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,Luciana Gerdes,Helder Louvandini,Partha Ray,Adibe Luiz Abdalla,Elisabete Aparecida De Nadai Fernandes,Lucas William Mendes,Caroline Rymer,Vagner Ovani Da Silva

doi:10.3389/fmicb.2021.768480

Patricia Spoto Corrêa, Carolina Rodriguez Jimenez + Show 8 more

Open Access

https://doi.org/10.3389/fmicb.2021.768480

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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.

Highlights

Brazil is the largest beef exporter in the world with an annual export of 2.49 million tons of carcass weight in 2019 (ABIEC, 2020; USDA, 2020)
We investigated the fecal microbiome by characterizing the functional metagenome and the composition of microbial communities in the feces of beef cattle raised under semi-intensive or traditional management systems
Fecal concentration of As and Pb was higher in beef cattle from T systems, whereas the concentration of Zn and P was higher in the feces of beef cattle from I systems (Table 1)

Summary

Introduction

Brazil is the largest beef exporter in the world with an annual export of 2.49 million tons of carcass weight in 2019 (ABIEC, 2020; USDA, 2020). The predominant breed found in more than 90% of commercial beef herds in Brazil is the Nelore (ABIEC, 2020). This breed is resilient in the Brazilian environment, and most importantly, it is well adapted to the traditional pasture-based beef production system. Most studies focused on the ruminal microbiota, which is understandable considering their substantial contribution to the generation of substrates for energy and protein supply to the host. The lower gut microbiota play an important role in animal health and immunity and contribute, to a lesser extent, to energy supply to the host (Zhang et al, 2019; O’Hara et al, 2020; Valerio et al, 2020). It is critical to characterize the fecal microbiota to understand their contribution to host health and nutrition and to understand the effect of management system on the fecal microbiota composition

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