Research Article: Diversity of Gut Microbiota Metabolic Pathways in 10 Pairs of Chinese Infant Twins

Date Published: September 1, 2016

Publisher: Public Library of Science

Author(s): Shaoming Zhou, Ruihuan Xu, Fusheng He, Jiaxiu Zhou, Yan Wang, Jianli Zhou, Mingbang Wang, Wenhao Zhou, Erwin G Zoetendal.


Early colonization of gut microbiota in human gut is a complex process. It remains unclear when gut microbiota colonization occurs and how it proceeds. In order to study gut microbiota composition in human early life, the present study recruited 10 healthy pairs of twins, including five monozygotic (MZ) and five dizygotic (DZ) twin pairs, whose age ranged from 0 to 6 years old. 20 fecal samples from these twins were processed by shotgun metagenomic sequencing, and their averaged data outputs were generated as 2G per sample. We used MEGAN5 to perform taxonomic and functional annotation of the metagenomic data, and systematically analyzed those 20 samples, including Jaccard index similarity, principle component, clustering, and correlation analyses. Our findings indicated that within our study group: 1) MZ-twins share more microbes than DZ twins or non-twin pairs, 2) gut microbiota distribution is relatively stable at metabolic pathways level, 3) age represents the strongest factor that can account for variation in gut microbiota, and 4) a clear metabolic pathway shift can be observed, which speculatively occurs around the age of 1 year old. This research will serve as a base for future studies of gut microbiota-related disease research.

Partial Text

The gut micobiota plays an important role in human health. However, the early colonization of microbiota in the human gut is a complex process and remains largely unclear. It is assumed that the microbiota colonization begin as early as during the first trimester urinary tract infection. Aagaard et al. systematically studied the placentas microbiota composition from 320 subjects, and compared them to other human body site microbiota. They revealed that placenta harbors a unique microbiota composition, although they are similar to the human oral microbiota [1]. Delivery mode is another factor that contributory to shape newborns gut microbiota during birth. Dominguez-Bello et al. revealed that vaginally delivered infants acquired microbiota similar to their own mother’s vaginal microbiota, and C-section infants harbored bacterial communities similar to mother’s skin surface [2]. The gut microbiota stabilization or maturation is affected by feeding model as well [3]. Furthermore, numerous researchs have indicated that antibiotics play an essential role in altering the gut microbiota and exert long-lasting effects during later life. Early exposure to low-dose antibiotics may disrupt metabolic homeostasis in microbiota of mice and lead to obesity [4, 5]. Decreased diversity of microbiota early in life has been associated with compromised immune development. Cahenzli et al. found that a failure to establish a critical level of diversity in the gut microbiota of developing mice may result in a long-term increasing in IgE levels, and then predispose mice to immune-mediated disorders [6]. Co-twins have been used to study how human genetics affect the composition of gut microbiota. However, only a few of phenotypic characteristics, mainly referring to age, rather than host genetics have been evaluated. Tims et al. [7] used 16S rRNA gene microarray to study the gut microbiota composition of 40 adult monozygotic (MZ) twin pairs, half of which were discordant with body mass index (BMI). Their results revealed that MZ twins have more similar microbiotas compared with unrelated subjects, and some gut microbes give rise to the BMI differences between twin pairs. So far, nevertheless, these studies have been mainly restricted to adults group [8] or the use of 16S rRNA gene based profiling [9]. To understand the composition of human gut microbiota during early life and to evaluate the effects of host genetics, we performed shotgun metagenomic sequencing of 10 pairs of Chinese twins, who ranged in age from 5 months to 6 years old. We systematically compared the diversity of gut microbiota between intra- and inter-twin pairs, and evaluated correlations between human phenotypes and gut microbiota at both the strain and pathway levels. We found a change in the genes involved in microbial metabolism when comparing the infants below one year of age with infants older than one year. Additionally, we also observed a trend that gut microbiota composition might begin to stabilize after 1 year old, and these changes, or the differences between younger infants (0–1 year old) and older babies (1–6 years old) were correlated with several functional pathways. Although there are certain limitations in our study, for example, we did not conduct continuous sampling and did not perform long-term follow-up, the current findings conduced to facilitate future studies.

In brief, by collecting infant twins and performing shotgun metagenome sequencing and systematic analysis, we found that twins share gut microbiota, which implicated that genetic factors contributing to gut microbiota composition. However, gut microbiota may also be strongly influenced by age, as attributing to differences in metabolic pathways, especially those bacterial groups involved in the genetic information processing and metabolism. There was a significant metabolic pathway shift observed in our study, including some novel metabolic pathways and others that have been associated with human disease, through comparing infants below 1 year of age to whom over 1year. Notwithstanding certain limitations (different time points come from different individuals), our findings will serve as a base for future research about gut microbe-related disease in infants.