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For: Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ. Adaptive Evolution within Gut Microbiomes of Healthy People. Cell Host Microbe 2019;25:656-667.e8. [PMID: 31028005 DOI: 10.1016/j.chom.2019.03.007] [Cited by in Crossref: 118] [Cited by in F6Publishing: 90] [Article Influence: 39.3] [Reference Citation Analysis]
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8 Yang C, Mogno I, Contijoch EJ, Borgerding JN, Aggarwala V, Li Z, Siu S, Grasset EK, Helmus DS, Dubinsky MC, Mehandru S, Cerutti A, Faith JJ. Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation. Cell Host Microbe 2020; 27: 467-475. e6. [PMID: 32075742 DOI: 10.1016/j.chom.2020.01.016] [Cited by in Crossref: 38] [Cited by in F6Publishing: 38] [Article Influence: 19.0] [Reference Citation Analysis]
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13 Turner CB, Buskirk SW, Harris KB, Cooper VS. Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection. Mol Ecol 2020;29:138-48. [PMID: 31725941 DOI: 10.1111/mec.15307] [Cited by in Crossref: 5] [Cited by in F6Publishing: 2] [Article Influence: 1.7] [Reference Citation Analysis]
14 Valguarnera E, Wardenburg JB. Good Gone Bad: One Toxin Away From Disease for Bacteroides fragilis. J Mol Biol 2020;432:765-85. [PMID: 31857085 DOI: 10.1016/j.jmb.2019.12.003] [Cited by in Crossref: 18] [Cited by in F6Publishing: 13] [Article Influence: 6.0] [Reference Citation Analysis]
15 Moltzau Anderson J, Lipinski S, Sommer F, Pan WH, Boulard O, Rehman A, Falk-Paulsen M, Stengel ST, Aden K, Häsler R, Bharti R, Künzel S, Baines JF, Chamaillard M, Rosenstiel P. NOD2 Influences Trajectories of Intestinal Microbiota Recovery After Antibiotic Perturbation. Cell Mol Gastroenterol Hepatol 2020;10:365-89. [PMID: 32289499 DOI: 10.1016/j.jcmgh.2020.03.008] [Cited by in Crossref: 8] [Cited by in F6Publishing: 7] [Article Influence: 4.0] [Reference Citation Analysis]
16 Tauzin AS, Pereira MR, Van Vliet LD, Colin PY, Laville E, Esque J, Laguerre S, Henrissat B, Terrapon N, Lombard V, Leclerc M, Doré J, Hollfelder F, Potocki-Veronese G. Investigating host-microbiome interactions by droplet based microfluidics. Microbiome 2020;8:141. [PMID: 33004077 DOI: 10.1186/s40168-020-00911-z] [Cited by in Crossref: 6] [Cited by in F6Publishing: 6] [Article Influence: 3.0] [Reference Citation Analysis]
17 Paoli L, Sunagawa S. Space, time and microdiversity: towards a resolution revolution in microbiomics. Environ Microbiol Rep 2021;13:31-5. [PMID: 33063432 DOI: 10.1111/1758-2229.12897] [Reference Citation Analysis]
18 Garud NR, Pollard KS. Population Genetics in the Human Microbiome. Trends Genet 2020;36:53-67. [PMID: 31780057 DOI: 10.1016/j.tig.2019.10.010] [Cited by in Crossref: 30] [Cited by in F6Publishing: 18] [Article Influence: 10.0] [Reference Citation Analysis]
19 Whitfill T, Oh J. Recoding the metagenome: microbiome engineering in situ. Curr Opin Microbiol 2019;50:28-34. [PMID: 31622928 DOI: 10.1016/j.mib.2019.09.005] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
20 Tierney BT, Yang Z, Luber JM, Beaudin M, Wibowo MC, Baek C, Mehlenbacher E, Patel CJ, Kostic AD. The Landscape of Genetic Content in the Gut and Oral Human Microbiome. Cell Host Microbe 2019;26:283-295.e8. [PMID: 31415755 DOI: 10.1016/j.chom.2019.07.008] [Cited by in Crossref: 79] [Cited by in F6Publishing: 56] [Article Influence: 26.3] [Reference Citation Analysis]
21 Zhang J, Knight R. Genomic mutations within the host microbiome: Adaptive evolution or purifying selection. Engineering 2022. [DOI: 10.1016/j.eng.2021.11.018] [Reference Citation Analysis]
22 Ross BD, Verster AJ, Radey MC, Schmidtke DT, Pope CE, Hoffman LR, Hajjar AM, Peterson SB, Borenstein E, Mougous JD. Human gut bacteria contain acquired interbacterial defence systems. Nature 2019;575:224-8. [PMID: 31666699 DOI: 10.1038/s41586-019-1708-z] [Cited by in Crossref: 42] [Cited by in F6Publishing: 35] [Article Influence: 14.0] [Reference Citation Analysis]
23 Campbell DE, Ly LK, Ridlon JM, Hsiao A, Whitaker RJ, Degnan PH. Infection with Bacteroides Phage BV01 Alters the Host Transcriptome and Bile Acid Metabolism in a Common Human Gut Microbe. Cell Rep 2020;32:108142. [PMID: 32937127 DOI: 10.1016/j.celrep.2020.108142] [Cited by in Crossref: 5] [Cited by in F6Publishing: 3] [Article Influence: 5.0] [Reference Citation Analysis]
24 Tan J, Kerstetter JE, Turcotte MM. Eco-evolutionary interaction between microbiome presence and rapid biofilm evolution determines plant host fitness. Nat Ecol Evol 2021;5:670-6. [PMID: 33707690 DOI: 10.1038/s41559-021-01406-2] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
25 Moffa S, Mezza T, Cefalo CMA, Cinti F, Impronta F, Sorice GP, Santoro A, Di Giuseppe G, Pontecorvi A, Giaccari A. The Interplay between Immune System and Microbiota in Diabetes. Mediators Inflamm 2019;2019:9367404. [PMID: 32082078 DOI: 10.1155/2019/9367404] [Cited by in Crossref: 9] [Cited by in F6Publishing: 4] [Article Influence: 3.0] [Reference Citation Analysis]
26 [DOI: 10.1101/2020.12.14.422699] [Cited by in Crossref: 3] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
27 Liu P, Zhang H, Wang Y, Chen X, Jin L, Xu L, Xiao M. Screening and characterization of an α-L-fucosidase from Bacteroides fragilis NCTC9343 for synthesis of fucosyl-N-acetylglucosamine disaccharides. Appl Microbiol Biotechnol 2020;104:7827-40. [PMID: 32715363 DOI: 10.1007/s00253-020-10759-w] [Cited by in Crossref: 4] [Cited by in F6Publishing: 3] [Article Influence: 2.0] [Reference Citation Analysis]
28 Levade I, Khan AI, Chowdhury F, Calderwood SB, Ryan ET, Harris JB, LaRocque RC, Bhuiyan TR, Qadri F, Weil AA, Shapiro BJ. A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients. mSystems 2021;6:e0088921. [PMID: 34427503 DOI: 10.1128/mSystems.00889-21] [Cited by in Crossref: 2] [Article Influence: 2.0] [Reference Citation Analysis]
29 D'Souza AW, Potter RF, Wallace M, Shupe A, Patel S, Sun X, Gul D, Kwon JH, Andleeb S, Burnham CD, Dantas G. Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces. Nat Commun 2019;10:4569. [PMID: 31594927 DOI: 10.1038/s41467-019-12563-1] [Cited by in Crossref: 16] [Cited by in F6Publishing: 13] [Article Influence: 5.3] [Reference Citation Analysis]
30 Bobay LM, Wissel EF, Raymann K. Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome. mSphere 2020;5:e00694-20. [PMID: 32848005 DOI: 10.1128/mSphere.00694-20] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
31 Bergallo M, Galliano I, Montanari P, Zaniol E, Graziano E, Calvi C, Alliaudi C, Daprà V, Savino F. Modulation of human endogenous retroviruses -H, -W and -K transcription by microbes. Microbes Infect 2020;22:366-70. [PMID: 32035224 DOI: 10.1016/j.micinf.2020.01.006] [Cited by in Crossref: 1] [Article Influence: 0.5] [Reference Citation Analysis]
32 Groussin M, Poyet M, Sistiaga A, Kearney SM, Moniz K, Noel M, Hooker J, Gibbons SM, Segurel L, Froment A, Mohamed RS, Fezeu A, Juimo VA, Lafosse S, Tabe FE, Girard C, Iqaluk D, Nguyen LTT, Shapiro BJ, Lehtimäki J, Ruokolainen L, Kettunen PP, Vatanen T, Sigwazi S, Mabulla A, Domínguez-Rodrigo M, Nartey YA, Agyei-Nkansah A, Duah A, Awuku YA, Valles KA, Asibey SO, Afihene MY, Roberts LR, Plymoth A, Onyekwere CA, Summons RE, Xavier RJ, Alm EJ. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell 2021;184:2053-2067.e18. [PMID: 33794144 DOI: 10.1016/j.cell.2021.02.052] [Cited by in Crossref: 6] [Cited by in F6Publishing: 7] [Article Influence: 6.0] [Reference Citation Analysis]
33 Hildebrand F. Ultra-resolution Metagenomics: When Enough Is Not Enough. mSystems 2021;:e0088121. [PMID: 34463579 DOI: 10.1128/mSystems.00881-21] [Reference Citation Analysis]
34 Franck M, de Toro-martín J, Vohl M. Eco-Evolutionary Dynamics of the Human-Gut Microbiota Symbiosis in a Changing Nutritional Environment. Evol Biol. [DOI: 10.1007/s11692-022-09569-x] [Reference Citation Analysis]
35 Feng L, Raman AS, Hibberd MC, Cheng J, Griffin NW, Peng Y, Leyn SA, Rodionov DA, Osterman AL, Gordon JI. Identifying determinants of bacterial fitness in a model of human gut microbial succession. Proc Natl Acad Sci U S A 2020;117:2622-33. [PMID: 31969452 DOI: 10.1073/pnas.1918951117] [Cited by in Crossref: 13] [Cited by in F6Publishing: 10] [Article Influence: 6.5] [Reference Citation Analysis]
36 Yaffe E, Relman DA. Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation. Nat Microbiol 2020;5:343-53. [PMID: 31873203 DOI: 10.1038/s41564-019-0625-0] [Cited by in Crossref: 38] [Cited by in F6Publishing: 22] [Article Influence: 12.7] [Reference Citation Analysis]
37 Martinson JNV, Walk ST. Escherichia coli Residency in the Gut of Healthy Human Adults. EcoSal Plus 2020;9. [PMID: 32978935 DOI: 10.1128/ecosalplus.ESP-0003-2020] [Cited by in Crossref: 2] [Article Influence: 1.0] [Reference Citation Analysis]
38 Fehlner-Peach H, Magnabosco C, Raghavan V, Scher JU, Tett A, Cox LM, Gottsegen C, Watters A, Wiltshire-Gordon JD, Segata N, Bonneau R, Littman DR. Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates. Cell Host Microbe 2019;26:680-690.e5. [PMID: 31726030 DOI: 10.1016/j.chom.2019.10.013] [Cited by in Crossref: 39] [Cited by in F6Publishing: 39] [Article Influence: 19.5] [Reference Citation Analysis]
39 Scanlan PD. Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales. mSystems 2021;6:e0083221. [PMID: 34427532 DOI: 10.1128/mSystems.00832-21] [Reference Citation Analysis]
40 Ramiro RS, Durão P, Bank C, Gordo I. Low mutational load and high mutation rate variation in gut commensal bacteria. PLoS Biol 2020;18:e3000617. [PMID: 32155146 DOI: 10.1371/journal.pbio.3000617] [Cited by in Crossref: 17] [Cited by in F6Publishing: 9] [Article Influence: 8.5] [Reference Citation Analysis]
41 Soverini M, Rampelli S, Turroni S, Brigidi P, Biagi E, Candela M. Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life? BMC Genomics 2020;21:678. [PMID: 32998695 DOI: 10.1186/s12864-020-07087-8] [Reference Citation Analysis]
42 Hwang S, Jo M, Hong JE, Park CO, Lee CG, Yun M, Rhee KJ. Zerumbone Suppresses Enterotoxigenic Bacteroides fragilis Infection-Induced Colonic Inflammation through Inhibition of NF-κΒ. Int J Mol Sci 2019;20:E4560. [PMID: 31540059 DOI: 10.3390/ijms20184560] [Cited by in Crossref: 7] [Cited by in F6Publishing: 8] [Article Influence: 2.3] [Reference Citation Analysis]
43 Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med 2020;12:71. [PMID: 32791981 DOI: 10.1186/s13073-020-00765-y] [Cited by in Crossref: 16] [Cited by in F6Publishing: 12] [Article Influence: 8.0] [Reference Citation Analysis]
44 Conwill A, Kuan AC, Damerla R, Poret AJ, Baker JS, Tripp AD, Alm EJ, Lieberman TD. Anatomy promotes neutral coexistence of strains in the human skin microbiome. Cell Host Microbe 2022:S1931-3128(21)00578-3. [PMID: 34995483 DOI: 10.1016/j.chom.2021.12.007] [Reference Citation Analysis]
45 Hoces D, Arnoldini M, Diard M, Loverdo C, Slack E. Growing, evolving and sticking in a flowing environment: understanding IgA interactions with bacteria in the gut. Immunology 2020;159:52-62. [PMID: 31777063 DOI: 10.1111/imm.13156] [Cited by in Crossref: 16] [Cited by in F6Publishing: 14] [Article Influence: 5.3] [Reference Citation Analysis]
46 Rottinghaus AG, Ferreiro A, Fishbein SRS, Dantas G, Moon TS. Genetically stable CRISPR-based kill switches for engineered microbes. Nat Commun 2022;13:672. [PMID: 35115506 DOI: 10.1038/s41467-022-28163-5] [Reference Citation Analysis]
47 Brito IL. Examining horizontal gene transfer in microbial communities. Nat Rev Microbiol 2021;19:442-53. [PMID: 33846600 DOI: 10.1038/s41579-021-00534-7] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
48 Kennedy MS, Chang EB. The microbiome: Composition and locations. Prog Mol Biol Transl Sci 2020;176:1-42. [PMID: 33814111 DOI: 10.1016/bs.pmbts.2020.08.013] [Cited by in Crossref: 2] [Article Influence: 1.0] [Reference Citation Analysis]
49 Koo H, Hakim JA, Crossman DK, Kumar R, Lefkowitz EJ, Morrow CD. Individualized recovery of gut microbial strains post antibiotics. NPJ Biofilms Microbiomes 2019;5:30. [PMID: 31632686 DOI: 10.1038/s41522-019-0103-8] [Cited by in Crossref: 10] [Cited by in F6Publishing: 10] [Article Influence: 3.3] [Reference Citation Analysis]
50 Pennycook JH, Scanlan PD. Ecological and evolutionary responses to antibiotic treatment in the human gut microbiota. FEMS Microbiol Rev 2021:fuab018. [PMID: 33822937 DOI: 10.1093/femsre/fuab018] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
51 Tyagi AM, Darby TM, Hsu E, Yu M, Pal S, Dar H, Li JY, Adams J, Jones RM, Pacifici R. The gut microbiota is a transmissible determinant of skeletal maturation. Elife 2021;10:e64237. [PMID: 33432923 DOI: 10.7554/eLife.64237] [Cited by in Crossref: 3] [Article Influence: 3.0] [Reference Citation Analysis]
52 Di Rienzi SC, Britton RA. Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners. Adv Nutr 2020;11:616-29. [PMID: 31696209 DOI: 10.1093/advances/nmz118] [Cited by in Crossref: 23] [Cited by in F6Publishing: 20] [Article Influence: 23.0] [Reference Citation Analysis]
53 Roodgar M, Good BH, Garud NR, Martis S, Avula M, Zhou W, Lancaster SM, Lee H, Babveyh A, Nesamoney S, Pollard KS, Snyder MP. Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. Genome Res 2021;31:1433-46. [PMID: 34301627 DOI: 10.1101/gr.265058.120] [Reference Citation Analysis]
54 Barroso-Batista J, Pedro MF, Sales-Dias J, Pinto CJG, Thompson JA, Pereira H, Demengeot J, Gordo I, Xavier KB. Specific Eco-evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility. Curr Biol 2020;30:1049-1062.e7. [PMID: 32142697 DOI: 10.1016/j.cub.2020.01.050] [Cited by in Crossref: 22] [Cited by in F6Publishing: 15] [Article Influence: 11.0] [Reference Citation Analysis]
55 Xiao Y, Yang C, Yu L, Tian F, Wu Y, Zhao J, Zhang H, Yang R, Chen W, Hill C, Cui Y, Zhai Q. Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model. Microbiome 2021;9:180. [PMID: 34470652 DOI: 10.1186/s40168-021-01108-8] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
56 Kolodny O, Schulenburg H. Microbiome-mediated plasticity directs host evolution along several distinct time scales. Philos Trans R Soc Lond B Biol Sci 2020;375:20190589. [PMID: 32772662 DOI: 10.1098/rstb.2019.0589] [Cited by in Crossref: 7] [Cited by in F6Publishing: 5] [Article Influence: 3.5] [Reference Citation Analysis]
57 Scanlan PD. Microbial evolution and ecological opportunity in the gut environment. Proc Biol Sci 2019;286:20191964. [PMID: 31744431 DOI: 10.1098/rspb.2019.1964] [Cited by in Crossref: 7] [Cited by in F6Publishing: 6] [Article Influence: 2.3] [Reference Citation Analysis]
58 Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh J. Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin. Cell 2020;180:454-470.e18. [PMID: 32004459 DOI: 10.1016/j.cell.2020.01.006] [Cited by in Crossref: 19] [Cited by in F6Publishing: 19] [Article Influence: 9.5] [Reference Citation Analysis]
59 Martin R, Dreßler H, Hattab G, Hackl T, Fischer MG, Heider D. MOSGA 2: Comparative genomics and validation tools. Comput Struct Biotechnol J 2021;19:5504-9. [PMID: 34712396 DOI: 10.1016/j.csbj.2021.09.024] [Reference Citation Analysis]
60 Schlomann BH, Parthasarathy R. Timescales of gut microbiome dynamics. Curr Opin Microbiol 2019;50:56-63. [PMID: 31689582 DOI: 10.1016/j.mib.2019.09.011] [Cited by in Crossref: 9] [Cited by in F6Publishing: 7] [Article Influence: 3.0] [Reference Citation Analysis]
61 Schwartz DJ, Langdon AE, Dantas G. Understanding the impact of antibiotic perturbation on the human microbiome. Genome Med. 2020;12:82. [PMID: 32988391 DOI: 10.1186/s13073-020-00782-x] [Cited by in Crossref: 22] [Cited by in F6Publishing: 27] [Article Influence: 11.0] [Reference Citation Analysis]
62 Aggarwala V, Mogno I, Li Z, Yang C, Britton GJ, Chen-Liaw A, Mitcham J, Bongers G, Gevers D, Clemente JC, Colombel JF, Grinspan A, Faith J. Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes. Nat Microbiol 2021;6:1309-18. [PMID: 34580445 DOI: 10.1038/s41564-021-00966-0] [Cited by in Crossref: 3] [Article Influence: 3.0] [Reference Citation Analysis]
63 Simonet C, McNally L. Kin selection explains the evolution of cooperation in the gut microbiota. Proc Natl Acad Sci U S A 2021;118:e2016046118. [PMID: 33526674 DOI: 10.1073/pnas.2016046118] [Cited by in Crossref: 1] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
64 Quistad SD, Doulcier G, Rainey PB. Experimental manipulation of selfish genetic elements links genes to microbial community function. Philos Trans R Soc Lond B Biol Sci 2020;375:20190681. [PMID: 32200751 DOI: 10.1098/rstb.2019.0681] [Cited by in Crossref: 6] [Cited by in F6Publishing: 7] [Article Influence: 3.0] [Reference Citation Analysis]
65 Dapa T, Ramiro RS, Pedro MF, Gordo I, Xavier KB. Diet leaves a genetic signature in a keystone member of the gut microbiota. Cell Host Microbe 2022:S1931-3128(22)00038-5. [PMID: 35085504 DOI: 10.1016/j.chom.2022.01.002] [Reference Citation Analysis]
66 Ho PY, Good BH, Huang KC. Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas. Elife 2022;11:e75168. [PMID: 35404785 DOI: 10.7554/eLife.75168] [Reference Citation Analysis]
67 Xiang H, Gan J, Zeng D, Li J, Yu H, Zhao H, Yang Y, Tan S, Li G, Luo C, Xie Z, Zhao G, Li H. Specific Microbial Taxa and Functional Capacity Contribute to Chicken Abdominal Fat Deposition. Front Microbiol 2021;12:643025. [PMID: 33815329 DOI: 10.3389/fmicb.2021.643025] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
68 Culyba MJ, Van Tyne D. Bacterial evolution during human infection: Adapt and live or adapt and die. PLoS Pathog 2021;17:e1009872. [PMID: 34499699 DOI: 10.1371/journal.ppat.1009872] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
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