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For: Philippe H, Douady CJ. Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 2003;6:498-505. [PMID: 14572543 DOI: 10.1016/j.mib.2003.09.008] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Number Cited by Other Article(s)
1
Liu F, Cai Z, Kang W, Chen W, Lu Y, Chen M, Zhao R. A New Method for Constructing High-Resolution Phylogenomic Topologies Using Core Gene-Associated MNP Markers: A Case Study From Agaricus bisporus. Microb Biotechnol 2025;18:e70070. [PMID: 39976373 PMCID: PMC11840843 DOI: 10.1111/1751-7915.70070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2024] [Accepted: 12/10/2024] [Indexed: 02/21/2025]  Open
2
da Silva TF, Glória RDA, Americo MF, Freitas ADS, de Jesus LCL, Barroso FAL, Laguna JG, Coelho-Rocha ND, Tavares LM, le Loir Y, Jan G, Guédon É, Azevedo VADC. Unlocking the Potential of Probiotics: A Comprehensive Review on Research, Production, and Regulation of Probiotics. Probiotics Antimicrob Proteins 2024;16:1687-1723. [PMID: 38539008 DOI: 10.1007/s12602-024-10247-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2024] [Indexed: 10/02/2024]
3
Wang Y, Wu X, Chen Y, Xu C, Wang Y, Wang Q. Phylogenomic analyses revealed widely occurring hybridization events across Elsholtzieae (Lamiaceae). Mol Phylogenet Evol 2024;198:108112. [PMID: 38806075 DOI: 10.1016/j.ympev.2024.108112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/14/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
4
Caetano DS, Quental TB. How Important Is Budding Speciation for Comparative Studies? Syst Biol 2023;72:1443-1453. [PMID: 37586404 DOI: 10.1093/sysbio/syad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/26/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]  Open
5
Farrell AA, Nesbø CL, Zhaxybayeva O. Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales. Genome Biol Evol 2023;15:evad156. [PMID: 37616556 PMCID: PMC10476701 DOI: 10.1093/gbe/evad156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]  Open
6
Fleming JF, Valero‐Gracia A, Struck TH. Identifying and addressing methodological incongruence in phylogenomics: A review. Evol Appl 2023;16:1087-1104. [PMID: 37360032 PMCID: PMC10286231 DOI: 10.1111/eva.13565] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/07/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]  Open
7
Santos RGD, Hurtado R, Rodrigues DLN, Lima A, Dos Anjos WF, Rifici C, Attili AR, Tiwari S, Jaiswal AK, Spier SJ, Mazzullo G, Morais-Rodrigues F, Gomide ACP, de Jesus LCL, Aburjaile FF, Brenig B, Cuteri V, Castro TLDP, Seyffert N, Santos A, Góes-Neto A, de Jesus Sousa T, Azevedo V. Comparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation. Res Microbiol 2023;174:103998. [PMID: 36375718 DOI: 10.1016/j.resmic.2022.103998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
8
Advances in Novel Animal Vitamin C Biosynthesis Pathways and the Role of Prokaryote-Based Inferences to Understand Their Origin. Genes (Basel) 2022;13:genes13101917. [PMID: 36292802 PMCID: PMC9602106 DOI: 10.3390/genes13101917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/04/2022]  Open
9
Dang C, Walkup JGV, Hungate BA, Franklin RB, Schwartz E, Morrissey EM. Phylogenetic organization in the assimilation of chemically distinct substrates by soil bacteria. Environ Microbiol 2021;24:357-369. [PMID: 34811865 DOI: 10.1111/1462-2920.15843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022]
10
Floridia-Yapur N, Rusman F, Diosque P, Tomasini N. Genome data vs MLST for exploring intraspecific evolutionary history in bacteria: Much is not always better. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021;93:104990. [PMID: 34224899 DOI: 10.1016/j.meegid.2021.104990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
11
Robertson J, Bessonov K, Schonfeld J, Nash JHE. Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance. Microb Genom 2021;6. [PMID: 32969786 PMCID: PMC7660255 DOI: 10.1099/mgen.0.000435] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
12
Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut. Microorganisms 2020;9:microorganisms9010008. [PMID: 33375064 PMCID: PMC7822027 DOI: 10.3390/microorganisms9010008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022]  Open
13
Fang H, Xu JB, Nie Y, Wu XL. Pan-genomic analysis reveals that the evolution of Dietzia species depends on their living habitats. Environ Microbiol 2020;23:861-877. [PMID: 32715552 DOI: 10.1111/1462-2920.15176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022]
14
The complex phylogenetic relationships of a 4mC/6mA DNA methyltransferase in prokaryotes. Mol Phylogenet Evol 2020;149:106837. [PMID: 32304827 DOI: 10.1016/j.ympev.2020.106837] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 01/30/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023]
15
Saroj DB, Gupta AK. Genome based safety assessment for Bacillus coagulans strain LBSC (DSM 17654) for probiotic application. Int J Food Microbiol 2020;318:108523. [DOI: 10.1016/j.ijfoodmicro.2020.108523] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 10/30/2019] [Accepted: 01/12/2020] [Indexed: 01/12/2023]
16
Srivastava A, Mohan S, Mauchline TH, Davies KG. Evidence for diversifying selection of genetic regions of encoding putative collagen-like host-adhesive fibers in Pasteuria penetrans. FEMS Microbiol Ecol 2019;95:5149496. [PMID: 30380051 PMCID: PMC6238073 DOI: 10.1093/femsec/fiy217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/29/2018] [Indexed: 11/16/2022]  Open
17
Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage. Appl Environ Microbiol 2019;85:AEM.00988-19. [PMID: 31126947 DOI: 10.1128/aem.00988-19] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/19/2019] [Indexed: 01/01/2023]  Open
18
Rossoni AW, Price DC, Seger M, Lyska D, Lammers P, Bhattacharya D, Weber APM. The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. eLife 2019;8:e45017. [PMID: 31149898 PMCID: PMC6629376 DOI: 10.7554/elife.45017] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023]  Open
19
Jeong H, Arif B, Caetano-Anollés G, Kim KM, Nasir A. Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation. Sci Rep 2019;9:5953. [PMID: 30976019 PMCID: PMC6459891 DOI: 10.1038/s41598-019-42227-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 03/27/2019] [Indexed: 12/21/2022]  Open
20
Bao H, Zhao JH, Zhu S, Wang S, Zhang J, Wang XY, Hua B, Liu C, Liu H, Liu SL. Genetic diversity and evolutionary features of type VI secretion systems in Salmonella. Future Microbiol 2019;14:139-154. [PMID: 30672329 DOI: 10.2217/fmb-2018-0260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
21
Beilsmith K, Thoen MPM, Brachi B, Gloss AD, Khan MH, Bergelson J. Genome-wide association studies on the phyllosphere microbiome: Embracing complexity in host-microbe interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019;97:164-181. [PMID: 30466152 DOI: 10.1111/tpj.14170] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/08/2018] [Accepted: 11/16/2018] [Indexed: 05/18/2023]
22
Liu C, Wright B, Allen-Vercoe E, Gu H, Beiko R. Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions. Genome Biol Evol 2018;10:2255-2265. [PMID: 30137329 PMCID: PMC6130602 DOI: 10.1093/gbe/evy178] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2018] [Indexed: 11/20/2022]  Open
23
Hassan Y, Zhou T. Addressing the mycotoxin deoxynivalenol contamination with soil-derived bacterial and enzymatic transformations targeting the C3 carbon. WORLD MYCOTOXIN J 2018. [DOI: 10.3920/wmj2017.2259] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
24
Zakharenko LP, Ivannikov AV, Ignatenko OM, Zakharov IK. Search for Canonical P Element in Genomes of Drosophilinae Subfamily Species. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
25
Zhao Q, Yue S, Bilal M, Hu H, Wang W, Zhang X. Comparative genomic analysis of 26 Sphingomonas and Sphingobium strains: Dissemination of bioremediation capabilities, biodegradation potential and horizontal gene transfer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017;609:1238-1247. [PMID: 28787798 DOI: 10.1016/j.scitotenv.2017.07.249] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 05/12/2023]
26
The complex resistomes of Paenibacillaceae reflect diverse antibiotic chemical ecologies. ISME JOURNAL 2017;12:885-897. [PMID: 29259290 DOI: 10.1038/s41396-017-0017-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/17/2017] [Accepted: 11/05/2017] [Indexed: 12/31/2022]
27
Functional horizontal gene transfer from bacteria to eukaryotes. Nat Rev Microbiol 2017;16:67-79. [DOI: 10.1038/nrmicro.2017.137] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
28
Malik SS, Azem-E-Zahra S, Kim KM, Caetano-Anollés G, Nasir A. Do Viruses Exchange Genes across Superkingdoms of Life? Front Microbiol 2017;8:2110. [PMID: 29163404 PMCID: PMC5671483 DOI: 10.3389/fmicb.2017.02110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/16/2017] [Indexed: 12/13/2022]  Open
29
Déraspe M, Raymond F, Boisvert S, Culley A, Roy PH, Laviolette F, Corbeil J. Phenetic Comparison of Prokaryotic Genomes Using k-mers. Mol Biol Evol 2017;34:2716-2729. [PMID: 28957508 PMCID: PMC5850840 DOI: 10.1093/molbev/msx200] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
30
Venter SN, Palmer M, Beukes CW, Chan WY, Shin G, van Zyl E, Seale T, Coutinho TA, Steenkamp ET. Practically delineating bacterial species with genealogical concordance. Antonie van Leeuwenhoek 2017;110:1311-1325. [DOI: 10.1007/s10482-017-0869-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/30/2017] [Indexed: 10/19/2022]
31
Bacterial Communities and Antibiotic Resistance Communities in a Full-Scale Hospital Wastewater Treatment Plant by High-Throughput Pyrosequencing. WATER 2016. [DOI: 10.3390/w8120580] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
32
Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine. Appl Environ Microbiol 2016;82:7019-7029. [PMID: 27663031 DOI: 10.1128/aem.02190-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/12/2016] [Indexed: 11/20/2022]  Open
33
Yin H, Wang G, Ma L, Yi SV, Zhang Z. What Signatures Dominantly Associate with Gene Age? Genome Biol Evol 2016;8:3083-3089. [PMID: 27609935 PMCID: PMC5174733 DOI: 10.1093/gbe/evw216] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
34
Sojo V, Dessimoz C, Pomiankowski A, Lane N. Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life. Mol Biol Evol 2016;33:2874-2884. [PMID: 27501943 PMCID: PMC5062322 DOI: 10.1093/molbev/msw164] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
35
Gupta RS. Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification. FEMS Microbiol Rev 2016;40:520-53. [PMID: 27279642 DOI: 10.1093/femsre/fuw011] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2016] [Indexed: 12/24/2022]  Open
36
Gouy R, Baurain D, Philippe H. Rooting the tree of life: the phylogenetic jury is still out. Philos Trans R Soc Lond B Biol Sci 2016;370:20140329. [PMID: 26323760 DOI: 10.1098/rstb.2014.0329] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
37
Zhang Y, Zhuang Y, Geng J, Ren H, Xu K, Ding L. Reduction of antibiotic resistance genes in municipal wastewater effluent by advanced oxidation processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016;550:184-191. [PMID: 26815295 DOI: 10.1016/j.scitotenv.2016.01.078] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 05/22/2023]
38
Eckshtain-Levi N, Shkedy D, Gershovits M, Da Silva GM, Tamir-Ariel D, Walcott R, Pupko T, Burdman S. Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits. Front Microbiol 2016;7:430. [PMID: 27092114 PMCID: PMC4821854 DOI: 10.3389/fmicb.2016.00430] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/17/2016] [Indexed: 11/13/2022]  Open
39
Khayi S, Blin P, Pédron J, Chong TM, Chan KG, Moumni M, Hélias V, Van Gijsegem F, Faure D. Population genomics reveals additive and replacing horizontal gene transfers in the emerging pathogen Dickeya solani. BMC Genomics 2015;16:788. [PMID: 26467299 PMCID: PMC4607151 DOI: 10.1186/s12864-015-1997-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/03/2015] [Indexed: 11/17/2022]  Open
40
Zakharevich NV, Averina OV, Klimina KM, Kudryavtseva AV, Kasianov AS, Makeev VJ, Danilenko VN. Complete Genome Sequence of Bifidobacterium longum GT15: Identification and Characterization of Unique and Global Regulatory Genes. MICROBIAL ECOLOGY 2015;70:819-834. [PMID: 25894918 DOI: 10.1007/s00248-015-0603-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
41
Doyle VP, Young RE, Naylor GJP, Brown JM. Can We Identify Genes with Increased Phylogenetic Reliability? Syst Biol 2015;64:824-37. [DOI: 10.1093/sysbio/syv041] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/09/2015] [Indexed: 12/19/2022]  Open
42
Spring S, Scheuner C, Göker M, Klenk HP. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 2015;6:281. [PMID: 25914684 PMCID: PMC4391266 DOI: 10.3389/fmicb.2015.00281] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/21/2015] [Indexed: 11/13/2022]  Open
43
Timilsina S, Jibrin MO, Potnis N, Minsavage GV, Kebede M, Schwartz A, Bart R, Staskawicz B, Boyer C, Vallad GE, Pruvost O, Jones JB, Goss EM. Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of Xanthomonas gardneri. Appl Environ Microbiol 2015;81:1520-9. [PMID: 25527544 PMCID: PMC4309686 DOI: 10.1128/aem.03000-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/14/2014] [Indexed: 01/29/2023]  Open
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Yang Y, Li B, Zou S, Fang HHP, Zhang T. Fate of antibiotic resistance genes in sewage treatment plant revealed by metagenomic approach. WATER RESEARCH 2014;62:97-106. [PMID: 24937359 DOI: 10.1016/j.watres.2014.05.019] [Citation(s) in RCA: 314] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 05/08/2023]
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Use of genome sequencing to assess nucleotide structure variation of Staphylococcus aureus strains cultured in spaceflight on Shenzhou-X, under simulated microgravity and on the ground. Microbiol Res 2014;170:61-8. [PMID: 25304992 DOI: 10.1016/j.micres.2014.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/31/2014] [Accepted: 09/02/2014] [Indexed: 01/10/2023]
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Lux TM, Lee R, Love J. Genome-wide phylogenetic analysis of the pathogenic potential of Vibrio furnissii. Front Microbiol 2014;5:435. [PMID: 25191313 PMCID: PMC4139957 DOI: 10.3389/fmicb.2014.00435] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/31/2014] [Indexed: 11/15/2022]  Open
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Steppe M, Van Nieuwerburgh F, Vercauteren G, Boyen F, Eeckhaut V, Deforce D, Haesebrouck F, Ducatelle R, Van Immerseel F. Safety assessment of the butyrate-producing Butyricicoccus pullicaecorum strain 25-3(T), a potential probiotic for patients with inflammatory bowel disease, based on oral toxicity tests and whole genome sequencing. Food Chem Toxicol 2014;72:129-37. [PMID: 25007784 DOI: 10.1016/j.fct.2014.06.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 06/18/2014] [Accepted: 06/26/2014] [Indexed: 02/09/2023]
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Zhang M, Pereira e Silva MDC, Chaib De Mares M, van Elsas JD. The mycosphere constitutes an arena for horizontal gene transfer with strong evolutionary implications for bacterial-fungal interactions. FEMS Microbiol Ecol 2014;89:516-26. [DOI: 10.1111/1574-6941.12350] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/24/2014] [Accepted: 04/25/2014] [Indexed: 11/29/2022]  Open
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Dröge J, Buczek D, Suzuki Y, Makałowski W. Amoebozoa possess lineage-specific globin gene repertoires gained by individual horizontal gene transfers. Int J Biol Sci 2014;10:689-701. [PMID: 25013378 PMCID: PMC4081604 DOI: 10.7150/ijbs.8327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/24/2014] [Indexed: 12/13/2022]  Open
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Som A. Causes, consequences and solutions of phylogenetic incongruence. Brief Bioinform 2014;16:536-48. [PMID: 24872401 DOI: 10.1093/bib/bbu015] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/05/2014] [Indexed: 11/14/2022]  Open
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