Abstract
In pigs, the gut microbiota composition plays a major role in the process of digestion, but is influenced by many external factors, especially diet. To be used in breeding applications, genotype by diet interactions on microbiota composition have to be quantified, as well as their impact on genetic covariances with feed efficiency (FE) and digestive efficiency (DE) traits. This study aimed at determining the impact of an alternative diet on variance components of microbiota traits (genera and alpha diversity indices), and estimating genetic correlations between microbiota and efficiency traits for pigs fed a conventional (CO) or a high fiber (HF) diet. Fecal microbes of 812 full-siblings fed a CO diet and 752 pigs fed the HF diet were characterized at 16 weeks of age by sequencing the V3-V4 region of the 16S rRNA gene. A total of 231 genera were identified. Digestibility coefficients of nitrogen, organic matter and energy were predicted analyzing the same fecal samples with near infrared spectrometry. Daily feed intake, feed conversion ratio, residual feed intake and average daily gain (ADG) were also recorded. The 71 genera with less than 20% of zeros were retained for genetic analyses. Heritability (h2) of microbiota traits were similar between diets (from null to 0.38 ± 0.12 in the CO diet and to 0.39 ± 0.12 in the HF diet). Only three out of the 24 genera and two alpha diversity indices with significant h2 in both diets had genetic correlations across diets significantly different from 0.99 (P < 0.05), indicating limited genetic by diet interactions for these traits. When both diets were analyzed jointly, 59 genera had h2 significantly different from zero. Based on the genetic correlations between these genera and ADG, FE and DE traits, three groups of genera could be identified. A group of 29 genera was favorably correlated with DE and FE traits, 14 genera were unfavorably correlated with DE traits, and the last group of 16 genera had correlations close to zero with production traits. However, genera favorably correlated with DE and FE traits were unfavorably correlated with ADG, and vice versa. Alpha diversity indices had correlation patterns similar to the first group. In the end, genetic by diet interactions on gut microbiota composition of growing pigs were limited in this study. Based on this study, microbiota-based traits could be used as proxies to improve FE and DE in growing pigs.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
1 This study is part of the MicroFeed project, under grant ANR-16-CE20-0003, and the Feed-a-Gene Project, funded from the European Union’s H2020 Programme under grant agreement n°633531. The authors would like to acknowledge the breeding companies Axiom and Nucleus for providing animals and co-funding VD’s Ph. D. thesis through France Génétique Porc. Finally, the authors thank the UEPR phenotyping station staff in Le Rheu for animal raising and data recording.
List of abbreviations
- ADG
- average daily gain
- CO
- conventional
- DC
- digestibility coefficient
- DFI
- daily feed intake
- FCR
- feed conversion ratio
- HF
- high fiber
- LW
- Large White
- Microbiota traits
- microbiota genera + alpha diversity indices
- NDF
- neutral detergent fiber
- NE
- net energy
- NIRS
- near infrared spectrometry
- OTU
- operational taxonomic unit
- PCR
- polymerase chain reaction
- RFI
- residual feed intake