Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems

Patricia Spoto Corrêa; Carolina Rodriguez Jimenez; Lucas William Mendes; Caroline Rymer; Partha Ray; Luciana Gerdes; Vagner Ovani da Silva; Elisabete Aparecida De Nadai Fernandes; Adibe Luiz Abdalla; Helder Louvandini

doi:10.3389/fmicb.2021.768480

Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems

Front Microbiol. 2021 Dec 8:12:768480. doi: 10.3389/fmicb.2021.768480. eCollection 2021.

Affiliations

¹ Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil.
² Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil.
³ Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom.
⁴ Reference Laboratory on Classification and Evaluation of Animal Products, Institute of Zootechnics, Nova Odessa, Brazil.
⁵ Radioisotopes Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil.

Abstract

The importance of beef production for economy of Brazil and the growing demand for animal protein across the globe warrant an improvement in the beef production system. Although most attention has been on modulation of the rumen microbiome to improve ruminant production, the role of the lower gut microbiome in host health and nutrition remains relatively unexplored. This work aimed to investigate the taxonomy and functional variations in the fecal microbiome of Brazilian beef cattle reared in two different production systems using a metagenomic approach. Sixty male beef cattle from six farms representing semi-intensive (I, n = 2) and traditional (T, n = 4) Brazilian beef production systems were enrolled in the study. Shotgun sequencing was used to characterize taxonomic and functional composition and diversity of the microbiome in fecal samples collected from each animal. Fecal samples were analyzed for copper (Cu), lead (Pb), nitrogen (N), phosphorous (P), selenium (Se), and zinc (Zn) and stable isotopes of carbon (¹³C) and nitrogen (¹⁵N). The fecal microbiome was influenced by the beef production systems with greater functional and lower taxonomic diversity in beef cattle feces from I systems compared with that from T systems. The concentration of N, P, and Zn was higher in beef cattle feces from I systems compared with that from T systems and was associated with taxonomic and functional profile of fecal microbiome in I system, suggesting the role of fecal nutrients in shaping system-specific microbiome. Semi-intensive management practices led to a more complex but less connected fecal microbiome in beef cattle. The microbial community in beef cattle feces from I systems was characterized by greater abundance of beneficial bacteria (phylum Firmicutes and butyrate-producing bacteria family Lachnospiraceae and genera Anaerostipes, Blautia, Butyrivibrio, Eubacterium, Roseburia, and Ruminococcus). In addition, the fecal abundance of microbial genes related to immune system, nutrient metabolism, and energy production was greater in beef cattle raised under I systems compared with that under T systems. Findings of the current study suggest that semi-intensive management practices could facilitate the development of a healthier and more efficient fecal microbiome in beef cattle by driving an increase in the abundance of beneficial bacteria and functional genes.

Keywords: beef cattle; fecal microbiome; metagenome; minerals; production system.