Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs
A large number of studies have highlighted the importance of gut microbiome composition in shaping fat deposition in mammals. Several studies have also highlighted how host genome controls the abundance of certain species that make up the gut microbiota. We propose a systematic approach to infer how...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2021-01-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037020305638 |
| _version_ | 1818871654568165376 |
|---|---|
| author | Francesco Tiezzi Justin Fix Clint Schwab Caleb Shull Christian Maltecca |
| author_facet | Francesco Tiezzi Justin Fix Clint Schwab Caleb Shull Christian Maltecca |
| author_sort | Francesco Tiezzi |
| collection | DOAJ |
| description | A large number of studies have highlighted the importance of gut microbiome composition in shaping fat deposition in mammals. Several studies have also highlighted how host genome controls the abundance of certain species that make up the gut microbiota. We propose a systematic approach to infer how the host genome can control the gut microbiome, which in turn contributes to the host phenotype determination. We implemented a mediation test that can be applied to measured and latent dependent variables to describe fat deposition in swine (Sus scrofa). In this study, we identify several host genomic features having a microbiome-mediated effects on fat deposition. This demonstrates how the host genome can affect the phenotypic trait by inducing a change in gut microbiome composition that leads to a change in the phenotype. Host genomic variants identified through our analysis are different than the ones detected in a traditional genome-wide association study. In addition, the use of latent dependent variables allows for the discovery of additional host genomic features that do not show a significant effect on the measured variables. Microbiome-mediated host genomic effects can help understand the genetic determination of fat deposition. Since their contribution to the overall genetic variance is usually not included in association studies, they can contribute to filling the missing heritability gap and provide further insights into the host genome – gut microbiome interplay. Further studies should focus on the portability of these effects to other populations as well as their preservation when pro-/pre-/anti-biotics are used (i.e. remediation). |
| first_indexed | 2024-12-19T12:26:21Z |
| format | Article |
| id | doaj.art-2be0d1f709db407ba3967135e79427dc |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-19T12:26:21Z |
| publishDate | 2021-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-2be0d1f709db407ba3967135e79427dc2022-12-21T20:21:33ZengElsevierComputational and Structural Biotechnology Journal2001-03702021-01-0119530544Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigsFrancesco Tiezzi0Justin Fix1Clint Schwab2Caleb Shull3Christian Maltecca4Department of Animal Science, North Carolina State University, Raleigh, NC, USA; Corresponding author at: 120 W Broughton Dr. 27695-7621, Raleigh, NC, USA.Acuity Ag Solutions, LLC, Carlyle, IL 62230, USAAcuity Ag Solutions, LLC, Carlyle, IL 62230, USA; The Maschhoffs, LLC, Carlyle, IL 62230, USAThe Maschhoffs, LLC, Carlyle, IL 62230, USADepartment of Animal Science, North Carolina State University, Raleigh, NC, USAA large number of studies have highlighted the importance of gut microbiome composition in shaping fat deposition in mammals. Several studies have also highlighted how host genome controls the abundance of certain species that make up the gut microbiota. We propose a systematic approach to infer how the host genome can control the gut microbiome, which in turn contributes to the host phenotype determination. We implemented a mediation test that can be applied to measured and latent dependent variables to describe fat deposition in swine (Sus scrofa). In this study, we identify several host genomic features having a microbiome-mediated effects on fat deposition. This demonstrates how the host genome can affect the phenotypic trait by inducing a change in gut microbiome composition that leads to a change in the phenotype. Host genomic variants identified through our analysis are different than the ones detected in a traditional genome-wide association study. In addition, the use of latent dependent variables allows for the discovery of additional host genomic features that do not show a significant effect on the measured variables. Microbiome-mediated host genomic effects can help understand the genetic determination of fat deposition. Since their contribution to the overall genetic variance is usually not included in association studies, they can contribute to filling the missing heritability gap and provide further insights into the host genome – gut microbiome interplay. Further studies should focus on the portability of these effects to other populations as well as their preservation when pro-/pre-/anti-biotics are used (i.e. remediation).http://www.sciencedirect.com/science/article/pii/S2001037020305638Causal effectGut microbiomeFat depositionLatent variables |
| spellingShingle | Francesco Tiezzi Justin Fix Clint Schwab Caleb Shull Christian Maltecca Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs Computational and Structural Biotechnology Journal Causal effect Gut microbiome Fat deposition Latent variables |
| title | Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs |
| title_full | Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs |
| title_fullStr | Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs |
| title_full_unstemmed | Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs |
| title_short | Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs |
| title_sort | gut microbiome mediates host genomic effects on phenotypes a case study with fat deposition in pigs |
| topic | Causal effect Gut microbiome Fat deposition Latent variables |
| url | http://www.sciencedirect.com/science/article/pii/S2001037020305638 |
| work_keys_str_mv | AT francescotiezzi gutmicrobiomemediateshostgenomiceffectsonphenotypesacasestudywithfatdepositioninpigs AT justinfix gutmicrobiomemediateshostgenomiceffectsonphenotypesacasestudywithfatdepositioninpigs AT clintschwab gutmicrobiomemediateshostgenomiceffectsonphenotypesacasestudywithfatdepositioninpigs AT calebshull gutmicrobiomemediateshostgenomiceffectsonphenotypesacasestudywithfatdepositioninpigs AT christianmaltecca gutmicrobiomemediateshostgenomiceffectsonphenotypesacasestudywithfatdepositioninpigs |