Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

ABSTRACT

Inflammatory Bowel Disease (IBD) is a chronic immune-mediated inflammatory disease of the gastrointestinal tract that is a growing public burden. Gut microbes and their interactions with hosts play a crucial role in disease pathogenesis and progression. These interactions are complex, spanning multiple physiological systems and data types, making comprehensive disease assessment difficult, and often overwhelming single-omic capabilities. Stool-based multi-omics is a promising approach for characterizing host-gut microbiome interactions using deep integration of technologies such as 16S rRNA sequencing, shotgun metagenomics, meta-transcriptomics, metabolomics, and metaproteomics. The wealth of information generated through multi-omic studies is poised to usher in advancements in IBD research and precision medicine. This review highlights historical and recent findings from stool-based muti-omic studies that have contributed to unraveling IBD’s complexity. Finally, we discuss common pitfalls, issues, and limitations, and how future pipelines should address them to standardize multi-omics in IBD research and beyond.

Related collections

Most cited references 108

Record: found
Abstract: found
Article: found

Is Open Access

Structure, Function and Diversity of the Healthy Human Microbiome

Tatiana Vishnivetskaya, Jeroen Raes (2014)

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin, and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics, and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analyzed the largest cohort and set of distinct, clinically relevant body habitats to date. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families, and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology, and translational applications of the human microbiome.

0 comments Cited 2304 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Human gut microbiome viewed across age and geography

Tanya Yatsunenko, Federico E Rey, Mark Manary … (2012)

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ between human populations when viewed from the perspective of component microbial lineages, encoded metabolic functions, stage of postnatal development, and environmental exposures, we characterized bacterial species present in fecal samples obtained from 531 individuals representing healthy Amerindians from the Amazonas of Venezuela, residents of rural Malawian communities, and inhabitants of USA metropolitan areas, as well as the gene content of 110 of their microbiomes. This cohort encompassed infants, children, teenagers and adults, parents and offspring, and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the representation of genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial species assemblages and functional gene repertoires were noted between individuals residing in the USA compared to the other two countries. These distinctive features are evident in early infancy as well as adulthood. In addition, the similarity of fecal microbiomes among family members extends across cultures. These findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations, and the impact of Westernization.

0 comments Cited 1543 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

mixOmics: An R package for ‘omics feature selection and multiple data integration

Florian Rohart, Benoît Gautier, Amrit Singh … (2017)

The advent of high throughput technologies has led to a wealth of publicly available ‘omics data coming from different sources, such as transcriptomics, proteomics, metabolomics. Combining such large-scale biological data sets can lead to the discovery of important biological insights, provided that relevant information can be extracted in a holistic manner. Current statistical approaches have been focusing on identifying small subsets of molecules (a ‘molecular signature’) to explain or predict biological conditions, but mainly for a single type of ‘omics. In addition, commonly used methods are univariate and consider each biological feature independently. We introduce mixOmics, an R package dedicated to the multivariate analysis of biological data sets with a specific focus on data exploration, dimension reduction and visualisation. By adopting a systems biology approach, the toolkit provides a wide range of methods that statistically integrate several data sets at once to probe relationships between heterogeneous ‘omics data sets. Our recent methods extend Projection to Latent Structure (PLS) models for discriminant analysis, for data integration across multiple ‘omics data or across independent studies, and for the identification of molecular signatures. We illustrate our latest mixOmics integrative frameworks for the multivariate analyses of ‘omics data available from the package.

0 comments Cited 1172 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Journal

Journal ID (nlm-ta): Gut Microbes

Journal ID (iso-abbrev): Gut Microbes

Title: Gut Microbes

Publisher: Taylor & Francis

ISSN (Print): 1949-0976

ISSN (Electronic): 1949-0984

Publication date (Electronic, pub): 11 December 2022

Publication date (Electronic, collection): 2022

Publication date PMC-release: 11 December 2022

Volume: 14

Issue: 1

Electronic Location Identifier: 2154092

Affiliations

[a ]Department of Pharmacology, University of California San Diego; , La Jolla, CA, USA

[b ]Skaggs School of Pharmacy, University of California San Diego; , La Jolla, CA, USA

[c ]Center for Microbiome Innovation, University of California San Diego; , La Jolla, CA, USA

[d ]Department of Pediatrics, University of California San Diego; , La Jolla, CA, USA

[e ]Department of Bioengineering, University of California San Diego; , La Jolla, CA, USA

[f ]Department of Computer Science and Engineering, University of California San Diego; , La Jolla, CA, USA

[g ]Division of Gastroenterology and Hepatology, Northwestern University; , Chicago, IL, USA

Author notes

CONTACT Carlos Gonzalez c6gonzalez@ 123456health.ucsd.edu Department of Pharmacology, University of California San Diego; , La Jolla, CA, USA

Author information

Consuelo Sauceda https://orcid.org/0000-0002-1487-6631

Carlos G. Gonzalez https://orcid.org/0000-0002-4673-4048

Article

Publisher ID: 2154092

DOI: 10.1080/19490976.2022.2154092

PMC ID: 9746627

PubMed ID: 36503356

SO-VID: 42ecddad-ff47-452a-9651-dfcfe9a3c07a

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Stool multi-omics for the study of host–microbe interactions in inflammatory bowel disease

Read this article at

ABSTRACT

Related collections

Microbial Genomics

Most cited references 108

Structure, Function and Diversity of the Healthy Human Microbiome

Human gut microbiome viewed across age and geography

mixOmics: An R package for ‘omics feature selection and multiple data integration

Author and article information

Journal

Affiliations

Author notes

Author information

Article

History

Page count

Categories

Comments

Comment on this article

Similar content 511

Cited by 5

Most referenced authors 3,560