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Tytgat HLP, Binia A, Austin S, Grathwohl D, Sprenger N. Human Milk Oligosaccharides, Important Milk Bioactives for Child Health: A Perspective. Nestle Nutr Inst Workshop Ser 2023; 97:30-40. [PMID: 37023733 DOI: 10.1159/000528992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/18/2022] [Indexed: 04/08/2023]
Abstract
Human milk contains all nutritive and bioactive compounds to give infants the best possible start in life. Human milk bioactives cover a broad range of components, including immune cells, antimicrobial proteins, microbes, and human milk oligosaccharides (HMOs). Over the last decade, HMOs have gained special attention as their industrial production has allowed the study of their structure-function relation in reductionist experimental setups. This has shed light on how HMOs steer microbiome and immune system development in early life but also how HMOs affect infant health (e.g., antibiotic use, respiratory tract infections). We are on the verge of a new era where we can examine human milk as a complex biological system. This allows not only study of the mode of action and causality of individual human milk components but also investigation of synergistic effects that might exist between different bioactives. This new wave in human milk research is largely fueled by significant advances in analytical tools in the field of systems biology and network analysis. It will be exciting to explore how human milk composition is affected by different factors, how different human milk compounds work together, and how this influences healthy infant development.
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Affiliation(s)
- Hanne L P Tytgat
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Aristea Binia
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Sean Austin
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Dominik Grathwohl
- Clinical Development Research Unit, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Norbert Sprenger
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
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Martin FP, Tytgat HLP, Krogh Pedersen H, Moine D, Eklund AC, Berger B, Sprenger N. Host-microbial co-metabolites modulated by human milk oligosaccharides relate to reduced risk of respiratory tract infections. Front Nutr 2022; 9:935711. [PMID: 35990340 PMCID: PMC9386273 DOI: 10.3389/fnut.2022.935711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022] Open
Abstract
Human milk oligosaccharides (HMOs) are structurally diverse oligosaccharides present in breast milk, supporting the development of the gut microbiota and immune system. Previously, 2-HMO (2'fucosyllactose, lacto-N-neotetraose) compared to control formula feeding was associated with reduced risk of lower respiratory tract infections (LRTIs), in part linked to lower acetate and higher bifidobacteria proportions. Here, our objective was to gain further insight into additional molecular pathways linking the 2-HMO formula feeding and LRTI mitigation. From the same trial, we measured the microbiota composition and 743 known biochemical species in infant stool at 3 months of age using shotgun metagenomic sequencing and untargeted mass spectrometry metabolomics. We used multivariate analysis to identify biochemicals associated to 2-HMO formula feeding and LRTI and integrated those findings with the microbiota compositional data. Three molecular pathways stood out: increased gamma-glutamylation and N-acetylation of amino acids and decreased inflammatory signaling lipids. Integration of stool metagenomic data revealed some Bifidobacterium and Bacteroides species to be implicated. These findings deepen our understanding of the infant gut/microbiome co-metabolism in early life and provide evidence for how such metabolic changes may influence immune competence at distant mucosal sites such as the airways.
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Affiliation(s)
- François-Pierre Martin
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Hanne L P Tytgat
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | - Deborah Moine
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | - Bernard Berger
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Norbert Sprenger
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
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Karcher N, Nigro E, Punčochář M, Blanco-Míguez A, Ciciani M, Manghi P, Zolfo M, Cumbo F, Manara S, Golzato D, Cereseto A, Arumugam M, Bui TPN, Tytgat HLP, Valles-Colomer M, de Vos WM, Segata N. Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. Genome Biol 2021; 22:209. [PMID: 34261503 PMCID: PMC8278651 DOI: 10.1186/s13059-021-02427-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored. RESULTS We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon. CONCLUSIONS We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria.
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Affiliation(s)
| | - Eleonora Nigro
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Anna Cereseto
- Department CIBIO, University of Trento, Trento, Italy
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thi Phuong Nam Bui
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Current address: Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- IEO, European Institute of Oncology IRCCS, Milan, Italy.
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Tytgat HLP, Rasinkangas P, Ritari J, Reunanen J, Aalvink S, Lin CW, Palva A, Douillard FP, de Vos WM. Selection and characterization of a SpaCBA pilus-secreting food-grade derivative of Lacticaseibacillus rhamnosus GG. Appl Microbiol Biotechnol 2021; 105:1123-1131. [PMID: 33417041 PMCID: PMC7843469 DOI: 10.1007/s00253-020-11051-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/25/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022]
Abstract
Many studies have established the functional properties of Lacticaseibacillus rhamnosus GG, previously known as Lactobacillus rhamnosus GG, marketed worldwide as a probiotic. The extraordinary capacity of L. rhamnosus GG to bind to human mucus and influence the immune system especially stand out. Earlier, we have shown the key role of its SpaCBA sortase-dependent pili encoded by the spaCBA-srtC1 gene cluster herein. These heterotrimeric pili consist of a shaft pilin SpaA, a basal pilin SpaB, and tip pilin SpaC that contains a mucus-binding domain. Here, we set out to characterize a food-grade non-GMO mutant of L. rhamnosus GG, strain PA11, which secretes its pilins, rather than coupling them to the cell surface, due to a defect in the housekeeping sortase A. The sortase-negative strain PA11 was extensively characterized using functional genomics and biochemical approaches and found to secrete the SpaCBA pili into the supernatant. Given the functional importance and uniqueness of the mucus-binding pili of L. rhamnosus GG, strain PA11 offers novel opportunities towards the characterization and further therapeutic application of SpaCBA pili and their low-cost, large-scale production. •Creation of pilus-secreting mutant (PA11) of the key probiotic LGG. •Strain PA11 is defective in a functional housekeeping sortase SrtA. •Strain PA11 opens novel biotherapeutic application avenues. Graphical abstract![]()
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Affiliation(s)
- Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Pia Rasinkangas
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.,DuPont Nutrition & Biosciences, Kantvik, Finland
| | - Jarmo Ritari
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.,Finnish Red Cross Blood Service, Helsinki, Finland
| | - Justus Reunanen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.,University of Oulu, Oulu, Finland
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Chia-Wei Lin
- Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland
| | - Airi Palva
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - François P Douillard
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.,Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands. .,Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland. .,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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Rasinkangas P, Tytgat HLP, Ritari J, Reunanen J, Salminen S, Palva A, Douillard FP, de Vos WM. Characterization of Highly Mucus-Adherent Non-GMO Derivatives of Lacticaseibacillus rhamnosus GG. Front Bioeng Biotechnol 2020; 8:1024. [PMID: 32974330 PMCID: PMC7466733 DOI: 10.3389/fbioe.2020.01024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/05/2020] [Indexed: 01/30/2023] Open
Abstract
Lacticaseibacillus rhamnosus GG is one of the best studied lactic acid bacteria in the context of probiotic effects. L. rhamnosus GG has been shown to prevent diarrhea in children and adults and has been implicated to have mitigating or preventive effects in several disorders connected to microbiota dysbiosis. The probiotic effects are largely attributed to its adhesive heterotrimeric sortase-dependent pili, encoded by the spaCBA-srtC1 gene cluster. Indeed, the strain-specific SpaCBA pili have been shown to contribute to adherence, biofilm formation and host signaling. In this work we set out to generate non-GMO derivatives of L. rhamnosus GG that adhere stronger to mucus compared to the wild-type strain using chemical mutagenesis. We selected 13 derivatives that showed an increased mucus-adherent phenotype. Deep shotgun resequencing of the strains enabled division of the strains into three classes, two of which revealed SNPs (single nucleotide polymorphisms) in the spaA and spaC genes encoding the shaft and tip adhesive pilins, respectively. Strikingly, the other class derivatives demonstrated less clear genotype – phenotype relationships, illustrating that pili biogenesis and structure is also affected by other processes. Further characterization of the different classes of derivatives was performed by PacBio SMRT sequencing and RNAseq analysis, which resulted in the identification of molecular candidates driving pilin biosynthesis and functionality. In conclusion, we report on the generation and characterization of three classes of strongly adherent L. rhamnosus GG derivatives that show an increase in adhesion to mucus. These are of special interest as they provide a window on processes and genes driving piliation and its control in L. rhamnosus GG and offer a variety of non-GMO derivatives of this key probiotic strain that are applicable in food products.
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Affiliation(s)
- Pia Rasinkangas
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Jarmo Ritari
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Justus Reunanen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Airi Palva
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - François P Douillard
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Willem M de Vos
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands.,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Ligthart K, Belzer C, de Vos WM, Tytgat HLP. Bridging Bacteria and the Gut: Functional Aspects of Type IV Pili. Trends Microbiol 2020; 28:340-348. [PMID: 32298612 DOI: 10.1016/j.tim.2020.02.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 12/14/2022]
Abstract
Cell-surface-located proteinaceous appendages, such as flagella and fimbriae or pili, are ubiquitous in bacterial communities. Here, we focus on conserved type IV pili (T4P) produced by bacteria in the intestinal tract, one of the most densely populated human ecosystems. Computational analysis revealed that approximately 30% of known intestinal bacteria are predicted to produce T4P. To rationalize how T4P allow intestinal bacteria to interact with their environment, other microbiota members, and host cells, we review their established role in gut commensals and pathogens with respect to adherence, motility, and biofilm formation, as well as protein secretion and DNA uptake. This work indicates that T4P are widely spread among the known members of the intestinal microbiota and that their contribution to human health might be underestimated.
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Affiliation(s)
- Kate Ligthart
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands; Research Program Human Microbiome, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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van der Veer C, Hertzberger RY, Bruisten SM, Tytgat HLP, Swanenburg J, de Kat Angelino-Bart A, Schuren F, Molenaar D, Reid G, de Vries H, Kort R. Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota. Microbiome 2019; 7:49. [PMID: 30925932 PMCID: PMC6441167 DOI: 10.1186/s40168-019-0667-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/15/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND A vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we investigated whether L. crispatus strains isolated from the vaginal tract of women with Lactobacillus-dominated vaginal microbiota (LVM) are pheno- or genotypically distinct from L. crispatus strains isolated from vaginal samples with dysbiotic vaginal microbiota (DVM). RESULTS We studied 33 L. crispatus strains (n = 16 from LVM; n = 17 from DVM). Comparison of these two groups of strains showed that, although strain differences existed, both groups degraded various carbohydrates, produced similar amounts of organic acids, inhibited Neisseria gonorrhoeae growth, and did not produce biofilms. Comparative genomics analyses of 28 strains (n = 12 LVM; n = 16 DVM) revealed a novel, 3-fragmented glycosyltransferase gene that was more prevalent among strains isolated from DVM. Most L. crispatus strains showed growth on glycogen-supplemented growth media. Strains that showed less-efficient (n = 6) or no (n = 1) growth on glycogen all carried N-terminal deletions (respectively, 29 and 37 amino acid deletions) in a putative pullulanase type I protein. DISCUSSION L. crispatus strains isolated from LVM were not phenotypically distinct from L. crispatus strains isolated from DVM; however, the finding that the latter were more likely to carry a 3-fragmented glycosyltransferase gene may indicate a role for cell surface glycoconjugates, which may shape vaginal microbiota-host interactions. Furthermore, the observation that variation in the pullulanase type I gene is associated with growth on glycogen discourages previous claims that L. crispatus cannot directly utilize glycogen.
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Affiliation(s)
- Charlotte van der Veer
- Department of Infectious Diseases, Public Health Service, GGD, Amsterdam, The Netherlands
| | - Rosanne Y Hertzberger
- Department of Molecular Cell Biology, Faculty of Science, O|2 Lab Building, VU University, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Sylvia M Bruisten
- Department of Infectious Diseases, Public Health Service, GGD, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | | | - Jorne Swanenburg
- Department of Molecular Cell Biology, Faculty of Science, O|2 Lab Building, VU University, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Netherlands Organization for Applied Scientific Research (TNO), Microbiology and Systems Biology, Zeist, The Netherlands
| | - Alie de Kat Angelino-Bart
- Netherlands Organization for Applied Scientific Research (TNO), Microbiology and Systems Biology, Zeist, The Netherlands
| | - Frank Schuren
- Netherlands Organization for Applied Scientific Research (TNO), Microbiology and Systems Biology, Zeist, The Netherlands
| | - Douwe Molenaar
- Department of Molecular Cell Biology, Faculty of Science, O|2 Lab Building, VU University, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Gregor Reid
- Canadian R&D Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, Canada
- Departments of Microbiology and Immunology, and Surgery, Western University, London, Ontario, Canada
| | - Henry de Vries
- Department of Infectious Diseases, Public Health Service, GGD, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Remco Kort
- Department of Molecular Cell Biology, Faculty of Science, O|2 Lab Building, VU University, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
- Netherlands Organization for Applied Scientific Research (TNO), Microbiology and Systems Biology, Zeist, The Netherlands.
- ARTIS-Micropia, Amsterdam, The Netherlands.
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Tytgat HLP, Nobrega FL, van der Oost J, de Vos WM. Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut? Trends Microbiol 2018; 27:17-25. [PMID: 30219265 DOI: 10.1016/j.tim.2018.08.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/29/2018] [Accepted: 08/15/2018] [Indexed: 02/06/2023]
Abstract
Bacterial communities are known to impact human health and disease. Mixed species biofilms, mostly pathogenic in nature, have been observed in dental and gastric infections as well as in intestinal diseases, chronic gut wounds and colon cancer. Apart from the appendix, the presence of thick polymicrobial biofilms in the healthy gut mucosa is still debated. Polymicrobial biofilms containing potential pathogens appear to be an early-warning signal of developing disease and can be regarded as a tipping point between a healthy and a diseased state of the gut mucosa. Key biofilm-forming pathogens and associated molecules hold promise as biomarkers. Criteria to distinguish microcolonies from biofilms are crucial to provide clarity when reporting biofilm-related phenomena in health and disease in the gut.
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Affiliation(s)
- Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands; Institute of Microbiology, Swiss Federal Institute of Technology, ETH Zurich, 8093 Zurich, Switzerland.
| | - Franklin L Nobrega
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands; Kavli Institute of Nanoscience and Department of BioNanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands; Faculty of Medicine, Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, 00290 Helsinki, Finland.
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Abstract
The Human Microbiome, as well as the exploration of the microorganisms inhabiting the human body, are not only integral to the field of microbiology but represent an intrinsic part of all human beings. Consequently, along with scientists, artists have been inspired by the microbiome: transforming it in to tangible artefacts in order to critically question, reflect on and break down the barrier between humans and their microcohabitants. By artistic means, artists help us to understand how microbial research topics are inevitably affected by societal influences, including (health) politics, economics and the arts. Fifty Percent Human is a multidisciplinary artistic research project that aims to reshape our understanding of the human body and its environment as well as to explore possibilities for conscious coexistence in order to bridge the gap between science and society.
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Affiliation(s)
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Institute of Microbiology, Swiss Federal Institute of Technology, ETH Zurich, Zürich, Switzerland
| | - Birgit Nemec
- Department for History and Ethics of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Ruth Schmidt
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- INRS-Institut Armand-Frappier, Université du Québec, Quebec City, QC, Canada
| | - Loo Wee Chia
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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Tytgat HLP, Schoofs G, Vanderleyden J, Van Damme EJM, Wattiez R, Lebeer S, Leroy B. Systematic Exploration of the Glycoproteome of the Beneficial Gut Isolate Lactobacillus rhamnosus GG. J Mol Microbiol Biotechnol 2016; 26:345-58. [PMID: 27463506 DOI: 10.1159/000447091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/25/2016] [Indexed: 11/19/2022] Open
Abstract
Glycoproteins form an interesting class of macromolecules involved in bacterial-host interactions, but they are not yet widely explored in Gram-positive and beneficial species. Here, an integrated and widely applicable approach was followed to identify putative bacterial glycoproteins, combining proteome fractionation with 2D protein and glycostained gels and lectin blots. This approach was validated for the microbiota isolate Lactobacillus rhamnosus GG. The approach resulted in a list of putative glycosylated proteins receiving a 'glycosylation score'. Ultimately, we could identify 41 unique glycosylated proteins in L. rhamnosus GG (6 top-confidence, 10 high-confidence and 25 putative hits; classification based on glycosylation score). Most glycoproteins are associated with the cell wall and membrane. Identified glycoproteins include proteins involved in transport, translation, and sugar metabolism processes. A robust screening resulted in a comprehensive mapping of glycoproteins in L. rhamnosus GG. Our results reflect the glycosylation of sugar metabolism enzymes, transporters, and other proteins crucial for cell physiology. We hypothesize that protein glycosylation can confer an extra level of regulation, for example by affecting enzyme functions. This is the first systematic study of the glycoproteome of a probiotic and beneficial gut isolate.
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Affiliation(s)
- Hanne L P Tytgat
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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Tytgat HLP, de Vos WM. Sugar Coating the Envelope: Glycoconjugates for Microbe-Host Crosstalk. Trends Microbiol 2016; 24:853-861. [PMID: 27374775 DOI: 10.1016/j.tim.2016.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/31/2016] [Accepted: 06/09/2016] [Indexed: 12/14/2022]
Abstract
Tremendous progress has been made on mapping the mainly bacterial members of the human intestinal microbiota. Knowledge on what is out there, or rather what is inside, needs to be complemented with insight on how these bacteria interact with their biotic environment. Bacterial glycoconjugates, that is, the collection of all glycan-modified molecules, are ideal modulators of such interactions. Their enormous versatility and diversity results in a species-specific glycan barcode, providing a range of ligands for host interaction. Recent reports on the functional importance of glycosylation of important bacterial ligands in beneficial and pathogenic species underpin this. Glycoconjugates, and glycoproteins in particular, are an underappreciated, potentially crucial, factor in understanding bacteria-host interactions of old friends and foes.
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Affiliation(s)
- Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands; Institute of Microbiology, Swiss Federal Institute of Technology, ETH Zurich, 8093 Zurich, Switzerland
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands; Faculty of Medicine, Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, 00290 Helsinki, Finland.
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Tytgat HLP, van Teijlingen NH, Sullan RMA, Douillard FP, Rasinkangas P, Messing M, Reunanen J, Satokari R, Vanderleyden J, Dufrêne YF, Geijtenbeek TBH, de Vos WM, Lebeer S. Probiotic Gut Microbiota Isolate Interacts with Dendritic Cells via Glycosylated Heterotrimeric Pili. PLoS One 2016; 11:e0151824. [PMID: 26985831 PMCID: PMC4795749 DOI: 10.1371/journal.pone.0151824] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/06/2016] [Indexed: 02/06/2023] Open
Abstract
Mapping of the microbial molecules underlying microbiota-host interactions is key to understand how microbiota preserve mucosal homeostasis. A pivotal family of such bacterial molecules are pili. Pili are proteinaceous cell wall appendages with a well-documented role in adhesion, whilst their role in immune interaction with the host is less established. Gram-positive pili are often posttranslationally modified by sortase-specific cleavage reactions and the formation of intramolecular peptide bonds. Here we report glycosylation as a new level of posttranslational modification of sortase-dependent pili of a beneficial microbiota species and its role in immune modulation. We focused on the SpaCBA pili of the model probiotic and beneficial human gut microbiota isolate Lactobacillus rhamnosus GG. A unique combination of molecular techniques, nanoscale mechanical and immunological approaches led to the identification of mannose and fucose residues on the SpaCBA pili. These glycans on the pili are recognized by human dendritic cells via the C-type lectin receptor DC-SIGN, a key carbohydrate-dependent immune tailoring pattern recognition receptor. This specific lectin-sugar interaction is moreover of functional importance and modulated the cytokine response of dendritic cells. This provides insight into the direct role bacterial glycoproteins can play in the immunomodulation of the host. Modification of the complex heterotrimeric pili of a model probiotic and microbiota isolate with mannose and fucose is of importance for the functional interaction with the host immune lectin receptor DC-SIGN on human dendritic cells. Our findings shed light on the yet underappreciated role of glycoconjugates in bacteria-host interactions.
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Affiliation(s)
- Hanne L. P. Tytgat
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Bioscience Engineering, Environmental Ecology & Applied Microbiology, University of Antwerp, Antwerp, Belgium
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Nienke H. van Teijlingen
- Academic Medical Center, Department of Experimental Immunology, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruby May A. Sullan
- Institute of Life Sciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Pia Rasinkangas
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Marcel Messing
- Immunobiology Research Program and Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Justus Reunanen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Reetta Satokari
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jos Vanderleyden
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Yves F. Dufrêne
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Teunis B. H. Geijtenbeek
- Academic Medical Center, Department of Experimental Immunology, University of Amsterdam, Amsterdam, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Immunobiology Research Program and Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Sarah Lebeer
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Bioscience Engineering, Environmental Ecology & Applied Microbiology, University of Antwerp, Antwerp, Belgium
- * E-mail:
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Borgdorff H, Armstrong SD, Tytgat HLP, Xia D, Ndayisaba GF, Wastling JM, van de Wijgert JHHM. Unique Insights in the Cervicovaginal Lactobacillus iners and L. crispatus Proteomes and Their Associations with Microbiota Dysbiosis. PLoS One 2016; 11:e0150767. [PMID: 26963809 PMCID: PMC4786256 DOI: 10.1371/journal.pone.0150767] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/17/2016] [Indexed: 02/02/2023] Open
Abstract
Background A Lactobacillus-dominated cervicovaginal microbiota (VMB) protects women from adverse reproductive health outcomes, but the role of L. iners in the VMB is poorly understood. Our aim was to explore the association between the cervicovaginal L. iners and L. crispatus proteomes and VMB composition. Methods The vaginal proteomes of 50 Rwandan women at high HIV risk, grouped into four VMB groups (based on 16S rDNA microarray results), were investigated by mass spectrometry using cervicovaginal lavage (CVL) samples. Only samples with positive 16S results for L. iners and/or L. crispatus within each group were included in subsequent comparative protein analyses: Lactobacillus crispatus-dominated VMB cluster (with 16S-proven L. iners (ni) = 0, and with 16S-proven L. crispatus (nc) = 5), L. iners-dominated VMB cluster (ni = 11, nc = 4), moderate dysbiosis (ni = 12, nc = 2); and severe dysbiosis (ni = 8, nc = 2). The relative abundances of proteins that were considered specific for L. iners and L. crispatus were compared among VMB groups. Results Forty Lactobacillus proteins were identified of which 7 were specific for L. iners and 11 for L. crispatus. The relative abundances of L. iners DNA starvation/stationary phase protection protein (DPS), and the glycolysis enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and glucose-6-phosphate isomerase (GPI), were significantly decreased in women with L. iners-containing dysbiosis compared to women with a L. iners-dominated VMB, independent of vaginal pH and L. iners abundance. Furthermore, L. iners DPS, GAPDH, GPI, and fructose-bisphosphate aldolase (ALDO) were significantly negatively associated with vaginal pH. Glycolysis enzymes of L. crispatus showed a similar negative, but nonsignificant, trend related to dysbiosis. Conclusions Most identified Lactobacillus proteins had conserved intracellular functions, but their high abundance in CVL supernatant might imply an additional extracellular (moonlighting) role. Our findings suggest that these proteins can be important in maintaining a Lactobacillus-dominated VMB. Functional studies are needed to investigate their roles in vaginal bacterial communities and whether they can be used to prevent vaginal dysbiosis.
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Affiliation(s)
- Hanneke Borgdorff
- Amsterdam Institute for Global Health and Development (AIGHD) and Department of Global Health, Academic Medical Center, Amsterdam, The Netherlands
| | - Stuart D. Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Hanne L. P. Tytgat
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Centre of Microbial and Plant Genetics, Catholic University Leuven, Leuven, Belgium
- Laboratory of Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Dong Xia
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | - Jonathan M. Wastling
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Faculty of Natural Sciences, Keele University, Keele, United Kingdom
| | - Janneke H. H. M. van de Wijgert
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Rinda Ubuzima, Kigali, Rwanda
- * E-mail:
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Tytgat HLP, Schoofs G, Driesen M, Proost P, Van Damme EJM, Vanderleyden J, Lebeer S. Endogenous biotin-binding proteins: an overlooked factor causing false positives in streptavidin-based protein detection. Microb Biotechnol 2014; 8:164-8. [PMID: 25211245 PMCID: PMC4321382 DOI: 10.1111/1751-7915.12150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 11/29/2022] Open
Abstract
Biotinylation is widely used in DNA, RNA and protein probing assays as this molecule has generally no impact on the biological activity of its substrate. During the streptavidin-based detection of glycoproteins in Lactobacillus rhamnosus GG with biotinylated lectin probes, a strong positive band of approximately 125 kDa was observed, present in different cellular fractions. This potential glycoprotein reacted heavily with concanavalin A (ConA), a lectin that specifically binds glucose and mannose residues. Surprisingly, this protein of 125 kDa could not be purified using a ConA affinity column. Edman degradation of the protein, isolated via cation and anion exchange chromatography, lead to the identification of the band as pyruvate carboxylase, an enzyme of 125 kDa that binds biotin as a cofactor. Detection using only the streptavidin conjugate resulted in more false positive signals of proteins, also in extracellular fractions, indicating biotin-associated proteins. Indeed, biotin is a known cofactor of numerous carboxylases. The potential occurence of false positive bands with biotinylated protein probes should thus be considered when using streptavidin-based detection, e.g. by developing a blot using only the streptavidin conjugate. To circumvent these false positives, alternative approaches like detection based on digoxigenin labelling can also be used.
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Affiliation(s)
- Hanne L P Tytgat
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium; Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Leuven, Belgium
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Sánchez-Rodríguez A, Tytgat HLP, Winderickx J, Vanderleyden J, Lebeer S, Marchal K. A network-based approach to identify substrate classes of bacterial glycosyltransferases. BMC Genomics 2014; 15:349. [PMID: 24885406 PMCID: PMC4039749 DOI: 10.1186/1471-2164-15-349] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 04/16/2014] [Indexed: 01/03/2023] Open
Abstract
Background Bacterial interactions with the environment- and/or host largely depend on the bacterial glycome. The specificities of a bacterial glycome are largely determined by glycosyltransferases (GTs), the enzymes involved in transferring sugar moieties from an activated donor to a specific substrate. Of these GTs their coding regions, but mainly also their substrate specificity are still largely unannotated as most sequence-based annotation flows suffer from the lack of characterized sequence motifs that can aid in the prediction of the substrate specificity. Results In this work, we developed an analysis flow that uses sequence-based strategies to predict novel GTs, but also exploits a network-based approach to infer the putative substrate classes of these predicted GTs. Our analysis flow was benchmarked with the well-documented GT-repertoire of Campylobacter jejuni NCTC 11168 and applied to the probiotic model Lactobacillus rhamnosus GG to expand our insights in the glycosylation potential of this bacterium. In L. rhamnosus GG we could predict 48 GTs of which eight were not previously reported. For at least 20 of these GTs a substrate relation was inferred. Conclusions We confirmed through experimental validation our prediction of WelI acting upstream of WelE in the biosynthesis of exopolysaccharides. We further hypothesize to have identified in L. rhamnosus GG the yet undiscovered genes involved in the biosynthesis of glucose-rich glycans and novel GTs involved in the glycosylation of proteins. Interestingly, we also predict GTs with well-known functions in peptidoglycan synthesis to also play a role in protein glycosylation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-349) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Sarah Lebeer
- Department of Microbial and Molecular Systems, KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, box 2460, Leuven B-3001, Belgium.
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Tytgat HLP, Sánchez-Rodríguez A, Schoofs G, Verhoeven TLA, De Keersmaecker SCJ, Marchal K, Vanderleyden J, Lebeer S. A combined approach to study the protein glycosylation potential of Lactobacillus rhamnosus GG (LGG). Commun Agric Appl Biol Sci 2012; 77:15-19. [PMID: 22558749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Hanne L P Tytgat
- Centre of Microbial and Plant Genetics, KULeuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
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