A Summary of Microbial Research in Animals

Why do we need to perform microbial research in animals?

Enormous amounts of microorganisms live both within and on animal, the animal and its microorganisms exchange energy substances, transmit information to each other and form a holistic system. The impact of microorganisms on animal health is mainly reflected in mutual benefit sharing and symbiosis. If the number of microorganisms is out of balance, disease will occur, so it is necessary to maintain the balance of micro-ecology. Selective utilization of the diversity of microbial species and their functions provides opportunities to improve animal health and productivity. The rapid development of molecular biology methods, especially sequencing technology, has brought great benefit to the research of microorganisms in animals. In this article, we give a summary of microbial research in livestock industry and labs.

1. Microbial risk assessment

To ensure the health of lab and farm animals, microbial testing is needed to detect pathogenic and parasitic microbes. The primary methods include RT-PCR, high-throughput sequencing, immunoassay, and microbial culture. And commercially available kits have been developed for microbial testing. Here, we take cattle and poultry microbiology testing as examples to understand the application of microbial testing in livestock industry.

Cattle microbiology testing

• Early and accurate identification of pathogenic and parasitic microorganisms involved in breeding environment and livestock. For example, mastitis testing brings great benefits in controlling the disease at farm level.
• RT-PCR based test for Staphylococcus aureus, Streptococcus agalactia, Streptococcus dysgalactia, Streptococcus uberisand Mycoplasma bovis.
• Milk culture for identification of microbes, probably offering advice on the use of antibiotic.

Poultry microbiology testing

• Breeding and flock management
• Real-time PCR experiments for rapid screening of Salmonella and serovar identification from feces, boot swabs, dust, poultry feed and feed ingredients.
• Other targets such as avian influenza and Newcastle disease are also assayed.

Egg & poultry meat production

• RT-PCR assays for genetically modified organisms and meat species identification
• RT-PCR assays for screening of pathogens and quality indicators (such as Salmonella, Campylobacter, Listeria, and coli) from poultry meat, egg, and other environmental samples.

2. Alimentary tract microbiome analysis

The alimentary tract of a ruminant is colonized by millions of microorganisms that lives in a symbiotic relationship with the host. Therefore, knowledge of the microbial composition of the gut can provide insights into improving animal health and productivity. High-throughput sequencing (such as 16S/18S/ITS amplicon sequencing) is a powerful technology to explore the gut microbial composition of ruminants, microbial functions, microbe-host interactions, and environment/disease factors that affects microbial activities. By comparing the microbial composition of alimentary tract between healthy and diseased animals, microbial probiotics can probably be discovered and developed. Microbial probiotics represent living microorganisms that have beneficial effect after consumption.

3. Functional microbial genomics

Functional microbial genomics is performed to elucidate microbiome functions that effects host performance, differentiate beneficial, neutral, and detrimental microorganisms, and experimentally manipulate the taxonomic makeup of microbiomes to improve animal health and productivity. The principal approaches to investigating microbiome function include correlation analyses, single-cell sequencing, whole-community metagenomics and metatranscriptomics, experimental manipulation, synthetic microbiomes, and microbiome engineering by artificial selection.