H2Oh No! The importance of reporting your water source in your in vivo microbiome studies

Abstract

Water is a fundamental part of any in vivo microbiome experiment however, it is also one of the most overlooked and underreported variables within the literature. Currently there is no established standard for drinking water quality set by the Canadian Council on Animal Care. Most water treatment methods focus on inhibiting bacterial growth within the water while prolonging the shelf-life of bottles once poured. When reviewing the literature, it is clear that some water treatment methods, such as water acidification, alter the gut microbiome of experimental animals resulting in dramatic differences in disease phenotype progression. Furthermore, The Jackson Lab, one of the world's leading animal vendors, provides acidified water to their in-house animals and is often cited in the literature as having a dramatically different gut microbiome than animals acquired from either Charles River or Taconic. While we recognize that it is impossible to standardize water across all animal facilities currently conducting microbiome research, we hope that by drawing attention to the issue in this commentary, researchers will consider water source as an experimental variable and report their own water sources to facilitate experimental reproducibility. Moreover, researchers should be cognisant of potential phenotypic differences observed between commercial animal vendors due to changes in the gut microbiome as a result of various sources of water used.

Keywords: Gut microbiome; Jax vs Taconic Non-obese diabetic mice; acidified water; bacteriome; drinking water source; experimental variable; Muc2-/- mice; spontaneous colitis model; in vivo; mice; microbial ecology.

Figure 1.

The majority of microbiome research literature does not report the complete details of water source. Of the 76 primary research articles surveyed for the current commentary, 62% of the articles did not state any information regarding the water source provided to their in vivo animals (47 articles.) While 24% stated some aspect of their water source, but not enough to be repeated by another researcher (18 articles.) Only 14% of the articles listed what the current authors would consider adequate detail with regards to the water source being provided to experimental animals (11 articles.).

Figure 2.

Summary of differences observed in C57Bl/6 mice obtained from the top three commercial animal vendors: Charles River, Taconic and Jax®.

Figure 3.

The fecal microbiome clusters to water source in a mouse model of spontaneous colitis. Beta-diversity between two in vivo facilities supplying different water sources to Muc2^−/− mice show clear clustering based on Bray-Curtis dissimilarity measures. Red dots represent the UBC Okanagan cohort (receiving acidified water at pH of ~2.3 via the addition of HCL) and blue dots represent the UBC Vancouver cohort (who received autoclaved municipal tap water.).