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.
Highlights
Today, biologists in agricultural science, regardless of the organism of their interest, focus significant attention on the microbiota, i.e., the complex communities of microorganisms colonizing host animals, fish, and plants [1]
Meta-analyses of 16S rRNA genes from different body parts of animals, fish, and plants are frequently performed expecting that some changes of microbiota will explain the effectiveness of treatments such as feed changes, fertilizer amendment, or gene knockouts on host organisms, which have been conducted with aims to improve productivity and sustainability in agriculture [2]
Microbiota datasets obtained from livestock animals, aquaculture fish, and crop plants grown may significantly be affected by complex environmental factors such as climates, cultivation scales, and uses of antibiotics and fertilizers, which can vary between different countries and regions
Summary
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. 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. 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
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