The claim of primacy of human gut Bacteroides ovatus in dietary cellobiose degradation

References

• Golisch B, Lei Z, Tamura K, Brumer H. Configured for the human gut microbiota: molecular mechanisms of dietary β‑glucan utilization. ACS Chem Biol. 2021;16(11):2087–18. doi:10.1021/acschembio.1c00563.
   PubMed Web of Science ®Google Scholar
• Macy JM, Farrand JR, Montgomery L. Cellulolytic and non-cellulolytic bacteria in rat gastrointestinal tracts. Appl Environ Microbiol. 1982;44(6):1428–1434. doi:10.1128/aem.44.6.1428-1434.1982.
   PubMed Web of Science ®Google Scholar
• Varel VH, Fryda SJ, Robinson IM. Cellulolytic bacteria from pig large intestine. Appl Environ Microbiol. 1984;47(1):219–221. doi:10.1128/aem.47.1.219-221.1984.
   PubMed Web of Science ®Google Scholar
• Varel VH, Pond WG. Characteristics of a new cellulolytic Clostridium sp. isolated from pig intestinal tract. Appl Environ Microbiol. 1992;58(5):1645–1649. doi:10.1128/aem.58.5.1645-1649.1992.
   PubMed Web of Science ®Google Scholar
• Robert C, Del’Homme C, Bernalier-Donadille A. Interspecies H2 transfer in cellulose degradation between fibrolytic bacteria and H2-utilizing microorganisms from the human colon. FEMS Microbiol Lett. 2001;205(2):209–214. doi:10.1016/S0378-1097(01)00467-0.
   PubMed Web of Science ®Google Scholar
• Robert C, Chassard C, Lawson PA, Bernalier-Donadille A. Bacteroides cellulosilyticus sp. nov., a cellulolytic bacterium from the human gut microbial community. Int J Syst Evol Microbiol. 2007;57(7):1516–1520. doi:10.1099/ijs.0.64998-0.
   PubMedGoogle Scholar
• Chassard C, Delmas E, Robert C, Bernalier- Donadille A. The cellulose-degrading microbial community of the human gut varies according to the presence or absence of methanogens. FEMS Microbiol Ecol. 2010;74(1):205–213. Available from. doi:10.1111/j.1574-6941.2010.00941.x.
   PubMed Web of Science ®Google Scholar
• Chassard C, Delmas E, Robert C, Lawson PA, Bernalier-Donadille A. Ruminococcus champanellensis sp. nov., a cellulose-degrading bacterium from human gut microbiota. Int J Syst Evol Microbiol. 2012;62(1):138–143. doi:10.1099/ijs.0.027375-0.
   PubMed Web of Science ®Google Scholar
• Julliand V, de Vaux A, Millet L, Fonty G. Identification of Ruminococcus flavefaciens as the predominant cellulolytic bacterial species of the equine cecum. Appl Environ Microbiol. 1999;65(8):3738–3741. doi:10.1128/AEM.65.8.3738-3741.1999.
   PubMed Web of Science ®Google Scholar
• Katole SB, Das A, Agarwal N, Prakash B, Saha SK, Saini M, Sharma AK. Influence of work on nutrient utilisation in semicaptive Asian elephants (Elephas maximus). J Appl Anim Res. 2014;42(4):380–388. doi:10.1080/09712119.2013.875904.
   Web of Science ®Google Scholar
• Varel VH, Tanner RS, Woese CR. Clostridium herbivorans sp. nov., a cellulolytic anaerobe from the pig intestine. Int J Syst Bacteriol. 1995;45(3):490–494. doi:10.1099/00207713-45-3-490.
   PubMedGoogle Scholar
• Shinkai T, Kobayashi Y. Localization of ruminal cellulolytic bacteria on plant fibrous materials as determined by fluorescence in situ hybridization and real-time PCR. Appl Environ Microbiol. 2007;73(5):1646–1652. doi:10.1128/AEM.01896-06.
   PubMed Web of Science ®Google Scholar
• Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012;3(4):289–306. doi:10.4161/gmic.19897.
   PubMed Web of Science ®Google Scholar
• Li H, Qu J, Li T, Wirth S, Zhang Y, Zhao X, Li X. Diet simplification selects for high gut microbial diversity and strong fermenting ability in high-altitude pikas. Appl Microbiol Biotechnol. 2018;105(15):6739–6751. doi:10.1007/s00253-018-9097-z.
   Google Scholar
• Montgomery L, Macy JM. Characterization of rat cecum cellulolytic bacteria. Appl Environ Microbiol. 1982;44(6):1435–1443. doi:10.1128/aem.44.6.1435-1443.1982.
   PubMed Web of Science ®Google Scholar
• Bryant MP, Robinson IM, Chu H. Observations on the nutrition of Bacteroides succinogenes-A ruminal cellulolytic bacterium. J Dairy Sci. 1959;42(11):1831–1847. doi:10.3168/jds.S0022-0302(59)90815-X.
   Web of Science ®Google Scholar
• Neumann AP, McCormick CA, Suen G. Fibrobacter communities in the gastrointestinal tracts of diverse hindgut-fermenting herbivores are distinct from those of the rumen. Environ Microbiol. 2017;19(9):3768–3783. doi:10.1111/1462-2920.13878.
   PubMed Web of Science ®Google Scholar
• Amann RI, Lin C, Key R, Montgomery L, Stahl DA. Diversity Among Fibrobacter isolates: towards a phylogenetic classification. Syst Appl Microbiol. 1992;15(1):23–31. doi:10.1016/S0723-2020(11)80133-5.
   Web of Science ®Google Scholar
• Cummings JH, Macfarlane GT. The control and consequences of bacterial fermentation in the human colon. J Appl Bacteriol. 1991;70(6):443–459. doi:10.1111/j.1365-2672.1991.tb02739.x.
   PubMedGoogle Scholar
• Wedekind KJ, Mansfield HR, Montgomery L. Enumeration and isolation of cellulolytic and hemicellulolytic bacteria from human feces. Appl Environ Microbiol. 1988;54(6):1530–1535. doi:10.1128/aem.54.6.1530-1535.1988.
   PubMed Web of Science ®Google Scholar
• Chassard C, Delmas E, Robert C, Bernalier-Donadille A. The cellulose-degrading microbial community of the human gut varies according to the presence or absence of methanogens. FEMS Microbiol Ecol. 2010;74(1):205–213. doi:10.1111/j.1574-6941.2010.00941.x.
   PubMed Web of Science ®Google Scholar
• Robert C, Bernalier-Donadille A. The cellulolytic microflora of the human colon: evidence of microcrystalline cellulose-degrading bacteria in methane-excreting subjects. FEMS Microbiol Ecol. 2003;46(1):81–89. doi:10.1016/S0168-6496(03)00207-1.
   PubMed Web of Science ®Google Scholar
• Froidurot A, Julliand V. Cellulolytic bacteria in the large intestine of mammals. Gut Microbes. 2022;14(1):2031694. doi:10.1080/19490976.2022.2031694.
   PubMed Web of Science ®Google Scholar
• Yeoman CJ, Fields CJ, Lepercq P, Ruiz P, Forano E, White BA, Mosoni P. In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminococcus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses. mBio. 2021;12(2):e03533–3520. 10.1128/mBio.03533-20.
   PubMed Web of Science ®Google Scholar
• Moraïs S, David YB, Bensoussan L, Duncan SH, Koropatkin NM, Martens EC, Flint HJ, Bayer EA. Cellulose degradation in the human gut: ruminococcus champanellensis expands the cellulosome paradigm. Environ Microbiol. 2016;18(2):542–556. doi:10.1111/1462-2920.13047.
   PubMed Web of Science ®Google Scholar
• Violot S, Aghajari N, Czjzek M, Feller G, Sonan GK, Gouet P, Gerday C, Haser R, Receveur-Bréchot V. Structure of a full length psychrophilic cellulase from Pseudoalteromonas haloplanktis revealed by X-ray diffraction and small angle X-ray scattering. J Mol Biol. 2005;348(5):1211–1224. doi:10.1016/j.jmb.20-05.03.026.
   PubMed Web of Science ®Google Scholar
• Zhu Y, Han L, Hefferon KL, Silvaggi NR, Wilson DB, McBride MJ, Spormann AM. Periplasmic cytophaga hutchinsonii endoglucanases are required for use of crystalline cellulose as the sole source of carbon and energy. Appl Environ Microbiol. 2016;82(15):4835–4845. doi:10.1128/AEM.01298-16.
   PubMed Web of Science ®Google Scholar
• Cao J, Deng Q, Gao D, He B, Yin S, Qian L, Wang J, Wang Q. A novel bifunctional glucanase exhibiting high production of glucose and cellobiose from rumen bacterium. Int J Biol Macromol. 2021;173:136–145. doi:10.1016/j.ijbiomac.2021.01.113.
   PubMed Web of Science ®Google Scholar
• Liu N, Li H, Chevrette MG, Zhang L, Cao L, Zhou H, Zhou X, Zhou Z, Pope PB, Currie CR, et al. Functional metagenomics reveals abundant polysaccharide degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite. Isme J. 2019;13(1):104–117. doi:10.1038/s41396-018-0255-1.
   PubMed Web of Science ®Google Scholar
• Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, Abbott DW, Henrissat B, Gilbert HJ, Bolam DN, et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 2011;9(12):e1001221. doi:10.1371/journal.pbi-o.1001221.
   PubMed Web of Science ®Google Scholar
• Tamura K, Hemsworth GR, Déjean G, Rogers TE, Pudlo NA, Urs K, Jain N, Davies JG, Martens EC, Brumer H. Molecular mechanism by which prominent human gut Bacteroidetes utilize mixed-linkage beta-glucans, major health-promoting cereal polysaccharides. Cell Rep. 2017;21(2):417–430. doi:10.1016/j.celrep.2017.09.049.
   PubMed Web of Science ®Google Scholar
• Grondin JM, Tamura K, Déjean G, Abbott DW, Brumer H, O’Toole G. Polysaccharide utilization loci: fueling microbial communities. J Bacteriol. 2017;199(15):e00860–16. doi:10.1128/J-B.00860-16.
   PubMed Web of Science ®Google Scholar
• Li M, Li S, Guo X, Guo C, Wang Y, Du Z, Zhang Z, Xie C, Ding K. Discrete genetic loci in human gut Bacteroides thetaiotaomicron confer pectin metabolism. Carbohydr Polym. 2021;272:118534. doi:10.1016/j.carbpol.2021.1-18534.
   PubMed Web of Science ®Google Scholar
• Ndeh D, Rogowski A, Cartmell A, Luis AS, Baslé A, Gray J, Venditto I, Briggs J, Zhang X, Labourel A, et al. Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature. 2017;544:65–70. doi:10.1038/nature21725.
   PubMed Web of Science ®Google Scholar
• Luis AS, Briggs J, Zhang X, Farnell B, Ndeh D, Labourel A, Baslé A, Cartmell A, Terrapon N, Stott K, et al. Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Nature Microbiol. 2018;3(2):210–219. doi:10.1038/s41564-017-0079-1.
   PubMed Web of Science ®Google Scholar
• Qian K, Chen S, Wang J, Sheng K, Wang Y, Zhang M. A β-N-acetylhexosaminidase Amuc_2109 from Akkermansia muciniphila protects against dextran sulfate sodium-induced colitis in mice by enhancing intestinal barrier and modulating gut microbiota. Food Funct. 2022;13(4):2216–2227. doi:10.1039/d1fo04094d.
   PubMed Web of Science ®Google Scholar
• Gao C, Major A, Rendon D, Lugo M, Jackson V, Shi Z, Mori-Akiyama Y, Versalovic J. Histamine H2 Receptor-Mediated Suppression of Intestinal Inflammation by Probiotic Lactobacillus reuteri. mBio. 2015;6(6):e01358–1315. doi:10.1128/mBio.01358-15.
   PubMed Web of Science ®Google Scholar
• Alexander JK. Characteristics of cellobiose phosphorylase. J Bacteriol. 1961;81(6):903–910. doi:10.1128/jb.81.6.903-910.1961.
   PubMed Web of Science ®Google Scholar
• Romano AH, Brino G, Peterkofsky A, Reizer J. Regulation of β-Galactoside transport and accumulation in heterofermentative lactic acid bacteria. J Bacteriol. 1987;169(12):5589–5596. doi:10.1128/jb.169.12.5589-5596.1987.
   PubMed Web of Science ®Google Scholar
• Thompson J, Gentry-Weeks CR, Nguyen NY, Folk JE, Robrish SA. Purification from Fusobacterium mortiferum ATCC 25557 of a 6-phosphoryl-O-a-D-glucopyranosyl: 6-phosphoglucohydrolase that hydrolyzes maltose 6-phosphate and related phospho-a-D-glucosides. J Bacteriol. 1995;177(9):2505–2512. doi:10.1128/jb.177.9.2505-2512.1995.
   PubMed Web of Science ®Google Scholar
• Garg R, Srivastava R, Brahma V, Verma L, Karthikeyan S, Sahni G. Biochemical and structural characterization of a novel halotolerant cellulase from soil metagenome. Sci Rep. 2016;6:39634. doi:10.1038/srep39634.
   PubMed Web of Science ®Google Scholar
• Dutoit R, Delsaute M, Collet L, Wauven CV, Elder DV, Berlemont R, Richel A, Galleni M, Bauvois C. Crystal structure determination of Pseudomonas stutzeri A1501 endoglucanase Cel5A: the search for a molecular basis for glycosynthesis in GH5_5 enzymes. Acta Crystallogr D Struct Biol. 2019;75(Pt 6):605–615. doi:10.1107/S2059798319007113.
   PubMedGoogle Scholar
• Lombard V, Ramulu HG, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42(D1):D490–D495. doi:10.1093/nar/gkt1178.
   PubMed Web of Science ®Google Scholar
• Svartström O, Alneberg J, Terrapon N, Lombard V, Bruijn I, Malmsten J, Dalin AM, Muller EE, Shah P, Wilmes P, et al. Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. Isme J. 2017;11(11):2538–2551. doi:10.1038/ismej.2017.108.
   PubMed Web of Science ®Google Scholar
• Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, Liachko I, Snelling TG, Dewhurst RG, Walker AW. Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nat Commun. 2018;9(1):870. doi:10.1038/s41467-018-03317-6.
   PubMedGoogle Scholar
• Watanabe H, Tokuda G. Cellulolytic systems in insects. Annu Rev Entomol. 2010;55:609–632. doi:10.1146/annurev-ento-112408-085319.
   PubMed Web of Science ®Google Scholar
• Kern M, McGeehan JE, Streeter SD, Martin RNA, Besser K, Elias L, Eborall W, Malyon GP, Payne CM, Himmel ME, et al. Structural characterization of a unique marine animal family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance. Proc Natl Acad Sci U S A. 2013;110(25):10189–10194. doi:10.1073/pnas.1301502110.
   PubMed Web of Science ®Google Scholar
• Fischer F, Romero R, Hellhund A, Linne U, Bertrams W, Pinkenburg O, Eldin HS, Binder K, Jacob R, Walker A, et al. Dietary cellulose induces anti-inflammatory immunity and transcriptional programs via maturation of the intestinal microbiota. Gut Microbes. 2022;12(1):1–17. doi:10.1080/19490976.2020.1829962.
   Web of Science ®Google Scholar
• Meulen RV, Makras L, Verbrugghe K, Adriany T, Vuyst LD. In vitro kinetic analysis of oligofructose consumption by Bacteroides and Bifidobacterium spp. indicates different degradation mechanisms. Appl Environ Microbiol. 2006;72(2):1006–1012. doi:10.1128/AEM.72.2.1006-1012.2006.
   PubMed Web of Science ®Google Scholar
• Wilson KH, Blitchington RB, Greene RC. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol. 1990;28(9):1942–1946. doi:10.1128/jcm.28.9.1942-1946.1990.
   PubMed Web of Science ®Google Scholar
• Rakoff-Nahoum S, Coyne MJ, Comstock LE. An ecological network of polysaccharide utilization among human intestinal symbionts. Curr Biol. 2014;24(1):40–49. doi:10.1016/j.cub.2013.10.077.
   PubMed Web of Science ®Google Scholar
• Leth ML, Ejby M, Workman C, Ewald DA, Pedersen SS, Sternberg C, Bahl ML, Licht TR, Aachmann FL, Westereng B, et al. Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut. Nature Microbiol. 2018;3(5):570–580. doi:10.1038/s41564-018-0132-8.
   PubMed Web of Science ®Google Scholar
• Love ML, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi:10.1186/s13059-014-0550-8.
   PubMed Web of Science ®Google Scholar
• Luis AS, Briggs J, Zhang XY, Farnell B, Ndeh D, Labourel A, Baslé A, Cartmell A, Terrapon N, Stott K, et al. Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Nature Microbiol. 2018;3(2):210–219. doi:10.1038/s41564-017-0079-1.
   PubMed Web of Science ®Google Scholar
• Laverde D, Wobser D, Romero-Saavedra F, Hogendorf W, Marel G, Berthold M, Kropec A, Codee J, Huebner J, Miyaji EN. Synthetic teichoic acid conjugate vaccine against nosocomial Gram-positive bacteria. PLoS One. 2014;9(10):e110953. doi:10.1371/journal.pone.01109-53.
   PubMed Web of Science ®Google Scholar
• Rogowski A, Briggs JA, Mortimer JC, Tryfona T, Terrapon N, Lowe EC, Baslé A, Morland C, Day AM, Zheng H, et al. Glycan complexity dictates microbial resource allocation in the large intestine. Nat Commun. 2015;6:7481. doi:10.1038/ncomms8481.
   PubMed Web of Science ®Google Scholar
• Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596(7873):583–589. doi:10.1038/s41586-021-03819-2.
   PubMed Web of Science ®Google Scholar
• Steinegger M, Mirdita M, Söding J. Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold. Nat Methods. 2019;16(7):603–606. doi:10.1038/s41592-019-0437-4.
   PubMed Web of Science ®Google Scholar
• Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics. 2007;23(10):1282–1288. doi:10.1093/bioinformatics/btm098.
   PubMed Web of Science ®Google Scholar
• Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, Crusoe MR, Kale V, Potter SC, Richardson LJ. Mgnify: the microbiome analysis resource in 2020. Nucleic Acids Res. 2020;48(D1):D570–D578. doi:10.1093/nar/gkz1035.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Liu H, Yang S, Luo R, Chen HF. Well-balanced force field ff 03 CMAP for folded and disordered proteins. J Chem Theory Comput. 2019;15(12):6769–6780. doi:10.1021/acs.jctc.9b00623.
   PubMed Web of Science ®Google Scholar
• Li Z, Yan X, Wei Q, Gao X, Wang S, Cui S. PointSite: a point cloud segmentation tool for identification of protein ligand binding atoms. J Chem Inf Model. 2022;62(11):2835–2845. doi:10.1021/acs.jcim.1c01512.
   PubMed Web of Science ®Google Scholar
• Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455–461. doi:10.1002/jcc.21334.
   PubMed Web of Science ®Google Scholar
• Zheng L, Meng J, Jiang K, Lan H, Wang Z, Lin M, Li W, Guo H, Wei Y, Mu Y. Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term. Brief Bioinform. 2022;23(3). bbac051. doi:10.1093/bib/bbac051.
   Web of Science ®Google Scholar