Engineering the microbiome for animal health and conservation

Abstract

Interest in animal microbiomes as therapeutics is rapidly expanding, as techniques to study the microbial world decrease in cost and increase in accessibility and case studies from human medicine receive widespread attention. In this review, we summarize the current state of techniques to modify the microbiome to improve animal health, focusing on applications in domestic pets, farm animals, and in wild settings for conservation. We discuss options for modifying the microbiome, including community-wide changes such as fecal microbiota transplants, prebiotics, probiotics, and antibiotics, and more targeted approaches such as phage therapy and CRISPR-Cas. We conclude that although much remains to be done in untangling the basic biology of microbiome-directed therapies in animals, the rapid progress currently being made in human medicine and the examples to date of application of probiotics and other microbiome-directed therapies in taxa ranging from horses to salamanders to bees suggest excellent prospects for these technologies as they are further developed and as data on both the benefits and risks are carefully and systematically collected. Impact statement Considering the clear effects of microbiota on important aspects of animal biology and development (including in humans), this topic is timely and broadly appealing, as it compels us to consider the possibilities of altering the microbiome (without antibiotics) to positively affect animal health. In this review, we highlight three general approaches to manipulating the microbiome that have demonstrated success and promise for use in animal health. We also point out knowledge gaps where further inquiry would most benefit the field. Our paper not only provides a short and digestible overview of the current state of application, but also calls for further exploration of the microbial diversity at hand to expand our toolkit, while also leveraging the diversity and flexibility of animal systems to better understand mechanisms of efficacy.

Disease Exposure and Antifungal Bacteria on Skin of Invasive Cane Toads, Australia

“…Our results indicate that the skin bacterial communities on toads from sites overlapping the B. dendrobatidis distribution contain more putative B. dendrobatidis –inhibitory bacteria than is the case for toads from sites not yet invaded by the pathogen. Rather than following predictions regarding immunocompetence at the invasion front, this pattern suggests that B. dendrobatidis –inhibitory bacteria are selected for where the disease is present, in concordance with the adaptive microbiome hypothesis presented by Jin Song et al ( 7 ). Outside of the B. dendrobatidis range, selection for anti– B. dendrobatidis microbes is relaxed; inhibitory microbes represent less of the community, and some disappear.…”

Comparison of the ruminal and fecal microbiotas in beef calves supplemented or not with concentrate

“…The bovine gastrointestinal microbial population is composed of a consortium of microorganisms that exist in a symbiotic relationship with the host animal. Moreover, this gastrointestinal microbiota plays an important role in the host animal's metabolism and homeostasis [1,2]. Next-generation DNA sequencing techniques have made determining nucleotide sequences increasingly affordable and has reached a point where personalized microbiology is a conceivable reality [3].…”

Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum

“…In light of the various threats that koalas face, from chlamydia infection to wildfires ( Polkinghorne, Hanger & Timms, 2013 ), and the growing interest in rescuing and treating them in sanctuaries and zoos, it is important to identify beneficial members of their microbiome. This could (i) help decide which antibiotic compounds to choose during chlamydia treatment in order to maximize persistence of beneficial members in the koala gut microbiome and (ii) guide the development of probiotic cocktails during recovery ( Jin Song et al, 2019 ).…”