Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values
The gut microbiota is involved in the productivity of beef cattle, but the impact of different analysis strategies on microbial composition is unclear. Ruminal samples were obtained from Beefmaster calves (<i>n</i> = 10) at both extremes of residual feed intake (RFI) values (5 with the l...
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MDPI AG
2023-03-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/3/663 |
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| author | Nelson Manzanares-Miranda Jose F. Garcia-Mazcorro Eduardo B. Pérez-Medina Anakaren Vaquera-Vázquez Alejandro Martínez-Ruiz Yareellys Ramos-Zayas Jorge R. Kawas |
| author_facet | Nelson Manzanares-Miranda Jose F. Garcia-Mazcorro Eduardo B. Pérez-Medina Anakaren Vaquera-Vázquez Alejandro Martínez-Ruiz Yareellys Ramos-Zayas Jorge R. Kawas |
| author_sort | Nelson Manzanares-Miranda |
| collection | DOAJ |
| description | The gut microbiota is involved in the productivity of beef cattle, but the impact of different analysis strategies on microbial composition is unclear. Ruminal samples were obtained from Beefmaster calves (<i>n</i> = 10) at both extremes of residual feed intake (RFI) values (5 with the lowest and 5 with the highest RFI) from two consecutive days. Samples were processed using two different DNA extraction methods. The V3 and V4 regions of the 16S rRNA gene were amplified using PCR and sequenced with a MiSeq instrument (Illumina). We analyzed 1.6 million 16S sequences from all 40 samples (10 calves, 2 time points, and 2 extraction methods). The abundance of most microbes was significantly different between DNA extraction methods but not between high-efficiency (LRFI) and low-efficiency (HRFI) animals. Exceptions include the genus <i>Succiniclasticum</i> (lower in LRFI, <i>p</i> = 0.0011), and others. Diversity measures and functional predictions were also mostly affected by DNA extraction methods, but some pathways showed significant differences between RFI levels (e.g., methylglyoxal degradation, higher in LRFI, <i>p</i> = 0.006). The results suggest that the abundance of some ruminal microbes is associated with feed efficiency and serves as a cautionary tale for the interpretation of results obtained with a single DNA extraction method. |
| first_indexed | 2024-03-11T06:09:04Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T06:09:04Z |
| publishDate | 2023-03-01 |
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| series | Microorganisms |
| spelling | doaj.art-27f4d17ea400492b8d7c015c56278cd32023-11-17T12:45:22ZengMDPI AGMicroorganisms2076-26072023-03-0111366310.3390/microorganisms11030663Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI ValuesNelson Manzanares-Miranda0Jose F. Garcia-Mazcorro1Eduardo B. Pérez-Medina2Anakaren Vaquera-Vázquez3Alejandro Martínez-Ruiz4Yareellys Ramos-Zayas5Jorge R. Kawas6Centro de Investigación en Producción Agropecuaria (CIPA), Universidad Autónoma de Nuevo León (UANL), Linares 67700, MexicoResearch and Development, MNA de Mexico, San Nicolas de los Garza 66477, MexicoResearch and Development, MNA de Mexico, San Nicolas de los Garza 66477, MexicoLaboratorio de Biología Molecular, Laboratorio Central Regional del Norte (LCRN), Guadalupe 67100, MexicoLaboratorio de Biología Molecular, Laboratorio Central Regional del Norte (LCRN), Guadalupe 67100, MexicoResearch and Development, MNA de Mexico, San Nicolas de los Garza 66477, MexicoPosgrado Conjunto Agronomía-Veterinaria, UANL, General Escobedo 66054, MexicoThe gut microbiota is involved in the productivity of beef cattle, but the impact of different analysis strategies on microbial composition is unclear. Ruminal samples were obtained from Beefmaster calves (<i>n</i> = 10) at both extremes of residual feed intake (RFI) values (5 with the lowest and 5 with the highest RFI) from two consecutive days. Samples were processed using two different DNA extraction methods. The V3 and V4 regions of the 16S rRNA gene were amplified using PCR and sequenced with a MiSeq instrument (Illumina). We analyzed 1.6 million 16S sequences from all 40 samples (10 calves, 2 time points, and 2 extraction methods). The abundance of most microbes was significantly different between DNA extraction methods but not between high-efficiency (LRFI) and low-efficiency (HRFI) animals. Exceptions include the genus <i>Succiniclasticum</i> (lower in LRFI, <i>p</i> = 0.0011), and others. Diversity measures and functional predictions were also mostly affected by DNA extraction methods, but some pathways showed significant differences between RFI levels (e.g., methylglyoxal degradation, higher in LRFI, <i>p</i> = 0.006). The results suggest that the abundance of some ruminal microbes is associated with feed efficiency and serves as a cautionary tale for the interpretation of results obtained with a single DNA extraction method.https://www.mdpi.com/2076-2607/11/3/663beef cattlefeed efficiencyresidual feed intakeruminal microbiota<i>Succiniclasticum</i> |
| spellingShingle | Nelson Manzanares-Miranda Jose F. Garcia-Mazcorro Eduardo B. Pérez-Medina Anakaren Vaquera-Vázquez Alejandro Martínez-Ruiz Yareellys Ramos-Zayas Jorge R. Kawas Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values Microorganisms beef cattle feed efficiency residual feed intake ruminal microbiota <i>Succiniclasticum</i> |
| title | Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values |
| title_full | Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values |
| title_fullStr | Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values |
| title_full_unstemmed | Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values |
| title_short | Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values |
| title_sort | microbial populations in ruminal liquid samples from young beefmaster bulls at both extremes of rfi values |
| topic | beef cattle feed efficiency residual feed intake ruminal microbiota <i>Succiniclasticum</i> |
| url | https://www.mdpi.com/2076-2607/11/3/663 |
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