• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4619882)   Today's Articles (59)   Subscriber (49404)
For: Winand R, Bogaerts B, Hoffman S, Lefevre L, Delvoye M, Van Braekel J, Fu Q, Roosens NHC, De Keersmaecker SCJ, Vanneste K. TARGETING THE 16S RRNA GENE FOR BACTERIAL IDENTIFICATION IN COMPLEX MIXED SAMPLES: COMPARATIVE EVALUATION OF SECOND (ILLUMINA) AND THIRD (OXFORD NANOPORE TECHNOLOGIES) GENERATION SEQUENCING TECHNOLOGIES. Int J Mol Sci 2019;21:ijms21010298. [PMID: 31906254 PMCID: PMC6982111 DOI: 10.3390/ijms21010298] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Hilliam Y, Armbruster CR, Rapsinski GJ, Marshall CW, Moore J, Koirala J, Krainz L, Gaston JR, Cooper VS, Lee SE, Bomberger JM. Cystic fibrosis pathogens persist in the upper respiratory tract following initiation of elexacaftor/tezacaftor/ivacaftor therapy. Microbiol Spectr 2024;12:e0078724. [PMID: 38916354 PMCID: PMC11302335 DOI: 10.1128/spectrum.00787-24] [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: 03/26/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024]  Open
2
Silva VF, Mouriño JLP, Martins ML, Carvalho PLPF, Rodrigues ED, Gatlin DM, Griffin MJ, Older CE, Yamamoto FY. Dietary supplementation of mineral nanoparticles for channel catfish (Ictalurus punctatus). FISH PHYSIOLOGY AND BIOCHEMISTRY 2024:10.1007/s10695-024-01378-7. [PMID: 39066863 DOI: 10.1007/s10695-024-01378-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/12/2024] [Indexed: 07/30/2024]
3
Widén J, Morén J, Mölling P, Fagerström A, Enblad P, Eriksson BM, Ronne-Engström E, Sundqvist M, Westman G. Diagnosis of external ventricular drainage related infections with real-time 16S PCR and third-generation 16S sequencing. Infect Dis (Lond) 2024;56:521-530. [PMID: 38530119 DOI: 10.1080/23744235.2024.2331260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/11/2024] [Indexed: 03/27/2024]  Open
4
Santamarina-García G, Amores G, Llamazares D, Hernández I, Javier R Barron L, Virto M. Phenotypic and genotypic characterization of antimicrobial resistances reveals the effect of the production chain in reducing resistant lactic acid bacteria in an artisanal raw ewe milk PDO cheese. Food Res Int 2024;187:114308. [PMID: 38763625 DOI: 10.1016/j.foodres.2024.114308] [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: 01/17/2024] [Revised: 03/27/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024]
5
Ota Y, Yasunaga K, Mahazu S, Prah I, Nagai S, Hayashi T, Suzuki M, Yoshida M, Hoshino Y, Akeda Y, Suzuki T, Gu Y, Saito R. Comparative evaluation of analytical pipelines for illumina short- and nanopore long-read 16S rRNA gene amplicon sequencing with mock microbial communities. J Microbiol Methods 2024;221:106929. [PMID: 38599390 DOI: 10.1016/j.mimet.2024.106929] [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: 12/26/2023] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 04/12/2024]
6
Cenzato D, Lipták Z. A survey of BWT variants for string collections. BIOINFORMATICS (OXFORD, ENGLAND) 2024;40:btae333. [PMID: 38788221 DOI: 10.1093/bioinformatics/btae333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/13/2024] [Accepted: 05/23/2024] [Indexed: 05/26/2024]
7
Scarano C, Veneruso I, De Simone RR, Di Bonito G, Secondino A, D’Argenio V. The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences. Biomolecules 2024;14:568. [PMID: 38785975 PMCID: PMC11117673 DOI: 10.3390/biom14050568] [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: 04/08/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]  Open
8
Yeo K, Connell J, Bouras G, Smith E, Murphy W, Hodge JC, Krishnan S, Wormald PJ, Valentine R, Psaltis AJ, Vreugde S, Fenix KA. A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues. Arch Microbiol 2024;206:248. [PMID: 38713383 PMCID: PMC11076400 DOI: 10.1007/s00203-024-03985-7] [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: 03/13/2024] [Accepted: 04/28/2024] [Indexed: 05/08/2024]
9
Traylor A, Lee PW, Hsieh K, Wang TH. Improving bacteria identification from digital melt assay via oligonucleotide-based temperature calibration. Anal Chim Acta 2024;1297:342371. [PMID: 38438240 PMCID: PMC11082877 DOI: 10.1016/j.aca.2024.342371] [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: 11/10/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 03/06/2024]
10
Ly YT, Leuko S, Moeller R. An overview of the bacterial microbiome of public transportation systems-risks, detection, and countermeasures. Front Public Health 2024;12:1367324. [PMID: 38528857 PMCID: PMC10961368 DOI: 10.3389/fpubh.2024.1367324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024]  Open
11
He B, Shan T, Xu J, Zhong X, Zhang J, Han R, Yang Q, Wu J. Full-length transcriptome profiling of Acanthopanax gracilistylus provides new insight into the kaurenoic acid biosynthesis pathway. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024;30:383-399. [PMID: 38633273 PMCID: PMC11018598 DOI: 10.1007/s12298-024-01436-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/04/2024] [Accepted: 03/12/2024] [Indexed: 04/19/2024]
12
Głowienka-Stodolak M, Bagińska-Drabiuk K, Szubert S, Hennig EE, Horala A, Dąbrowska M, Micek M, Ciebiera M, Zeber-Lubecka N. Human Papillomavirus Infections and the Role Played by Cervical and Cervico-Vaginal Microbiota-Evidence from Next-Generation Sequencing Studies. Cancers (Basel) 2024;16:399. [PMID: 38254888 PMCID: PMC10814012 DOI: 10.3390/cancers16020399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024]  Open
13
Bajaj JS, O'Leary JG, Jakab SS, Fagan A, Sikaroodi M, Gillevet PM. Gut microbiome profiles to exclude the diagnosis of hepatic encephalopathy in patients with cirrhosis. Gut Microbes 2024;16:2392880. [PMID: 39189586 DOI: 10.1080/19490976.2024.2392880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/15/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024]  Open
14
Zymovets V, Rakhimova O, Wadelius P, Schmidt A, Brundin M, Kelk P, Landström M, Vestman NR. Exploring the impact of oral bacteria remnants on stem cells from the Apical papilla: mineralization potential and inflammatory response. Front Cell Infect Microbiol 2023;13:1257433. [PMID: 38089810 PMCID: PMC10711090 DOI: 10.3389/fcimb.2023.1257433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023]  Open
15
Fu KL, Chiu MJ, Wara-Aswapati N, Yang CN, Chang LC, Guo YL, Ni YH, Chen YW. Oral microbiome and serological analyses on association of Alzheimer's disease and periodontitis. Oral Dis 2023;29:3677-3687. [PMID: 35950713 DOI: 10.1111/odi.14348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/15/2022] [Accepted: 08/05/2022] [Indexed: 11/27/2022]
16
Arasu A, Prabha N, Devi D, Issac PK, Alarjani KM, Al Farraj DA, Aljeidi RA, Hussein DS, Mohan M, Tayyeb JZ, Guru A, Arockiaraj J. Antimicrobial Efficacy of Allium cepa and Zingiber officinale Against the Milk-Borne Pathogen Listeria monocytogenes. J Microbiol 2023;61:993-1011. [PMID: 38048022 DOI: 10.1007/s12275-023-00086-w] [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: 07/19/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 12/05/2023]
17
Zhang T, Li H, Ma S, Cao J, Liao H, Huang Q, Chen W. The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling. Appl Environ Microbiol 2023;89:e0060523. [PMID: 37800969 PMCID: PMC10617388 DOI: 10.1128/aem.00605-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/04/2023] [Indexed: 10/07/2023]  Open
18
Amieva-Balmori M, García-Mazcorro JF, Martínez-Conejo A, Hernández-Ramírez GA, García-Zermeño KR, Rodríguez-Aguilera O, Aja-Cadena M, Barradas-Cortés M, Quigley EMM, Remes-Troche JM. Fecal bacterial microbiota in constipated patients before and after eight weeks of daily Bifidobacterium infantis 35624 administration. REVISTA DE GASTROENTEROLOGIA DE MEXICO (ENGLISH) 2023;88:369-380. [PMID: 35810091 DOI: 10.1016/j.rgmxen.2022.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 10/17/2022]
19
Wong SP, Er YX, Tan SM, Lee SC, Rajasuriar R, Lim YAL. Oral and Gut Microbiota Dysbiosis is Associated with Mucositis Severity in Autologous Hematopoietic Stem Cell Transplantation: Evidence from an Asian Population. Transplant Cell Ther 2023;29:633.e1-633.e13. [PMID: 37422196 DOI: 10.1016/j.jtct.2023.06.016] [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: 04/16/2023] [Revised: 06/17/2023] [Accepted: 06/26/2023] [Indexed: 07/10/2023]
20
Rey-Velasco X, Deulofeu-Capo O, Sanz-Sáez I, Cardelús C, Ferrera I, Gasol JM, Sánchez O. Expanding success in the isolation of abundant marine bacteria after reduction in grazing and viral pressure and increase in nutrient availability. Microbiol Spectr 2023;11:e0089023. [PMID: 37747249 PMCID: PMC10580928 DOI: 10.1128/spectrum.00890-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/03/2023] [Indexed: 09/26/2023]  Open
21
Çelik Doğan C, Yüksel Dolgun HT, İkiz S, Kırkan Ş, Parın U. Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis. Foods 2023;12:3538. [PMID: 37835192 PMCID: PMC10572611 DOI: 10.3390/foods12193538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]  Open
22
Mesloub Y, Beury D, Vandermeeren F, Caboche S. CuReSim-LoRM: A Tool to Simulate Metabarcoding Long Reads. Int J Mol Sci 2023;24:14005. [PMID: 37762307 PMCID: PMC10531135 DOI: 10.3390/ijms241814005] [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: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023]  Open
23
Paul B. Concatenated 16S rRNA sequence analysis improves bacterial taxonomy. F1000Res 2023;11:1530. [PMID: 37767069 PMCID: PMC10521043 DOI: 10.12688/f1000research.128320.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 09/29/2023]  Open
24
Eke M, Tougeron K, Hamidovic A, Tinkeu LSN, Hance T, Renoz F. Deciphering the functional diversity of the gut microbiota of the black soldier fly (Hermetia illucens): recent advances and future challenges. Anim Microbiome 2023;5:40. [PMID: 37653468 PMCID: PMC10472620 DOI: 10.1186/s42523-023-00261-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]  Open
25
Strutt JPB, Natarajan M, Lee E, Teo DBL, Sin WX, Cheung KW, Chew M, Thazin K, Barone PW, Wolfrum JM, Williams RBH, Rice SA, Springs SL. Machine learning-based detection of adventitious microbes in T-cell therapy cultures using long-read sequencing. Microbiol Spectr 2023;11:e0135023. [PMID: 37646508 PMCID: PMC10580871 DOI: 10.1128/spectrum.01350-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/03/2023] [Indexed: 09/01/2023]  Open
26
Dass M, Singh Y, Ghai M. A Review on Microbial Species for Forensic Body Fluid Identification in Healthy and Diseased Humans. Curr Microbiol 2023;80:299. [PMID: 37491404 PMCID: PMC10368579 DOI: 10.1007/s00284-023-03413-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/08/2023] [Indexed: 07/27/2023]
27
Zhu J, Lu J, Weng H. Single-cell RNA sequencing for the study of kidney disease. Mol Med 2023;29:85. [PMID: 37400792 DOI: 10.1186/s10020-023-00693-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023]  Open
28
Stevens BM, Creed TB, Reardon CL, Manter DK. Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil. Sci Rep 2023;13:9323. [PMID: 37291169 PMCID: PMC10250467 DOI: 10.1038/s41598-023-36101-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023]  Open
29
Jaworska MM, Pecyna P, Jaskiewicz K, Rydzanicz M, Kaluzna M, Pawlaczyk K, Ploski R, Nowak-Malczewska DM, Karolak JA, Gajecka M. Differences in the composition of the bacterial element of the urinary tract microbiome in patients undergoing dialysis and patients after kidney transplantation. Front Microbiol 2023;14:1187625. [PMID: 37350786 PMCID: PMC10282556 DOI: 10.3389/fmicb.2023.1187625] [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: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023]  Open
30
Varliero G, Lebre PH, Stevens MI, Czechowski P, Makhalanyane T, Cowan DA. The use of different 16S rRNA gene variable regions in biogeographical studies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023;15:216-228. [PMID: 36810880 PMCID: PMC10464692 DOI: 10.1111/1758-2229.13145] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/23/2023] [Indexed: 05/06/2023]
31
Marascio N, Scarlata GGM, Romeo F, Cicino C, Trecarichi EM, Quirino A, Torti C, Matera G, Russo A. The Role of Gut Microbiota in the Clinical Outcome of Septic Patients: State of the Art and Future Perspectives. Int J Mol Sci 2023;24:ijms24119307. [PMID: 37298258 DOI: 10.3390/ijms24119307] [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: 04/27/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]  Open
32
Cha T, Kim HH, Keum J, Kwak MJ, Park JY, Hoh JK, Kim CR, Jeon BH, Park HK. Gut microbiome profiling of neonates using Nanopore MinION and Illumina MiSeq sequencing. Front Microbiol 2023;14:1148466. [PMID: 37256051 PMCID: PMC10225602 DOI: 10.3389/fmicb.2023.1148466] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023]  Open
33
Zorz J, Li C, Chakraborty A, Gittins DA, Surcon T, Morrison N, Bennett R, MacDonald A, Hubert CRJ. SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis. ISME COMMUNICATIONS 2023;3:33. [PMID: 37081077 PMCID: PMC10119094 DOI: 10.1038/s43705-023-00239-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 04/22/2023]
34
Szoboszlay M, Schramm L, Pinzauti D, Scerri J, Sandionigi A, Biazzo M. Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required. Microorganisms 2023;11:microorganisms11030804. [PMID: 36985377 PMCID: PMC10059749 DOI: 10.3390/microorganisms11030804] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023]  Open
35
Nakamura A, Komatsu M. Performance evaluation of whole genome metagenomics sequencing with the MinION nanopore sequencer: Microbial community analysis and antimicrobial resistance gene detection. J Microbiol Methods 2023;206:106688. [PMID: 36764487 DOI: 10.1016/j.mimet.2023.106688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
36
Lee AWT, Chan CTM, Wong LLY, Yip CY, Lui WT, Cheng KC, Leung JSL, Lee LK, Wong ITF, Ng TTL, Lao HY, Siu GKH. Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing. Front Microbiol 2023;14:1164632. [PMID: 37125165 PMCID: PMC10133568 DOI: 10.3389/fmicb.2023.1164632] [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: 02/13/2023] [Accepted: 03/14/2023] [Indexed: 05/02/2023]  Open
37
Enespa, Chandra P. Tool and techniques study to plant microbiome current understanding and future needs: an overview. Commun Integr Biol 2022;15:209-225. [PMID: 35967908 PMCID: PMC9367660 DOI: 10.1080/19420889.2022.2082736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
38
Fasullo M, Dolan M. The continuing evolution of barcode applications: Functional toxicology to cell lineage. Exp Biol Med (Maywood) 2022;247:2119-2127. [PMID: 36113119 PMCID: PMC9837303 DOI: 10.1177/15353702221121600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]  Open
39
Ju Y, Pu M, Sun K, Song G, Geng J. Nanopore Electrochemistry for Pathogen Detection. Chem Asian J 2022;17:e202200774. [PMID: 36069587 DOI: 10.1002/asia.202200774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Indexed: 11/05/2022]
40
Oral Microbiome in Orthodontic Acrylic Retainer. Polymers (Basel) 2022;14:polym14173583. [PMID: 36080658 PMCID: PMC9459992 DOI: 10.3390/polym14173583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022]  Open
41
Nie F, Wang L, Huang Y, Yang P, Gong P, Feng Q, Yang C. Characteristics of Microbial Distribution in Different Oral Niches of Oral Squamous Cell Carcinoma. Front Cell Infect Microbiol 2022;12:905653. [PMID: 36046741 PMCID: PMC9421053 DOI: 10.3389/fcimb.2022.905653] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 04/28/2022] [Indexed: 11/15/2022]  Open
42
Lobanov V, Gobet A, Joyce A. Ecosystem-specific microbiota and microbiome databases in the era of big data. ENVIRONMENTAL MICROBIOME 2022;17:37. [PMID: 35842686 PMCID: PMC9287977 DOI: 10.1186/s40793-022-00433-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/29/2022] [Indexed: 05/05/2023]
43
Curry KD, Wang Q, Nute MG, Tyshaieva A, Reeves E, Soriano S, Wu Q, Graeber E, Finzer P, Mendling W, Savidge T, Villapol S, Dilthey A, Treangen TJ. Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nat Methods 2022;19:845-853. [PMID: 35773532 PMCID: PMC9939874 DOI: 10.1038/s41592-022-01520-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022]
44
Nwachukwu BC, Babalola OO. Metagenomics: A Tool for Exploring Key Microbiome With the Potentials for Improving Sustainable Agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.886987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
45
Elgendy MY, Sherif AH, Kenawy AM, Abdelsalam M. Phenotypic and molecular characterization of the causative agents of edwardsiellosis causing Nile tilapia (Oreochromis niloticus) summer mortalities. Microb Pathog 2022;169:105620. [PMID: 35690232 DOI: 10.1016/j.micpath.2022.105620] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/26/2022]
46
Omi M, Matsuo Y, Araki-Sasaki K, Oba S, Yamada H, Hirota K, Takahashi K. 16S rRNA nanopore sequencing for the diagnosis of ocular infection: a feasibility study. BMJ Open Ophthalmol 2022;7:bmjophth-2021-000910. [PMID: 36161861 PMCID: PMC9131114 DOI: 10.1136/bmjophth-2021-000910] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/29/2022] [Indexed: 11/16/2022]  Open
47
A Potential Predictive Role of the Scalp Microbiome Profiling in Patients with Alopecia Areata: Staphylococcus caprae, Corynebacterium, and Cutibacterium Species. Microorganisms 2022;10:microorganisms10050864. [PMID: 35630309 PMCID: PMC9148078 DOI: 10.3390/microorganisms10050864] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023]  Open
48
Savio C, Mugo-Kamiri L, Upfold JK. Bugs in Bugs: The Role of Probiotics and Prebiotics in Maintenance of Health in Mass-Reared Insects. INSECTS 2022;13:376. [PMID: 35447818 PMCID: PMC9025317 DOI: 10.3390/insects13040376] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 02/07/2023]
49
Skipper PJA, Skipper LK, Dixon RA. A metagenomic analysis of the bacterial microbiome of limestone, and the role of associated biofilms in the biodeterioration of heritage stone surfaces. Sci Rep 2022;12:4877. [PMID: 35318388 PMCID: PMC8940931 DOI: 10.1038/s41598-022-08851-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022]  Open
50
Tamošiūnė I, Andriūnaitė E, Vinskienė J, Stanys V, Rugienius R, Baniulis D. Enduring Effect of Antibiotic Timentin Treatment on Tobacco In Vitro Shoot Growth and Microbiome Diversity. PLANTS (BASEL, SWITZERLAND) 2022;11:832. [PMID: 35336713 PMCID: PMC8954828 DOI: 10.3390/plants11060832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
PrevPage 1 of 2 12Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA