Horizontal gene transfer and adaptive evolution in bacteria
Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of...
Saved in:
| Published in: | Nature reviews. Microbiology Vol. 20; no. 4; pp. 206 - 218 |
|---|---|
| Main Authors: | , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
London
Nature Publishing Group UK
01.04.2022
Nature Publishing Group |
| Subjects: | |
| ISSN: | 1740-1526, 1740-1534, 1740-1534 |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Abstract | Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.
Bacterial DNA transfers between cells in numerous ways and becomes integrated into the genome, with diverse consequences for bacterial genomes. In this Review, Arnold, Huang and Hanage discuss the underlying theory used to infer the selective forces acting on transferred DNA and how they shape patterns of genomic variation. |
|---|---|
| AbstractList | Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.Bacterial DNA transfers between cells in numerous ways and becomes integrated into the genome, with diverse consequences for bacterial genomes. In this Review, Arnold, Huang and Hanage discuss the underlying theory used to infer the selective forces acting on transferred DNA and how they shape patterns of genomic variation. Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments. Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments. Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments. Bacterial DNA transfers between cells in numerous ways and becomes integrated into the genome, with diverse consequences for bacterial genomes. In this Review, Arnold, Huang and Hanage discuss the underlying theory used to infer the selective forces acting on transferred DNA and how they shape patterns of genomic variation. |
| Author | Arnold, Brian J. Hanage, William P. Huang, I-Ting |
| Author_xml | – sequence: 1 givenname: Brian J. orcidid: 0000-0002-8629-5465 surname: Arnold fullname: Arnold, Brian J. email: brianjohnarnold@gmail.com organization: Department of Computer Science, Princeton University, Center for Statistics and Machine Learning, Princeton University – sequence: 2 givenname: I-Ting surname: Huang fullname: Huang, I-Ting organization: Department of Organismic and Evolutionary Biology, Harvard University – sequence: 3 givenname: William P. orcidid: 0000-0002-6319-7336 surname: Hanage fullname: Hanage, William P. email: whanage@hsph.harvard.edu organization: Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/34773098$$D View this record in MEDLINE/PubMed |
| BookMark | eNp9kU1LAzEQhoNUtK3-AQ-y4MXL6uRrk8WTiF9Q8KLnkGazJWWb1GRX0F9vaquCB0-Zw_NMZuadoJEP3iJ0guECA5WXiWEu6hIILgEqDiXbQ2MsGJSYUzb6qUl1iCYpLQEI54IcoEPKhKBQyzG6egjRfQTf665YWG-LPmqfWhsL7ZtCN3rduzdb2LfQDb0LvnC-mGvT2-j0EdpvdZfs8e6dope72-ebh3L2dP94cz0rDRW8L7HFNWEwp6ZpsTENq1hLuARKJNPcGmOEMI2sKW2orGpRt5QKbaCVuayyN0Xn277rGF4Hm3q1csnYrtPehiEpwmvBATiDjJ79QZdhiD5Pp0jFoKokzv9M0emOGuYr26h1dCsd39X3WTIgt4CJIaVoW2Vcrzf75_O4TmFQmwTUNgGVE1BfCSiWVfJH_e7-r0S3UsqwX9j4O_Y_1idNQpY_ |
| CitedBy_id | crossref_primary_10_1016_j_jmb_2025_169403 crossref_primary_10_1007_s10142_023_01109_w crossref_primary_10_1038_s41467_025_60116_6 crossref_primary_10_1099_jmm_0_001923 crossref_primary_10_1186_s12866_024_03391_5 crossref_primary_10_1016_j_micres_2025_128048 crossref_primary_10_1186_s40168_025_02065_2 crossref_primary_10_1016_j_algal_2024_103460 crossref_primary_10_1016_j_jhazmat_2025_138980 crossref_primary_10_1016_j_chemosphere_2023_139905 crossref_primary_10_1038_s41467_024_54408_6 crossref_primary_10_1186_s40793_024_00570_9 crossref_primary_10_1038_s41576_023_00688_5 crossref_primary_10_1016_j_chom_2024_05_017 crossref_primary_10_3390_genes13112071 crossref_primary_10_1016_j_chom_2024_05_015 crossref_primary_10_1080_03036758_2024_2345315 crossref_primary_10_1038_s41576_023_00620_x crossref_primary_10_1093_femsle_fnae027 crossref_primary_10_1016_j_envres_2024_119153 crossref_primary_10_3389_fmicb_2022_889551 crossref_primary_10_1021_acs_jpcb_5c02436 crossref_primary_10_1128_msphere_01010_24 crossref_primary_10_3389_fmicb_2023_1271138 crossref_primary_10_3390_ncrna11030036 crossref_primary_10_3389_fmicb_2022_854792 crossref_primary_10_1038_s41467_022_33054_w crossref_primary_10_1080_21505594_2024_2322961 crossref_primary_10_3390_microorganisms13040908 crossref_primary_10_1007_s13752_024_00478_0 crossref_primary_10_1016_j_marpolbul_2024_116939 crossref_primary_10_1126_science_adl0799 crossref_primary_10_3390_agronomy14061295 crossref_primary_10_1007_s10142_023_01206_w crossref_primary_10_1038_s41522_025_00793_9 crossref_primary_10_3389_fmicb_2025_1625724 crossref_primary_10_1093_molbev_msad028 crossref_primary_10_21105_joss_07773 crossref_primary_10_1016_j_cej_2025_159666 crossref_primary_10_1016_j_meegid_2024_105654 crossref_primary_10_1038_s41467_023_36086_y crossref_primary_10_1093_femsle_fnae005 crossref_primary_10_1016_j_chemosphere_2024_142264 crossref_primary_10_1016_j_fochms_2024_100236 crossref_primary_10_1371_journal_pbio_3002632 crossref_primary_10_1128_aem_00095_24 crossref_primary_10_1128_msystems_00562_22 crossref_primary_10_1016_j_jare_2024_12_044 crossref_primary_10_1111_evo_14432 crossref_primary_10_3390_su162410922 crossref_primary_10_1111_1749_4877_12714 crossref_primary_10_1134_S2079086423060154 crossref_primary_10_1007_s13225_023_00530_7 crossref_primary_10_1111_mmi_15209 crossref_primary_10_1016_j_watres_2024_121855 crossref_primary_10_1038_s41564_023_01531_7 crossref_primary_10_1039_D4RA06117A crossref_primary_10_1128_msystems_00365_24 crossref_primary_10_1128_jcm_00266_24 crossref_primary_10_1186_s13059_025_03634_2 crossref_primary_10_1038_s41467_025_61035_2 crossref_primary_10_1038_s42003_023_04753_x crossref_primary_10_1093_molbev_msae272 crossref_primary_10_26599_NR_2025_94907821 crossref_primary_10_1038_s41586_024_07486_x crossref_primary_10_3389_fmicb_2022_913662 crossref_primary_10_1016_j_biortech_2024_131306 crossref_primary_10_1093_molbev_msaf107 crossref_primary_10_1128_spectrum_00517_25 crossref_primary_10_2478_johr_2022_0009 crossref_primary_10_1016_j_jenvman_2024_122930 crossref_primary_10_1093_femsle_fnae068 crossref_primary_10_1002_adtp_202400412 crossref_primary_10_1016_j_jhazmat_2024_136359 crossref_primary_10_1007_s12602_023_10128_9 crossref_primary_10_1038_s41467_022_31858_4 crossref_primary_10_3390_ijms24021153 crossref_primary_10_1186_s12934_025_02759_0 crossref_primary_10_1016_j_envint_2023_108318 crossref_primary_10_3389_fmicb_2024_1460335 crossref_primary_10_1016_j_envres_2024_118172 crossref_primary_10_1016_j_algal_2023_103128 crossref_primary_10_1016_j_jenvman_2022_115944 crossref_primary_10_1111_1348_0421_13222 crossref_primary_10_1093_gbe_evaf079 crossref_primary_10_3389_fbioe_2025_1620652 crossref_primary_10_1038_s41559_025_02827_z crossref_primary_10_1093_molbev_msaf128 crossref_primary_10_1016_j_tim_2023_12_008 crossref_primary_10_1111_cpr_13236 crossref_primary_10_1371_journal_pone_0315160 crossref_primary_10_1016_j_copbio_2022_102885 crossref_primary_10_1016_j_watres_2022_119060 crossref_primary_10_1016_j_watres_2022_119062 crossref_primary_10_1371_journal_pbio_3002796 crossref_primary_10_1016_j_envpol_2025_126686 crossref_primary_10_3390_ijms24031967 crossref_primary_10_1016_j_ecoenv_2022_114247 crossref_primary_10_1016_j_jhazmat_2025_139824 crossref_primary_10_1016_j_ejmech_2024_116840 crossref_primary_10_1016_j_fm_2025_104895 crossref_primary_10_1093_jambio_lxaf201 crossref_primary_10_3390_ijms241411761 crossref_primary_10_1111_ele_14447 crossref_primary_10_3389_fcell_2022_988866 crossref_primary_10_3390_microorganisms12112375 crossref_primary_10_1093_nar_gkaf932 crossref_primary_10_1016_j_scitotenv_2024_172251 crossref_primary_10_1080_22221751_2024_2352435 crossref_primary_10_1099_mgen_0_001021 crossref_primary_10_1038_s41579_024_01041_1 crossref_primary_10_1126_science_ade0705 crossref_primary_10_3390_microorganisms11112725 crossref_primary_10_1016_j_jhazmat_2025_137932 crossref_primary_10_1186_s43170_023_00201_2 crossref_primary_10_1007_s00284_025_04373_0 crossref_primary_10_1002_ps_70067 crossref_primary_10_1080_1040841X_2024_2423159 crossref_primary_10_1093_molbev_msaf166 crossref_primary_10_3390_microorganisms13040779 crossref_primary_10_1073_pnas_2205041119 crossref_primary_10_1128_msystems_00083_22 crossref_primary_10_1016_j_epidem_2025_100817 crossref_primary_10_3390_antibiotics12121708 crossref_primary_10_1002_1873_3468_14906 crossref_primary_10_1038_s41579_023_00890_6 crossref_primary_10_1099_mgen_0_001279 crossref_primary_10_1016_j_pt_2025_04_002 crossref_primary_10_1016_j_jece_2025_117915 crossref_primary_10_1099_mgen_0_001034 crossref_primary_10_1371_journal_pbio_3002460 crossref_primary_10_1016_j_microc_2023_109268 crossref_primary_10_1093_jambio_lxad127 crossref_primary_10_1002_ps_8638 crossref_primary_10_3390_v15071525 crossref_primary_10_1093_genetics_iyaf115 crossref_primary_10_1093_molbev_msae066 crossref_primary_10_1111_1462_2920_16311 crossref_primary_10_7554_eLife_78533 crossref_primary_10_1093_femsec_fiac103 crossref_primary_10_3389_fmicb_2022_939406 crossref_primary_10_1186_s12915_024_01937_7 crossref_primary_10_3389_fmicb_2023_1214081 crossref_primary_10_1016_j_envpol_2023_123067 crossref_primary_10_3389_fmicb_2023_1157888 crossref_primary_10_3390_microorganisms10051040 crossref_primary_10_3389_fcimb_2024_1343858 crossref_primary_10_1007_s00284_024_03648_2 crossref_primary_10_1093_molbev_msaf060 crossref_primary_10_1093_glycob_cwac069 crossref_primary_10_1128_jb_00066_25 crossref_primary_10_1146_annurev_micro_112723_083001 crossref_primary_10_1007_s00248_024_02390_3 crossref_primary_10_1038_s41467_024_45154_w crossref_primary_10_5772_geet_21 crossref_primary_10_1038_s41467_024_55581_4 crossref_primary_10_1093_ismejo_wrae043 crossref_primary_10_1002_mlf2_12077 crossref_primary_10_1016_j_mib_2023_102424 crossref_primary_10_1093_ismejo_wrae167 crossref_primary_10_1093_ismejo_wraf014 crossref_primary_10_1021_acs_est_5c06928 crossref_primary_10_3390_microorganisms12091920 crossref_primary_10_1093_ismejo_wraf137 crossref_primary_10_1016_j_margen_2024_101083 crossref_primary_10_1155_jotm_7857069 crossref_primary_10_1016_j_envint_2025_109385 crossref_primary_10_4142_jvs_23265 crossref_primary_10_1007_s12602_022_10017_7 crossref_primary_10_1016_j_emcon_2025_100578 crossref_primary_10_1016_j_jhazmat_2024_134343 crossref_primary_10_1094_PHYTO_02_25_0042_FI crossref_primary_10_3389_fcimb_2025_1526028 crossref_primary_10_1128_spectrum_00858_25 crossref_primary_10_3390_genes14040949 crossref_primary_10_3390_d17040220 crossref_primary_10_2478_aoas_2024_0111 crossref_primary_10_1007_s12672_024_01590_0 crossref_primary_10_1093_nar_gkae899 crossref_primary_10_1016_j_tim_2025_03_009 crossref_primary_10_1128_msystems_01538_24 crossref_primary_10_1021_acsestwater_5c00540 crossref_primary_10_1007_s00203_024_03850_7 crossref_primary_10_1371_journal_pcbi_1011532 crossref_primary_10_1016_j_aquaculture_2025_742524 crossref_primary_10_1002_mlf2_12132 crossref_primary_10_1093_nar_gkae1265 crossref_primary_10_1155_2022_3348695 crossref_primary_10_1093_nsr_nwaf128 crossref_primary_10_1021_acs_est_4c13010 crossref_primary_10_1016_j_envpol_2024_124592 crossref_primary_10_1128_cmr_00175_23 crossref_primary_10_1016_j_ecoenv_2023_115124 crossref_primary_10_1016_j_jwpe_2024_106636 crossref_primary_10_1128_spectrum_00917_25 crossref_primary_10_3390_d16050268 crossref_primary_10_1016_j_copbio_2023_102898 crossref_primary_10_3390_micro5020018 crossref_primary_10_1038_s41598_022_23690_z crossref_primary_10_1360_SST_2024_0258 crossref_primary_10_1128_cmr_00118_23 crossref_primary_10_3390_microorganisms12112317 crossref_primary_10_1016_j_cej_2022_140195 crossref_primary_10_3390_antibiotics13070661 crossref_primary_10_3390_microorganisms11020407 crossref_primary_10_3389_fpls_2024_1435440 crossref_primary_10_1016_j_fm_2023_104327 crossref_primary_10_1016_j_scitotenv_2024_174466 crossref_primary_10_1093_evolinnean_kzae023 crossref_primary_10_1016_j_watres_2025_124357 crossref_primary_10_1093_plcell_koaf195 crossref_primary_10_1038_s41598_024_83952_w crossref_primary_10_1371_journal_pone_0301172 crossref_primary_10_3389_fmicb_2024_1367490 crossref_primary_10_1186_s12864_023_09245_0 crossref_primary_10_1016_j_envres_2023_117739 crossref_primary_10_1101_gr_277340_122 crossref_primary_10_1111_tpj_17057 crossref_primary_10_1016_j_ympev_2025_108359 crossref_primary_10_3390_ijms26020621 crossref_primary_10_1080_10408398_2022_2081127 crossref_primary_10_1016_j_biortech_2025_132036 crossref_primary_10_1016_j_ympev_2024_108197 crossref_primary_10_1128_spectrum_03688_22 crossref_primary_10_1002_adma_202406910 crossref_primary_10_1111_nph_70329 crossref_primary_10_1093_femsre_fuaf045 crossref_primary_10_1021_acsabm_4c01872 crossref_primary_10_1128_msystems_00211_22 crossref_primary_10_1016_j_jhazmat_2024_135624 crossref_primary_10_1016_j_psep_2024_07_033 crossref_primary_10_1093_nargab_lqae061 crossref_primary_10_1007_s13225_025_00550_5 crossref_primary_10_1016_j_jhazmat_2023_132099 crossref_primary_10_1016_j_wasman_2024_04_048 crossref_primary_10_1016_j_envpol_2025_126817 crossref_primary_10_1016_j_envpol_2025_126938 crossref_primary_10_1186_s40168_024_01963_1 crossref_primary_10_1093_nar_gkad130 crossref_primary_10_3389_fbioe_2025_1612226 crossref_primary_10_1016_j_tibtech_2024_12_011 crossref_primary_10_1016_j_gde_2022_101950 crossref_primary_10_1016_j_mib_2024_102431 crossref_primary_10_3390_microorganisms12050986 crossref_primary_10_1111_1758_2229_70175 crossref_primary_10_3390_antibiotics12010024 crossref_primary_10_1016_j_tig_2024_02_001 crossref_primary_10_3390_antibiotics11121794 crossref_primary_10_3390_toxins17060311 crossref_primary_10_1016_j_cell_2024_08_008 crossref_primary_10_1016_j_ijantimicag_2024_107225 crossref_primary_10_1128_msystems_00887_24 crossref_primary_10_1016_j_tim_2024_02_002 crossref_primary_10_1080_10889868_2025_2510989 crossref_primary_10_1128_spectrum_02453_24 crossref_primary_10_1007_s00203_023_03557_1 crossref_primary_10_1016_j_watres_2024_122590 crossref_primary_10_1016_j_micpath_2024_107275 crossref_primary_10_1016_j_plaphy_2024_109359 crossref_primary_10_1128_aem_01220_22 crossref_primary_10_1016_j_ebiom_2023_104532 crossref_primary_10_1134_S0026261724606043 crossref_primary_10_3389_fmicb_2023_1148263 crossref_primary_10_1016_j_margen_2024_101122 crossref_primary_10_1016_j_tim_2023_07_009 crossref_primary_10_1038_s41559_024_02421_9 crossref_primary_10_1093_nar_gkad1172 crossref_primary_10_1073_pnas_2417628122 crossref_primary_10_1016_j_scitotenv_2023_168908 crossref_primary_10_3390_antibiotics14080843 crossref_primary_10_1091_mbc_E20_08_0564 crossref_primary_10_1016_j_jhazmat_2024_133774 crossref_primary_10_3390_microorganisms11010215 crossref_primary_10_1128_spectrum_00915_24 crossref_primary_10_1016_j_jmb_2024_168924 crossref_primary_10_26508_lsa_202201833 crossref_primary_10_1128_spectrum_03265_24 crossref_primary_10_1093_nargab_lqae142 crossref_primary_10_1128_msystems_01089_24 crossref_primary_10_1016_j_watres_2024_122375 crossref_primary_10_1111_1462_2920_16630 crossref_primary_10_1093_nar_gkad138 crossref_primary_10_1073_pnas_2311127121 crossref_primary_10_1093_bfgp_elac051 crossref_primary_10_1038_s41467_025_57825_3 crossref_primary_10_1038_s43705_023_00317_6 crossref_primary_10_1016_j_jhazmat_2024_136824 crossref_primary_10_1128_mmbr_00041_23 crossref_primary_10_1016_j_jhazmat_2023_133238 crossref_primary_10_1186_s40793_024_00610_4 crossref_primary_10_1016_j_jhazmat_2024_134885 crossref_primary_10_1016_j_cub_2024_06_030 crossref_primary_10_1038_s41545_025_00446_6 crossref_primary_10_1016_j_watres_2024_121198 crossref_primary_10_1007_s00203_024_04152_8 crossref_primary_10_3390_genes13101895 crossref_primary_10_1093_bib_bbaf149 crossref_primary_10_1016_j_cell_2022_12_001 crossref_primary_10_1016_j_still_2025_106655 crossref_primary_10_1016_j_cell_2022_06_014 crossref_primary_10_1016_j_biocontrol_2025_105699 crossref_primary_10_1042_BST20221395 crossref_primary_10_1093_nargab_lqaf005 crossref_primary_10_1016_j_jgar_2024_11_003 crossref_primary_10_1016_j_soilbio_2024_109553 crossref_primary_10_1038_s41467_025_55834_w crossref_primary_10_1038_s41522_024_00597_3 crossref_primary_10_1128_spectrum_00260_24 crossref_primary_10_1016_j_scitotenv_2024_174618 crossref_primary_10_1002_advs_202502193 crossref_primary_10_1186_s40793_025_00701_w crossref_primary_10_1016_j_jclepro_2022_135371 crossref_primary_10_1371_journal_pbio_3002901 crossref_primary_10_3390_ijms26189193 crossref_primary_10_1186_s12864_022_08678_3 crossref_primary_10_1016_j_micres_2024_128041 crossref_primary_10_1093_femsre_fuae006 crossref_primary_10_3390_d14070502 crossref_primary_10_1016_j_colsurfb_2022_112833 crossref_primary_10_3389_fmicb_2025_1663069 crossref_primary_10_1016_j_ebiom_2025_105781 crossref_primary_10_1038_s41396_023_01463_4 crossref_primary_10_1016_j_fbio_2024_105405 crossref_primary_10_3390_microorganisms13081861 crossref_primary_10_1016_j_watres_2024_121887 crossref_primary_10_1016_j_ibiod_2025_106211 crossref_primary_10_1016_j_watres_2024_122730 crossref_primary_10_1016_j_watres_2024_122972 crossref_primary_10_3390_microorganisms10040700 crossref_primary_10_1016_j_jenvman_2023_118071 crossref_primary_10_1186_s42523_025_00442_8 crossref_primary_10_1111_1751_7915_14335 crossref_primary_10_1097_PXH_0000000000000019 crossref_primary_10_1128_msystems_00706_24 crossref_primary_10_1016_j_jhazmat_2024_134811 crossref_primary_10_1038_s41587_025_02639_3 crossref_primary_10_3201_eid3001_221927 crossref_primary_10_1016_j_tim_2024_04_014 crossref_primary_10_3390_w16111575 crossref_primary_10_1186_s12862_025_02360_4 crossref_primary_10_1016_j_jhazmat_2024_135902 crossref_primary_10_3389_fmicb_2023_1118264 crossref_primary_10_3390_microorganisms13081732 crossref_primary_10_3389_fmicb_2025_1541524 crossref_primary_10_1016_j_micres_2025_128340 crossref_primary_10_3390_vetsci12050484 crossref_primary_10_1016_j_envpol_2023_122766 crossref_primary_10_1016_j_ecoenv_2025_118991 crossref_primary_10_1038_s41564_025_02091_8 crossref_primary_10_1093_nar_gkaf488 crossref_primary_10_1073_pnas_2317182121 crossref_primary_10_1093_nar_gkae155 crossref_primary_10_1186_s13059_024_03443_z crossref_primary_10_1186_s40793_023_00461_5 crossref_primary_10_1016_j_scib_2023_09_001 crossref_primary_10_1093_femsre_fuae019 crossref_primary_10_3390_ijms24032610 crossref_primary_10_1113_JP284410 crossref_primary_10_1016_j_micres_2025_128232 crossref_primary_10_1016_j_jclepro_2024_144177 crossref_primary_10_1016_j_marpolbul_2024_117059 crossref_primary_10_1016_j_micinf_2024_105462 crossref_primary_10_1002_chem_202401399 crossref_primary_10_1016_j_mib_2025_102628 crossref_primary_10_2147_IDR_S388354 crossref_primary_10_1099_mgen_0_000931 crossref_primary_10_1371_journal_pone_0301642 crossref_primary_10_1016_j_apsoil_2025_106013 crossref_primary_10_1016_j_apsoil_2025_106375 crossref_primary_10_1139_cjm_2024_0168 crossref_primary_10_1016_j_jhazmat_2025_137692 crossref_primary_10_1093_nargab_lqaf083 crossref_primary_10_1007_s00284_024_04044_6 crossref_primary_10_1080_1040841X_2025_2555938 crossref_primary_10_1073_pnas_2318160121 crossref_primary_10_1111_1751_7915_14408 crossref_primary_10_1146_annurev_earth_031621_070542 crossref_primary_10_1099_mgen_0_000939 crossref_primary_10_1016_j_jhazmat_2025_139638 crossref_primary_10_1038_s41522_024_00588_4 crossref_primary_10_1093_discim_kyad025 crossref_primary_10_1016_j_scitotenv_2024_171530 crossref_primary_10_1038_s41579_025_01157_y crossref_primary_10_1016_j_envres_2025_120920 crossref_primary_10_1038_s41559_023_02269_5 crossref_primary_10_1016_j_cell_2024_07_028 crossref_primary_10_23902_trkjnat_1171052 crossref_primary_10_1016_j_chom_2024_06_002 crossref_primary_10_1016_j_foodres_2024_115299 crossref_primary_10_1016_j_jhazmat_2024_133922 crossref_primary_10_1186_s12862_023_02112_2 crossref_primary_10_1016_j_ijbiomac_2025_139980 crossref_primary_10_1128_msphere_00114_25 crossref_primary_10_54203_scil_2025_wvj22 crossref_primary_10_1038_s42003_023_05745_7 crossref_primary_10_1038_s41522_025_00773_z crossref_primary_10_1016_j_tig_2024_01_007 crossref_primary_10_3389_fmicb_2025_1512923 crossref_primary_10_1007_s00210_025_04194_9 crossref_primary_10_1038_s41597_024_03908_7 crossref_primary_10_3389_fmicb_2025_1537073 crossref_primary_10_1016_j_watres_2024_122676 crossref_primary_10_3389_fmicb_2022_1034440 crossref_primary_10_1038_s41598_025_86098_5 crossref_primary_10_1186_s40168_023_01695_8 crossref_primary_10_3390_microbiolres16060118 crossref_primary_10_1038_s41467_023_39964_7 crossref_primary_10_1016_j_envpol_2025_126048 crossref_primary_10_1016_j_scitotenv_2024_178020 crossref_primary_10_1016_j_tim_2025_07_009 crossref_primary_10_1016_j_ijbiomac_2025_140979 crossref_primary_10_1128_spectrum_01466_24 crossref_primary_10_3390_foods14020216 crossref_primary_10_3389_fmars_2023_985514 crossref_primary_10_1016_j_ymben_2025_08_005 |
| Cites_doi | 10.1038/s41396-020-0655-x 10.1101/782573 10.1101/568709 10.1371/journal.pgen.1006508 10.1007/0-387-27651-3_7 10.1128/mBio.01033-18 10.1101/227413 10.1371/journal.pgen.1000601 10.1038/s41579-019-0311-5 10.1093/molbev/msz225 10.1371/journal.pgen.1000304 10.1007/978-94-007-2941-4_37 10.1128/mBio.02430-19 10.1371/journal.pgen.1003458 10.1016/j.tree.2013.08.003 10.1128/9781555819743.ch18 10.1038/s41564-017-0067-5 10.1371/journal.ppat.1002129 10.1038/nrg2526 10.1371/journal.pbio.0030130 10.3389/fmicb.2018.02365 10.3391/mbi.2017.8.1.01 10.1038/nature24287 10.1002/1521-1878(200012)22:12<1115::AID-BIES9>3.0.CO;2-R 10.1371/journal.pbio.3000878 10.1128/jb.173.22.7257-7268.1991 10.1371/journal.pgen.1002222 10.1016/j.cell.2019.06.033 10.1016/j.jtbi.2005.08.037 10.1016/S0168-9525(01)02447-7 10.1016/j.tim.2009.02.002 10.1146/annurev-micro-102215-095325 10.1128/mBio.01419-18 10.1093/molbev/msx309 10.1086/285644 10.1186/1471-2164-13-196 10.1098/rspb.2013.2609 10.1073/pnas.2005331117 10.1016/j.ymben.2012.07.004 10.1073/pnas.98.1.182 10.1073/pnas.95.21.12619 10.1038/nature10571 10.1371/journal.pcbi.1002735 10.1534/genetics.120.303401 10.1111/j.1574-6976.2012.00353.x 10.1371/journal.pbio.0050225 10.1093/gbe/evw077 10.3389/fmicb.2018.02980 10.1016/j.tim.2015.07.006 10.1038/ng1686 10.1016/S0923-2508(03)00071-8 10.1093/molbev/msv237 10.1073/pnas.1405336111 10.1093/genetics/143.4.1843 10.1073/pnas.0807339105 10.1016/j.cell.2011.01.015 10.1111/j.1574-6976.1997.tb00349.x 10.1371/journal.pbio.1002394 10.1093/molbev/mss163 10.1093/gbe/evp016 10.1093/molbev/msv009 10.1126/science.1218198 10.1126/science.aac5992 10.1073/pnas.90.10.4384 10.7554/eLife.08490 10.1093/molbev/msu082 10.1093/gbe/evs016 10.1093/molbev/mss279 10.1038/ismej.2017.36 10.1099/mgen.0.000184 10.1146/annurev.micro.60.080805.142300 10.1534/genetics.104.036939 10.1093/molbev/msu076 10.1073/pnas.1900570116 10.1128/MMBR.00038-08 10.1093/genetics/152.4.1459 10.1073/pnas.1906958116 10.1073/pnas.1614083113 10.1038/s41467-017-00808-w 10.1111/1574-6976.12067 10.1038/s41467-020-16669-9 10.1534/genetics.117.300662 10.1038/s41576-020-0244-x 10.1093/infdis/jis703 10.1371/journal.pgen.1007199 10.1371/journal.pcbi.1004041 10.1038/ismej.2016.88 10.1093/nar/gkz656 10.1126/science.285.5434.1745 10.1371/journal.pcbi.1006242 10.1038/s41564-017-0066-6 10.1016/j.cell.2021.01.029 10.1073/pnas.1119910109 10.1111/jeb.13132 10.1093/molbev/msx066 10.1073/pnas.94.18.9763 10.1038/nature08937 10.1016/j.resmic.2007.09.004 10.1093/nar/gkr928 10.1016/j.gde.2004.09.003 10.1038/ng1227 10.1016/j.chom.2019.10.022 10.1038/nature18927 10.1099/mgen.0.000338 10.3109/10409230903505596 10.1186/s12862-018-1272-4 10.1126/science.1086568 10.1093/gbe/evt002 10.1186/1471-2148-6-82 10.1186/s12915-015-0131-7 10.1016/j.cub.2007.03.032 10.1534/genetics.113.157172 10.1093/bib/bby042 10.1371/journal.pbio.3000102 10.1038/s41592-018-0293-7 10.1126/science.aaa4456 10.1101/gr.4746406 10.1038/ismej.2015.241 10.1242/jeb.114306 10.1038/nrmicro2235 10.1038/nrmicro3199 10.1128/JB.182.4.1016-1023.2000 10.1186/1741-7015-12-1 10.1126/science.283.5400.404 10.1073/pnas.0905137106 |
| ContentType | Journal Article |
| Copyright | Springer Nature Limited 2021 2021. Springer Nature Limited. Springer Nature Limited 2021. |
| Copyright_xml | – notice: Springer Nature Limited 2021 – notice: 2021. Springer Nature Limited. – notice: Springer Nature Limited 2021. |
| DBID | AAYXX CITATION CGR CUY CVF ECM EIF NPM 3V. 7QL 7RV 7U9 7X7 7XB 88A 88E 88I 8AO 8C1 8FD 8FE 8FH 8FI 8FJ 8FK ABUWG AEUYN AFKRA AZQEC BBNVY BENPR BHPHI BKSAR C1K CCPQU DWQXO FR3 FYUFA GHDGH GNUQQ H94 HCIFZ K9. KB0 LK8 M0S M1P M2P M7N M7P NAPCQ P64 PCBAR PHGZM PHGZT PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS Q9U RC3 7X8 |
| DOI | 10.1038/s41579-021-00650-4 |
| DatabaseName | CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed ProQuest Central (Corporate) Bacteriology Abstracts (Microbiology B) Nursing & Allied Health Database Virology and AIDS Abstracts Health & Medical Collection ProQuest Central (purchase pre-March 2016) Biology Database (Alumni Edition) Medical Database (Alumni Edition) Science Database (Alumni Edition) ProQuest Pharma Collection Public Health Database Technology Research Database ProQuest SciTech Collection ProQuest Natural Science Collection Hospital Premium Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) ProQuest Central (Alumni) ProQuest One Sustainability ProQuest Central UK/Ireland ProQuest Central Essentials Biological Science Database ProQuest Central Natural Science Collection ProQuest Earth, Atmospheric & Aquatic Science Collection Environmental Sciences and Pollution Management ProQuest One ProQuest Central Engineering Research Database Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student AIDS and Cancer Research Abstracts SciTech Premium Collection ProQuest Health & Medical Complete (Alumni) Nursing & Allied Health Database (Alumni Edition) ProQuest Biological Science Collection Health & Medical Collection (Alumni Edition) PML(ProQuest Medical Library) Science Database Algology Mycology and Protozoology Abstracts (Microbiology C) Biological Science Database Nursing & Allied Health Premium Biotechnology and BioEngineering Abstracts Earth, Atmospheric & Aquatic Science Database ProQuest Central Premium ProQuest One Academic ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China ProQuest Central Basic Genetics Abstracts MEDLINE - Academic |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) ProQuest Central Student ProQuest Central Essentials SciTech Premium Collection ProQuest Central China Environmental Sciences and Pollution Management ProQuest One Applied & Life Sciences ProQuest One Sustainability Health Research Premium Collection Natural Science Collection Health & Medical Research Collection Biological Science Collection ProQuest Central (New) ProQuest Medical Library (Alumni) Virology and AIDS Abstracts ProQuest Science Journals (Alumni Edition) ProQuest Biological Science Collection ProQuest One Academic Eastern Edition Earth, Atmospheric & Aquatic Science Database ProQuest Hospital Collection Health Research Premium Collection (Alumni) Biological Science Database ProQuest Hospital Collection (Alumni) Biotechnology and BioEngineering Abstracts Nursing & Allied Health Premium ProQuest Health & Medical Complete ProQuest One Academic UKI Edition ProQuest Nursing & Allied Health Source (Alumni) Engineering Research Database ProQuest One Academic ProQuest One Academic (New) Technology Research Database ProQuest One Academic Middle East (New) ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) ProQuest One Community College ProQuest One Health & Nursing ProQuest Natural Science Collection ProQuest Pharma Collection ProQuest Biology Journals (Alumni Edition) ProQuest Central Earth, Atmospheric & Aquatic Science Collection ProQuest Health & Medical Research Collection Genetics Abstracts Health and Medicine Complete (Alumni Edition) ProQuest Central Korea Bacteriology Abstracts (Microbiology B) Algology Mycology and Protozoology Abstracts (Microbiology C) AIDS and Cancer Research Abstracts ProQuest Public Health ProQuest Central Basic ProQuest Science Journals ProQuest Nursing & Allied Health Source ProQuest SciTech Collection ProQuest Medical Library ProQuest Central (Alumni) MEDLINE - Academic |
| DatabaseTitleList | ProQuest Central Student MEDLINE MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: BENPR name: ProQuest Central url: https://www.proquest.com/central sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1740-1534 |
| EndPage | 218 |
| ExternalDocumentID | 34773098 10_1038_s41579_021_00650_4 |
| Genre | Journal Article Review |
| GroupedDBID | --- .55 0R~ 123 29M 36B 39C 3V. 4.4 53G 70F 7RV 7X7 88A 88E 88I 8AO 8C1 8CJ 8FE 8FH 8FI 8FJ 8R4 8R5 AAEEF AARCD AAWYQ AAYZH AAZLF ABAWZ ABDBF ABJNI ABLJU ABUWG ACGFO ACGFS ACMJI ACPRK ACUHS ADBBV ADFRT AENEX AEUYN AFBBN AFKRA AFRAH AFSHS AGAYW AGHTU AHBCP AHMBA AHOSX AHSBF AIBTJ ALFFA ALIPV ALMA_UNASSIGNED_HOLDINGS AMTXH ARMCB ASPBG AVWKF AXYYD AZFZN AZQEC BBNVY BENPR BHPHI BKEYQ BKKNO BKSAR BPHCQ BVXVI CCPQU CS3 D1J DB5 DU5 DWQXO EAD EAP EAS EBS EE. EJD EMB EMK EMOBN ESX EX3 EXGXG F5P FEDTE FQGFK FSGXE FYUFA GNUQQ HCIFZ HMCUK HVGLF HZ~ IAO IH2 IHR INH INR ITC LGEZI LK8 LOTEE M0L M1P M2P M7P MM. N9A NADUK NAPCQ NNMJJ NXXTH O9- ODYON P2P PCBAR PQQKQ PROAC PSQYO Q2X QF4 QM4 QN7 QO4 RNR RNT RNTTT SHXYY SIXXV SNYQT SOJ SV3 TAOOD TBHMF TDRGL TSG TUS UKHRP WOW X7M AAYXX ABFSG ACSTC AEZWR AFANA AFHIU AGSTI AHWEU AIXLP ALPWD ATHPR CITATION CGR CUY CVF ECM EIF NPM 7QL 7U9 7XB 8FD 8FK C1K FR3 H94 K9. M7N P64 PHGZM PHGZT PJZUB PKEHL PPXIY PQEST PQGLB PQUKI PRINS Q9U RC3 7X8 |
| ID | FETCH-LOGICAL-c375t-1e19240b3cdf1ccd464f25803284a5eccc77cd8933d386979f337ac0f879f60b3 |
| IEDL.DBID | M2P |
| ISICitedReferencesCount | 492 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000717903600001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1740-1526 1740-1534 |
| IngestDate | Sun Nov 09 13:47:05 EST 2025 Sun Nov 30 04:03:49 EST 2025 Wed Feb 19 02:24:41 EST 2025 Tue Nov 18 22:11:21 EST 2025 Sat Nov 29 03:06:05 EST 2025 Fri Feb 21 02:38:50 EST 2025 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 4 |
| Language | English |
| License | 2021. Springer Nature Limited. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c375t-1e19240b3cdf1ccd464f25803284a5eccc77cd8933d386979f337ac0f879f60b3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Review-3 content type line 23 |
| ORCID | 0000-0002-6319-7336 0000-0002-8629-5465 |
| PMID | 34773098 |
| PQID | 2640668193 |
| PQPubID | 27584 |
| PageCount | 13 |
| ParticipantIDs | proquest_miscellaneous_2597500540 proquest_journals_2640668193 pubmed_primary_34773098 crossref_citationtrail_10_1038_s41579_021_00650_4 crossref_primary_10_1038_s41579_021_00650_4 springer_journals_10_1038_s41579_021_00650_4 |
| PublicationCentury | 2000 |
| PublicationDate | 2022-04-01 |
| PublicationDateYYYYMMDD | 2022-04-01 |
| PublicationDate_xml | – month: 04 year: 2022 text: 2022-04-01 day: 01 |
| PublicationDecade | 2020 |
| PublicationPlace | London |
| PublicationPlace_xml | – name: London – name: England |
| PublicationTitle | Nature reviews. Microbiology |
| PublicationTitleAbbrev | Nat Rev Microbiol |
| PublicationTitleAlternate | Nat Rev Microbiol |
| PublicationYear | 2022 |
| Publisher | Nature Publishing Group UK Nature Publishing Group |
| Publisher_xml | – name: Nature Publishing Group UK – name: Nature Publishing Group |
| References | Redfield (CR28) 2006; 6 Lozupone (CR9) 2008; 105 Chu, Sprouffske, Wagner (CR62) 2017; 30 Shapiro, David, Friedman, Alm (CR67) 2009; 17 Johnsborg, Eldholm, Håvarstein (CR15) 2007; 158 Hasegawa, Suzuki, Maeda (CR24) 2018; 9 Pál, Papp, Lercher (CR118) 2005; 37 Engelstädter, Moradigaravand (CR65) 2014; 281 Wall (CR26) 2016; 70 Garud, Good, Hallatschek, Pollard (CR2) 2019; 17 Messer, Petrov (CR87) 2013 Hao, Golding (CR101) 2006; 16 Castillo-Ramírez (CR132) 2011 Good, Rouzine, Balick, Hallatschek, Desai (CR76) 2012; 109 Cui (CR88) 2015; 32 Vos (CR55) 2015; 23 Haegeman, Weitz (CR98) 2012; 13 Maddamsetti, Lenski (CR94) 2018; 14 Hughes (CR99) 2005; 169 Vos, Eyre-walker (CR14) 2017 Bendall (CR70) 2016; 10 Croucher (CR41) 2016; 14 Rajeev, Malanowska, Gardner (CR36) 2009; 73 Cain (CR115) 2020; 21 Dubey, Ben-Yehuda (CR21) 2011; 144 Waterworth (CR54) 2020 Arnold (CR63) 2019 Shapiro (CR13) 2017; 2 Didelot, Wilson (CR122) 2015; 11 Bradley, Nayfach, Pollard (CR10) 2018; 14 Guglielmini, Quintais, Garcillán-Barcia, de la Cruz, Rocha (CR20) 2011; 7 Frye, Nilsen, Tønjum, Ambur (CR27) 2013 Cohan (CR85) 1994; 143 Durrant, Li, Siranosian, Montgomery, Bhatt (CR35) 2020; 27 Puigbò, Lobkovsky, Kristensen, Wolf, Koonin (CR110) 2014; 12 Dillon, Thakur, Almeida, Guttman (CR134) 2019 Crits-Christoph, Olm, Diamond, Bouma-Gregson, Banfield (CR72) 2020 Lobkovsky, Wolf, Koonin (CR103) 2013; 5 Daubin, Szollosi (CR127) 2016 Bertelli, Tilley, Brinkman (CR128) 2019; 20 Yahara, Didelot, Ansari, Sheppard, Falush (CR125) 2014; 31 CR131 Miralles, Gerrish, Moya, Elena (CR74) 1999; 285 Lawrence, Roth (CR45) 1996; 143 Marttinen (CR121) 2012; 40 Bárdy (CR23) 2020; 11 Hallet, Sherratt (CR34) 1997; 21 Moradigaravand, Engelstädter (CR59) 2012; 8 Domingo-Sananes, McInerney (CR107) 2019 Parkhill (CR51) 2003; 35 Kryazhimskiy, Plotkin (CR130) 2008 Evans (CR114) 2015; 218 Johnston, Martin, Fichant, Polard, Claverys (CR16) 2014; 12 Brito (CR113) 2016; 535 Hickman, Chandler, Dyda (CR37) 2010; 45 Campbell (CR47) 2003; 154 Dykhuizen, Green (CR5) 1991; 173 Wyres (CR33) 2013; 207 Pensar (CR90) 2019; 47 Wadsworth, Arnold, Sater, Grad (CR39) 2018; 9 Azarian (CR108) 2020; 18 Camarillo-Guerrero (CR19) 2021; 184 Mira, Ochman, Moran (CR43) 2001; 17 Smith, Smith, O’Rourke, Spratt (CR4) 1993; 90 Mcinerney, Mcnally, Connell (CR12) 2017; 2 Skwark (CR89) 2016 Frazão, Sousa, Lässig, Gordo (CR3) 2019; 116 Arnold (CR58) 2018; 208 Cohan (CR83) 2017 Kuo, Ochman (CR44) 2009; 1 Siguier, Gourbeyre, Chandler (CR30) 2014; 38 Bobay, Touchon, Rocha (CR109) 2014; 111 Cohan, Perry (CR106) 2007; 17 Yahara (CR64) 2016; 33 Rodriguez-Valera (CR79) 2009; 7 Collins, Higgs (CR96) 2012; 29 Slomka (CR93) 2020; 216 Baumdicker, Hess, Pfaffelhuber (CR97) 2012; 4 Dion, Oechslin, Moineau (CR29) 2020 Whelan, Rusilowicz, McInerney (CR92) 2020; 6 Charlesworth (CR105) 2009 Cohen, Kessler, Levine (CR56) 2005; 94 Fondi (CR84) 2016; 8 Poulsen (CR117) 2019; 116 Chu (CR48) 2017; 8 Majewski (CR32) 2000; 182 Corander (CR78) 2018; 2017 Woods (CR73) 2020; 117 Hendry (CR53) 2018 Ansari, Didelot (CR119) 2014; 196 Pimentel, Zhang (CR17) 2018; 9 Cooper (CR60) 2007; 5 Moran, Plague (CR52) 2004; 14 Maynard Smith, Feil, Smith (CR1) 2000; 22 Andreani, Hesse, Vos (CR11) 2017; 11 Shapiro (CR68) 2012; 336 CR123 Apagyi, Fraser, Croucher (CR42) 2018; 35 Majewski, Cohan (CR86) 1999; 152 Ramiro, Durão, Bank, Gordo (CR81) 2020 Rocha (CR129) 2006; 239 Arevalo, VanInsberghe, Elsherbini, Gore, Polz (CR40) 2019; 178 Winkler, Kao (CR61) 2012; 14 Holt (CR82) 2009; 106 Cohan (CR66) 2007 Roux, Hallam, Woyke, Sullivan (CR18) 2015; 4 Lee, Doak, Popodi, Foster, Tang (CR50) 2016; 44 Porter, Chang, Conow, Dunham, Friesen (CR71) 2017; 11 Oliveira, Touchon, Cury, Rocha (CR38) 2017; 8 Rosen, Davison, Bhaya, Fisher (CR69) 2015; 348 Abe, Nomura, Suzuki (CR22) 2020; 96 Feil (CR6) 2001; 98 Van Passel, Marri, Ochman (CR100) 2008; 4 Lin, Kussell (CR120) 2019; 16 Seitz, Blokesch (CR25) 2013; 37 Sela, Wolf, Koonin (CR104) 2016; 113 Good, McDonald, Barrick, Lenski, Desai (CR80) 2017; 551 Vulić, Dionisio, Taddei, Radman (CR31) 1997; 94 Daubin, Moran, Ochman (CR126) 2003; 301 David (CR133) 2017; 13 Hehemann (CR46) 2010; 464 De Visser, Zeyl, Gerrish, Blanchard, Lenski (CR75) 1999; 283 Knöppel, Lind, Lustig, Näsvall, Andersson (CR95) 2014; 31 Bobay, Ochman (CR112) 2018; 18 Mostowy (CR124) 2017; 34 CR102 Lynch (CR111) 2006; 60 Smillie (CR8) 2011; 480 Takeuchi, Cordero, Koonin, Kaneko (CR77) 2015; 13 Levin, Cornejo (CR57) 2009 Bobay, Rocha, Touchon (CR49) 2013; 30 Puranen (CR91) 2018; 4 Wu (CR116) 2015; 350 Suerbaum (CR7) 1998; 95 S Puranen (650_CR91) 2018; 4 P Bárdy (650_CR23) 2020; 11 M Fondi (650_CR84) 2016; 8 FM Cohan (650_CR85) 1994; 143 BJ Shapiro (650_CR67) 2009; 17 LM Bobay (650_CR109) 2014; 111 S Castillo-Ramírez (650_CR132) 2011 P Seitz (650_CR25) 2013; 37 P Marttinen (650_CR121) 2012; 40 NA Moran (650_CR52) 2004; 14 RJ Redfield (650_CR28) 2006; 6 C Pál (650_CR118) 2005; 37 J Winkler (650_CR61) 2012; 14 K Yahara (650_CR64) 2016; 33 MR Domingo-Sananes (650_CR107) 2019 V Daubin (650_CR127) 2016 J Corander (650_CR78) 2018; 2017 JO Mcinerney (650_CR12) 2017; 2 RS Ramiro (650_CR81) 2020 E Cohen (650_CR56) 2005; 94 B Charlesworth (650_CR105) 2009 A Knöppel (650_CR95) 2014; 31 TG Evans (650_CR114) 2015; 218 BE Poulsen (650_CR117) 2019; 116 FM Cohan (650_CR83) 2017 BJ Shapiro (650_CR68) 2012; 336 SC Waterworth (650_CR54) 2020 D Wall (650_CR26) 2016; 70 LM Bobay (650_CR49) 2013; 30 T Hendry (650_CR53) 2018 650_CR131 ZT Pimentel (650_CR17) 2018; 9 S Suerbaum (650_CR7) 1998; 95 AB Hickman (650_CR37) 2010; 45 L Rajeev (650_CR36) 2009; 73 BH Good (650_CR80) 2017; 551 P Puigbò (650_CR110) 2014; 12 S David (650_CR133) 2017; 13 PW Messer (650_CR87) 2013 GP Dubey (650_CR21) 2011; 144 MG Durrant (650_CR35) 2020; 27 M Dillon (650_CR134) 2019 JH Hehemann (650_CR46) 2010; 464 RD Holt (650_CR82) 2009; 106 B Hallet (650_CR34) 1997; 21 X Didelot (650_CR122) 2015; 11 J Guglielmini (650_CR20) 2011; 7 M Vulić (650_CR31) 1997; 94 CB Wadsworth (650_CR39) 2018; 9 MWJ Van Passel (650_CR100) 2008; 4 FM Cohan (650_CR66) 2007 BJ Arnold (650_CR58) 2018; 208 PH Bradley (650_CR10) 2018; 14 RE Collins (650_CR96) 2012; 29 F Baumdicker (650_CR97) 2012; 4 H Hasegawa (650_CR24) 2018; 9 ND Chu (650_CR48) 2017; 8 FM Cohan (650_CR106) 2007; 17 J Pensar (650_CR90) 2019; 47 O Johnsborg (650_CR15) 2007; 158 K Abe (650_CR22) 2020; 96 HY Chu (650_CR62) 2017; 30 P Siguier (650_CR30) 2014; 38 S Roux (650_CR18) 2015; 4 JG Lawrence (650_CR45) 1996; 143 TF Cooper (650_CR60) 2007; 5 M Lynch (650_CR111) 2006; 60 A Ansari (650_CR119) 2014; 196 CS Smillie (650_CR8) 2011; 480 M Vos (650_CR55) 2015; 23 J Engelstädter (650_CR65) 2014; 281 H Lee (650_CR50) 2016; 44 AL Hughes (650_CR99) 2005; 169 A Crits-Christoph (650_CR72) 2020 AK Cain (650_CR115) 2020; 21 J Majewski (650_CR32) 2000; 182 M Lin (650_CR120) 2019; 16 K Yahara (650_CR125) 2014; 31 NA Andreani (650_CR11) 2017; 11 EPC Rocha (650_CR129) 2006; 239 M Vos (650_CR14) 2017 C Johnston (650_CR16) 2014; 12 SS Porter (650_CR71) 2017; 11 650_CR102 DE Dykhuizen (650_CR5) 1991; 173 IL Brito (650_CR113) 2016; 535 CA Lozupone (650_CR9) 2008; 105 D Moradigaravand (650_CR59) 2012; 8 S Slomka (650_CR93) 2020; 216 C-H Kuo (650_CR44) 2009; 1 R Miralles (650_CR74) 1999; 285 A Campbell (650_CR47) 2003; 154 N Frazão (650_CR3) 2019; 116 JM Smith (650_CR4) 1993; 90 C Bertelli (650_CR128) 2019; 20 J Majewski (650_CR86) 1999; 152 KJ Apagyi (650_CR42) 2018; 35 JAGM De Visser (650_CR75) 1999; 283 J Maynard Smith (650_CR1) 2000; 22 Y Cui (650_CR88) 2015; 32 BJ Shapiro (650_CR13) 2017; 2 R Mostowy (650_CR124) 2017; 34 I Sela (650_CR104) 2016; 113 KL Wyres (650_CR33) 2013; 207 A Mira (650_CR43) 2001; 17 MB Dion (650_CR29) 2020 M Skwark (650_CR89) 2016 NJ Croucher (650_CR41) 2016; 14 NR Garud (650_CR2) 2019; 17 S Kryazhimskiy (650_CR130) 2008 EJ Feil (650_CR6) 2001; 98 AE Lobkovsky (650_CR103) 2013; 5 ML Bendall (650_CR70) 2016; 10 N Takeuchi (650_CR77) 2015; 13 L Bobay (650_CR112) 2018; 18 W Hao (650_CR101) 2006; 16 650_CR123 LF Camarillo-Guerrero (650_CR19) 2021; 184 J Parkhill (650_CR51) 2003; 35 M Wu (650_CR116) 2015; 350 R Maddamsetti (650_CR94) 2018; 14 BH Good (650_CR76) 2012; 109 PH Oliveira (650_CR38) 2017; 8 B Haegeman (650_CR98) 2012; 13 V Daubin (650_CR126) 2003; 301 SA Frye (650_CR27) 2013 P Arevalo (650_CR40) 2019; 178 B Arnold (650_CR63) 2019 BR Levin (650_CR57) 2009 M Rosen (650_CR69) 2015; 348 T Azarian (650_CR108) 2020; 18 LC Woods (650_CR73) 2020; 117 F Rodriguez-Valera (650_CR79) 2009; 7 FJ Whelan (650_CR92) 2020; 6 |
| References_xml | – volume: 27 start-page: 140 year: 2020 end-page: 153.e9 ident: CR35 article-title: A bioinformatic analysis of integrative mobile genetic elements highlights their role in bacterial adaptation publication-title: Cell Host Microbe – volume: 47 start-page: e112 year: 2019 end-page: e112 ident: CR90 article-title: Genome-wide epistasis and co-selection study using mutual information publication-title: Nucleic Acids Res. – volume: 106 start-page: 19659 year: 2009 end-page: 19665 ident: CR82 article-title: Bringing the Hutchinsonian niche into the 21st century: ecological and evolutionary perspectives publication-title: Proc. Natl Acad. Sci. USA – volume: 11 start-page: 248 year: 2017 end-page: 262 ident: CR71 article-title: Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium publication-title: ISME J. – volume: 143 start-page: 965 year: 1994 end-page: 986 ident: CR85 article-title: The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes publication-title: Am. Nat. – year: 2020 ident: CR72 article-title: Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow publication-title: ISME J. doi: 10.1038/s41396-020-0655-x – year: 2019 ident: CR107 article-title: Selection-based model of prokaryote pangenomes publication-title: bioRxiv doi: 10.1101/782573 – volume: 94 start-page: 1 year: 2005 end-page: 4 ident: CR56 article-title: Recombination dramatically speeds up evolution of finite populations publication-title: Phys. Rev. Lett. – volume: 8 start-page: 1 year: 2017 end-page: 10 ident: CR38 article-title: The chromosomal organization of horizontal gene transfer in bacteria publication-title: Nat. Commun. – volume: 31 start-page: 1593 year: 2014 end-page: 1605 ident: CR125 article-title: Efficient inference of recombination hot regions in bacterial genomes publication-title: Mol. Biol. Evol. – year: 2020 ident: CR81 article-title: Low mutational load allows for high mutation rate variation in gut commensal bacteria publication-title: PLoS Biol. doi: 10.1101/568709 – volume: 116 start-page: 17906 year: 2019 end-page: 17915 ident: CR3 article-title: Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut publication-title: Proc. Natl Acad. Sci. USA – volume: 12 start-page: 1 year: 2014 end-page: 19 ident: CR110 article-title: Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes publication-title: BMC Med. – volume: 34 start-page: 1167 year: 2017 end-page: 1182 ident: CR124 article-title: Efficient inference of recent and ancestral recombination within bacterial populations publication-title: Mol. Biol. Evol. – volume: 6 year: 2020 ident: CR92 article-title: Coinfinder: detecting significant associations and dissociations in pangenomes publication-title: Microb. Genomics – volume: 208 start-page: 1247 year: 2018 end-page: 1260 ident: CR58 article-title: Weak epistasis may drive adaptation in recombining bacteria publication-title: Genetics – volume: 21 start-page: 526 year: 2020 end-page: 540 ident: CR115 article-title: A decade of advances in transposon-insertion sequencing publication-title: Nat. Rev. Genet. – volume: 2 start-page: 1 year: 2017 end-page: 5 ident: CR12 article-title: Why prokaryotes have pangenomes publication-title: Nat. Publ. Gr. – volume: 17 start-page: 589 year: 2001 end-page: 596 ident: CR43 article-title: Deletional bias and the evolution of bacterial genomes publication-title: Trends Genet. – year: 2016 ident: CR89 article-title: Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1006508 – year: 2007 ident: CR66 article-title: Periodic selection and ecological diversity in bacteria publication-title: Selective Sweep doi: 10.1007/0-387-27651-3_7 – volume: 33 start-page: 456 year: 2016 end-page: 471 ident: CR64 article-title: The landscape of realized homologous recombination in pathogenic bacteria publication-title: Mol. Biol. Evol. – volume: 9 start-page: 1 year: 2018 end-page: 10 ident: CR17 article-title: Evolution of the natural transformation protein, ComEC, in Bacteria publication-title: Front. Microbiol. – year: 2018 ident: CR53 article-title: Ongoing transposon-mediated genome reduction in the luminous bacterial symbionts of deep-sea ceratioid anglerfishes publication-title: mBio doi: 10.1128/mBio.01033-18 – volume: 29 start-page: 3413 year: 2012 end-page: 3425 ident: CR96 article-title: Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome publication-title: Mol. Biol. Evol. – volume: 60 start-page: 327 year: 2006 end-page: 349 ident: CR111 article-title: Streamlining and simplification of microbial genome architecture publication-title: Annu.Rev.Microbiol. – year: 2019 ident: CR134 article-title: Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex publication-title: Genome Biol. doi: 10.1101/227413 – volume: 14 start-page: 487 year: 2012 end-page: 495 ident: CR61 article-title: Harnessing recombination to speed adaptive evolution in Escherichia coli publication-title: Metab. Eng. – year: 2009 ident: CR57 article-title: The population and evolutionary dynamics of homologous gene recombination in bacteria publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1000601 – volume: 40 start-page: 1 year: 2012 end-page: 12 ident: CR121 article-title: Detection of recombination events in bacterial genomes from large population samples publication-title: Nucleic Acids Res. – volume: 169 start-page: 533 year: 2005 end-page: 538 ident: CR99 article-title: Evidence for abundant slightly deleterious polymorphisms in bacterial populations publication-title: Genetics – volume: 8 start-page: 35 year: 2012 end-page: 37 ident: CR59 article-title: The effect of bacterial recombination on adaptation on fitness landscapes with limited peak accessibility publication-title: PLoS Comput. Biol. – year: 2020 ident: CR29 article-title: Phage diversity, genomics and phylogeny publication-title: Nat. Rev. Microbiol. doi: 10.1038/s41579-019-0311-5 – volume: 7 start-page: 828 year: 2009 end-page: 836 ident: CR79 article-title: Explaining microbial population genomics through phage predation publication-title: Nat. Rev. Microbiol. – volume: 152 start-page: 1459 year: 1999 end-page: 1474 ident: CR86 article-title: Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity publication-title: Genetics – volume: 218 start-page: 1925 year: 2015 end-page: 1935 ident: CR114 article-title: Considerations for the use of transcriptomics in identifying the ‘genes that matter’ for environmental adaptation publication-title: J. Exp. Biol. – volume: 9 start-page: 1 year: 2018 end-page: 6 ident: CR24 article-title: Horizontal plasmid transfer by transformation in Escherichia coli: environmental factors and possible mechanisms publication-title: Front. Microbiol. – volume: 6 start-page: 1 year: 2006 end-page: 15 ident: CR28 article-title: Evolution of competence and DNA uptake specificity in the Pasteurellaceae publication-title: BMC Evol. Biol. – volume: 464 start-page: 908 year: 2010 end-page: 912 ident: CR46 article-title: Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota publication-title: Nature – volume: 18 start-page: 15 year: 2018 ident: CR112 article-title: Factors driving effective population size and pan-genome evolution in bacteria publication-title: BMC Evol. Biol. – ident: CR123 – volume: 12 start-page: 181 year: 2014 end-page: 196 ident: CR16 article-title: Bacterial transformation: distribution, shared mechanisms and divergent control publication-title: Nat. Rev. Microbiol. – volume: 17 year: 2019 ident: CR2 article-title: Evolutionary dynamics of bacteria in the gut microbiome within and across hosts publication-title: PLoS Biol. – volume: 90 start-page: 4384 year: 1993 end-page: 4388 ident: CR4 article-title: How clonal are bacteria? publication-title: Proc. Natl Acad. Sci. USA – volume: 13 start-page: 1 year: 2015 end-page: 11 ident: CR77 article-title: Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection publication-title: BMC Biol. – volume: 13 start-page: 1 year: 2017 end-page: 21 ident: CR133 article-title: Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila publication-title: PLoS Genet. – volume: 158 start-page: 767 year: 2007 end-page: 778 ident: CR15 article-title: Natural genetic transformation: prevalence, mechanisms and function publication-title: Res. Microbiol. – volume: 178 start-page: 820 year: 2019 end-page: 834.e14 ident: CR40 article-title: A reverse ecology approach based on a biological definition of microbial populations publication-title: Cell – volume: 154 start-page: 277 year: 2003 end-page: 282 ident: CR47 article-title: Prophage insertion sites publication-title: Res. Microbiol. – volume: 2 start-page: 1005860 year: 2017 ident: CR13 article-title: The population genetics of pangenomes publication-title: Nat. Microbiol. – volume: 285 start-page: 1745 year: 1999 end-page: 1747 ident: CR74 article-title: Clonal interference and the evolution of RNA viruses publication-title: Science – volume: 70 start-page: 143 year: 2016 end-page: 160 ident: CR26 article-title: Kin recognition in bacteria publication-title: Annu. Rev. Microbiol. – year: 2019 ident: CR63 article-title: Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msz225 – volume: 283 start-page: 404 year: 1999 end-page: 406 ident: CR75 article-title: Diminishing returns from mutation supply rate in asexual populations publication-title: Science – volume: 143 start-page: 1843 year: 1996 end-page: 1860 ident: CR45 article-title: Selfish operons: horizontal transfer may drive the evolution of gene clusters publication-title: Genetics – volume: 14 start-page: 627 year: 2004 end-page: 633 ident: CR52 article-title: Genomic changes following host restriction in bacteria publication-title: Curr. Opin. Genet. Dev. – volume: 8 start-page: 1388 year: 2016 end-page: 1400 ident: CR84 article-title: “Every gene is everywhere but the environment selects”: global geolocalization of gene sharing in environmental samples through network analysis publication-title: Genome Biol. Evol. – volume: 96 start-page: 1 year: 2020 end-page: 12 ident: CR22 article-title: Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism publication-title: FEMS Microbiol. Ecol. – volume: 23 start-page: 598 year: 2015 end-page: 605 ident: CR55 article-title: Rates of lateral gene transfer in prokaryotes: high but why? publication-title: Trends Microbiol. – volume: 196 start-page: 253 year: 2014 end-page: 265 ident: CR119 article-title: Inference of the properties of the recombination process from whole bacterial genomes publication-title: Genetics – year: 2008 ident: CR130 article-title: The population genetics of dN/dS publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1000304 – volume: 105 start-page: 15076 year: 2008 end-page: 15081 ident: CR9 article-title: The convergence of carbohydrate active gene repertoires in human gut microbes publication-title: Proc. Natl Acad. Sci. USA – ident: CR102 – year: 2016 ident: CR127 article-title: Horizontal gene transfer and the tree of life publication-title: Cold Spring Harb. Perspect. Biol. doi: 10.1007/978-94-007-2941-4_37 – volume: 109 start-page: 4950 year: 2012 end-page: 4955 ident: CR76 article-title: Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations publication-title: Proc. Natl Acad. Sci. USA – volume: 11 start-page: 1 year: 2015 end-page: 18 ident: CR122 article-title: ClonalFrameML: efficient inference of recombination in whole bacterial genomes publication-title: PLoS Comput. Biol. – volume: 348 start-page: 1019 year: 2015 end-page: 1024 ident: CR69 article-title: Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche publication-title: Science – volume: 4 year: 2018 ident: CR91 article-title: SuperDCA for genome-wide epistasis analysis publication-title: Microb. Genomics – ident: CR131 – year: 2020 ident: CR54 article-title: Horizontal gene transfer to a defensive symbiont with a reduced genome in a multipartite beetle microbiome publication-title: mBio doi: 10.1128/mBio.02430-19 – volume: 9 start-page: 1 year: 2018 end-page: 17 ident: CR39 article-title: Azithromycin resistance through interspecific acquisition of an epistasis-dependent efflux pump component and transcriptional regulator in Neisseria gonorrhoeae publication-title: mBio – volume: 8 start-page: 1 year: 2017 end-page: 13 ident: CR48 article-title: A mobile element in mutS drives hypermutation in a marine Vibrio publication-title: mBio – volume: 21 start-page: 157 year: 1997 end-page: 178 ident: CR34 article-title: Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements publication-title: FEMS Microbiol. Rev. – volume: 1 start-page: 145 year: 2009 end-page: 152 ident: CR44 article-title: Deletional bias across the three domains of life publication-title: Genome Biol. Evol. – volume: 5 start-page: 1899 year: 2007 end-page: 1905 ident: CR60 article-title: Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli publication-title: PLoS Biol. – volume: 216 start-page: 543 year: 2020 end-page: 558 ident: CR93 article-title: Experimental evolution of bacillus subtilis reveals the evolutionary dynamics of horizontal gene transfer and suggests adaptive and neutral effects publication-title: Genetics – year: 2013 ident: CR27 article-title: Dialects of the DNA uptake sequence in Neisseriaceae publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1003458 – volume: 31 start-page: 1220 year: 2014 end-page: 1227 ident: CR95 article-title: Minor fitness costs in an experimental model of horizontal gene transfer in bacteria publication-title: Mol. Biol. Evol. – volume: 144 start-page: 590 year: 2011 end-page: 600 ident: CR21 article-title: Intercellular nanotubes mediate bacterial communication publication-title: Cell – volume: 22 start-page: 1115 year: 2000 end-page: 1122 ident: CR1 article-title: Population structure and evolutionary dynamics of pathogenic bacteria publication-title: Bioessays – volume: 4 start-page: 443 year: 2012 end-page: 456 ident: CR97 article-title: The infinitely many genes model for the distributed genome of bacteria publication-title: Genome Biol. Evol. – volume: 98 start-page: 182 year: 2001 end-page: 187 ident: CR6 article-title: Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences publication-title: Proc. Natl Acad. Sci. USA – volume: 13 year: 2012 ident: CR98 article-title: A neutral theory of genome evolution and the frequency distribution of genes publication-title: BMC Genomics – volume: 5 start-page: 233 year: 2013 end-page: 242 ident: CR103 article-title: Gene frequency distributions reject a neutral model of genome evolution publication-title: Genome Biol. Evol. – volume: 4 year: 2008 ident: CR100 article-title: The emergence and fate of horizontally acquired genes in Escherichia coli publication-title: PLoS Comput. Biol. – volume: 11 year: 2020 ident: CR23 article-title: Structure and mechanism of DNA delivery of a gene transfer agent publication-title: Nat. Commun. – year: 2013 ident: CR87 article-title: Population genomics of rapid adaptation by soft selective sweeps publication-title: Trends Ecol. Evol. doi: 10.1016/j.tree.2013.08.003 – volume: 17 start-page: 196 year: 2009 end-page: 204 ident: CR67 article-title: Looking for Darwin’s footprints in the microbial world publication-title: Trends Microbiol. – volume: 95 start-page: 12619 year: 1998 end-page: 12624 ident: CR7 article-title: Free recombination within Helicobacter pylori publication-title: PNAS – volume: 336 start-page: 48 year: 2012 end-page: 51 ident: CR68 article-title: Population genomics of early events in the ecological differentiation of bacteria publication-title: Science – year: 2017 ident: CR83 article-title: Transmission in the origins of bacterial diversity, from ecotypes to phyla publication-title: Microbiol. Spectr. doi: 10.1128/9781555819743.ch18 – volume: 30 start-page: 737 year: 2013 end-page: 751 ident: CR49 article-title: The adaptation of temperate bacteriophages to their host genomes publication-title: Mol. Biol. Evol. – volume: 182 start-page: 1016 year: 2000 end-page: 1023 ident: CR32 article-title: Barriers to genetic exchange between bacterial species: transformation publication-title: J. Bacteriol. – volume: 32 start-page: 1396 year: 2015 end-page: 1410 ident: CR88 article-title: Epidemic clones, oceanic gene pools, and Eco-LD in the free living marine pathogen Vibrio parahaemolyticus publication-title: Mol. Biol. Evol. – volume: 350 start-page: aac5992 year: 2015 ident: CR116 article-title: Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides publication-title: Science (80-.) – volume: 35 start-page: 575 year: 2018 end-page: 581 ident: CR42 article-title: Transformation asymmetry and the evolution of the bacterial accessory genome publication-title: Mol. Biol. Evol. – volume: 17 start-page: 373 year: 2007 end-page: 386 ident: CR106 article-title: A systematics for discovering the fundamental units of bacterial diversity publication-title: Curr. Biol. – volume: 111 start-page: 12127 year: 2014 end-page: 12132 ident: CR109 article-title: Pervasive domestication of defective prophages by bacteria publication-title: Proc. Natl Acad. Sci. USA – volume: 37 start-page: 336 year: 2013 end-page: 363 ident: CR25 article-title: Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria publication-title: FEMS Microbiol. Rev. – volume: 480 start-page: 241 year: 2011 end-page: 244 ident: CR8 article-title: Ecology drives a global network of gene exchange connecting the human microbiome publication-title: Nature – volume: 16 start-page: 199 year: 2019 end-page: 204 ident: CR120 article-title: Inferring bacterial recombination rates from large-scale sequencing datasets publication-title: Nat. Methods – volume: 173 start-page: 7257 year: 1991 end-page: 7268 ident: CR5 article-title: Recombination in Escherichia coli and the definition of biological species publication-title: J. Bacteriol. – volume: 535 start-page: 435 year: 2016 end-page: 439 ident: CR113 article-title: Mobile genes in the human microbiome are structured from global to individual scales publication-title: Nature – volume: 4 start-page: 1 year: 2015 end-page: 20 ident: CR18 article-title: Viral dark matter and virus–host interactions resolved from publicly available microbial genomes publication-title: eLife – volume: 207 start-page: 439 year: 2013 end-page: 449 ident: CR33 article-title: Pneumococcal capsular switching: a historical perspective publication-title: J. Infect. Dis. – volume: 94 start-page: 9763 year: 1997 end-page: 9767 ident: CR31 article-title: Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria publication-title: Proc. Natl Acad. Sci. USA – volume: 7 year: 2011 ident: CR20 article-title: The repertoire of ice in prokaryotes underscores the unity, diversity, and ubiquity of conjugation publication-title: PLoS Genet. – volume: 301 start-page: 829 year: 2003 end-page: 832 ident: CR126 article-title: Phylogenetics and the cohesion of bacterial genomes publication-title: Science – volume: 117 start-page: 26868 year: 2020 end-page: 26875 ident: CR73 article-title: Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation publication-title: Proc. Natl Acad. Sci. USA – volume: 45 start-page: 50 year: 2010 end-page: 69 ident: CR37 article-title: Integrating prokaryotes and eukaryotes: DNA transposases in light of structure publication-title: Crit. Rev. Biochem. Mol. Biol. – volume: 44 start-page: 7109 year: 2016 end-page: 7119 ident: CR50 article-title: Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli publication-title: Nucleic Acids Res. – volume: 10 start-page: 1589 year: 2016 end-page: 1601 ident: CR70 article-title: Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations publication-title: ISME J. – year: 2017 ident: CR14 article-title: Are pangenomes adaptive or not? publication-title: Nat. Microbiol. doi: 10.1038/s41564-017-0067-5 – volume: 551 start-page: 45 year: 2017 end-page: 50 ident: CR80 article-title: The dynamics of molecular evolution over 60,000 generations publication-title: Nature – volume: 14 start-page: 1 year: 2018 end-page: 30 ident: CR94 article-title: Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection publication-title: PLoS Genet. – volume: 281 start-page: 20132609 year: 2014 ident: CR65 article-title: Adaptation through genetic time travel? Fluctuating selection can drive the evolution of bacterial transformation publication-title: Proc. R. Soc. B Biol. Sci. – volume: 73 start-page: 300 year: 2009 end-page: 309 ident: CR36 article-title: Challenging a paradigm: the role of DNA homology in tyrosine recombinase reactions publication-title: Microbiol. Mol. Biol. Rev. – volume: 14 start-page: 1 year: 2016 end-page: 42 ident: CR41 article-title: Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict publication-title: PLoS Biol. – volume: 14 year: 2018 ident: CR10 article-title: Phylogeny-corrected identification of microbial gene families relevant to human gut colonization publication-title: PLoS Computational Biol. – volume: 18 year: 2020 ident: CR108 article-title: Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae publication-title: PLoS Biol. – volume: 239 start-page: 226 year: 2006 end-page: 235 ident: CR129 article-title: Comparisons of dN/dS are time dependent for closely related bacterial genomes publication-title: J. Theor. Biol. – volume: 38 start-page: 865 year: 2014 end-page: 891 ident: CR30 article-title: Bacterial insertion sequences: their genomic impact and diversity publication-title: FEMS Microbiol. Rev. – year: 2011 ident: CR132 article-title: The impact of recombination on dN/dS within recently emerged bacterial clones publication-title: PLoS Pathog. doi: 10.1371/journal.ppat.1002129 – volume: 37 start-page: 1372 year: 2005 end-page: 1375 ident: CR118 article-title: Adaptive evolution of bacterial metabolic networks by horizontal gene transfer publication-title: Nat. Genet. – volume: 116 start-page: 10072 year: 2019 end-page: 10080 ident: CR117 article-title: Defining the core essential genome of Pseudomonas aeruginosa publication-title: Proc. Natl Acad. Sci. USA – volume: 16 start-page: 636 year: 2006 end-page: 643 ident: CR101 article-title: The fate of laterally transferred genes: life in the fast lane to adaptation or death publication-title: Genome Res. – volume: 35 start-page: 32 year: 2003 end-page: 40 ident: CR51 article-title: Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica publication-title: Nat. Genet. – volume: 2017 start-page: 1950 year: 2018 end-page: 1960 ident: CR78 article-title: Frequency-dependent selection in vaccine-associated pneumococcal population dynamics publication-title: Nat. Ecol. Evol. – year: 2009 ident: CR105 article-title: Effective population size and patterns of molecular evolution and variation publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2526 – volume: 20 start-page: 1685 year: 2019 end-page: 1698 ident: CR128 article-title: Microbial genomic island discovery, visualization and analysis publication-title: Brief. Bioinform. – volume: 11 start-page: 1719 year: 2017 end-page: 1721 ident: CR11 article-title: Prokaryote genome fluidity is dependent on effective population size publication-title: ISME J. – volume: 184 start-page: 1098 year: 2021 end-page: 1109.e9 ident: CR19 article-title: Massive expansion of human gut bacteriophage diversity publication-title: Cell – volume: 113 start-page: 11399 year: 2016 end-page: 11407 ident: CR104 article-title: Theory of prokaryotic genome evolution publication-title: Proc. Natl Acad. Sci. USA – volume: 30 start-page: 1692 year: 2017 end-page: 1711 ident: CR62 article-title: The role of recombination in evolutionary adaptation of Escherichia coli to a novel nutrient publication-title: J. Evol. Biol. – ident: 650_CR102 doi: 10.1371/journal.pbio.0030130 – year: 2013 ident: 650_CR27 publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1003458 – volume: 9 start-page: 1 year: 2018 ident: 650_CR24 publication-title: Front. Microbiol. doi: 10.3389/fmicb.2018.02365 – volume: 2017 start-page: 1950 year: 2018 ident: 650_CR78 publication-title: Nat. Ecol. Evol. – volume: 8 start-page: 1 year: 2017 ident: 650_CR48 publication-title: mBio doi: 10.3391/mbi.2017.8.1.01 – volume: 551 start-page: 45 year: 2017 ident: 650_CR80 publication-title: Nature doi: 10.1038/nature24287 – volume: 22 start-page: 1115 year: 2000 ident: 650_CR1 publication-title: Bioessays doi: 10.1002/1521-1878(200012)22:12<1115::AID-BIES9>3.0.CO;2-R – volume: 18 year: 2020 ident: 650_CR108 publication-title: PLoS Biol. doi: 10.1371/journal.pbio.3000878 – volume: 173 start-page: 7257 year: 1991 ident: 650_CR5 publication-title: J. Bacteriol. doi: 10.1128/jb.173.22.7257-7268.1991 – volume: 7 year: 2011 ident: 650_CR20 publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1002222 – volume: 178 start-page: 820 year: 2019 ident: 650_CR40 publication-title: Cell doi: 10.1016/j.cell.2019.06.033 – volume: 239 start-page: 226 year: 2006 ident: 650_CR129 publication-title: J. Theor. Biol. doi: 10.1016/j.jtbi.2005.08.037 – year: 2020 ident: 650_CR54 publication-title: mBio doi: 10.1128/mBio.02430-19 – year: 2009 ident: 650_CR57 publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1000601 – volume: 17 start-page: 589 year: 2001 ident: 650_CR43 publication-title: Trends Genet. doi: 10.1016/S0168-9525(01)02447-7 – volume: 17 start-page: 196 year: 2009 ident: 650_CR67 publication-title: Trends Microbiol. doi: 10.1016/j.tim.2009.02.002 – volume: 70 start-page: 143 year: 2016 ident: 650_CR26 publication-title: Annu. Rev. Microbiol. doi: 10.1146/annurev-micro-102215-095325 – volume: 9 start-page: 1 year: 2018 ident: 650_CR39 publication-title: mBio doi: 10.1128/mBio.01419-18 – year: 2019 ident: 650_CR107 publication-title: bioRxiv doi: 10.1101/782573 – volume: 2 start-page: 1 year: 2017 ident: 650_CR12 publication-title: Nat. Publ. Gr. – volume: 35 start-page: 575 year: 2018 ident: 650_CR42 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msx309 – volume: 143 start-page: 965 year: 1994 ident: 650_CR85 publication-title: Am. Nat. doi: 10.1086/285644 – volume: 13 year: 2012 ident: 650_CR98 publication-title: BMC Genomics doi: 10.1186/1471-2164-13-196 – volume: 281 start-page: 20132609 year: 2014 ident: 650_CR65 publication-title: Proc. R. Soc. B Biol. Sci. doi: 10.1098/rspb.2013.2609 – volume: 117 start-page: 26868 year: 2020 ident: 650_CR73 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.2005331117 – volume: 14 start-page: 487 year: 2012 ident: 650_CR61 publication-title: Metab. Eng. doi: 10.1016/j.ymben.2012.07.004 – year: 2007 ident: 650_CR66 publication-title: Selective Sweep doi: 10.1007/0-387-27651-3_7 – year: 2011 ident: 650_CR132 publication-title: PLoS Pathog. doi: 10.1371/journal.ppat.1002129 – volume: 13 start-page: 1 year: 2017 ident: 650_CR133 publication-title: PLoS Genet. – volume: 98 start-page: 182 year: 2001 ident: 650_CR6 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.98.1.182 – volume: 95 start-page: 12619 year: 1998 ident: 650_CR7 publication-title: PNAS doi: 10.1073/pnas.95.21.12619 – volume: 480 start-page: 241 year: 2011 ident: 650_CR8 publication-title: Nature doi: 10.1038/nature10571 – volume: 8 start-page: 35 year: 2012 ident: 650_CR59 publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1002735 – volume: 216 start-page: 543 year: 2020 ident: 650_CR93 publication-title: Genetics doi: 10.1534/genetics.120.303401 – volume: 37 start-page: 336 year: 2013 ident: 650_CR25 publication-title: FEMS Microbiol. Rev. doi: 10.1111/j.1574-6976.2012.00353.x – volume: 5 start-page: 1899 year: 2007 ident: 650_CR60 publication-title: PLoS Biol. doi: 10.1371/journal.pbio.0050225 – year: 2008 ident: 650_CR130 publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1000304 – volume: 8 start-page: 1388 year: 2016 ident: 650_CR84 publication-title: Genome Biol. Evol. doi: 10.1093/gbe/evw077 – volume: 9 start-page: 1 year: 2018 ident: 650_CR17 publication-title: Front. Microbiol. doi: 10.3389/fmicb.2018.02980 – volume: 23 start-page: 598 year: 2015 ident: 650_CR55 publication-title: Trends Microbiol. doi: 10.1016/j.tim.2015.07.006 – volume: 37 start-page: 1372 year: 2005 ident: 650_CR118 publication-title: Nat. Genet. doi: 10.1038/ng1686 – volume: 154 start-page: 277 year: 2003 ident: 650_CR47 publication-title: Res. Microbiol. doi: 10.1016/S0923-2508(03)00071-8 – volume: 33 start-page: 456 year: 2016 ident: 650_CR64 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msv237 – volume: 44 start-page: 7109 year: 2016 ident: 650_CR50 publication-title: Nucleic Acids Res. – volume: 111 start-page: 12127 year: 2014 ident: 650_CR109 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.1405336111 – volume: 143 start-page: 1843 year: 1996 ident: 650_CR45 publication-title: Genetics doi: 10.1093/genetics/143.4.1843 – volume: 96 start-page: 1 year: 2020 ident: 650_CR22 publication-title: FEMS Microbiol. Ecol. – volume: 105 start-page: 15076 year: 2008 ident: 650_CR9 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.0807339105 – volume: 144 start-page: 590 year: 2011 ident: 650_CR21 publication-title: Cell doi: 10.1016/j.cell.2011.01.015 – volume: 21 start-page: 157 year: 1997 ident: 650_CR34 publication-title: FEMS Microbiol. Rev. doi: 10.1111/j.1574-6976.1997.tb00349.x – volume: 14 start-page: 1 year: 2016 ident: 650_CR41 publication-title: PLoS Biol. doi: 10.1371/journal.pbio.1002394 – year: 2013 ident: 650_CR87 publication-title: Trends Ecol. Evol. doi: 10.1016/j.tree.2013.08.003 – volume: 29 start-page: 3413 year: 2012 ident: 650_CR96 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/mss163 – year: 2020 ident: 650_CR29 publication-title: Nat. Rev. Microbiol. doi: 10.1038/s41579-019-0311-5 – volume: 1 start-page: 145 year: 2009 ident: 650_CR44 publication-title: Genome Biol. Evol. doi: 10.1093/gbe/evp016 – volume: 4 year: 2008 ident: 650_CR100 publication-title: PLoS Comput. Biol. – volume: 32 start-page: 1396 year: 2015 ident: 650_CR88 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msv009 – volume: 336 start-page: 48 year: 2012 ident: 650_CR68 publication-title: Science doi: 10.1126/science.1218198 – volume: 350 start-page: aac5992 year: 2015 ident: 650_CR116 publication-title: Science (80-.) doi: 10.1126/science.aac5992 – volume: 90 start-page: 4384 year: 1993 ident: 650_CR4 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.90.10.4384 – volume: 4 start-page: 1 year: 2015 ident: 650_CR18 publication-title: eLife doi: 10.7554/eLife.08490 – volume: 31 start-page: 1593 year: 2014 ident: 650_CR125 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msu082 – volume: 4 start-page: 443 year: 2012 ident: 650_CR97 publication-title: Genome Biol. Evol. doi: 10.1093/gbe/evs016 – volume: 30 start-page: 737 year: 2013 ident: 650_CR49 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/mss279 – volume: 11 start-page: 1719 year: 2017 ident: 650_CR11 publication-title: ISME J. doi: 10.1038/ismej.2017.36 – volume: 4 year: 2018 ident: 650_CR91 publication-title: Microb. Genomics doi: 10.1099/mgen.0.000184 – volume: 60 start-page: 327 year: 2006 ident: 650_CR111 publication-title: Annu.Rev.Microbiol. doi: 10.1146/annurev.micro.60.080805.142300 – volume: 169 start-page: 533 year: 2005 ident: 650_CR99 publication-title: Genetics doi: 10.1534/genetics.104.036939 – volume: 31 start-page: 1220 year: 2014 ident: 650_CR95 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msu076 – volume: 116 start-page: 10072 year: 2019 ident: 650_CR117 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.1900570116 – year: 2016 ident: 650_CR127 publication-title: Cold Spring Harb. Perspect. Biol. doi: 10.1007/978-94-007-2941-4_37 – volume: 73 start-page: 300 year: 2009 ident: 650_CR36 publication-title: Microbiol. Mol. Biol. Rev. doi: 10.1128/MMBR.00038-08 – volume: 152 start-page: 1459 year: 1999 ident: 650_CR86 publication-title: Genetics doi: 10.1093/genetics/152.4.1459 – volume: 116 start-page: 17906 year: 2019 ident: 650_CR3 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.1906958116 – volume: 113 start-page: 11399 year: 2016 ident: 650_CR104 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.1614083113 – ident: 650_CR131 – volume: 8 start-page: 1 year: 2017 ident: 650_CR38 publication-title: Nat. Commun. doi: 10.1038/s41467-017-00808-w – volume: 38 start-page: 865 year: 2014 ident: 650_CR30 publication-title: FEMS Microbiol. Rev. doi: 10.1111/1574-6976.12067 – volume: 11 year: 2020 ident: 650_CR23 publication-title: Nat. Commun. doi: 10.1038/s41467-020-16669-9 – volume: 208 start-page: 1247 year: 2018 ident: 650_CR58 publication-title: Genetics doi: 10.1534/genetics.117.300662 – volume: 21 start-page: 526 year: 2020 ident: 650_CR115 publication-title: Nat. Rev. Genet. doi: 10.1038/s41576-020-0244-x – volume: 207 start-page: 439 year: 2013 ident: 650_CR33 publication-title: J. Infect. Dis. doi: 10.1093/infdis/jis703 – volume: 14 start-page: 1 year: 2018 ident: 650_CR94 publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1007199 – volume: 11 start-page: 1 year: 2015 ident: 650_CR122 publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1004041 – year: 2020 ident: 650_CR72 publication-title: ISME J. doi: 10.1038/s41396-020-0655-x – volume: 11 start-page: 248 year: 2017 ident: 650_CR71 publication-title: ISME J. doi: 10.1038/ismej.2016.88 – volume: 47 start-page: e112 year: 2019 ident: 650_CR90 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkz656 – volume: 285 start-page: 1745 year: 1999 ident: 650_CR74 publication-title: Science doi: 10.1126/science.285.5434.1745 – volume: 14 year: 2018 ident: 650_CR10 publication-title: PLoS Computational Biol. doi: 10.1371/journal.pcbi.1006242 – volume: 2 start-page: 1005860 year: 2017 ident: 650_CR13 publication-title: Nat. Microbiol. doi: 10.1038/s41564-017-0066-6 – volume: 184 start-page: 1098 year: 2021 ident: 650_CR19 publication-title: Cell doi: 10.1016/j.cell.2021.01.029 – volume: 109 start-page: 4950 year: 2012 ident: 650_CR76 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.1119910109 – volume: 30 start-page: 1692 year: 2017 ident: 650_CR62 publication-title: J. Evol. Biol. doi: 10.1111/jeb.13132 – volume: 34 start-page: 1167 year: 2017 ident: 650_CR124 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msx066 – year: 2019 ident: 650_CR134 publication-title: Genome Biol. doi: 10.1101/227413 – volume: 94 start-page: 9763 year: 1997 ident: 650_CR31 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.94.18.9763 – volume: 464 start-page: 908 year: 2010 ident: 650_CR46 publication-title: Nature doi: 10.1038/nature08937 – volume: 158 start-page: 767 year: 2007 ident: 650_CR15 publication-title: Res. Microbiol. doi: 10.1016/j.resmic.2007.09.004 – volume: 40 start-page: 1 year: 2012 ident: 650_CR121 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkr928 – volume: 14 start-page: 627 year: 2004 ident: 650_CR52 publication-title: Curr. Opin. Genet. Dev. doi: 10.1016/j.gde.2004.09.003 – volume: 35 start-page: 32 year: 2003 ident: 650_CR51 publication-title: Nat. Genet. doi: 10.1038/ng1227 – volume: 27 start-page: 140 year: 2020 ident: 650_CR35 publication-title: Cell Host Microbe doi: 10.1016/j.chom.2019.10.022 – volume: 535 start-page: 435 year: 2016 ident: 650_CR113 publication-title: Nature doi: 10.1038/nature18927 – volume: 6 year: 2020 ident: 650_CR92 publication-title: Microb. Genomics doi: 10.1099/mgen.0.000338 – year: 2016 ident: 650_CR89 publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1006508 – volume: 45 start-page: 50 year: 2010 ident: 650_CR37 publication-title: Crit. Rev. Biochem. Mol. Biol. doi: 10.3109/10409230903505596 – ident: 650_CR123 doi: 10.1371/journal.pcbi.1004041 – volume: 18 start-page: 15 year: 2018 ident: 650_CR112 publication-title: BMC Evol. Biol. doi: 10.1186/s12862-018-1272-4 – volume: 301 start-page: 829 year: 2003 ident: 650_CR126 publication-title: Science doi: 10.1126/science.1086568 – volume: 5 start-page: 233 year: 2013 ident: 650_CR103 publication-title: Genome Biol. Evol. doi: 10.1093/gbe/evt002 – volume: 6 start-page: 1 year: 2006 ident: 650_CR28 publication-title: BMC Evol. Biol. doi: 10.1186/1471-2148-6-82 – volume: 13 start-page: 1 year: 2015 ident: 650_CR77 publication-title: BMC Biol. doi: 10.1186/s12915-015-0131-7 – volume: 17 start-page: 373 year: 2007 ident: 650_CR106 publication-title: Curr. Biol. doi: 10.1016/j.cub.2007.03.032 – year: 2018 ident: 650_CR53 publication-title: mBio doi: 10.1128/mBio.01033-18 – volume: 196 start-page: 253 year: 2014 ident: 650_CR119 publication-title: Genetics doi: 10.1534/genetics.113.157172 – volume: 94 start-page: 1 year: 2005 ident: 650_CR56 publication-title: Phys. Rev. Lett. – volume: 20 start-page: 1685 year: 2019 ident: 650_CR128 publication-title: Brief. Bioinform. doi: 10.1093/bib/bby042 – volume: 17 year: 2019 ident: 650_CR2 publication-title: PLoS Biol. doi: 10.1371/journal.pbio.3000102 – year: 2009 ident: 650_CR105 publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2526 – volume: 16 start-page: 199 year: 2019 ident: 650_CR120 publication-title: Nat. Methods doi: 10.1038/s41592-018-0293-7 – volume: 348 start-page: 1019 year: 2015 ident: 650_CR69 publication-title: Science doi: 10.1126/science.aaa4456 – volume: 16 start-page: 636 year: 2006 ident: 650_CR101 publication-title: Genome Res. doi: 10.1101/gr.4746406 – volume: 10 start-page: 1589 year: 2016 ident: 650_CR70 publication-title: ISME J. doi: 10.1038/ismej.2015.241 – year: 2017 ident: 650_CR14 publication-title: Nat. Microbiol. doi: 10.1038/s41564-017-0067-5 – year: 2017 ident: 650_CR83 publication-title: Microbiol. Spectr. doi: 10.1128/9781555819743.ch18 – volume: 218 start-page: 1925 year: 2015 ident: 650_CR114 publication-title: J. Exp. Biol. doi: 10.1242/jeb.114306 – volume: 7 start-page: 828 year: 2009 ident: 650_CR79 publication-title: Nat. Rev. Microbiol. doi: 10.1038/nrmicro2235 – volume: 12 start-page: 181 year: 2014 ident: 650_CR16 publication-title: Nat. Rev. Microbiol. doi: 10.1038/nrmicro3199 – volume: 182 start-page: 1016 year: 2000 ident: 650_CR32 publication-title: J. Bacteriol. doi: 10.1128/JB.182.4.1016-1023.2000 – year: 2019 ident: 650_CR63 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msz225 – volume: 12 start-page: 1 year: 2014 ident: 650_CR110 publication-title: BMC Med. doi: 10.1186/1741-7015-12-1 – volume: 283 start-page: 404 year: 1999 ident: 650_CR75 publication-title: Science doi: 10.1126/science.283.5400.404 – volume: 106 start-page: 19659 year: 2009 ident: 650_CR82 publication-title: Proc. Natl Acad. Sci. USA doi: 10.1073/pnas.0905137106 – year: 2020 ident: 650_CR81 publication-title: PLoS Biol. doi: 10.1101/568709 |
| SSID | ssj0025572 |
| Score | 2.734448 |
| SecondaryResourceType | review_article |
| Snippet | Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although... |
| SourceID | proquest pubmed crossref springer |
| SourceType | Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 206 |
| SubjectTerms | 631/158/855 631/326/41/2529 631/326/41/2530 631/326/41/2537 Algorithms Bacteria Bacteria - genetics Biomedical and Life Sciences Computational Biology Deoxyribonucleic acid DNA Evolution Evolution & development Evolution, Molecular Gene transfer Gene Transfer, Horizontal Genome, Bacterial - genetics Genomes Genomics Horizontal transfer Infectious Diseases Life Sciences Medical Microbiology Microbiology Parasitology Phylogeny Positive selection Review Article Signatures Virology |
| Title | Horizontal gene transfer and adaptive evolution in bacteria |
| URI | https://link.springer.com/article/10.1038/s41579-021-00650-4 https://www.ncbi.nlm.nih.gov/pubmed/34773098 https://www.proquest.com/docview/2640668193 https://www.proquest.com/docview/2597500540 |
| Volume | 20 |
| WOSCitedRecordID | wos000717903600001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVPQU databaseName: Nursing & Allied Health Database customDbUrl: eissn: 1740-1534 dateEnd: 20241212 omitProxy: false ssIdentifier: ssj0025572 issn: 1740-1526 databaseCode: 7RV dateStart: 20031001 isFulltext: true titleUrlDefault: https://search.proquest.com/nahs providerName: ProQuest |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV3da9swED_6NdjL1o9185YGFfq2itqWbUn0oaylIQ9tCKEreTOyJEOhOGmSFra_fidZSSllfenLIbBki7vz3U866Q7gSMWpNprltEo4o1lVGSpkXVBulJCZsKrwufRur_hgIMZjOQwbbvNwrHJpE72hNhPt9shP0HGjd0T_xc6mD9RVjXLR1VBCYx02Edkk7kjXdTpcLbjy3BdvQtAdU_RTRbg0EzNxMkfHxSV1BxQ8SqHZS8f0Cm2-ipR6B9T7_N6pb8OnAD3Jr1ZXdmDNNrvwoS1G-WcPTvs45u_E3Y4kqFWWLDymtTOiGkOUUVNnGYl9CspK7hpStbme1Rf43bu8uejTUFqBasbzBU2sW3jFFdOmTrQ2WZHVaS5ccr1M5ShWzbk2iGWYYaKQXNaMcaXjWmCzwHH7sNFMGvsNCBM8LYQsrK6Qz7JGSCF0pXDVbbGhVQTJkq-lDnnHXfmL-9LHv5koW1mUKIvSy6LMIvi5GjNts2682buz5HsZ_sB5-cz0CA5Xj_HfcQER1djJI_bB1VTuQWsEX1sxrz7HMo7GT4oIjpdyf375_-fy_e25_ICPqbs_4Y_-dGBjMXu0B7ClnxZ381kX1vno1tEx91QgFRdJFzbPLwfDUddrt6N8-A_gEPfn |
| linkProvider | ProQuest |
| linkToHtml | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1R3JbtQw9KkUEL2wdgkUMBKcwGomdrwIIYSAaqoOox4K6s04tiNVQpnpzLSofBTfyLOTTIUqeuuBW6TYzkvenrcBvLR54bxjJa0GklFeVZ4qXQsqvVWaq2BF6qX3bSTHY3V0pA9W4HdfCxPTKnuZmAS1n7j4j3wHFTdqR9Rf7P30hMapUTG62o_QaMliP5z_RJdt_m7vE-L3VVHsfj78OKTdVAHqmCwXdBCiz5FXzPl64JzngtdFqWJfOW5LfCMnpfNxCr1nSmipa8akdXmt8FLgPjz3BtzksbNYTBUsDpYOXlmmYVFo5OcU9aLoinRypnbmqCilpjEhIllFlP-tCC9Zt5cis0nh7d773z7VfbjbmdbkQ8sLD2AlNA_hdjts8_wRvB0ijL8msfqTINcEskg2e5gR23hivZ1GyU_CWceM5LghVdvL2q7D12uBfANWm0kTtoAwJQuhtAiuQrzqGk0m5SordB7wwtkMBj0ejev6qsfxHj9Miu8zZVrcG8S9Sbg3PIPXyz3TtqvIlau3ezybTsLMzQWSM3ixvI2yIQZ8bBMmp7gGvcUyGeUZbLZktXwc4xKFu1YZvOnp7OLwf8Py-GpYnsOd4eGXkRntjfefwFoRa0VSmtM2rC5mp-Ep3HJni-P57FniHALfr5v-_gApG04X |
| linkToPdf | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1R3batRA9FC3Kr54t8ZWHUGf7LDZTDIXShG1XVpalkVU-jZOZiZQKNl1d1upn-bX9cwk2SLFvvXBt0BmJic595wbwFuTZtZZVtByIBjNy9JRqSpOhTNS5dIbHnvpfT8Uo5E8OlLjFfjT1cKEtMpOJkZB7SY2_CPvo-JG7Yj6i_WrNi1ivDP8MP1JwwSpEGntxmk0JHLgz3-h-zbf3t9BXL_LsuHu1897tJ0wQC0TxYIOfPA_0pJZVw2sdTnPq6yQocdcbgp8OyuEdWEivWOSK6EqxoSxaSXxkuM-PPcWrAo0MvIerH7aHY2_LN29ooijo9DkTylqSd6W7KRM9ueoNoWiIT0i2kg0_1stXrF1r8Rpo_obPvifP9xDuN8a3eRjwyWPYMXXj-FOM4bz_Als7SGMvyehLpQgP3myiNa8nxFTO2KcmQadQPxZy6bkuCZl0-XaPIVvNwL5M-jVk9o_B8KkyLhU3NsScawqNKakLQ1XqccLaxIYdDjVtu24HgZ_nOgY-WdSN3SgkQ50pAOdJ_B-uWfa9Bu5dvVGh3Pdyp65vkR4Am-Wt1FqhFCQqf3kFNegH1lEcz2BtYbElo9juUCxr2QCmx3NXR7-b1heXA_La7iLZKcP90cH63AvC0UkMf9pA3qL2al_Cbft2eJ4PnvVshGBHzdNgBc58Vgx |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Horizontal+gene+transfer+and+adaptive+evolution+in+bacteria&rft.jtitle=Nature+reviews.+Microbiology&rft.au=Arnold%2C+Brian+J&rft.au=I-Ting%2C+Huang&rft.au=Hanage%2C+William+P&rft.date=2022-04-01&rft.pub=Nature+Publishing+Group&rft.issn=1740-1526&rft.eissn=1740-1534&rft.volume=20&rft.issue=4&rft.spage=206&rft.epage=218&rft_id=info:doi/10.1038%2Fs41579-021-00650-4&rft.externalDBID=HAS_PDF_LINK |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1740-1526&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1740-1526&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1740-1526&client=summon |