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Warmbrunn MV, Boulund U, Aron-Wisnewsky J, de Goffau MC, Abeka RE, Davids M, Bresser LRF, Levin E, Clement K, Galenkamp H, Ferwerda B, van den Born BJJH, Kurilshikov A, Fu J, Zwinderman AH, Soeters MR, van Raalte DH, Herrema H, Groen AK, Nieuwdorp M. Networks of gut bacteria relate to cardiovascular disease in a multi-ethnic population: the HELIUS study. Cardiovasc Res 2024; 120:372-384. [PMID: 38289866 PMCID: PMC10981523 DOI: 10.1093/cvr/cvae018] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/25/2023] [Accepted: 11/30/2023] [Indexed: 02/01/2024] Open
Abstract
AIMS Gut microbiota have been linked to blood lipid levels and cardiovascular diseases (CVDs). The composition and abundance of gut microbiota trophic networks differ between ethnicities. We aim to evaluate the relationship between gut microbiotal trophic networks and CVD phenotypes. METHODS AND RESULTS We included cross-sectional data from 3860 individuals without CVD history from 6 ethnicities living in the Amsterdam region participating in the prospective Healthy Life in Urban Setting (HELIUS) study. Genetic variants were genotyped, faecal gut microbiota were profiled, and blood and anthropometric parameters were measured. A machine learning approach was used to assess the relationship between CVD risk (Framingham score) and gut microbiota stratified by ethnicity. Potential causal relationships between gut microbiota composition and CVD were inferred by performing two-sample Mendelian randomization with hard CVD events from the Pan-UK Biobank and microbiome genome-wide association studies summary data from a subset of the HELIUS cohort (n = 4117). Microbial taxa identified to be associated with CVD by machine learning and Mendelian randomization were often ethnic-specific, but some concordance across ethnicities was found. The microbes Akkermansia muciniphila and Ruminococcaceae UCG-002 were protective against ischaemic heart disease in African-Surinamese and Moroccans, respectively. We identified a strong inverse association between blood lipids, CVD risk, and the combined abundance of the correlated microbes Christensenellaceae-Methanobrevibacter-Ruminococcaceae (CMR). The CMR cluster was also identified in two independent cohorts and the association with triglycerides was replicated. CONCLUSION Certain gut microbes can have a potentially causal relationship with CVD events, with possible ethnic-specific effects. We identified a trophic network centred around Christensenellaceae, Methanobrevibacter, and various Ruminococcaceae, frequently lacking in South-Asian Surinamese, to be protective against CVD risk and associated with low triglyceride levels.
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Affiliation(s)
- Moritz V Warmbrunn
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ulrika Boulund
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Judith Aron-Wisnewsky
- Nutrition and Obesities: Systemic Approaches Research Unit (Nutriomics), Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Nutrition Department, Assistantea Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Centres de Recherche en Nutrition Humaine, Paris, Ile de France, France
| | - Marcus C de Goffau
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- HorAIzon BV, 2625 GZ Delft, The Netherlands
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Meibergdreef 69, 1105 BK Amsterdam, The Netherlands
| | - Rosamel E Abeka
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mark Davids
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Lucas R F Bresser
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- HorAIzon BV, 2625 GZ Delft, The Netherlands
| | - Evgeni Levin
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- HorAIzon BV, 2625 GZ Delft, The Netherlands
| | - Karine Clement
- Nutrition and Obesities: Systemic Approaches Research Unit (Nutriomics), Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Nutrition Department, Assistantea Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Centres de Recherche en Nutrition Humaine, Paris, Ile de France, France
| | - Henrike Galenkamp
- Department of Public Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Bart Ferwerda
- Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Bert-Jan J H van den Born
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Alexander Kurilshikov
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Aeilko H Zwinderman
- Department of Public Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Maarten R Soeters
- Department of Endocrinology and Metabolism, Internal Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Daniel H van Raalte
- Department of Internal Medicine, Amsterdam University Medical Center (UMC), Vrije Universiteit (VU) University Medical Center, Amsterdam, The Netherlands
| | - Hilde Herrema
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Albert K Groen
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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Gaccioli F, Stephens K, Sovio U, Jessop F, Wong HS, Lager S, Cook E, de Goffau MC, Le Doare K, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS. Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants. Nat Microbiol 2023; 8:2338-2348. [PMID: 38030897 PMCID: PMC10686823 DOI: 10.1038/s41564-023-01528-2] [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: 06/23/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Streptococcus agalactiae (Group B Streptococcus; GBS) is a common cause of sepsis in neonates. Previous work detected GBS DNA in the placenta in ~5% of women before the onset of labour, but the clinical significance of this finding is unknown. Here we re-analysed this dataset as a case control study of neonatal unit (NNU) admission. Of 436 infants born at term (≥37 weeks of gestation), 7/30 with placental GBS and 34/406 without placental GBS were admitted to the NNU (odds ratio (OR) 3.3, 95% confidence interval (CI) 1.3-7.8). We then performed a validation study using non-overlapping subjects from the same cohort. This included a further 239 cases of term NNU admission and 686 term controls: 16/36 with placental GBS and 223/889 without GBS were admitted to the NNU (OR 2.4, 95% CI 1.2-4.6). Of the 36 infants with placental GBS, 10 were admitted to the NNU with evidence of probable but culture-negative sepsis (OR 4.8, 95% CI 2.2-10.3), 2 were admitted with proven GBS sepsis (OR 66.6, 95% CI 7.3-963.7), 6 were admitted and had chorioamnionitis (inflammation of the foetal membranes) (OR 5.3, 95% CI 2.0-13.4), and 5 were admitted and had funisitis (inflammation of the umbilical cord) (OR 6.7, 95% CI 12.5-17.7). Foetal cytokine storm (two or more pro-inflammatory cytokines >10 times median control levels in umbilical cord blood) was present in 36% of infants with placental GBS DNA and 4% of cases where the placenta was negative (OR 14.2, 95% CI 3.6-60.8). Overall, ~1 in 200 term births had GBS detected in the placenta, which was associated with infant NNU admission and morbidity.
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Affiliation(s)
- Francesca Gaccioli
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Katie Stephens
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Flora Jessop
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Hilary S Wong
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Susanne Lager
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Emma Cook
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Marcus C de Goffau
- Wellcome Trust Sanger Institute, Hinxton, UK
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Kirsty Le Doare
- Centre for Neonatal and Paediatric Infectious Diseases Research, St George's University of London, London, UK
| | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK.
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK.
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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Aggarwal D, Rajan D, Bellis KL, Betteridge E, Brennan J, de Sousa C, Parkhill J, Peacock SJ, de Goffau MC, Wagner J, Harrison EM. Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination. Microb Genom 2023; 9:001115. [PMID: 37843887 PMCID: PMC10634443 DOI: 10.1099/mgen.0.001115] [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: 08/01/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
16S rRNA gene sequencing is widely used to characterize human and environmental microbiomes. Sequencing at scale facilitates better powered studies but is limited by cost and time. We identified two areas in our 16S rRNA gene library preparation protocol where modifications could provide efficiency gains, including (1) pooling of multiple PCR amplifications per sample to reduce PCR drift and (2) manual preparation of mastermix to reduce liquid handling. Using nasal samples from healthy human participants and a serially diluted mock microbial community, we compared alpha and beta diversity, and compositional abundance where the PCR amplification was conducted in triplicate, duplicate or as a single reaction, and where manually prepared or premixed mastermix was used. One hundred and fifty-eight 16S rRNA gene sequencing libraries were prepared, including a replicate experiment. Comparing PCR pooling strategies, we found no significant difference in high-quality read counts and alpha diversity, and beta diversity by Bray-Curtis index clustered by replicate on principal coordinate analysis (PCoA) and non-metric dimensional scaling (NMDS) analysis. Choice of mastermix had no significant impact on high-quality read and alpha diversity, and beta diversity by Bray-Curtis index clustered by replicate in PCoA and NMDS analysis. Importantly, we observed contamination and variability of rare species (<0.01 %) across replicate experiments; the majority of contaminants were accounted for by removal of species present at <0.1 %, or were linked to reagents (including a primer stock). We demonstrate no requirement for pooling of PCR amplifications or manual preparation of PCR mastermix, resulting in a more efficient 16S rRNA gene PCR protocol.
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Affiliation(s)
- Dinesh Aggarwal
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Diana Rajan
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Katherine L. Bellis
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Joe Brennan
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Catarina de Sousa
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - CARRIAGE Study Team‡
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Tytgat Institute for Liver and Intestinal Research, University of Amsterdam, Amsterdam, Netherlands
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Marcus C. de Goffau
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Tytgat Institute for Liver and Intestinal Research, University of Amsterdam, Amsterdam, Netherlands
| | - Josef Wagner
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ewan M. Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
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van der Vossen EWJ, Davids M, Bresser LRF, Galenkamp H, van den Born BJH, Zwinderman AH, Levin E, Nieuwdorp M, de Goffau MC. Gut microbiome transitions across generations in different ethnicities in an urban setting-the HELIUS study. Microbiome 2023; 11:99. [PMID: 37158898 PMCID: PMC10165778 DOI: 10.1186/s40168-023-01488-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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/03/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND During the course of history, various important lifestyle changes have caused profound transitions of the gut microbiome. These include the introduction of agriculture and animal husbandry, a shift from a nomadic to a more sedentary lifestyle, and recently increased levels of urbanization and a transition towards a more Western lifestyle. The latter is linked with shifts in the gut microbiome that have a reduced fermentative capability and which are commonly associated with diseases of affluence. In this study, in which 5193 subjects are included, we investigated the direction of microbiome shifts that occur in various ethnicities living in Amsterdam by comparing 1st and 2nd generation participants. We furthermore validated part of these findings with a cohort of subjects that moved from rural Thailand to the USA. RESULTS The abundance of the Prevotella cluster, which includes P. copri and the P. stercorea trophic network, diminished in the 2nd generation Moroccans and Turks but also in younger Dutch, whilst the Western-associated Bacteroides/Blautia/Bifidobacterium (BBB) cluster, which has an inverse correlation with α-diversity, increased. At the same time, the Christensenellaceae/Methanobrevibacter/Oscillibacter trophic network, which is positively associated with α-diversity and a healthy BMI, decreased in younger Turks and Dutch. Large compositional shifts were not observed in South-Asian and African Surinamese, in whom the BBB cluster is already dominant in the 1st generation, but ASV-level shifts towards certain species, associated amongst others with obesity, were observed. CONCLUSION The Moroccan and Turkish populations, but also the Dutch population are transitioning towards a less complex and fermentative less capable configuration of the gut microbiota, which includes a higher abundance of the Western-associated BBB cluster. The Surinamese, whom have the highest prevalence of diabetes and other diseases of affluence, are already dominated by the BBB cluster. Given the continuous increase in diseases of affluence, this devolution towards low-diversity and fermentatively less capable gut microbiome compositions in urban environments is a worrying development. Video Abstract.
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Affiliation(s)
- Eduard W J van der Vossen
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Mark Davids
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Lucas R F Bresser
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Horaizon BV, Marshalllaan 2, 2625 GZ, Delft, The Netherlands
| | - Henrike Galenkamp
- Department of Public and Occupational Health, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Bert-Jan H van den Born
- Department of Public and Occupational Health, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Department of Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Evgeni Levin
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Horaizon BV, Marshalllaan 2, 2625 GZ, Delft, The Netherlands
| | - Max Nieuwdorp
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
- Department of Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
| | - Marcus C de Goffau
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
- Sanger Institute, Cambridge, UK.
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Wijdeveld M, van Olst N, van der Vossen EWJ, de Brauw M, Acherman YIZ, de Goffau MC, Gerdes VEA, Nieuwdorp M. Identifying Gut Microbiota associated with Gastrointestinal Symptoms upon Roux-en-Y Gastric Bypass. Obes Surg 2023:10.1007/s11695-023-06610-6. [PMID: 37093508 DOI: 10.1007/s11695-023-06610-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
PURPOSE Roux-en-Y gastric bypasses (RYGB) are frequently accompanied by long-term gastrointestinal (GI) symptoms. Direct mechanistic insight into the causation of these symptoms is lacking, but changes in the intestinal microbiome have been proposed to play a role. With this study, we aimed to investigate whether a microbial predisposition exists before RYGB which is associated with GI symptoms during follow-up and to evaluate which microbial groups are involved. MATERIALS AND METHODS In total, 67 RYGB patients were included. Shotgun metagenomic sequencing was performed on fecal samples obtained just before and 1 year after surgery. To assess GI symptoms, patients filled out Gastrointestinal Quality of Life Index (GIQLI) questionnaires and were divided into groups based on their total GIQLI score and change in score (postsurgery versus baseline). Extremely randomized tree predictor models were used to identify the most distinctive microbial species associated with postoperative GI symptoms. RESULTS Beta diversity differed significantly between baseline and 1-year post-surgery samples, with the post-surgery microbiome resembling a more dysbiotic profile. The most predictive species regarding total GIQLI (AUC 0.77) or delta GIQLI score (AUC 0.83) were identified. Many of these species are known butyrate producers or species known to support them and/or species with anti-inflammatory properties, including Coprococcus eutactus, Faecalibacterium prausnitzii, and Ruminococcus callidus. CONCLUSION Beneficial commensal gut microbiota related to a high GI score were associated to adequate intestinal fermentative capacity, suggesting these species might have protective properties against postoperative GI malfunctioning.
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Affiliation(s)
- Madelief Wijdeveld
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, Room D3-211, 1105, AZ, Amsterdam, The Netherlands.
| | - Nienke van Olst
- Department of Bariatric Surgery, Spaarne Gasthuis, Spaarnepoort 1, 2134, Hoofddorp, The Netherlands
| | - Eduard W J van der Vossen
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, Room D3-211, 1105, AZ, Amsterdam, The Netherlands
| | - Maurits de Brauw
- Department of Bariatric Surgery, Spaarne Gasthuis, Spaarnepoort 1, 2134, Hoofddorp, The Netherlands
| | - Yair I Z Acherman
- Department of Bariatric Surgery, Spaarne Gasthuis, Spaarnepoort 1, 2134, Hoofddorp, The Netherlands
| | - Marcus C de Goffau
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, Room D3-211, 1105, AZ, Amsterdam, The Netherlands
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Meibergdreef 69, 1105, BK, Amsterdam, The Netherlands
- Sanger Institute, Saffron Walden, Cambridge, CB10 1RQ, UK
| | - Victor E A Gerdes
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, Room D3-211, 1105, AZ, Amsterdam, The Netherlands
- Department of Bariatric Surgery, Spaarne Gasthuis, Spaarnepoort 1, 2134, Hoofddorp, The Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, Room D3-211, 1105, AZ, Amsterdam, The Netherlands
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6
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Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 2023; 613:639-649. [PMID: 36697862 DOI: 10.1038/s41586-022-05546-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/09/2022] [Indexed: 01/26/2023]
Abstract
Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.
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Affiliation(s)
- Katherine M Kennedy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Marcus C de Goffau
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- Wellcome Sanger Institute, Cambridge, UK
| | - Maria Elisa Perez-Muñoz
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Marie-Claire Arrieta
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thorsten Braun
- Department of Obstetrics and Experimental Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frederic D Bushman
- Department of Microbiology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joel Dore
- Université Paris-Saclay, INRAE, MetaGenoPolis, AgroParisTech, MICALIS, Jouy-en-Josas, France
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, USA
- UC Davis Genome Center, University of California, Davis, Davis, CA, USA
| | - Michal A Elovitz
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephanie C Ganal-Vonarburg
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michael G Gänzle
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, MA, USA
- Department of Medicine and Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lindsay J Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Chair of Intestinal Microbiome, ZIEL-Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Curtis Huttenhower
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liza Konnikova
- Departments of Pediatrics and Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Andrew J Macpherson
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ruth C Massey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Hannover Braunschweig site, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Trevor D Lawley
- Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Liam O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jeroen Raes
- VIB Center for Microbiology, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Eran Segal
- Weizmann Institute of Science, Rehovot, Israel
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
- European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Deborah M Sloboda
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, Ontario, Canada
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Harry Sokol
- Gastroenterology Department, AP-HP, Saint Antoine Hospital, Centre de Recherche Saint-Antoine, CRSA, INSERM and Sorbonne Université, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Gerald W Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alan W Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Moran Yassour
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jens Walter
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
- Department of Medicine, University College Cork, Cork, Ireland.
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7
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van der Vossen EWJ, de Goffau MC, Levin E, Nieuwdorp M. Recent insights into the role of microbiome in the pathogenesis of obesity. Therap Adv Gastroenterol 2022; 15:17562848221115320. [PMID: 35967920 PMCID: PMC9373125 DOI: 10.1177/17562848221115320] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Obesity is a risk factor for many chronic diseases and its rising prevalence the last couple of decades is a healthcare concern in many countries. Obesity is a multifactorial problem that is not only limited in its causation by diet and lack of exercise. Genetics but also environmental factors such as the gut microbiome should similarly be taken into account. A plethora of articles have been published, that from various different angles, attempt to disentangle the complex interaction between gut microbiota and obesity. Examples range from the effect of the gut microbiota on the host immune system to the pathophysiological pathways in which microbial-derived metabolites affect obesity. Various discordant gut microbiota findings are a result of this complexity. In this review, in addition to summarizing the classical role of the gut microbiome in the pathogenesis of obesity, we attempt to view both the healthy and obesogenic effects of the gut microbiota as a consequence of the presence or absence of collective guilds/trophic networks. Lastly, we propose avenues and strategies for the future of gut microbiome research concerning obesity.
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Affiliation(s)
- Eduard W. J. van der Vossen
- Department of Experimental Vascular Medicine,
Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The
Netherlands
| | - Marcus C. de Goffau
- Department of Experimental Vascular Medicine,
Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The
Netherlands
| | - Evgeni Levin
- Department of Experimental Vascular Medicine,
Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The
Netherlands,Horaizon BV, Delft, The Netherlands
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8
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Bourgonje AR, Roo-Brand G, Lisotto P, Sadaghian Sadabad M, Reitsema RD, de Goffau MC, Faber KN, Dijkstra G, Harmsen HJM. Patients With Inflammatory Bowel Disease Show IgG Immune Responses Towards Specific Intestinal Bacterial Genera. Front Immunol 2022; 13:842911. [PMID: 35693832 PMCID: PMC9174456 DOI: 10.3389/fimmu.2022.842911] [Citation(s) in RCA: 10] [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: 12/24/2021] [Accepted: 04/25/2022] [Indexed: 12/26/2022] Open
Abstract
Introduction Inflammatory bowel disease (IBD) is characterized by a disturbed gut microbiota composition. Patients with IBD have both elevated mucosal and serum levels of IgG-antibodies directed against bacterial antigens, including flagellins. In this study, we aimed to determine to which intestinal bacteria the humoral immune response is directed to in patients with IBD. Methods Fecal and serum samples were collected from patients with IBD (n=55) and age- and sex-matched healthy controls (n=55). Fecal samples were incubated with autologous serum and IgG-coated fractions were isolated by magnetic-activated cell sorting (MACS) and its efficiency was assessed by flow cytometry. The bacterial composition of both untreated and IgG-coated fecal samples was determined by 16S rRNA-gene Illumina sequencing. Results IgG-coated fecal samples were characterized by significantly lower microbial diversity compared to the fecal microbiome. Both in patients with IBD and controls, serum IgG responses were primarily directed to Streptococcus, Lactobacillus, Lactococcus, Enterococcus, Veillonella and Enterobacteriaceae, as well as against specific Lachnospiraceae bacteria, including Coprococcus and Dorea (all P<0.001), and to Ruminococcus gnavus-like bacteria (P<0.05). In contrast, serological IgG responses against typical commensal, anaerobic and colonic microbial species were rather low, e.g. to the Lachnospiraceae members Roseburia and Blautia, to Faecalibacterium, as well as to Bacteroides. Patients with IBD showed more IgG-coating of Streptococcus, Lactobacillus, and Lactococcus bacteria compared to healthy controls (all P<0.05). No differences in IgG-coated bacterial fractions were observed between Crohn's disease and ulcerative colitis, between active or non-active disease, nor between different disease locations. Conclusion The IgG immune response is specifically targeted at distinct intestinal bacterial genera that are typically associated with the small intestinal microbiota, whereas responses against more colonic-type commensals are lower, which was particularly the case for patients with IBD. These findings may be indicative of a strong immunological exposure to potentially pathogenic intestinal bacteria in concordance with relative immune tolerance against commensal bacteria.
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Affiliation(s)
- Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Geesje Roo-Brand
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Paola Lisotto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mehdi Sadaghian Sadabad
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Rosanne D Reitsema
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Marcus C de Goffau
- Department of Vascular Medicine, University of Amsterdam, Amsterdam University Medical Center, Amsterdam, Netherlands.,Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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9
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van der Vossen EWJ, Bastos D, Stols-Gonçalves D, de Goffau MC, Davids M, Pereira JPB, Li Yim AYF, Henneman P, Netea MG, de Vos WM, de Jonge W, Groen AK, Nieuwdorp M, Levin E. Effects of fecal microbiota transplant on DNA methylation in subjects with metabolic syndrome. Gut Microbes 2022; 13:1993513. [PMID: 34747338 PMCID: PMC8583152 DOI: 10.1080/19490976.2021.1993513] [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
Accumulating evidence shows that microbes with their theater of activity residing within the human intestinal tract (i.e., the gut microbiome) influence host metabolism. Some of the strongest results come from recent fecal microbial transplant (FMT) studies that relate changes in intestinal microbiota to various markers of metabolism as well as the pathophysiology of insulin resistance. Despite these developments, there is still a limited understanding of the multitude of effects associated with FMT on the general physiology of the host, beyond changes in gut microbiome composition. We examined the effect of either allogenic (lean donor) or autologous FMTs on the gut microbiome, plasma metabolome, and epigenomic (DNA methylation) reprogramming in peripheral blood mononuclear cells in individuals with metabolic syndrome measured at baseline (pre-FMT) and after 6 weeks (post-FMT). Insulin sensitivity was determined with a stable isotope-based 2 step hyperinsulinemic clamp and multivariate machine learning methodology was used to uncover discriminative microbes, metabolites, and DNA methylation loci. A larger gut microbiota shift was associated with an allogenic than with autologous FMT. Furthemore, the data results of the the allogenic FMT group data indicates that the introduction of new species can potentially modulate the plasma metabolome and (as a result) the epigenome. Most notably, the introduction of Prevotella ASVs directly correlated with methylation of AFAP1, a gene involved in mitochondrial function, insulin sensitivity, and peripheral insulin resistance (Rd, rate of glucose disappearance). FMT was found to have notable effects on the gut microbiome but also on the host plasma metabolome and the epigenome of immune cells providing new avenues of inquiry in the context of metabolic syndrome treatment for the manipulation of host physiology to achieve improved insulin sensitivity.
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Affiliation(s)
- Eduard W. J. van der Vossen
- Department of Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Diogo Bastos
- Department of Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands,Horaizon BV, Delft, The Netherlands
| | - Daniela Stols-Gonçalves
- Department of Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Marcus C. de Goffau
- Department of Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands,Wellcome Sanger Institute, Cambridge, UK
| | - Mark Davids
- Department of Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Joao P. B. Pereira
- Department of Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands,Horaizon BV, Delft, The Netherlands
| | - Andrew Y. F. Li Yim
- Department of Genome Diagnostics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Genome Diagnostics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mihai G. Netea
- Department of Experimental Internal Medicine, Radboud University, Nijmegen, The Netherlands,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (Limes), University of Bonn, Bonn, Germany
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Wouter de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Albert K. Groen
- Department of Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands,CONTACT Max Nieuwdorp
| | - Evgeni Levin
- Department of Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands,Horaizon BV, Delft, The Netherlands,Evgeni Levin Department of Vascular Medicine, Amsterdam University Medical Center, Meibergdreef 9, Room G1-143, Amsterdam1105 AZ, The Netherlands
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10
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de Goffau MC, Jallow AT, Sanyang C, Prentice AM, Meagher N, Price DJ, Revill PA, Parkhill J, Pereira DIA, Wagner J. Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network. Nat Microbiol 2022; 7:132-144. [PMID: 34972822 PMCID: PMC8727306 DOI: 10.1038/s41564-021-01023-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 02/07/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023]
Abstract
Distinct bacterial trophic networks exist in the gut microbiota of individuals in industrialized and non-industrialized countries. In particular, non-industrialized gut microbiomes tend to be enriched with Prevotella species. To study the development of these Prevotella-rich compositions, we investigated the gut microbiota of children aged between 7 and 37 months living in rural Gambia (616 children, 1,389 stool samples, stratified by 3-month age groups). These infants, who typically eat a high-fibre, low-protein diet, were part of a double-blind, randomized iron intervention trial (NCT02941081) and here we report the secondary outcome. We found that child age was the largest discriminating factor between samples and that anthropometric indices (collection time points, season, geographic collection site, and iron supplementation) did not significantly influence the gut microbiome. Prevotella copri, Faecalibacterium prausnitzii and Prevotella stercorea were, on average, the most abundant species in these 1,389 samples (35%, 11% and 7%, respectively). Distinct bacterial trophic network clusters were identified, centred around either P. stercorea or F. prausnitzii and were found to develop steadily with age, whereas P. copri, independently of other species, rapidly became dominant after weaning. This dataset, set within a critical gut microbial developmental time frame, provides insights into the development of Prevotella-rich gut microbiomes, which are typically understudied and are underrepresented in western populations.
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Affiliation(s)
- Marcus C de Goffau
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Amadou T Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Chilel Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Niamh Meagher
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Melbourne, Australia
| | - David J Price
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Melbourne, Australia
| | - Peter A Revill
- Victorian Infectious Disease Reference Laboratory, the Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Dora I A Pereira
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Josef Wagner
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Victorian Infectious Disease Reference Laboratory, the Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia.
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11
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Heida FH, Kooi EMW, Wagner J, Nguyen TY, Hulscher JBF, van Zoonen AGJF, Bos AF, Harmsen HJM, de Goffau MC. Weight shapes the intestinal microbiome in preterm infants: results of a prospective observational study. BMC Microbiol 2021; 21:219. [PMID: 34289818 PMCID: PMC8293572 DOI: 10.1186/s12866-021-02279-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 02/21/2021] [Accepted: 06/28/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The intestinal microbiome in preterm infants differs markedly from term infants. It is unclear whether the microbiome develops over time according to infant specific factors. METHODS We analysed (clinical) metadata - to identify the main factors influencing the microbiome composition development - and the first meconium and faecal samples til the 4th week via 16 S rRNA amplican sequencing. RESULTS We included 41 infants (gestational age 25-30 weeks; birth weight 430-990 g. Birth via Caesarean section (CS) was associated with placental insufficiency during pregnancy and lower BW. In meconium samples and in samples from weeks 2 and 3 the abundance of Escherichia and Bacteroides (maternal faecal representatives) were associated with vaginal delivery while Staphylococcus (skin microbiome representative) was associated with CS. Secondly, irrespective of the week of sampling or the mode of birth, a transition was observed as children children gradually increased in weight from a microbiome dominated by Staphylococcus (Bacilli) towards a microbiome dominated by Enterobacteriaceae (Gammaproteobacteria). CONCLUSIONS Our data show that the mode of delivery affects the meconium microbiome composition. They also suggest that the weight of the infant at the time of sampling is a better predictor for the stage of progression of the intestinal microbiome development/maturation than postconceptional age as it less confounded by various infant-specific factors.
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Affiliation(s)
- Fardou H Heida
- Division of Obstetrics & Gynecology, Isala Klinieken, University of Groningen, Zwolle, the Netherlands. .,Division of Pediatric Surgery Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
| | - Elisabeth M W Kooi
- Division of Neonatology Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Josef Wagner
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, Melbourne, Australia
| | - Thi-Yen Nguyen
- Division of Pediatric Surgery Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jan B F Hulscher
- Division of Pediatric Surgery Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Anne G J F van Zoonen
- Division of Pediatric Surgery Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Arend F Bos
- Division of Neonatology Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hermie J M Harmsen
- Division of Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marcus C de Goffau
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Parasites and Microboes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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12
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de Goffau MC, Charnock-Jones DS, Smith GCS, Parkhill J. Batch effects account for the main findings of an in utero human intestinal bacterial colonization study. Microbiome 2021; 9:6. [PMID: 33436099 PMCID: PMC7805227 DOI: 10.1186/s40168-020-00949-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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] [Indexed: 05/17/2023]
Abstract
A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their sequence data and identified a batch effect which violates the underlying assumptions of the bioinformatic method used for contamination removal. This batch effect resulted in Micrococcus not being identified as a contaminant in the original work and being falsely assigned to the fetal samples. We further provide evidence that the micrographs presented by Rackaityte et al. are unlikely to show Micrococci or other bacteria as the size of the particles shown exceeds that of related bacterial cells. Finally, phylogenetic analysis showed that the microbes cultured from the fetal samples differed significantly from those detected by sequencing. Overall, our findings show that the presence of Micrococcus in the fetal gut is not supported by the primary sequence data. Our findings underline important aspects of the nature of contamination for both sequencing and culture approaches in microbiome studies and the appropriate use of automated contamination identification tools.
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Affiliation(s)
- Marcus C de Goffau
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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13
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Bharucha T, Oeser C, Balloux F, Brown JR, Carbo EC, Charlett A, Chiu CY, Claas ECJ, de Goffau MC, de Vries JJC, Eloit M, Hopkins S, Huggett JF, MacCannell D, Morfopoulou S, Nath A, O'Sullivan DM, Reoma LB, Shaw LP, Sidorov I, Simner PJ, Van Tan L, Thomson EC, van Dorp L, Wilson MR, Breuer J, Field N. STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies. Lancet Infect Dis 2020; 20:e251-e260. [PMID: 32768390 PMCID: PMC7406238 DOI: 10.1016/s1473-3099(20)30199-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.
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Affiliation(s)
- Tehmina Bharucha
- Department of Biochemistry, University of Oxford, Oxford, UK; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos.
| | - Clarissa Oeser
- Centre for Molecular Epidemiology and Translational Research, University College London, London, UK
| | | | - Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children, London, UK
| | - Ellen C Carbo
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Andre Charlett
- Statistics, Modelling and Economics Department, Public Health England, London, UK
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Marcus C de Goffau
- Wellcome Sanger Institute, Hinxton, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jutte J C de Vries
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
| | - Susan Hopkins
- Healthcare-Associated Infection and Antimicrobial Resistance, Public Health England, London, UK; Infectious Diseases Unit, Royal Free Hospital, London, UK
| | - Jim F Huggett
- National Measurement Laboratory, LGC, Teddington, UK; School of Biosciences & Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | - Duncan MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, London, UK
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institutes of Health, Bethesda, MD, USA
| | | | - Lauren B Reoma
- Section of Infections of the Nervous System, National Institutes of Health, Bethesda, MD, USA
| | - Liam P Shaw
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Igor Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Le Van Tan
- Emerging Infections Group, Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Michael R Wilson
- Weill Institute for Neurosciences and Department of Neurology, University of California, San Francisco, CA, USA
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK; Great Ormond Street Hospital for Children, London, UK
| | - Nigel Field
- Centre for Molecular Epidemiology and Translational Research, University College London, London, UK
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14
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Gaccioli F, Lager S, de Goffau MC, Sovio U, Dopierala J, Gong S, Cook E, Sharkey A, Moffett A, Lee WK, Delles C, Venturini C, Breuer J, Parkhill J, Peacock SJ, Charnock-Jones DS, Smith GCS. Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia. Nat Microbiol 2020; 5:901-908. [PMID: 32367053 PMCID: PMC7610361 DOI: 10.1038/s41564-020-0711-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 03/18/2020] [Indexed: 12/16/2022]
Abstract
Pre-eclampsia (typically characterized by new-onset hypertension and proteinuria in the second half of pregnancy) represents a major determinant of the global burden of disease1,2. Its pathophysiology involves placental dysfunction, but the mechanism is unclear. Viral infection can cause organ dysfunction, but its role in placentally related disorders of human pregnancy is unknown3. We addressed this using RNA sequencing metagenomics4-6 of placental samples from normal and complicated pregnancies. Here, we show that human herpesvirus 6 (HHV-6, A or B) RNA was detected in 6.1% of cases of pre-eclampsia and 2.2% of other pregnancies. Fetal genotyping demonstrated that 70% of samples with HHV-6 RNA in the placenta exhibited inherited, chromosomally integrated HHV-6 (iciHHV-6). We genotyped 467 pre-eclampsia cases and 3,854 controls and found an excess of iciHHV-6 in the cases (odds ratio of 2.8, 95% confidence intervals of 1.4-5.6, P = 0.008). We validated this finding by comparing iciHHV-6 in a further 740 cases with controls from large-scale population studies (odds ratio of 2.5, 95% confidence intervals of 1.4-4.4, P = 0.0013). We conclude that iciHHV-6 results in the transcription of viral RNA in the human placenta and predisposes the mother to pre-eclampsia.
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Affiliation(s)
- Francesca Gaccioli
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Susanne Lager
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Marcus C de Goffau
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Justyna Dopierala
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Functional Genomics, GlaxoSmithKline Limited, Stevenage, UK
| | - Sungsam Gong
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Emma Cook
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Andrew Sharkey
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ashley Moffett
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wai Kwong Lee
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Cristina Venturini
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
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15
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Ruohtula T, de Goffau MC, Nieminen JK, Honkanen J, Siljander H, Hämäläinen AM, Peet A, Tillmann V, Ilonen J, Niemelä O, Welling GW, Knip M, Harmsen HJ, Vaarala O. Maturation of Gut Microbiota and Circulating Regulatory T Cells and Development of IgE Sensitization in Early Life. Front Immunol 2019; 10:2494. [PMID: 31749800 PMCID: PMC6842923 DOI: 10.3389/fimmu.2019.02494] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 05/21/2019] [Accepted: 10/07/2019] [Indexed: 12/19/2022] Open
Abstract
Recent studies suggest that the cross-talk between the gut microbiota and human immune system during the first year of life is an important regulator of the later development of atopic diseases. We explored the changes in the gut microbiota, blood regulatory T cells, and atopic sensitization in a birth-cohort of Estonian and Finnish children followed from 3 to 36 months of age. We describe here an infant Treg phenotype characterized by high Treg frequency, the maturation of Treg population characterized by a decrease in their frequency accompanied with an increase in the highly activated Treg cells. These changes in Treg population associated first with the relative abundance of Bifidobacterium longum followed by increasing colonization with butyrate producing bacteria. High bifidobacterial abundance in the neonatal microbiota appeared to be protective, while colonization with Bacteroides and E. coli was associated with later risk of allergy. Estonian children with lower risk of IgE mediated allergic diseases than Finnish children showed an earlier maturation of the gut microbiota, detected as earlier switch to an increasing abundance of butyrate-producing bacteria, combined with an earlier maturation of Treg cell phenotype and total IgE production. The children with established allergic diseases by age 3 showed a decreased abundance of butyrate producing Faecalibacterium. These results suggest that as well as the maintenance of a bifidobacterial dominated gut microbiota is important during the first weeks of life, the overtake by butyrate producing bacteria seems to be a beneficial shift, which should not be postponed.
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Affiliation(s)
| | - Marcus C de Goffau
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | | | - Heli Siljander
- Children's Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Anu-Maaria Hämäläinen
- Department of Pediatrics, Jorvi Hospital, Helsinki University Hospital, Espoo, Finland
| | - Aleksandr Peet
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Vallo Tillmann
- Department of Pediatrics, Tartu University Hospital, University of Tartu, Tartu, Estonia
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Onni Niemelä
- Department of Laboratory Medicine and Medical Research Unit, Seinäjoki Central Hospital and University of Tampere, Seinäjoki, Finland
| | - Gjalt W Welling
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Mikael Knip
- Clinicum, University of Helsinki, Helsinki, Finland.,Children's Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Hermie J Harmsen
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Outi Vaarala
- Clinicum, University of Helsinki, Helsinki, Finland
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16
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Denham EL, Piersma S, Rinket M, Reilman E, de Goffau MC, van Dijl JM. Differential expression of a prophage-encoded glycocin and its immunity protein suggests a mutualistic strategy of a phage and its host. Sci Rep 2019; 9:2845. [PMID: 30808982 PMCID: PMC6391423 DOI: 10.1038/s41598-019-39169-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 08/28/2018] [Accepted: 12/31/2018] [Indexed: 01/12/2023] Open
Abstract
Sublancin 168 is a highly potent and stable antimicrobial peptide secreted by the Gram-positive bacterium Bacillus subtilis. Production of sublancin gives B. subtilis a major competitive growth advantage over a range of other bacteria thriving in the same ecological niches, the soil and plant rhizosphere. B. subtilis protects itself against sublancin by producing the cognate immunity protein SunI. Previous studies have shown that both the sunA gene for sublancin and the sunI immunity gene are encoded by the prophage SPβ. The sunA gene is under control of several transcriptional regulators. Here we describe the mechanisms by which sunA is heterogeneously expressed within a population, while the sunI gene encoding the immunity protein is homogeneously expressed. The key determinants in heterogeneous sunA expression are the transcriptional regulators Spo0A, AbrB and Rok. Interestingly, these regulators have only a minor influence on sunI expression and they have no effect on the homogeneous expression of sunI within a population of growing cells. Altogether, our findings imply that the homogeneous expression of sunI allows even cells that are not producing sublancin to protect themselves at all times from the active sublancin produced at high levels by their isogenic neighbors. This suggests a mutualistic evolutionary strategy entertained by the SPβ prophage and its Bacillus host, ensuring both stable prophage maintenance and a maximal competitive advantage for the host at minimal costs.
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Affiliation(s)
- Emma L Denham
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.,Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Sjouke Piersma
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Marleen Rinket
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Ewoud Reilman
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Marcus C de Goffau
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.,Wellcome Sanger Institute, Cambridge, UK
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.
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17
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Salter SJ, Scott P, Page AJ, Tracey A, de Goffau MC, Cormie C, Ochoa-Montaño B, Ling CL, Tangmanakit J, Turner P, Parkhill J. 'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs. Microb Genom 2019; 5. [PMID: 30720420 PMCID: PMC6421346 DOI: 10.1099/mgen.0.000247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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] [Indexed: 01/05/2023] Open
Abstract
'Candidatus Ornithobacterium hominis' represents a new member of the Flavobacteriaceae detected in 16S rRNA gene surveys of people from South-East Asia, Africa and Australia. It frequently colonizes the infant nasopharynx at high proportional abundance, and we demonstrate its presence in 42 % of nasopharyngeal swabs from 12-month-old children in the Maela refugee camp in Thailand. The species, a Gram-negative bacillus, has not yet been cultured, but the cells can be identified in mixed samples by fluorescent hybridization. Here, we report seven genomes assembled from metagenomic data, two to improved draft standard. The genomes are approximately 1.9 Mb, sharing 62 % average amino acid identity with the only other member of the genus, the bird pathogen Ornithobacterium rhinotracheale. The draft genomes encode multiple antibiotic-resistance genes, competition factors, Flavobacterium johnsoniae-like gliding motility genes and a homologue of the Pasteurella multocida mitogenic toxin. Intra- and inter-host genome comparison suggests that colonization with this bacterium is both persistent and strain exclusive.
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Affiliation(s)
| | - Paul Scott
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Andrew J Page
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK.,†Present address: Quadram Institute Bioscience, Norwich, UK
| | - Alan Tracey
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | | | - Claire Cormie
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Bernardo Ochoa-Montaño
- 2Department of Biochemistry, University of Cambridge, Cambridge, UK.,‡Present address: Illumina Cambridge Ltd, Little Chesterford, UK
| | - Clare L Ling
- 3Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,4Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiraporn Tangmanakit
- 3Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Paul Turner
- 4Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,5Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
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18
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Lager S, de Goffau MC, Sovio U, Peacock SJ, Parkhill J, Stephen Charnock-Jones D, Smith GCS. Correction to: Detecting eukaryotic microbiota with single-cell sensitivity in human tissue. Microbiome 2018; 6:188. [PMID: 30342557 PMCID: PMC6195996 DOI: 10.1186/s40168-018-0576-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The author reported an error in an equation in the article [1].
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Affiliation(s)
- Susanne Lager
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | | | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Wellcome Trust Sanger Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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19
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Lager S, de Goffau MC, Sovio U, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS. Detecting eukaryotic microbiota with single-cell sensitivity in human tissue. Microbiome 2018; 6:151. [PMID: 30172254 PMCID: PMC6119588 DOI: 10.1186/s40168-018-0529-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/09/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Fetal growth restriction, pre-eclampsia, and pre-term birth are major adverse pregnancy outcomes. These complications are considerable contributors to fetal/maternal morbidity and mortality worldwide. A significant proportion of these cases are thought to be due to dysfunction of the placenta. However, the underlying mechanisms of placental dysfunction are unclear. The aim of the present study was to investigate whether adverse pregnancy outcomes are associated with evidence of placental eukaryotic infection. RESULTS We modified the 18S Illumina Amplicon Protocol of the Earth Microbiome Project and made it capable of detecting just a single spiked-in genome copy of Plasmodium falciparum, Saccharomyces cerevisiae, or Toxoplasma gondii among more than 70,000 human cells. Using this method, we were unable to detect eukaryotic pathogens in placental biopsies in instances of adverse pregnancy outcome (n = 199) or in healthy controls (n = 99). CONCLUSIONS Eukaryotic infection of the placenta is not an underlying cause of the aforementioned pregnancy complications. Possible clinical applications for this non-targeted, yet extremely sensitive, eukaryotic screening method are manifest.
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Affiliation(s)
- Susanne Lager
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | | | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Wellcome Trust Sanger Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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20
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Salter SJ, Turner C, Watthanaworawit W, de Goffau MC, Wagner J, Parkhill J, Bentley SD, Goldblatt D, Nosten F, Turner P. A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children. PLoS Negl Trop Dis 2017; 11:e0005975. [PMID: 28968382 PMCID: PMC5638608 DOI: 10.1371/journal.pntd.0005975] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 10/12/2017] [Accepted: 09/19/2017] [Indexed: 11/19/2022] Open
Abstract
A longitudinal study was undertaken in infants living in the Maela refugee camp on the Thailand-Myanmar border between 2007 and 2010. Nasopharyngeal swabs were collected monthly, from birth to 24 months of age, with additional swabs taken if the infant was diagnosed with pneumonia according to WHO clinical criteria. At the time of collection, swabs were cultured for Streptococcus pneumoniae and multiple serotype carriage was assessed. The bacterial 16S rRNA gene profiles of 544 swabs from 21 infants were analysed to see how the microbiota changes with age, respiratory infection, antibiotic consumption and pneumococcal acquisition. The nasopharyngeal microbiota is a somewhat homogenous community compared to that of other body sites. In this cohort it is dominated by five taxa: Moraxella, Streptococcus, Haemophilus, Corynebacterium and an uncharacterized Flavobacteriaceae taxon of 93% nucleotide similarity to Ornithobacterium. Infant age correlates with certain changes in the microbiota across the cohort: Staphylococcus and Corynebacterium are associated with the first few months of life while Moraxella and the uncharacterised Flavobacteriaceae increase in proportional abundance with age. Respiratory illness and antibiotic use often coincide with an unpredictable perturbation of the microbiota that differs from infant to infant and in different illness episodes. The previously described interaction between Dolosigranulum and Streptococcus was observed in these data. Monthly sampling demonstrates that the nasopharyngeal microbiota is in flux throughout the first two years of life, and that in this refugee camp population the pool of potential bacterial colonisers may be limited. The nasopharynx hosts a community of microbes that first colonise us during infancy and that changes as we grow. Colonisation with certain species is a risk factor for developing respiratory infections such as pneumonia, while other species can have a protective influence. In this study we use molecular methods to identify the bacteria present in nasopharyngeal swabs taken regularly from children in a refugee camp in Thailand. The microbiota develops with age, with early colonisers such as Corynebacterium or Staphylococcus being eventually outgrown by Moraxella and an uncultured taxon described here as unclassified Flavobacteriaceae I. There is evidence in the cohort of Streptococcus pneumoniae being frequently carried and transmitted throughout the first two years of life. We found that the microbiota profiles were not unique or distinguishable between individuals in this study, which is unlike studies in high income, low density populations.
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Affiliation(s)
- Susannah J. Salter
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail:
| | - Claudia Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | - Josef Wagner
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - David Goldblatt
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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21
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Glasner C, de Goffau MC, van Timmeren MM, Schulze ML, Jansen B, Tavakol M, van Wamel WJB, Stegeman CA, Kallenberg CGM, Arends JP, Rossen JW, Heeringa P, van Dijl JM. Genetic loci of Staphylococcus aureus associated with anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitides. Sci Rep 2017; 7:12211. [PMID: 28939882 PMCID: PMC5610336 DOI: 10.1038/s41598-017-12450-z] [Citation(s) in RCA: 19] [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: 01/27/2017] [Accepted: 09/06/2017] [Indexed: 01/08/2023] Open
Abstract
The proteinase 3 (PR3)-positive anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV) granulomatosis with polyangiitis (GPA) has been associated with chronic nasal S. aureus carriage, which is a risk factor for disease relapse. The present study was aimed at comparing the genetic make-up of S. aureus isolates from PR3-ANCA-positive GPA patients with that of isolates from patients suffering from myeloperoxidase (MPO)-ANCA-positive AAV, and isolates from healthy controls. Based on a DNA microarray-based approach, we show that not only PR3-ANCA-positive GPA patients, but also MPO-ANCA-positive AAV patients mainly carried S. aureus types that are prevalent in the general population. Nonetheless, our data suggests that MPO-ANCA-associated S. aureus isolates may be distinct from healthy control- and PR3-ANCA-associated isolates. Furthermore, several genetic loci of S. aureus are associated with either PR3-ANCA- or MPO-ANCA-positive AAV, indicating a possible role for pore-forming toxins, such as leukocidins, in PR3-ANCA-positive GPA. Contrary to previous studies, no association between AAV and superantigens was detected. Our findings also show that a lowered humoral immune response to S. aureus is common for PR3-ANCA- and MPO-ANCA-positive AAV. Altogether, our observations imply that the presence or absence of particular virulence genes of S. aureus isolates from AAV patients contributes to disease progression and/or relapse.
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Affiliation(s)
- Corinna Glasner
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Marcus C de Goffau
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Mirjan M van Timmeren
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Mirja L Schulze
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Benita Jansen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Mehri Tavakol
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - Willem J B van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - Coen A Stegeman
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cees G M Kallenberg
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Jan P Arends
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - John W Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Peter Heeringa
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.
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22
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Abstract
The microbiota in our gut performs many different essential functions that help us to stay healthy. These functions include vitamin production, regulation of lipid metabolism and short chain fatty acid production as fuel for epithelial cells and regulation of gene expression. There is a very numerous and diverse microbial community present in the gut, especially in the colon, with reported numbers of species that vary between 400 and 1500, for some those we even do not yet have culture representatives.A healthy gut microbiota is important for maintaining a healthy host. An aberrant microbiota can cause diseases of different nature and at different ages ranging from allergies at early age to IBD in young adults. This shows that our gut microbiota needs to be treated well to stay healthy. In this chapter we describe what we consider a healthy microbiota and discuss what the role of the microbiota is in various diseases. Research into these described dysbiosis conditions could lead to new strategies for treatment and/or management of our microbiota to improve health.
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Affiliation(s)
- Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, 30001, 9700, Groningen, The Netherlands.
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Heida FH, van Zoonen AG, Hulscher JB, Te Kiefte BJ, Wessels R, Kooi EM, Bos AF, Harmsen HJ, de Goffau MC. Reply to Cassir et al. Clin Infect Dis 2016; 62:1618-20. [PMID: 27045124 DOI: 10.1093/cid/ciw205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | | | | | | | - Elisabeth M Kooi
- Neonatology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Arend F Bos
- Neonatology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, The Netherlands
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Heida FH, van Zoonen AGJF, Hulscher JBF, Te Kiefte BJC, Wessels R, Kooi EMW, Bos AF, Harmsen HJM, de Goffau MC. A Necrotizing Enterocolitis-Associated Gut Microbiota Is Present in the Meconium: Results of a Prospective Study. Clin Infect Dis 2016; 62:863-870. [PMID: 26787171 DOI: 10.1093/cid/ciw016] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/16/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Anomalous intestinal microbiota development is supposedly associated with development of necrotizing enterocolitis (NEC). Our aim in this study was to identify the intestinal microbiota of patients at risk for NEC. METHODS In a prospective trial that investigated prognostic factors for development of NEC in high-risk neonates (NTR4153), 11 NEC cases were gestational age/birthweight matched with controls (ratio of 1:2). Feces were collected twice a week. We used the first feces sample of each patient (meconium), as well as the last 2 feces samples prior to development of NEC. DNA was extracted, and the bacterial 16S rRNA genes were analyzed on a MiSeq sequencer. RESULTS The presence and abundance of Clostridium perfringens (8.4%) and Bacteroides dorei (0.9%) in meconium were increased in neonates who developed NEC compared with controls (0.1% and 0.2%; both species, P < .001). In post-meconium samples, the abundance of staphylococci became negatively associated with NEC development (P = .1 and P = .01 for consecutive samples); Clostridium perfringens continued to be more prevalent in NEC cases. Early enteral feeding and, in particular, breast milk were correlated with an increase in lactate-producing bacilli in post-meconium samples (ρ = -0.45; P = .004). CONCLUSIONS A NEC-associated gut microbiota can be identified in meconium samples; C. perfringens continues to be associated with NEC from the first meconium till just before NEC onset. In contrast, in post-meconium, increased numbers of staphylococci were negatively associated with NEC. These findings suggest causality but this causality should be verified in trials of induced infection in animals, targeted antibiotics, and/or probiotics. CLINICAL TRIALS REGISTRATION CALIFORNIA trial, registered under trial number NTR4153 in the Dutch Trial Registry.
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Affiliation(s)
- Fardou H Heida
- Department of Pediatric Surgery.,Department of Medical Microbiology
| | | | | | | | | | - Elisabeth M W Kooi
- Department of Neonatology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Arend F Bos
- Department of Neonatology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, The Netherlands
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Sadaghian Sadabad M, Regeling A, de Goffau MC, Blokzijl T, Weersma RK, Penders J, Faber KN, Harmsen HJM, Dijkstra G. The ATG16L1-T300A allele impairs clearance of pathosymbionts in the inflamed ileal mucosa of Crohn's disease patients. Gut 2015; 64:1546-52. [PMID: 25253126 DOI: 10.1136/gutjnl-2014-307289] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [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] [Received: 03/23/2014] [Accepted: 09/09/2014] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Crohn's disease (CD) is caused by a complex interplay among genetic, microbial and environmental factors. ATG16L1 is an important genetic factor involved in innate immunity, including autophagy and phagocytosis of microbial components from the gut. We investigated the effect of inflammation on the composition of microbiota in the ileal mucosa of CD patients in relation to the ATG16L1 risk status. DESIGN Biopsies (n=35) were obtained from inflamed and non-inflamed regions of the terminal ileum of 11 CD patients homozygous for the ATG16L1 risk allele (ATG16L1-T300A) and 9 CD patients homozygous for the ATG16L1 protective allele (ATG16L1-T300). Biopsy DNA was extracted and the bacterial composition analysed by pyrosequencing. Intracellular survival rates of adherent-invasive Escherichia coli (AIEC) were analysed by determining colony forming units after exposure to monocytes isolated from healthy volunteers homozygous for the ATG16L1 risk or protective allele. RESULTS Inflamed ileal tissue from patients homozygous for the ATG16L1 risk allele contained increased numbers of Fusobacteriaceae, whereas inflamed ileal tissue of patients homozygous for the ATG16L1 protective allele showed decreased numbers of Bacteroidaceae and Enterobacteriaceae and increased Lachnospiraceae. The ATG16L1 allele did not affect the bacterial composition in the non-inflamed ileal tissue. Monocytes homozygous for the ATG16L1 risk allele showed impaired killing of AIEC under inflammatory conditions compared with those homozygous for the ATG16L1 protective allele. CONCLUSIONS CD patients homozygous for the ATG16L1-T300A risk allele show impaired clearance of pathosymbionts in ileal inflammation indicating that ATG16L1 is essential for effective elimination of pathosymbionts upon inflammation.
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Affiliation(s)
- Mehdi Sadaghian Sadabad
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anouk Regeling
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcus C de Goffau
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tjasso Blokzijl
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John Penders
- Department of Medical Microbiology, School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Timmermans AJ, Harmsen HJM, Bus-Spoor C, Buijssen KJDA, van As-Brooks C, de Goffau MC, Tonk RH, van den Brekel MWM, Hilgers FJM, van der Laan BFAM. Biofilm formation on the Provox ActiValve: Composition and ingrowth analyzed by Illumina paired-end RNA sequencing, fluorescence in situ hybridization, and confocal laser scanning microscopy. Head Neck 2015; 38 Suppl 1:E432-40. [DOI: 10.1002/hed.24014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 12/18/2014] [Accepted: 01/06/2015] [Indexed: 11/10/2022] Open
Affiliation(s)
- Adriana J. Timmermans
- Department of Head and Neck Oncology and Surgery; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Hermie J. M. Harmsen
- Department of Medical Microbiology; University of Groningen, University Medical Center; Groningen Groningen The Netherlands
| | - Carien Bus-Spoor
- Department of Medical Microbiology; University of Groningen, University Medical Center; Groningen Groningen The Netherlands
| | | | - Corina van As-Brooks
- Department of Head and Neck Oncology and Surgery; The Netherlands Cancer Institute; Amsterdam The Netherlands
- Department of Clinical Affairs; Atos Medical AB; Hörby Sweden
| | - Marcus C. de Goffau
- Department of Medical Microbiology; University of Groningen, University Medical Center; Groningen Groningen The Netherlands
| | - Rudi H. Tonk
- Department of Medical Microbiology; University of Groningen, University Medical Center; Groningen Groningen The Netherlands
| | - Michiel W. M. van den Brekel
- Department of Head and Neck Oncology and Surgery; The Netherlands Cancer Institute; Amsterdam The Netherlands
- Institute of Phonetic Sciences, University of Amsterdam; Amsterdam The Netherlands
- Department of Oral and Maxillofacial Surgery; Academic Medical Center; Amsterdam The Netherlands
| | - Frans J. M. Hilgers
- Department of Head and Neck Oncology and Surgery; The Netherlands Cancer Institute; Amsterdam The Netherlands
- Institute of Phonetic Sciences, University of Amsterdam; Amsterdam The Netherlands
- Department of Oral and Maxillofacial Surgery; Academic Medical Center; Amsterdam The Netherlands
| | - Bernard F. A. M. van der Laan
- Department of Otorhinolaryngology and Head and Neck Oncology and Surgery; University of Groningen, University Medical Center; Groningen Groningen The Netherlands
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de Goffau MC, Fuentes S, van den Bogert B, Honkanen H, de Vos WM, Welling GW, Hyöty H, Harmsen HJM. Aberrant gut microbiota composition at the onset of type 1 diabetes in young children. Diabetologia 2014; 57:1569-77. [PMID: 24930037 DOI: 10.1007/s00125-014-3274-0] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/02/2014] [Indexed: 12/13/2022]
Abstract
AIMS/HYPOTHESIS Recent studies indicate that an aberrant gut microbiota is associated with the development of type 1 diabetes, yet little is known about the microbiota in children who have diabetes at an early age. To this end, the microbiota of children aged 1-5 years with new-onset type 1 diabetes was compared with the microbiota of age-matched healthy controls. METHODS A deep global analysis of the gut microbiota composition was established by phylogenetic microarray analysis using a Human Intestinal Tract Chip (HITChip). RESULTS Principal component analyses highlighted the importance of age when comparing age-matched pairs. In pairs younger than 2.9 years, the combined abundance of the class Bacilli (notably streptococci) and the phylum Bacteroidetes was higher in diabetic children, whereas the combined abundance of members of Clostridium clusters IV and XIVa was higher in the healthy controls. Controls older than 2.9 years were characterised by a higher fraction of butyrate-producing species within Clostridium clusters IV and XIVa than was seen in the corresponding diabetic children or in children from the younger age groups, while the diabetic children older than 2.9 years could be differentiated by having an increased microbial diversity. CONCLUSIONS/INTERPRETATION The results from both age groups suggest that non-diabetic children have a more balanced microbiota in which butyrate-producing species appear to hold a pivotal position.
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Affiliation(s)
- Marcus C de Goffau
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, HPC EB80, 9713 GZ, Groningen, The Netherlands
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van Oosten M, Schäfer T, Gazendam JAC, Ohlsen K, Tsompanidou E, de Goffau MC, Harmsen HJM, Crane LMA, Lim E, Francis KP, Cheung L, Olive M, Ntziachristos V, van Dijl JM, van Dam GM. Real-time in vivo imaging of invasive- and biomaterial-associated bacterial infections using fluorescently labelled vancomycin. Nat Commun 2014; 4:2584. [PMID: 24129412 DOI: 10.1038/ncomms3584] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 09/10/2013] [Indexed: 01/29/2023] Open
Abstract
Invasive and biomaterial-associated infections in humans are often difficult to diagnose and treat. Here, guided by recent advances in clinically relevant optical imaging technologies, we explore the use of fluorescently labelled vancomycin (vanco-800CW) to specifically target and detect infections caused by Gram-positive bacteria. The application potential of vanco-800CW for real-time in vivo imaging of bacterial infections is assessed in a mouse myositis model and a human post-mortem implant model. We show that vanco-800CW can specifically detect Gram-positive bacterial infections in our mouse myositis model, discriminate bacterial infections from sterile inflammation in vivo and detect biomaterial-associated infections in the lower leg of a human cadaver. We conclude that vanco-800CW has a high potential for enhanced non-invasive diagnosis of infections with Gram-positive bacteria and is a promising candidate for early-phase clinical trials.
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Affiliation(s)
- Marleen van Oosten
- 1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1, PO Box 30001, 9700 RB Groningen, The Netherlands [2] Division of Surgical Oncology, Department of Surgery, BioOptical Imaging Center, University of Groningen, UMCG, Hanzeplein 1, PO Box 30001, 9700 RB Groningen, The Netherlands
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de Goffau MC, Luopajärvi K, Knip M, Ilonen J, Ruohtula T, Härkönen T, Orivuori L, Hakala S, Welling GW, Harmsen HJ, Vaarala O. Fecal microbiota composition differs between children with β-cell autoimmunity and those without. Diabetes 2013; 62:1238-44. [PMID: 23274889 PMCID: PMC3609581 DOI: 10.2337/db12-0526] [Citation(s) in RCA: 393] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The role of the intestinal microbiota as a regulator of autoimmune diabetes in animal models is well-established, but data on human type 1 diabetes are tentative and based on studies including only a few study subjects. To exclude secondary effects of diabetes and HLA risk genotype on gut microbiota, we compared the intestinal microbiota composition in children with at least two diabetes-associated autoantibodies (n = 18) with autoantibody-negative children matched for age, sex, early feeding history, and HLA risk genotype using pyrosequencing. Principal component analysis indicated that a low abundance of lactate-producing and butyrate-producing species was associated with β-cell autoimmunity. In addition, a dearth of the two most dominant Bifidobacterium species, Bifidobacterium adolescentis and Bifidobacterium pseudocatenulatum, and an increased abundance of the Bacteroides genus were observed in the children with β-cell autoimmunity. We did not find increased fecal calprotectin or IgA as marker of inflammation in children with β-cell autoimmunity. Functional studies related to the observed alterations in the gut microbiome are warranted because the low abundance of bifidobacteria and butyrate-producing species could adversely affect the intestinal epithelial barrier function and inflammation, whereas the apparent importance of the Bacteroides genus in development of type 1 diabetes is insufficiently understood.
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Affiliation(s)
- Marcus C. de Goffau
- Department of Medical Microbiology, University Medical Center Groningen and University of Groningen, Groningen, the Netherlands
| | - Kristiina Luopajärvi
- Immune Response Unit, Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
| | - Mikael Knip
- Children’s Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, Turku, Finland; and the
- Department of Clinical Immunology, University of Eastern Finland, Kuopio, Finland
| | - Terhi Ruohtula
- Immune Response Unit, Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
| | - Taina Härkönen
- Children’s Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Laura Orivuori
- Immune Response Unit, Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
| | - Saara Hakala
- Immune Response Unit, Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
| | - Gjalt W. Welling
- Department of Medical Microbiology, University Medical Center Groningen and University of Groningen, Groningen, the Netherlands
| | - Hermie J. Harmsen
- Department of Medical Microbiology, University Medical Center Groningen and University of Groningen, Groningen, the Netherlands
| | - Outi Vaarala
- Immune Response Unit, Department of Vaccination and Immune Protection, National Institute for Health and Welfare, Helsinki, Finland
- Corresponding author: Outi Vaarala,
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de Boer VCJ, de Goffau MC, Arts ICW, Hollman PCH, Keijer J. SIRT1 stimulation by polyphenols is affected by their stability and metabolism. Mech Ageing Dev 2006; 127:618-27. [PMID: 16603228 DOI: 10.1016/j.mad.2006.02.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 02/06/2006] [Accepted: 02/23/2006] [Indexed: 12/20/2022]
Abstract
Silent information regulator two ortholog 1 (SIRT1) is the human ortholog of the yeast sir2 protein; one of the most important regulators of lifespan extension by caloric restriction in several organisms. Dietary polyphenols, abundant in vegetables, fruits, cereals, wine and tea, were reported to stimulate the deacetylase activity of recombinant SIRT1 protein and could therefore be potential regulators of aging associated processes. However, inconsistent data between effects of polyphenols on the recombinant SIRT1 and on in vivo SIRT1, led us to investigate the influence of (1) stability of polyphenols under experimental conditions and (2) metabolism of polyphenols in human HT29 cells, on stimulation of SIRT1. With an improved SIRT1 deacetylation assay we found three new polyphenolic stimulators. Epigallocatechin galate (EGCg, 1.76-fold), epicatechin galate (ECg, 1.85-fold) and myricetin (3.19-fold) stimulated SIRT1 under stabilizing conditions, whereas without stabilization, these polyphenols strongly inhibited SIRT1, probably due to H2O2 formation. Using metabolically active HT29 cells we were able to show that quercetin (a stimulator of recombinant SIRT1) could not stimulate intracellular SIRT1. The major quercetin metabolite in humans, quercetin 3-O-glucuronide, slightly inhibited the recombinant SIRT1 activity which explains the lack of stimulatory action of quercetin in HT29 cells. This study shows that the stimulation of SIRT1 is strongly affected by polyphenol stability and metabolism, therefore extrapolation of in vitro SIRT1 stimulation results to physiological effects should be done with caution.
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Affiliation(s)
- Vincent C J de Boer
- RIKILT-Institute of Food Safety, Wageningen University and Research Centre, Wageningen, The Netherlands
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