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For: Ayling M, Clark MD, Leggett RM. New approaches for metagenome assembly with short reads. Brief Bioinform 2021;21:584-594. [PMID: 30815668 PMCID: PMC7299287 DOI: 10.1093/bib/bbz020] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Barchi A, Massimino L, Mandarino FV, Vespa E, Sinagra E, Almolla O, Passaretti S, Fasulo E, Parigi TL, Cagliani S, Spanò S, Ungaro F, Danese S. Microbiota profiling in esophageal diseases: Novel insights into molecular staining and clinical outcomes. Comput Struct Biotechnol J 2024;23:626-637. [PMID: 38274997 PMCID: PMC10808859 DOI: 10.1016/j.csbj.2023.12.026] [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: 08/22/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024]  Open
2
Liu C, Tang Z, Li L, Kang Y, Teng Y, Yu Y. Enhancing antimicrobial resistance detection with MetaGeneMiner: Targeted gene extraction from metagenomes. Chin Med J (Engl) 2024:00029330-990000000-01108. [PMID: 38934052 DOI: 10.1097/cm9.0000000000003182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Indexed: 06/28/2024]  Open
3
Zavadska D, Henry N, Auladell A, Berney C, Richter DJ. Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes. PLoS One 2024;19:e0303697. [PMID: 38843225 PMCID: PMC11156365 DOI: 10.1371/journal.pone.0303697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/29/2024] [Indexed: 06/09/2024]  Open
4
Chen Z, Grim CJ, Ramachandran P, Meng J. Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing. Microbiol Spectr 2024;12:e0011724. [PMID: 38687063 DOI: 10.1128/spectrum.00117-24] [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: 01/22/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024]  Open
5
Xiao Y, Hao T. New insights on ecological roles of waste activated sludge in nutrient-stressed co-digestion. BIORESOURCE TECHNOLOGY 2024;402:130836. [PMID: 38744398 DOI: 10.1016/j.biortech.2024.130836] [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: 01/03/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
6
Zampolli J, De Giani A, Rossi M, Finazzi M, Di Gennaro P. Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas. Front Microbiol 2024;15:1380953. [PMID: 38863750 PMCID: PMC11165352 DOI: 10.3389/fmicb.2024.1380953] [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: 02/02/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024]  Open
7
Lin A, Torres CM, Hobbs EC, Bardhan J, Aley SB, Spencer CT, Taylor KL, Chiang T. Computational and Systems Biology Advances to Enable Bioagent Agnostic Signatures. Health Secur 2024;22:130-139. [PMID: 38483337 PMCID: PMC11044874 DOI: 10.1089/hs.2023.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]  Open
8
Lin A, Torres C, Hobbs EC, Bardhan J, Aley S, Spencer CT, Taylor KL, Chiang T. Computational and Systems Biology Advances to Enable Bioagent Agnostic Signatures. ARXIV 2024:arXiv:2310.13898v3. [PMID: 37961741 PMCID: PMC10635321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
9
Li Y, Miyani B, Faust RA, David RE, Xagoraraki I. A broad wastewater screening and clinical data surveillance for virus-related diseases in the metropolitan Detroit area in Michigan. Hum Genomics 2024;18:14. [PMID: 38321488 PMCID: PMC10845806 DOI: 10.1186/s40246-024-00581-0] [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: 09/01/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024]  Open
10
Kim C, Pongpanich M, Porntaveetus T. Unraveling metagenomics through long-read sequencing: a comprehensive review. J Transl Med 2024;22:111. [PMID: 38282030 PMCID: PMC10823668 DOI: 10.1186/s12967-024-04917-1] [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: 10/15/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024]  Open
11
Li Y, Miyani B, Childs KL, Shiu SH, Xagoraraki I. Effect of wastewater collection and concentration methods on assessment of viral diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;908:168128. [PMID: 37918732 DOI: 10.1016/j.scitotenv.2023.168128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
12
Baltoumas FA, Karatzas E, Liu S, Ovchinnikov S, Sofianatos Y, Chen IM, Kyrpides N, Pavlopoulos G. NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes. Nucleic Acids Res 2024;52:D502-D512. [PMID: 37811892 PMCID: PMC10767849 DOI: 10.1093/nar/gkad800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023]  Open
13
Cerk K, Ugalde‐Salas P, Nedjad CG, Lecomte M, Muller C, Sherman DJ, Hildebrand F, Labarthe S, Frioux C. Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing. Microb Biotechnol 2024;17:e14396. [PMID: 38243750 PMCID: PMC10832553 DOI: 10.1111/1751-7915.14396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 11/27/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]  Open
14
Fu P, Wu Y, Zhang Z, Qiu Y, Wang Y, Peng Y. VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data. Brief Bioinform 2023;25:bbad444. [PMID: 38048079 PMCID: PMC10753531 DOI: 10.1093/bib/bbad444] [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: 04/27/2023] [Revised: 10/26/2023] [Accepted: 11/11/2023] [Indexed: 12/05/2023]  Open
15
Chen L, Chen A, Zhang XD, T Robles MS, Han HS, Xiao Y, Xiao G, Pipas JM, Weitz DA. High-sensitivity whole-genome recovery of single viral species in environmental samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566948. [PMID: 38014300 PMCID: PMC10680796 DOI: 10.1101/2023.11.13.566948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
16
Walsh LH, Coakley M, Walsh AM, O'Toole PW, Cotter PD. Bioinformatic approaches for studying the microbiome of fermented food. Crit Rev Microbiol 2023;49:693-725. [PMID: 36287644 DOI: 10.1080/1040841x.2022.2132850] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/11/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
17
Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, Nickols WA, Piccinno G, Piperni E, Punčochář M, Valles-Colomer M, Tett A, Giordano F, Davies R, Wolf J, Berry SE, Spector TD, Franzosa EA, Pasolli E, Asnicar F, Huttenhower C, Segata N. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol 2023;41:1633-1644. [PMID: 36823356 PMCID: PMC10635831 DOI: 10.1038/s41587-023-01688-w] [Citation(s) in RCA: 141] [Impact Index Per Article: 141.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
18
Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad A, Roux S, Call L, Ivanova NN, Chen IM, Paez-Espino D, Karatzas E, Iliopoulos I, Konstantinidis K, Tiedje JM, Pett-Ridge J, Baker D, Visel A, Ouzounis CA, Ovchinnikov S, Buluç A, Kyrpides NC. Unraveling the functional dark matter through global metagenomics. Nature 2023;622:594-602. [PMID: 37821698 PMCID: PMC10584684 DOI: 10.1038/s41586-023-06583-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/30/2023] [Indexed: 10/13/2023]
19
Magdy Wasfy R, Mbaye B, Borentain P, Tidjani Alou M, Murillo Ruiz ML, Caputo A, Andrieu C, Armstrong N, Million M, Gerolami R. Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study. Microorganisms 2023;11:2437. [PMID: 37894093 PMCID: PMC10608849 DOI: 10.3390/microorganisms11102437] [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: 08/20/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]  Open
20
Ho H, Chovatia M, Egan R, He G, Yoshinaga Y, Liachko I, O’Malley R, Wang Z. Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning. PeerJ 2023;11:e16129. [PMID: 37753177 PMCID: PMC10519199 DOI: 10.7717/peerj.16129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/28/2023] [Indexed: 09/28/2023]  Open
21
Liang X, Zhang J, Kim Y, Ho J, Liu K, Keenum I, Gupta S, Davis B, Hepp SL, Zhang L, Xia K, Knowlton KF, Liao J, Vikesland PJ, Pruden A, Heath LS. ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization. Front Genet 2023;14:1219297. [PMID: 37811141 PMCID: PMC10558085 DOI: 10.3389/fgene.2023.1219297] [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: 05/08/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023]  Open
22
Muralitharan RR, Snelson M, Meric G, Coughlan MT, Marques FZ. Guidelines for microbiome studies in renal physiology. Am J Physiol Renal Physiol 2023;325:F345-F362. [PMID: 37440367 DOI: 10.1152/ajprenal.00072.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023]  Open
23
Mak L, Meleshko D, Danko DC, Barakzai WN, Maharjan S, Belchikov N, Hajirasouliha I. Ariadne: synthetic long read deconvolution using assembly graphs. Genome Biol 2023;24:197. [PMID: 37641111 PMCID: PMC10463629 DOI: 10.1186/s13059-023-03033-5] [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: 03/24/2022] [Accepted: 08/07/2023] [Indexed: 08/31/2023]  Open
24
Zhang ZF, Liu LR, Pan YP, Pan J, Li M. Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments. MICROBIOME 2023;11:188. [PMID: 37612768 PMCID: PMC10464287 DOI: 10.1186/s40168-023-01630-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
25
Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023;14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
26
Mineeva O, Danciu D, Schölkopf B, Ley RE, Rätsch G, Youngblut ND. ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning. PLoS Comput Biol 2023;19:e1011001. [PMID: 37126495 PMCID: PMC10174551 DOI: 10.1371/journal.pcbi.1011001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 05/11/2023] [Accepted: 03/06/2023] [Indexed: 05/02/2023]  Open
27
Esquerra-Ruvira B, Baquedano I, Ruiz R, Fernandez A, Montoliu L, Mojica FJM. Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering. Microb Biotechnol 2023. [PMID: 37097160 DOI: 10.1111/1751-7915.14266] [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: 02/06/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]  Open
28
Rong Lee M, Kim JC, Eun Park S, Kim WJ, Su Kim J. Detection of Viral Genes in Metarhizium anisopliae JEF-290-infected longhorned tick, Haemaphysalis longicornis using transcriptome analysis. J Invertebr Pathol 2023;198:107926. [PMID: 37087092 DOI: 10.1016/j.jip.2023.107926] [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: 10/15/2022] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 04/24/2023]
29
Yorki S, Shea T, Cuomo CA, Walker BJ, LaRocque RC, Manson AL, Earl AM, Worby CJ. Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes. Brief Bioinform 2023;24:bbad050. [PMID: 36804804 PMCID: PMC10025444 DOI: 10.1093/bib/bbad050] [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: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/26/2023] [Indexed: 02/23/2023]  Open
30
Soto MA, Desai D, Bannon C, LaRoche J, Bertrand EM. Cobalamin producers and prokaryotic consumers in the Northwest Atlantic. Environ Microbiol 2023. [PMID: 36861357 DOI: 10.1111/1462-2920.16363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/26/2023] [Indexed: 03/03/2023]
31
Wang T, Wang XW, Lee-Sarwar KA, Litonjua AA, Weiss ST, Sun Y, Maslov S, Liu YY. Predicting metabolomic profiles from microbial composition through neural ordinary differential equations. NAT MACH INTELL 2023;5:284-293. [PMID: 38223254 PMCID: PMC10786629 DOI: 10.1038/s42256-023-00627-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023]
32
Lu Y, Ge C, Cai B, Xu Q, Kong R, Chang S. Antibody sequences assembly method based on weighted de Bruijn graph. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:6174-6190. [PMID: 37161102 DOI: 10.3934/mbe.2023266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
33
Morrison AG, Sarkar S, Umar S, Lee STM, Thomas SM. The Contribution of the Human Oral Microbiome to Oral Disease: A Review. Microorganisms 2023;11:318. [PMID: 36838283 PMCID: PMC9962706 DOI: 10.3390/microorganisms11020318] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023]  Open
34
Martin S, Ayling M, Patrono L, Caccamo M, Murcia P, Leggett RM. Capturing variation in metagenomic assembly graphs with MetaCortex. Bioinformatics 2023;39:6986127. [PMID: 36722204 PMCID: PMC9889960 DOI: 10.1093/bioinformatics/btad020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/10/2022] [Accepted: 01/11/2023] [Indexed: 01/13/2023]  Open
35
Mangalea MR, Keift K, Duerkop BA, Anantharaman K. Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data. Methods Mol Biol 2023;2649:317-337. [PMID: 37258871 DOI: 10.1007/978-1-0716-3072-3_17] [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] [Indexed: 06/02/2023]
36
Santana-Pereira ALR. Identification of PKS Gene Clusters from Metagenomic Libraries Using a Next-Generation Sequencing Approach. Methods Mol Biol 2023;2555:73-90. [PMID: 36306079 DOI: 10.1007/978-1-0716-2795-2_5] [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: 06/16/2023]
37
Mendes CI, Vila-Cerqueira P, Motro Y, Moran-Gilad J, Carriço JA, Ramirez M. LMAS: evaluating metagenomic short de novo assembly methods through defined communities. Gigascience 2022;12:6963325. [PMID: 36576131 PMCID: PMC9795473 DOI: 10.1093/gigascience/giac122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/26/2022] [Accepted: 11/16/2022] [Indexed: 12/29/2022]  Open
38
Vuong P, Wise MJ, Whiteley AS, Kaur P. Ten simple rules for investigating (meta)genomic data from environmental ecosystems. PLoS Comput Biol 2022;18:e1010675. [PMID: 36480496 PMCID: PMC9731419 DOI: 10.1371/journal.pcbi.1010675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
39
Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022;12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
40
Critical Assessment of Short-Read Assemblers for the Metagenomic Identification of Foodborne and Waterborne Pathogens Using Simulated Bacterial Communities. Microorganisms 2022;10:microorganisms10122416. [PMID: 36557669 PMCID: PMC9784204 DOI: 10.3390/microorganisms10122416] [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: 11/10/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]  Open
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Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice. Genes (Basel) 2022;13:genes13122280. [PMID: 36553546 PMCID: PMC9777648 DOI: 10.3390/genes13122280] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/09/2022]  Open
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Sun J, Qiu Z, Egan R, Ho H, Li Y, Wang Z. Persistent memory as an effective alternative to random access memory in metagenome assembly. BMC Bioinformatics 2022;23:513. [PMID: 36451083 PMCID: PMC9710083 DOI: 10.1186/s12859-022-05052-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/11/2022] [Indexed: 12/05/2022]  Open
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Zhong Z, Tang H, Shen T, Ma X, Zhao F, Kwok LY, Sun Z, Bilige M, Zhang H. Bifidobacterium animalis subsp. lactis Probio-M8 undergoes host adaptive evolution by glcU mutation and translocates to the infant's gut via oral-/entero-mammary routes through lactation. MICROBIOME 2022;10:197. [PMID: 36419187 PMCID: PMC9682673 DOI: 10.1186/s40168-022-01398-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
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Tims S, Marsaux C, Pinto A, Daly A, Karall D, Kuhn M, Santra S, Roeselers G, Knol J, MacDonald A, Scholl-Bürgi S. Altered gut microbiome diversity and function in patients with propionic acidemia. Mol Genet Metab 2022;137:308-322. [PMID: 36274442 DOI: 10.1016/j.ymgme.2022.09.012] [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: 06/24/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022]
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Srinivas M, O’Sullivan O, Cotter PD, van Sinderen D, Kenny JG. The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods. Foods 2022;11:3297. [PMCID: PMC9601669 DOI: 10.3390/foods11203297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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Bai X, Ren J, Sun F. MLR-OOD: A Markov Chain Based Likelihood Ratio Method for Out-Of-Distribution Detection of Genomic Sequences. J Mol Biol 2022;434:167586. [PMID: 35427634 PMCID: PMC10433695 DOI: 10.1016/j.jmb.2022.167586] [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] [Received: 01/16/2022] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 12/23/2022]
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Zhang T, Zhou J, Gao W, Jia Y, Wei Y, Wang G. Complex genome assembly based on long-read sequencing. Brief Bioinform 2022;23:6657663. [PMID: 35940845 DOI: 10.1093/bib/bbac305] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/20/2022] [Accepted: 07/06/2022] [Indexed: 11/12/2022]  Open
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Sim M, Lee J, Wy S, Park N, Lee D, Kwon D, Kim J. Generation and application of pseudo-long reads for metagenome assembly. Gigascience 2022;11:giac044. [PMID: 35579554 PMCID: PMC9112764 DOI: 10.1093/gigascience/giac044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/10/2022] [Accepted: 04/03/2022] [Indexed: 12/13/2022]  Open
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Satjarak A, Golinski GK, Trest MT, Graham LE. Microbiome and related structural features of Earth's most archaic plant indicate early plant symbiosis attributes. Sci Rep 2022;12:6423. [PMID: 35443766 PMCID: PMC9021317 DOI: 10.1038/s41598-022-10186-z] [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] [Received: 09/17/2021] [Accepted: 04/04/2022] [Indexed: 11/09/2022]  Open
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Altermann E, Tegetmeyer HE, Chanyi RM. The evolution of bacterial genome assemblies - where do we need to go next? MICROBIOME RESEARCH REPORTS 2022;1:15. [PMID: 38046358 PMCID: PMC10688829 DOI: 10.20517/mrr.2022.02] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/08/2022] [Accepted: 03/24/2022] [Indexed: 12/05/2023]
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