How Can We Define “Optimal Microbiota?”: A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture

Abstract

All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.

Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream

“…As in previous studies with this species, the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes dominate the autochthonous microbiota of the intestine [36,41,43]. In all animals, Proteobacteria, as facultative anaerobic organisms, commonly dominate these types of niches due to their highly exible metabolic properties [71]. In accordance with the abundance values found in this study, the Proteobacteria family Vibrionaceae has been described to be one of the most abundant symbionts in marine sh [72,73].…”

“…The present results showed a higher abundance of Clostridiaceae in the fast-growth families (11%) when compared to the intermediate and slow-growth families (6 and 7%, respectively). The positive effects of Clostridiales on growth and feed e ciency have been attributed to the production of shortchain fatty acids, with many demonstrated positive effects on animal health, including anti-in ammatory properties, epithelial barrier strengthening and disease resistance [18,71,93].…”

Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework

“…The origin of the microbiota samples explained the majority of differences in alpha diversity patterns. Such differences in diversity were expected as each source compartment possesses its own microbial signature (Thompson et al, 2017;Ikeda-Ohtsubo et al, 2018;Reese and Dunn, 2018). Although, our study was focused on an agricultural food chain, the obtained alpha diversity results using 515F-806R primer pair are comparable with Earth Microbiome Project’s (EMP) findings, where similar primer pair was used to amplify diverse free-living and host-associated microbial communities (Thompson et al, 2017).…”

Cannabis Microbiome and the Role of Endophytes in Modulating the Production of Secondary Metabolites: An Overview

“…During recent years, the impact of microbial communities on shaping the host immune system and fitness of their host has gained attention [30]. The composition of microbiota residing in a host is affected by environmental conditions such as temperature, pH, and nutrient availability [31]. The overuse of xenobiotics in agriculture, along with the emergence of antibiotic and pesticide-resistance strains in agriculture and human medicine, can affect the host capacity to interact properly with the microbiota [30].…”