{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T22:10:31Z","timestamp":1792447831732,"version":"4.5.0"},"reference-count":62,"publisher":"National Academy of Sciences","issue":"47","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2014,11,25]]},"abstract":"<jats:title>Significance<\/jats:title>\n                  <jats:p>In animals, gut microbes are essential for digestion. Here, we show that bacteria outside the gut can also play a critical role in digestion. In shipworms, wood-eating marine bivalves, endosymbiotic bacteria are found within specialized cells in the gills. We show that these endosymbionts produce wood-degrading enzymes that are selectively transported to the shipworm\u2019s bacteria-free gut, where wood digestion occurs. Because only selected wood-degrading enzymes are transported, the shipworm system naturally identifies those endosymbiont enzymes most relevant to lignocellulose deconstruction without interference from other microbial proteins. Thus, this work expands the known biological repertoire of bacterial endosymbionts to include digestion of food and identifies previously undescribed enzymes and enzyme combinations of potential value to biomass-based industries, such as cellulosic biofuel production.<\/jats:p>","DOI":"10.1073\/pnas.1413110111","type":"journal-article","created":{"date-parts":[[2014,11,10]],"date-time":"2014-11-10T23:42:34Z","timestamp":1415662954000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":92,"title":["Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk"],"prefix":"10.1073","volume":"111","author":[{"given":"Roberta M.","family":"O\u2019Connor","sequence":"first","affiliation":[{"name":"Tufts Medical Center, Boston, MA 02111;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer M.","family":"Fung","sequence":"additional","affiliation":[{"name":"Ocean Genome Legacy Center of New England Biolabs, Marine Sciences Center, Northeastern University, Nahant, MA 01908;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koty H.","family":"Sharp","sequence":"additional","affiliation":[{"name":"James Center for Molecular and Life Sciences, Eckerd College, St. Petersburg, FL 33711;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jack S.","family":"Benner","sequence":"additional","affiliation":[{"name":"New England Biolabs, Ipswich, MA 01938;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Colleen","family":"McClung","sequence":"additional","affiliation":[{"name":"New England Biolabs, Ipswich, MA 01938;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shelley","family":"Cushing","sequence":"additional","affiliation":[{"name":"New England Biolabs, Ipswich, MA 01938;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth R.","family":"Lamkin","sequence":"additional","affiliation":[{"name":"Harvard University, Boston, MA 02115;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexey I.","family":"Fomenkov","sequence":"additional","affiliation":[{"name":"New England Biolabs, Ipswich, MA 01938;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernard","family":"Henrissat","sequence":"additional","affiliation":[{"name":"Architecture et Fonction des Macromol\u00e9cules Biologiques, Centre National de la Recherche Scientifique, Unit\u00e9 Mixte de Recherches 7257, Case 932, Campus de Luminy, 13288 Marseille Cedex 09, France;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuri Y.","family":"Londer","sequence":"additional","affiliation":[{"name":"New England Biolabs, Ipswich, MA 01938;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew B.","family":"Scholz","sequence":"additional","affiliation":[{"name":"Institute for Cyber Enabled Research, Michigan State University, East Lansing, MI 48824-1226;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janos","family":"Posfai","sequence":"additional","affiliation":[{"name":"New England Biolabs, Ipswich, MA 01938;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Malfatti","sequence":"additional","affiliation":[{"name":"Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susannah G.","family":"Tringe","sequence":"additional","affiliation":[{"name":"Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanja","family":"Woyke","sequence":"additional","affiliation":[{"name":"Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rex R.","family":"Malmstrom","sequence":"additional","affiliation":[{"name":"Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devin","family":"Coleman-Derr","sequence":"additional","affiliation":[{"name":"Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marvin A.","family":"Altamia","sequence":"additional","affiliation":[{"name":"Marine Sciences Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Dedrick","sequence":"additional","affiliation":[{"name":"Boston College, Chestnut Hill, MA 02467; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan T.","family":"Kaluziak","sequence":"additional","affiliation":[{"name":"Ocean Genome Legacy Center of New England Biolabs, Marine Sciences Center, Northeastern University, Nahant, MA 01908;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margo G.","family":"Haygood","sequence":"additional","affiliation":[{"name":"Institute of Environmental Health, Oregon Health &amp; Sciences University, Portland, OR 97239-3098"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel L.","family":"Distel","sequence":"additional","affiliation":[{"name":"Ocean Genome Legacy Center of New England Biolabs, Marine Sciences Center, Northeastern University, Nahant, MA 01908;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2014,11,10]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","unstructured":"DL Distel The biology of marine wood boring bivalves and their bacterial endosymbionts. 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Nucleic Acids Res 42, D490\u2013D495 (2014).","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_4_25_2","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/nar\/29.1.22","article-title":"The COG database: New developments in phylogenetic classification of proteins from complete genomes","volume":"29","author":"Tatusov RL","year":"2001","unstructured":"RL Tatusov, , The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29, 22\u201328 (2001).","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_4_26_2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/1754-6834-5-45","article-title":"Novel enzymes for the degradation of cellulose","volume":"5","author":"Horn SJ","year":"2012","unstructured":"SJ Horn, G Vaaje-Kolstad, B Westereng, VG Eijsink, Novel enzymes for the degradation of cellulose. 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Biochim Biophys Acta 1778, 1735\u20131756 (2008).","journal-title":"Biochim Biophys Acta"},{"key":"e_1_3_4_28_2","doi-asserted-by":"crossref","first-page":"8919","DOI":"10.1073\/pnas.1407687111","article-title":"GroEL from the endosymbiont Buchnera aphidicola betrays the aphid by triggering plant defense","volume":"111","author":"Chaudhary R","year":"2014","unstructured":"R Chaudhary, HS Atamian, Z Shen, SP Briggs, I Kaloshian, GroEL from the endosymbiont Buchnera aphidicola betrays the aphid by triggering plant defense. Proc Natl Acad Sci USA 111, 8919\u20138924 (2014).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_29_2","doi-asserted-by":"crossref","first-page":"e74656","DOI":"10.1371\/journal.pone.0074656","article-title":"Proteomic investigation of aphid honeydew reveals an unexpected diversity of proteins","volume":"8","author":"Sabri A","year":"2013","unstructured":"A Sabri, , Proteomic investigation of aphid honeydew reveals an unexpected diversity of proteins. 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Bulletin of the Bureau of Fisheries 37, 191\u2013231 (1908).","journal-title":"Bulletin of the Bureau of Fisheries"},{"key":"e_1_3_4_32_2","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.ymben.2010.11.004","article-title":"Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli","volume":"13","author":"Chen X","year":"2011","unstructured":"X Chen, AP Alonso, DK Allen, JL Reed, Y Shachar-Hill, Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli. 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Appl Environ Microbiol 73, 5261\u20135267 (2007).","journal-title":"Appl Environ Microbiol"},{"key":"e_1_3_4_43_2","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"Larkin MA","year":"2007","unstructured":"MA Larkin, , Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947\u20132948 (2007).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_44_2","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models","volume":"22","author":"Stamatakis A","year":"2006","unstructured":"A Stamatakis, RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688\u20132690 (2006).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_45_2","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/nmeth.2109","article-title":"jModelTest 2: More models, new heuristics and parallel computing","volume":"9","author":"Darriba D","year":"2012","unstructured":"D Darriba, GL Taboada, R Doallo, D Posada, jModelTest 2: More models, new heuristics and parallel computing. Nat Methods 9, 772 (2012).","journal-title":"Nat Methods"},{"key":"e_1_3_4_46_2","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1093\/bioinformatics\/17.8.754","article-title":"MRBAYES: Bayesian inference of phylogenetic trees","volume":"17","author":"Huelsenbeck JP","year":"2001","unstructured":"JP Huelsenbeck, F Ronquist, MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754\u2013755 (2001).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_47_2","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1128\/AEM.01733-10","article-title":"mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization","volume":"77","author":"Yilmaz LS","year":"2011","unstructured":"LS Yilmaz, S Parnerkar, DR Noguera, mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization. Appl Environ Microbiol 77, 1118\u20131122 (2011).","journal-title":"Appl Environ Microbiol"},{"key":"e_1_3_4_48_2","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: Algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino DR","year":"2008","unstructured":"DR Zerbino, E Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18, 821\u2013829 (2008).","journal-title":"Genome Res"},{"key":"e_1_3_4_49_2","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1517\/14622416.5.4.433","article-title":"Solexa Ltd","volume":"5","author":"Bennett S","year":"2004","unstructured":"S Bennett, Solexa Ltd. Pharmacogenomics 5, 433\u2013438 (2004).","journal-title":"Pharmacogenomics"},{"key":"e_1_3_4_50_2","doi-asserted-by":"crossref","first-page":"63","DOI":"10.4056\/sigs.632","article-title":"The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes","volume":"1","author":"Mavromatis K","year":"2009","unstructured":"K Mavromatis, , The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Stand Genomic Sci 1, 63\u201367 (2009).","journal-title":"Stand Genomic Sci"},{"key":"e_1_3_4_51_2","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1126\/science.1162986","article-title":"Real-time DNA sequencing from single polymerase molecules","volume":"323","author":"Eid J","year":"2009","unstructured":"J Eid, , Real-time DNA sequencing from single polymerase molecules. Science 323, 133\u2013138 (2009).","journal-title":"Science"},{"key":"e_1_3_4_52_2","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/S0076-6879(10)72001-2","article-title":"Real-time DNA sequencing from single polymerase molecules","volume":"472","author":"Korlach J","year":"2010","unstructured":"J Korlach, , Real-time DNA sequencing from single polymerase molecules. Methods Enzymol 472, 431\u2013455 (2010).","journal-title":"Methods Enzymol"},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","first-page":"e29","DOI":"10.1093\/nar\/gkr1146","article-title":"Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing","volume":"40","author":"Clark TA","year":"2012","unstructured":"TA Clark, , Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res 40, e29 (2012).","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_4_54_2","doi-asserted-by":"crossref","first-page":"e159","DOI":"10.1093\/nar\/gkq543","article-title":"A flexible and efficient template format for circular consensus sequencing and SNP detection","volume":"38","author":"Travers KJ","year":"2010","unstructured":"KJ Travers, CS Chin, DR Rank, JS Eid, SW Turner, A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 38, e159 (2010).","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_4_55_2","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/nmeth.2474","article-title":"Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data","volume":"10","author":"Chin CS","year":"2013","unstructured":"CS Chin, , Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10, 563\u2013569 (2013).","journal-title":"Nat Methods"},{"key":"e_1_3_4_56_2","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead B","year":"2012","unstructured":"B Langmead, SL Salzberg, Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357\u2013359 (2012).","journal-title":"Nat Methods"},{"key":"e_1_3_4_57_2","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li H","year":"2009","unstructured":"H Li, , The Sequence Alignment\/Map format and SAMtools. Bioinformatics; 1000 Genome Project Data Processing Subgroup 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_58_2","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1002\/pmic.200700764","article-title":"Physical and computational analysis of the yeast Kluyveromyces lactis secreted proteome","volume":"8","author":"Swaim CL","year":"2008","unstructured":"CL Swaim, BP Anton, SS Sharma, CH Taron, JS Benner, Physical and computational analysis of the yeast Kluyveromyces lactis secreted proteome. Proteomics 8, 2714\u20132723 (2008).","journal-title":"Proteomics"},{"key":"e_1_3_4_59_2","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1186\/1471-2148-12-186","article-title":"Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)","volume":"12","author":"Aspeborg H","year":"2012","unstructured":"H Aspeborg, PM Coutinho, Y Wang, 3rd H Brumer, B Henrissat, Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5). BMC Evol Biol 12, 186 (2012).","journal-title":"BMC Evol Biol"},{"key":"e_1_3_4_60_2","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.pep.2008.06.014","article-title":"Addressing Shewanella oneidensis \u201ccytochromome\u201d: The first step towards high-throughput expression of cytochromes c","volume":"62","author":"Londer YY","year":"2008","unstructured":"YY Londer, SE Giuliani, T Peppler, FR Collart, Addressing Shewanella oneidensis \u201ccytochromome\u201d: The first step towards high-throughput expression of cytochromes c. Protein Expr Purif 62, 128\u2013137 (2008).","journal-title":"Protein Expr Purif"},{"key":"e_1_3_4_61_2","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nmeth.1318","article-title":"Enzymatic assembly of DNA molecules up to several hundred kilobases","volume":"6","author":"Gibson DG","year":"2009","unstructured":"DG Gibson, , Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6, 343\u2013345 (2009).","journal-title":"Nat Methods"},{"key":"e_1_3_4_62_2","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/S0021-9258(18)71980-7","article-title":"A photometric adaptation of the Somogyi method for the determination of glucose","volume":"153","author":"Nelson N","year":"1944","unstructured":"N Nelson, A photometric adaptation of the Somogyi method for the determination of glucose. J Biol Chem 153, 375\u2013380 (1944).","journal-title":"J Biol Chem"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.1413110111","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T12:35:25Z","timestamp":1747139725000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.1413110111"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,10]]},"references-count":62,"journal-issue":{"issue":"47","published-print":{"date-parts":[[2014,11,25]]}},"alternative-id":["10.1073\/pnas.1413110111"],"URL":"https:\/\/doi.org\/10.1073\/pnas.1413110111","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,10]]},"assertion":[{"value":"2014-11-10","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}