Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways.
Genomics
Geographic areas
Microbial genomics
Microbial metabolism
Journal
iScience
ISSN: 2589-0042
Titre abrégé: iScience
Pays: United States
ID NLM: 101724038
Informations de publication
Date de publication:
20 Oct 2023
20 Oct 2023
Historique:
received:
18
04
2023
revised:
14
05
2023
accepted:
18
09
2023
medline:
16
10
2023
pubmed:
16
10
2023
entrez:
16
10
2023
Statut:
epublish
Résumé
A comprehensive metagenomics-based investigation of the microorganisms present within milk kefir communities from across the globe was carried out with a view to defining the milk kefir pan-metagenome, including details relating to core and non-core components. Milk kefir samples, generated by inoculating full fat, pasteurized cow's milk with 64 kefir grains sourced from 25 different countries, were analyzed. We identified core features, including a consistent pattern of domination by representatives from the species
Identifiants
pubmed: 37841598
doi: 10.1016/j.isci.2023.108004
pii: S2589-0042(23)02081-3
pmc: PMC10568436
doi:
Types de publication
Journal Article
Langues
eng
Pagination
108004Informations de copyright
© 2023 The Author(s).
Déclaration de conflit d'intérêts
The authors declare no conflicting interest.
Références
Microorganisms. 2021 Oct 16;9(10):
pubmed: 34683479
Nat Biotechnol. 2021 May;39(5):578-585
pubmed: 33349699
Nucleic Acids Res. 2020 Sep 18;48(16):8883-8900
pubmed: 32766782
Int J Antimicrob Agents. 2005 May;25(5):404-8
pubmed: 15848295
Nutrients. 2019 Aug 05;11(8):
pubmed: 31387262
Virol J. 2019 Feb 1;16(1):15
pubmed: 30709355
mSystems. 2016 Oct 4;1(5):
pubmed: 27822552
F1000Res. 2013 Sep 18;2:191
pubmed: 24555091
Nutrients. 2019 Jun 01;11(6):
pubmed: 31159409
Front Nutr. 2022 May 23;9:902642
pubmed: 35719144
Front Microbiol. 2019 Jan 31;10:4
pubmed: 30766512
Elife. 2021 May 04;10:
pubmed: 33944776
Nucleic Acids Res. 2020 Jan 8;48(D1):D445-D453
pubmed: 31586394
J Dairy Sci. 2007 Apr;90(4):1920-8
pubmed: 17369232
Bioinformatics. 2015 May 15;31(10):1674-6
pubmed: 25609793
Br J Nutr. 2006 May;95(5):939-46
pubmed: 16611384
Nat Biotechnol. 2019 Dec;37(12):1408-1412
pubmed: 31748692
Crit Rev Microbiol. 2022 Oct 26;:1-33
pubmed: 36287644
J Am Diet Assoc. 2003 May;103(5):582-7
pubmed: 12728216
ISME J. 2017 Dec;11(12):2864-2868
pubmed: 28742071
Bioinformatics. 2019 Feb 1;35(3):526-528
pubmed: 30016406
Br J Nutr. 2021 Jan 28;125(2):129-138
pubmed: 32684173
Curr Protoc Bioinformatics. 2020 Mar;69(1):e96
pubmed: 32162851
Food Chem. 2014 Jan 15;143:17-21
pubmed: 24054206
Nutrients. 2022 Apr 06;14(7):
pubmed: 35406140
Curr Nutr Rep. 2020 Sep;9(3):184-192
pubmed: 32472367
Bioinformatics. 2017 Dec 01;33(23):3740-3748
pubmed: 28961782
Science. 2010 Aug 20;329(5994):913-4
pubmed: 20724626
Nat Microbiol. 2021 Feb;6(2):196-208
pubmed: 33398099
Front Microbiol. 2017 Feb 14;8:206
pubmed: 28261168
Int J Syst Evol Microbiol. 2019 Jun;71(3):
pubmed: 33650946
Int J Syst Evol Microbiol. 2019 Jan;69(1A):S1-S111
pubmed: 26596770
Immunobiology. 2007;212(8):647-54
pubmed: 17869642
J Bacteriol. 1992 Dec;174(24):8057-64
pubmed: 1459954
Microbiome. 2021 Feb 1;9(1):37
pubmed: 33522966
Genome Res. 2017 Apr;27(4):626-638
pubmed: 28167665
Genome Biol. 2011 Jun 24;12(6):R60
pubmed: 21702898
Biometrics. 2006 Mar;62(1):245-53
pubmed: 16542252
Microbiome. 2020 May 18;8(1):67
pubmed: 32423436
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31
pubmed: 19855009
Nat Commun. 2019 Jul 17;10(1):3136
pubmed: 31316056
Front Microbiol. 2016 May 04;7:647
pubmed: 27199969
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
Nutrients. 2020 Jan 28;12(2):
pubmed: 32013044
Nat Commun. 2020 May 19;11(1):2500
pubmed: 32427907
Microbiome. 2018 Sep 15;6(1):158
pubmed: 30219103