Predicting feed efficiency of Angus steers using the gastrointestinal microbiome
Microbial composition of the gastrointestinal tracts is an important factor affecting the variation in feed efficiency in ruminants. Several studies have investigated the composition of the ruminal and fecal microbiotas, as well as their impacts on feed efficiency and digestion. In addition, next-ge...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-03-01
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| Series: | Animal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1751731124000338 |
| _version_ | 1797256447811125248 |
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| author | M. Congiu J. Lourenco A. Cesarani U. Lamichhane N.P.P. Macciotta C. Dimauro |
| author_facet | M. Congiu J. Lourenco A. Cesarani U. Lamichhane N.P.P. Macciotta C. Dimauro |
| author_sort | M. Congiu |
| collection | DOAJ |
| description | Microbial composition of the gastrointestinal tracts is an important factor affecting the variation in feed efficiency in ruminants. Several studies have investigated the composition of the ruminal and fecal microbiotas, as well as their impacts on feed efficiency and digestion. In addition, next-generation DNA sequencing techniques have allowed us to gain a better understanding of such microbiomes. In this study, the beef cattle microbiome data were analyzed using both a multivariate and a univariate approach and the results were compared. Moreover, a statistical procedure to classify calves in two groups with extreme Residual Feed Intake (RFI) values, using their microbiota profile, was developed. Both fecal and ruminal samples were collected from 63 Angus steers at two different time points for evaluation of their microbiomes: at the beginning and at the end of the feedlot. An additional fecal sample was collected at weaning. A total of 149 and 119 bacterial families (BFs) were retrieved from the ruminal and fecal samples, respectively. A Canonical Discriminant Analysis (CDA) was used to investigate whether BFs were able to distinguish between rumen and fecal samples. A sub-sample of 28 steers was divided in two groups based on their feed efficiency status: positive or negative for RFI. Fecal samples collected at weaning were used to assign the positive and negative RFI animals to their corresponding groups using both Stepwise Discriminant Analysis and CDA. Results revealed that CDA was able to distinguish between rumen and fecal samples. Peptostreptococcaceae was the family most associated with the fecal samples, whereas Prevotellaceae the most associated with the ruminal samples. The CDA using 19 BFs selected from the stepwise was able to correctly assign all animals to the proper RFI groups (negative or positive). Rhizobiaceae was the family most associated with negative RFI, whereas Comamonadacea was the family most linked with positive RFI. The results from this study showed that the multivariate approach can be used to improve microbiome data analysis, as well as to predict feed efficiency in beef cattle using information derived from the fecal microbiome. |
| first_indexed | 2024-03-07T16:54:14Z |
| format | Article |
| id | doaj.art-dae7db02f1884de4b592e253a2a2efa1 |
| institution | Directory Open Access Journal |
| issn | 1751-7311 |
| language | English |
| last_indexed | 2024-04-24T22:21:54Z |
| publishDate | 2024-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Animal |
| spelling | doaj.art-dae7db02f1884de4b592e253a2a2efa12024-03-20T06:09:00ZengElsevierAnimal1751-73112024-03-01183101102Predicting feed efficiency of Angus steers using the gastrointestinal microbiomeM. Congiu0J. Lourenco1A. Cesarani2U. Lamichhane3N.P.P. Macciotta4C. Dimauro5Dipartimento di Agraria, University of Sassari, Sassari 07100, Italy; Department of Animal and Dairy Science, University of Georgia, Athens 30602, GA, USADepartment of Animal and Dairy Science, University of Georgia, Athens 30602, GA, USADipartimento di Agraria, University of Sassari, Sassari 07100, Italy; Department of Animal and Dairy Science, University of Georgia, Athens 30602, GA, USA; Corresponding author at: Viale Italia 39, Sassari (SS) 07100, Italy.Department of Animal and Dairy Science, University of Georgia, Athens 30602, GA, USADipartimento di Agraria, University of Sassari, Sassari 07100, ItalyDipartimento di Agraria, University of Sassari, Sassari 07100, ItalyMicrobial composition of the gastrointestinal tracts is an important factor affecting the variation in feed efficiency in ruminants. Several studies have investigated the composition of the ruminal and fecal microbiotas, as well as their impacts on feed efficiency and digestion. In addition, next-generation DNA sequencing techniques have allowed us to gain a better understanding of such microbiomes. In this study, the beef cattle microbiome data were analyzed using both a multivariate and a univariate approach and the results were compared. Moreover, a statistical procedure to classify calves in two groups with extreme Residual Feed Intake (RFI) values, using their microbiota profile, was developed. Both fecal and ruminal samples were collected from 63 Angus steers at two different time points for evaluation of their microbiomes: at the beginning and at the end of the feedlot. An additional fecal sample was collected at weaning. A total of 149 and 119 bacterial families (BFs) were retrieved from the ruminal and fecal samples, respectively. A Canonical Discriminant Analysis (CDA) was used to investigate whether BFs were able to distinguish between rumen and fecal samples. A sub-sample of 28 steers was divided in two groups based on their feed efficiency status: positive or negative for RFI. Fecal samples collected at weaning were used to assign the positive and negative RFI animals to their corresponding groups using both Stepwise Discriminant Analysis and CDA. Results revealed that CDA was able to distinguish between rumen and fecal samples. Peptostreptococcaceae was the family most associated with the fecal samples, whereas Prevotellaceae the most associated with the ruminal samples. The CDA using 19 BFs selected from the stepwise was able to correctly assign all animals to the proper RFI groups (negative or positive). Rhizobiaceae was the family most associated with negative RFI, whereas Comamonadacea was the family most linked with positive RFI. The results from this study showed that the multivariate approach can be used to improve microbiome data analysis, as well as to predict feed efficiency in beef cattle using information derived from the fecal microbiome.http://www.sciencedirect.com/science/article/pii/S1751731124000338Discriminant AnalysisMicrobiotaMultivariate analysisResidual Feed IntakeRumen |
| spellingShingle | M. Congiu J. Lourenco A. Cesarani U. Lamichhane N.P.P. Macciotta C. Dimauro Predicting feed efficiency of Angus steers using the gastrointestinal microbiome Animal Discriminant Analysis Microbiota Multivariate analysis Residual Feed Intake Rumen |
| title | Predicting feed efficiency of Angus steers using the gastrointestinal microbiome |
| title_full | Predicting feed efficiency of Angus steers using the gastrointestinal microbiome |
| title_fullStr | Predicting feed efficiency of Angus steers using the gastrointestinal microbiome |
| title_full_unstemmed | Predicting feed efficiency of Angus steers using the gastrointestinal microbiome |
| title_short | Predicting feed efficiency of Angus steers using the gastrointestinal microbiome |
| title_sort | predicting feed efficiency of angus steers using the gastrointestinal microbiome |
| topic | Discriminant Analysis Microbiota Multivariate analysis Residual Feed Intake Rumen |
| url | http://www.sciencedirect.com/science/article/pii/S1751731124000338 |
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