Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome

Abstract

Murine models are widely used to explore host-microbe interactions because of the challenges and limitations inherent to human studies. However, microbiome studies in murine models are not without their nuances. Inter-individual variations in gut microbiota are frequent even in animals housed within the same room. We therefore sought to find an efficient and effective standard operating procedure (SOP) to minimize these effects to improve consistency and reproducibility in murine microbiota studies. Mice were housed in a single room under specific-pathogen free conditions. Soiled cage bedding was routinely mixed weekly and distributed among all cages from weaning (three weeks old) until the onset of the study. Females and males were separated by sex and group-housed (up to five mice/cage) at weaning. 16S rRNA gene analyses of fecal samples showed that this protocol significantly reduced pre-study variability of gut microbiota amongst animals compared to other conventional measures used to normalize microbiota when large experimental cohorts have been required. A significant and consistent effect size was observed in gut microbiota when mice were switched from regular chow to purified diet in both sexes. However, sex and aging appeared to be independent drivers of gut microbial assemblage and should be taken into account in studies of this nature. In summary, we report a practical and effective pre-study SOP for normalizing the gut microbiome of murine cohorts that minimizes inter-individual variability and resolves co-housing problems inherent to male mice. This SOP may increase quality, rigor, and reproducibility of data acquisition and analysis.

Depletion of Foxp3+ regulatory T cells is accompanied by an increase in the relative abundance of Firmicutes in the murine gut microbiome

“…29 Furthermore, the variables cage, breeding and experiment number were variables that were associated with significant differences in the gut microbiota composition, which is in line with other murine studies. 29 Furthermore, the variables cage, breeding and experiment number were variables that were associated with significant differences in the gut microbiota composition, which is in line with other murine studies.…”

“…In addition, we found significant inter-individual variation in the murine gut microbiome, a finding that has been reported previously. 29 Furthermore, the variables cage, breeding and experiment number were variables that were associated with significant differences in the gut microbiota composition, which is in line with other murine studies. [30][31][32] According to the number of significantly different abundant genera, the variation of the gut microbiota between the cages and individual experiments had the highest impact on the gut microbiota in our study.…”

Faecal microbiota and functional capacity associated with weaning weight in meat rabbits

“…breast-milk feeding and ingest the soft faeces of dams) and indigenous environment microbiome (Hufeldt, et al, 2010;Rogers, et al, 2014;Ericsson, et al, 2015;Yang, et al, 2017;Korpela, et al, 2018;Martinez, et al, 2018). Previous studies investigated the role of sex in adult animals' gut microbiota suggested that the significant difference of gut microbial composition between sexes was caused by sex hormones (Org, et al, 2016;Miyoshi, et al, 2018). However, Steegenga, et al (2014) indicated that these sexual microbial differences do not present in the young animals and are only detected after puberty.…”

The microgenderome revealed: sex differences in bidirectional interactions between the microbiota, hormones, immunity and disease susceptibility

“…Indeed, while Bacteroidetes and Firmicutes dominate in the microbiota of many laboratory rodents (e.g., mice, rats, hamsters) [35–37], marked differences between the rodent and human GIT microbiota at the genus level indicate that rodent studies may not be generalizable to humans [38]. Furthermore, individual rodents may vary greatly in their microbiota even when co-housed; thus, rigorous experimental techniques are required to ensure consistency in experiments [39]. …”

“…Many studies have shown that the GIT microbiota composition differs in adult male and female rodents [39, 43–46]. For example, while the pro-inflammatory Lactobacillaceae are more abundant in females, the highly pro-inflammatory Ruminococcaceae and Rikenellaceae are more prevalent in males [43].…”