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Microorganisms
Volume 11
Issue 3
10.3390/microorganisms11030663
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Article

Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values

by
Nelson Manzanares-Miranda
1,†,
Jose F. Garcia-Mazcorro
2,†,
Eduardo B. Pérez-Medina
2,
Anakaren Vaquera-Vázquez
3,
Alejandro Martínez-Ruiz
3,
Yareellys Ramos-Zayas
2,4 and
Jorge R. Kawas
4,5,*
1
Centro de Investigación en Producción Agropecuaria (CIPA), Universidad Autónoma de Nuevo León (UANL), Linares 67700, Mexico
2
Research and Development, MNA de Mexico, San Nicolas de los Garza 66477, Mexico
3
Laboratorio de Biología Molecular, Laboratorio Central Regional del Norte (LCRN), Guadalupe 67100, Mexico
4
Posgrado Conjunto Agronomía-Veterinaria, UANL, General Escobedo 66054, Mexico
5
Facultad de Agronomía, UANL, General Escobedo 66054, Mexico
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Microorganisms 2023, 11(3), 663; https://doi.org/10.3390/microorganisms11030663
Submission received: 17 January 2023 / Revised: 14 February 2023 / Accepted: 1 March 2023 / Published: 6 March 2023
(This article belongs to the Special Issue Beneficial Microbes and Gastrointestinal Microbiota)
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Abstract

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 (n = 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 Succiniclasticum (lower in LRFI, p = 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, p = 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.
Keywords: beef cattle; feed efficiency; residual feed intake; ruminal microbiota; Succiniclasticum beef cattle; feed efficiency; residual feed intake; ruminal microbiota; Succiniclasticum

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MDPI and ACS Style

Manzanares-Miranda, N.; Garcia-Mazcorro, J.F.; Pérez-Medina, E.B.; Vaquera-Vázquez, A.; Martínez-Ruiz, A.; Ramos-Zayas, Y.; Kawas, J.R. Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values. Microorganisms 2023, 11, 663. https://doi.org/10.3390/microorganisms11030663

AMA Style

Manzanares-Miranda N, Garcia-Mazcorro JF, Pérez-Medina EB, Vaquera-Vázquez A, Martínez-Ruiz A, Ramos-Zayas Y, Kawas JR. Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values. Microorganisms. 2023; 11(3):663. https://doi.org/10.3390/microorganisms11030663

Chicago/Turabian Style

Manzanares-Miranda, Nelson, Jose F. Garcia-Mazcorro, Eduardo B. Pérez-Medina, Anakaren Vaquera-Vázquez, Alejandro Martínez-Ruiz, Yareellys Ramos-Zayas, and Jorge R. Kawas. 2023. "Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values" Microorganisms 11, no. 3: 663. https://doi.org/10.3390/microorganisms11030663

APA Style

Manzanares-Miranda, N., Garcia-Mazcorro, J. F., Pérez-Medina, E. B., Vaquera-Vázquez, A., Martínez-Ruiz, A., Ramos-Zayas, Y., & Kawas, J. R. (2023). Microbial Populations in Ruminal Liquid Samples from Young Beefmaster Bulls at Both Extremes of RFI Values. Microorganisms, 11(3), 663. https://doi.org/10.3390/microorganisms11030663

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