Machine Learning Data Analysis Highlights the Role of
Alloprevorella
Parasutterella
autism spectrum disorder
dysbiosis
gut microbiota
machine learning data analysis
targeted metagenomics
Journal
Biomedicines
ISSN: 2227-9059
Titre abrégé: Biomedicines
Pays: Switzerland
ID NLM: 101691304
Informations de publication
Date de publication:
19 Aug 2022
19 Aug 2022
Historique:
received:
20
06
2022
revised:
10
08
2022
accepted:
15
08
2022
entrez:
26
8
2022
pubmed:
27
8
2022
medline:
27
8
2022
Statut:
epublish
Résumé
In recent years, the involvement of the gut microbiota in disease and health has been investigated by sequencing the 16S gene from fecal samples. Dysbiotic gut microbiota was also observed in Autism Spectrum Disorder (ASD), a neurodevelopmental disorder characterized by gastrointestinal symptoms. However, despite the relevant number of studies, it is still difficult to identify a typical dysbiotic profile in ASD patients. The discrepancies among these studies are due to technical factors (i.e., experimental procedures) and external parameters (i.e., dietary habits). In this paper, we collected 959 samples from eight available projects (540 ASD and 419 Healthy Controls, HC) and reduced the observed bias among studies. Then, we applied a Machine Learning (ML) approach to create a predictor able to discriminate between ASD and HC. We tested and optimized three algorithms: Random Forest, Support Vector Machine and Gradient Boosting Machine. All three algorithms confirmed the importance of five different genera, including
Identifiants
pubmed: 36009575
pii: biomedicines10082028
doi: 10.3390/biomedicines10082028
pmc: PMC9405825
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : Regione Lazio
ID : "ProgettiStrategici 2019" Project N.A0320-2019-28090 "HGP-T21"
Organisme : Ministero della Salute
ID : RF-2018-12366931
Références
Gut Pathog. 2020 Feb 03;12:6
pubmed: 32025243
Nutrients. 2021 Feb 21;13(2):
pubmed: 33669978
PLoS One. 2011 Jan 27;6(1):e16393
pubmed: 21297998
Front Psychiatry. 2020 Jun 10;11:541
pubmed: 32587537
Sci Rep. 2021 Jan 29;11(1):2618
pubmed: 33514807
Sci Rep. 2021 Jul 12;11(1):14304
pubmed: 34253750
Bioinformatics. 2012 Mar 15;28(6):882-3
pubmed: 22257669
Front Microbiol. 2021 Feb 19;12:634511
pubmed: 33737920
Brain Behav Immun. 2014 Mar;37:197-206
pubmed: 24333160
BMC Bioinformatics. 2020 Aug 21;21(Suppl 10):352
pubmed: 32838759
Mol Nutr Food Res. 2017 May;61(5):
pubmed: 28012235
Clin Transl Med. 2019 May 13;8(1):16
pubmed: 31081530
Sci Rep. 2018 Jan 25;8(1):1597
pubmed: 29371629
BMC Microbiol. 2019 Oct 22;19(1):230
pubmed: 31640566
Front Aging Neurosci. 2019 Jun 18;11:130
pubmed: 31275138
Nat Commun. 2022 Jan 17;13(1):342
pubmed: 35039521
EBioMedicine. 2017 Oct;24:166-178
pubmed: 28965876
Cell. 2019 May 30;177(6):1600-1618.e17
pubmed: 31150625
Front Immunol. 2021 Aug 12;12:722206
pubmed: 34484230
Front Bioeng Biotechnol. 2020 Jan 24;8:6
pubmed: 32039191
Nat Methods. 2016 Jul;13(7):581-3
pubmed: 27214047
Front Pharmacol. 2019 Sep 13;10:1035
pubmed: 31572201
Genomics Proteomics Bioinformatics. 2019 Feb;17(1):26-38
pubmed: 31026579
PLoS One. 2013 Apr 22;8(4):e61217
pubmed: 23630581
Microbiome. 2017 Mar 3;5(1):27
pubmed: 28253908
PLoS One. 2015 Oct 01;10(10):e0137725
pubmed: 26427004
Sci Rep. 2019 Jan 22;9(1):287
pubmed: 30670726
PLoS One. 2013 Jul 03;8(7):e68322
pubmed: 23844187
Brief Bioinform. 2022 Jan 17;23(1):
pubmed: 34791021
Microbiome. 2017 Feb 22;5(1):24
pubmed: 28222761
Sci Rep. 2021 Feb 25;11(1):4565
pubmed: 33633172
Comput Struct Biotechnol J. 2021 Jan 27;19:1092-1107
pubmed: 33680353
PLoS Comput Biol. 2016 Jul 11;12(7):e1004977
pubmed: 27400279
mSystems. 2018 May 15;3(3):
pubmed: 29795809
mSystems. 2019 Sep 3;4(5):
pubmed: 31481602
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
Biomed Pharmacother. 2020 Apr;124:109873
pubmed: 31986412
Clin Psychopharmacol Neurosci. 2017 Feb 28;15(1):47-52
pubmed: 28138110
Gut Microbes. 2020 May 3;11(3):453-464
pubmed: 31530087
Database (Oxford). 2021 Apr 29;2021:
pubmed: 33914028
Microbiome. 2018 Oct 18;6(1):185
pubmed: 30336775
FEMS Microbiol Lett. 2011 Sep;322(1):51-9
pubmed: 21658104
Behav Brain Res. 2015 Jan 15;277:32-48
pubmed: 25078296
Int J Mol Sci. 2021 Mar 15;22(6):
pubmed: 33804088
Adv Exp Med Biol. 2019;1118:253-269
pubmed: 30747427
Int Dent J. 2018 Feb;68(1):39-46
pubmed: 28771699
Gut Microbes. 2020 Sep 2;11(5):1246-1267
pubmed: 32312186
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
Brain Sci. 2020 Apr 19;10(4):
pubmed: 32325848
Gut Microbes. 2022 Jan-Dec;14(1):2051999
pubmed: 35311453
PLoS One. 2014 Nov 07;9(11):e112445
pubmed: 25380056
Cell Mol Gastroenterol Hepatol. 2016 Dec 11;3(2):218-230
pubmed: 28275689
Gut. 2006 Feb;55(2):205-11
pubmed: 16188921
FEMS Microbiol Ecol. 2007 Nov;62(2):142-60
pubmed: 17892477
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21
pubmed: 21062823
Front Microbiol. 2018 Dec 19;9:3146
pubmed: 30619212
Sci Rep. 2016 Sep 30;6:34055
pubmed: 27687977
ISME J. 2019 Jun;13(6):1520-1534
pubmed: 30742017
Physiol Behav. 2015 Jan;138:179-87
pubmed: 25446201
Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14691-6
pubmed: 20679230
Microorganisms. 2019 Aug 19;7(8):
pubmed: 31430948
Front Psychiatry. 2019 Feb 11;10:34
pubmed: 30804820
Genome Med. 2021 Jan 20;13(1):10
pubmed: 33472701
Food Res Int. 2020 Dec;138(Pt B):109778
pubmed: 33288164
Med Microecol. 2020 Jun;4:
pubmed: 34368751
J Proteomics. 2022 Jan 16;251:104407
pubmed: 34763095
J Oral Microbiol. 2019 Dec 12;12(1):1702806
pubmed: 31893019
J Med Microbiol. 2020 Apr;69(4):558-571
pubmed: 32213246
Front Genet. 2019 Jun 25;10:579
pubmed: 31293616
J Psychiatr Res. 2020 Oct;129:149-159
pubmed: 32912596
BMC Nutr. 2020 Dec 11;6(1):72
pubmed: 33303023
Int J Mol Sci. 2019 Apr 29;20(9):
pubmed: 31035684
Nat Methods. 2013 Jan;10(1):57-9
pubmed: 23202435
BioData Min. 2017 Dec 8;10:35
pubmed: 29234465
Commun Biol. 2020 Aug 28;3(1):474
pubmed: 32859925
Microbiome. 2018 May 17;6(1):90
pubmed: 29773078
Microb Ecol. 2018 Nov;76(4):1102-1114
pubmed: 29564487
PLoS One. 2013 Oct 09;8(10):e76993
pubmed: 24130822
PLoS Comput Biol. 2014 Apr 03;10(4):e1003531
pubmed: 24699258
Anaerobe. 2018 Feb;49:121-131
pubmed: 29274915
Gut Microbes. 2015;6(3):207-13
pubmed: 25835343
Front Microbiol. 2022 Jun 09;13:871086
pubmed: 35756062
Microb Pathog. 2020 Dec;149:104568
pubmed: 33096147
BMC Gastroenterol. 2011 Mar 16;11:22
pubmed: 21410934
J Dev Behav Pediatr. 2006 Apr;27(2 Suppl):S128-36
pubmed: 16685179
J Gastroenterol Hepatol. 2018 Nov;33(11):1844-1852
pubmed: 29744928
Nat Biotechnol. 2019 Aug;37(8):852-857
pubmed: 31341288
Pathogens. 2019 Aug 13;8(3):
pubmed: 31412603