Publications by authors named "Dirk Haller"

169 Publications

Longitudinal Profiles of Dietary and Microbial Metabolites in Formula- and Breastfed Infants.

Front Mol Biosci 2021 28;8:660456. Epub 2021 May 28.

Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany.

The early-life metabolome of the intestinal tract is dynamically influenced by colonization of gut microbiota which in turn is affected by nutrition, i.e. breast milk or formula. A detailed examination of fecal metabolites was performed to investigate the effect of probiotics in formula compared to control formula and breast milk within the first months of life in healthy neonates. A broad metabolomics approach was conceptualized to describe fecal polar and semi-polar metabolites affected by feeding type within the first year of life. Fecal metabolomes were clearly distinct between formula- and breastfed infants, mainly originating from diet and microbial metabolism. Unsaturated fatty acids and human milk oligosaccharides were increased in breastfed, whereas Maillard products were found in feces of formula-fed children. Altered microbial metabolism was represented by bile acids and aromatic amino acid metabolites. Elevated levels of sulfated bile acids were detected in stool samples of breastfed infants, whereas secondary bile acids were increased in formula-fed infants. Microbial co-metabolism was supported by significant correlation between chenodeoxycholic or lithocholic acid and members of Clostridia. Fecal metabolites showed strong inter- and intra-individual behavior with features uniquely present in certain infants and at specific time points. Nevertheless, metabolite profiles converged at the end of the first year, coinciding with solid food introduction.
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http://dx.doi.org/10.3389/fmolb.2021.660456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8195334PMC
May 2021

Intestinal microbiota in health and disease - Seeding multidisciplinary research in Germany.

Authors:
Dirk Haller

Int J Med Microbiol 2021 Jul 5;311(5):151514. Epub 2021 Jun 5.

Chair of Nutrition and Immunology, Technical University of Munich, Germany.

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http://dx.doi.org/10.1016/j.ijmm.2021.151514DOI Listing
July 2021

Network analysis methods for studying microbial communities: A mini review.

Comput Struct Biotechnol J 2021 4;19:2687-2698. Epub 2021 May 4.

Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany.

Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities in complex and contiguous environments. They engage in numerous inter- and intra- kingdom interactions which can be inferred from microbiome profiling data. In particular, network-based approaches have proven helpful in deciphering complex microbial interaction patterns. Here we give an overview of state-of-the-art methods to infer intra-kingdom interactions ranging from simple correlation- to complex conditional dependence-based methods. We highlight common biases encountered in microbial profiles and discuss mitigation strategies employed by different tools and their trade-off with increased computational complexity. Finally, we discuss current limitations that motivate further method development to infer inter-kingdom interactions and to robustly and comprehensively characterize microbial environments in the future.
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http://dx.doi.org/10.1016/j.csbj.2021.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131268PMC
May 2021

MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes.

Microb Biotechnol 2021 07 3;14(4):1757-1770. Epub 2021 Jun 3.

Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany.

Environmental and host-associated microbial communities are complex ecosystems, of which many members are still unknown. Hence, it is challenging to study community dynamics and important to create model systems of reduced complexity that mimic major community functions. Therefore, we developed MiMiC, a computational approach for data-driven design of simplified communities from shotgun metagenomes. We first built a comprehensive database of species-level bacterial and archaeal genomes (n = 22 627) consisting of binary (presence/absence) vectors of protein families (Pfam = 17 929). MiMiC predicts the composition of minimal consortia using an iterative scoring system based on maximal match-to-mismatch ratios between this database and the Pfam binary vector of any input metagenome. Pfam vectorization retained enough resolution to distinguish metagenomic profiles between six environmental and host-derived microbial communities (n = 937). The calculated number of species per minimal community ranged between 5 and 11, with MiMiC selected communities better recapitulating the functional repertoire of the original samples than randomly selected species. The inferred minimal communities retained habitat-specific features and were substantially different from communities consisting of most abundant members. The use of a mixture of known microbes revealed the ability to select 23 of 25 target species from the entire genome database. MiMiC is open source and available at https://github.com/ClavelLab/MiMiC.
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http://dx.doi.org/10.1111/1751-7915.13845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8313253PMC
July 2021

Development of a Highly Sensitive Ultra-High-Performance Liquid Chromatography Coupled to Electrospray Ionization Tandem Mass Spectrometry Quantitation Method for Fecal Bile Acids and Application on Crohn's Disease Studies.

J Agric Food Chem 2021 May 23;69(17):5238-5251. Epub 2021 Apr 23.

Chair for Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, D-85354 Freising, Germany.

In addition to their important role in fat digestion, bile acids are increasingly being used as markers for various diseases. The large diversity of bile acids results from the conversion of primary and conjugated bile acids into secondary bile acids by deconjugation and dehydroxylation reactions mediated by the intestinal microbiota. Here, we describe a fast and sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for absolute quantitation of 45 bile acids in human or mouse feces in combination with a simple workup and extraction procedure. Method validation outlined excellent limits of detection and quantitation, linearity, selectivity, recovery, extraction loss, and precision. To investigate the connection between microbiome alterations and bile acid metabolism, the method was applied on a Crohn's disease study including patients with histologically documented active disease or remission as well as on a model using humanized mice. As the complex mechanism including genetic and environmental factors leading to the development of Crohn's disease is so far not completely understood, the study investigates the microbial metabolism of bile acids and the potential use of bile acid profiles to predict disease state.
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http://dx.doi.org/10.1021/acs.jafc.1c00769DOI Listing
May 2021

Auto-aggressive CXCR6 CD8 T cells cause liver immune pathology in NASH.

Nature 2021 Apr 24;592(7854):444-449. Epub 2021 Mar 24.

Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University Innsbruck, Innsbruck, Austria.

Nonalcoholic steatohepatitis (NASH) is a manifestation of systemic metabolic disease related to obesity, and causes liver disease and cancer. The accumulation of metabolites leads to cell stress and inflammation in the liver, but mechanistic understandings of liver damage in NASH are incomplete. Here, using a preclinical mouse model that displays key features of human NASH (hereafter, NASH mice), we found an indispensable role for T cells in liver immunopathology. We detected the hepatic accumulation of CD8 T cells with phenotypes that combined tissue residency (CXCR6) with effector (granzyme) and exhaustion (PD1) characteristics. Liver CXCR6 CD8 T cells were characterized by low activity of the FOXO1 transcription factor, and were abundant in NASH mice and in patients with NASH. Mechanistically, IL-15 induced FOXO1 downregulation and CXCR6 upregulation, which together rendered liver-resident CXCR6 CD8 T cells susceptible to metabolic stimuli (including acetate and extracellular ATP) and collectively triggered auto-aggression. CXCR6 CD8 T cells from the livers of NASH mice or of patients with NASH had similar transcriptional signatures, and showed auto-aggressive killing of cells in an MHC-class-I-independent fashion after signalling through P2X7 purinergic receptors. This killing by auto-aggressive CD8 T cells fundamentally differed from that by antigen-specific cells, which mechanistically distinguishes auto-aggressive and protective T cell immunity.
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http://dx.doi.org/10.1038/s41586-021-03233-8DOI Listing
April 2021

Associations between habitual diet, metabolic disease, and the gut microbiota using latent Dirichlet allocation.

Microbiome 2021 03 16;9(1):61. Epub 2021 Mar 16.

Independent Research Unit Clinical Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.

Background: The gut microbiome impacts human health through various mechanisms and is involved in the development of a range of non-communicable diseases. Diet is a well-known factor influencing microbe-host interaction in health and disease. However, very few findings are based on large-scale analysis using population-based studies. Our aim was to investigate the cross-sectional relationship between habitual dietary intake and gut microbiota structure in the Cooperative Health Research in the Region of Augsburg (KORA) FF4 study.

Results: Fecal microbiota was analyzed using 16S rRNA gene amplicon sequencing. Latent Dirichlet allocation (LDA) was applied to samples from 1992 participants to identify 20 microbial subgroups within the study population. Each participant's gut microbiota was subsequently described by a unique composition of these 20 subgroups. Associations between habitual dietary intake, assessed via repeated 24-h food lists and a Food Frequency Questionnaire, and the 20 subgroups, as well as between prevalence of metabolic diseases/risk factors and the subgroups, were assessed with multivariate-adjusted Dirichlet regression models. After adjustment for multiple testing, eight of 20 microbial subgroups were significantly associated with habitual diet, while nine of 20 microbial subgroups were associated with the prevalence of one or more metabolic diseases/risk factors. Subgroups 5 (Faecalibacterium, Lachnospiracea incertae sedis, Gemmiger, Roseburia) and 14 (Coprococcus, Bacteroides, Faecalibacterium, Ruminococcus) were particularly strongly associated with diet. For example, participants with a high probability for subgroup 5 were characterized by a higher Alternate Healthy Eating Index and Mediterranean Diet Score and a higher intake of food items such as fruits, vegetables, legumes, and whole grains, while participants with prevalent type 2 diabetes mellitus were characterized by a lower probability for subgroup 5.

Conclusions: The associations between habitual diet, metabolic diseases, and microbial subgroups identified in this analysis not only expand upon current knowledge of diet-microbiota-disease relationships, but also indicate the possibility of certain microbial groups to be modulated by dietary intervention, with the potential of impacting human health. Additionally, LDA appears to be a powerful tool for interpreting latent structures of the human gut microbiota. However, the subgroups and associations observed in this analysis need to be replicated in further studies. Video abstract.
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http://dx.doi.org/10.1186/s40168-020-00969-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7967986PMC
March 2021

Recent advances in culture-based gut microbiome research.

Int J Med Microbiol 2021 Apr 25;311(3):151485. Epub 2021 Feb 25.

Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany; ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany. Electronic address:

Gut microbes affect the physiology of their hosts. Studying their diversity and functions is thus of utmost importance as it will open new avenues towards the discovery of new biomolecules and the treatment of diseases. Gut microbiome research is currently boosted by the unification of metagenomics, which has dominated the field in the last two decades, and cultivation, which is experiencing a renaissance. Each of these approaches has advantages and drawbacks that can be overcome if used synergistically. In this brief article, we summarize recent literature and own studies on the cultivation of gut microbes, provide a succinct status quo of cultured fractions and collections of isolates, and give short opinions on challenges and next steps to take.
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http://dx.doi.org/10.1016/j.ijmm.2021.151485DOI Listing
April 2021

Modeling microbe-host interaction in the pathogenesis of Crohn's disease.

Int J Med Microbiol 2021 Apr 25;311(3):151489. Epub 2021 Feb 25.

Technical University of Munich, Chair of Nutrition and Immunology, School of Life Sciences, 85354 Freising, Germany; Technical University of Munich, ZIEL Institute for Food & Health, Germany. Electronic address:

Alterations in the gut microbiota structure and function are thought to play an important role in the pathogenesis of Crohn's disease (CD). The rapid advancement of high-throughput sequencing technologies led to the identification of microbiome risk signatures associated with distinct disease phenotypes and progressing disease entities. Functional validation of the identified microbiome signatures is essential to understand the underlying mechanisms of microbe-host interactions. Germfree mouse models are available to study the functional role of disease-conditioning complex gut microbial ecosystems (dysbiosis) or pathobionts (single bacteria) in the pathogenesis of CD-like inflammation. Here, we discuss the clinical and mechanistic relevance and limitations of gnotobiotic mouse models in the context of CD. In addition, we will address the role of diet as an essential external factor modulating microbiome changes, potentially underlying disease initiation and development.
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http://dx.doi.org/10.1016/j.ijmm.2021.151489DOI Listing
April 2021

Microbe-Mucus Interface in the Pathogenesis of Colorectal Cancer.

Cancers (Basel) 2021 Feb 4;13(4). Epub 2021 Feb 4.

Department of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany.

Overlying gastrointestinal epithelial cells is the transparent mucus layer that separates the lumen from the host. The dynamic mucus layer serves to lubricate the mucosal surface, to protect underlying epithelial cells, and as a transport medium between luminal contents and epithelial cells. Furthermore, it provides a habitat for commensal bacteria and signals to the underlying immune system. Mucins are highly glycosylated proteins, and their glycocode is tissue-specific and closely linked to the resident microbiota. Aberrant mucin expression and glycosylation are linked to chronic inflammation and gastrointestinal cancers, including colorectal cancer (CRC). Aberrant mucus production compromises the mucus layer and allows bacteria to come into close contact with the intestinal epithelium, potentially triggering unfavorable host responses and the subsequent development of tumors. Here, we review our current understanding of the interaction between the intestinal microbiota and mucus in healthy and CRC subjects. Deep knowledge of the intricate mechanisms of microbe-mucus interactions may contribute to the development of novel treatment strategies for CRC, in which a dysfunctional mucus layer is observed.
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http://dx.doi.org/10.3390/cancers13040616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7913824PMC
February 2021

Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis.

PLoS One 2021 8;16(2):e0246367. Epub 2021 Feb 8.

Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain.

Background: Personalized medicine requires finding relationships between variables that influence a patient's phenotype and predicting an outcome. Sparse generalized canonical correlation analysis identifies relationships between different groups of variables. This method requires establishing a model of the expected interaction between those variables. Describing these interactions is challenging when the relationship is unknown or when there is no pre-established hypothesis. Thus, our aim was to develop a method to find the relationships between microbiome and host transcriptome data and the relevant clinical variables in a complex disease, such as Crohn's disease.

Results: We present here a method to identify interactions based on canonical correlation analysis. We show that the model is the most important factor to identify relationships between blocks using a dataset of Crohn's disease patients with longitudinal sampling. First the analysis was tested in two previously published datasets: a glioma and a Crohn's disease and ulcerative colitis dataset where we describe how to select the optimum parameters. Using such parameters, we analyzed our Crohn's disease data set. We selected the model with the highest inner average variance explained to identify relationships between transcriptome, gut microbiome and clinically relevant variables. Adding the clinically relevant variables improved the average variance explained by the model compared to multiple co-inertia analysis.

Conclusions: The methodology described herein provides a general framework for identifying interactions between sets of omic data and clinically relevant variables. Following this method, we found genes and microorganisms that were related to each other independently of the model, while others were specific to the model used. Thus, model selection proved crucial to finding the existing relationships in multi-omics datasets.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0246367PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7870068PMC
August 2021

Mitochondrial Metabolism in the Intestinal Stem Cell Niche-Sensing and Signaling in Health and Disease.

Front Cell Dev Biol 2020 5;8:602814. Epub 2021 Jan 5.

Chair of Nutrition and Immunology, Technische Universität München, Freising-Weihenstephan, Germany.

Mitochondrial metabolism, dynamics, and stress responses in the intestinal stem cell niche play a pivotal role in regulating intestinal epithelial cell homeostasis, including self-renewal and differentiation. In addition, mitochondria are increasingly recognized for their involvement in sensing the metabolic environment and their capability of integrating host and microbial-derived signals. Gastrointestinal diseases such as inflammatory bowel diseases and colorectal cancer are characterized by alterations of intestinal stemness, the microbial milieu, and mitochondrial metabolism. Thus, mitochondrial function emerges at the interface of determining health and disease, and failure to adapt mitochondrial function to environmental cues potentially results in aberrant tissue responses. A mechanistic understanding of the underlying role of mitochondrial fitness in intestinal pathologies is still in its infancy, and therapies targeting mitochondrial (dys)function are currently lacking. This review discusses mitochondrial signaling and metabolism in intestinal stem cells and Paneth cells as critical junction translating host- and microbe-derived signals into epithelial responses. Consequently, we propose mitochondrial fitness as a hallmark for intestinal epithelial cell plasticity, determining the regenerative capacity of the epithelium.
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http://dx.doi.org/10.3389/fcell.2020.602814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7813778PMC
January 2021

Environmental signals rather than layered ontogeny imprint the function of type 2 conventional dendritic cells in young and adult mice.

Nat Commun 2021 01 19;12(1):464. Epub 2021 Jan 19.

Faculty of Medicine, Biomedical Center, Institute for Cardiovascular Physiology and Pathophysiology, LMU Munich, 82152, Planegg-Martinsried, Germany.

Conventional dendritic cells (cDC) are key activators of naive T cells, and can be targeted in adults to induce adaptive immunity, but in early life are considered under-developed or functionally immature. Here we show that, in early life, when the immune system develops, cDC2 exhibit a dual hematopoietic origin and, like other myeloid and lymphoid cells, develop in waves. Developmentally distinct cDC2 in early life, despite being distinguishable by fate mapping, are transcriptionally and functionally similar. cDC2 in early and adult life, however, are exposed to distinct cytokine environments that shape their transcriptional profile and alter their ability to sense pathogens, secrete cytokines and polarize T cells. We further show that cDC2 in early life, despite being distinct from cDC2 in adult life, are functionally competent and can induce T cell responses. Our results thus highlight the potential of harnessing cDC2 for boosting immunity in early life.
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http://dx.doi.org/10.1038/s41467-020-20659-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7815729PMC
January 2021

Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome.

Nat Genet 2021 02 18;53(2):147-155. Epub 2021 Jan 18.

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.

The intestinal microbiome is implicated as an important modulating factor in multiple inflammatory, neurologic and neoplastic diseases. Recent genome-wide association studies yielded inconsistent, underpowered and rarely replicated results such that the role of human host genetics as a contributing factor to microbiome assembly and structure remains uncertain. Nevertheless, twin studies clearly suggest host genetics as a driver of microbiome composition. In a genome-wide association analysis of 8,956 German individuals, we identified 38 genetic loci to be associated with single bacteria and overall microbiome composition. Further analyses confirm the identified associations of ABO histo-blood groups and FUT2 secretor status with Bacteroides and Faecalibacterium spp. Mendelian randomization analysis suggests causative and protective effects of gut microbes, with clade-specific effects on inflammatory bowel disease. This holistic investigative approach of the host, its genetics and its associated microbial communities as a 'metaorganism' broaden our understanding of disease etiology, and emphasize the potential for implementing microbiota in disease treatment and management.
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http://dx.doi.org/10.1038/s41588-020-00747-1DOI Listing
February 2021

Comparing Circadian Rhythmicity in the Human Gut Microbiome.

STAR Protoc 2020 Dec 26;1(3):100148. Epub 2020 Oct 26.

ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.

Targeted sequencing of 16S rRNA genes enables the analysis of microbiomes. Here, we describe a protocol for the collection, storage, and preparation of fecal samples. We describe how we cluster similar sequences and assign bacterial taxonomies. Using diversity analysis and machine learning, we can extract disease-associated features. We also describe a circadian analysis to identify the presence or absence of rhythms in taxonomies. Differences in rhythmicity between cohorts can contribute to determining disease-associated bacterial signatures. For complete details on the use and execution of this protocol, please refer to Reitmeier et al. (2020).
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http://dx.doi.org/10.1016/j.xpro.2020.100148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7757335PMC
December 2020

A Phenotyping Platform to Characterize Healthy Individuals Across Four Stages of Life - The Study.

Front Nutr 2020 28;7:582387. Epub 2020 Oct 28.

ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.

Nutritional habits and requirements are changing over the lifespan, but the dynamics of nutritional issues and the diet-health relationship in the major stages of the human life cycle are not sufficiently understood. A human phenotyping research platform for nutrition studies was established to recruit and phenotype selected population groups across different stages of life. The project is the backbone of the highly interdisciplinary competence cluster of nutrition research aiming to identify dietary determinants of a healthy life throughout the lifespan and to develop healthier and tasty convenience foods with high consumer acceptance. The phenotyping program included anthropometry, body composition analysis, assessment of energy metabolism, health and functional status, multisensory perception, metabolic phenotyping, lifestyle, sociodemography, chronobiology, and assessment of dietary intake including food preferences and aversions. In total, 503 healthy volunteers at four defined phases of life including 3-5-year old children ( = 44), young adults aged 18-25 years ( = 94), adults aged 40-65 years ("middle agers," = 205), and older adults aged 75-85 years ( = 160) were recruited and comprehensively phenotyped. Plasma, serum, buffy coat, urine, feces and saliva samples were collected and stored at -80°C. Significant differences in anthropometric and metabolic parameters between the four groups were found. A major finding was the decrease in fat-free mass and the concomitant increase in % body fat in both sexes across the adult lifespan. The dataset will provide novel information on differences in diet-related parameters over the lifespan and is available for targeted analyses. We expect that this novel platform approach will have implications for the development of innovative food products tailored to promote healthy eating throughout life. DRKS, DRKS00009797. Registered on 20 January 2016, https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&_ID=DRKS00009797.
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http://dx.doi.org/10.3389/fnut.2020.582387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7657309PMC
October 2020

Organoids to Study Intestinal Nutrient Transport, Drug Uptake and Metabolism - Update to the Human Model and Expansion of Applications.

Front Bioeng Biotechnol 2020 11;8:577656. Epub 2020 Sep 11.

Chair of Nutrition and Immunology, Technische Universität München, Munich, Germany.

Intestinal transport and sensing processes and their interconnection to metabolism are relevant to pathologies such as malabsorption syndromes, inflammatory diseases, obesity and type 2 diabetes. Constituting a highly selective barrier, intestinal epithelial cells absorb, metabolize, and release nutrients into the circulation, hence serving as gatekeeper of nutrient availability and metabolic health for the whole organism. Next to nutrient transport and sensing functions, intestinal transporters including peptide transporter 1 (PEPT1) are involved in the absorption of drugs and prodrugs, including certain inhibitors of angiotensin-converting enzyme, protease inhibitors, antivirals, and peptidomimetics like β-lactam antibiotics. Here, we verify the applicability of 3D organoids for investigation of intestinal biochemical processes related to transport and metabolism of nutrients and drugs. Establishing a variety of methodologies including illustration of transporter-mediated nutrient and drug uptake and metabolomics approaches, we highlight intestinal organoids as robust and reliable tool in this field of research. Currently used models to study intestinal nutrient absorption, drug transport and enterocyte metabolism, such as Caco-2 cells or rodent explant models are of limited value due to their cancer and non-human origin, respectively. Particularly species differences result in poorly correlative data and findings obtained in these models cannot be extrapolated reliably to humans, as indicated by high failure rates in drug development pipelines. In contrast, human intestinal organoids represent a superior model of the intestinal epithelium and might help to implement the 3Rs (Reduction, Refinement and Replacement) principle in basic science as well as the preclinical and regulatory setup.
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http://dx.doi.org/10.3389/fbioe.2020.577656DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7516017PMC
September 2020

Comprehensive Lifestyle-Modification in Patients with Ulcerative Colitis-A Randomized Controlled Trial.

J Clin Med 2020 Sep 24;9(10). Epub 2020 Sep 24.

Department of Internal and Integrative Medicine, Evang. Kliniken Essen-Mitte, Faculty of Medicine, University of Duisburg-Essen, Am Deimelsberg 34 a, 45276 Essen, Germany.

Patients with ulcerative colitis suffer from impaired health-related quality of life (HrQoL). Comprehensive lifestyle-modification might increase HrQoL and decrease disease activity. Ninety-seven patients in clinical remission with impaired HrQoL were randomly assigned to a 10 week comprehensive lifestyle-modification program (LSM; = 47; 50.28 ± 11.90 years) or control ( = 50; 45.54 ± 12.49 years) that received a single workshop of intense training in naturopathic self-help strategies. Primary outcome was HrQoL (Inflammatory Bowel Disease Questionnaire; IBDQ) at week 12. Secondary outcomes included IBDQ subscales; generic HrQoL; disease activity and microbiome. Both groups showed improvement in HrQoL from baseline to post-treatment at week 12. The IBDQ sum score showed no significant group difference ( = 0.251). If patients attended more than 50% of the training sessions, a significant group effect ( = 0.034) was evident in favor of LSM. In addition, the SF-36 mental component summary ( = 0.002) was significantly different between the groups in favor of LSM. Disease activity microbiome and adverse events did not differ. Both a single workshop and a 10-week comprehensive lifestyle-modification program can improve HrQoL in patients with ulcerative colitis in remission with no apparent effects on clinical disease activity. A treatment difference was observed when examining a subsample of patients who attended ≥ 50% of sessions.
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http://dx.doi.org/10.3390/jcm9103087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7599849PMC
September 2020

Infusion of donor feces affects the gut-brain axis in humans with metabolic syndrome.

Mol Metab 2020 12 8;42:101076. Epub 2020 Sep 8.

Department of Endocrinology and Metabolism, Amsterdam University Medical Centers, location AMC, Amsterdam, the Netherlands.

Objective: Increasing evidence indicates that intestinal microbiota play a role in diverse metabolic processes via intestinal butyrate production. Human bariatric surgery data suggest that the gut-brain axis is also involved in this process, but the underlying mechanisms remain unknown.

Methods: We compared the effect of fecal microbiota transfer (FMT) from post-Roux-en-Y gastric bypass (RYGB) donors vs oral butyrate supplementation on (I-FP-CIT-determined) brain dopamine transporter (DAT) and serotonin transporter (SERT) binding as well as stable isotope-determined insulin sensitivity at baseline and after 4 weeks in 24 male and female treatment-naïve metabolic syndrome subjects. Plasma metabolites and fecal microbiota were also determined at these time points.

Results: We observed an increase in brain DAT after donor FMT compared to oral butyrate that reduced this binding. However, no effect on body weight and insulin sensitivity was demonstrated after post-RYGB donor feces transfer in humans with metabolic syndrome. Increases in fecal levels of Bacteroides uniformis were significantly associated with an increase in DAT, whereas increases in Prevotella spp. showed an inverse association. Changes in the plasma metabolites glycine, betaine, methionine, and lysine (associated with the S-adenosylmethionine cycle) were also associated with altered striatal DAT expression.

Conclusions: Although more and larger studies are needed, our data suggest a potential gut microbiota-driven modulation of brain dopamine and serotonin transporters in human subjects with obese metabolic syndrome. These data also suggest the presence of a gut-brain axis in humans that can be modulated.

Ntr Registration: 4488.
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http://dx.doi.org/10.1016/j.molmet.2020.101076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536740PMC
December 2020

Mechanisms of Interactions between Bile Acids and Plant Compounds-A Review.

Int J Mol Sci 2020 Sep 5;21(18). Epub 2020 Sep 5.

Fraunhofer Institute for Process Engineering and Packaging (IVV), 85354 Freising, Germany.

Plant compounds are described to interact with bile acids during small intestinal digestion. This review will summarise mechanisms of interaction between bile acids and plant compounds, challenges in in vivo and in vitro analyses, and possible consequences on health. The main mechanisms of interaction assume that increased viscosity during digestion results in reduced micellar mobility of bile acids, or that bile acids and plant compounds are associated or complexed at the molecular level. Increasing viscosity during digestion due to specific dietary fibres is considered a central reason for bile acid retention. Furthermore, hydrophobic interactions are proposed to contribute to bile acid retention in the small intestine. Although frequently hypothesised, no mechanism of permanent binding of bile acids by dietary fibres or indigestible protein fractions has yet been demonstrated. Otherwise, various polyphenolic structures were recently associated with reduced micellar solubility and modification of steroid and bile acid excretion but underlying molecular mechanisms of interaction are not yet fully understood. Therefore, future research activities need to consider the complex composition and cell-wall structures as influenced by processing when investigating bile acid interactions. Furthermore, influences of bile acid interactions on gut microbiota need to be addressed to clarify their role in bile acid metabolism.
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http://dx.doi.org/10.3390/ijms21186495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7555273PMC
September 2020

Integrated microbiota and metabolite profiles link Crohn's disease to sulfur metabolism.

Nat Commun 2020 08 28;11(1):4322. Epub 2020 Aug 28.

Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany.

Gut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn's disease patients undergoing autologous hematopoietic stem cell transplantation, and investigational therapy that induces drug free remission in a subset of patients. Via comparison of patients who responded and maintained remission, responded but experienced disease relapse and patients who did not respond to therapy, we identify shared functional signatures that correlate with disease activity despite the variability of gut microbiota profiles at taxonomic level. These signatures reflect the disease state when transferred to gnotobiotic mice. Taken together, the integration of microbiome and metabolite profiles from human cohort and mice improves the predictive modelling of disease outcome, and allows the identification of a network of bacteria-metabolite interactions involving sulfur metabolism as a key mechanism linked to disease activity in Crohn's disease.
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http://dx.doi.org/10.1038/s41467-020-17956-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7456324PMC
August 2020

Activating Transcription Factor 6 Mediates Inflammatory Signals in Intestinal Epithelial Cells Upon Endoplasmic Reticulum Stress.

Gastroenterology 2020 10 13;159(4):1357-1374.e10. Epub 2020 Jul 13.

Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany. Electronic address:

Background & Aims: Excess and unresolved endoplasmic reticulum (ER) stress in intestinal epithelial cells (IECs) promotes intestinal inflammation. Activating transcription factor 6 (ATF6) is one of the signaling mediators of ER stress. We studied the pathways that regulate ATF6 and its role for inflammation in IECs.

Methods: We performed an RNA interference screen, using 23,349 unique small interfering RNAs targeting 7783 genes and a luciferase reporter controlled by an ATF6-dependent ERSE (ER stress-response element) promoter, to identify proteins that activate or inhibit the ATF6 signaling pathway in HEK293 cells. To validate the screening results, intestinal epithelial cell lines (Caco-2 cells) were transfected with small interfering RNAs or with a plasmid overexpressing a constitutively active form of ATF6. Caco-2 cells with a CRISPR-mediated disruption of autophagy related 16 like 1 gene (ATG16L1) were used to study the effect of ATF6 on ER stress in autophagy-deficient cells. We also studied intestinal organoids derived from mice that overexpress constitutively active ATF6, from mice with deletion of the autophagy related 16 like 1 or X-Box binding protein 1 gene in IECs (Atg16l1 or Xbp1, which both develop spontaneous ileitis), from patients with Crohn's disease (CD) and healthy individuals (controls). Cells and organoids were incubated with tunicamycin to induce ER stress and/or chemical inhibitors of newly identified activator proteins of ATF6 signaling, and analyzed by real-time polymerase chain reaction and immunoblots. Atg16l1 and control (Atg16l1) mice were given intraperitoneal injections of tunicamycin and were treated with chemical inhibitors of ATF6 activating proteins.

Results: We identified and validated 15 suppressors and 7 activators of the ATF6 signaling pathway; activators included the regulatory subunit of casein kinase 2 (CSNK2B) and acyl-CoA synthetase long chain family member 1 (ACSL1). Knockdown or chemical inhibition of CSNK2B and ACSL1 in Caco-2 cells reduced activity of the ATF6-dependent ERSE reporter gene, diminished transcription of the ATF6 target genes HSP90B1 and HSPA5 and reduced NF-κB reporter gene activation on tunicamycin stimulation. Atg16l1 and or Xbp1 organoids showed increased expression of ATF6 and its target genes. Inhibitors of ACSL1 or CSNK2B prevented activation of ATF6 and reduced CXCL1 and tumor necrosis factor (TNF) expression in these organoids on induction of ER stress with tunicamycin. Injection of mice with inhibitors of ACSL1 or CSNK2B significantly reduced tunicamycin-mediated intestinal inflammation and IEC death and expression of CXCL1 and TNF in Atg16l1 mice. Purified ileal IECs from patients with CD had higher levels of ATF6, CSNK2B, and HSPA5 messenger RNAs than controls; early-passage organoids from patients with active CD show increased levels of activated ATF6 protein, incubation of these organoids with inhibitors of ACSL1 or CSNK2B reduced transcription of ATF6 target genes, including TNF.

Conclusions: Ileal IECs from patients with CD have higher levels of activated ATF6, which is regulated by CSNK2B and HSPA5. ATF6 increases expression of TNF and other inflammatory cytokines in response to ER stress in these cells and in organoids from Atg16l1 and Xbp1 mice. Strategies to inhibit the ATF6 signaling pathway might be developed for treatment of inflammatory bowel diseases.
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http://dx.doi.org/10.1053/j.gastro.2020.06.088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7923714PMC
October 2020

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes.

Cell Host Microbe 2020 08 2;28(2):258-272.e6. Epub 2020 Jul 2.

ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany; Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany. Electronic address:

Lifestyle, obesity, and the gut microbiome are important risk factors for metabolic disorders. We demonstrate in 1,976 subjects of a German population cohort (KORA) that specific microbiota members show 24-h oscillations in their relative abundance and identified 13 taxa with disrupted rhythmicity in type 2 diabetes (T2D). Cross-validated prediction models based on this signature similarly classified T2D. In an independent cohort (FoCus), disruption of microbial oscillation and the model for T2D classification was confirmed in 1,363 subjects. This arrhythmic risk signature was able to predict T2D in 699 KORA subjects 5 years after initial sampling, being most effective in combination with BMI. Shotgun metagenomic analysis functionally linked 26 metabolic pathways to the diurnal oscillation of gut bacteria. Thus, a cohort-specific risk pattern of arrhythmic taxa enables classification and prediction of T2D, suggesting a functional link between circadian rhythms and the microbiome in metabolic diseases.
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http://dx.doi.org/10.1016/j.chom.2020.06.004DOI Listing
August 2020

Partial enteral nutrition has no benefit on bone health but improves growth in paediatric patients with quiescent or mild Crohn's disease.

Clin Nutr 2020 12 22;39(12):3786-3796. Epub 2020 Apr 22.

Department of Paediatrics, Dr von Hauner Children's Hospital, LMU Munich, Munich, Germany. Electronic address:

Background And Aims: Exclusive enteral nutrition induces remission, improves bone health and growth in paediatric Crohn's disease (CD) patients, but is highly demanding for patients. We investigated efficacy of partial enteral nutrition (PEN) on bone health, growth and course in CD patients and assessed microbial and metabolic changes induced by PEN.

Methods: We performed a two centre, non-randomized controlled intervention study in quiescent CD patients aged <19 years. Patients in intervention group received a liquid formula providing ~25% of daily energy for one year. At baseline, after 3, 6, 9 and 12 months, we collected data on bone, muscle (peripheral quantitative computertomography), anthropometry, disease activity (weighted paediatric CD activity index), metabolomic profile (liquid chromatography mass spectrometry), and faecal microbiome (16S rRNA gene sequencing).

Results: Of 41 CD patients, 22 received the intervention (PEN) (mean age 15.0 ± 1.9 years, 50% male), 19 served as controls (non-PEN) (12.8 ± 3.1 years, 58% male). At baseline, mean bone quality was comparable to reference population with no improvement during the intervention. Relapse rate was low (8/41, PEN 4/22 and non-PEN 4/19, ns). PEN was not associated with microbiota community changes (beta diversity) but significantly reduced species diversity. Metabolome changes with upregulation of phosphatidylcholines in PEN patients are likely related to lipid and fatty acid composition of the formula. PEN significantly improved growth in a subgroup with Tanner stage 1-3.

Conclusion: In our cohort of paediatric CD patients, PEN did not affect bone health but improved growth in patients with a potential to grow.
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http://dx.doi.org/10.1016/j.clnu.2020.04.012DOI Listing
December 2020

Investigation of Adiposity Measures and Operational Taxonomic unit (OTU) Data Transformation Procedures in Stool Samples from a German Cohort Study Using Machine Learning Algorithms.

Microorganisms 2020 Apr 10;8(4). Epub 2020 Apr 10.

Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.

The analysis of the gut microbiome with respect to health care prevention and diagnostic purposes is increasingly the focus of current research. We analyzed around 2000 stool samples from the KORA (Cooperative Health Research in the Region of Augsburg) cohort using high-throughput 16S rRNA gene amplicon sequencing representing a total microbial diversity of 2089 operational taxonomic units (OTUs). We evaluated the combination of three different components to assess the reflection of obesity related to microbiota profiles: (i) four prediction methods (i.e., partial least squares (PLS), support vector machine regression (SVMReg), random forest (RF), and M5Rules); (ii) five OTU data transformation approaches (i.e., no transformation, relative abundance without and with log-transformation, as well as centered and isometric log-ratio transformations); and (iii) predictions from nine measurements of obesity (i.e., body mass index, three measures of body shape, and five measures of body composition). Our results showed a substantial impact of all three components. The applications of SVMReg and PLS in combination with logarithmic data transformations resulted in considerably predictive models for waist circumference-related endpoints. These combinations were at best able to explain almost 40% of the variance in obesity measurements based on stool microbiota data (i.e., OTUs) only. A reduced loss in predictive performance was seen after sex-stratification in waist-height ratio compared to other waist-related measurements. Moreover, our analysis showed that the contribution of OTUs less prevalent and abundant is minor concerning the predictive power of our models.
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http://dx.doi.org/10.3390/microorganisms8040547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7232268PMC
April 2020

Mitochondrial impairment drives intestinal stem cell transition into dysfunctional Paneth cells predicting Crohn's disease recurrence.

Gut 2020 11 28;69(11):1939-1951. Epub 2020 Feb 28.

Chair of Nutrition and Immunology, Technische Universität München, Freising-Weihenstephan, Germany

Objective: Reduced Paneth cell (PC) numbers are observed in inflammatory bowel diseases and impaired PC function contributes to the ileal pathogenesis of Crohn's disease (CD). PCs reside in proximity to Lgr5 intestinal stem cells (ISC) and mitochondria are critical for ISC-renewal and differentiation. Here, we characterise ISC and PC appearance under inflammatory conditions and describe the role of mitochondrial function for ISC niche-maintenance.

Design: Ileal tissue samples from patients with CD, mouse models for mitochondrial dysfunction (Hsp60) and CD-like ileitis (TNF), and intestinal organoids were used to characterise PCs and ISCs in relation to mitochondrial function.

Results: In patients with CD and TNF mice, inflammation correlated with reduced numbers of Lysozyme-positive granules in PCs and decreased expression in crypt regions. Disease-associated changes in PC and ISC appearance persisted in non-inflamed tissue regions of patients with CD and predicted the risk of disease recurrence after surgical resection. ISC-specific deletion of Hsp60 and inhibition of mitochondrial respiration linked mitochondrial function to the aberrant PC phenotype. Consistent with reduced stemness in vivo, crypts from inflamed TNF mice fail to grow into organoids ex vivo. Dichloroacetate-mediated inhibition of glycolysis, forcing cells to shift to mitochondrial respiration, improved ISC niche function and rescued the ability of TNF mice-derived crypts to form organoids.

Conclusion: We provide evidence that inflammation-associated mitochondrial dysfunction in the intestinal epithelium triggers a metabolic imbalance, causing reduced stemness and acquisition of a dysfunctional PC phenotype. Blocking glycolysis might be a novel drug target to antagonise PC dysfunction in the pathogenesis of CD.
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http://dx.doi.org/10.1136/gutjnl-2019-319514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7569388PMC
November 2020

ER Stress and the UPR in Shaping Intestinal Tissue Homeostasis and Immunity.

Front Immunol 2019 4;10:2825. Epub 2019 Dec 4.

Chair of Nutrition and Immunology, Technical University of Munich, Munich, Germany.

An imbalance in the correct protein folding milieu of the endoplasmic reticulum (ER) can cause ER stress, which leads to the activation of the unfolded protein response (UPR). The UPR constitutes a highly conserved and intricately regulated group of pathways that serve to restore ER homeostasis through adaptation or apoptosis. Numerous studies over the last decade have shown that the UPR plays a critical role in shaping immunity and inflammation, resulting in the recognition of the UPR as a key player in pathological processes including complex inflammatory, autoimmune and neoplastic diseases. The intestinal epithelium, with its many highly secretory cells, forms an important barrier and messenger between the luminal environment and the host immune system. It is not surprising, that numerous studies have associated ER stress and the UPR with intestinal diseases such as inflammatory bowel disease (IBD) and colorectal cancer (CRC). In this review, we discuss our current understanding of the roles of ER stress and the UPR in shaping immune responses and maintaining tissue homeostasis. Furthermore, the role played by the UPR in disease, with emphasis on IBD and CRC, is described here. As a key player in immunity and inflammation, the UPR has been increasingly recognized as an important pharmacological target in the development of therapeutic strategies for immune-mediated pathologies. We summarize available strategies targeting the UPR and their therapeutic implications. Understanding the balance between homeostasis and pathophysiology, as well as means of manipulating this balance, provides an important avenue for future research.
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http://dx.doi.org/10.3389/fimmu.2019.02825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6904315PMC
October 2020

Microbial Signals Link Westernized Diet to Metabolic Inflammation: More Evidence to Resolve Controversies.

Cell Mol Gastroenterol Hepatol 2020 6;9(2):343-344. Epub 2019 Dec 6.

Department of Nutrition and Immunology, Technische Universität, München, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jcmgh.2019.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6997444PMC
August 2020

Retention of Primary Bile Acids by Lupin Cell Wall Polysaccharides Under In Vitro Digestion Conditions.

Nutrients 2019 Sep 5;11(9). Epub 2019 Sep 5.

ZIEL-Institute for Food & Health, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany.

Interference of dietary fibres with the enterohepatic circulation of bile acids is proposed as a mechanism for lowering cholesterol. We investigated how lupin hull and cotyledon dietary fibres interact with primary bile acids using an in vitro model under simulated upper gastrointestinal conditions. Cell wall polysaccharides were isolated and extracted to separate pectin-like, hemicellulosic, and lignocellulosic structures. Lupin hull consisted mainly of structural components rich in cellulose. The viscosity of the in vitro digesta of lupin hull was low, showing predominantly liquid-like viscoelastic properties. On the other hand, lupin cotyledon fibre retarded bile acid release due to increased viscosity of the in vitro digesta, which was linked with high contents of pectic polymers forming an entangled network. Molecular interactions with bile acids were not measured for the hull but for the cotyledon, as follows: A total of 1.29 µmol/100 mg DM of chenodesoxycholic acids were adsorbed. Molecular interactions of cholic and chenodesoxycholic acids were evident for lignin reference material but did not account for the adsorption of the lupin cotyledon. Furthermore, none of the isolated and fractionated cell wall materials showed a significant adsorptive capacity, thus disproving a major role of lupin cell wall polysaccharides in bile acid adsorption.
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http://dx.doi.org/10.3390/nu11092117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769765PMC
September 2019
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