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For: Parks DH, Rigato F, Vera-Wolf P, Krause L, Hugenholtz P, Tyson GW, Wood DLA. Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome. Front Microbiol 2021;12:643682. [PMID: 33959106 PMCID: PMC8093879 DOI: 10.3389/fmicb.2021.643682] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/11/2021] [Indexed: 12/12/2022]  Open
Number Cited by Other Article(s)
1
Brito J, Grosicki GJ, Robinson AT, Coburn JW, Costa PB, Holmes KE, Lyon G, Hakonsson Z, Conti F, Galpin AJ. Hormonal birth control is associated with altered gut microbiota β-diversity in physically active females across the menstrual cycle: a pilot trial. J Appl Physiol (1985) 2025;138:739-745. [PMID: 39951399 DOI: 10.1152/japplphysiol.00008.2025] [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: 01/15/2025] [Revised: 01/28/2025] [Accepted: 02/05/2025] [Indexed: 02/16/2025]  Open
2
Pribyl AL, Hugenholtz P, Cooper MA. A decade of advances in human gut microbiome-derived biotherapeutics. Nat Microbiol 2025;10:301-312. [PMID: 39779879 DOI: 10.1038/s41564-024-01896-3] [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: 04/05/2024] [Accepted: 11/20/2024] [Indexed: 01/11/2025]
3
Flintoff JM, Pattinson C, Ahamed S, Ali S, Bagley A, Broszczak D, Crewther B, de Waal L, Edmed SL, Fernando T, Fookes C, Frentiu FD, Hunt AP, Lipp OV, McMaster B, Mengersen K, Ney L, Oon SL, Pandey A, Pandit P, Peake JM, Perera MMN, Perlo V, Punyadeera C, Schmidt L, Smith SS, Spann K, Stewart I, Sullivan KA, Young D, Kerr G, Parker TJ. Predictive biomarkers of performance under stress: a two-phase study protocol to develop a wearable monitoring system. BMJ Open Sport Exerc Med 2025;11:e002410. [PMID: 39897983 PMCID: PMC11784218 DOI: 10.1136/bmjsem-2024-002410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 12/19/2024] [Indexed: 02/04/2025]  Open
4
Angel NZ, Sullivan MJ, Alsheikh-Hussain A, Fang L, MacDonald S, Pribyl A, Wills B, Tyson GW, Hugenholtz P, Parks DH, Griffin P, Wood DLA. Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens. Gut Pathog 2025;17:4. [PMID: 39827146 PMCID: PMC11742996 DOI: 10.1186/s13099-024-00673-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2024] [Accepted: 12/24/2024] [Indexed: 01/22/2025]  Open
5
Puller V, Plaza Oñate F, Prifti E, de Lahondès R. Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines. Microb Genom 2025;11:001330. [PMID: 39804694 PMCID: PMC11728698 DOI: 10.1099/mgen.0.001330] [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: 05/13/2024] [Accepted: 11/06/2024] [Indexed: 01/16/2025]  Open
6
Davies JM, Teh JJ, Ewais T, Begun J. Does Improving Depression Symptoms in Young Adults With Inflammatory Bowel Disease Alter Their Microbiome? Inflamm Bowel Dis 2024;30:2428-2439. [PMID: 38839073 PMCID: PMC11630472 DOI: 10.1093/ibd/izae121] [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: 08/08/2023] [Indexed: 06/07/2024]
7
Mitchell LK, Heussler HS, Burgess CJ, Rehman A, Steinert RE, Davies PSW. Gastrointestinal, Behaviour and Anxiety Outcomes in Autistic Children Following an Open Label, Randomised Pilot Study of Synbiotics vs Synbiotics and Gut-Directed Hypnotherapy. J Autism Dev Disord 2024:10.1007/s10803-024-06588-9. [PMID: 39417900 DOI: 10.1007/s10803-024-06588-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2024] [Indexed: 10/19/2024]
8
Shaw J, Yu YW. Rapid species-level metagenome profiling and containment estimation with sylph. Nat Biotechnol 2024:10.1038/s41587-024-02412-y. [PMID: 39379646 DOI: 10.1038/s41587-024-02412-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 08/28/2024] [Indexed: 10/10/2024]
9
Van Uffelen A, Posadas A, Roosens NHC, Marchal K, De Keersmaecker SCJ, Vanneste K. Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities. Sci Data 2024;11:864. [PMID: 39127718 PMCID: PMC11316826 DOI: 10.1038/s41597-024-03672-8] [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: 02/09/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024]  Open
10
Vasileva S, Yap CX, Whitehouse AJ, Gratten J, Eyles D. Absence of association between maternal adverse events and long-term gut microbiome outcomes in the Australian autism biobank. Brain Behav Immun Health 2024;39:100814. [PMID: 39027090 PMCID: PMC11254947 DOI: 10.1016/j.bbih.2024.100814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 07/20/2024]  Open
11
Nganou-Makamdop K, Douek DC. The Gut and the Translocated Microbiomes in HIV Infection: Current Concepts and Future Avenues. Pathog Immun 2024;9:168-194. [PMID: 38807656 PMCID: PMC11132393 DOI: 10.20411/pai.v9i1.693] [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: 03/05/2024] [Accepted: 05/03/2024] [Indexed: 05/30/2024]  Open
12
Erhardt R, Steels E, Harnett JE, Taing MW, Steadman KJ. Effects of a prebiotic formulation on the composition of the faecal microbiota of people with functional constipation. Eur J Nutr 2024;63:777-784. [PMID: 38165420 DOI: 10.1007/s00394-023-03292-9] [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: 10/10/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
13
Kan CM, Tsang HF, Pei XM, Ng SSM, Yim AKY, Yu ACS, Wong SCC. Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis. Int J Mol Sci 2024;25:3333. [PMID: 38542307 PMCID: PMC10970082 DOI: 10.3390/ijms25063333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 11/11/2024]  Open
14
Valencia EM, Maki KA, Dootz JN, Barb JJ. Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines. Sci Data 2024;11:81. [PMID: 38233447 PMCID: PMC10794705 DOI: 10.1038/s41597-023-02877-7] [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: 05/26/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024]  Open
15
Bugnot AB, Dafforn KA, Erickson K, McGrath A, O'Connor WA, Gribben PE. Reintroducing a keystone bioturbator can facilitate microbial bioremediation in urban polluted sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023;324:121419. [PMID: 36906055 DOI: 10.1016/j.envpol.2023.121419] [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: 10/24/2022] [Revised: 01/23/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
16
Wright RJ, Comeau AM, Langille MGI. From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools. Microb Genom 2023;9:mgen000949. [PMID: 36867161 PMCID: PMC10132073 DOI: 10.1099/mgen.0.000949] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 12/07/2022] [Indexed: 03/04/2023]  Open
17
Ibañez-Lligoña M, Colomer-Castell S, González-Sánchez A, Gregori J, Campos C, Garcia-Cehic D, Andrés C, Piñana M, Pumarola T, Rodríguez-Frias F, Antón A, Quer J. Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses. Viruses 2023;15:587. [PMID: 36851800 PMCID: PMC9965957 DOI: 10.3390/v15020587] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]  Open
18
Portik DM, Brown CT, Pierce-Ward NT. Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets. BMC Bioinformatics 2022;23:541. [PMID: 36513983 PMCID: PMC9749362 DOI: 10.1186/s12859-022-05103-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]  Open
19
Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S. Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. MICROBIOME 2022;10:212. [PMID: 36464731 PMCID: PMC9721005 DOI: 10.1186/s40168-022-01410-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
20
Solari SM, Young RB, Marcelino VR, Forster SC. expam-high-resolution analysis of metagenomes using distance trees. Bioinformatics 2022;38:4814-4816. [PMID: 36029242 PMCID: PMC9563691 DOI: 10.1093/bioinformatics/btac591] [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: 05/23/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]  Open
21
Sindi AS, Stinson LF, Lean SS, Chooi YH, Leghi GE, Netting MJ, Wlodek ME, Muhlhausler BS, Geddes DT, Payne MS. Effect of a reduced fat and sugar maternal dietary intervention during lactation on the infant gut microbiome. Front Microbiol 2022;13:900702. [PMID: 36060782 PMCID: PMC9428759 DOI: 10.3389/fmicb.2022.900702] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022]  Open
22
Chakoory O, Comtet-Marre S, Peyret P. RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties. NAR Genom Bioinform 2022;4:lqac070. [PMID: 36159175 PMCID: PMC9492272 DOI: 10.1093/nargab/lqac070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/04/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022]  Open
23
Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements. Microbiol Spectr 2022;10:e0191521. [PMID: 35234490 PMCID: PMC8941912 DOI: 10.1128/spectrum.01915-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
24
Speight RE, Navone L, Gebbie LK, Blinco JAL, Bryden WL. Platforms to accelerate biomanufacturing of enzyme and probiotic animal feed supplements: discovery considerations and manufacturing implications. ANIMAL PRODUCTION SCIENCE 2022. [DOI: 10.1071/an21342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
25
Synbiotics Easing Renal Failure by Improving Gut Microbiology II (SYNERGY II): A Feasibility Randomized Controlled Trial. Nutrients 2021;13:nu13124481. [PMID: 34960037 PMCID: PMC8708915 DOI: 10.3390/nu13124481] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 01/14/2023]  Open
26
Pryor J, Eslick GD, Talley NJ, Duncanson K, Keely S, Hoedt EC. Clinical medicine journals lag behind science journals with regards to "microbiota sequence" data availability. Clin Transl Med 2021;11:e656. [PMID: 34870904 PMCID: PMC8647683 DOI: 10.1002/ctm2.656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022]  Open
27
Yap CX, Henders AK, Alvares GA, Wood DLA, Krause L, Tyson GW, Restuadi R, Wallace L, McLaren T, Hansell NK, Cleary D, Grove R, Hafekost C, Harun A, Holdsworth H, Jellett R, Khan F, Lawson LP, Leslie J, Frenk ML, Masi A, Mathew NE, Muniandy M, Nothard M, Miller JL, Nunn L, Holtmann G, Strike LT, de Zubicaray GI, Thompson PM, McMahon KL, Wright MJ, Visscher PM, Dawson PA, Dissanayake C, Eapen V, Heussler HS, McRae AF, Whitehouse AJO, Wray NR, Gratten J. Autism-related dietary preferences mediate autism-gut microbiome associations. Cell 2021;184:5916-5931.e17. [PMID: 34767757 DOI: 10.1016/j.cell.2021.10.015] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/14/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022]
28
McFarlane C, Krishnasamy R, Stanton T, Savill E, Snelson M, Mihala G, Morrison M, Johnson DW, Campbell KL. Diet Quality and Protein-Bound Uraemic Toxins: Investigation of Novel Risk Factors and the Role of Microbiome in Chronic Kidney Disease. J Ren Nutr 2021;32:542-551. [PMID: 34776340 DOI: 10.1053/j.jrn.2021.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 09/16/2021] [Accepted: 10/03/2021] [Indexed: 02/06/2023]  Open
29
Pribyl AL, Parks DH, Angel NZ, Boyd JA, Hasson AG, Fang L, MacDonald SL, Wills BA, Wood DLA, Krause L, Tyson GW, Hugenholtz P. Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME COMMUNICATIONS 2021;1:14. [PMID: 37938632 PMCID: PMC9645250 DOI: 10.1038/s43705-021-00014-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/14/2021] [Accepted: 04/06/2021] [Indexed: 05/04/2023]
30
Chan S, Morrison M, Hawley CM, Campbell SB, Francis RS, Isbel NM, Pascoe EM, Johnson DW. Characteristics of the gastrointestinal microbiota in paired live kidney donors and recipients. Nephrology (Carlton) 2021;26:471-478. [PMID: 33501716 DOI: 10.1111/nep.13853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 01/08/2023]
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