The rumen microbiome composition from Raramuri Criollo and European cattle in an extensive system

Authors: MAYNEZ-PEREZ, ADRIAN - Universidad Autonoma De Chihuahua; JAHUEY-MARTINEZ, FRANCISCO - Universidad Autonoma De Chihuahua; MARTINEZ-QUINTANA, JOSE - Universidad Autonoma De Chihuahua; HUME, MICHAEL - Retired ARS Employee; Anderson, Robin; CORRAL-LUNA, AGUSTIN - Universidad Autonoma De Chihuahua; RODRIGUEZ-ALMEIDA, FELIPE - Universidad Autonoma De Chihuahua; CASTILLO-CASTILLO, YAMICELA - Universidad Autonoma De Chihuahua; FELIX-PORTILLO, MONSERRATH - Universidad Autonoma De Chihuahua

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2024
Publication Date: 10/31/2024
Citation: Maynez-Perez, A., Jahuey-Martinez, F., Martinez-Quintana, J.A., Hume, M., Anderson, R.C., Corral-Luna, A., Rodriguez-Almeida, F., Castillo-Castillo, Y., Felix-Portillo, M. 2024. The rumen microbiome composition from Raramuri Criollo and European cattle in an extensive system. Microorganisms. 12(11). Article 2203. https://doi.org/10.3390/microorganisms12112203.
DOI: https://doi.org/10.3390/microorganisms12112203

Interpretive Summary: Understanding the relationship between native cattle of southwestern North America, called Raramuri Criollo cattle (RC), and the microbial ecosystem of their gastrointestinal tract, will help identify advantageous characteristics of these cattle to improve the sustainability of current beef production systems. Our objective was to characterize the rumen microbiome of RC in comparison to the European sourced breeds, Angus and Herefords. Gut contents were collected from 63 cows grazing in the same paddock during 45 d, in dry and in rainy seasons. DNA from gut contents was isolated and analyzed to compare the genetic similarity of the microbial populations. Results revealed differences between the populations of gut microbes collected from the native cattle and the European cattle and these differences were clearly impacted by the season. Results indicated that the microbial populations in the gut of the native cattle were better adapted to hostile environmental conditions by having microbial groups specialized in the degradation of highly fibrous grasses. These results will help livestock producers select and breed cattle more able to thrive in the dry regions of the southwestern parts of North America.

Technical Abstract: Understanding the relationship between Raramuri Criollo cattle (RC) and their microbial ruminal ecosystem will help identify advantageous characteristics of adapted cattle as alternatives to reach sustainable beef production systems. Our objective was to characterize the rumen microbiome of RC in comparison to Angus and Hereford breeds (European, E) and the cross between them (ExRC). Ruminal fluid was collected from 63 cows in their second productive cycle after grazing in the same paddock during 45 d, in dry (n=28) and rain (n=35) seasons. DNA from ruminal fluid was isolated for 16s rRNA gene next generation sequencing. The data were analyzed with QIIME2 and compared against SILVA 16s rRNA database. Beta diversity was different (p<0.05) between RC and E in both seasons. A microbial core was represented by the most abundant phyla. Planctomycetes and Spirochaetes represented above 1% in the rain season and below 1% in the dry one, whereas Euryarchaeota was below 1% and around 3%, respectively. LEfSe analysis identified differentiated (p<0.05) key microbial groups that explain the differences between lineages at different taxonomic levels, reflecting the ability of the rumen ecosystem of RC cattle to adapt to hostile environmental conditions by having microbial groups specialized in the degradation of highly fibrous content.