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For: Gupta RS. Identification of Conserved Indels that are Useful for Classification and Evolutionary Studies. J Microbiol Methods 2014. [DOI: 10.1016/bs.mim.2014.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Number Cited by Other Article(s)
1
Rudra B, Gupta RS. Molecular Markers Specific for the Pseudomonadaceae Genera Provide Novel and Reliable Means for the Identification of Other Pseudomonas Strains/spp. Related to These Genera. Genes (Basel) 2025;16:183. [PMID: 40004512 PMCID: PMC11855360 DOI: 10.3390/genes16020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 01/28/2025] [Accepted: 01/31/2025] [Indexed: 02/27/2025]  Open
2
Patel I, Bello S, Gupta RS. Phylogenomic and molecular marker based studies to clarify the evolutionary relationships amongst Anoxybacillus species and demarcation of the family Anoxybacillaceae and some of its constituent genera. Int J Syst Evol Microbiol 2024;74:006528. [PMID: 39287972 PMCID: PMC11407518 DOI: 10.1099/ijsem.0.006528] [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: 06/18/2024] [Accepted: 09/06/2024] [Indexed: 09/19/2024]  Open
3
Montecillo JAV. Genomics of the Thermophilic Bacterium Thermosulfidibacter takaii Reveals Novel Lineage of Deep-Branching Bacterial Phylum. Indian J Microbiol 2024;64:762-772. [PMID: 39011009 PMCID: PMC11246332 DOI: 10.1007/s12088-024-01214-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/21/2024] [Indexed: 07/17/2024]  Open
4
Malhotra M, Bello S, Gupta RS. Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus. Syst Appl Microbiol 2024;47:126499. [PMID: 38428338 DOI: 10.1016/j.syapm.2024.126499] [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: 09/19/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
5
Montecillo JAV, Billacura MP, Billacura MDG. Reclassification of Aestuariicella albida as Pseudomaricurvus albidus comb. nov. and Aestuariicella hydrocarbonica as Pseudomaricurvus hydrocarbonicus comb. nov. Based on Comparative Genomics and Molecular Synapomorphies. Curr Microbiol 2024;81:159. [PMID: 38689166 DOI: 10.1007/s00284-024-03683-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/30/2024] [Indexed: 05/02/2024]
6
Bello S, McQuay S, Rudra B, Gupta RS. Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers. Int J Syst Evol Microbiol 2024;74. [PMID: 38319314 DOI: 10.1099/ijsem.0.006247] [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] [Indexed: 02/07/2024]  Open
7
Rudra B, Gupta RS. Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera. Front Microbiol 2024;14:1273665. [PMID: 38249459 PMCID: PMC10797017 DOI: 10.3389/fmicb.2023.1273665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/17/2023] [Indexed: 01/23/2024]  Open
8
Bello S, Mudassir SH, Rudra B, Gupta RS. Phylogenomic and molecular markers based studies on Staphylococcaceae and Gemella species. Proposals for an emended family Staphylococcaceae and three new families (Abyssicoccaceae fam. nov., Salinicoccaceae fam. nov. and Gemellaceae fam. nov.) harboring four new genera, Lacicoccus gen. nov., Macrococcoides gen. nov., Gemelliphila gen. nov., and Phocicoccus gen. nov. Antonie Van Leeuwenhoek 2023;116:937-973. [PMID: 37523090 DOI: 10.1007/s10482-023-01857-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023]
9
Montecillo JAV. Phylogenomics and molecular marker-based analyses of the order Nevskiales: Proposal for the creation of Steroidobacterales ord. nov. and Peristeroidobacter gen. nov. Res Microbiol 2023:104057. [PMID: 37037310 DOI: 10.1016/j.resmic.2023.104057] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 04/12/2023]
10
Montecillo JAV. Phylogenomics and comparative genomic analyses support the creation of the novel family Ignatzschineriaceae fam. nov. comprising the genera Ignatzschineria and Wohlfahrtiimonas within the order Cardiobacteriales. Res Microbiol 2023;174:103988. [PMID: 35973557 DOI: 10.1016/j.resmic.2022.103988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/08/2022] [Accepted: 08/05/2022] [Indexed: 01/11/2023]
11
Montecillo JAV, Bae H. Reclassification of Brevibacterium frigoritolerans as Peribacillus frigoritolerans comb. nov. based on phylogenomics and multiple molecular synapomorphies. Int J Syst Evol Microbiol 2022;72. [DOI: 10.1099/ijsem.0.005389] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
12
Gupta RS, Suggett C. Conserved Signatures in Protein Sequences Reliably Demarcate Different Clades of Rodents/Glires Species and Consolidate Their Evolutionary Relationships. Genes (Basel) 2022;13:genes13020288. [PMID: 35205335 PMCID: PMC8871558 DOI: 10.3390/genes13020288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 01/18/2023]  Open
13
Khadka B, Gupta RS. Conserved molecular signatures in the spike protein provide evidence indicating the origin of SARS-CoV-2 and a Pangolin-CoV (MP789) by recombination(s) between specific lineages of Sarbecoviruses. PeerJ 2021;9:e12434. [PMID: 35028194 PMCID: PMC8592051 DOI: 10.7717/peerj.12434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/14/2021] [Indexed: 01/01/2023]  Open
14
Joshi A, Thite S, Karodi P, Joseph N, Lodha T. Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera. Front Microbiol 2021;12:722369. [PMID: 34707580 PMCID: PMC8543038 DOI: 10.3389/fmicb.2021.722369] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022]  Open
15
Chen S, Rudra B, Gupta RS. Phylogenomics and molecular signatures support division of the order Neisseriales into emended families Neisseriaceae and Chromobacteriaceae and three new families Aquaspirillaceae fam. nov., Chitinibacteraceae fam. nov., and Leeiaceae fam. nov. Syst Appl Microbiol 2021;44:126251. [PMID: 34600238 DOI: 10.1016/j.syapm.2021.126251] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/22/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
16
Rudra B, Gupta RS. Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera. Int J Syst Evol Microbiol 2021;71. [PMID: 34546867 DOI: 10.1099/ijsem.0.005011] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
17
Saini N, Gupta RS. A robust phylogenetic framework for members of the order Legionellales and its main genera (Legionella, Aquicella, Coxiella and Rickettsiella) based on phylogenomic analyses and identification of molecular markers demarcating different clades. Antonie van Leeuwenhoek 2021;114:957-982. [PMID: 33881638 DOI: 10.1007/s10482-021-01569-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/01/2021] [Indexed: 12/29/2022]
18
Cutiño-Jiménez AM, Menck CFM, Cambas YT, Díaz-Pérez JC. Protein signatures to identify the different genera within the Xanthomonadaceae family. Braz J Microbiol 2020;51:1515-1526. [PMID: 32488841 DOI: 10.1007/s42770-020-00304-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/18/2020] [Indexed: 11/26/2022]  Open
19
Gupta RS, Patel S. Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures. Front Microbiol 2020;10:2821. [PMID: 32010063 PMCID: PMC6971209 DOI: 10.3389/fmicb.2019.02821] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022]  Open
20
Pot B, Salvetti E, Mattarelli P, Felis GE. The potential impact of the Lactobacillus name change: The results of an expert meeting organised by the Lactic Acid Bacteria Industrial Platform (LABIP). Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
21
Khadka B, Chatterjee T, Gupta BP, Gupta RS. Genomic Analyses Identify Novel Molecular Signatures Specific for the Caenorhabditis and other Nematode Taxa Providing Novel Means for Genetic and Biochemical Studies. Genes (Basel) 2019;10:E739. [PMID: 31554175 PMCID: PMC6826867 DOI: 10.3390/genes10100739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/06/2019] [Accepted: 09/17/2019] [Indexed: 11/20/2022]  Open
22
Hu D, Zang Y, Mao Y, Gao B. Identification of Molecular Markers That Are Specific to the Class Thermoleophilia. Front Microbiol 2019;10:1185. [PMID: 31178855 PMCID: PMC6544083 DOI: 10.3389/fmicb.2019.01185] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/09/2019] [Indexed: 12/26/2022]  Open
23
Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures. INFECTION GENETICS AND EVOLUTION 2018;66:130-151. [DOI: 10.1016/j.meegid.2018.09.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/12/2018] [Accepted: 09/19/2018] [Indexed: 11/21/2022]
24
A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera. Antonie van Leeuwenhoek 2018;112:561-588. [PMID: 30392177 DOI: 10.1007/s10482-018-1188-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/14/2018] [Indexed: 01/01/2023]
25
Hu D, Cha G, Gao B. A Phylogenomic and Molecular Markers Based Analysis of the Class Acidimicrobiia. Front Microbiol 2018;9:987. [PMID: 29867887 PMCID: PMC5962788 DOI: 10.3389/fmicb.2018.00987] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/27/2018] [Indexed: 01/22/2023]  Open
26
Gupta RS, Sawnani S, Adeolu M, Alnajar S, Oren A. Phylogenetic framework for the phylum Tenericutes based on genome sequence data: proposal for the creation of a new order Mycoplasmoidales ord. nov., containing two new families Mycoplasmoidaceae fam. nov. and Metamycoplasmataceae fam. nov. harbouring Eperythrozoon, Ureaplasma and five novel genera. Antonie van Leeuwenhoek 2018;111:1583-1630. [PMID: 29556819 DOI: 10.1007/s10482-018-1047-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/08/2018] [Indexed: 12/19/2022]
27
Gupta RS, Lo B, Son J. Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera. Front Microbiol 2018;9:67. [PMID: 29497402 PMCID: PMC5819568 DOI: 10.3389/fmicb.2018.00067] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023]  Open
28
Alnajar S, Khadka B, Gupta RS. Ribonucleotide Reductases from Bifidobacteria Contain Multiple Conserved Indels Distinguishing Them from All Other Organisms: In Silico Analysis of the Possible Role of a 43 aa Bifidobacteria-Specific Insert in the Class III RNR Homolog. Front Microbiol 2017;8:1409. [PMID: 28824557 PMCID: PMC5535262 DOI: 10.3389/fmicb.2017.01409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/11/2017] [Indexed: 01/05/2023]  Open
29
Ho J, Adeolu M, Khadka B, Gupta RS. Identification of distinctive molecular traits that are characteristic of the phylum "Deinococcus-Thermus" and distinguish its main constituent groups. Syst Appl Microbiol 2016;39:453-463. [PMID: 27506333 DOI: 10.1016/j.syapm.2016.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/14/2016] [Accepted: 07/21/2016] [Indexed: 12/30/2022]
30
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
31
Campbell C, Adeolu M, Gupta RS. Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov. Int J Syst Evol Microbiol 2015;65:3203-3215. [PMID: 25999592 DOI: 10.1099/ijs.0.000347] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
32
Phylogenomic and molecular demarcation of the core members of the polyphyletic pasteurellaceae genera actinobacillus, haemophilus, and pasteurella. Int J Genomics 2015;2015:198560. [PMID: 25821780 PMCID: PMC4363679 DOI: 10.1155/2015/198560] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/19/2015] [Accepted: 01/26/2015] [Indexed: 12/18/2022]  Open
33
Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE, Gupta RS. A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie van Leeuwenhoek 2014;107:467-85. [DOI: 10.1007/s10482-014-0344-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/28/2014] [Indexed: 01/10/2023]
34
Gupta RS, Naushad S, Baker S. Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov. Int J Syst Evol Microbiol 2014;65:1050-1069. [PMID: 25428416 DOI: 10.1099/ijs.0.070136-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
35
Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades. Anaerobe 2014;28:182-98. [PMID: 24969840 DOI: 10.1016/j.anaerobe.2014.06.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/10/2014] [Accepted: 06/12/2014] [Indexed: 02/05/2023]
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