Gut microbial similarity in twins is driven by shared environment and aging

Abstract

Background: Human gut microbiome composition is influenced by genetics, diet and environmental factors. We investigated the microbial composition in several gastrointestinal (GI) compartments to evaluate the impact of genetics, delivery mode, diet, household sharing and aging on microbial similarity in monozygotic and dizygotic twins.

Methods: Fecal, biopsy and saliva samples were obtained from total 108 twins. DNA and/or RNA was extracted and the region V1-V2 of the 16S rRNA gene was amplified and sequenced. Bray-Curtis similarity was used for further microbiome comparisons, Mann-Whitney test was applied to evaluate the significant differences between groups and Spearman test was applied to reveal potential correlations between data.

Findings: The global bacterial profiles were grouped into two clusters separating the upper and lower GI. The upper GI microbiome composition was strictly dependent on the Helicobacter pylori status. With a positivity rate of 55%, H. pylori completely colonized the stomach and separated infected twins from non-infected twins irrespective of zygosity status. Lower GI microbiome similarity between the twins was defined mainly by household-sharing and aging; whereas delivery mode and host genetics had no influence. There was a progredient decrease in the bacterial similarity with aging. Shared vs. non-shared phylotypes analysis showed that in both siblings the shared phylotypes progressively diminished with aging, while the non-shared phylotypes increased.

Interpretation: Our findings strongly highlight the aging and shared household as they key determinants in gut microbial similarity and drift in twins irrespective of their zygotic state.

Funding: This work was supported by the grant of the Research Council of Lithuania (Project no. APP-2/2016) and also partially supported by the funds of European Commission through the "European funds for regional development" (EFRE) as well as by the regional Ministry of Economy, Science and Digitalization as part of the "LiLife" Project as part of the "Autonomy in old Age" research group (Project ID: ZS/2018/11/95324).

Keywords: 16S rRNA sequencing; Aging; Equality; Helicobacter pylori; Microbiome; Shared household; Stomach.

Figure 1

Graphical abstract. Design of the study.

Figure 2

A. Group-average agglomerative hierarchical clustering of studied samples, based on the global bacterial profile at phylotype-level along the upper GI (saliva, corpus and antrum) and fecal samples. B to F: Most abundant genera detected in corpus, antrum and saliva in H. pylori negative (N) and positive (P) individuals as well as in dizygotic (DZ) and monozygotic (MZ) twins. Percentages shown the Bray-Curtis similarities between twin pairs. G: Heatmap at family-level with the most abundant taxa representing the microbiome in saliva, antrum, corpus and feces.

Figure 3

A. Principal Coordinates Analysis (PCoA) of the bacterial communities in the upper GI (DNA_S for saliva, DNA_C or RNA_C for corpus DNA_A or RNA_A for antrum) at phylotype-level based on the Bray-Curtis similarity matrix. Samples from corpus and antrum of patients infected by H. pylori are denoted as Hp. B: Percentage of Bray-Curtis similarities of the bacterial communities in twin pairs in saliva corpus and antrum between monozygotic twins (MZ) and dizygotic twins (DZ).

Figure 4

A. Group-average agglomerative hierarchical clustering of 198 fecal samples at phylotype-level. Concordant twins (Con) are denoted in bold in contrast to non-concordant (Non-Con). Light blue and dark blue denoted monozygotic (MZ) and dizygotic (DZ) twins, respectively as well as light brown and dark brown denoted shared and non-shared household twins, respectively. B to E: Bray-Curtis similarities of the bacterial communities in twin pairs and a priori defined groups (one dot represents two twins). Statistically differences are shown as *** if p value < 0.001 and **** if p value < 0.0001 and ns denotes no statistical differences.

Figure 5

Spearman correlations (rho) between Bray-Curtis similarities of the bacterial communities in twins pairs (one dot represents two twins) and the body mass index ratio (BMI-ratio) (A), Kilocalories (Kcal) intake ratio (B), and carbohydrates, proteins (C) and lipid (D) intake ratios, respectively.

Figure 6

A. Overview of the age on the different cohort of twins published so far compared to this study. If it was published, for each study is shown the minimum and the maximum of age, as well as the standard deviation and the median. B: Spearman correlation (rho) in twin pairs (one dot represents two twins) between their age and their percentage of similarity of the bacterial communities. C: Differences on the age between concordant (Con) twins and non-concordant (Non-Con) twins according to the Bray-Curtis similarities shown in Fig. 4. **** denotes p value < 0.0001. D: Spearman correlation (rho) between the number of phylotypes shared (light green) and non-shared (dark green) between twins paired (TP).

Figure 7

Abundances of the most predominant genera detected in fecal samples. Samples are sorted in increasing percentage of Bray-Curtis similarity and in twin pairs side-by-side, as well as divided in 7 groups due to space limitation, showing magnified the first group (A) and the last group (G) and in small sizes groups B to F.