Browse dbCAN-PUL Entries

PULID Characterization Method(s) Substrate Organism Publication Publish Date Type Num Genes Num CAZymes CazyFamily
PUL0010 enzyme activity assay, liquid chromatography and mass spectrometry xylan Geobacillus thermodenitrificans 28616644
Synergistic hydrolysis of xylan using novel xylanases, beta-xylosidases, and an alpha-L-arabinofuranosidase from Geobacillus thermodenitrificans NG80-2. Appl Microbiol Biotechnol. 2017 Aug;101(15):6023-6037. doi: 10.1007/s00253-017-8341-2. Epub 2017 Jun 14.
2017 Aug degradation 42 9 GH43, GH43_11, GH10, GH39, GH67, GH10, CBM22, GH52, CE4, GH51
PUL0013 Northern Blot, RT-PCR, isothermal titration calorimetry, electrophoretic mobility shift assay arabinan Geobacillus stearothermophilus 21460081
The L-Arabinan utilization system of Geobacillus stearothermophilus. J Bacteriol. 2011 Jun;193(11):2838-50. doi: 10.1128/JB.00222-11. Epub 2011 Apr 1.
2011 Jun degradation 56 11 GH43_5, GH43, GH43, GH43_4, GH51, GH51, GH127, CE4, GH52, GH10, GH67, GH39, GH43_11
PUL0029 enzyme activity assay arabinogalactan Bifidobacterium longum 30564851
Degradative enzymes for type II arabinogalactan side chains in Bifidobacterium longum subsp. longum. Appl Microbiol Biotechnol. 2019 Feb;103(3):1299-1310. doi: 10.1007/s00253-018-9566-4. Epub 2018 Dec 18.
2019 Feb degradation 24 8 GH43_24, GH43, CBM13, GH30, GH30_5, GH146, GH43_22, GH43, GH43_34, GH43_22, GH43, GH43_26, GH43_27, GH43, GH43_22, GH43_22
PUL0044 qRT-PCR, enzyme activity assay arabinoxylan Bacteroides ovatus 26112186, 32266006
Glycan complexity dictates microbial resource allocation in the large intestine. Multimodular fused acetyl-feruloyl esterases from soil and gut Bacteroidetes improve xylanase depolymerization of recalcitrant biomass. Nat Commun. 2015 Jun 26;6:7481. doi: 10.1038/ncomms8481. Biotechnol Biofuels. 2020 Mar 31;13:60. doi: 10.1186/s13068-020-01698-9. eCollection 2020.
2015 Jun 26,2020 degradation 33 16 GH43, GH43_10, GH3, GH43_12, GH43, GH31, GH97, CBM6, GH43, GH43_29, GH43_12, GH43, GH30_8, CBM35, GH98, GH115, CE6, CE1, CBM6, GH43, GH43_29, GH95, GH30, GH115
PUL0045 qRT-PCR arabinoxylan Bacteroides ovatus 26112186
Glycan complexity dictates microbial resource allocation in the large intestine. Nat Commun. 2015 Jun 26;6:7481. doi: 10.1038/ncomms8481.
2015 Jun 26 degradation 11 5 GH67, GH43_1, GH43, GH10, CBM4, GH10
PUL0063 bicinchoninic acid (BCA) reducing-sugar assay, enzymatic product analysis, affinity gel electrophoresis, isothermal titration calorimetry xyloglucan Bacteroides ovatus 31420336
Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol. 2019 Oct 1;85(20):e01491-19. doi: 10.1128/AEM.01491-19. Print 2019 Oct 15.
2019 Oct 15 degradation 16 8 GH3, GH2, GH31, GH9, GH5_4, GH43, GH43_12, GH43_12, GH3
PUL0065 bicinchoninic acid (BCA) reducing-sugar assay, enzymatic product analysis, affinity gel electrophoresis, isothermal titration calorimetry xyloglucan Bacteroides uniformis 31420336
Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol. 2019 Oct 1;85(20):e01491-19. doi: 10.1128/AEM.01491-19. Print 2019 Oct 15.
2019 Oct 15 degradation 13 6 GH43_12, GH43, GH5_4, GH5, GH31, GH2, GH3, GH95
PUL0066 bicinchoninic acid (BCA) reducing-sugar assay, enzymatic product analysis, affinity gel electrophoresis, isothermal titration calorimetry xyloglucan Bacteroides fluxus 31420336
Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol. 2019 Oct 1;85(20):e01491-19. doi: 10.1128/AEM.01491-19. Print 2019 Oct 15.
2019 Oct 15 degradation 13 6 GH43_12, GH43, GH5, GH5_4, GH31, GH2, GH3, GH95
PUL0084 label-free quantitative proteomics, functional enrichment analysis, enzyme activity assay lignocellulose Ruminiclostridium papyrosolvens 31338125
Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation. Biotechnol Biofuels. 2019 Jul 15;12:183. doi: 10.1186/s13068-019-1522-8. eCollection 2019.
2019 degradation 12 12 GH10, CBM6, GH43_29, GH43, CBM6, CE1, CBM6, GH43_10, CBM6, GH62, CBM6, GH43_29, GH43, CBM6, GH27, CBM6, GH59, CBM6, GH62, CE6, CBM6, GH95, CBM32, CE1, CBM6, GH30_8, CBM6
PUL0114 recombinant protein expression, enzyme activity assay arabinofuranose Ruminiclostridium cellulolyticum 31198441
The xyl-doc gene cluster of Ruminiclostridium cellulolyticum encodes GH43- and GH62-alpha-l-arabinofuranosidases with complementary modes of action. Biotechnol Biofuels. 2019 Jun 10;12:144. doi: 10.1186/s13068-019-1483-y. eCollection 2019.
2019 degradation 14 14 GH43, GH43_16, CBM6, GH10, CBM6, GH43, GH43_29, CBM6, CE1, CBM6, GH43_10, CBM6, GH62, CBM6, GH43, GH43_29, CBM6, GH146, CBM22, GH27, CBM6, GH59, CBM6, GH2, CBM6, GH62, CE6, CBM6, CBM32, GH95, CBM6, GH30_8, CBM6
PUL0128 RT-PCR, enzyme activity assay hemicellulose Bifidobacterium longum subsp. longum JCM 1217 30635377
Two Novel alpha-l-Arabinofuranosidases from Bifidobacterium longum subsp. longum Belonging to Glycoside Hydrolase Family 43 Cooperatively Degrade Arabinan. Appl Environ Microbiol. 2019 Mar 6;85(6):e02582-18. doi: 10.1128/AEM.02582-18. Print 2019 Mar 15.
2019 Mar 15 degradation 24 8 GH43, GH43_24, GH30_5, GH30, CBM13, GH146, GH43, GH43_34, GH43_22, GH43, GH43_22, GH43_26, GH43_27, GH43, GH43_22, GH43_22
PUL0135 enzyme activity assay, substrate binding assay pectin Pseudoalteromonas sp. 30341080
Biochemical Reconstruction of a Metabolic Pathway from a Marine Bacterium Reveals Its Mechanism of Pectin Depolymerization. Appl Environ Microbiol. 2018 Dec 13;85(1):e02114-18. doi: 10.1128/AEM.02114-18. Print 2019 Jan 1.
2019 Jan 1 degradation 21 8 CE12, CE4, GH28, GH105, GH105, GH43, GH43_10, CE8, PL1_2
PUL0140 sequence homology analysis xylose Bifidobacterium animalis subsp. animalis 30306201
Staying alive: growth and survival of Bifidobacterium animalis subsp. animalis under in vitro and in vivo conditions. Appl Microbiol Biotechnol. 2018 Dec;102(24):10645-10663. doi: 10.1007/s00253-018-9413-7. Epub 2018 Oct 10.
2018 Dec degradation 11 5 GH43, GH43_12, GH43, GH43_11, GH43_10
PUL0160 mass spectrometry, sequence homology analysis alpha-mannan Salegentibacter sp. Hel_I_6 30246424
Alpha- and beta-mannan utilization by marine Bacteroidetes. Environ Microbiol. 2018 Nov;20(11):4127-4140. doi: 10.1111/1462-2920.14414. Epub 2018 Oct 16.
2018 Nov degradation 33 10 GH92, GH92, GH43, GH43_34, GH125, CBM32, GH92, GH92, GH92, GH76, GH2, GH92
PUL0169 enzyme activity assay, qRT-PCR arabinofuranooligosaccharide Xanthomonas euvesicatoria 30092047
Functional characterization of unique enzymes in Xanthomonas euvesicatoria related to degradation of arabinofurano-oligosaccharides on hydroxyproline-rich glycoproteins. PLoS One. 2018 Aug 9;13(8):e0201982. doi: 10.1371/journal.pone.0201982. eCollection 2018.
2018 degradation 9 3 GH146, GH43, GH43_29, GH121
PUL0189 RNA-Seq, RT-PCR, qPCR pectin Bacteroides xylanisolvens 26920945
Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics. 2016 Feb 27;17:147. doi: 10.1186/s12864-016-2472-1.
2016 Feb 27 degradation 17 7 GH95, GH140, CBM67, GH78, GH33, GH28, GH78, CBM67, GH43_18, GH43, PL1, CE8, PL1_2, GH92
PUL0190 RNA-Seq, RT-PCR, qPCR pectin Bacteroides xylanisolvens 26920945
Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics. 2016 Feb 27;17:147. doi: 10.1186/s12864-016-2472-1.
2016 Feb 27 degradation 15 5 GH51, GH146, GH43, GH43_4, GH43_4, GH51, GH43_29
PUL0192 RNA-Seq, RT-PCR, qPCR pectin Bacteroides xylanisolvens 26920945
Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics. 2016 Feb 27;17:147. doi: 10.1186/s12864-016-2472-1.
2016 Feb 27 degradation 27 12 GH106, GH28, GH28, CE12, GH2, GH43_18, GH43_34, GH43, CBM32, GH42, GH28, PL11, PL11_1, PL26, CE12, GH105, PL11_1, GH105
PUL0218 enzyme activity assay arabinose, arabinan termite gut metagenome 25304507
Investigating the function of an arabinan utilization locus isolated from a termite gut community. Appl Environ Microbiol. 2015 Jan;81(1):31-9. doi: 10.1128/AEM.02257-14. Epub 2014 Oct 10.
2015 Jan degradation 24 5 GH51, GH97, GH146, GH43_4, GH43, GH43_4, GH51, GH43_29
PUL0224 RT-PCR, qRT-PCR cellulose Ruminiclostridium cellulolyticum 23418511
A two-component system (XydS/R) controls the expression of genes encoding CBM6-containing proteins in response to straw in Clostridium cellulolyticum. PLoS One. 2013;8(2):e56063. doi: 10.1371/journal.pone.0056063. Epub 2013 Feb 13.
2013 degradation 16 14 GH43_16, GH43, CBM6, GH10, CBM6, GH43, GH43_29, CBM6, CBM6, CE1, GH43_10, CBM6, GH62, CBM6, GH43, GH43_29, CBM6, GH146, CBM22, GH27, CBM6, GH59, CBM6, GH2, CBM6, GH62, CBM6, CE6, CBM32, GH95, CBM6, GH30_8, CBM6
PUL0228 qRT-PCR, enzyme activity assay, high performance anion exchange chromatography arabinan Bacteroides thetaiotaomicron 22686399, 21339299
Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system. The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases. Mol Microbiol. 2012 Aug;85(3):478-91. doi: 10.1111/j.1365-2958.2012.08123.x. Epub 2012 Jul 5. J Biol Chem. 2011 Apr 29;286(17):15483-95. doi: 10.1074/jbc.M110.215962. Epub 2011 Feb 21.
2012 Aug,2011 Apr 29 degradation 10 4 GH43, GH43_4, GH43_4, GH51, GH43_29
PUL0229 RT-PCR aldouronate Paenibacillus sp. JDR-2 17921311
Structure, function, and regulation of the aldouronate utilization gene cluster from Paenibacillus sp. strain JDR-2. J Bacteriol. 2007 Dec;189(24):8863-70. doi: 10.1128/JB.01141-07. Epub 2007 Oct 5.
2007 Dec degradation 8 3 GH67, CBM22, GH10, GH43_12, GH43
PUL0274 RT-qPCR xylobiose, xylooligosaccharide Bifidobacterium animalis subsp. lactis 23663691
Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04. BMC Genomics. 2013 May 10;14:312. doi: 10.1186/1471-2164-14-312.
2013 May 10 degradation 12 4 GH43, GH43_12, GH43_11, GH43, GH43_10
PUL0289 enzyme activity assay xylan Flavobacterium johnsoniae 29588659
A novel acetyl xylan esterase enabling complete deacetylation of substituted xylans. Biotechnol Biofuels. 2018 Mar 22;11:74. doi: 10.1186/s13068-018-1074-3. eCollection 2018.
2018 degradation 12 7 GH97, GH3, CBM22, GH43_10, GH43, GH146, GH115, CE0, CE6, CE1, GH43_12
PUL0294 gene trait matching exercise xylooligosaccharide Bifidobacterium longum 29310579
Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains. BMC Genomics. 2018 Jan 8;19(1):33. doi: 10.1186/s12864-017-4388-9.
2018 Jan 8 degradation 12 2 GH120, GH43, GH43_12, GH43_11, GH43
PUL0295 gene trait matching exercise arabinan Bifidobacterium longum 29310579
Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains. BMC Genomics. 2018 Jan 8;19(1):33. doi: 10.1186/s12864-017-4388-9.
2018 Jan 8 degradation 9 5 GH43_22, GH43_34, GH43, GH43_22, GH43_26, GH43, GH43_27, GH43, GH43_22, GH43, GH43_22
PUL0296 gene trait matching exercise arabinan Bifidobacterium longum 29310579
Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains. BMC Genomics. 2018 Jan 8;19(1):33. doi: 10.1186/s12864-017-4388-9.
2018 Jan 8 degradation 4 1 GH43, GH43_22
PUL0300 gene trait matching exercise arabinoxylan Bifidobacterium longum 29310579
Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains. BMC Genomics. 2018 Jan 8;19(1):33. doi: 10.1186/s12864-017-4388-9.
2018 Jan 8 degradation 14 5 GH43_26, GH43, GH43_27, GH43, GH43_4, GH43_4, GH51
PUL0302 RT-qPCR, isothermal titration calorimetry, enzyme activity assay, gene deletion mutant and growth assay arabinan Bacteroides thetaiotaomicron 29255254
Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Nat Microbiol. 2018 Feb;3(2):210-219. doi: 10.1038/s41564-017-0079-1. Epub 2017 Dec 18.
2018 Feb degradation 22 6 GH51, GH146, GH43_4, GH43, GH43_4, GH51, GH43_29
PUL0309 enzyme activity assay, substrate binding assay, isothermal titration calorimetry arabinan Caldanaerobius polysaccharolyticus 28710263
Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus. Appl Environ Microbiol. 2017 Aug 31;83(18):e00794-17. doi: 10.1128/AEM.00794-17. Print 2017 Sep 15.
2017 Sep 15 degradation 12 6 GH43_4, GH43, GH127, GH51, GH27, GH51, GH146
PUL0328 microarray, gas chromatography and mass spectrometry xylan Gramella flava 28261179
Characterization of Potential Polysaccharide Utilization Systems in the Marine Bacteroidetes Gramella Flava JLT2011 Using a Multi-Omics Approach. Front Microbiol. 2017 Feb 14;8:220. doi: 10.3389/fmicb.2017.00220. eCollection 2017.
2017 degradation 10 4 GH127, CBM13, GH43, GH43_26, GH2, GH5, GH5_13
PUL0329 microarray, gas chromatography and mass spectrometry xylan Gramella flava 28261179
Characterization of Potential Polysaccharide Utilization Systems in the Marine Bacteroidetes Gramella Flava JLT2011 Using a Multi-Omics Approach. Front Microbiol. 2017 Feb 14;8:220. doi: 10.3389/fmicb.2017.00220. eCollection 2017.
2017 degradation 25 7 GH43_10, GH43, CBM22, GH43, GH43_12, GH43, GH43_1, GH3, GH67, GH10, GH115, CE15
PUL0345 qRT-PCR, enzyme activity assay xylan Bacteroides intestinalis 27681607
Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan. Sci Rep. 2016 Sep 29;6:34360. doi: 10.1038/srep34360.
2016 Sep 29 degradation 31 13 CBM4, GH10, GH35, GH43_12, GH43, GH10, GH43_1, GH43, GH67, GH8, CE6, GH95, CE0, CE1, GH5, GH5_21, GH10, CBM0, GH115
PUL0346 gene deletion mutant and growth assay xylooligosaccharide uncultured bacterium 27573446
Functional characterization of a gene locus from an uncultured gut Bacteroides conferring xylo-oligosaccharides utilization to Escherichia coli. Mol Microbiol. 2016 Nov;102(4):579-592. doi: 10.1111/mmi.13480. Epub 2016 Sep 14.
2016 Nov degradation 15 5 GH43, GH43_29, GH43, GH43_12, GH43, GH43_1, GH10, GH16
PUL0354 microarray lactose, host glycan Bacteroides thetaiotaomicron 16968696
Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J Biol Chem. 2006 Nov 24;281(47):36269-79. doi: 10.1074/jbc.M606509200. Epub 2006 Sep 12.
2006 Nov 24 degradation 8 3 GH93, GH0, GH43_31, GH43, GH43_31
PUL0358 microarray lactose, host glycan Bacteroides thetaiotaomicron 16968696
Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J Biol Chem. 2006 Nov 24;281(47):36269-79. doi: 10.1074/jbc.M606509200. Epub 2006 Sep 12.
2006 Nov 24 degradation 4 4 CBM32, GH35, GH43_19, GH43, GH43_9, GH43_19, GH43, GH51
PUL0386 ion trap liquid chromatography, mass spectrometry, target decoy database analysis, high performance anion exchange chromatography hemicellulose Ruminiclostridium cellulolyticum 20013800
Modulation of cellulosome composition in Clostridium cellulolyticum: adaptation to the polysaccharide environment revealed by proteomic and carbohydrate-active enzyme analyses. Proteomics. 2010 Feb;10(3):541-54. doi: 10.1002/pmic.200900311.
2010 Feb degradation 11 11 GH43, CBM6, GH43_16, GH10, CBM6, GH43_29, GH43, CBM6, CE1, CBM6, GH43_10, CBM6, GH62, CBM6, GH43_29, GH43, CBM6, GH146, CBM22, GH27, CBM6, GH59, CBM6, GH2, CBM6
PUL0395 isothermal calorimetric titration, electrophoretic mobility shift assay, Northern Blot arabinose, arabinan Geobacillus stearothermophilus 21460081
The L-Arabinan utilization system of Geobacillus stearothermophilus. J Bacteriol. 2011 Jun;193(11):2838-50. doi: 10.1128/JB.00222-11. Epub 2011 Apr 1.
2011 Jun degradation 25 5 GH43, GH43_5, GH43, GH43_4, CBM54, GH51, GH51, GH127
PUL0402 Northern Blot, enzyme activity assay xylan, xylose Lactococcus lactis subsp. lactis IO-1 11282589
Genetic evidence for a defective xylan degradation pathway in Lactococcus lactis. Appl Environ Microbiol. 2001 Apr;67(4):1445-52. doi: 10.1128/AEM.67.4.1445-1452.2001.
2001 Apr degradation 6 1 GH43_11, GH43
PUL0435 mass spectrometry, high performance anion exchange chromatography glucose Chitinophaga pinensis 28069559
Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis. J Proteomics. 2017 Mar 6;156:63-74. doi: 10.1016/j.jprot.2017.01.003. Epub 2017 Jan 6.
2017 Mar 6 degradation 13 4 GH43, GH43_34, GH30, GH30_1, GH30, GH30_3, GH16
PUL0456 microarray, RNA-Seq xylan Prevotella bryantii 20622018
Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes. J Biol Chem. 2010 Sep 24;285(39):30261-73. doi: 10.1074/jbc.M110.141788. Epub 2010 Jul 9.
2010 Sep 24 degradation 13 6 CE6, GH43_10, GH43, GH43_1, GH43, GH10, GH67
PUL0457 high performance anion exchange chromatography, enzyme activity assay, RNA-Seq xylooligosaccharide Lactobacillus rossiae 27142164
Cloning, expression and characterization of a beta-D-xylosidase from Lactobacillus rossiae DSM 15814(T). Microb Cell Fact. 2016 May 3;15:72. doi: 10.1186/s12934-016-0473-z.
2016 May 3 degradation 7 1 GH43_11, GH43
PUL0468 microarray, qPCR host glycan Bacteroides thetaiotaomicron 18996345
Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe. 2008 Nov 13;4(5):447-57. doi: 10.1016/j.chom.2008.09.007.
2008 Nov 13 degradation 47 2 GH43, GH43_26, GH76
PUL0476 growth assay hemicellulose, pectin Flavobacterium johnsoniae 19717629
Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol. 2009 Nov;75(21):6864-75. doi: 10.1128/AEM.01495-09. Epub 2009 Aug 28.
2009 Nov degradation 11 6 GH5, GH5_13, GH43_18, GH2, GH43, GH43_26, GH43_31, GH29, CBM32
PUL0479 growth assay pectin Flavobacterium johnsoniae 19717629
Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol. 2009 Nov;75(21):6864-75. doi: 10.1128/AEM.01495-09. Epub 2009 Aug 28.
2009 Nov degradation 20 12 GH43, GH43_34, GH43_19, GH27, GH2, GH95, GH51, GH28, GH28, GH2, GH92, GH92, GH89
PUL0481 growth assay, enzyme activity assay hemicellulose Flavobacterium johnsoniae 19717629, 32266006
Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Multimodular fused acetyl-feruloyl esterases from soil and gut Bacteroidetes improve xylanase depolymerization of recalcitrant biomass. Appl Environ Microbiol. 2009 Nov;75(21):6864-75. doi: 10.1128/AEM.01495-09. Epub 2009 Aug 28. Biotechnol Biofuels. 2020 Mar 31;13:60. doi: 10.1186/s13068-020-01698-9. eCollection 2020.
2009 Nov,2020 degradation 13 7 GH97, GH3, GH43, GH43_10, CBM22, GH146, GH115, GH43_12, GH3
PUL0482 growth assay pectin Flavobacterium johnsoniae 19717629
Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol. 2009 Nov;75(21):6864-75. doi: 10.1128/AEM.01495-09. Epub 2009 Aug 28.
2009 Nov degradation 27 17 GH78, CBM67, GH142, GH95, GH78, CBM67, GH143, GH43_18, GH43, GH28, GH140, PL1, CE8, PL1_2, PL1, CE8, PL1_2, CE8, GH127, PL1, PL1_2, GH139, GH106, GH2, GH137, GH78
PUL0484 growth assay pectin Flavobacterium johnsoniae 19717629
Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol. 2009 Nov;75(21):6864-75. doi: 10.1128/AEM.01495-09. Epub 2009 Aug 28.
2009 Nov degradation 12 8 CE12, GH28, PL10, CE8, PL10_1, GH43_10, GH43, GH105, GH105, GH105, GH28
PUL0520 clone and expression, enzyme activity assay xylobiose, xylodextrin Klebsiella oxytoca 14532050
Cloning, characterization, and functional expression of the Klebsiella oxytoca xylodextrin utilization operon (xynTB) in Escherichia coli. Appl Environ Microbiol. 2003 Oct;69(10):5957-67. doi: 10.1128/AEM.69.10.5957-5967.2003.
2003 Oct degradation 2 1 GH43, GH43_11
PUL0530 microarray, qPCR rhamnogalacturonan Bacteroides thetaiotaomicron 22205877
Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.
2011 Dec degradation 54 21 PL1, CE8, PL1_2, GH2, GH139, GH106, GH2, GH2, GH137, GH2, CBM57, GH138, GH78, GH141, GH127, GH95, GH105, GH140, GH78, GH33, CBM67, GH28, GH78, CBM67, GH143, GH142, GH43_18, GH43, PL1, CE8, PL1_2
PUL0532 RNA-Seq arabinan, pectin Bacteroides cellulosilyticus 23976882
Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol. 2013;11(8):e1001637. doi: 10.1371/journal.pbio.1001637. Epub 2013 Aug 20.
2013 degradation 17 5 GH51, GH43_4, GH43, GH43_4, GH43, GH146, GH51
PUL0535 RNA-Seq arabinogalactan Bacteroides cellulosilyticus 23976882
Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol. 2013;11(8):e1001637. doi: 10.1371/journal.pbio.1001637. Epub 2013 Aug 20.
2013 degradation 9 2 GH16, GH43, GH43_24, GH16
PUL0545 RNA-Seq arabinan Bacteroides cellulosilyticus 23976882
Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol. 2013;11(8):e1001637. doi: 10.1371/journal.pbio.1001637. Epub 2013 Aug 20.
2013 degradation 10 5 GH43_2, CBM6, GH43, GH3, GH43_17, GH9, GH43_7, CBM13, CE1
PUL0552 RNA-Seq arabinan Bacteroides cellulosilyticus 23976882
Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol. 2013;11(8):e1001637. doi: 10.1371/journal.pbio.1001637. Epub 2013 Aug 20.
2013 degradation 7 4 PL1_2, CE8, PL1, GH43_18, GH43, GH142, GH143, GH78, CBM67
PUL0553 RT-PCR, qPCR xylan Bacteroides xylanisolvens 27142817
Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level. BMC Genomics. 2016 May 4;17:326. doi: 10.1186/s12864-016-2680-8.
2016 May 4 degradation 21 13 GH43_10, GH43, CBM6, GH3, GH43, GH43_12, GH31, GH97, CBM66, CBM6, GH43, GH43_29, GH43, GH43_12, CBM4, CBM0, GH10, GH5_21, CE1, CE6, CBM6, GH43_29, GH95, GH115
PUL0558 gene deletion mutant and growth assay, growth assay, enzyme activity assay rhamnogalacturonan Bacteroides thetaiotaomicron 28329766
Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature. 2017 Apr 6;544(7648):65-70. doi: 10.1038/nature21725. Epub 2017 Mar 22.
2017 Apr 6 degradation 50 20 GH2, GH139, GH106, GH2, GH2, GH2, CBM57, GH137, GH138, GH78, GH141, GH127, GH95, GH105, GH140, CBM67, GH33, GH78, GH28, CBM67, GH78, GH142, GH143, GH43_18, GH43, CE8, PL1_2, PL1
PUL0560 microarray, qPCR arabinogalactan Bacteroides thetaiotaomicron 18996345, 22205877
Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. Cell Host Microbe. 2008 Nov 13;4(5):447-57. doi: 10.1016/j.chom.2008.09.007. PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.
2008 Nov 13,2011 Dec degradation 30 4 PL27, GH43_24, GH43, GH43_24, GH35, CBM32
PUL0563 microarray, qPCR arabinogalactan Bacteroides thetaiotaomicron 18996345, 22205877
Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. Cell Host Microbe. 2008 Nov 13;4(5):447-57. doi: 10.1016/j.chom.2008.09.007. PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.
2008 Nov 13,2011 Dec degradation 14 7 GH127, GH43, GH43_34, GH154, GH43, GH16, GH43_24, GH43_24, GH145, GH105
PUL0564 microarray, qPCR rhamnogalacturonan Bacteroides thetaiotaomicron 18996345, 22205877
Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. Cell Host Microbe. 2008 Nov 13;4(5):447-57. doi: 10.1016/j.chom.2008.09.007. PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.
2008 Nov 13,2011 Dec degradation 39 23 GH106, GH28, GH28, CE12, GH2, GH43, GH43_18, GH42, GH28, CE4, CE0, GH28, GH2, GH27, CBM35, GH35, PL9, PL9_1, PL26, CE12, GH105, PL11, PL11_1, GH105, CE4, CE0, CE6, GH2, PL9_1
PUL0599 liquid chromatography and mass spectrometry, differential gene expression xylan Clostridium cellulovorans 26020016
Elucidation of the recognition mechanisms for hemicellulose and pectin in Clostridium cellulovorans using intracellular quantitative proteome analysis. AMB Express. 2015 May 23;5:29. doi: 10.1186/s13568-015-0115-6. eCollection 2015.
2015 degradation 7 1 GH43, GH43_11
PUL0617 RNA-Seq xylan Prevotella sp. PINT 33113351
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp. Cell Host Microbe. 2020 Dec 9;28(6):838-852.e6. doi: 10.1016/j.chom.2020.09.012. Epub 2020 Oct 27.
2020 Dec 9 degradation 14 6 GH67, GH10, GH43, GH43_1, GH43_35, GH43, GH5_21, GH5, GH10, CBM0, CBM4, 3.2.1.8
PUL0622 RNA-Seq xylan Prevotella sp. PROD 33113351
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp. Cell Host Microbe. 2020 Dec 9;28(6):838-852.e6. doi: 10.1016/j.chom.2020.09.012. Epub 2020 Oct 27.
2020 Dec 9 degradation 15 5 CBM35, CBM2, PL11_1, PL11, GH3, 3.2.1.55, CBM6, 3.2.1.37, GH43_7, CBM13, GH43, PL11_1, CBM35, CE12, PL11, CBM2, GH2
PUL0624 RNA-Seq xylan Prevotella sp. PMUR 33113351
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp. Cell Host Microbe. 2020 Dec 9;28(6):838-852.e6. doi: 10.1016/j.chom.2020.09.012. Epub 2020 Oct 27.
2020 Dec 9 degradation 11 3 CBM13, GH43, GH43_24, GH43_19, GH51, GH128
PUL0625 RNA-Seq xylan Prevotella sp. PMUR 33113351
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp. Cell Host Microbe. 2020 Dec 9;28(6):838-852.e6. doi: 10.1016/j.chom.2020.09.012. Epub 2020 Oct 27.
2020 Dec 9 degradation 18 9 GH43_12, GH43, GH115, GH43, GH43_10, GH97, CBM6, GH43_29, GH43, CBM22, CE1, CBM48, CBM51, CBM32, GH95, CBM13, GH115, GH30_8
PUL0626 high performance anion exchange chromatography arabinan Lactobacillus crispatus DSM29598 33119797
Characterization of two extracellular arabinanases in Lactobacillus crispatus. Appl Microbiol Biotechnol. 2020 Dec;104(23):10091-10103. doi: 10.1007/s00253-020-10979-0. Epub 2020 Oct 29.
2020 Dec degradation 24 8 GH43, CBM54, GH43_4, GH2, GH43, GH43_4, GH127, GH51, GH43, CBM42, GH43_26, GH51, GH27, CBM51
PUL0630 enzyme activity assay, affinity gel electrophoresis xylan termite gut metagenome 33187992
Multimodularity of a GH10 Xylanase Found in the Termite Gut Metagenome. Appl Environ Microbiol. 2021 Jan 15;87(3):e01714-20. doi: 10.1128/AEM.01714-20. Print 2021 Jan 15.
2021 Jan 15 degradation 9 5 GH10, CBM4, CBM0, 3.2.1.8, GH115, GH11, CBM6, CBM36, CBM0, 3.2.1.8, GH10, CBM9, CBM22, GH43, GH43_1
PUL0643 enzyme activity assay, liquid chromatography, high performance anion exchange chromatography, qRT-PCR, crystallization arabinoxylan Bacteroides intestinalis DSM 17393 33469030
Degradation of complex arabinoxylans by human colonic Bacteroidetes. Nat Commun. 2021 Jan 19;12(1):459. doi: 10.1038/s41467-020-20737-5.
2021 Jan 19 degradation 12 7 CBM48, CE1, GH43, GH43_7, CBM13, CBM48, CE1, CE6, CBM48, CE1, GH43_17, CBM6, GH3, GH43, CBM6, GH43_2
PUL0644 enzyme activity assay, liquid chromatography, high performance anion exchange chromatography, qRT-PCR, crystallization arabinoxylan Bacteroides cellulosilyticus DSM 14838 33469030
Degradation of complex arabinoxylans by human colonic Bacteroidetes. Nat Commun. 2021 Jan 19;12(1):459. doi: 10.1038/s41467-020-20737-5.
2021 Jan 19 degradation 10 6 GH43, GH43_2, CBM6, GH43_17, GH10, CBM48, CE1, CE1, GH43, CBM13, GH43_7, CBM48, CE1
PUL0645 enzyme activity assay, liquid chromatography, high performance anion exchange chromatography, qRT-PCR, crystallization arabinoxylan Bacteroides oleiciplenus YIT 12058 33469030
Degradation of complex arabinoxylans by human colonic Bacteroidetes. Nat Commun. 2021 Jan 19;12(1):459. doi: 10.1038/s41467-020-20737-5.
2021 Jan 19 degradation 10 5 GH43, GH43_2, CBM6, GH3, CBM6, GH43_17, GH43_7, GH43, CBM13, CE1, CBM48
PUL0648 high performance anion exchange chromatography, substrate binding assay, thin layer chromatography, NMR, mass spectrometry, crystallization glucuronoarabinoxylan Dysgonomonas mossii DSM 22836 33667545
A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases. J Biol Chem. 2021 Jan-Jun;296:100500. doi: 10.1016/j.jbc.2021.100500. Epub 2021 Mar 2.
2021 Jan-Jun degradation 37 20 CBM0, 3.2.1.8, CBM4, GH10, GH43_12, GH43, GH43, GH43_1, GH10, GH146, CBM48, CE1, CBM6, CBM36, GH8, 3.2.1.156, CE6, CBM2, GH43_29, GH43, CBM22, CBM42, CBM66, CBM6, CBM6, GH43_29, GH43, GH97, GH31, GH51, CBM2, GH43_29, GH43, CBM22, CBM42, CBM6, CBM48, CE1, GH10, GH43_10, GH43, GH115, GH10, GH43, GH43_1, GH67
PUL0664 thin layer chromatography, clone and expression, recombinant protein expression arabinogalactan protein Bacteroides plebeius DSM17135 34340552
Sulfation of Arabinogalactan Proteins Confers Privileged Nutrient Status to Bacteroides plebeius. mBio. 2021 Aug 31;12(4):e0136821. doi: 10.1128/mBio.01368-21. Epub 2021 Aug 3.
2021 Aug 31 degradation 17 8 GH49, GH2, GH36, GH27, GH28, GH43, GH43, GH2
PUL0666 UHPLC-MS, RNA-seq, RT-qPCR pectin Bacteroides thetaiotaomicron VPI-5482 34420703
Discrete genetic loci in human gut Bacteroides thetaiotaomicron confer pectin metabolism. Carbohydr Polym. 2021 Nov 15;272:118534. doi: 10.1016/j.carbpol.2021.118534. Epub 2021 Aug 6.
2021 Nov 15 degradation 5 4 GH35, GH43, GH51
PUL0668 UHPLC-MS, RNA-seq, RT-qPCR pectin Bacteroides thetaiotaomicron VPI-5482 34420703
Discrete genetic loci in human gut Bacteroides thetaiotaomicron confer pectin metabolism. Carbohydr Polym. 2021 Nov 15;272:118534. doi: 10.1016/j.carbpol.2021.118534. Epub 2021 Aug 6.
2021 Nov 15 degradation 17 8 GH43, GH28, PL9, PL26, CE12, GH105
PUL0669 clone, high performance anion exchange chromatography, enzymatic product analysis xylan Bacteroides eggerthii 1_2_48FAA 34480044
Characterization of a novel multidomain CE15-GH8 enzyme encoded by a polysaccharide utilization locus in the human gut bacterium Bacteroides eggerthii. Sci Rep. 2021 Sep 3;11(1):17662. doi: 10.1038/s41598-021-96659-z.
2021 Sep 3 degradation 24 12 CE15, GH8, GH95, GH43