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Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics.

Authors :
Schmartz GP
Rehner J
Gund MP
Keller V
Molano LG
Rupf S
Hannig M
Berger T
Flockerzi E
Seitz B
Fleser S
Schmitt-Grohé S
Kalefack S
Zemlin M
Kunz M
Götzinger F
Gevaerd C
Vogt T
Reichrath J
Diehl L
Hecksteden A
Meyer T
Herr C
Gurevich A
Krug D
Hegemann J
Bozhueyuek K
Gulder TAM
Fu C
Beemelmanns C
Schattenberg JM
Kalinina OV
Becker A
Unger M
Ludwig N
Seibert M
Stein ML
Hanna NL
Martin MC
Mahfoud F
Krawczyk M
Becker SL
Müller R
Bals R
Keller A
Source :
Nature communications [Nat Commun] 2024 Sep 26; Vol. 15 (1), pp. 8261. Date of Electronic Publication: 2024 Sep 26.
Publication Year :
2024

Abstract

The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.<br /> (© 2024. The Author(s).)

Details

Language :
English
ISSN :
2041-1723
Volume :
15
Issue :
1
Database :
MEDLINE
Journal :
Nature communications
Publication Type :
Academic Journal
Accession number :
39327438
Full Text :
https://doi.org/10.1038/s41467-024-52598-7