Cargando…

Single-cell analysis and spatial resolution of the gut microbiome

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 etiolog...

Descripción completa

Detalles Bibliográficos
Autores principales: Madhu, Bhoomi, Miller, Brittany M., Levy, Maayan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10582963/
https://www.ncbi.nlm.nih.gov/pubmed/37860069
http://dx.doi.org/10.3389/fcimb.2023.1271092
_version_ 1785122455057072128
author Madhu, Bhoomi
Miller, Brittany M.
Levy, Maayan
author_facet Madhu, Bhoomi
Miller, Brittany M.
Levy, Maayan
author_sort Madhu, Bhoomi
collection PubMed
description 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.
format Online
Article
Text
id pubmed-10582963
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-105829632023-10-19 Single-cell analysis and spatial resolution of the gut microbiome Madhu, Bhoomi Miller, Brittany M. Levy, Maayan Front Cell Infect Microbiol Cellular and Infection Microbiology 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. Frontiers Media S.A. 2023-10-04 /pmc/articles/PMC10582963/ /pubmed/37860069 http://dx.doi.org/10.3389/fcimb.2023.1271092 Text en Copyright © 2023 Madhu, Miller and Levy https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cellular and Infection Microbiology
Madhu, Bhoomi
Miller, Brittany M.
Levy, Maayan
Single-cell analysis and spatial resolution of the gut microbiome
title Single-cell analysis and spatial resolution of the gut microbiome
title_full Single-cell analysis and spatial resolution of the gut microbiome
title_fullStr Single-cell analysis and spatial resolution of the gut microbiome
title_full_unstemmed Single-cell analysis and spatial resolution of the gut microbiome
title_short Single-cell analysis and spatial resolution of the gut microbiome
title_sort single-cell analysis and spatial resolution of the gut microbiome
topic Cellular and Infection Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10582963/
https://www.ncbi.nlm.nih.gov/pubmed/37860069
http://dx.doi.org/10.3389/fcimb.2023.1271092
work_keys_str_mv AT madhubhoomi singlecellanalysisandspatialresolutionofthegutmicrobiome
AT millerbrittanym singlecellanalysisandspatialresolutionofthegutmicrobiome
AT levymaayan singlecellanalysisandspatialresolutionofthegutmicrobiome