Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
11 2021
11 2021
Historique:
received:
18
05
2021
accepted:
01
09
2021
pubmed:
5
9
2021
medline:
11
3
2022
entrez:
4
9
2021
Statut:
ppublish
Résumé
The number of publicly available microbiome samples is continually growing. As data set size increases, bottlenecks arise in standard analytical pipelines. Faith's phylogenetic diversity (Faith's PD) is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's phylogenetic diversity (SFPhD) enables calculation of this widely adopted diversity metric at a much larger scale by implementing a computationally efficient algorithm. The algorithm reduces the amount of computational resources required, resulting in more accessible software with a reduced carbon footprint, as compared to previous approaches. The new algorithm produces identical results to the previous method. We further demonstrate that the phylogenetic aspect of Faith's PD provides increased power in detecting diversity differences between younger and older populations in the FINRISK study's metagenomic data.
Identifiants
pubmed: 34479875
pii: gr.275777.121
doi: 10.1101/gr.275777.121
pmc: PMC8559715
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2131-2137Subventions
Organisme : British Heart Foundation
ID : CH/12/2/29428
Pays : United Kingdom
Organisme : NIEHS NIH HHS
ID : R01 ES027595
Pays : United States
Organisme : British Heart Foundation
ID : RG/13/13/30194
Pays : United Kingdom
Organisme : British Heart Foundation
ID : RG/18/13/33946
Pays : United Kingdom
Informations de copyright
© 2021 Armstrong et al.; Published by Cold Spring Harbor Laboratory Press.
Références
Cell Host Microbe. 2019 Jun 12;25(6):789-802.e5
pubmed: 31194939
Nature. 2017 Nov 23;551(7681):457-463
pubmed: 29088705
Microorganisms. 2021 Jun 07;9(6):
pubmed: 34200249
Proc Biol Sci. 2017 Oct 25;284(1865):
pubmed: 29070718
mSystems. 2021 Mar 16;6(2):
pubmed: 33727399
Nat Biotechnol. 2020 Sep;38(9):1079-1086
pubmed: 32341564
Appl Environ Microbiol. 2009 Aug;75(15):5111-20
pubmed: 19502440
Nat Methods. 2018 Nov;15(11):847-848
pubmed: 30377368
Nat Commun. 2016 Jul 05;7:12083
pubmed: 27377774
BMC Genomics. 2018 Nov 6;19(1):799
pubmed: 30400812
Adv Sci (Weinh). 2021 May 02;8(12):2100707
pubmed: 34194954
mSystems. 2017 Mar 7;2(2):
pubmed: 28289731
Nat Commun. 2021 May 11;12(1):2671
pubmed: 33976176
Gigascience. 2012 Jul 12;1(1):7
pubmed: 23587224
Nat Commun. 2019 May 16;10(1):2200
pubmed: 31097702
Int J Mol Sci. 2009 Nov 03;10(11):4723-41
pubmed: 20087461
Nature. 2012 Jun 13;486(7402):207-14
pubmed: 22699609
Nat Biotechnol. 2018 Nov;36(10):996-1004
pubmed: 30148503
mSystems. 2018 Nov 13;3(6):
pubmed: 30443602
mSystems. 2019 Jun 25;4(4):
pubmed: 31239397
PeerJ. 2017 Aug 30;5:e3720
pubmed: 28875074
Appl Environ Microbiol. 2006 Jul;72(7):5069-72
pubmed: 16820507
mSystems. 2019 Feb 12;4(1):
pubmed: 30801021
Nat Microbiol. 2016 Oct 03;1:16177
pubmed: 27694806
mSystems. 2018 May 15;3(3):
pubmed: 29795809
Nature. 2020 Sep;585(7825):357-362
pubmed: 32939066
ISME J. 2010 Jan;4(1):17-27
pubmed: 19710709
ISME J. 2012 Mar;6(3):610-8
pubmed: 22134646
Pac Symp Biocomput. 2012;:247-58
pubmed: 22174280
Genome Biol. 2019 Nov 1;20(1):219
pubmed: 31672155
mSystems. 2019 May 14;4(4):
pubmed: 31098397
mSystems. 2017 Feb 21;2(1):
pubmed: 28251186
Nat Methods. 2018 Oct;15(10):796-798
pubmed: 30275573
Int J Epidemiol. 2018 Jun 1;47(3):696-696i
pubmed: 29165699
Nat Methods. 2018 Jul;15(7):475-476
pubmed: 29967506
Eur J Public Health. 2015 Jun;25(3):539-46
pubmed: 25422363
ISME J. 2016 Jan;10(1):170-82
pubmed: 26090993
Appl Environ Microbiol. 2005 Dec;71(12):8228-35
pubmed: 16332807
Cell Host Microbe. 2014 Mar 12;15(3):382-392
pubmed: 24629344
Nat Chem Biol. 2021 Feb;17(2):146-151
pubmed: 33199911
Nat Commun. 2019 Dec 2;10(1):5477
pubmed: 31792218