HUMAN-MICROBIOME INTERACTIONS

Colonisation, succession and evolution of the human gastrointestinal microbiome from birth to infancy (the COSMIC study)

The vast majority of scientific evidence indicates that humans are born germ-free. Birth is considered the time when microorganisms start to colonise the body including the gut, skin and lungs. It has long been suspected that this early colonisation may set the course for later health. In particular, caesarean section delivery (CSD) likely disrupts mother-to-neonate transmission of microbiota which may in turn be linked to the higher propensity of CSD-born individuals to develop immune system-linked conditions including allergies, chronic immune disorders and metabolic disorders. Understanding the links between birth mode, microbial transmission and early immune system stimulation is therefore important especially in view of the rise in the rate of CSD worldwide. To investigate the aforementioned links, we recruited mother-infant pairs and collected samples at the main delivery unit in Luxembourg with a particular focus on the first few days postpartum (up to day 5 postpartum).

Through the collection of appropriately preserved samples, we were able to demonstrate a delayed colonisation by bacteria, archaea and microeukaryotes during the first days of life. Given that the collected infant stool samples contain limited amounts of microbial biomass, we developed the necessary wet- and dry-lab methodologies to generate artefact-free high-resolution metagenomic data. We identified differences in encoded functions between microbiomes of vaginally delivered (VD) and CSD neonates. Several functional pathways were over-represented in VD neonates, including lipopolysaccharide (LPS) biosynthesis, flagellar assembly, bacterial chemotaxis and two-component systems. Through de novo genome reconstructions, we were able to link these enriched functions to individual-specific strains, which were transmitted from mothers to neonates in case of VD. The stimulation of primary human immune cells with immunogenic LPS isolated from early stool samples of VD neonates resulted in the production of higher levels of tumour necrosis factor (TNF-α) and interleukin 18 (IL-18). Accordingly, the observed levels of TNF-α and IL-18 in neonatal blood plasma were higher in the case of VD. Taken together, our results demonstrate that CSD disrupts mother-to-neonate transmission of specific microbial gut strains, linked functional repertoires and immune-stimulatory potential during a critical window for neonatal immune system priming. Based on our findings, we are investigating the longer-term impacts of differences in microbiome colonisation on the human immune system and assessing new approaches aimed at restoring the early colonising microbiota in the case of CSD. Based on our data, such approaches require the transfer of function-conferring strains from the maternal gut in accordance with personalised medicine approaches.

Collaborators: Carine de Beaufort, Centre Hospitalier de Luxembourg (CHL; Luxembourg-City, Luxembourg); Integrated BioBank of Luxembourg (IBBL; Dudelange, Luxembourg); Anders Andersson, KTH Royal Institute of Technology and SciLifeLab (Stockholm, Sweden).

Publications:

Greenhalgh K., Meyer K.M., Aagaard K.M., Wilmes P.* (2016) The human gut microbiome in health: establishment and resilience of microbiota over a lifetime. Environmental Microbiology 18:2103-16 (doi: 10.1111/1462-2920.13318). 

Wampach L., Heintz-Buschart A., Hogan A., Muller E.E.L., Narayanasamy S., Laczny C.L., Hugerth L.W., Bindl L., Bottu J., Andersson A.F., de Beaufort C., Wilmes P. (2017) Colonization and succession within the human gut microbiome by archaea, bacteria and microeukaryotes during the first year of life. Frontiers in Microbiology 8:1-21 (doi: 10.3389/fmicb.2017.00738).

Wampach L., Heintz-Buschart A., Fritz J.V., Herold M., Narayanasamy S., Kaysen A., Hogan A., Bindl L., Bottu J., Sjöqvist C., Ramiro-Garcia J., May P., Andersson A.F., de Beaufort C., Wilmes P. (2018) Birth mode is associated with earliest gut microbiome functions and immunostimulatory potential. Nature Communications 9:5091 (doi: 10.1038/s41467-018-07631-x).

Funding: Luxembourg National Research Fund (FNR) Aides à la Formation Recherche (AFR); Fondation André et Henriette Losch.

Organismal and functional biogeography of the human gastrointestinal tract and its potential involvement in colorectal cancer

The human body is home to microbial communities whose member cells as well as genes outnumber our own. The largest part of the human microbiome resides in the gastrointestinal tract and it greatly influences human health and disease. Metagenomic DNA from faecal samples has been analysed in detail in recent years to understand the structure and function of the gastrointestinal microbiome. Links between colonization patterns and human well-being or disease have been identified. Here, we are using an integrated omics approach to identify potential links between gut microbial community structure and function, and colorectal cancers. In addition, differences/commonalities between the oral microbiome and the colonic microbiota are being studied.

First results demonstrate that transmission to, and subsequent colonisation of, the large intestine by oral microbes is common among healthy individuals. In addition there are increased levels of transmission in patients suffering from colorectal cancer or rheumatoid arthritis, suggesting oral-gut transmission of several microbes may play a role in the progression of chronic diseases. These findings establish the mouth as a potential source of gut microbial species and demonstrate that microbes linked to colorectal cancer may originate from within the body rather than the environment. It must now be assessed whether interventions in the oral microbial community may impact the gut microbiome and its effects on human health.

Collaborator: Peer Bork, European Molecular Biology Laboratory (Heidelberg, Germany)

Publications:

Schmidt T.S.B., Hayward M.R., Coelho L.P., Li S.S., Costea P.I., Voigt A.Y., Maistrenko O.M., Alves R.J., Bergsten E., de Beaufort C., Sobhani I., Heintz-Buschart A., Sunagawa S., Zeller G., Wilmes P., Bork P. (2019) Extensive transmission of microbes along the gastrointestinal tract. eLife 8:e42693 (doi: 10.7554/eLife.42693).

Funding: FNR INTER CORE programme grant "microCancer".

Diabetes multiplex family study (the MUST study)

Recent evidence from high-resolution molecular studies suggests links between microbial dysbiosis in the gastrointestinal tract and a number of complex chronic diseases including diabetes mellitus. The present study forms a pilot study for the larger Luxembourg-based Diabetes Multiplex Family Study (MUST). Within the pilot study, we investigate the interplay of the gastrointestinal microbiota, lifestyle and genetic background in an observational study of families with two or more individuals affected by type 1 diabetes mellitus (T1DM). Faecal samples which have undergone comprehensive biomolecular extractions are currently analysed using a multi-omics approach. Anthropometric data, including demographics, medical history, health status, medication, and dietary habits of all study participants were collected and are integrated with molecular data.

By building on our integrated wet- and dry-lab methodological framework for integrated multi-omic analyses of microbial communities, we resolved the taxonomic and functional attributes of gastrointestinal microbiota in four Luxembourg families with multiple cases of T1DM. Analysis of intra- and inter-individual variation demonstrated that family membership has a pronounced effect on the structural and functional composition of the gastrointestinal microbiome. In the context of T1DM, consistent taxonomic differences were absent across families, but certain human exocrine pancreatic proteins including α-amylases were found at lower levels. Microbial genes whose expression was associated with the levels of the human proteins included enzyme-coding genes conferring different metabolic traits. Interestingly, genes involved in thiamine (vitamin B1) biosynthesis were significantly reduced in expression in the context of T1DM. Thiamine deficiency had been described in T1DM and this has been linked to the exacerbation of the disease. Our work demonstrates that this deficiency is at least partially due to impacts on the functions expressed by the gut microbiome, thereby providing a mechanistic understanding of how the gut microbiome plays a role in key disease processes. Furthermore, based on the reconstructed genomes, we found that the differentially genes in question were encoded and expressed by distinct microbial taxa in different individuals. In other words, functional differences do not necessarily depend on specific taxa. This represents an essential consideration for the field as studies have so far primarily aimed at identifying taxonomic differences between healthy and diseased individuals thereby emulating the concepts of infection biology from over a century. However, our work clearly demonstrates that differences may be apparent in the “functional microbiome”, independent of taxonomic differences. Therefore, future studies into the gut microbiome in the context of disease should consider identification of functional genes of interest first, followed by the linkage to constituent taxa along the premise of “function first, taxa second”.

Collaborators: Carine de Beaufort, Centre Hospitalier de Luxembourg (CHL; Luxembourg-City, Luxembourg); Integrated BioBank of Luxembourg (IBBL; Dudelange, Luxembourg).

Publications:

Heintz-Buschart A., May P., Laczny C., Lebrun L., Bellora C., Krishna A., Wampach L., Schneider J., Hogan A., de Beaufort C., Wilmes P. (2017) Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes. Nature Microbiology 2:16180 (doi: 10.1038/nmicrobiol.2016.180).

Heintz-Buschart A. and Wilmes P. (2018) Human gut microbiome: function matters. Trends in Microbiology 26:563-574 (doi: 10.1016/j.tim.2017.11.002).

Non-invasive microbiome-derived multi-omic biomarkers for the early-stage detection and stratification of Parkinson’s disease (MiBiPa)

Parkinson’s disease (PD) is a neurodegenerative disease with characteristic motor symptoms that are commonly accompanied by pathological α-synuclein aggregation. Presently the propagation of α-synuclein aggregation in PD is proposed to start in the periphery, i.e. in the enteric nervous system and the olfactory bulb. Our study focuses on these two ports of entry for potential pathogenic agents in PD. We hypothesize that changes in microbial community structure and function in the gastrointestinal tract as well as the nasal cavity accompany PD from its onset, progression through its most specific prodrome REM sleep behaviour disorder (RBD) to manifest PD. We aim to (i) develop a microbiome biomarker model for Parkinson’s disease based on microbiome structural and functional signatures in faeces and/or nasal lavages, (ii) validate the biomarker, (iii) assess its applicability for early diagnosis of high-risk cohorts (such as RBD patients), and (iv) contribute to the understanding of the disease development by characterizing PD-specific microbiota. This is of particular relevance in relation to the development of future disease-modifying neuroprotective therapies that would require intervention at the earliest stages of disease but also to identify preventive strategies for PD.

Collaborators: Brit Mollenhauer, Paracelsus Elena Klinik Kassel (Kassel, Germany); Wolfgang Oertel, Philipps-University Marburg (Marburg, Germany).

Publication:

Heintz-Buschart A., Pandey U., Wicke T., Sixel-Döring F., Janzen A., Sittig-Wiegand E., Trenkwalder C., Oertel W.H., Mollenhauer B., Wilmes P. (2018) The nasal and gut microbiome in Parkinson’s disease and idiopathic rapid eye movement sleep behavior disorder. Movement Disorders 33:88-98 (doi: 10.1002/mds.27105).

Funding: FNR CORE programme grant “MiBiPa”; Michael J. Fox Foundation grant “MiBiPa PLUS”; Rotary Espoir-en-Tête 2016, 2018, 2019

Small RNA-mediated human-microbial cross-talk

The human gastrointestinal tract is densely populated by several bacterial species and imbalances in the microbiota affect human health. Bacteria are known to change the expression of genes to cope with modified environments and bacterial sRNAs play crucial roles in such responses. Furthermore, several studies have postulated that bacterial sRNAs influence bacterial pathogenesis. In the present projects, we are characterising the functions of sRNAs (primarily exported sRNAs) which we have identified in the gastrointestinal tract and in enteric bacteria to understand whether these molecules may play roles in interspecies communication including with the human host.

Collaborator: Esther N.M. Nolte-'t Hoen (Utrecht University, Dept Biochemistry & Cell Biology, Fac Veterinary Medicine, Netherlands); Julien Godet (Laboratoire de Biophotonique et Pharmacologie, UMR CNRS 7213, Faculté de Pharmacie)

Publications:

Ghosal A., Upadhyaya B.B., Fritz J.V., Heintz-Buschart A., Desai M.S., Dilimulati Y., Huang D., Baumuratov A., Wang K., Galas D., Wilmes P. (2015) The extracellular RNA complement of Escherichia coli. MicrobiologyOpen 4:252-266 (doi: 10.1002/mbo3.235).

Joëlle V. Fritz; Extracellular RNA in Bacteria, http://exrna.org/extracellular-rna-bacteria/

Fritz J.F., Heintz-Buschart A., Ghosal A., Wampach L., Etheridge A., Galas D., Wilmes P. (2016) Sources and functions of extracellular small RNAs in human circulation. Annual Review of Nutrition 36:301-336 (doi: 10.1146/annurev-nutr-071715-050711).

Heintz-Buschart A., Yusuf D., Kaysen A., Etheridge A., Fritz J.V., May P., de Beaufort C., Upadhyaya B.B., Ghosal A., Galas D., Wilmes P. (2018) Small RNA profiling of low biomass samples: identification and removal of contaminants. BMC Biology, 16:52 (doi: 10.1186/s12915-018-0522-7).

Funding: FNR COREJunior programme grant “BEaR”, FNR INTER CORE programme grant "microCancer".

Changes in the gastrointestinal microbiome and immune status during chemotherapy and immune ablative intervention in humans

Chemotherapeutic treatments for malignant diseases are known to greatly impact patients’ gut microbiota. Resulting imbalances at the mucosal interface may culminate in mucositis, which is considered the major complication associated with chemotherapy and radiotherapy. In addition, a frequent adverse effect of allogeneic stem cell transplantation (allo-HSCT) potentially linked to the microbiome is graft-versus-host disease.

In this project, we are investigating changes to the composition of the gut microbiome during and after different cancer treatment regimens and allo-HSCT. Specifically, we aim to correlate the detected shifts in the microbiome with development or amplification of treatment side effects and overall outcome. Ultimately, this could enable to identify patients at risk based on their specific GIT microbiome profile and to develop individually tailored treatments.

Collaborators: Jochen Schneider, Luxembourg Centre for Systems Biomedicine, University of Luxembourg (Esch-sur-Alzette, Luxembourg); Norbert Graf, Arne Simon and Jörg Bittenbring, Saarland University Medical Center (Homburg, Germany).

Publications:

Noor F., Kaysen A., Wilmes P., Schneider J. (2018) The gut microbiota and hematopoietic stem cell transplantation: challenges and potentials.  Journal of Innate Immunity, in press (doi: 10.1159/000492943).

Kaysen A., Heintz-Buschart A., Muller E.E.L., Narayanasamy S., Wampach L., Laczny C.C., Graf N., Simon A., Franke K., Bittenbring J., Wilmes P., Schneider J.G. (2017) Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation. Translational Research 186:79-94 (doi: 10.1016/j.trsl.2017.06.008).

Funding: Internal Research Project of University of Luxembourg “ImMicroDyn”.