Working Towards Microbiome Research Standards

Working Towards Microbiome Research Standards Microbiome research continues at an amazing pace, but labs around the world are racing ahead with few agreed-upon standards. This makes communication difficult and may undermine reproducibility.

Growing Call for Microbiome Standards

There are groups advocating for common standards, such as The Microbiome Coalition, and the subject frequently comes up at scientific conferences.

In 2015, Julian R. Marchesi and Jacques Ravel published a paper suggesting a standard vocabulary, The vocabulary of microbiome research: a proposal1. A standard vocabulary is needed to assure scientists are able to communicate effectively when publishing, presenting, or having discussions.

A 2016 editorial in Nature Microbiology stated that "if the vast potential for microbiome research is to be translated into scientific advances and real world applications, the development of standard operating procedures will be necessary to ensure reproducibility and gain regulatory approval2."

Also in 2016, the US National Institute of Standards and Technology held a workshop to "seek input on defining reference materials, data, and methods for human microbiome community measurements." You can review these presentations on the workshop website.

Standardized Lab Mice Support Reproducibility

One of the primary research tools used to study the microbiome are mice. With thousands of mouse strains available and hundreds of labs performing studies, the potential variability between experiments is extensive. Add hundreds of seemingly minor choices in housing modalities, diet, and water sources and it is difficult to imagine duplicating an intra-lab microbiome study, let alone inter-lab study.

In a recent paper, McCoy et al. discuss the need for gut microbiome standardization in control and experimental mice. "Lack of experimental reproducibility between research groups has highlighted the necessity for rigorously controlled experimental designs in order to standardize the microbiota between control and experimental animals3."

Lab Animal Magazine recently devoted an entire supplement to reproducibility in lab animals. In the editors' introduction, they state that "the articles are connected by a common message: some of our current practices using animal models are flawed and can lead not only to irreproducible results, but failures to validate models and translate findings from the lab to the clinic4." Lack of standards and defined, common language may lead to irreproducible results.

All the way back to Little and Castle, numerous scientists and organizations strived toward the standardization of laboratory mice. With the advent of the emerging microbiome research field, a new set of standards must be established.

Germ-Free Mice and Microbiome Research

One critical tool for microbiome research is germ-free mice. These mice can be associated with individual microbes or pre-selected communities to develop animal models of human disease.

Germ-free mice should be screened to a common health standard and generated on a defined genetic background to assure intra- and inter-lab consistency and assure reproducibility. The only commercial source of genetically defined, germ-free mice is Taconic Biosciences, with germ-free C57BL/6N, BALB/c, and Swiss Webster strains available. Through rigorous controls and testing, these mice are consistent from study to study and can be used with confidence.

You can learn more about these models on Taconic's microbiome pages, which contain resources to help you utilize germ-free mice in your own laboratory animal facilities.

You Can Help Define Standards

The microbiome may hold the answers to many of today's questions about disease causality. Unlocking those answers will require standardization across all aspects of microbiome research.

Here are three ways you can participate in the development of shared microbiome standards:

  • Join the discussion and debate on microbiome standards.
  • Carefully consider the vocabulary you use when publishing and discussing your research.
  • Always use defined sources of standardized research reagents, including laboratory mice.
1. Julian R. Marchesi and Jacques Ravel. The vocabulary of microbiome research: a proposal. Microbiome 2015 3:31.
2. Editorial. Raising standards in microbiome research. Nature Microbiology 1, Article number: 16112 2016.
3. McCoy, KD, Geuking, MB and Ronchi, F. Gut Microbiome Standardization in Control and Experimental Mice. Curr Protoc Immunol. 2017 Apr 3; 117:23.
4. Editorial. Confidence in Preclinical Research. Lab Animal 2017 46, 101 - 102.