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Early life determinants induce sustainable changes in the gut microbiome of six-year-old children.

ABSTRACT: While the association between early life determinants and the development of the gut microbiome composition in infancy has been widely investigated, a potential persistent influence of early life determinants on the gut microbial community after its stabilization at later childhood remains largely unknown. Therefore, we aimed to identify the association between several early life determinants and the gut microbiome composition in six-year-old children from the LISA birth cohort. A total number of 166 fecal samples were analyzed using 16S rRNA gene-based barcoding to assess bacterial diversity pattern. The bacterial profiles were investigated for their association with maternal smoking during pregnancy, mode of delivery, breastfeeding, antibiotic treatment between one and two years of age, gender and socioeconomic status (SES). While alpha and beta diversity of the infants' gut microbiome remained unaffected, amplicon sequence variants (ASVs) annotated to Firmicutes and Actinobacteria responded to early life determinants, mostly to feeding practice and antibiotics use. ASVs associated to Bacteriodetes remained unaffected. Our findings indicate that early life determinants could have a long-term sustainable effect on the gut microflora of six-year-old children, however, associations with early life determinates are weaker than reported for infants.

SUBMITTER: Gschwendtner S

PROVIDER: S-EPMC6722248 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Early life determinants induce sustainable changes in the gut microbiome of six-year-old children.

Gschwendtner Silvia S Kang Hyena H Thiering Elisabeth E Kublik Susanne S Fösel Bärbel B Schulz Holger H Krauss-Etschmann Susanne S Heinrich Joachim J Schöler Anne A Schloter Michael M Standl Marie M

Scientific reports 20190903 1

While the association between early life determinants and the development of the gut microbiome composition in infancy has been widely investigated, a potential persistent influence of early life determinants on the gut microbial community after its stabilization at later childhood remains largely unknown. Therefore, we aimed to identify the association between several early life determinants and the gut microbiome composition in six-year-old children from the LISA birth cohort. A total number o ...[more]

PMID: 31481742

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Project description:BackgroundThe human gut microbiome is recognized as an important determinant of human health, yet little is known about how dietary habits are related to the microbiome in post-weaned, pre-pubescent children.ObjectiveThe goal of this work was to link quantitative dietary intake with microbiome features in a diverse population of children consuming a predominantly Western diet.DesignThis was a cross-sectional study.Participants/settingsEnglish- or Spanish-speaking families with healthy children between the ages of 2 and 9 years were recruited from a community-based, early childhood learning center in suburban Los Angeles, California between June and September 2014.Main outcome measuresChildren included in the analyses (n=75) contributed three fecal samples and three quantitative 24-hour dietary recalls using the multiple-pass method with an average of 5.7 days between samples. Microbial communities of each fecal sample were characterized using Illumina sequencing of the 16S ribosomal RNA gene. Dietary recalls were analyzed using the Automated Self-Administered 24-Hour Recall Dietary Assessment Tool.Statistical analysis performedAssociations between dietary factors and microbiome features were assessed using the Kruskal-Wallis test, Spearman rank correlations, or permutational multivariate analysis of variance. For demographic and health-related variables, χ2 analyses were used to test for differences between age groups for categorical variables.ResultsOur results show that age is correlated with three metrics of microbiome diversity (P<0.05) and is associated with both community structure (P=0.0488) and membership (P=0.0002). Several dietary food groups and nutrients were likewise associated with microbiome features. For example, consumption of non-whole-grain foods was associated with community structure (P=0.0089) and membership (P=0.0057), but not diversity (P>0.05). Likewise, the relative abundance of several bacterial taxa were linked to consumption of particular food groups and/or nutrients, as illustrated by the positive associations between total fruit (Pfalsediscovery rate<0.05) and fiber (Pfalsediscovery rate<0.05) consumption with the relative abundance of the Lachnospira genera.ConclusionsThis hypothesis-generating study demonstrates that the composition of the child gut microbiome remains dynamic beyond the age of 3 years and responds to dietary differences across individuals. In particular, non-whole-grain foods fortified with vitamins and minerals appear to be associated with the composition of the microbiome. Future interventional or model organism-based studies will be needed to test these associations between diet and microbiome composition.

Project description:BackgroundCurrently, few studies focus on the association between gut microbiota and systemic lupus erythematosus (SLE), and much less studies consider the effect of drug usage. Proton pump inhibitors (PPIs) are commonly used to treat drug-related gastrointestinal damage in SLE patients. Therefore, the purpose of this study is to examine the gut microbiota of SLE patients using PPIs.MethodsFecal samples from 20 SLE patients with PPIs (P-SLE), 20 SLE patients without PPIs (NP-SLE) and 17 healthy controls (HCs) were obtained. The structure of the bacterial community in the fecal samples was analyzed by 16S rRNA gene sequencing. Redundancy analysis (RDA) was performed to observe the relationship between clinical variables and microbiome composition in P-SLE and NP-SLE patients. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, functional capabilities of microbiota were estimated. Network analysis was performed to analyze the association of metabolic pathway alterations with altered gut microbiota in P-SLE and NP-SLE patients.ResultsP-SLE patients exhibited increased alpha-diversity and an altered composition of the gut microbiota compared with NP-SLE patients. The alpha-diversity of NP-SLE patients was significantly lower than HCs but also of P-SLE patients, whose alpha-diversity had become similar to HCs. Compared with NP-SLE patients, the relative abundances of Lactobacillus, Roseburia, Oxalobacter, and Desulfovibrio were increased, while those of Veillonella, Escherichia, Morganella, Pseudomonas and Stenotrophomonas were decreased in P-SLE patients. RDA indicated that PPI use was the only significant exploratory variable for the microbiome composition when comparing SLE patients. KEGG analysis showed that 16 metabolic pathways were significantly different between NP-SLE and P-SLE patients. These metabolic pathways were mainly associated with changes in Escherichia, Roseburia, Stenotrophomonas, Morganella and Alipipes as determined by the network analysis.ConclusionsPPI use is associated with an improved microbiome composition of SLE patients as it 1) increases alpha-diversity levels back to normal, 2) increases the abundance of various (beneficial) commensals, and 3) decreases the abundance of certain opportunistic pathogenic genera such as Escherichia. Validation studies with higher patient numbers are however recommended to explore these patterns in more detail.

Project description:Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events.

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Early life determinants induce sustainable changes in the gut microbiome of six-year-old children.

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Early life determinants induce sustainable changes in the gut microbiome of six-year-old children.

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