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Lykkebo CA, Mortensen MS, Davidsen N, Bahl MI, Ramhøj L, Granby K, Svingen T, Licht TR. Antibiotic induced restructuring of the gut microbiota does not affect oral uptake and accumulation of perfluorooctane sulfonic acid (PFOS) in rats. Environ Pollut 2023; 334:122179. [PMID: 37454717 DOI: 10.1016/j.envpol.2023.122179] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/20/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Perfluorooctane sulfonic acid (PFOS) is a manmade legacy compound belonging to the group of persistent per- and polyfluorinated substances (PFAS). While many adverse health effects of PFOS have been identified, knowledge about its effect on the intestinal microbiota is scarce. The microbial community inhabiting the gut of mammals plays an important role in health, for instance by affecting the uptake, excretion, and bioavailability of some xenobiotic toxicants. Here, we investigated (i) the effect of vancomycin-mediated microbiota modulation on the uptake of PFOS in adult Sprague-Dawley rats, and (ii) the effects of PFOS exposure on the rat microbiota composition. Four groups of twelve rats were exposed daily for 7 days with either 3 mg/kg PFOS plus 8 mg/kg vancomycin, only PFOS, only vancomycin, or a corn oil control. Vancomycin-induced modulation of the gut microbiota composition did not affect uptake of branched and linear PFOS over a period of 7 days, measured in serum samples. 16S rRNA amplicon sequencing of faecal and intestinal samples revealed that vancomycin treatment lowered microbial alpha-diversity, while PFOS increased the microbial diversity in vancomycin-treated as well as in non-antibiotic treated animals, possibly because an observed decrease in the Enterobacteriaceae abundance allows other microbial species to propagate. Colonic short-chain fatty acids were significantly lower in vancomycin-treated animals but remained unaffected by PFOS. Our results suggest that PFOS exposure may disturb the intestinal microbiota, but that antibiotic-induced modulation of the intestinal ecosystem does not affect systemic uptake of PFOS in rats.
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Affiliation(s)
- Claus Asger Lykkebo
- National Food Institute, Technical University of Denmark, Kgs, Lyngby, DK-2800, Denmark.
| | | | - Nichlas Davidsen
- National Food Institute, Technical University of Denmark, Kgs, Lyngby, DK-2800, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kgs, Lyngby, DK-2800, Denmark
| | - Louise Ramhøj
- National Food Institute, Technical University of Denmark, Kgs, Lyngby, DK-2800, Denmark
| | - Kit Granby
- National Food Institute, Technical University of Denmark, Kgs, Lyngby, DK-2800, Denmark
| | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kgs, Lyngby, DK-2800, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs, Lyngby, DK-2800, Denmark.
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Procházková N, Venlet N, Hansen ML, Lieberoth CB, Dragsted LO, Bahl MI, Licht TR, Kleerebezem M, Lauritzen L, Roager HM. Effects of a wholegrain-rich diet on markers of colonic fermentation and bowel function and their associations with the gut microbiome: a randomised controlled cross-over trial. Front Nutr 2023; 10:1187165. [PMID: 37324737 PMCID: PMC10267323 DOI: 10.3389/fnut.2023.1187165] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
Background Diets rich in whole grains are associated with health benefits. Yet, it remains unclear whether the benefits are mediated by changes in gut function and fermentation. Objective We explored the effects of whole-grain vs. refined-grain diets on markers of colonic fermentation and bowel function, as well as their associations with the gut microbiome. Methods Fifty overweight individuals with increased metabolic risk and a high habitual intake of whole grains (~69 g/day) completed a randomised cross-over trial with two 8-week dietary intervention periods comprising a whole-grain diet (≥75 g/day) and a refined-grain diet (<10 g/day), separated by a washout period of ≥6 weeks. A range of markers of colonic fermentation and bowel function were assessed before and after each intervention. Results The whole-grain diet increased the levels of faecal butyrate (p = 0.015) and caproate (p = 0.013) compared to the refined-grain diet. No changes in other faecal SCFA, BCFA or urinary levels of microbial-derived proteolytic markers between the two interventions were observed. Similarly, faecal pH remained unchanged. Faecal pH did however increase (p = 0.030) after the refined-grain diet compared to the baseline. Stool frequency was lower at the end of the refined-grain period compared to the end of the whole-grain diet (p = 0.001). No difference in faecal water content was observed between the intervention periods, however, faecal water content increased following the whole-grain period compared to the baseline (p = 0.007). Dry stool energy density was unaffected by the dietary interventions. Nevertheless, it explained 4.7% of the gut microbiome variation at the end of the refined-grain diet, while faecal pH and colonic transit time explained 4.3 and 5%, respectively. Several butyrate-producers (e.g., Faecalibacterium, Roseburia, Butyriciococcus) were inversely associated with colonic transit time and/or faecal pH, while the mucin-degraders Akkermansia and Ruminococcaceae showed the opposite association. Conclusion Compared with the refined-grain diet, the whole-grain diet increased faecal butyrate and caproate concentrations as well as stool frequency, emphasising that differences between whole and refined grains affect both colonic fermentation and bowel habits.
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Affiliation(s)
- Nicola Procházková
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Naomi Venlet
- Host-Microbe Interactomics, Wageningen University and Research, Wageningen, Netherlands
| | - Mathias L. Hansen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Christian B. Lieberoth
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Lars Ove Dragsted
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Martin I. Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michiel Kleerebezem
- Host-Microbe Interactomics, Wageningen University and Research, Wageningen, Netherlands
| | - Lotte Lauritzen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
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Dimopoulou C, Bongers M, Pedersen M, Bahl MI, Sommer MOA, Laursen MF, Licht TR. An engineered Escherichia coli Nissle 1917 increase the production of indole lactic acid in the gut. FEMS Microbiol Lett 2023; 370:7110978. [PMID: 37028942 DOI: 10.1093/femsle/fnad027] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023] Open
Abstract
The expanding knowledge of the health impacts of the metabolic activities of the gut microbiota reinforces the current interest in engineered probiotics. Tryptophan metabolites, in particular indole lactic acid (ILA), are attractive candidates as potential therapeutic agents. ILA is a promising compound with multiple beneficial effects including amelioration colitis in rodent models of necrotizing enterocolitis, as well as improved infant immune system maturation. In this work we engineered and characterized in vitro and in vivo an Escherichia coli Nissle 1917 strain that produces ILA. The 2-step metabolic pathway comprises aminotransferases native of E. coli and a dehydrogenase introduced from Bifidobacterium longum subspecies infantis. Our results show a robust engineered probiotic that produces 73.4 ± 47.2 nmol and 149 ± 123.6 nmol of ILA per gram of fecal and cecal matter, respectively, three days after colonization in a mouse model. In addition, hereby is reported an engineered-probiotic-related increase of ILA in the systemic circulation of the treated mice. This strain serves as proof of concept for the transfer of capacity to produce ILA in vivo and as ILA emerges as a potent microbial metabolite against gastrointestinal inflammation, further development of this strain offers efficient options for ILA-focused therapeutic interventions in situ.
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Affiliation(s)
- Chrysoula Dimopoulou
- National Food Institute, Kemitorvet, Building 202, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mareike Bongers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikael Pedersen
- National Food Institute, Kemitorvet, Building 202, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Kemitorvet, Building 202, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Martin Frederik Laursen
- National Food Institute, Kemitorvet, Building 202, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Kemitorvet, Building 202, Technical University of Denmark, Kgs. Lyngby, Denmark
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Bondegaard PW, Torp AM, Guerra P, Kristensen KA, Christfort JF, Krogfelt KA, Nielsen LH, Zor K, Boisen A, Mortensen MS, Bahl MI, Licht TR. Delivery of E. coli Nissle to the mouse gut by mucoadhesive microcontainers does not improve its competitive ability against strains linked to ulcerative colitis. FEMS Microbiol Lett 2023; 370:fnad110. [PMID: 37863838 PMCID: PMC10612143 DOI: 10.1093/femsle/fnad110] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 10/22/2023] Open
Abstract
For patients with ulcerative colitis (UC), administration of the probiotic E. coli Nissle (EcN) holds promise for alleviation of disease symptoms. The mechanisms are unclear, but it has been hypothesised that a capacity of the probiotic to outcompete potentially detrimental UC-associated E. coli strains plays an important role. However, this could previously not be confirmed in a mouse model of competition between EcN and two UC-associated strains, as reported by Petersen et al. 2011. In the present study, we re-evaluated the idea, hypothesising that delivery of EcN by a micro device dosing system (microcontainers), designed for delivery into the intestinal mucus, could support colonisation and confer a competition advantage compared to classical oral dosing. Six groups of mice were pre-colonised with one of two UC-associated E. coli strains followed by oral delivery of EcN, either in capsules containing microcontainers with freeze-dried EcN powder, capsules containing freeze-dried EcN powder, or as a fresh sucrose suspension. Co-colonisation between the probiotic and the disease-associated strains was observed regardless of dosing method, and no competition advantages linked to microcontainer delivery were identified within this setup. Other approaches are thus needed if the competitive capacity of EcN in the gut should be improved.
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Affiliation(s)
- Pi Westi Bondegaard
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Anders Meyer Torp
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Priscila Guerra
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Katja Ann Kristensen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Karen Angeliki Krogfelt
- Department of Science and Environment, Molecular and Medical Biology, Roskilde University, Roskilde, 4000, Denmark
| | - Line Hagner Nielsen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Kinga Zor
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Anja Boisen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
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Davidsen N, Ramhøj L, Lykkebo CA, Kugathas I, Poulsen R, Rosenmai AK, Evrard B, Darde TA, Axelstad M, Bahl MI, Hansen M, Chalmel F, Licht TR, Svingen T. Corrigendum to "PFOS-induced thyroid hormone system disrupted rats display organ-specific changes in their transcriptomes" [Environ. Pollut. 305 (2022) 119340]. Environ Pollut 2023; 317:120709. [PMID: 36462679 DOI: 10.1016/j.envpol.2022.120709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Nichlas Davidsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Louise Ramhøj
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Claus Asger Lykkebo
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Indusha Kugathas
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Rikke Poulsen
- Department of Environmental Science, Aarhus University, Roskilde DK, 4000, Denmark
| | | | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | | | - Marta Axelstad
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Roskilde DK, 4000, Denmark
| | - Frederic Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
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Abstract
Accumulating evidence indicates that gut transit time is a key factor in shaping the gut microbiota composition and activity, which are linked to human health. Both population-wide and small-scale studies have identified transit time as a top covariate contributing to the large interindividual variation in the faecal microbiota composition. Despite this, transit time is still rarely being considered in the field of the human gut microbiome. Here, we review the latest research describing how and why whole gut and segmental transit times vary substantially between and within individuals, and how variations in gut transit time impact the gut microbiota composition, diversity and metabolism. Furthermore, we discuss the mechanisms by which the gut microbiota may causally affect gut motility. We argue that by taking into account the interindividual and intraindividual differences in gut transit time, we can advance our understanding of diet-microbiota interactions and disease-related microbiome signatures, since these may often be confounded by transient or persistent alterations in transit time. Altogether, a better understanding of the complex, bidirectional interactions between the gut microbiota and transit time is required to better understand gut microbiome variations in health and disease.
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Affiliation(s)
- Nicola Procházková
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Gwen Falony
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Lars Ove Dragsted
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University, Kgs. Lyngby, Denmark
| | - Jeroen Raes
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
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7
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Wei S, Bahl MI, Baunwall SMD, Dahlerup JF, Hvas CL, Licht TR. Gut microbiota differs between treatment outcomes early after fecal microbiota transplantation against recurrent Clostridioides difficile infection. Gut Microbes 2022; 14:2084306. [PMID: 36519447 PMCID: PMC9176232 DOI: 10.1080/19490976.2022.2084306] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
AbstarctIn fecal microbiota transplantation (FMT) against recurrent Clostridioides difficile infection (CDI), clinical outcomes are usually determined after 8 weeks. We hypothesized that the intestinal microbiota changes earlier than this timepoint, and analyzed fecal samples obtained 1 week after treatment from 64 patients diagnosed with recurrent CDI and included in a randomized clinical trial, where the infection was treated with either vancomycin-preceded FMT (N = 24), vancomycin (N = 16) or fidaxomicin (N = 24). In comparison with non-responders, patients with sustained resolution after FMT had increased microbial alpha diversity, enrichment of Ruminococcaceae and Lachnospiraceae, depletion of Enterobacteriaceae, more pronounced donor microbiota engraftment, and resolution of gut microbiota dysbiosis. We found that a constructed index, based on markers for the identified genera Escherichia and Blautia, successfully predicted clinical outcomes at Week 8, which exemplifies a way to utilize clinically feasible methods to predict treatment failure. Microbiota changes were restricted to patients who received FMT rather than antibiotic monotherapy, indicating that FMT confers treatment response in a different way than antibiotics. We suggest that early identification of microbial community structures after FMT is of clinical value to predict response to the treatment.
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Affiliation(s)
- Shaodong Wei
- National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Jens Frederik Dahlerup
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus N, Denmark
| | - Christian Lodberg Hvas
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus N, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark,CONTACT Tine Rask Licht National Food Institute, Technical University of Denmark, Kemitorvet 2022800, Kgs Lyngby, Denmark
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Boekhorst J, Venlet N, Procházková N, Hansen ML, Lieberoth CB, Bahl MI, Lauritzen L, Pedersen O, Licht TR, Kleerebezem M, Roager HM. Stool energy density is positively correlated to intestinal transit time and related to microbial enterotypes. Microbiome 2022; 10:223. [PMID: 36510309 PMCID: PMC9743556 DOI: 10.1186/s40168-022-01418-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/08/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND It has been hypothesised that the gut microbiota causally affects obesity via its capacity to extract energy from the diet. Yet, evidence elucidating the role of particular human microbial community structures and determinants of microbiota-dependent energy harvest is lacking. RESULTS Here, we investigated whether energy extraction from the diet in 85 overweight adults, estimated by dry stool energy density, was associated with intestinal transit time and variations in microbial community diversity and overall structure stratified as enterotypes. We hypothesised that a slower intestinal transit would allow for more energy extraction. However, opposite of what we expected, the stool energy density was positively associated with intestinal transit time. Stratifications into enterotypes showed that individuals with a Bacteroides enterotype (B-type) had significantly lower stool energy density, shorter intestinal transit times, and lower alpha-diversity compared to individuals with a Ruminococcaceae enterotype (R-type). The Prevotella (P-type) individuals appeared in between the B- and R-type. The differences in stool energy density between enterotypes were not explained by differences in habitual diet, intake of dietary fibre or faecal bacterial cell counts. However, the R-type individuals showed higher urinary and faecal levels of microbial-derived proteolytic metabolites compared to the B-type, suggesting increased colonic proteolysis in the R-type individuals. This could imply a less effective colonic energy extraction in the R-type individuals compared to the B-type individuals. Notably, the R-type had significantly lower body weight compared to the B-type. CONCLUSIONS Our findings suggest that gut microbial energy harvest is diversified among individuals by intestinal transit time and associated gut microbiome ecosystem variations. A better understanding of these associations could support the development of personalised nutrition and improved weight-loss strategies. Video Abstract.
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Affiliation(s)
- Jos Boekhorst
- Host-Microbe Interactomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Naomi Venlet
- Host-Microbe Interactomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Nicola Procházková
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Mathias L. Hansen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Christian B. Lieberoth
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Martin I. Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lotte Lauritzen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michiel Kleerebezem
- Host-Microbe Interactomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
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9
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Wei S, Jespersen ML, Baunwall SMD, Myers PN, Smith EM, Dahlerup JF, Rasmussen S, Nielsen HB, Licht TR, Bahl MI, Hvas CL. Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report. Microbiome 2022; 10:193. [PMID: 36352460 PMCID: PMC9647999 DOI: 10.1186/s40168-022-01394-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/13/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) effectively prevents the recurrence of Clostridioides difficile infection (CDI). Long-term engraftment of donor-specific microbial consortia may occur in the recipient, but potential further transfer to other sites, including the vertical transmission of donor-specific strains to future generations, has not been investigated. Here, we report, for the first time, the cross-generational transmission of specific bacterial strains from an FMT donor to a pregnant patient with CDI and further to her child, born at term, 26 weeks after the FMT treatment. METHODS A pregnant woman (gestation week 12 + 5) with CDI was treated with FMT via colonoscopy. She gave vaginal birth at term to a healthy baby. Fecal samples were collected from the feces donor, the mother (before FMT, and 1, 8, 15, 22, 26, and 50 weeks after FMT), and the infant (meconium at birth and 3 and 6 months after birth). Fecal samples were profiled by deep metagenomic sequencing for strain-level analysis. The microbial transfer was monitored using single nucleotide variants in metagenomes and further compared to a collection of metagenomic samples from 651 healthy infants and 58 healthy adults. RESULTS The single FMT procedure led to an uneventful and sustained clinical resolution in the patient, who experienced no further CDI-related symptoms up to 50 weeks after treatment. The gut microbiota of the patient with CDI differed considerably from the healthy donor and was characterized as low in alpha diversity and enriched for several potential pathogens. The FMT successfully normalized the patient's gut microbiota, likely by donor microbiota transfer and engraftment. Importantly, our analysis revealed that some specific strains were transferred from the donor to the patient and then further to the infant, thus demonstrating cross-generational microbial transfer. CONCLUSIONS The evidence for cross-generational strain transfer following FMT provides novel insights into the dynamics and engraftment of bacterial strains from healthy donors. The data suggests FMT treatment of pregnant women as a potential strategy to introduce beneficial strains or even bacterial consortia to infants, i.e., neonatal seeding. Video Abstract.
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Affiliation(s)
- Shaodong Wei
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
| | - Marie Louise Jespersen
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simon Mark Dahl Baunwall
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Emilie Milton Smith
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
| | - Jens Frederik Dahlerup
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800, Kgs Lyngby, Denmark.
| | - Christian Lodberg Hvas
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
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10
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Christensen L, Hjorth MF, Krych L, Licht TR, Lauritzen L, Magkos F, Roager HM. Prevotella abundance and salivary amylase gene copy number predict fat loss in response to wholegrain diets. Front Nutr 2022; 9:947349. [PMID: 36071931 PMCID: PMC9441811 DOI: 10.3389/fnut.2022.947349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
Background Salivary amylase (AMY1) gene copy number (CN) and Prevotella abundance in the gut are involved in carbohydrate digestion in the upper and lower gastrointestinal tract, respectively; and have been suggested as prognostic biomarkers for weight loss among overweight individuals consuming diets rich in fiber and wholegrains. Objective We hypothesized that Prevotella abundance would be linked to greater loss of body fat after wholegrain consumption among individuals with low AMY1 CN, but not in those with high AMY1 CN. Methods We reanalyzed data from two independent randomized ad libitum wholegrain interventions (fiber intake ∼33 g/d for 6–8 weeks), to investigate the relationship between baseline Prevotella abundance and body fat loss among healthy, overweight participants stratified into two groups by median AMY1 CN. Individuals with no detected Prevotella spp. were excluded from the main analysis. Results In both studies, individuals with low AMY1 CN exhibited a positive correlation between baseline Prevotella abundance and fat loss after consuming the wholegrain diet (r > 0.5, P < 0.05), but no correlation among participants with high AMY1 CN (P ≥ 0.6). Following consumption of the refined wheat control diets, there were no associations between baseline Prevotella abundance and changes in body fat in any of the AMY1 groups. Conclusion These results suggest that Prevotella abundance together with AMY1 CN can help predict fat loss in response to ad libitum wholegrain diets, highlighting the potential of these biomarkers in personalized obesity management.
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Affiliation(s)
- Lars Christensen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Lars Christensen,
| | | | - Lukasz Krych
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lotte Lauritzen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Faidon Magkos
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
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11
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Davidsen N, Ramhøj L, Lykkebo CA, Kugathas I, Poulsen R, Rosenmai AK, Evrard B, Darde TA, Axelstad M, Bahl MI, Hansen M, Chalmel F, Licht TR, Svingen T. PFOS-induced thyroid hormone system disrupted rats display organ-specific changes in their transcriptomes. Environ Pollut 2022; 305:119340. [PMID: 35460815 DOI: 10.1016/j.envpol.2022.119340] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Perfluorooctanesulfonic acid (PFOS) is a persistent anthropogenic chemical that can affect the thyroid hormone system in humans and animals. In adults, thyroid hormones (THs) are regulated by the hypothalamic-pituitary-thyroid (HPT) axis, but also by organs such as the liver and potentially the gut microbiota. PFOS and other xenobiotics can therefore disrupt the TH system at various locations and through different mechanisms. To start addressing this, we exposed adult male rats to 3 mg PFOS/kg/day for 7 days and analysed effects on multiple organs and pathways simultaneously by transcriptomics. This included four primary organs involved in TH regulation, namely hypothalamus, pituitary, thyroid, and liver. To investigate a potential role of the gut microbiota in thyroid hormone regulation, two additional groups of animals were dosed with the antibiotic vancomycin (8 mg/kg/day), either with or without PFOS. PFOS exposure decreased thyroxine (T4) and triiodothyronine (T3) without affecting thyroid stimulating hormone (TSH), resembling a state of hypothyroxinemia. PFOS exposure resulted in 50 differentially expressed genes (DEGs) in the hypothalamus, 68 DEGs in the pituitary, 71 DEGs in the thyroid, and 181 DEGs in the liver. A concomitant compromised gut microbiota did not significantly change effects of PFOS exposure. Organ-specific DEGs did not align with TH regulating genes; however, genes associated with vesicle transport and neuronal signaling were affected in the hypothalamus, and phase I and phase II metabolism in the liver. This suggests that a decrease in systemic TH levels may activate the expression of factors altering trafficking, metabolism and excretion of TH. At the transcriptional level, little evidence suggests that the pituitary or thyroid gland is involved in PFOS-induced TH system disruption.
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Affiliation(s)
- Nichlas Davidsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Louise Ramhøj
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Claus Asger Lykkebo
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Indusha Kugathas
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Rikke Poulsen
- Department of Environmental Science, Aarhus University, Roskilde, DK-4000, Denmark
| | | | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | | | - Marta Axelstad
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Roskilde, DK-4000, Denmark
| | - Frederic Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark.
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12
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Holst AQ, Jois H, Laursen MF, Sommer MOA, Licht TR, Bahl MI. Human milk oligosaccharides induce acute yet reversible compositional changes in the gut microbiota of conventional mice linked to a reduction of butyrate levels. Microlife 2022; 3:uqac006. [PMID: 37223362 PMCID: PMC10117735 DOI: 10.1093/femsml/uqac006] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/21/2022] [Accepted: 05/16/2022] [Indexed: 05/25/2023]
Abstract
Human Milk Oligosaccharides (HMOs) are glycans with prebiotic properties known to drive microbial selection in the infant gut, which in turn influences immune development and future health. Bifidobacteria are specialized in HMO degradation and frequently dominate the gut microbiota of breastfed infants. However, some species of Bacteroidaceae also degrade HMOs, which may prompt selection also of these species in the gut microbiota. To investigate to what extent specific HMOs affect the abundance of naturally occurring Bacteroidaceae species in a complex mammalian gut environment, we conducted a study in 40 female NMRI mice administered three structurally different HMOs, namely 6'sialyllactose (6'SL, n = 8), 3-fucosyllactose (3FL, n = 16), and Lacto-N-Tetraose (LNT, n = 8), through drinking water (5%). Compared to a control group receiving unsupplemented drinking water (n = 8), supplementation with each of the HMOs significantly increased both the absolute and relative abundance of Bacteroidaceae species in faecal samples and affected the overall microbial composition analyzed by 16s rRNA amplicon sequencing. The compositional differences were mainly attributed to an increase in the relative abundance of the genus Phocaeicola (formerly Bacteroides) and a concomitant decrease of the genus Lacrimispora (formerly Clostridium XIVa cluster). During a 1-week washout period performed specifically for the 3FL group, this effect was reversed. Short-chain fatty acid analysis of faecal water revealed a decrease in acetate, butyrate and isobutyrate levels in animals supplemented with 3FL, which may reflect the observed decrease in the Lacrimispora genus. This study highlights HMO-driven Bacteroidaceae selection in the gut environment, which may cause a reduction of butyrate-producing clostridia.
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Affiliation(s)
- Andrea Qvortrup Holst
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Harshitha Jois
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Glycom / DSM, DK-2970 Hørsholm, Denmark
| | | | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK 2800 Kgs. Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Martin Iain Bahl
- Corresponding author: National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark. Tel: +45 35 88 70 36; E-mail:
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13
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Locke AV, Larsen JM, Graversen KB, Licht TR, Bahl MI, Bøgh KL. Amoxicillin does not affect the development of cow’s milk allergy in a Brown Norway rat model. Scand J Immunol 2022; 95:e13148. [PMID: 35152475 PMCID: PMC9285443 DOI: 10.1111/sji.13148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 08/28/2021] [Revised: 01/12/2022] [Accepted: 02/04/2022] [Indexed: 11/29/2022]
Abstract
The use of antibiotics as well as changes in the gut microbiota have been linked to development of food allergy in childhood. It remains unknown whether administration of a single clinically relevant antibiotic directly promotes food allergy development when administrated during the sensitisation phase in an experimental animal model. We investigated whether the antibiotic amoxicillin affected gut microbiota composition, development of cow's milk allergy (CMA) and frequencies of allergic effector cells and regulatory T cells in the intestine. Brown Norway rats were given daily oral gavages of amoxicillin for six weeks and whey protein concentrate (WPC) with or without cholera toxin three times per week for the last five weeks. Microbiota composition in faeces and small intestine was analysed by 16S rRNA sequencing. The development of CMA was assessed by WPC‐specific IgE in serum, ear swelling response to WPC and body hypothermia following oral gavage of WPC. Allergic effector cells were analysed by histology, and frequencies of regulatory and activated T cells were analysed by flow cytometry. Amoxicillin administration reduced faecal microbiota diversity, reduced the relative abundance of Firmicutes and increased the abundance of Bacteroidetes and Proteobacteria. Despite these effects, amoxicillin did not affect the development of CMA, nor the frequencies of allergic effector cells or regulatory T cells. Thus, amoxicillin does not carry a direct risk for food allergy development when administrated in an experimental model of allergic sensitisation to WPC via the gut. This finding suggests that confounding factors may better explain the epidemiological link between antibiotic use and food allergy.
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Affiliation(s)
| | | | | | - Tine Rask Licht
- National Food Institute Technical University of Denmark Kgs. Lyngby Denmark
| | - Martin Iain Bahl
- National Food Institute Technical University of Denmark Kgs. Lyngby Denmark
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14
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Armetta J, Schantz-Klausen M, Shepelin D, Vazquez-Uribe R, Bahl MI, Laursen MF, Licht TR, Sommer MO. Escherichia coli Promoters with Consistent Expression throughout the Murine Gut. ACS Synth Biol 2021; 10:3359-3368. [PMID: 34842418 DOI: 10.1021/acssynbio.1c00325] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Advanced microbial therapeutics have great potential as a novel modality to diagnose and treat a wide range of diseases. Yet, to realize this potential, robust parts for regulating gene expression and consequent therapeutic activity in situ are needed. In this study, we characterized the expression level of more than 8000 variants of the Escherichia coli sigma factor 70 (σ70) promoter in a range of different environmental conditions and growth states using fluorescence-activated cell sorting and deep sequencing. Sampled conditions include aerobic and anaerobic culture in the laboratory as well as growth in several locations of the murine gastrointestinal tract. We found that σ70 promoters in E. coli generally maintain consistent expression levels across the murine gut (R2: 0.55-0.85, p value < 1 × 10-5), suggesting a limited environmental influence but a higher variability between in vitro and in vivo expression levels, highlighting the challenges of translating in vitro promoter activity to in vivo applications. Based on these data, we design the Schantzetta library, composed of eight promoters spanning a wide expression range and displaying a high degree of robustness in both laboratory and in vivo conditions (R2 = 0.98, p = 0.000827). This study provides a systematic assessment of the σ70 promoter activity in E. coli as it transits the murine gut leading to the definition of robust expression cassettes that could be a valuable tool for reliable engineering and development of advanced microbial therapeutics.
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Affiliation(s)
- Jeremy Armetta
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Michael Schantz-Klausen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Denis Shepelin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | | | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Morten O.A. Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
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15
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Graversen KB, Larsen JM, Pedersen SS, Sørensen LV, Christoffersen HF, Jacobsen LN, Halken S, Licht TR, Bahl MI, Bøgh KL. Partially Hydrolysed Whey Has Superior Allergy Preventive Capacity Compared to Intact Whey Regardless of Amoxicillin Administration in Brown Norway Rats. Front Immunol 2021; 12:705543. [PMID: 34531857 PMCID: PMC8438296 DOI: 10.3389/fimmu.2021.705543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/05/2021] [Accepted: 08/13/2021] [Indexed: 12/25/2022] Open
Abstract
Background It remains largely unknown how physicochemical properties of hydrolysed infant formulas influence their allergy preventive capacity, and results from clinical and animal studies comparing the preventive capacity of hydrolysed infant formula with conventional infant formula are inconclusive. Thus, the use of hydrolysed infant formula for allergy prevention in atopy-prone infants is highly debated. Furthermore, knowledge on how gut microbiota influences allergy prevention remains scarce. Objective To gain knowledge on (1) how physicochemical properties of hydrolysed whey products influence the allergy preventive capacity, (2) whether host microbiota disturbance influences allergy prevention, and (3) to what extent hydrolysed whey products influence gut microbiota composition. Methods The preventive capacity of four different ad libitum administered whey products was investigated in Brown Norway rats with either a conventional or an amoxicillin-disturbed gut microbiota. The preventive capacity of products was evaluated as the capacity to reduce whey-specific sensitisation and allergic reactions to intact whey after intraperitoneal post-immunisations with intact whey. Additionally, the direct effect of the whey products on the growth of gut bacteria derived from healthy human infant donors was evaluated by in vitro incubation. Results Two partially hydrolysed whey products with different physicochemical characteristics were found to be superior in preventing whey-specific sensitisation compared to intact and extensively hydrolysed whey products. Daily oral amoxicillin administration, initiated one week prior to intervention with whey products, disturbed the gut microbiota but did not impair the prevention of whey-specific sensitisation. The in vitro incubation of infant faecal samples with whey products indicated that partially hydrolysed whey products might confer a selective advantage to enterococci. Conclusions Our results support the use of partially hydrolysed whey products for prevention of cow’s milk allergy in atopy-predisposed infants regardless of their microbiota status. However, possible direct effects of partially hydrolysed whey products on gut microbiota composition warrants further investigation.
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Affiliation(s)
| | - Jeppe Madura Larsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | | | | | | | - Susanne Halken
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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16
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Seidelin JB, Bahl MI, Licht TR, Mead BE, Karp JM, Johansen JV, Riis LB, Galera MR, Woetmann A, Bjerrum JT. Acute Experimental Barrier Injury Triggers Ulcerative Colitis-Specific Innate Hyperresponsiveness and Ulcerative Colitis-Type Microbiome Changes in Humans. Cell Mol Gastroenterol Hepatol 2021; 12:1281-1296. [PMID: 34118489 PMCID: PMC8455368 DOI: 10.1016/j.jcmgh.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 01/13/2023]
Abstract
BACKGROUND AND AIMS The trigger hypothesis opens the possibility of anti-flare initiation therapies by stating that ulcerative colitis (UC) flares originate from inadequate responses to acute mucosal injuries. However, experimental evidence is restricted by a limited use of suitable human models. We thus aimed to investigate the acute mucosal barrier injury responses in humans with and without UC using an experimental injury model. METHODS A standardized mucosal break was inflicted in the sigmoid colon of 19 patients with UC in endoscopic and histological remission and 20 control subjects. Postinjury responses were assessed repeatedly by high-resolution imaging and sampling to perform Geboes scoring, RNA sequencing, and injury niche microbiota 16S ribosomal RNA gene sequencing. RESULTS UC patients had more severe endoscopic postinjury inflammation than did control subjects (P < .01), an elevated modified Geboes score (P < .05), a rapid induction of innate response gene sets (P < .05) and antimicrobial peptides (P < .01), and engagement of neutrophils (P < .01). Innate lymphoid cell type 3 (ILC3) markers were increased preinjury (P < .01), and ILC3 activating cytokines were highly induced postinjury, resulting in an increase in ILC3-type cytokine interleukin-17A. Across groups, the postinjury mucosal microbiome had higher bacterial load (P < .0001) and lower α-diversity (P < .05). CONCLUSIONS UC patients in remission respond to mucosal breaks by an innate hyperresponse engaging resident regulatory ILC3s and a subsequent adaptive activation. The postinjury inflammatory bowel disease-like microbiota diversity decrease is irrespective of diagnosis, suggesting that the dysbiosis is secondary to host injury responses. We provide a model for the study of flare initiation in the search for antitrigger-directed therapies.
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Affiliation(s)
- Jakob Benedict Seidelin
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark,Correspondence Address correspondence to: Jakob Benedict Seidelin, MD, PhD, DMSc, Department of Gastroenterology D112M, Herlev Hospital, University of Copenhagen, 1 Borgmester Ib Juuls Vej, DK-2730 Herlev, Denmark. fax: 45 44 94 04 56.
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Benjamin E. Mead
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical and Engineering Science and Harvard Medical School, Cambridge, Massachusetts,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts,Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, Massachusetts
| | - Jeffrey M. Karp
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical and Engineering Science and Harvard Medical School, Cambridge, Massachusetts,Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Harvard Medical School, Boston, Massachusetts,Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Cambridge, Massachusetts
| | - Jens Vilstrup Johansen
- Bioinformatics Core Facility, Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Lene Buhl Riis
- Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Marina Ramírez Galera
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark,LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Anders Woetmann
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark,LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Tveiten Bjerrum
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
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17
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Laursen MF, Pekmez CT, Larsson MW, Lind MV, Yonemitsu C, Larnkjær A, Mølgaard C, Bode L, Dragsted LO, Michaelsen KF, Licht TR, Bahl MI. Maternal milk microbiota and oligosaccharides contribute to the infant gut microbiota assembly. ISME Commun 2021; 1:21. [PMID: 36737495 PMCID: PMC9723702 DOI: 10.1038/s43705-021-00021-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/10/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023]
Abstract
Breastfeeding protects against diseases, with potential mechanisms driving this being human milk oligosaccharides (HMOs) and the seeding of milk-associated bacteria in the infant gut. In a cohort of 34 mother-infant dyads we analyzed the microbiota and HMO profiles in breast milk samples and infant's feces. The microbiota in foremilk and hindmilk samples of breast milk was compositionally similar, however hindmilk had higher bacterial load and absolute abundance of oral-associated bacteria, but a lower absolute abundance of skin-associated Staphylococcus spp. The microbial communities within both milk and infant's feces changed significantly over the lactation period. On average 33% and 23% of the bacterial taxa detected in infant's feces were shared with the corresponding mother's milk at 5 and 9 months of age, respectively, with Streptococcus, Veillonella and Bifidobacterium spp. among the most frequently shared. The predominant HMOs in feces associated with the infant's fecal microbiota, and the dominating infant species B. longum ssp. infantis and B. bifidum correlated inversely with HMOs. Our results show that breast milk microbiota changes over time and within a feeding session, likely due to transfer of infant oral bacteria during breastfeeding and suggest that milk-associated bacteria and HMOs direct the assembly of the infant gut microbiota.
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Affiliation(s)
| | - Ceyda T Pekmez
- Department of Nutrition, Exercise, and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Melanie Wange Larsson
- Department of Nutrition, Exercise, and Sports, University of Copenhagen, Frederiksberg, Denmark
- Department of Nursing and Nutrition, University College Copenhagen, Copenhagen, Denmark
| | - Mads Vendelbo Lind
- Department of Nutrition, Exercise, and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Chloe Yonemitsu
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California San Diego, La Jolla, CA, USA
| | - Anni Larnkjær
- Department of Nutrition, Exercise, and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Christian Mølgaard
- Department of Nutrition, Exercise, and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California San Diego, La Jolla, CA, USA
| | - Lars Ove Dragsted
- Department of Nutrition, Exercise, and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Kim F Michaelsen
- Department of Nutrition, Exercise, and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
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18
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Andersen D, Roager HM, Zhang L, Moll JM, Frandsen HL, Danneskiold-Samsøe NB, Hansen AK, Kristiansen K, Licht TR, Brix S. Systems-wide effects of short-term feed deprivation in obese mice. Sci Rep 2021; 11:5716. [PMID: 33707503 PMCID: PMC7952545 DOI: 10.1038/s41598-021-85020-z] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 02/18/2021] [Indexed: 11/09/2022] Open
Abstract
While prolonged fasting induces significant metabolic changes in humans and mice, less is known about systems-wide metabolic changes in response to short-term feed deprivation, which is used in experimental animal studies prior to metabolic challenge tests. We here performed a systems biology-based investigation of connections between gut bacterial composition and function, inflammatory and metabolic parameters in the intestine, liver, visceral adipose tissue, blood and urine in high-fat fed, obese mice that were feed deprived up to 12 h. The systems-wide analysis revealed that feed deprivation linked to enhanced intestinal butyric acid production and expression of the gene encoding the pro-thermogenic uncoupling protein UCP1 in visceral adipose tissue of obese mice. Ucp1 expression was also positively associated with Il33 expression in ileum, colon and adipose tissue as well as with the abundance of colonic Porphyromonadaceae, the latter also correlating to cecal butyric acid levels. Collectively, the data highlighted presence of a multi-tiered system of inter-tissue communication involving intestinal, immune and metabolic functions which is affected by feed deprivation in obese mice, thus pointing to careful use of short-feed deprivation in metabolic studies using obese mice.
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Affiliation(s)
- Daniel Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Henrik Munch Roager
- National Food Institute, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Nutrition, Exercise and Sports, University of Copenhagen, 1958, Frederiksberg C, Denmark
| | - Li Zhang
- National Food Institute, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Janne Marie Moll
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | | | - Niels Banhos Danneskiold-Samsøe
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Axel Kornerup Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
- Institute of Metagenomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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19
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Laursen MF, Bahl MI, Licht TR. Settlers of our inner surface - Factors shaping the gut microbiota from birth to toddlerhood. FEMS Microbiol Rev 2021; 45:6081092. [PMID: 33428723 PMCID: PMC8371275 DOI: 10.1093/femsre/fuab001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 09/04/2020] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
During the first 3 years of life, the microbial ecosystem within the human gut undergoes a process that is unlike what happens in this ecosystem at any other time of our life. This period in time is considered a highly important developmental window, where the gut microbiota is much less resilient and much more responsive to external and environmental factors than seen in the adult gut. While advanced bioinformatics and clinical correlation studies have received extensive focus within studies of the human microbiome, basic microbial growth physiology has attracted much less attention, although it plays a pivotal role to understand the developing gut microbiota during early life. In this review, we will thus take a microbial ecology perspective on the analysis of factors that influence the temporal development of the infant gut microbiota. Such factors include sources of microbes that seed the intestinal environment, physico-chemical (abiotic) conditions influencing microbial growth and the availability of nutrients needed by the intestinal microbes.
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Affiliation(s)
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby
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20
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Kamguyan K, Torp AM, Christfort JF, Guerra PR, Licht TR, Hagner Nielsen L, Zor K, Boisen A. Colon-Specific Delivery of Bioactive Agents Using Genipin-Cross-Linked Chitosan Coated Microcontainers. ACS Appl Bio Mater 2020. [DOI: 10.1021/acsabm.0c01333] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Khorshid Kamguyan
- The Danish National Research Foundation and Villum Foundation’s Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Anders Meyer Torp
- The National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Juliane Fjelrad Christfort
- The Danish National Research Foundation and Villum Foundation’s Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Priscila R. Guerra
- The National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Tine Rask Licht
- The National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Line Hagner Nielsen
- The Danish National Research Foundation and Villum Foundation’s Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kinga Zor
- The Danish National Research Foundation and Villum Foundation’s Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Anja Boisen
- The Danish National Research Foundation and Villum Foundation’s Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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21
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Laursen MF, Larsson MW, Lind MV, Larnkjær A, Mølgaard C, Michaelsen KF, Bahl MI, Licht TR. Intestinal Enterococcus abundance correlates inversely with excessive weight gain and increased plasma leptin in breastfed infants. FEMS Microbiol Ecol 2020; 96:5818758. [PMID: 32275305 PMCID: PMC7183236 DOI: 10.1093/femsec/fiaa066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 12/02/2019] [Accepted: 04/03/2020] [Indexed: 01/04/2023] Open
Abstract
Epidemiological evidence indicates that breastfeeding provides protection against development of overweight/obesity. Nonetheless, a small subgroup of infants undergo excessive weight gain during exclusive breastfeeding, a phenomenon that remains unexplained. Breast milk contains both gut-seeding microbes and substrates for microbial growth in the gut of infants, and a large body of evidence suggests a role for gut microbes in host metabolism. Based on the recently established SKOT III cohort, we investigated the role of the infant gut microbiota in excessive infant weight gain during breastfeeding, including 30 exclusively breastfed infants, 13 of which exhibited excessive weight gain and 17 controls which exhibited normal weight gain during infancy. Infants undergoing excessive weight gain during breastfeeding had a reduced abundance of gut Enterococcus as compared with that observed in the controls. Within the complete cohort, Enterococcus abundance correlated inversely with age/gender-adjusted body-weight, body-mass index and waist circumference, body fat and levels of plasma leptin. The reduced abundance of Enterococcus in infants with excessive weight gain was coupled to a lower content of Enterococcus in breast milk samples of their mothers than seen for mothers in the control group. Together, this suggests that lack of breast milk-derived gut-seeding Enterococci may contribute to excessive weight gain in breastfed infants.
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Affiliation(s)
- Martin Frederik Laursen
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800 Kgs Lyngby, Denmark
| | - Melanie Wange Larsson
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Nørre Allé 51, 2200 Copenhagen N, Denmark.,Department of Nursing and Nutrition, University College Copenhagen, Humletorvet 3, 1799 Copenhagen V, Denmark
| | - Mads Vendelbo Lind
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Nørre Allé 51, 2200 Copenhagen N, Denmark
| | - Anni Larnkjær
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Nørre Allé 51, 2200 Copenhagen N, Denmark
| | - Christian Mølgaard
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Nørre Allé 51, 2200 Copenhagen N, Denmark
| | - Kim F Michaelsen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Nørre Allé 51, 2200 Copenhagen N, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800 Kgs Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kemitorvet 202, 2800 Kgs Lyngby, Denmark
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22
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Nielsen RL, Helenius M, Garcia SL, Roager HM, Aytan-Aktug D, Hansen LBS, Lind MV, Vogt JK, Dalgaard MD, Bahl MI, Jensen CB, Muktupavela R, Warinner C, Aaskov V, Gøbel R, Kristensen M, Frøkiær H, Sparholt MH, Christensen AF, Vestergaard H, Hansen T, Kristiansen K, Brix S, Petersen TN, Lauritzen L, Licht TR, Pedersen O, Gupta R. Data integration for prediction of weight loss in randomized controlled dietary trials. Sci Rep 2020; 10:20103. [PMID: 33208769 PMCID: PMC7674420 DOI: 10.1038/s41598-020-76097-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 04/06/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022] Open
Abstract
Diet is an important component in weight management strategies, but heterogeneous responses to the same diet make it difficult to foresee individual weight-loss outcomes. Omics-based technologies now allow for analysis of multiple factors for weight loss prediction at the individual level. Here, we classify weight loss responders (N = 106) and non-responders (N = 97) of overweight non-diabetic middle-aged Danes to two earlier reported dietary trials over 8 weeks. Random forest models integrated gut microbiome, host genetics, urine metabolome, measures of physiology and anthropometrics measured prior to any dietary intervention to identify individual predisposing features of weight loss in combination with diet. The most predictive models for weight loss included features of diet, gut bacterial species and urine metabolites (ROC-AUC: 0.84–0.88) compared to a diet-only model (ROC-AUC: 0.62). A model ensemble integrating multi-omics identified 64% of the non-responders with 80% confidence. Such models will be useful to assist in selecting appropriate weight management strategies, as individual predisposition to diet response varies.
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Affiliation(s)
- Rikke Linnemann Nielsen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Marianne Helenius
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Sara L Garcia
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark.,National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Derya Aytan-Aktug
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.,National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Mads Vendelbo Lind
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Josef K Vogt
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Marlene Danner Dalgaard
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Martin I Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Cecilia Bang Jensen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Rasa Muktupavela
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Vincent Aaskov
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Rikke Gøbel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Mette Kristensen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Frøkiær
- Institute for Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Henrik Vestergaard
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark.,Department of Medicine, Bornholms Hospital, Rønne, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Lotte Lauritzen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark.
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark.
| | - Ramneek Gupta
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark. .,Novo Nordisk Research Centre Oxford, Oxford, OX3 7FZ, UK.
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23
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Bahl MI, Jørgensen SMD, Skriver AH, Larsen NA, Wang M, Licht TR, Dahlerup JF, Hvas CL. Faecal microbiota transplantation for eradication of co-infection with Clostridioides difficile and extensively drug-resistant KPC-producing Klebsiella pneumoniae. Scand J Gastroenterol 2020; 55:626-630. [PMID: 32324085 DOI: 10.1080/00365521.2020.1753806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Clostridioides difficile infection may be complicated by co-infection with other pathogens. We here describe the successful use of faecal microbiota transplantation to eradicate concomitant C. difficile and extensively drug-resistant (XDR) KPC-producing Klebsiella pneumoniae. Donor microbiota efficiently engrafted in the patient, and a donor-like microbial assemblage persisted in the patient during six months follow-up. The report explores the potential for the donor microbiota to eradicate and replace multi-resistant microorganisms.
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Affiliation(s)
- Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | | | - Nanna Alsig Larsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikala Wang
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jens Frederik Dahlerup
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Christian Lodberg Hvas
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
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24
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Graversen KB, Bahl MI, Larsen JM, Ballegaard ASR, Licht TR, Bøgh KL. Short-Term Amoxicillin-Induced Perturbation of the Gut Microbiota Promotes Acute Intestinal Immune Regulation in Brown Norway Rats. Front Microbiol 2020; 11:496. [PMID: 32292395 PMCID: PMC7135894 DOI: 10.3389/fmicb.2020.00496] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 01/24/2020] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
The intestinal gut microbiota is essential for maintaining host health. Concerns have been raised about the possible connection between antibiotic use, causing microbiota disturbances, and the increase in allergic and autoimmune diseases observed during the last decades. To elucidate the putative connection between antibiotic use and immune regulation, we have assessed the effects of the antibiotic amoxicillin on immune regulation, protein uptake, and bacterial community structure in a Brown Norway rat model. Daily intra-gastric administration of amoxicillin resulted in an immediate and dramatic shift in fecal microbiota, characterized by a reduction of within sample (α) diversity, reduced variation between animals (β diversity), increased relative abundance of Bacteroidetes and Gammaproteobacteria, with concurrent reduction of Firmicutes, compared to a water control group. In the small intestine, amoxicillin also affected microbiota composition significantly, but in a different way than observed in feces. The small intestine of control animals was vastly dominated by Lactobacillus, but this genus was much less abundant in the amoxicillin group. Instead, multiple different genera expanded after amoxicillin administration, with high variation between individual animals, thus the small intestinal α and β diversity were higher in the amoxicillin group compared to controls. After 1 week of daily amoxicillin administration, total fecal IgA level, relative abundance of small intestinal regulatory T cells and goblet cell numbers were higher in the amoxicillin group compared to controls. Several bacterial genera, including Escherichia/Shigella, Klebsiella (Gammaproteobacteria), and Bifidobacterium, for which the relative abundance was higher in the small intestine in the amoxicillin group than in controls, were positively correlated with the fraction of small intestinal regulatory T cells. Despite of epidemiologic studies showing an association between early life antibiotic consumption and later prevalence of inflammatory bowel diseases and food allergies, our findings surprisingly indicated that amoxicillin-induced perturbation of the gut microbiota promotes acute immune regulation. We speculate that the observed increase in relative abundance of small intestinal regulatory T cells is partly mediated by immunomodulatory lipopolysaccharides derived from outgrowth of Gammaproteobacteria.
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Affiliation(s)
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jeppe Madura Larsen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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25
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Asgari S, Pourjavadi A, Licht TR, Boisen A, Ajalloueian F. Polymeric carriers for enhanced delivery of probiotics. Adv Drug Deliv Rev 2020; 161-162:1-21. [PMID: 32702378 DOI: 10.1016/j.addr.2020.07.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022]
Abstract
Probiotics are live microorganisms (usually bacteria), which are defined by their ability to confer health benefits to the host, if administered adequately. Probiotics are not only used as health supplements but have also been applied in various attempts to prevent and treat gastrointestinal (GI) and non-gastrointestinal diseases such as diarrhea, colon cancer, obesity, diabetes, and inflammation. One of the challenges in the use of probiotics is putative loss of viability by the time of administration. It can be due to procedures that the probiotic products go through during fabrication, storage, or administration. Biocompatible and biodegradable polymers with specific moieties or pH/enzyme sensitivity have shown great potential as carriers of the bacteria for 1) better viability, 2) longer storage times, 3) preservation from the aggressive environment in the stomach and 4) topographically targeted delivery of probiotics. In this review, we focus on polymeric carriers and the procedures applied for encapsulation of the probiotics into them. At the end, some novel methods for specific probiotic delivery, possibilities to improve the targeted delivery of probiotics and some challenges are discussed.
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26
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Jørgensen SMD, Hvas CL, Dahlerup JF, Mikkelsen S, Ehlers L, Hammeken LH, Licht TR, Bahl MI, Erikstrup C. Banking feces: a new frontier for public blood banks? Transfusion 2019; 59:2776-2782. [PMID: 31241182 PMCID: PMC6852397 DOI: 10.1111/trf.15422] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
Abstract
Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridioides difficile infection and is potentially beneficial in other microbiota-related disorders. The provision of FMT in routine clinical practice requires an extensive infrastructure that is reliant on voluntary donors. Alongside an increasing demand for FMT, the logistic barriers of a large-scale donor-dependent operation and the difficulties among health authorities to regulate FMT limit the dissemination of sustainable FMT services. Blood centers are large organizations that handle a multitude of donor-dependent operations on a daily basis. Blood and feces share many of the same dependencies, and feces may present a new opportunity for the blood services to handle. In this paper, we describe how an FMT service may be established and embedded within the blood service infrastructure, and we explain the benefits of using blood donors as feces donors. We further explore the current indications of FMT, the challenges related to the lack of legislation, and the future perspectives for blood banks to meet a new and increasing demand.
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Affiliation(s)
| | | | | | - Susan Mikkelsen
- Department of Clinical ImmunologyAarhus University HospitalAarhusDenmark
| | - Lars Ehlers
- Department of Business and Management, Danish Centre for Healthcare ImprovementsAalborg UniversityAalborgDenmark
| | - Lianna Hede Hammeken
- Department of Business and Management, Danish Centre for Healthcare ImprovementsAalborg UniversityAalborgDenmark
| | - Tine Rask Licht
- National Food InstituteTechnical University of DenmarkKgs. LyngbyDenmark
| | - Martin Iain Bahl
- National Food InstituteTechnical University of DenmarkKgs. LyngbyDenmark
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27
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28
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Roager HM, Vogt JK, Kristensen M, Hansen LBS, Ibrügger S, Mærkedahl RB, Bahl MI, Lind MV, Nielsen RL, Frøkiær H, Gøbel RJ, Landberg R, Ross AB, Brix S, Holck J, Meyer AS, Sparholt MH, Christensen AF, Carvalho V, Hartmann B, Holst JJ, Rumessen JJ, Linneberg A, Sicheritz-Pontén T, Dalgaard MD, Blennow A, Frandsen HL, Villas-Bôas S, Kristiansen K, Vestergaard H, Hansen T, Ekstrøm CT, Ritz C, Nielsen HB, Pedersen OB, Gupta R, Lauritzen L, Licht TR. Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial. Gut 2019; 68:83-93. [PMID: 29097438 PMCID: PMC6839833 DOI: 10.1136/gutjnl-2017-314786] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To investigate whether a whole grain diet alters the gut microbiome and insulin sensitivity, as well as biomarkers of metabolic health and gut functionality. DESIGN 60 Danish adults at risk of developing metabolic syndrome were included in a randomised cross-over trial with two 8-week dietary intervention periods comprising whole grain diet and refined grain diet, separated by a washout period of ≥6 weeks. The response to the interventions on the gut microbiome composition and insulin sensitivity as well on measures of glucose and lipid metabolism, gut functionality, inflammatory markers, anthropometry and urine metabolomics were assessed. RESULTS 50 participants completed both periods with a whole grain intake of 179±50 g/day and 13±10 g/day in the whole grain and refined grain period, respectively. Compliance was confirmed by a difference in plasma alkylresorcinols (p<0.0001). Compared with refined grain, whole grain did not significantly alter glucose homeostasis and did not induce major changes in the faecal microbiome. Also, breath hydrogen levels, plasma short-chain fatty acids, intestinal integrity and intestinal transit time were not affected. The whole grain diet did, however, compared with the refined grain diet, decrease body weight (p<0.0001), serum inflammatory markers, interleukin (IL)-6 (p=0.009) and C-reactive protein (p=0.003). The reduction in body weight was consistent with a reduction in energy intake, and IL-6 reduction was associated with the amount of whole grain consumed, in particular with intake of rye. CONCLUSION Compared with refined grain diet, whole grain diet did not alter insulin sensitivity and gut microbiome but reduced body weight and systemic low-grade inflammation. TRIAL REGISTRATION NUMBER NCT01731366; Results.
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Affiliation(s)
- Henrik Munch Roager
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Josef K Vogt
- Department of Bio and Heath Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mette Kristensen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Frederiksberg, Denmark
| | - Lea Benedicte S Hansen
- Department of Bio and Heath Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sabine Ibrügger
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Frederiksberg, Denmark
| | - Rasmus B Mærkedahl
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Frederiksberg, Denmark,Department of Veterinary Disease Biology, Faculty of Science, University of Copenhagen, Copenhagen, Frederiksberg, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mads Vendelbo Lind
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Frederiksberg, Denmark,Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Rikke L Nielsen
- Department of Bio and Heath Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Hanne Frøkiær
- Department of Veterinary Disease Biology, Faculty of Science, University of Copenhagen, Copenhagen, Frederiksberg, Denmark
| | - Rikke Juul Gøbel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Rikard Landberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Alastair B Ross
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jesper Holck
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anne S Meyer
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Vera Carvalho
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bolette Hartmann
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jens Juul Holst
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jüri Johannes Rumessen
- Research Unit and Department of Gastroenterology, Herlev and Gentofte Hospital, Copenhagen, Denmark
| | - Allan Linneberg
- Research Centre for Prevention and Health, Copenhagen, Denmark,Department of Clinical Experimental Research, Rigshospitalet, Copenhagen, Denmark,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Sicheritz-Pontén
- Department of Bio and Heath Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marlene D Dalgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andreas Blennow
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Silas Villas-Bôas
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Vestergaard
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark,Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Claus T Ekstrøm
- Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Christian Ritz
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Frederiksberg, Denmark
| | - Henrik Bjørn Nielsen
- Department of Bio and Heath Informatics, Technical University of Denmark, Kongens Lyngby, Denmark,Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Oluf Borbye Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Ramneek Gupta
- Department of Bio and Heath Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lotte Lauritzen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Frederiksberg, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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29
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Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJY, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Dworzynski P, Nielsen HB, Bäckhed F, Doré J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Madsen L, Kristiansen K. Correction: Amendments: Author Correction: A catalog of the mouse gut metagenome. Nat Biotechnol 2019; 37:102. [DOI: 10.1038/nbt0119-102a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Leth ML, Ejby M, Workman C, Ewald DA, Pedersen SS, Sternberg C, Bahl MI, Licht TR, Aachmann FL, Westereng B, Abou Hachem M. Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut. Nat Microbiol 2018; 3:570-580. [PMID: 29610517 DOI: 10.1038/s41564-018-0132-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/19/2018] [Indexed: 12/11/2022]
Abstract
Metabolism of dietary glycans is pivotal in shaping the human gut microbiota. However, the mechanisms that promote competition for glycans among gut commensals remain unclear. Roseburia intestinalis, an abundant butyrate-producing Firmicute, is a key degrader of the major dietary fibre xylan. Despite the association of this taxon to a healthy microbiota, insight is lacking into its glycan utilization machinery. Here, we investigate the apparatus that confers R. intestinalis growth on different xylans. R. intestinalis displays a large cell-attached modular xylanase that promotes multivalent and dynamic association to xylan via four xylan-binding modules. This xylanase operates in concert with an ATP-binding cassette transporter to mediate breakdown and selective internalization of xylan fragments. The transport protein of R. intestinalis prefers oligomers of 4-5 xylosyl units, whereas the counterpart from a model xylan-degrading Bacteroides commensal targets larger ligands. Although R. intestinalis and the Bacteroides competitor co-grew in a mixed culture on xylan, R. intestinalis dominated on the preferred transport substrate xylotetraose. These findings highlight the differentiation of capture and transport preferences as a possible strategy to facilitate co-growth on abundant dietary fibres and may offer a unique route to manipulate the microbiota based on glycan transport preferences in therapeutic interventions to boost distinct taxa.
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Affiliation(s)
- Maria Louise Leth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Morten Ejby
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Christopher Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - David Adrian Ewald
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Signe Schultz Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Claus Sternberg
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Finn Lillelund Aachmann
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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Nielsen LN, Roager HM, Casas ME, Frandsen HL, Gosewinkel U, Bester K, Licht TR, Hendriksen NB, Bahl MI. Glyphosate has limited short-term effects on commensal bacterial community composition in the gut environment due to sufficient aromatic amino acid levels. Environ Pollut 2018; 233:364-376. [PMID: 29096310 DOI: 10.1016/j.envpol.2017.10.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/03/2017] [Accepted: 10/05/2017] [Indexed: 05/20/2023]
Abstract
Recently, concerns have been raised that residues of glyphosate-based herbicides may interfere with the homeostasis of the intestinal bacterial community and thereby affect the health of humans or animals. The biochemical pathway for aromatic amino acid synthesis (Shikimate pathway), which is specifically inhibited by glyphosate, is shared by plants and numerous bacterial species. Several in vitro studies have shown that various groups of intestinal bacteria may be differently affected by glyphosate. Here, we present results from an animal exposure trial combining deep 16S rRNA gene sequencing of the bacterial community with liquid chromatography mass spectrometry (LC-MS) based metabolic profiling of aromatic amino acids and their downstream metabolites. We found that glyphosate as well as the commercial formulation Glyfonova®450 PLUS administered at up to fifty times the established European Acceptable Daily Intake (ADI = 0.5 mg/kg body weight) had very limited effects on bacterial community composition in Sprague Dawley rats during a two-week exposure trial. The effect of glyphosate on prototrophic bacterial growth was highly dependent on the availability of aromatic amino acids, suggesting that the observed limited effect on bacterial composition was due to the presence of sufficient amounts of aromatic amino acids in the intestinal environment. A strong correlation was observed between intestinal concentrations of glyphosate and intestinal pH, which may partly be explained by an observed reduction in acetic acid produced by the gut bacteria. We conclude that sufficient intestinal levels of aromatic amino acids provided by the diet alleviates the need for bacterial synthesis of aromatic amino acids and thus prevents an antimicrobial effect of glyphosate in vivo. It is however possible that the situation is different in cases of human malnutrition or in production animals.
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Affiliation(s)
- Lene Nørby Nielsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Henrik M Roager
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Henrik L Frandsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ulrich Gosewinkel
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Kai Bester
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
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Hjorth MF, Roager HM, Larsen TM, Poulsen SK, Licht TR, Bahl MI, Zohar Y, Astrup A. Pre-treatment microbial Prevotella-to-Bacteroides ratio, determines body fat loss success during a 6-month randomized controlled diet intervention. Int J Obes (Lond) 2017; 42:580-583. [PMID: 28883543 PMCID: PMC5880576 DOI: 10.1038/ijo.2017.220] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/04/2017] [Accepted: 08/22/2017] [Indexed: 12/25/2022]
Abstract
On the basis of the abundance of specific bacterial genera, the human gut microbiota can be divided into two relatively stable groups that might have a role in personalized nutrition. We studied these simplified enterotypes as prognostic markers for successful body fat loss on two different diets. A total of 62 participants with increased waist circumference were randomly assigned to receive an ad libitum New Nordic Diet (NND) high in fiber/whole grain or an Average Danish Diet for 26 weeks. Participants were grouped into two discrete enterotypes by their relative abundance of Prevotella spp. divided by Bacteroides spp. (P/B ratio) obtained by quantitative PCR analysis. Modifications of dietary effects of pre-treatment P/B group were examined by linear mixed models. Among individuals with high P/B the NND resulted in a 3.15 kg (95% confidence interval (CI): 1.55; 4.76, P<0.001) larger body fat loss compared with ADD, whereas no differences was observed among individuals with low P/B (0.88 kg (95% CI: −0.61; 2.37, P=0.25)). Consequently, a 2.27 kg (95% CI: 0.09; 4.45, P=0.041) difference in responsiveness to the diets were found between the two groups. In summary, subjects with high P/B ratio appeared more susceptible to lose body fat on diets high in fiber and whole grain than subjects with a low P/B ratio.
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Affiliation(s)
- M F Hjorth
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - H M Roager
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - T M Larsen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - S K Poulsen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark.,Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - T R Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - M I Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Y Zohar
- Gelesis Inc., Boston, MA, USA
| | - A Astrup
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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33
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Laursen MF, Laursen RP, Larnkjær A, Michaelsen KF, Bahl MI, Licht TR. Administration of two probiotic strains during early childhood does not affect the endogenous gut microbiota composition despite probiotic proliferation. BMC Microbiol 2017; 17:175. [PMID: 28818050 PMCID: PMC5561568 DOI: 10.1186/s12866-017-1090-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/11/2017] [Indexed: 01/16/2023] Open
Abstract
Background Probiotics are increasingly applied to prevent and treat a range of infectious, immune related and gastrointestinal diseases. Despite this, the mechanisms behind the putative effects of probiotics are poorly understood. One of the suggested modes of probiotic action is modulation of the endogenous gut microbiota, however probiotic intervention studies in adults have failed to show significant effects on gut microbiota composition. The gut microbiota of young children is known to be unstable and more responsive to external factors than that of adults. Therefore, potential effects of probiotic intervention on gut microbiota may be easier detectable in early life. We thus investigated the effects of a 6 month placebo-controlled probiotic intervention with Bifidobacterium animalis subsp. lactis (BB-12®) and Lactobacillus rhamnosus (LGG®) on gut microbiota composition and diversity in more than 200 Danish infants (N = 290 enrolled; N = 201 all samples analyzed), as assessed by 16S rRNA amplicon sequencing. Further, we evaluated probiotic presence and proliferation by use of specific quantitative polymerase chain reaction (qPCR). Results Probiotic administration did not significantly alter gut microbiota community structure or diversity as compared to placebo. The probiotic strains were detected in 91.3% of the fecal samples from children receiving probiotics and in 1% of the placebo treated children. Baseline gut microbiota was not found to predict the ability of probiotics to establish in the gut after the 6 month intervention. Within the probiotics group, proliferation of the strains LGG® and BB-12® in the gut was detected in 44.7% and 83.5% of the participants, respectively. A sub-analysis of the gut microbiota including only individuals with detected growth of the probiotics LGG® or BB-12® and comparing these to placebo revealed no differences in community structure or diversity. Conclusion Six months of probiotic administration during early life did not change gut microbiota community structure or diversity, despite active proliferation of the administered probiotic strains. Therefore, alteration of the healthy infant gut microbiota is not likely to be a prominent mechanism by which these specific probiotics works to exert beneficial effects on host health. Trial registration NCT02180581. Registered 30 June 2014. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1090-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Frederik Laursen
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800, Lyngby, Denmark
| | - Rikke Pilmann Laursen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, DK-1958, Frederiksberg C, Denmark
| | - Anni Larnkjær
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, DK-1958, Frederiksberg C, Denmark
| | - Kim F Michaelsen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, DK-1958, Frederiksberg C, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800, Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800, Lyngby, Denmark.
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Xiao L, Sonne SB, Feng Q, Chen N, Xia Z, Li X, Fang Z, Zhang D, Fjære E, Midtbø LK, Derrien M, Hugenholtz F, Tang L, Li J, Zhang J, Liu C, Hao Q, Vogel UB, Mortensen A, Kleerebezem M, Licht TR, Yang H, Wang J, Li Y, Arumugam M, Wang J, Madsen L, Kristiansen K. High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice. Microbiome 2017; 5:43. [PMID: 28390422 PMCID: PMC5385073 DOI: 10.1186/s40168-017-0258-6] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 03/16/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND It is well known that the microbiota of high-fat (HF) diet-induced obese mice differs from that of lean mice, but to what extent, this difference reflects the obese state or the diet is unclear. To dissociate changes in the gut microbiota associated with high HF feeding from those associated with obesity, we took advantage of the different susceptibility of C57BL/6JBomTac (BL6) and 129S6/SvEvTac (Sv129) mice to diet-induced obesity and of their different responses to inhibition of cyclooxygenase (COX) activity, where inhibition of COX activity in BL6 mice prevents HF diet-induced obesity, but in Sv129 mice accentuates obesity. RESULTS Using HiSeq-based whole genome sequencing, we identified taxonomic and functional differences in the gut microbiota of the two mouse strains fed regular low-fat or HF diets with or without supplementation with the COX-inhibitor, indomethacin. HF feeding rather than obesity development led to distinct changes in the gut microbiota. We observed a robust increase in alpha diversity, gene count, abundance of genera known to be butyrate producers, and abundance of genes involved in butyrate production in Sv129 mice compared to BL6 mice fed either a LF or a HF diet. Conversely, the abundance of genes involved in propionate metabolism, associated with increased energy harvest, was higher in BL6 mice than Sv129 mice. CONCLUSIONS The changes in the composition of the gut microbiota were predominantly driven by high-fat feeding rather than reflecting the obese state of the mice. Differences in the abundance of butyrate and propionate producing bacteria in the gut may at least in part contribute to the observed differences in obesity propensity in Sv129 and BL6 mice.
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Affiliation(s)
| | - Si Brask Sonne
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Qiang Feng
- BGI-Shenzhen, Shenzhen, 518083 China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ning Chen
- BGI-Shenzhen, Shenzhen, 518083 China
| | | | | | | | | | - Even Fjære
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- National Institute of Nutrition and Seafood Research (NIFES), Postboks 2029, Nordnes, N-5817 Bergen, Norway
| | - Lisa Kolden Midtbø
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- National Institute of Nutrition and Seafood Research (NIFES), Postboks 2029, Nordnes, N-5817 Bergen, Norway
| | - Muriel Derrien
- Laboratory of Microbiology, Wageningen University, 6701 AK Wageningen, The Netherlands
- Present address: Danone Research, TI Food and Nutrition, Paris, France
| | - Floor Hugenholtz
- Laboratory of Microbiology, Wageningen University, 6701 AK Wageningen, The Netherlands
| | | | - Junhua Li
- BGI-Shenzhen, Shenzhen, 518083 China
| | | | - Chuan Liu
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Qin Hao
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ulla Birgitte Vogel
- National Research Centre for the Working Environment, DK-2100 Copenhagen, Denmark
| | - Alicja Mortensen
- National Food Institute, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Michiel Kleerebezem
- Laboratory of Microbiology, Wageningen University, 6701 AK Wageningen, The Netherlands
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083 China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058 China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083 China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058 China
| | | | - Manimozhiyan Arumugam
- BGI-Shenzhen, Shenzhen, 518083 China
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, DK-2100 Denmark
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083 China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Lise Madsen
- BGI-Shenzhen, Shenzhen, 518083 China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- National Institute of Nutrition and Seafood Research (NIFES), Postboks 2029, Nordnes, N-5817 Bergen, Norway
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, 518083 China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
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35
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Zhang L, Bahl MI, Roager HM, Fonvig CE, Hellgren LI, Frandsen HL, Pedersen O, Holm JC, Hansen T, Licht TR. Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans. ISME J 2016; 11:676-690. [PMID: 27858930 DOI: 10.1038/ismej.2016.151] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 08/19/2016] [Accepted: 09/20/2016] [Indexed: 12/24/2022]
Abstract
Microbiota transplantation to germ-free animals is a powerful method to study involvement of gut microbes in the aetiology of metabolic syndrome. Owing to large interpersonal variability in gut microbiota, studies with broad coverage of donors are needed to elucidate the establishment of human-derived microbiotas in mice, factors affecting this process and resulting impact on metabolic health. We thus transplanted faecal microbiotas from humans (16 obese and 16 controls) separately into 64 germ-free Swiss Webster mice caged in pairs within four isolators, with two isolators assigned to each phenotype, thereby allowing us to explore the extent of microbial spread between cages in a well-controlled environment. Despite high group-wise similarity between obese and control human microbiotas, transplanted mice in the four isolators developed distinct gut bacterial composition and activity, body mass gain, and insulin resistance. Spread of microbes between cages within isolators interacted with establishment of the transplanted microbiotas in mice, and contributed to the transmission of metabolic phenotypes. Our findings highlight the impact of donor variability and reveal that inter-individual spread of microbes contributes to the development of metabolic traits. This is of major importance for design of animal studies, and indicates that environmental transfer of microbes between individuals may affect host metabolic traits.
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Affiliation(s)
- Li Zhang
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | | | - Cilius Esmann Fonvig
- The Children's Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars I Hellgren
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | | | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens-Christian Holm
- The Children's Obesity Clinic, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Søborg, Denmark
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36
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Kiilerich P, Myrmel LS, Fjære E, Hao Q, Hugenholtz F, Sonne SB, Derrien M, Pedersen LM, Petersen RK, Mortensen A, Licht TR, Rømer MU, Vogel UB, Waagbø LJ, Giallourou N, Feng Q, Xiao L, Liu C, Liaset B, Kleerebezem M, Wang J, Madsen L, Kristiansen K. Effect of a long-term high-protein diet on survival, obesity development, and gut microbiota in mice. Am J Physiol Endocrinol Metab 2016; 310:E886-99. [PMID: 27026084 DOI: 10.1152/ajpendo.00363.2015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 03/28/2016] [Indexed: 01/12/2023]
Abstract
Female C57BL/6J mice were fed a regular low-fat diet or high-fat diets combined with either high or low protein-to-sucrose ratios during their entire lifespan to examine the long-term effects on obesity development, gut microbiota, and survival. Intake of a high-fat diet with a low protein/sucrose ratio precipitated obesity and reduced survival relative to mice fed a low-fat diet. By contrast, intake of a high-fat diet with a high protein/sucrose ratio attenuated lifelong weight gain and adipose tissue expansion, and survival was not significantly altered relative to low-fat-fed mice. Our findings support the notion that reduced survival in response to high-fat/high-sucrose feeding is linked to obesity development. Digital gene expression analyses, further validated by qPCR, demonstrated that the protein/sucrose ratio modulated global gene expression over time in liver and adipose tissue, affecting pathways related to metabolism and inflammation. Analysis of fecal bacterial DNA using the Mouse Intestinal Tract Chip revealed significant changes in the composition of the gut microbiota in relation to host age and dietary fat content, but not the protein/sucrose ratio. Accordingly, dietary fat rather than the protein/sucrose ratio or adiposity is a major driver shaping the gut microbiota, whereas the effect of a high-fat diet on survival is dependent on the protein/sucrose ratio.
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Affiliation(s)
- Pia Kiilerich
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lene Secher Myrmel
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark; National Institute of Nutrition and Seafood Research, Bergen, Norway
| | - Even Fjære
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark; National Institute of Nutrition and Seafood Research, Bergen, Norway
| | - Qin Hao
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Si Brask Sonne
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Muriel Derrien
- Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - Lone Møller Pedersen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Koefoed Petersen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alicja Mortensen
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Maria Unni Rømer
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, University of Copenhagen, Denmark
| | | | | | | | | | | | | | - Bjørn Liaset
- National Institute of Nutrition and Seafood Research, Bergen, Norway
| | - Michiel Kleerebezem
- Top Institute Food and Nutrition, Wageningen, The Netherlands; Host Microbe Interactomics Group, Wageningen University, Wageningen, The Netherlands
| | - Jun Wang
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark; BGI-Shenzhen, Shenzhen, China, Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia; Macau University of Science and Technology, Taipa, Macau, China; Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China
| | - Lise Madsen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark; National Institute of Nutrition and Seafood Research, Bergen, Norway; BGI-Shenzhen, Shenzhen, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark; BGI-Shenzhen, Shenzhen, China,
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O'Brien Andersen L, Karim AB, Roager HM, Vigsnæs LK, Krogfelt KA, Licht TR, Stensvold CR. Associations between common intestinal parasites and bacteria in humans as revealed by qPCR. Eur J Clin Microbiol Infect Dis 2016; 35:1427-31. [PMID: 27230509 DOI: 10.1007/s10096-016-2680-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/13/2016] [Indexed: 02/05/2023]
Abstract
Several studies have shown associations between groups of intestinal bacterial or specific ratios between bacterial groups and various disease traits. Meanwhile, little is known about interactions and associations between eukaryotic and prokaryotic microorganisms in the human gut. In this work, we set out to investigate potential associations between common single-celled parasites such as Blastocystis spp. and Dientamoeba fragilis and intestinal bacteria. Stool DNA from patients with intestinal symptoms were selected based on being Blastocystis spp.-positive (B+)/negative (B-) and D. fragilis-positive (D+)/negative (D-), and split into four groups of 21 samples (B+ D+, B+ D-, B- D+, and B- D-). Quantitative PCR targeting the six bacterial taxa Bacteroides, Prevotella, the butyrate-producing clostridial clusters IV and XIVa, the mucin-degrading Akkermansia muciniphila, and the indigenous group of Bifidobacterium was subsequently performed, and the relative abundance of these bacteria across the four groups was compared. The relative abundance of Bacteroides in B- D- samples was significantly higher compared with B+ D- and B+ D+ samples (P < 0.05 and P < 0.01, respectively), and this association was even more significant when comparing all parasite-positive samples with parasite-negative samples (P < 0.001). Additionally, our data revealed that a low abundance of Prevotella and a higher abundance of Clostridial cluster XIVa was associated with parasite-negative samples (P < 0.05 and P < 0.01, respectively). Our data support the theory that Blastocystis alone or combined with D. fragilis is associated with gut microbiota characterized by low relative abundances of Bacteroides and Clostridial cluster XIVa and high levels of Prevotella.
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Affiliation(s)
- L O'Brien Andersen
- Unit of Mycology and Parasitology, Department of Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - A B Karim
- Unit of Mycology and Parasitology, Department of Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - H M Roager
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - L K Vigsnæs
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - K A Krogfelt
- Unit of Mycology and Parasitology, Department of Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - T R Licht
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - C R Stensvold
- Unit of Mycology and Parasitology, Department of Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark.
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38
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Tulstrup MVL, Christensen EG, Carvalho V, Linninge C, Ahrné S, Højberg O, Licht TR, Bahl MI. Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class. PLoS One 2015; 10:e0144854. [PMID: 26691591 PMCID: PMC4686753 DOI: 10.1371/journal.pone.0144854] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/24/2015] [Indexed: 01/25/2023] Open
Abstract
Antibiotics are frequently administered orally to treat bacterial infections not necessarily related to the gastrointestinal system. This has adverse effects on the commensal gut microbial community, as it disrupts the intricate balance between specific bacterial groups within this ecosystem, potentially leading to dysbiosis. We hypothesized that modulation of community composition and function induced by antibiotics affects intestinal integrity depending on the antibiotic administered. To address this a total of 60 Wistar rats (housed in pairs with 6 cages per group) were dosed by oral gavage with either amoxicillin (AMX), cefotaxime (CTX), vancomycin (VAN), metronidazole (MTZ), or water (CON) daily for 10-11 days. Bacterial composition, alpha diversity and caecum short chain fatty acid levels were significantly affected by AMX, CTX and VAN, and varied among antibiotic treatments. A general decrease in diversity and an increase in the relative abundance of Proteobacteria was observed for all three antibiotics. Additionally, the relative abundance of Bifidobacteriaceae was increased in the CTX group and both Lactobacillaceae and Verrucomicrobiaceae were increased in the VAN group compared to the CON group. No changes in microbiota composition or function were observed following MTZ treatment. Intestinal permeability to 4 kDa FITC-dextran decreased after CTX and VAN treatment and increased following MTZ treatment. Plasma haptoglobin levels were increased by both AMX and CTX but no changes in expression of host tight junction genes were found in any treatment group. A strong correlation between the level of caecal succinate, the relative abundance of Clostridiaceae 1 family in the caecum, and the level of acute phase protein haptoglobin in blood plasma was observed. In conclusion, antibiotic-induced changes in microbiota may be linked to alterations in intestinal permeability, although the specific interactions remain to be elucidated as changes in permeability did not always result from major changes in microbiota and vice versa.
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Affiliation(s)
- Monica Vera-Lise Tulstrup
- Division of Diet, Disease prevention and Toxicology, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Ellen Gerd Christensen
- Division of Diet, Disease prevention and Toxicology, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Vera Carvalho
- Division of Diet, Disease prevention and Toxicology, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Caroline Linninge
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Siv Ahrné
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Ole Højberg
- Department of Animal Science, Aarhus University, Tjele, Denmark
| | - Tine Rask Licht
- Division of Diet, Disease prevention and Toxicology, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Martin Iain Bahl
- Division of Diet, Disease prevention and Toxicology, National Food Institute, Technical University of Denmark, Søborg, Denmark
- * E-mail:
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Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJY, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Dworzynski P, Nielsen HB, Bäckhed F, Doré J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Madsen L, Kristiansen K. A catalog of the mouse gut metagenome. Nat Biotechnol 2015; 33:1103-8. [PMID: 26414350 DOI: 10.1038/nbt.3353] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/20/2015] [Indexed: 12/28/2022]
Abstract
We established a catalog of the mouse gut metagenome comprising ∼2.6 million nonredundant genes by sequencing DNA from fecal samples of 184 mice. To secure high microbiome diversity, we used mouse strains of diverse genetic backgrounds, from different providers, kept in different housing laboratories and fed either a low-fat or high-fat diet. Similar to the human gut microbiome, >99% of the cataloged genes are bacterial. We identified 541 metagenomic species and defined a core set of 26 metagenomic species found in 95% of the mice. The mouse gut microbiome is functionally similar to its human counterpart, with 95.2% of its Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups in common. However, only 4.0% of the mouse gut microbial genes were shared (95% identity, 90% coverage) with those of the human gut microbiome. This catalog provides a useful reference for future studies.
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Affiliation(s)
- Liang Xiao
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Qiang Feng
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Suisha Liang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Si Brask Sonne
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zhongkui Xia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Xinmin Qiu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Xiaoping Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Hua Long
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Jianfeng Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Dongya Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Chuan Liu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Zhiwei Fang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Joyce Chou
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Jacob Glanville
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Qin Hao
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dorota Kotowska
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Colding
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Donghai Wu
- Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences (Chinese University Hong Kong), Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Jao Yiu Sung
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences (Chinese University Hong Kong), Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Qiaoyi Liang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences (Chinese University Hong Kong), Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Junhua Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Huijue Jia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Zhou Lan
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Valentina Tremaroli
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Piotr Dworzynski
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - H Bjørn Nielsen
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden.,The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Joël Doré
- Institut National de la Recherche Agronomique (Microbiologie de l'Alimentation au Service de la Santé), Jouy en Josas, France.,Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France
| | | | - S Dusko Ehrlich
- Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, UK
| | - John C Lin
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Manimozhiyan Arumugam
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jun Wang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, China
| | - Lise Madsen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,National Institute of Nutrition and Seafood Research, Bergen, Norway
| | - Karsten Kristiansen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Laursen MF, Zachariassen G, Bahl MI, Bergström A, Høst A, Michaelsen KF, Licht TR. Having older siblings is associated with gut microbiota development during early childhood. BMC Microbiol 2015; 15:154. [PMID: 26231752 PMCID: PMC4522135 DOI: 10.1186/s12866-015-0477-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/06/2015] [Indexed: 12/15/2022] Open
Abstract
Background Evidence suggests that early life infections, presence of older siblings and furred pets in the household affect the risk of developing allergic diseases through altered microbial exposure. Recently, low gut microbial diversity during infancy has also been linked with later development of allergies. We investigated whether presence of older siblings, furred pets and early life infections affected gut microbial communities at 9 and 18 months of age and whether these differences were associated with the cumulative prevalence of atopic symptoms of eczema and asthmatic bronchitis at 3 years of age. Bacterial compositions and diversity indices were determined in fecal samples collected from 114 infants in the SKOT I cohort at age 9 and 18 months by 16S rRNA gene sequencing. These were compared to the presence of older siblings, furred pets and early life infections and the cumulative prevalence of diagnosed asthmatic bronchitis and self-reported eczema at 3 years of age. Results The number of older siblings correlated positively with bacterial diversity (p = 0.030), diversity of the phyla Firmicutes (p = 0.013) and Bacteroidetes (p = 0.004) and bacterial richness (p = 0.006) at 18 months. Further, having older siblings was associated with increased relative abundance of several bacterial taxa at both 9 and 18 months of age. Compared to the effect of having siblings, presence of household furred pets and early life infections had less pronounced effects on the gut microbiota. Gut microbiota characteristics were not significantly associated with cumulative occurrence of eczema and asthmatic bronchitis during the first 3 years of life. Conclusions Presence of older siblings is associated with increased gut microbial diversity and richness during early childhood, which could contribute to the substantiation of the hygiene hypothesis. However, no associations were found between gut microbiota and atopic symptoms of eczema and asthmatic bronchitis during early childhood and thus further studies are required to elucidate whether sibling-associated gut microbial changes influence development of allergies later in childhood. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0477-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Frederik Laursen
- Division of Diet, Disease Prevention and Toxicology, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860, Søborg, Denmark.
| | - Gitte Zachariassen
- H.C. Andersen Children's Hospital, Odense University Hospital, Sdr. Boulevard 29, DK-5000, Odense C, Denmark.
| | - Martin Iain Bahl
- Division of Diet, Disease Prevention and Toxicology, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860, Søborg, Denmark.
| | - Anders Bergström
- Division of Diet, Disease Prevention and Toxicology, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860, Søborg, Denmark. .,Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 30, DK-1958, Frederiksberg C, Denmark.
| | - Arne Høst
- H.C. Andersen Children's Hospital, Odense University Hospital, Sdr. Boulevard 29, DK-5000, Odense C, Denmark.
| | - Kim F Michaelsen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 30, DK-1958, Frederiksberg C, Denmark.
| | - Tine Rask Licht
- Division of Diet, Disease Prevention and Toxicology, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860, Søborg, Denmark
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Christensen EG, Licht TR, Leser TD, Bahl MI. Dietary xylo-oligosaccharide stimulates intestinal bifidobacteria and lactobacilli but has limited effect on intestinal integrity in rats. BMC Res Notes 2014; 7:660. [PMID: 25238818 PMCID: PMC4179812 DOI: 10.1186/1756-0500-7-660] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [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: 02/26/2014] [Accepted: 09/16/2014] [Indexed: 12/30/2022] Open
Abstract
Background Consumption of prebiotics may modulate gut microbiota, subsequently affecting the bacterial composition, metabolite profile, and human health. Previous studies indicate that also changes in intestinal integrity may occur. In order to explore this further we have investigated the effect of the putative prebiotic xylo-oligosaccharides (XOS) on the gut microbiota and intestinal integrity in male Wistar rats. As changes in intestinal integrity may be related to the expected bifidogenic effect of XOS, we additionally addressed effects of supplementation with a commensal Bifidobacterium pseudolongum (BIF) isolated from the same breed of laboratory rats. Results Changes in faecal and caecal bacterial composition determined by 16S rRNA gene sequencing and quantitative PCR for selected bacterial groups revealed that the overall bacterial composition did not differ markedly between the control (CON), XOS, and BIF groups, when correcting for multiple comparisons. However as hypothesised, the relative abundance of Bifidobacterium spp. was increased in XOS-fed rats as compared to CON in faecal samples after the intervention. Also Lactobacillus spp. was increased in both the XOS and BIF groups in caecum content compared to CON. Intestinal permeability determined in vivo by FITC-dextran permeability and in vitro using extracted caecum water in trans-epithelial resistance (TER) assay showed no effect on intestinal integrity in either the XOS or the BIF groups. However, the expression of occludin, which is part of the tight junction complex, was increased in the XOS group compared to the CON group. Conclusions Supplementation with XOS or a commensal Bifidobacterium pseudolongum had very limited effects on intestinal integrity in rats as only significant change in expression of a single tight junction protein gene was found for the XOS group.
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Affiliation(s)
| | | | | | - Martin Iain Bahl
- Division of Food Microbiology, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, Søborg DK-2860, Denmark.
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42
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Sulek K, Vigsnaes LK, Schmidt LR, Holck J, Frandsen HL, Smedsgaard J, Skov TH, Meyer AS, Licht TR. A combined metabolomic and phylogenetic study reveals putatively prebiotic effects of high molecular weight arabino-oligosaccharides when assessed by in vitro fermentation in bacterial communities derived from humans. Anaerobe 2014; 28:68-77. [DOI: 10.1016/j.anaerobe.2014.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 03/27/2014] [Accepted: 05/19/2014] [Indexed: 12/26/2022]
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Wesolowska-Andersen A, Bahl MI, Carvalho V, Kristiansen K, Sicheritz-Pontén T, Gupta R, Licht TR. Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome 2014; 2:19. [PMID: 24949196 PMCID: PMC4063427 DOI: 10.1186/2049-2618-2-19] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/25/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND In recent years, studies on the human intestinal microbiota have attracted tremendous attention. Application of next generation sequencing for mapping of bacterial phylogeny and function has opened new doors to this field of research. However, little attention has been given to the effects of choice of methodology on the output resulting from such studies. RESULTS IN THIS STUDY WE CONDUCTED A SYSTEMATIC COMPARISON OF THE DNA EXTRACTION METHODS USED BY THE TWO MAJOR COLLABORATIVE EFFORTS: The European MetaHIT and the American Human Microbiome Project (HMP). Additionally, effects of homogenizing the samples before extraction were addressed. We observed significant differences in distribution of bacterial taxa depending on the method. While eukaryotic DNA was most efficiently extracted by the MetaHIT protocol, DNA from bacteria within the Bacteroidetes phylum was most efficiently extracted by the HMP protocol. CONCLUSIONS Whereas it is comforting that the inter-individual variation clearly exceeded the variation resulting from choice of extraction method, our data highlight the challenge of comparing data across studies applying different methodologies.
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Affiliation(s)
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Søborg DK-2860, Denmark
| | - Vera Carvalho
- National Food Institute, Technical University of Denmark, Søborg DK-2860, Denmark
| | - Karsten Kristiansen
- Department of Biology, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence analysis, Technical University of Denmark, Lyngby DK-2800, Denmark
| | - Ramneek Gupta
- Center for Biological Sequence analysis, Technical University of Denmark, Lyngby DK-2800, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Søborg DK-2860, Denmark
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44
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Holch A, Ingmer H, Licht TR, Gram L. Listeria monocytogenes strains encoding premature stop codons in inlA invade mice and guinea pig fetuses in orally dosed dams. J Med Microbiol 2013; 62:1799-1806. [DOI: 10.1099/jmm.0.057505-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Listeria monocytogenes is an important food-borne bacterial pathogen and listeriosis can result in abortions in pregnant women. The bacterium can colonize food-processing environments, where specific molecular subtypes can persist for years. The purpose of this study was to determine the virulence potential of a group of food-processing persistent L. monocytogenes strains encoding a premature stop codon in inlA (encoding internalin A) by using two orally dosed models, pregnant mice and pregnant guinea pigs. A food-processing persistent strain of L. monocytogenes invaded placentas (n = 58; 10 % positive) and fetuses (3 % positive) of pregnant mice (n = 9 animals per strain), similar to a genetically manipulated murinized strain, EGD-e InlA
m*
(n = 61; 3 and 2 %, respectively). In pregnant guinea pigs (n = 9 animals per bacterial strain), a maternofetal strain (from a human fetal clinical fatal case) was isolated from 34 % of placenta samples (n = 50), whereas both food-processing persistent strains were found in 5 % of placenta samples (n = 36 or 37). One of the food-processing persistent strains, N53-1, was found in up to 8 % of guinea pig fetal liver and brain samples, whereas the maternofetal control was found in 6 % of fetal tissue samples. As the food-processing persistent strains carry a premature stop codon in inlA but are invasive in orally dosed pregnant mice and guinea pigs, we hypothesize that listerial crossing of the placental barrier can occur by a mechanism that is independent of an interaction between E-cadherin and InlA.
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Affiliation(s)
- Anne Holch
- National Food Institute, Technical University of Denmark, Søltofts Plads, Bldg 221, DK-2800 Kongens Lyngby, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860 Søborg, Denmark
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Bldg 221, DK-2800 Kongens Lyngby, Denmark
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45
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Christensen EG, Licht TR, Kristensen M, Bahl MI. Bifidogenic effect of whole-grain wheat during a 12-week energy-restricted dietary intervention in postmenopausal women. Eur J Clin Nutr 2013; 67:1316-21. [DOI: 10.1038/ejcn.2013.207] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/27/2013] [Accepted: 09/14/2013] [Indexed: 12/13/2022]
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Vigsnæs LK, Brynskov J, Steenholdt C, Wilcks A, Licht TR. Gram-negative bacteria account for main differences between faecal microbiota from patients with ulcerative colitis and healthy controls. Benef Microbes 2013; 3:287-97. [PMID: 22968374 DOI: 10.3920/bm2012.0018] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Detailed knowledge about the composition of the intestinal microbiota may be critical to unravel the pathogenesis of ulcerative colitis (UC), a human chronic inflammatory bowel disease, since the intestinal microbes are expected to influence some of the key mechanisms involved in the inflammatory process of the gut mucosa. The aim of this study was to investigate the faecal microbiota in patients either with UC in remission (n=6) or with active disease (n=6), and in healthy controls (n=6). The composition of Gram-negative bacteria and Gram-positive bacteria was examined. Antigenic structures of Gram-negative bacteria such as lipopolysaccharides have been related to the inflammatory responses and pathogenesis of inflammatory bowel disease. Dice cluster analysis and principal component analysis of faecal microbiota profiles obtained by denaturing gradient gel electrophoresis and quantitative PCR, respectively, revealed that the composition of faecal bacteria from UC patients with active disease differed from the healthy controls and that this difference should be ascribed to Gram-negative bacteria. The analysis did not show any clear grouping of UC patients in remission. Even with the relatively low number of subjects in each group, we were able to detect a statistically significant underrepresentation of Lactobacillus spp. and Akkermansia muciniphila in UC patients with clinically active disease compared to the healthy controls. In line with previous communications, we have shown that the microbiota in UC patients with active disease differ from that in healthy controls. Our findings indicate that alterations in the composition of the Gram-negative bacterial population, as well as reduced numbers of lactobacilli and A. muciniphila may play a role in UC.
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Affiliation(s)
- L K Vigsnæs
- Division of Food Microbiology, National Food Institute, Technical University of Denmark, Søborg, Denmark.
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47
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Vigsnaes LK, van den Abbeele P, Sulek K, Frandsen HL, Steenholdt C, Brynskov J, Vermeiren J, van de Wiele T, Licht TR. Microbiotas from UC patients display altered metabolism and reduced ability of LAB to colonize mucus. Sci Rep 2013; 3:1110. [PMID: 23346367 PMCID: PMC3552269 DOI: 10.1038/srep01110] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [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: 11/09/2012] [Accepted: 12/06/2012] [Indexed: 12/17/2022] Open
Abstract
We compared fecal microbial communities derived either from Ulcerative Colitis (UC) patients in remission (n = 4) or in relapse (n = 4), or from healthy subjects (n = 4). These communities were used for inoculation of a dynamic in vitro gut model, which contained integrated mucin-covered microcosms. We found that the microbiota of the ‘mucus’ largely differed from that of the ‘lumen’. This was partly due to decreased mucus-associated populations of lactic acid producing bacterial populations (LAB), as LAB originating from UC patients had a significantly decreased capacity to colonize the mucin-covered microcosms as compared to those originating from healthy subjects. We found significant differences between the metabolomes of UC patients in relapse and remission, respectively, while the metabolome of patients in remission resembled that of healthy subjects. These novel findings constitute an important contribution to the understanding of the complex etiology of UC.
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Hildebrand F, Ebersbach T, Nielsen HB, Li X, Sonne SB, Bertalan M, Dimitrov P, Madsen L, Qin J, Wang J, Raes J, Kristiansen K, Licht TR. A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). BMC Genomics 2012; 13:514. [PMID: 23020652 PMCID: PMC3472315 DOI: 10.1186/1471-2164-13-514] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [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: 06/22/2012] [Accepted: 09/24/2012] [Indexed: 01/08/2023] Open
Abstract
Background Guinea pig (Cavia porcellus) is an important model for human intestinal research. We have characterized the faecal microbiota of 60 guinea pigs using Illumina shotgun metagenomics, and used this data to compile a gene catalogue of its prevalent microbiota. Subsequently, we compared the guinea pig microbiome to existing human gut metagenome data from the MetaHIT project. Results We found that the bacterial richness obtained for human samples was lower than for guinea pig samples. The intestinal microbiotas of both species were dominated by the two phyla Bacteroidetes and Firmicutes, but at genus level, the majority of identified genera (320 of 376) were differently abundant in the two hosts. For example, the guinea pig contained considerably more of the mucin-degrading Akkermansia, as well as of the methanogenic archaea Methanobrevibacter than found in humans. Most microbiome functional categories were less abundant in guinea pigs than in humans. Exceptions included functional categories possibly reflecting dehydration/rehydration stress in the guinea pig intestine. Finally, we showed that microbiological databases have serious anthropocentric biases, which impacts model organism research. Conclusions The results lay the foundation for future gastrointestinal research applying guinea pigs as models for humans.
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Affiliation(s)
- Falk Hildebrand
- National Food Institute, Technical University of Denmark, Denmark
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49
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Bahl MI, Bergström A, Licht TR. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett 2012; 329:193-7. [PMID: 22325006 DOI: 10.1111/j.1574-6968.2012.02523.x] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 12/21/2011] [Accepted: 02/03/2012] [Indexed: 12/11/2022] Open
Abstract
Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study, DNA was extracted either directly or following freeze storage of three homogenized human fecal samples using three different extraction methods. No consistent differences were observed in DNA yields between extractions on fresh and frozen samples; however, differences were observed between extraction methods. Quantitative PCR analysis was subsequently performed on all DNA samples using six different primer pairs targeting 16S rRNA genes of significant bacterial groups, and the community composition was evaluated by comparing specific ratios of the calculated abundances. In seven of nine cases, the Firmicutes to Bacteroidetes 16S rRNA gene ratio was significantly higher in fecal samples that had been frozen compared to identical samples that had not. This effect was further supported by qPCR analysis of bacterial groups within these two phyla. The results demonstrate that storage conditions of fecal samples may adversely affect the determined Firmicutes to Bacteroidetes ratio, which is a frequently used biomarker in gut microbiology.
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Affiliation(s)
- Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Søborg, Denmark
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50
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Fink LN, Metzdorff SB, Zeuthen LH, Nellemann C, Kristensen MB, Licht TR, Frøkiær H. Establishment of tolerance to commensal bacteria requires a complex microbiota and is accompanied by decreased intestinal chemokine expression. Am J Physiol Gastrointest Liver Physiol 2012; 302:G55-65. [PMID: 21960522 DOI: 10.1152/ajpgi.00428.2010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Intricate regulation of tolerance to the intestinal commensal microbiota acquired at birth is critical. We hypothesized that epithelial cell tolerance toward early gram-positive and gram-negative colonizing bacteria is established immediately after birth, as has previously been shown for endotoxin. Gene expression in the intestine of mouse pups born to dams that were either colonized with a conventional microbiota or monocolonized (Lactobacillus acidophilus or Eschericia coli) or germ free was examined on day 1 and day 6 after birth. Intestinal epithelial cells from all groups of pups were stimulated ex vivo with L. acidophilus and E. coli to assess tolerance establishment. Intestine from pups exposed to a conventional microbiota displayed lower expression of Ccl2, Ccl3, Cxcl1, Cxcl2, and Tslp than germ-free mice, whereas genes encoding proteins in Toll-like receptor signaling pathways and cytokines were upregulated. When comparing pups on day 1 and day 6 after birth, a specific change in gene expression pattern was evident in all groups of mice. Tolerance to ex vivo stimulation with E. coli was only established in conventional animals. Colonization of the intestine was reflected in the spleen displaying downregulation of Cxcl2 compared with germ-free animals on day 1 after birth. Colonization reduced the expression of genes involved in antigen presentation in the intestine-draining mesenteric lymph nodes, but not in the popliteal lymph nodes, as evidenced by gene expression on day 23 after birth. We propose that microbial detection systems in the intestine are upregulated by colonization with a diverse microbiota, whereas expression of proinflammatory chemokines is reduced to avoid excess recruitment of immune cells to the maturing intestine.
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Affiliation(s)
- L N Fink
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
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