A Comparative Review on Microbiota Manipulation: Lessons From Fish, Plants, Livestock, and Human Research

Abstract

During recent years the impact of microbial communities on the health of their host (being plants, fish, and terrestrial animals including humans) has received increasing attention. The microbiota provides the host with nutrients, induces host immune development and metabolism, and protects the host against invading pathogens (1–6). Through millions of years of co-evolution bacteria and hosts have developed intimate relationships. Microbial colonization shapes the host immune system that in turn can shape the microbial composition (7–9). However, with the large scale use of antibiotics in agriculture and human medicine over the last decades an increase of diseases associated with so-called dysbiosis has emerged. Dysbiosis refers to either a disturbed microbial composition (outgrowth of possible pathogenic species) or a disturbed interaction between bacteria and the host (10). Instead of using more antibiotics to treat dysbiosis there is a need to develop alternative strategies to combat disturbed microbial control. To this end, we can learn from nature itself. For example, the plant root (or “rhizosphere”) microbiome of sugar beet contains several bacterial species that suppress the fungal root pathogen Rhizoctonia solani, an economically important fungal pathogen of this crop (11). Likewise, commensal bacteria present on healthy human skin produce antimicrobial molecules that selectively kill skin pathogen Staphylococcus aureus. Interestingly, patients with atopic dermatitis (inflammation of the skin) lacked antimicrobial peptide secreting commensal skin bacteria (12). In this review, we will give an overview of microbial manipulation in fish, plants, and terrestrial animals including humans to uncover conserved mechanisms and learn how we might restore microbial balance increasing the resilience of the host species.

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

“…The microbiome is a term that describes the collective genome of microbial communities, the so-called microbiota, which is associated with humans, animals, and plants. 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 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]. Compared to the number of studies on the microbiota of human subjects, there is a minimal number of studies focusing on economically agricultural crops.…”

Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota

“…This includes common strategies that aim to modulate the sh microbiota through the diet in order to improve disease resistance, nutrient digestibility, tolerance to stress, and reproduction [17]. More recently, however, procedures such as faecal microbiota transplantation (FMT) have be touted as a prospective, more holistic approach that has the capacity to improve outcomes by modulating the entire microbial community and facilitating the re-establishment of defunct species [18,19]. First developed in 1958 to cure pseudomembranous enterocolitis in humans [20], FMT has since been used to successfully treat a range of other conditions including, among others, Clostridioides di cile infection, in ammatory bowel disease (IBD), and obesity [21].…”

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

“…Intestinal microbiota is key for many host functions, such as digestion, nutrient absorption and metabolism, disease resistance, and immune training and function. Its importance in health has led to an increasing interest in manipulating these populations to improve animal welfare, not only in humans, but also in livestock and sh [34]. Due to its economic value, many studies on gilthead sea bream intestinal microbiota have been conducted.…”