Expanded microbiome niches of RAG-deficient patients.
RAG deficiency
RNA virus
antimicrobial resistance
bacteria
human microbiome
inborn error of immunity
metagenomic assembled genome
nares
skin
Journal
Cell reports. Medicine
ISSN: 2666-3791
Titre abrégé: Cell Rep Med
Pays: United States
ID NLM: 101766894
Informations de publication
Date de publication:
17 10 2023
17 10 2023
Historique:
received:
13
09
2022
revised:
28
11
2022
accepted:
31
08
2023
medline:
23
10
2023
pubmed:
28
9
2023
entrez:
27
9
2023
Statut:
ppublish
Résumé
The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize skin, nares, and gut microbiota of patients with recombination-activating gene (RAG) deficiency-a rare genetically defined inborn error of immunity (IEI) that results in a broad spectrum of clinical phenotypes. Integrating de novo assembly of metagenomes from RAG-deficient patients with reference genome catalogs provides an expansive multi-kingdom view of microbial diversity. RAG-deficient patient microbiomes exhibit inter-individual variation, including expansion of opportunistic pathogens (e.g., Corynebacterium bovis, Haemophilus influenzae), and a relative loss of body site specificity. We identify 35 and 27 bacterial species derived from skin/nares and gut microbiomes, respectively, which are distinct to RAG-deficient patients compared to healthy individuals. Underscoring IEI patients as potential reservoirs for viral persistence and evolution, we further characterize the colonization of eukaryotic RNA viruses (e.g., Coronavirus 229E, Norovirus GII) in this patient population.
Identifiants
pubmed: 37757827
pii: S2666-3791(23)00372-5
doi: 10.1016/j.xcrm.2023.101205
pmc: PMC10591041
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
101205Investigateurs
Jim Thomas
(J)
James Mullikin
(J)
Alice Young
(A)
Gerry Bouffard
(G)
Betty Barnabas
(B)
Shelise Brooks
(S)
Chloe Buchter
(C)
Juyun Crawford
(J)
Joel Han
(J)
Shi-Ling Ho
(SL)
Richelle Legaspi
(R)
Quino Maduro
(Q)
Holly Marfani
(H)
Casandra Montemayor
(C)
Karen Schandler
(K)
Brian Schmidt
(B)
Christina Sison
(C)
Mal Stantripop
(M)
Sean Black
(S)
Mila Dekhtyar
(M)
Cathy Masiello
(C)
Jenny McDowell
(J)
Morgan Park
(M)
Pam Thomas
(P)
Meg Vemulapalli
(M)
Informations de copyright
Published by Elsevier Inc.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare that they have no competing interests.
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