Colonization and succession of the human gastrointestinal microbiome in neonates and infants at high risk of metabolic disease in adulthood

Doctoral thesis (2018)

Recent studies have highlighted that the human gastrointestinal microbiome not only maintains important functions for the human host, but is also intimately linked to the development of the neonatal ... [more ▼]

Recent studies have highlighted that the human gastrointestinal microbiome not only maintains important functions for the human host, but is also intimately linked to the development of the neonatal immune system. Therefore, earliest perturbations to the initial colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. While the rate of caesarean section deliveries is increasing worldwide, it still remains unclear to what extent a caesarean section delivery (CSD) or other perturbations affect the colonization and succession of the gastrointestinal microbiome and might eventually impact the immune development of a neonate. Although much research has been performed on bacterial colonization and succession to date, far less is known about the other two domains of life, archaea and eukaryotes. Furthermore, it remains unclear whether a delivery by caesarean section causes a disruption of mother-to-infant transmission of microbiota and whether this affects human physiology early on, with potentially persistent effects in later life. Over the course of this thesis, a multitude of objectives was tackled. First of all, the description of microbial communities and trends over time within the neonatal and infant gut microbiome, and the study of the early colonization and succession by members of the three domains of life. Second, the careful application of high-throughput approaches on earliest low biomass samples, the detection of functional repertoires and strains transferred from mothers to neonates, and the analysis of the immunostimulatory potential of neonatal gut microbiomes in relation to delivery mode with likely effects on the later health status. In a first study based on 15 infants and using a combination of 16S and 18S rRNA gene amplicon sequencing and quantitative real-time PCR, earliest differences among the three domains of life according to delivery mode were detected as early as three days postpartum. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The findings complement previous observations of a delay in colonization and succession of CSD infants, which likely affects not only bacteria but also archaea and microeukaryotes. Based on the observation that the first 5 days postpartum showed significant differing trends between delivery modes and considering the fact that the very first days postpartum are generally under-studied, this highlighted the importance to perform more in-depth analyses of these microbiome samples. In a next step, based on 12 mother-neonate pairs, high-resolution, metagenomic analysis of the gut microbiomes of mothers and neonates was performed to resolve the earliest colonizing microbiome. After data curation and in accordance with the observed changes in community composition for both cohorts, differences with respect to encoded metabolic functions between the microbiomes of vaginally delivered (VD) or CSD neonates as early as day 3 were observed. Several functional pathways were over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis. Genes encoding proteins involved in these functions were linked to specific strains, which were vertically transmitted from the respective mothers. Based on the candidate’s work, more follow-up work on LPS was done by a colleague with a background in immunology. Isolated LPS from faecal samples collected at day 3 had a higher immunostimulatory potential in VD neonates and cytokines measured in plasma collected at the same day presented an increased immune reaction in VD neonates. Collectively, these results suggest that vaginal delivery favours vertical transmission of specific gastrointestinal strains from mother to neonate, while caesarean section may impede this process and thereby decrease linked functional repertoires and immunostimulatory potential with potential effects on human physiology later in life. Taken together, the results obtained from both cohorts strongly indicate that maternal and neonatal factors, such as antibiotics intake or milk diet, but most importantly the delivery mode, have the potential to influence the initial neonatal bacterial, archaeal and microeukaryotic colonization of the gut microbiome shortly postpartum, with the potential to impact the neonatal immune development, which could thereby affect the later health status. [less ▲]

Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host-Microbiota Interactions.

in Microbial Proteomics (2018)

The gastrointestinal microbiome plays a central role in health and disease. Imbalances in the microbiome, also referred to as dysbiosis, have recently been associated with a number of human idiopathic ... [more ▼]

The gastrointestinal microbiome plays a central role in health and disease. Imbalances in the microbiome, also referred to as dysbiosis, have recently been associated with a number of human idiopathic diseases ranging from metabolic to neurodegenerative. However, to causally link specific microorganisms or dysbiotic communities with tissue-specific and/or systemic disease-associated phenotypes, systematic in vivo studies are fundamental. Gnotobiotic mouse models have proven to be particularly useful for the elucidation of microbiota-associated characteristics as they provide a means to conduct targeted perturbations followed by analyses of induced localized and systemic effects. Here, we describe a methodology in the framework of systems biology which allows the comprehensive isolation of high quality biomolecular fractions (DNA, RNA, proteins and metabolites) from limited and/or heterogeneous sample material derived from murine brain, liver, and colon tissues, as well as from intestinal contents (fecal pellets and fecal masses). The obtained biomolecular fractions are compatible with current high-throughput genomic, transcriptomic, proteomic, and metabolomic analyses. The resulting data fulfills the premise of systematic measurements and allows the detailed study of tissue-specific and/or systemic effects of host-microbiota interactions in relation to health and disease. [less ▲]

Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation.

in Translational Research: the Journal of Laboratory and Clinical Medicine (2017)

In patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), treatment-induced changes to the gastrointestinal tract (GIT) microbiome have been linked to adverse outcomes, most ... [more ▼]

In patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), treatment-induced changes to the gastrointestinal tract (GIT) microbiome have been linked to adverse outcomes, most notably graft-versus-host disease (GvHD). However, it is presently unknown whether this relationship is causal or consequential. Here, we performed an integrated meta-omic analysis to probe deeper into the GIT microbiome changes during allo-HSCT and its accompanying treatments. We used 16S and 18S rRNA gene amplicon sequencing to resolve archaea, bacteria, and eukaryotes within the GIT microbiomes of 16 patients undergoing allo-HSCT for the treatment of hematologic malignancies. These results revealed a major shift in the GIT microbiome after allo-HSCT including a marked reduction in bacterial diversity, accompanied by only limited changes in eukaryotes and archaea. An integrated analysis of metagenomic and metatranscriptomic data was performed on samples collected from a patient before and after allo-HSCT for acute myeloid leukemia. This patient developed severe GvHD, leading to death 9 months after allo-HSCT. In addition to drastically decreased bacterial diversity, the post-treatment microbiome showed a higher overall number and higher expression levels of antibiotic resistance genes (ARGs). One specific Escherichia coli strain causing a paravertebral abscess was linked to GIT dysbiosis, suggesting loss of intestinal barrier integrity. The apparent selection for bacteria expressing ARGs suggests that prophylactic antibiotic administration may adversely affect the overall treatment outcome. We therefore assert that such analyses including information about the selection of pathogenic bacteria expressing ARGs may assist clinicians in "personalizing" regimens for individual patients to improve overall outcomes. [less ▲]

Erratum: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.

in Nature Microbiology (2016), 2

Early dynamics of the gastrointestinal microbiome in infants at risk of metabolic disease in adulthood.

Poster (2015, June)

Early dynamics of the gastrointestinal microbiome in infants at risk of metabolic disease in adulthood

Poster (2015, March)

Integrated Omic Analyses of the Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus

Poster (2014, April 30)

Meta-omic Analyses of the Microbiome in a Family Study of Diabetes Mellitus

Poster (2013, October)