Assessments of fish gut microbiota during development, and in response to environmental and dietary change

Background: With human population proliferating at an ever alarming rate, and with billions of individuals presently living on the planet starving or suffering from nutrient deficiencies, producing more fish can make an important contribution. The nutritional benefits of fish consumption have a positive link to increased food security and decreased poverty rates in developing countries. Fish, particularly produced through aquaculture, is commonly cheaper than other animal feed, and can be consumed by lower income individuals. Fish also contains much higher protein levels, as well as other important minerals and vitamins. Increased availability of fish can mean better health and a more diverse diet.
Undoubtedly promoting and maintaining fish health is paramount for enhancing fish production.
Extensive research has shown that microbes that reside in the intestine have important roles in maintaining and promoting the health of the host. They can breakdown some food materials to some essential nutrients and vitamins important to maintaining immunity, health and well-being of the host. The microbes also protect the gut from colonization by pathogenic bacteria.
The identity of fish gut microbial composition and how they can be influenced by environmental, dietary and developmental factors is in its infancy. There are carnivorous, herbivorous and omnivorous fish which naturally select specific diets. We do not know if their digestive physiology can adapt to consume commercial feed. This knowledge is important of formulation of appropriate feed to avoid digestive problems.
In this project, a group of scientists knowledgeable in nutrition, intestinal physiology/microbiology and intestinal adaptation to dietary change aim to assess the impact of i) habitat (farms), ii) fish species of different dietary habits, iii) diet and iv) fish maturation, on the microbial populations that reside in the fish intestine.
The intestinal content of 1) adult carnivorous, herbivorous and omnivorous fish obtained from different locations (farms) and 2) fry of the same species, grown under controlled conditions and maintained on different defined diets, will be used. Using modern technologies, the precise composition of microbial populations, and the nutrients they produce, will be determined. Other bodily parameters such as growth, food conversion ratio, and gut morphology will be assessed.
Anticipated outcomes are:
Proving information on microbial populations that reside in intestines of herbivorous, carnivorous and omnivorous fish.
Identifying contributions of environment, diet and fish species on the composition and activity of gut microbes.
Gaining knowledge on the responses of predominant microbial populations to environment, diet, host and developmental signals.
Impact: Characterization of gut microbiota during fish maturation and in fish with different dietary habits will allow scientifically-based feed (feed supplement) formulation to enhance selective gut microbial populations that promote fish growth, health and productivity.
Benefits from this research are to:
Fish: The correct diet will maintain and promote fish health and welfare, prevent disease and increase productivity.
The public: Increasing availability of fish means better health and more diverse diet.
Society and Economy: Contributing towards wealth creation and economic prosperity. Commercial aquaculture has the potential to stimulate economic growth and create jobs.
R&D investment from global business.
The commercialisation and exploitation of scientific knowledge, leading to interaction with industries.

General aim: to comprehensively assess the impact of habitat, species, diet and fish maturation on the intestinal microbiota of three different classes of fish: herbivores (grass carp; Ctenopharyngodon idella), omnivores (common carp; Cyprinus carpio) and carnivores (rainbow trout; Oncorhynchus mykiss). In addition to quantitatively determine the levels of microbial-derived metabolites within the intestinal tracts of the same fish.

Obtaining fish from different locations (farms) we aim to identify i) whether host type or habitat has the greater influence on intestinal microbiota and metabolites, within the same species, ii) inter-individual variation within the same species raised in the same habitat, and iii) differences in microbiota and metabolites between disparate species.

Growing fry under controlled conditions and maintained on defined diets we aim to determine influences of diet and/or ontogenetic signals on resident gut microbiota and metabolites during different maturation stages (fry; adolescent; adult).

Bacterial metabolites will be measured in intestinal contents.
Feed consumption rate, fish weight and gut morphology will be assessed during feeding trials.

Methodology: Bacterial DNA will be extracted from fish intestinal contents, purified and quantified. Next-generation sequencing will be used to analyze 16S rRNA gene sequences. Raw sequencing reads will be subjected to bioinfomatic analyses in order to provide the phylogenetic framework for describing community structure, allowing characterization of microbial ecosystems, its richness and diversity. Bacterial metabolites will be measured by gas chromatography and quantified in relation to an internal standard. Feed consumption rate, weight and gut morphology will be determined by measuring various body parameters and by morphometric analyses.

Academic Impact:
The outcome of this research will act as a platform for further studies in fish addressing issues such as the identification of safe and effective replacements for antibiotics, effect of environmental change and exposure to toxins and pollutants.

The outcome of this project will provide new knowledge that enhances scientific advancement nationally and internationally. It will offer valuable information for scientists and practitioners of diverse disciplines including physiologists, veterinarians, nutritionists, microbiologists, molecular biologists and geneticists. It will contribute to developing expertise and knowledge in multi-disciplinary areas.

Economic and Social Impact:
The audience benefiting from this research are:
The public: Increasing availability of fish means better health and more diverse diet.
Society and Economy: Contributing towards wealth creation and economic prosperity. Commercial aquaculture has the potential to stimulate economic growth and create jobs.
R&D investment from global business.
The commercialisation and exploitation of scientific knowledge, leading to interaction with industries.