1. Leading the way in Agriculture and Rural Research, Education and Consulting
Overview of Microbiome Research
- Agriculture and Food -
Professor Rainer Roehe
4. Soil - ecosystem
Healthy soil
ecosystem
Protects roots from
diseases and
parasites
Improves structure
of soil particles
Decompose organic
matter toward
humus
Fixation of nitrogen
and other nutrients
Provides nutrients to plants and produces
hormones to stimulate plant grow
Alleviation of stress
factors (draught,
contamination,
salinity, etc.)
7. Industry of plant beneficial microorganisms
• Bio-fertility inoculants
– Nitrogen-Fixing Microbes
– Phosphate Solubilizing Microbes
• Bio-Control microrganisms
– Antibiosis
– Competition for space and nutrients
– Enzymatic activity
– Induced resistance
Bacillus mycoides B38V
(Di Franco et al., 2002;
Ambrosini et al., 2016 )
8. Deep Sequencing of DNA from rumen
microbes
Metagenomic analysis
Domain
e.g.
Archaea,
Bacteria
Phylum
e.g.
Bacterioidetes,
Proteobacteria
Genus
e.g.
Methano-
brevibacter,
Methano-
sphaera
Microbial
enzyme genes
e.g.
KEGG gene
ortholog
Proteins within
KEGG ortholog
Microbial community
Gene-
centric
15. Selection using rumen microbial
information
R2 = 0.81
20 genes
Sampling
rumen fluid in
the abattoir or
live animals
Determination
of the
abundance of
microbial genes
Prediction of
feed efficiency
Prediction of
methane
emission
Prediction of
animal health
R2 = 0.88 R2 = ???
EBV FCE EBV CH4
EBV
Health
49 genes X genes
Roehe et al. (2016) PLOS Genetics
16. Selection using microbial information
x genes
Sampling soil
and plant
microbes
Determination
of the
abundance of
microbial genes
Prediction of
plant yield
Prediction of
nutrient
efficiency
Prediction of
plant health
Breeding
yield
Breeding
efficiency
Breeding
health
x genes X genes
Nutrition
yield
Nutrition
efficiency
Nutrition
health
https://microbewiki.kenyon.edu/
17. Microbiome Research & Developments
Microbiome
Soil health
Plant
production &
health
Animal production
& health
Manure &
waste
management
Bio-digester
High Quality
Food
18. Microorganism in food production
• Fermentation
– Yeast (Saccharomyces cerevisiae; Bread, Wine)
– Bacteria (Lactobacillus sp.; Cheese, Probiotics)
– Moulds (Penicillium sp.; Cambert, Blue cheese)
• Biotechnological techniques
– wide variety of products
– high quality & safer foods
– highly controlled conditions
19. Gene editing of microbes or plants
• Inserting, deleting or replacing DNA in a gene
– Engineered by nucleases
• Double-strand breaks at a desired location in
the gene
– Nucleases
• CRISPR-Cas9 system
20. Conclusions
• Precision
– Soil management
– Plant breeding, nutrition, management
– Animal breeding, nutrition, management
• Improved waste management
• Control and improvement
– Fermentation food products
– Bio-digesters
• Microbial genes as Biomarker
• Microbial products for soil, plant and animals
• Microbes directly producing food
22. The research is funded by:
The Scottish Government (RESAS) and
Biotechnology and Biological Sciences Research Council (BBSRC)
Aligned research is sponsored through:
Department for Environment, Food and Rural Affairs (Defra),
English Beef and Lamb Executive Ltd. (EBLEX)
and Quality Meat Scotland (QMS)
Other collaborators:
Acknowledgements
