Single-cell analysis and spatial resolution of the gut microbiome.
genomics
microbiome
sequencing
single cell
spatial resolution
Journal
Frontiers in cellular and infection microbiology
ISSN: 2235-2988
Titre abrégé: Front Cell Infect Microbiol
Pays: Switzerland
ID NLM: 101585359
Informations de publication
Date de publication:
2023
2023
Historique:
received:
01
08
2023
accepted:
11
09
2023
medline:
23
10
2023
pubmed:
20
10
2023
entrez:
20
10
2023
Statut:
epublish
Résumé
Over the past decade it has become clear that various aspects of host physiology, metabolism, and immunity are intimately associated with the microbiome and its interactions with the host. Specifically, the gut microbiome composition and function has been shown to play a critical role in the etiology of different intestinal and extra-intestinal diseases. While attempts to identify a common pattern of microbial dysbiosis linked with these diseases have failed, multiple studies show that bacterial communities in the gut are spatially organized and that disrupted spatial organization of the gut microbiome is often a common underlying feature of disease pathogenesis. As a result, focus over the last few years has shifted from analyzing the diversity of gut microbiome by sequencing of the entire microbial community, towards understanding the gut microbiome in spatial context. Defining the composition and spatial heterogeneity of the microbiome is critical to facilitate further understanding of the gut microbiome ecology. Development in single cell genomics approach has advanced our understanding of microbial community structure, however, limitations in approaches exist. Single cell genomics is a very powerful and rapidly growing field, primarily used to identify the genetic composition of microbes. A major challenge is to isolate single cells for genomic analyses. This review summarizes the different approaches to study microbial genomes at single-cell resolution. We will review new techniques for microbial single cell sequencing and summarize how these techniques can be applied broadly to answer many questions related to the microbiome composition and spatial heterogeneity. These methods can be used to fill the gaps in our understanding of microbial communities.
Identifiants
pubmed: 37860069
doi: 10.3389/fcimb.2023.1271092
pmc: PMC10582963
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
1271092Subventions
Organisme : NIEHS NIH HHS
ID : P30 ES013508
Pays : United States
Organisme : NIAID NIH HHS
ID : T32 AI055400
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA014520
Pays : United States
Informations de copyright
Copyright © 2023 Madhu, Miller and Levy.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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