Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes
Abstract Background Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior studies have primarily focused on composition, we hypothesized that multi...
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| Format: | Article |
| Language: | English |
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BMC
2023-01-01
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| Series: | Microbiome |
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| Online Access: | https://doi.org/10.1186/s40168-022-01450-5 |
| _version_ | 1797952438032924672 |
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| author | Jonathan P. Jacobs Venu Lagishetty Megan C. Hauer Jennifer S. Labus Tien S. Dong Ryan Toma Momchilo Vuyisich Bruce D. Naliboff Jeffrey M. Lackner Arpana Gupta Kirsten Tillisch Emeran A. Mayer |
| author_facet | Jonathan P. Jacobs Venu Lagishetty Megan C. Hauer Jennifer S. Labus Tien S. Dong Ryan Toma Momchilo Vuyisich Bruce D. Naliboff Jeffrey M. Lackner Arpana Gupta Kirsten Tillisch Emeran A. Mayer |
| author_sort | Jonathan P. Jacobs |
| collection | DOAJ |
| description | Abstract Background Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior studies have primarily focused on composition, we hypothesized that multi-omics assessment of microbial function incorporating both metatranscriptomics and metabolomics would further delineate microbial profiles of IBS and its subtypes. Methods Fecal samples were collected from a racially/ethnically diverse cohort of 495 subjects, including 318 IBS patients and 177 healthy controls, for analysis by 16S rRNA gene sequencing (n = 486), metatranscriptomics (n = 327), and untargeted metabolomics (n = 368). Differentially abundant microbes, predicted genes, transcripts, and metabolites in IBS were identified by multivariate models incorporating age, sex, race/ethnicity, BMI, diet, and HAD-Anxiety. Inter-omic functional relationships were assessed by transcript/gene ratios and microbial metabolic modeling. Differential features were used to construct random forests classifiers. Results IBS was associated with global alterations in microbiome composition by 16S rRNA sequencing and metatranscriptomics, and in microbiome function by predicted metagenomics, metatranscriptomics, and metabolomics. After adjusting for age, sex, race/ethnicity, BMI, diet, and anxiety, IBS was associated with differential abundance of bacterial taxa such as Bacteroides dorei; metabolites including increased tyramine and decreased gentisate and hydrocinnamate; and transcripts related to fructooligosaccharide and polyol utilization. IBS further showed transcriptional upregulation of enzymes involved in fructose and glucan metabolism as well as the succinate pathway of carbohydrate fermentation. A multi-omics classifier for IBS had significantly higher accuracy (AUC 0.82) than classifiers using individual datasets. Diarrhea-predominant IBS (IBS-D) demonstrated shifts in the metatranscriptome and metabolome including increased bile acids, polyamines, succinate pathway intermediates (malate, fumarate), and transcripts involved in fructose, mannose, and polyol metabolism compared to constipation-predominant IBS (IBS-C). A classifier incorporating metabolites and gene-normalized transcripts differentiated IBS-D from IBS-C with high accuracy (AUC 0.86). Conclusions IBS is characterized by a multi-omics microbial signature indicating increased capacity to utilize fermentable carbohydrates—consistent with the clinical benefit of diets restricting this energy source—that also includes multiple previously unrecognized metabolites and metabolic pathways. These findings support the need for integrative assessment of microbial function to investigate the microbiome in IBS and identify novel microbiome-related therapeutic targets. Video Abstract |
| first_indexed | 2024-04-10T22:47:26Z |
| format | Article |
| id | doaj.art-b494a1d45506496484c5c0afc24609e1 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-04-10T22:47:26Z |
| publishDate | 2023-01-01 |
| publisher | BMC |
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| series | Microbiome |
| spelling | doaj.art-b494a1d45506496484c5c0afc24609e12023-01-15T12:16:42ZengBMCMicrobiome2049-26182023-01-0111111810.1186/s40168-022-01450-5Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypesJonathan P. Jacobs0Venu Lagishetty1Megan C. Hauer2Jennifer S. Labus3Tien S. Dong4Ryan Toma5Momchilo Vuyisich6Bruce D. Naliboff7Jeffrey M. Lackner8Arpana Gupta9Kirsten Tillisch10Emeran A. Mayer11Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los AngelesVatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los AngelesVatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los AngelesVatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los AngelesVatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los AngelesViome Life SciencesViome Life SciencesVatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los AngelesDivision of Behavioral Medicine, Department of Medicine, Jacobs School of Medicine, University at Buffalo, SUNYVatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los AngelesVatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los AngelesVatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los AngelesAbstract Background Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior studies have primarily focused on composition, we hypothesized that multi-omics assessment of microbial function incorporating both metatranscriptomics and metabolomics would further delineate microbial profiles of IBS and its subtypes. Methods Fecal samples were collected from a racially/ethnically diverse cohort of 495 subjects, including 318 IBS patients and 177 healthy controls, for analysis by 16S rRNA gene sequencing (n = 486), metatranscriptomics (n = 327), and untargeted metabolomics (n = 368). Differentially abundant microbes, predicted genes, transcripts, and metabolites in IBS were identified by multivariate models incorporating age, sex, race/ethnicity, BMI, diet, and HAD-Anxiety. Inter-omic functional relationships were assessed by transcript/gene ratios and microbial metabolic modeling. Differential features were used to construct random forests classifiers. Results IBS was associated with global alterations in microbiome composition by 16S rRNA sequencing and metatranscriptomics, and in microbiome function by predicted metagenomics, metatranscriptomics, and metabolomics. After adjusting for age, sex, race/ethnicity, BMI, diet, and anxiety, IBS was associated with differential abundance of bacterial taxa such as Bacteroides dorei; metabolites including increased tyramine and decreased gentisate and hydrocinnamate; and transcripts related to fructooligosaccharide and polyol utilization. IBS further showed transcriptional upregulation of enzymes involved in fructose and glucan metabolism as well as the succinate pathway of carbohydrate fermentation. A multi-omics classifier for IBS had significantly higher accuracy (AUC 0.82) than classifiers using individual datasets. Diarrhea-predominant IBS (IBS-D) demonstrated shifts in the metatranscriptome and metabolome including increased bile acids, polyamines, succinate pathway intermediates (malate, fumarate), and transcripts involved in fructose, mannose, and polyol metabolism compared to constipation-predominant IBS (IBS-C). A classifier incorporating metabolites and gene-normalized transcripts differentiated IBS-D from IBS-C with high accuracy (AUC 0.86). Conclusions IBS is characterized by a multi-omics microbial signature indicating increased capacity to utilize fermentable carbohydrates—consistent with the clinical benefit of diets restricting this energy source—that also includes multiple previously unrecognized metabolites and metabolic pathways. These findings support the need for integrative assessment of microbial function to investigate the microbiome in IBS and identify novel microbiome-related therapeutic targets. Video Abstracthttps://doi.org/10.1186/s40168-022-01450-5Irritable bowel syndromeBowel habit subtypesMicrobiomeMulti-omicsMetatranscriptomicsMetabolomics |
| spellingShingle | Jonathan P. Jacobs Venu Lagishetty Megan C. Hauer Jennifer S. Labus Tien S. Dong Ryan Toma Momchilo Vuyisich Bruce D. Naliboff Jeffrey M. Lackner Arpana Gupta Kirsten Tillisch Emeran A. Mayer Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes Microbiome Irritable bowel syndrome Bowel habit subtypes Microbiome Multi-omics Metatranscriptomics Metabolomics |
| title | Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes |
| title_full | Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes |
| title_fullStr | Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes |
| title_full_unstemmed | Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes |
| title_short | Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes |
| title_sort | multi omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes |
| topic | Irritable bowel syndrome Bowel habit subtypes Microbiome Multi-omics Metatranscriptomics Metabolomics |
| url | https://doi.org/10.1186/s40168-022-01450-5 |
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