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The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes
Open accessAbstract
BACKGROUND: The human gastrointestinal tract contains a complex community of microbes, fulfilling important health-promoting functions. However, this vast complexity of species hampers the assignment of responsible organisms to these functions. Recently, Akkermansia muciniphila, a new species from the deeply branched phylum Verrucomicrobia, was isolated from the human intestinal tract based on its capacity to efficiently use mucus as a carbon and nitrogen source. This anaerobic resident is associated with the protective mucus lining of the intestines. METHODOLOGY/PRINCIPAL FINDINGS: In order to uncover the functional potential of A. muciniphila, its genome was sequenced and annotated. It was found to contain numerous candidate mucinase-encoding genes, but lacking genes encoding canonical mucus-binding domains. Numerous phage-associated sequences found throughout the genome indicate that viruses have played an important part in the evolution of this species. Furthermore, we mined 37 GI tract metagenomes for the presence, and genetic diversity of Akkermansia sequences. Out of 37, eleven contained 16S ribosomal RNA gene sequences that are >95% identical to that of A. muciniphila. In addition, these libraries were found to contain large amounts of Akkermansia DNA based on average nucleotide identity scores, which indicated in one subject co-colonization by different Akkermansia phylotypes. An additional 12 libraries also contained Akkermansia sequences, making a total of ∼16 Mbp of new Akkermansia pangenomic DNA. The relative abundance of Akkermansia DNA varied between <0.01% to nearly 4% of the assembled metagenomic reads. Finally, by testing a large collection of full length 16S sequences, we find at least eight different representative species in the genus Akkermansia. CONCLUSIONS/SIGNIFICANCE: These large repositories allow us to further mine for genetic heterogeneity and species diversity in the genus Akkermansia, providing novel insight towards the functionality of this abundant inhabitant of the human intestinal tract.
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Citations
Cites
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
The gut microbiota as an environmental factor that regulates fat storage
Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407076101 · Cited by 6,245
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
Host-Bacterial Mutualism in the Human Intestine
Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277
Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium
Derrien, M., Vaughan, E. E., Plugge, C. M., & de Vos, W. M. (2004) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijs.0.02873-0 · Cited by 2,094
Self-citationPng, C. W., Lindén, S. K., Gilshenan, K. S., Zoetendal, E. G., McSweeney, C. S., Sly, L. I., McGuckin, M. A., & Florin, T. H. J. (2010) · American Journal of Gastroenterology · doi:10.1038/ajg.2010.281 · Cited by 1,364 · cited 1×
“Future studies, including proteomic analyses and functional screening of genomic libraries, can be expected to shed light on the involved enzymes, since recent analysis have confirmed the mucolytic activity of Akkermansia [34].”
BackgroundSelf-citationTransfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota
Hehemann, J.-H., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010) · Nature · doi:10.1038/nature08937 · Cited by 1,117
Towards the human intestinal microbiota phylogenetic core
Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J., Ugarte, E., Muñoz‐Tamayo, R., Paslier, D. L. E., Nalin, R., et al. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01982.x · Cited by 927 · cited 1×
“Subsequent analyses allow the quantification of the differences in colonization diversity between individuals, as well as their overlapping core microbiota [6,7].”
BackgroundComparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V. K., Srivastava, T. P., et al. (2007) · DNA Research · doi:10.1093/dnares/dsm018 · Cited by 869
Collado, M. C., Derrien, M., Isolauri, E., de Vos, W. M., & Salminen, S. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01477-07 · Cited by 706
Self-citation
Cited by
Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
Everard, A., Belzer, C., Geurts, L., Ouwerkerk, J. P., Druart, C., Bindels, L. B., Guiot, Y., Derrien, M., Muccioli, G. G., Delzenne, N. M., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219451110 · Cited by 4,511
Self-citationInfluence of diet on the gut microbiome and implications for human health
Singh, R. K., Chang, H.-W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., Abrouk, M., Farahnik, B., Nakamura, M., Zhu, T. H., et al. (2017) · Journal of Translational Medicine · doi:10.1186/s12967-017-1175-y · Cited by 2,599
Microbial degradation of complex carbohydrates in the gut
Flint, H. J., Scott, K. P., Duncan, S. H., Louis, P., & Forano, E. (2012) · Gut Microbes · doi:10.4161/gmic.19897 · Cited by 2,331
Dao, M. C., Everard, A., Aron-Wisnewsky, J., Sokolovska, N., Prifti, E., Verger, E. O., Kayser, B. D., Levenez, F., Chilloux, J., Hoyles, L., et al. (2016) · Gut · doi:10.1136/gutjnl-2014-308778 · Cited by 1,931
Akkermansia muciniphila: paradigm for next-generation beneficial microorganisms
Cani, P. D., Depommier, C., Derrien, M., Everard, A., & de Vos, W. M. (2022) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-022-00631-9 · Cited by 1,192
Self-citationKelly, J. R., Kennedy, P. J., Cryan, J. F., Dinan, T. G., Clarke, G., & Hyland, N. P. (2015) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2015.00392 · Cited by 1,110
Akkermansia muciniphila and its role in regulating host functions
Derrien, M., Belzer, C., & de Vos, W. M. (2017) · Microbial Pathogenesis · doi:10.1016/j.micpath.2016.02.005 · Cited by 1,044
Self-citationAkkermansia muciniphila is a promising probiotic
Zhang, T., Li, Q., Cheng, L., Buch, H., & Zhang, F. (2019) · Microbial Biotechnology · doi:10.1111/1751-7915.13410 · Cited by 708
Bedarf, J. R., Hildebrand, F., Coelho, L. P., Sunagawa, S., Bahram, M., Goeser, F., Bork, P., & Wüllner, U. (2017) · Genome Medicine · doi:10.1186/s13073-017-0428-y · Cited by 642
Shono, Y., Docampo, M. D., Peled, J. U., Perobelli, S. M., Velardi, E., Tsai, J. J., Slingerland, A. E., Smith, O. M., Young, L. F., Gupta, J., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aaf2311 · Cited by 592
Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis
Ansaldo, E., Slayden, L. C., Ching, K. L., Koch, M. A., Wolf, N. K., Plichta, D. R., Brown, E. M., Graham, D. B., Xavier, R. J., Moon, J. J., et al. (2019) · Science · doi:10.1126/science.aaw7479 · Cited by 566
The gut microbiota influences anticancer immunosurveillance and general health
Routy, B., Gopalakrishnan, V., Daillère, R., Zitvogel, L., Wargo, J. A., & Kroemer, G. (2018) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-018-0006-2 · Cited by 523
Human genetic variation and the gut microbiome in disease
Hall, A. B., Tolonen, A. C., & Xavier, R. J. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.63 · Cited by 517
Hänninen, A., Toivonen, R., Pöysti, S., Belzer, C., Plovier, H., Ouwerkerk, J. P., Emani, R., Cani, P. D., & De Vos, W. M. (2018) · Gut · doi:10.1136/gutjnl-2017-314508 · Cited by 359
Self-citationTurroni, F., Ventura, M., Buttó, L. F., Duranti, S., O’Toole, P. W., Motherway, M. O., & van Sinderen, D. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1318-0 · Cited by 336
Ottman, N., Davids, M., Suarez-Diez, M., Boeren, S., Schaap, P. J., Martins dos Santos, V. A. P., Smidt, H., Belzer, C., & de Vos, W. M. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.01014-17 · Cited by 269
Self-citationBrodmann, T., Endo, A., Gueimonde, M., Vinderola, G., Kneifel, W., de Vos, W. M., Salminen, S., & Gómez-Gallego, C. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01725 · Cited by 191
Tailford, L. E., Owen, C. D., Walshaw, J., Crost, E. H., Hardy-Goddard, J., Le Gall, G., de Vos, W. M., Taylor, G. L., & Juge, N. (2015) · Nature Communications · doi:10.1038/ncomms8624 · Cited by 183
Self-citationChemical and pathogen-induced inflammation disrupt the murine intestinal microbiome
Borton, M. A., Sabag-Daigle, A., Wu, J., Solden, L. M., O’Banion, B. S., Daly, R. A., Wolfe, R. A., Gonzalez, J. F., Wysocki, V. H., Ahmer, B. M. M., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0264-8 · Cited by 149
The role of Akkermansia muciniphila in obesity, diabetes and atherosclerosis
Hasani, A., Ebrahimzadeh, S., Hemmati, F., Khabbaz, A., Hasani, A., & Gholizadeh, P. (2021) · Journal of Medical Microbiology · doi:10.1099/jmm.0.001435 · Cited by 152
Ouyang, J., Lin, J., Isnard, S., Fombuena, B., Peng, X., Marette, A., Routy, B., Messaoudene, M., Chen, Y., & Routy, J.-P. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.00645 · Cited by 124
Safety aspects of next generation probiotics
Saarela, M. H. (2019) · Current Opinion in Food Science · doi:10.1016/j.cofs.2018.09.001 · Cited by 118
Kirmiz, N., Galindo, K., Cross, K. L., Luna, E., Rhoades, N., Podar, M., & Flores, G. E. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.02117-19 · Cited by 94
Cozzolino, A., Vergalito, F., Tremonte, P., Iorizzo, M., Lombardi, S. J., Sorrentino, E., Luongo, D., Coppola, R., Di Marco, R., & Succi, M. (2020) · Microorganisms · doi:10.3390/microorganisms8020189 · Cited by 84
Luna, E., Parkar, S. G., Kirmiz, N., Hartel, S., Hearn, E., Hossine, M., Kurdian, A., Mendoza, C., Orr, K., Padilla, L., et al. (2022) · Applied and Environmental Microbiology · doi:10.1128/aem.01487-21 · Cited by 73
Lorente-Picón, M., & Laguna, A. (2021) · Biomolecules · doi:10.3390/biom11030433 · Cited by 69
Evaluating the capacity of human gut microorganisms to colonize the zebrafish larvae (Danio rerio)
Valenzuela, M.-J., Caruffo, M., Herrera, Y., Medina, D. A., Coronado, M., Feijóo, C. G., Muñoz, S., Garrido, D., Troncoso, M., Figueroa, G., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01032 · Cited by 39
Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut
González, D., Morales-Olavarria, M., Vidal-Veuthey, B., & Cárdenas, J. P. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1238580 · Cited by 30
Genomic convergence between Akkermansia muciniphila in different mammalian hosts
Geerlings, S. Y., Ouwerkerk, J. P., Koehorst, J. J., Ritari, J., Aalvink, S., Stecher, B., Schaap, P. J., Paulin, L., de Vos, W. M., & Belzer, C. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02360-6 · Cited by 28
Recent insight into oligosaccharide uptake and metabolism in probiotic bacteria
Abou Hachem, M., Andersen, J. M., Barrangou, R., Møller, M. S., Fredslund, F., Majumder, A., Ejby, M., Lahtinen, S. J., Jacobsen, S., Lo Leggio, L., et al. (2013) · Biocatalysis and Biotransformation · doi:10.3109/10242422.2013.828048 · Cited by 25
Ouwerkerk, J. P., Tytgat, H. L. P., Elzinga, J., Koehorst, J., Van den Abbeele, P., Henrissat, B., Gueimonde, M., Cani, P. D., Van de Wiele, T., Belzer, C., et al. (2022) · Microorganisms · doi:10.3390/microorganisms10081605 · Cited by 23
Comparative Genomics and Pan-Genome Driven Prediction of a Reduced Genome of Akkermansia muciniphila
Bukhari, S. A. R., Irfan, M., Ahmad, I., & Chen, L. (2022) · Microorganisms · doi:10.3390/microorganisms10071350 · Cited by 18
Lv, N., Wang, C., Zhou, H., Ma, X., Yu, X., & Ren, D. (2024) · Foods · doi:10.3390/foods13131979 · Cited by 12
Gao, W., Xiao, M., Gu, Z., Fu, X., Ren, X., Yu, Y., Liu, Z., Zhu, C., Kong, Q., & Mou, H. (2022) · Molecular Genetics and Genomics · doi:10.1007/s00438-022-01937-8 · Cited by 10
Fatima, S., Butt, H. A., Aftab, A., & Bakhtiar, S. M. (2021) · Pakistan Journal of Biochemistry and Biotechnology · doi:10.52700/pjbb.v2i2.46 · Cited by 1
Metadata
- Authors
- van Passel, M. W. J., Kant, R., Zoetendal, E. G., Plugge, C. M., Derrien, M., Malfatti, S. A., Chain, P. S. G., Woyke, T., Palva, A., de Vos, W. M., & Smidt, H.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-03-03
- Volume
- 6
- Issue
- 3
- Pages
- e16876
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2068495545
- Cited by
- 423
- References
- 11
- FWCI
- 7.17
- Type
- journal article
- Language
- en
- Open access
- gold
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