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. 2025 Aug 1:16:1566722.
doi: 10.3389/fimmu.2025.1566722. eCollection 2025.

The critical role of diet, exercise, and sleep in shaping the gut microbiota of children with idiopathic short stature: a Retrospective study

Qin Zeng  1   2 , Jun Zhu  2   3 , Yanling Hu  1   2 , Shaoyu Su  1   2 , Jing Chen  1   2
Affiliations

The critical role of diet, exercise, and sleep in shaping the gut microbiota of children with idiopathic short stature: a Retrospective study

Qin Zeng et al. Front Immunol. .

Abstract

Objectives: To investigate the gut microbiota in children with varying degrees of idiopathic short stature (ISS) and to examine the relationship between their intestinal microbiota and lifestyle factors, including diet, exercise, medication, sleep, and psychological state.

Methods: A retrospective study involving 58 ISS children was conducted from May to October 2022. Lifestyle data were collected using questionnaires. Fecal samples were analyzed using 16S rRNA gene sequencing to assess microbiota diversity and composition. LEfSe analysis identified differential bacterial communities between ISS-2SD and ISS-3SD groups (LDA score ≥ 2.5). Spearman correlation analysis explored the relationship between microbiota diversity, dominant taxa, and lifestyle factors, visualized in a heatmap.

Results: No significant differences in alpha diversity of intestinal microbiota were observed among children with varying degrees of short stature at the ISS, but differences were noted in the dominant microbiota. The ISS-2SD group had Leptotrichiaceae and Sneathia as predominant members, whereas the ISS-3SD group was dominated by Lachnoclostridium, Thermous_scotoductus and Thermoles. Correlation analysis revealed that microbiota diversity was linked to diet, especially legume consumption (Shannon index: r=0.372, P=0.004; Simpson index: r=0.379, P=0.003). At the genus level, Prevotella was positively correlated with beverage intake (r=0.262, P=0.047) and sleep quality (r=0.324, P=0.013), while Ezakiella was negatively correlated with meat intake (r=-0.297, P=0.024), Other genera exhibited significant correlations with diet, exercise, and sleep.

Conclusion: Children with varying degrees of short stature exhibited differences in their dominant intestinal microbiota. Diet, exercise, and sleep appear to be significant factors influencing these microbial changes in ISS children.

Keywords: 16S rRNA gene sequencing; correlation analysis; idiopathic short stature; intestinal microbiota; lifestyle factors.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The Reviewer HZ declared a shared affiliation with the authors to the handling editor at the time of review.

Figures

Figure 1
Figure 1
Cumulative box chart of alpha diversity species. The horizontal axis represents the sample size; The vertical axis represents the number of ASVs after sampling.
Figure 2
Figure 2
Rarefaction curve. The horizontal axis represents the sequencing data volume, and the vertical axis represents the corresponding alpha diversity index. (A) Observed_species, (B) Chao 1, (C) Shannon index, (D) Simpson index, (E) Pielou’s index, (F) Dominance index.
Figure 3
Figure 3
Cumulative box chart of alpha diversity species. The chart shows the diversity of bacterial species in two subgroups: ISS-2SD (n=34) and ISS-3SD (n=24). The horizontal axis represents grouping, and the vertical axis represents the corresponding alpha index values. (A) Observed_species, (B) Chao 1, (C) Shannon index, (D) Simpson index, (E) Pielou’s index, (F) Dominance index.
Figure 4
Figure 4
Heatmap analysis of the top 10 gut microbiota genera in ISS-2SD (n=34) and ISS-3SD (n=24) groups.
Figure 5
Figure 5
Analysis of inter group microbial diversity. (A) Evolutionary diagram with circle sizes indicating abundance, colors for species differentiation, red and green nodes for key microbial groups, and species names in the legend. (B) LDA scores for species in ISS-2SD (n=34) and ISS-3SD (n=24) groups, with colors for group distinction and bar lengths for species contribution, showing only species with LDA ≥2.5.
Figure 6
Figure 6
Spearman correlation heatmap of factors associated with gut microbiota in ISS children. The vertical axis represents environmental factors, while the horizontal axis corresponds to microbial species. Heatmap values indicate Spearman’s correlation coefficients (ranging from -1 to 1), where negative correlations (r < 0) and positive correlations (r > 0) are depicted. Significance levels are denoted as follows: “*” for P<0.05 and “**” for P<0.01. (A) Correlation between gut microbiota diversity and lifestyle factors. (B) Correlation analysis of the top 10 genus-level microbes with overall lifestyle factors. (C) Correlation analysis of the top 10 genus-level microbes with dietary factors. (D) Correlation analysis of the top 10 genus-level microbes with exercise-related factors. (E) Correlation analysis of the top 10 genus-level microbes with sleep-related factors.
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