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. 2022 Dec 16;11(12):1827.
doi: 10.3390/antibiotics11121827.

Characterization of the Composition Variation of Healthy Human Gut Microbiome in Correlation with Antibiotic Usage and Yogurt Consumption

Shaofei Yan  1 , Xiaofan Zhang  2 , Xiaofang Jia  2 , Jiguo Zhang  2 , Xiaomin Han  1 , Chang Su  2 , Jianyun Zhao  1 , Wanglong Gou  3 , Jin Xu  1 , Bing Zhang  2
Affiliations

Characterization of the Composition Variation of Healthy Human Gut Microbiome in Correlation with Antibiotic Usage and Yogurt Consumption

Shaofei Yan et al. Antibiotics (Basel). .

Abstract

Antibiotic usage and yogurt consumption are the major interventions for gut microbiota, yet their shared characteristics and disparities in healthy human gut microbiome remain unclear. This study aimed to decipher the composition changes among healthy humans, comparing antibiotic usage and yogurt consumption. The relative bacterial abundances of 1113 fecal samples were collected from an ongoing, population-based longitudinal cohort study in China that covered lifestyle, diet, disease status and physical measurements, and biological indicators of participants were obtained by the sequencing of 16S rRNA. The samples were divided into three groups, which were antibiotic users (122), yogurt consumers (497) and controls (494), where data visualization, alpha diversity, beta diversity and LEfSe analysis were conducted. At the family level, the relative abundances of Streptococcaceae, Enterobacteriaceae and Enterococcaceae families in antibiotic users increased almost 50%, 70% and 200%, respectively, while yogurt consumption also increased relative abundances of Streptococcaceae and Enterococcaceae, but not Enterobacteriaceae. Alpha diversity analyses suggested that the microbiome of the antibiotic usage and yogurt consumption groups exhibited an alpha diversity lower than that of the control. LEfSe analysis showed that, at the family level, the number of biomarkers in the yogurt consumption and antibiotic usage group were respectively 5 and 7, lower than that of the control (13). This study demonstrated the importance in considering the potential assistance of yogurt consumption on ARG gene transfer from commensal bacteria to pathogens in the human gut, which may pose a risk for human health. Antibiotic usage and yogurt consumption share more identical changes on healthy human gut flora than disparities. Therefore, in order to understand the potential risks of antibiotic usage and yogurt consumption on antibiotic resistance transmission in human gut microbiota, further research needs to be undertaken.

Keywords: antibiotic usage; gut microbiota; metagenomics; yogurt consumption.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Composition of the Gut Microbiota of control, antibiotic usage and Yogurt consumption groups. (A) Gut microbiome composition at the phylum level; (B) Gut microbiome composition at the family level; (C) Heat tree demonstration of gut microbiome composition at the order level.
Figure 2
Figure 2
Alpha and Beta Diversity of the Gut Microbiome. (A) Alpha diversity evaluation at Chao1, Shannon, Simpson and observed indexes; (B) Beta diversity based on the PERMANOVA statistic method.
Figure 3
Figure 3
Biomarkers of different taxa level of the Gut Microbiome among antibiotic usage, Yogurt consumption and control (LEfSe analysis).
See this image and copyright information in PMC

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