Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations
Open accessAbstract
Background: Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out. Results: Here, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. We extend previous results of biogeographic stratification, identifying a new subspecies predominantly found in African individuals and showing that closely related non-human primates do not harbor E. rectale. Comparison of pairwise genetic and geographic distances between subspecies suggests that isolation by distance and co-dispersal with human populations might have contributed to shaping the contemporary population structure of E. rectale. We confirm that a relatively recently diverged E. rectale subspecies specific to Europe consistently lacks motility operons and that it is immotile in vitro, probably due to ancestral genetic loss. The same subspecies exhibits expansion of its carbohydrate metabolism gene repertoire including the acquisition of a genomic island strongly enriched in glycosyltransferase genes involved in exopolysaccharide synthesis. Conclusions: Our study provides new insights into the population structure and ecology of E. rectale and shows that shotgun metagenomes can enable population genomics studies of microbiota members at a resolution and scale previously attainable only by extensive isolate sequencing.
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Geographical origin is a major driver of intraspecific diversity, shaping host traits from diet to antibiotic exposure.
“Indeed, geographical origin is a major driver of intraspecific diversity, shaping host traits from diet to antibiotic exposure [94-97] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [95]
The Results and discussion section reports a correlation between geographic and genetic distances among E. rectale subspecies, supporting a geographic component to intraspecific diversity. The Discussion says isolation by distance is likely not the only influence and reports no significant association between subspecies and diet; it does not establish that geography shapes host diet or antibiotic exposure. (LLM, conf=0.85)
Experimental — accuracy not yet measuredA large fraction of the gut microbiome's individual uniqueness is encoded at the level of single strains.
“and a large fraction of this uniqueness is encoded at the level of single strains36–38.”
From Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma (2022) · cites this paper as [38]
The Introduction says human gut microbiota composition varies across individuals, and the Results and discussion document genetic differences among E. rectale strains. But the paper does not establish that a large fraction of individuals’ gut-microbiome uniqueness is encoded at the single-strain level across the microbiome; its strain analysis focuses on one species. The indexed passages provide section labels but no page numbers. (LLM, conf=0.82)
Experimental — accuracy not yet measured
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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works
KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077 · see citing works
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291 · see citing works
KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232 · see citing works
Prokka: rapid prokaryotic genome annotation
Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,512 · see citing works
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496 · see citing works
Prodigal: prokaryotic gene recognition and translation initiation site identification
Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,426 · see citing works
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Capella-Gutiérrez, S., Silla-Martinez, J., & Gabaldón, T. (2009) · Bioinform. · doi:10.1093/bioinformatics/btp348 · Cited by 12,052 · see citing works
Posterior summarization in Bayesian phylogenetics using tracer 1.7
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy032 · Cited by 11,159 · see citing works
Finding groups in data: an introduction to cluster analysis
(1991) · Choice Reviews Online · doi:10.5860/choice.28-4558 · Cited by 10,537 · see citing works
Li, D., Liu, C.-M., Luo, R., Sadakane, K., & Lam, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv033 · Cited by 9,781 · see citing works
UniProt: the Universal Protein knowledgebase
Apweiler, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh131 · Cited by 7,535 · see citing works
Finding Groups in Data: An Introduction to Cluster Analysis
Kaufman, L., & Rousseeuw, P. J. (1990) · Wiley Series in Probability and Statistics · doi:10.1002/9780470316801 · Cited by 7,344 · cited 6× · see citing works
“Clustering of core gene genetic distances using partitioning around medoids (PAM) [21] supported the existence of four subspecies (prediction strength consistently over 0.8 for k = 4, Additional file 1: Fig.”
MethodInfluentialBEAST 2: a software platform for Bayesian evolutionary analysis
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003537 · Cited by 6,527 · see citing works
The carbohydrate-active enzymes database (CAZy) in 2013
Lombard, V., Ramulu, H. G., Drula, É., Coutinho, P. M., & Henrissat, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1178 · Cited by 6,355 · see citing works
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V., & Henrissat, B. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn663 · Cited by 5,947 · see citing works
Roary: rapid large-scale prokaryote pan genome analysis
Page, A. J., Cummins, C. A., Hunt, M., Wong, V. K., Reuter, S., Holden, M. T. G., Fookes, M., Falush, D., Keane, J. A., & Parkhill, J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv421 · Cited by 5,736 · see citing works
Self-citationWright, S. (1943) · Genetics · doi:10.1093/genetics/28.2.114 · Cited by 5,620 · see citing works
Eddy, S. R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.755 · Cited by 5,515 · see citing works
metaSPAdes: a new versatile metagenomic assembler
Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496 · see citing works
UniProt: the universal protein knowledgebase
The UniProt Consortium (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1099 · Cited by 4,436 · see citing works
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848 · see citing works
Kang, D., Li, F., Kirton, E., Thomas, A., Egan, R. S., An, H., & Wang, Z. (2019) · PeerJ · doi:10.7717/peerj.7359 · Cited by 3,784 · see citing works
Mash: fast genome and metagenome distance estimation using MinHash
(2016) · Genome biology · doi:10.1186/s13059-016-0997-x · Cited by 3,373 · see citing works
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.004 · Cited by 3,315 · see citing works
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., von Mering, C., & Bork, P. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx148 · Cited by 2,709 · see citing works
The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624 · see citing works
Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health
Ríos-Covián, D., Ruas‐Madiedo, P., Margollés, A., Gueimonde, M., Reyes‐Gavilán, C. G. D. L., & Salazar, N. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00185 · Cited by 2,215 · see citing works
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185 · see citing works
Self-citationGenomic insights that advance the species definition for prokaryotes
Konstantinidis, K. T., & Tiedje, J. M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409727102 · Cited by 2,124 · see citing works
Anvi’o: an advanced analysis and visualization platform for ‘omics data
Eren, A. M., Esen, Ö. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., & Delmont, T. O. (2015) · PeerJ · doi:10.7717/peerj.1319 · Cited by 1,823 · see citing works
dbCAN: a web resource for automated carbohydrate-active enzyme annotation
Yin, Y., Mao, X., Yang, J., Chen, X., Mao, F., & Xu, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks479 · Cited by 1,800 · see citing works
Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591 · see citing works
Self-citationCentrifuge: rapid and sensitive classification of metagenomic sequences
Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016) · Genome Research · doi:10.1101/gr.210641.116 · Cited by 1,438 · see citing works
Potential of fecal microbiota for early-stage detection of colorectal cancer
Zeller, G., Tap, J., Voigt, A. Y., Sunagawa, S., Kultima, J. R., Costea, P. I., Amiot, A., Böhm, J., Brunetti, F., Habermann, N., et al. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145645 · Cited by 1,375 · see citing works
Self-citationA unified catalog of 204,938 reference genomes from the human gut microbiome
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367 · see citing works
Self-citationA new genomic blueprint of the human gut microbiota
Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314 · see citing works
Ferretti, P., Pasolli, E., Tett, A., Asnicar, F., Gorfer, V., Fedi, S., Armanini, F., Truong, D. T., Manara, S., Zolfo, M., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.06.005 · Cited by 1,292 · see citing works
Self-citationTraces of Human Migrations in Helicobacter pylori Populations
Falush, D., Wirth, T., Linz, B., Pritchard, J. K., Stephens, M., Kidd, M. S., Blaser, M. J., Graham, D. Y., Vacher, S., Perez-Perez, G. I., et al. (2003) · Science · doi:10.1126/science.1080857 · Cited by 1,019 · see citing works
Self-citationPhylogenetic Relationships of Butyrate-Producing Bacteria from the Human Gut
Barcenilla, A., Pryde, S. E., Martin, J. C., Duncan, S. H., Stewart, C. S., Henderson, C., & Flint, H. J. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.4.1654-1661.2000 · Cited by 996 · see citing works
Self-citationAn African origin for the intimate association between humans and Helicobacter pylori
Linz, B., Balloux, F., Moodley, Y., Manica, A., Liu, H., Roumagnac, P., Falush, D., Stamer, C., Prugnolle, F., der Merwe, V., et al. (2007) · Nature · doi:10.1038/nature05562 · Cited by 977 · see citing works
Self-citationMicrobial strain-level population structure and genetic diversity from metagenomes
Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C., & Segata, N. (2017) · Genome Research · doi:10.1101/gr.216242.116 · Cited by 839 · see citing works
Self-citationPhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
Segata, N., Börnigen, D., Morgan, X. C., & Huttenhower, C. (2013) · Nature Communications · doi:10.1038/ncomms3304 · Cited by 829 · see citing works
Self-citationNew insights from uncultivated genomes of the global human gut microbiome
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature · doi:10.1038/s41586-019-1058-x · Cited by 737 · see citing works
Cluster Validation by Prediction Strength
Tibshirani, R. J., & Walther, G. (2005) · Journal of Computational and Graphical Statistics · doi:10.1198/106186005x59243 · Cited by 662 · see citing works
Marcy, Y., Ouverney, C., Bik, E. M., Lösekann, T., Ivanova, N., Martín, H. G., Szeto, E., Platt, D., Hugenholtz, P., Relman, D. A., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704662104 · Cited by 632 · see citing works
Social networks predict gut microbiome composition in wild baboons
Tung, J., Barreiro, L. B., Burns, M. B., Grenier, J., Lynch, J., Grieneisen, L., Jeanne Altmann, A., Alberts, S. C., Blekhman, R., & Archie, E. A. (2015) · eLife · doi:10.7554/elife.05224 · Cited by 524 · see citing works
Accessible, curated metagenomic data through ExperimentHub
Pasolli, E., Schiffer, L., Manghi, P., Renson, A., Obenchain, V., Truong, D. T., Beghini, F., Malik, F., Ramos, M., Dowd, J. B., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4468 · Cited by 514 · see citing works
Self-citationTett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476 · see citing works
Self-citationMantel test in population genetics
Diniz‐Filho, J. A. F., Soares, T. N., Lima, J. S., et al. (2013) · Genetics and Molecular Biology · doi:10.1590/s1415-47572013000400002 · Cited by 475 · see citing works
Asnicar, F., Manara, S., Zolfo, M., Truong, D. T., Scholz, M., Armanini, F., Ferretti, P., Gorfer, V., Pedrotti, A., Tett, A., et al. (2017) · mSystems · doi:10.1128/msystems.00164-16 · Cited by 445 · see citing works
Self-citationLiu, M. Y., Gui, G., Wei, B. L., Preston, J. F., Oakford, L. X., Yüksel, Ü., Giedroc, D. P., & Romeo, T. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.28.17502 · Cited by 439 · see citing works
Lopez-Siles, M., Khan, T. M., Duncan, S. H., Harmsen, H. J. M., Garcia-Gil, L. J., & Flint, H. J. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.06858-11 · Cited by 433 · see citing works
Self-citationBiofilm Formation and Dispersal under the Influence of the Global Regulator CsrA of Escherichia coli
Jackson, D. W., Suzuki, K., Oakford, L. X., Simecka, J. W., Hart, M. E., & Romeo, T. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.1.290-301.2002 · Cited by 425 · see citing works
Strain-level microbial epidemiology and population genomics from shotgun metagenomics
Scholz, M., Ward, D. V., Pasolli, E., Tolio, T., Zolfo, M., Asnicar, F., Truong, D. T., Tett, A., Morrow, A. L., & Segata, N. (2016) · Nature Methods · doi:10.1038/nmeth.3802 · Cited by 374 · see citing works
Self-citationEvolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes
Amato, K. R., Sanders, J. G., Song, S. J., Nute, M., Metcalf, J. L., Thompson, L., Morton, J. T., Amir, A., McKenzie, V. J., Humphrey, G., et al. (2018) · The ISME Journal · doi:10.1038/s41396-018-0175-0 · Cited by 368 · see citing works
Age of the Association between Helicobacter pylori and Man
Moodley, Y., Linz, B., Bond, R., Nieuwoudt, M. J., Soodyall, H., Schlebusch, C. M., Bernhöft, S., Hale, J., Suerbaum, S., Mugisha, L., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002693 · Cited by 342 · see citing works
Ultra-deep, long-read nanopore sequencing of mock microbial community standards
Nicholls, S. M., Quick, J., Tang, S., & Loman, N. J. (2019) · GigaScience · doi:10.1093/gigascience/giz043 · Cited by 305 · see citing works
Gut microbiomes of wild great apes fluctuate seasonally in response to diet
Hicks, A. L., Lee, K. J., Couto-Rodriguez, M., Patel, J., Sinha, R., Guo, C., Olson, S. H., Seimon, A., Seimon, T. A., Ondzie, A. U., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04204-w · Cited by 271 · see citing works
Bruzzese, E., Callegari, M. L., Raia, V., Viscovo, S., Scotto, R., Ferrari, S., Morelli, L., Buccigrossi, V., Vecchio, A. L., Ruberto, E., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087796 · Cited by 217 · see citing works
Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes
The CAZypedia Consortium (2017) · Glycobiology · doi:10.1093/glycob/cwx089 · Cited by 215 · see citing works
Miyazaki, K., Martin, J. C., Marinšek-Logar, R., & Flint, H. J. (1997) · Anaerobe · doi:10.1006/anae.1997.0125 · Cited by 185 · see citing works
Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity
Segata, N. (2015) · Current Biology · doi:10.1016/j.cub.2015.05.040 · Cited by 183 · see citing works
Self-citationHorizontal versus Familial Transmission of Helicobacter pylori
Schwarz, S., Morelli, G., Kušećek, B., Manica, A., Balloux, F., Owen, R. J., Graham, D. Y., der Merwe, V., Achtman, M., & Suerbaum, S. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.1000180 · Cited by 174 · see citing works
Duncan, S. H., Russell, W. R., Quartieri, A., Rossi, M., Parkhill, J., Walker, A. W., & Flint, H. J. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13158 · Cited by 168 · see citing works
Self-citationRamakrishna, B., Jayakanthan, P., Pugazhendhi, S., & Kabeerdoss, J. (2015) · The Indian Journal of Medical Research · doi:10.4103/0971-5916.162091 · Cited by 144 · see citing works
Zhang, L., Gray, L., Novick, R. P., & Ji, G. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m205367200 · Cited by 142 · see citing works
Subspecies in the global human gut microbiome
Costea, P. I., Coelho, L. P., Sunagawa, S., Munch, R., Huerta‐Cepas, J., Forslund, S. K., Hildebrand, F., Kushugulova, A. R., Zeller, G., & Bork, P. (2017) · Molecular Systems Biology · doi:10.15252/msb.20177589 · Cited by 141 · see citing works
Self-citationSeasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest
Orkin, J. D., Campos, F. A., Myers, M. S., Cheves Hernandez, S. E., Guadamuz, A., & Melin, A. D. (2019) · The ISME Journal · doi:10.1038/s41396-018-0256-0 · Cited by 140 · see citing works
Fite, A., Macfarlane, S., Furrie, E., Bahrami, B., Cummings, J. H., Steinke, D. T., & Macfarlane, G. T. (2012) · Journal of Clinical Microbiology · doi:10.1128/jcm.02574-12 · Cited by 110 · see citing works
High-quality genome sequences of uncultured microbes by assembly of read clouds
Bishara, A., Moss, E. L., Kolmogorov, M., Parada, A. E., Weng, Z., Sidow, A., Dekas, A., Batzoglou, S., & Bhatt, A. S. (2018) · Nature Biotechnology · doi:10.1038/nbt.4266 · Cited by 110 · see citing works
Manara, S., Asnicar, F., Beghini, F., Bazzani, D., Cumbo, F., Zolfo, M., Nigro, E., Karcher, N., Manghi, P., Metzger, M., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1923-9 · Cited by 91 · see citing works
Self-citationGABAAR Modulator for Postpartum Depression
Módy, I. (2019) · Cell · doi:10.1016/j.cell.2018.12.016 · Cited by 65 · see citing works
Proposal of a neotype strain (A1-86) for Eubacterium rectale. Request for an Opinion
Duncan, S. H., & Flint, H. J. (2008) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.2008/004580-0 · Cited by 64 · see citing works
Self-citationSmall regulatory RNAs inPseudomonas aeruginosa
Sonnleitner, E., Romeo, A., & Bläsi, U. (2012) · RNA Biology · doi:10.4161/rna.19231 · Cited by 64 · see citing works
Neville, B. A., Sheridan, P. O., Harris, H. M. B., Coughlan, S., Flint, H. J., Duncan, S. H., Jeffery, I. B., Claesson, M. J., Ross, R. P., Scott, K. P., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068919 · Cited by 62 · see citing works
Self-citationBowers, R. M., Kyrpides, N. C., Stepanauskas, R., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt0218-196a · Cited by 60 · see citing works
A Population Genetics Pedigree Perspective on the Transmission of Helicobacter pylori
Delport, W., Cunningham, M., Olivier, B. J., Preisig, O., & der Merwe, V. (2006) · Genetics · doi:10.1534/genetics.106.057703 · Cited by 43 · see citing works
Kang, D. D., Li, F., Kirton, E., et al. (2019) · doi:10.7287/peerj.preprints.27522 · Cited by 35 · see citing works
Supplementary Data for Eubacterium rectale study
Karcher, N. (2020) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.3763190 · Cited by 1 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 4
- [19]Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, et al. bioRxiv. 2019:600593 Available from: https://www.biorxiv.org/content/10.1101/600593v1. [cited 2019 Jun 5]. · DOI
- [51]Manara S, Asnicar F, Beghini F et al. Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species. Genome Biol. 2019;20:299. PMC6935492 31883524
- [81]Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, et al: Eubacterium rectale Strain L2–21 Genome Assembly. NCBI RefSeq. Accession GCF_008122485.1. https://www.ncbi.nlm.nih.gov/assembly/GCF_008122485.1. August 2019.
- [82]Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, et al: Eubacterium rectale Strain T3Wbe13 Genome Assembly. NCBI RefSeq. Accession GCF_008123415.1. https://www.ncbi.nlm.nih.gov/assembly/GCF_008123415.1. Accessed August 2019.
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Self-citationA new genomic blueprint of the human gut microbiota
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Prevotella Diversity, Niches and Interactions with the Human Host
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Lee, K. A., Thomas, A. M., Bolte, L. A., Björk, J. R., de Ruijter, L. K., Armanini, F., Asnicar, F., Blanco-Miguez, A., Board, R., Calbet-Llopart, N., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01695-5 · Cited by 464 · see citing works
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Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis
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Selleri, E., Longhi, G., Tarracchini, C., Carolis, E. D., Petraro, S., Mancabelli, L., Milani, C., Turroni, F., Ventura, M., & Lugli, G. A. (2026) · Microbiome Research Reports · doi:10.20517/mrr.2026.19
- Authors
- Karcher, N., Pasolli, E., Asnicar, F., Huang, K. D., Tett, A., Manara, S., Armanini, F., Bain, D., Duncan, S. H., Louis, P., Zolfo, M., Manghi, P., Valles-Colomer, M., Raffaetà, R., Rota-Stabelli, O., Collado, M. C., Zeller, G., Falush, D., Maixner, F., Walker, A. W., Huttenhower, C., & Segata, N.
- Affiliations
- University of Trento (IT)
- University of Naples Federico II (IT)
- Fondazione Edmund Mach (IT)
- University of Aberdeen (GB)
- Free University of Bozen-Bolzano (IT)
- European Molecular Biology Laboratory (DE)
- University of Bath (GB)
- Eurac Research (IT)
- Broad Institute (US)
- Corresponding author
- Segata, Nicola
- ORCID
- Venue
- Genome Biology
- Published
- 2020-06-08
- Volume
- 21
- Issue
- 1
- Pages
- 138-138
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC7278147
- OpenAlex
- W3033825041
- Cited by
- 116
- References
- 83
- Citations by year
- 2026: 18 · 2025: 17 · 2024: 21 · 2023: 15 · 2022: 22 · 2021: 14 · 2020: 7 · 2019: 1
- FWCI
- 4.79
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Aberdeen University Research Archive (Aberdeen University) (submittedVersion)
- Institutional Research Information System (Università degli Studi di Trento) (submittedVersion, cc-by)
- CINECA IRIS Institutional Research Information System (Fondazione Edmund Mach) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- ARCA (Università Ca' Foscari Venezia) (submittedVersion, other-oa)
- Open Research (University of Surrey) (submittedVersion, other-oa)
- Funders
- H2020 European Research Council (716575)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- Eubacterium rectale, gut microbiota, population structure, phylogeography, subspecies, metagenome-assembled genomes, isolation by distance, carbohydrate metabolism, genomic islands, glycosyltransferases, exopolysaccharide biosynthesis, human gut bacteria, non-human primates
- MeSH terms
- Gastrointestinal Microbiome, Adolescent, Adult, Aged, Child, Child, Preschool, Eubacterium, Humans, Infant, Middle Aged, Genome, Bacterial, Glycosyltransferases, Carbohydrate Metabolism, Metagenome, Young Adult, Phylogeography
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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