A metaproteomic analysis of the piglet fecal microbiome across the weaning transition
Microbiome analysis has relied largely on metagenomics to characterize microbial populations and predict their functions. Here, we used a metaproteomic analysis of the fecal microbiome in piglets before and after weaning to compare protein abundances as they pertain to microbial populations specific...
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Frontiers Media S.A.
2025-05-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1504433/full |
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| author | Israel Rivera KaLynn Harlow KaLynn Harlow Robert N. Cole Robert O’Meally Wesley Garrett Weili Xiong William Oliver James E. Wells Katie Lynn Summers Nisan Chhetri Olga Postnikova Lea Rempel Matt Crouse Bryan Neville Cary Pirone Davies |
| author_facet | Israel Rivera KaLynn Harlow KaLynn Harlow Robert N. Cole Robert O’Meally Wesley Garrett Weili Xiong William Oliver James E. Wells Katie Lynn Summers Nisan Chhetri Olga Postnikova Lea Rempel Matt Crouse Bryan Neville Cary Pirone Davies |
| author_sort | Israel Rivera |
| collection | DOAJ |
| description | Microbiome analysis has relied largely on metagenomics to characterize microbial populations and predict their functions. Here, we used a metaproteomic analysis of the fecal microbiome in piglets before and after weaning to compare protein abundances as they pertain to microbial populations specific to either a milk- or plant-based diet. Fecal samples were collected from six piglets on the day of weaning and 4 weeks after transitioning to a standard nursery diet. Using the 12,554 protein groups identified in samples, we confirmed the shift in protein composition that takes place in response to the microbial succession following weaning and demonstrated the redundancy in metabolic processes between taxa. We identified taxa with roles as primary degraders based on corresponding proteins synthesized, thereby providing evidence for cross-feeding. Proteins associated with the breakdown of milk-specific carbohydrates were common among pre-weaned pigs, whereas the proteome of post-weaned piglets contained a greater abundance of proteins involved in the breaking down plant-specific carbohydrates. Furthermore, output revealed that production of propionate takes place via the propionaldehyde pathway in pre-weaned piglets, but changes to production via the succinate pathway in post-weaned piglets. Finally, a disproportionate quantity of carbohydrate-active enzymes (CAZymes) (~8%) were produced by fungi, which typically only represent ~0.1% of the microbiome taxa. Information gathered through this characterization of the metaproteome before and after weaning revealed important differences regarding the role of members in the microbial community, thereby providing information for the optimization of diets and products for both piglet and microbiome health. |
| format | Article |
| id | doaj-art-8f44aa9a4fda40e88dee3de5a020af32 |
| institution | DOAJ |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj-art-8f44aa9a4fda40e88dee3de5a020af322025-08-20T03:10:37ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-05-011610.3389/fmicb.2025.15044331504433A metaproteomic analysis of the piglet fecal microbiome across the weaning transitionIsrael Rivera0KaLynn Harlow1KaLynn Harlow2Robert N. Cole3Robert O’Meally4Wesley Garrett5Weili Xiong6William Oliver7James E. Wells8Katie Lynn Summers9Nisan Chhetri10Olga Postnikova11Lea Rempel12Matt Crouse13Bryan Neville14Cary Pirone Davies15Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, ARS, U.S. Department of Agriculture, Beltsville, MD, United StatesAnimal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, ARS, U.S. Department of Agriculture, Beltsville, MD, United StatesOak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, United StatesDepartment of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, United StatesDepartment of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, United StatesAnimal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, ARS, U.S. Department of Agriculture, Beltsville, MD, United StatesU.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, United StatesU.S. Meat Animal Research Center, ARS, U.S. Department of Agriculture, Clay Center, NE, United StatesU.S. Meat Animal Research Center, ARS, U.S. Department of Agriculture, Clay Center, NE, United StatesAnimal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, ARS, U.S. Department of Agriculture, Beltsville, MD, United StatesDepartment of Computer Science, College of Engineering, North Carolina State University, Raleigh, NC, United StatesAnimal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, ARS, U.S. Department of Agriculture, Beltsville, MD, United StatesU.S. Meat Animal Research Center, ARS, U.S. Department of Agriculture, Clay Center, NE, United StatesU.S. Meat Animal Research Center, ARS, U.S. Department of Agriculture, Clay Center, NE, United StatesU.S. Meat Animal Research Center, ARS, U.S. Department of Agriculture, Clay Center, NE, United StatesAnimal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, ARS, U.S. Department of Agriculture, Beltsville, MD, United StatesMicrobiome analysis has relied largely on metagenomics to characterize microbial populations and predict their functions. Here, we used a metaproteomic analysis of the fecal microbiome in piglets before and after weaning to compare protein abundances as they pertain to microbial populations specific to either a milk- or plant-based diet. Fecal samples were collected from six piglets on the day of weaning and 4 weeks after transitioning to a standard nursery diet. Using the 12,554 protein groups identified in samples, we confirmed the shift in protein composition that takes place in response to the microbial succession following weaning and demonstrated the redundancy in metabolic processes between taxa. We identified taxa with roles as primary degraders based on corresponding proteins synthesized, thereby providing evidence for cross-feeding. Proteins associated with the breakdown of milk-specific carbohydrates were common among pre-weaned pigs, whereas the proteome of post-weaned piglets contained a greater abundance of proteins involved in the breaking down plant-specific carbohydrates. Furthermore, output revealed that production of propionate takes place via the propionaldehyde pathway in pre-weaned piglets, but changes to production via the succinate pathway in post-weaned piglets. Finally, a disproportionate quantity of carbohydrate-active enzymes (CAZymes) (~8%) were produced by fungi, which typically only represent ~0.1% of the microbiome taxa. Information gathered through this characterization of the metaproteome before and after weaning revealed important differences regarding the role of members in the microbial community, thereby providing information for the optimization of diets and products for both piglet and microbiome health.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1504433/fullmetaproteomemicrobiomeweaningdigestionswine |
| spellingShingle | Israel Rivera KaLynn Harlow KaLynn Harlow Robert N. Cole Robert O’Meally Wesley Garrett Weili Xiong William Oliver James E. Wells Katie Lynn Summers Nisan Chhetri Olga Postnikova Lea Rempel Matt Crouse Bryan Neville Cary Pirone Davies A metaproteomic analysis of the piglet fecal microbiome across the weaning transition Frontiers in Microbiology metaproteome microbiome weaning digestion swine |
| title | A metaproteomic analysis of the piglet fecal microbiome across the weaning transition |
| title_full | A metaproteomic analysis of the piglet fecal microbiome across the weaning transition |
| title_fullStr | A metaproteomic analysis of the piglet fecal microbiome across the weaning transition |
| title_full_unstemmed | A metaproteomic analysis of the piglet fecal microbiome across the weaning transition |
| title_short | A metaproteomic analysis of the piglet fecal microbiome across the weaning transition |
| title_sort | metaproteomic analysis of the piglet fecal microbiome across the weaning transition |
| topic | metaproteome microbiome weaning digestion swine |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1504433/full |
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