Variations in rumen microbiota and host genome impacted feed efficiency in goat breeds
IntroductionImproving feed efficiency (FE) is a significant goal in animal breeding programs. Variations in FE and its relationship with rumen microbiota remain poorly understood across different goat breeds.MethodsThis study assessed the influence of the rumen microbiome and host genome on FE in 10...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2025-01-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1492742/full |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832582914431254528 |
|---|---|
| author | Alaa Emara Rabee Ibrahim Abou-souliman Ahmed I. Yousif Mebarek Lamara Mohamed A. El-Sherbieny Eman Ali Elwakeel Ahmed M. Sallam |
| author_facet | Alaa Emara Rabee Ibrahim Abou-souliman Ahmed I. Yousif Mebarek Lamara Mohamed A. El-Sherbieny Eman Ali Elwakeel Ahmed M. Sallam |
| author_sort | Alaa Emara Rabee |
| collection | DOAJ |
| description | IntroductionImproving feed efficiency (FE) is a significant goal in animal breeding programs. Variations in FE and its relationship with rumen microbiota remain poorly understood across different goat breeds.MethodsThis study assessed the influence of the rumen microbiome and host genome on FE in 10 Shami (SH) goats and 10 Zaraibi (ZA) goats, all of which were fed the same diet. The animals were genotyped using the Illumina 65KSNP chip arrays v2, and their rumen bacteria and archaea were investigated using PCR-amplicon sequencing of the 16S rRNA gene.ResultsThe results showed that the ZA goats exhibited higher FE than the SH goats (p < 0.05) and a greater relative abundance (p < 0.05) of rumen bacterial groups that are involved in the degradation of cellulose and hemicelluloses, such as Bacteroidota and Fibrobacterota, along with genera such as Prevotella, Lachnospiraceae AC2044 group, Lachnospiraceae NK3A20 group, and Succiniclasticum, which are linked to carbohydrate and nitrogen metabolism pathways. In addition, breed differences were found to affect the proportions of milk fatty acids. The association analysis identified 26 genome windows containing several putative candidate genes, such as TMEM241, AP4S1, FTO, HYAL2, BBS2, CD52, CRYBG2, PIGV, WDTC1, EEF1A2, GBA2, FNIP1, ACSL6, STARD10, VPS26B, ACAD8, GLB1L3, NRN1L, LCAT, and SLC7A6. These genes contributed to FE traits in Egyptian goats, as they are involved in obesity, metabolism, and the transport of energy, vitamins, fatty acids, proteins, and lipids through diverse biological pathways.DiscussionThis study suggests that specific genetic markers and rumen microbial traits could be used to identify high-efficient individuals in Egyptian goat breeds, and improving breeding strategies for FE. |
| format | Article |
| id | doaj-art-be7abff47771481fa737b8d9b53690de |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj-art-be7abff47771481fa737b8d9b53690de2025-01-29T06:45:47ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-01-011610.3389/fmicb.2025.14927421492742Variations in rumen microbiota and host genome impacted feed efficiency in goat breedsAlaa Emara Rabee0Ibrahim Abou-souliman1Ahmed I. Yousif2Mebarek Lamara3Mohamed A. El-Sherbieny4Eman Ali Elwakeel5Ahmed M. Sallam6Animal and Poultry Nutrition Department, Desert Research Center, Cairo, EgyptAnimal and Poultry Breeding Department, Desert Research Center, Cairo, EgyptAnimal Production Research Institute, Agricultural Research Center, Cairo, EgyptForest Research Institute, University of Quebec in Abitibi-Temiscamingue, Rouyn-Noranda, QC, CanadaAnimal Production Research Institute, Agricultural Research Center, Cairo, EgyptDepartment of Animal and Fish Production, Faculty of Agriculture, University of Alexandria, Alexandria, EgyptAnimal and Poultry Breeding Department, Desert Research Center, Cairo, EgyptIntroductionImproving feed efficiency (FE) is a significant goal in animal breeding programs. Variations in FE and its relationship with rumen microbiota remain poorly understood across different goat breeds.MethodsThis study assessed the influence of the rumen microbiome and host genome on FE in 10 Shami (SH) goats and 10 Zaraibi (ZA) goats, all of which were fed the same diet. The animals were genotyped using the Illumina 65KSNP chip arrays v2, and their rumen bacteria and archaea were investigated using PCR-amplicon sequencing of the 16S rRNA gene.ResultsThe results showed that the ZA goats exhibited higher FE than the SH goats (p < 0.05) and a greater relative abundance (p < 0.05) of rumen bacterial groups that are involved in the degradation of cellulose and hemicelluloses, such as Bacteroidota and Fibrobacterota, along with genera such as Prevotella, Lachnospiraceae AC2044 group, Lachnospiraceae NK3A20 group, and Succiniclasticum, which are linked to carbohydrate and nitrogen metabolism pathways. In addition, breed differences were found to affect the proportions of milk fatty acids. The association analysis identified 26 genome windows containing several putative candidate genes, such as TMEM241, AP4S1, FTO, HYAL2, BBS2, CD52, CRYBG2, PIGV, WDTC1, EEF1A2, GBA2, FNIP1, ACSL6, STARD10, VPS26B, ACAD8, GLB1L3, NRN1L, LCAT, and SLC7A6. These genes contributed to FE traits in Egyptian goats, as they are involved in obesity, metabolism, and the transport of energy, vitamins, fatty acids, proteins, and lipids through diverse biological pathways.DiscussionThis study suggests that specific genetic markers and rumen microbial traits could be used to identify high-efficient individuals in Egyptian goat breeds, and improving breeding strategies for FE.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1492742/fullgoat breedsfeed efficiencycaprine genomerumen fermentationbacteria and archaea |
| spellingShingle | Alaa Emara Rabee Ibrahim Abou-souliman Ahmed I. Yousif Mebarek Lamara Mohamed A. El-Sherbieny Eman Ali Elwakeel Ahmed M. Sallam Variations in rumen microbiota and host genome impacted feed efficiency in goat breeds Frontiers in Microbiology goat breeds feed efficiency caprine genome rumen fermentation bacteria and archaea |
| title | Variations in rumen microbiota and host genome impacted feed efficiency in goat breeds |
| title_full | Variations in rumen microbiota and host genome impacted feed efficiency in goat breeds |
| title_fullStr | Variations in rumen microbiota and host genome impacted feed efficiency in goat breeds |
| title_full_unstemmed | Variations in rumen microbiota and host genome impacted feed efficiency in goat breeds |
| title_short | Variations in rumen microbiota and host genome impacted feed efficiency in goat breeds |
| title_sort | variations in rumen microbiota and host genome impacted feed efficiency in goat breeds |
| topic | goat breeds feed efficiency caprine genome rumen fermentation bacteria and archaea |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1492742/full |
| work_keys_str_mv | AT alaaemararabee variationsinrumenmicrobiotaandhostgenomeimpactedfeedefficiencyingoatbreeds AT ibrahimabousouliman variationsinrumenmicrobiotaandhostgenomeimpactedfeedefficiencyingoatbreeds AT ahmediyousif variationsinrumenmicrobiotaandhostgenomeimpactedfeedefficiencyingoatbreeds AT mebareklamara variationsinrumenmicrobiotaandhostgenomeimpactedfeedefficiencyingoatbreeds AT mohamedaelsherbieny variationsinrumenmicrobiotaandhostgenomeimpactedfeedefficiencyingoatbreeds AT emanalielwakeel variationsinrumenmicrobiotaandhostgenomeimpactedfeedefficiencyingoatbreeds AT ahmedmsallam variationsinrumenmicrobiotaandhostgenomeimpactedfeedefficiencyingoatbreeds |