carbohydrate esterases, can be used to understand the carbohydrate flux in organisms made possible by the advent of genomics. This universal system can be used for the identification and classification of glycoside hydrolases and glycosyltransferases from hyperthermophiles.
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The Carbohydrate-Active Enzymes database (CAZy) in 2013
Nucleic Acids Research, 2014Co-Authors: Vincent Lombard, Hemalatha Golaconda Ramulu, Elodie Drula, Pedro M. Coutinho, Bernard HenrissatAbstract:The Carbohydrate-Active Enzymes database (CAZy; http://www.cazy.org) provides online and continuously updated access to a sequence-based family classification linking the sequence to the specificity and 3D structure of the Enzymes that assemble, modify and breakdown oligo- and polysaccharides. Functional and 3D structural information is added and curated on a regular basis based on the available literature. In addition to the use of the database by enzymologists seeking curated information on CAZymes, the dissemination of a stable nomenclature for these Enzymes is probably a major contribution of CAZy. The past few years have seen the expansion of the CAZy classification scheme to new families, the development of subfamilies in several families and the power of CAZy for the analysis of genomes and metagenomes. This article outlines the changes that have occurred in CAZy during the past 5 years and presents our novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes.
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Carbohydrate-Active Enzymes from pigmented Bacilli: a genomic approach to assess carbohydrate utilization and degradation.
BMC Microbiology, 2011Co-Authors: Nicola Manzo, Bernard Henrissat, Pedro M. Coutinho, Enrica D'apuzzo, Simon M. Cutting, Ezio RiccaAbstract:Background: Spore-forming Bacilli are Gram-positive bacteria commonly found in a variety of natural habitats, including soil, water and the gastro-intestinal (GI)-tract of animals. Isolates of various Bacillus species produce pigments, mostly carotenoids, with a putative protective role against UV irradiation and oxygen-reactive forms. Results: We report the annotation of carbohydrate active Enzymes (CAZymes) of two pigmented Bacilli isolated from the human GI-tract and belonging to the Bacillus indicus and B. firmus species. A high number of glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) were found in both isolates. A detailed analysis of CAZyme families, was performed and supported by growth data. Carbohydrates able to support growth as the sole carbon source negatively effected carotenoid formation in rich medium, suggesting that a catabolite repression-like mechanism controls carotenoid biosynthesis in both Bacilli. Experimental results on biofilm formation confirmed genomic data on the potentials of B. indicus HU36 to produce a levan-based biofilm, while mucin-binding and -degradation experiments supported genomic data suggesting the ability of both Bacilli to degrade mammalian glycans. Conclusions: CAZy analyses of the genomes of the two pigmented Bacilli, compared to other Bacillus species and validated by experimental data on carbohydrate utilization, biofilm formation and mucin degradation, suggests that the two pigmented Bacilli are adapted to the intestinal environment and are suited to grow in and colonize the human gut.
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Carbohydrate-Active Enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level
BMC Genomics, 2011Co-Authors: Evy Battaglia, Bernard Henrissat, Pedro M. Coutinho, Joost Brink, Isabelle Benoit, Ad Wiebenga, Ronald P De VriesAbstract:Rhizopus oryzae is a zygomycete filamentous fungus, well-known as a saprobe ubiquitous in soil and as a pathogenic/spoilage fungus, causing Rhizopus rot and mucomycoses. Carbohydrate Active enzyme (CAZy) annotation of the R. oryzae identified, in contrast to other filamentous fungi, a low number of glycoside hydrolases (GHs) and a high number of glycosyl transferases (GTs) and carbohydrate esterases (CEs). A detailed analysis of CAZy families, supported by growth data, demonstrates highly specialized plant and fungal cell wall degrading abilities distinct from ascomycetes and basidiomycetes. The specific genomic and growth features for degradation of easily digestible plant cell wall mono- and polysaccharides (starch, galactomannan, unbranched pectin, hexose sugars), chitin, chitosan, β-1,3-glucan and fungal cell wall fractions suggest specific adaptations of R. oryzae to its environment. CAZy analyses of the genome of the zygomycete fungus R. oryzae and comparison to ascomycetes and basidiomycete species revealed how evolution has shaped its genetic content with respect to carbohydrate degradation, after divergence from the Ascomycota and Basidiomycota.
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A hierarchical classification of polysaccharide lyases for glycogenomics
Biochemical Journal, 2010Co-Authors: Vincent Lombard, Thomas Bernard, Harry Brumer, Pedro M. Coutinho, Corinne Rancurel, Bernard HenrissatAbstract:Carbohydrate-Active Enzymes face large substrate diversity in a highly selective manner with only a limited number of available folds. They are therefore subjected to multiple divergent and convergent evolutionary events. This and their frequent modularity render their functional annotation in genomes difficult in a number of cases. A classification of polysaccharide lyases (the Enzymes that cleave polysaccharides using an elimination instead of a hydrolytic mechanism) is presented thoroughly for the first time. Based on the analysis of a large panel of experimentally characterized polysaccharide lyases, we examined the correlation of various enzyme properties with the three levels of the classification: fold, families and subfamilies. The resulting hierarchical classification, which should help annotate relevant genes in genomic efforts, is available and constantly updated at the Carbohydrate-Active Enzymes Database (www.cazy.org).
Xiaofei Li - One of the best experts on this subject based on the ideXlab platform.
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Development and application of a high throughput carbohydrate profiling technique for analyzing plant cell wall polysaccharides and carbohydrate active Enzymes.
Biotechnology for Biofuels, 2013Co-Authors: Xiaofei Li, Denis V. Rubtsov, Katja S. Johansen, Nuno Faria-blanc, Kristian B. R. M. Krogh, Simon R. Turner, Peter Jackson, Jennifer C. Mortimer, Paul DupreeAbstract:Background: Plant cell wall polysaccharide composition varies substantially between species, organs and genotypes. Knowledge of the structure and composition of these polysaccharides, accompanied by a suite of well characterised glycosyl hydrolases will be important for the success of lignocellulosic biofuels. Current methods used to characterise enzymatically released plant oligosaccharides are relatively slow. Results: A method and software was developed allowing the use of a DNA sequencer to profile oligosaccharides derived from plant cell wall polysaccharides (DNA sequencer-Assisted Saccharide analysis in High throughput, DASH). An ABI 3730xl, which can analyse 96 samples simultaneously by capillary electrophoresis, was used to separate fluorophore derivatised reducing mono- and oligo-saccharides from plant cell walls. Using electrophoresis mobility markers, oligosaccharide mobilities were standardised between experiments to enable reproducible oligosaccharide identification. These mobility markers can be flexibly designed to span the mobilities of oligosaccharides under investigation, and they have a fluorescence emission that is distinct from that of the saccharide labelling. Methods for relative and absolute quantitation of oligosaccharides are described. Analysis of a large number of samples is facilitated by the DASHboard software which was developed in parallel. Use of this method was exemplified by comparing xylan structure and content in Arabidopsis thaliana mutants affected in xylan synthesis. The product profiles of specific xylanases were also compared in order to identify Enzymes with unusual oligosaccharide products. Conclusions: The DASH method and DASHboard software can be used to carry out large-scale analyses of the compositional variation of plant cell walls and biomass, to compare plants with mutations in plant cell wall synthesis pathways, and to characterise novel carbohydrate active Enzymes.
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Development and application of a high throughput carbohydrate profiling technique for analyzing plant cell wall polysaccharides and carbohydrate active Enzymes
Biotechnology for Biofuels, 2013Co-Authors: Xiaofei Li, Denis V. Rubtsov, Katja S. Johansen, Nuno Faria-blanc, Kristian B. R. M. Krogh, Simon R. Turner, Peter Jackson, Jennifer C. Mortimer, Paul DupreeAbstract:Background: Plant cell wall polysaccharide composition varies substantially between species, organs and genotypes. Knowledge of the structure and composition of these polysaccharides, accompanied by a suite of well characterised glycosyl hydrolases will be important for the success of lignocellulosic biofuels. Current methods used to characterise enzymatically released plant oligosaccharides are relatively slow. Results: A method and software was developed allowing the use of a DNA sequencer to profile oligosaccharides derived from plant cell wall polysaccharides (DNA sequencer-Assisted Saccharide analysis in High throughput, DASH). An ABI 3730xl, which can analyse 96 samples simultaneously by capillary electrophoresis, was used to separate fluorophore derivatised reducing mono- and oligo-saccharides from plant cell walls. Using electrophoresis mobility markers, oligosaccharide mobilities were standardised between experiments to enable reproducible oligosaccharide identification. These mobility markers can be flexibly designed to span the mobilities of oligosaccharides under investigation, and they have a fluorescence emission that is distinct from that of the saccharide labelling. Methods for relative and absolute quantitation of oligosaccharides are described. Analysis of a large number of samples is facilitated by the DASHboard software which was developed in parallel. Use of this method was exemplified by comparing xylan structure and content in Arabidopsis thaliana mutants affected in xylan synthesis. The product profiles of specific xylanases were also compared in order to identify Enzymes with unusual oligosaccharide products. Conclusions: The DASH method and DASHboard software can be used to carry out large-scale analyses of the compositional variation of plant cell walls and biomass, to compare plants with mutations in plant cell wall synthesis pathways, and to characterise novel carbohydrate active Enzymes. © 2013 Li et al.; licensee BioMed Central Ltd.
J H Hehemann - One of the best experts on this subject based on the ideXlab platform.
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transfer of carbohydrate active Enzymes from marine bacteria to japanese gut microbiota
Nature, 2010Co-Authors: Gaelle Correc, J H Hehemann, Tristan Barbeyron, William Helbert, Mirjam CzjzekAbstract:One of the useful roles performed by the human gut microbiota is to supply digestive Enzymes missing from the human genome. For instance, polysaccharides from the terrestrial plants that have been part of the human diet throughout evolution are broken down in the gut by carbohydrate active Enzymes, or CAZymes, many of them highly specific Enzymes from Bacteroides spp. bacteria. Little is known about the gut Enzymes acting on edible marine algae such as nori, sea lettuce and wakame, common in Japanese cuisine. Now CAZymes able to digest sulphated polysaccharides from Porphyra sp. marine red algae have been identified in marine Bacteroides isolates. And surprisingly, genome data mining reveals that this enzyme is present in gut bacteria from Japanese — but not American — individuals. This demonstrates that the gene transfer has taken place — recently in evolutionary terms — from a marine environmental bacterium to the Japanese gut bacterium Bacteroides plebeius. Porphyra are otherwise known as nori and used traditionally in sushi, so it seems probable that contact with non-sterile food may be a general factor in stocking gut microbes with a varied arsenal of CAZymes. One of the roles of the human gut microbiota is to break down nutrients using bacterial Enzymes that are lacking from the human genome. It is now shown that the gut microbiota of Japanese, but not American, individuals contains porphyranases, Enzymes that digest sulphated polysaccharides which are present in the marine environment only. These findings indicate that diet can select for gene content of the human microbiota. Gut microbes supply the human body with energy from dietary polysaccharides through carbohydrate active Enzymes, or CAZymes1, which are absent in the human genome. These Enzymes target polysaccharides from terrestrial plants that dominated diet throughout human evolution2. The array of CAZymes in gut microbes is highly diverse, exemplified by the human gut symbiont Bacteroides thetaiotaomicron3, which contains 261 glycoside hydrolases and polysaccharide lyases, as well as 208 homologues of susC and susD-genes coding for two outer membrane proteins involved in starch utilization1,4. A fundamental question that, to our knowledge, has yet to be addressed is how this diversity evolved by acquiring new genes from microbes living outside the gut. Here we characterize the first porphyranases from a member of the marine Bacteroidetes, Zobellia galactanivorans, active on the sulphated polysaccharide porphyran from marine red algae of the genus Porphyra. Furthermore, we show that genes coding for these porphyranases, agarases and associated proteins have been transferred to the gut bacterium Bacteroides plebeius isolated from Japanese individuals5. Our comparative gut metagenome analyses show that porphyranases and agarases are frequent in the Japanese population6 and that they are absent in metagenome data7 from North American individuals. Seaweeds make an important contribution to the daily diet in Japan (14.2 g per person per day)8, and Porphyra spp. (nori) is the most important nutritional seaweed, traditionally used to prepare sushi9,10. This indicates that seaweeds with associated marine bacteria may have been the route by which these novel CAZymes were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.