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Prince N, Peralta Marzal LN, Markidi A, Ahmed S, Adolfs Y, Pasterkamp RJ, Kumar H, Roeselers G, Garssen J, Kraneveld AD, Perez-Pardo P. Prebiotic diet normalizes aberrant immune and behavioral phenotypes in a mouse model of autism spectrum disorder. Acta Pharmacol Sin 2024:10.1038/s41401-024-01268-x. [PMID: 38589690 DOI: 10.1038/s41401-024-01268-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Autism spectrum disorder (ASD) is a cluster of neurodevelopmental disorders characterized by deficits in communication and behavior. Increasing evidence suggests that the microbiota-gut-brain axis and the likely related immune imbalance may play a role in the development of this disorder. Gastrointestinal deficits and gut microbiota dysfunction have been linked to the development or severity of autistic behavior. Therefore, treatments that focus on specific diets may improve gastrointestinal function and aberrant behavior in individuals with ASD. In this study, we investigated whether a diet containing specific prebiotic fibers, namely, 3% galacto-oligosaccharide/fructo-oligosaccharide (GOS/FOS; 9:1), can mitigate the adverse effects of in utero exposure to valproic acid (VPA) in mice. Pregnant BALB/cByJ dams were injected with VPA (600 mg/kg, sc.) or phosphate-buffered saline (PBS) on gestational day 11 (G11). Male offspring were divided into four groups: (1) in utero PBS-exposed with a control diet, (2) in utero PBS-exposed with GOS/FOS diet, (3) in utero VPA-exposed with a control diet, and (4) in utero VPA-exposed with GOS/FOS diet. Dietary intervention started from birth and continued throughout the duration of the experiment. We showed that the prebiotic diet normalized VPA-induced alterations in male offspring, including restoration of key microbial taxa, intestinal permeability, peripheral immune homeostasis, reduction of neuroinflammation in the cerebellum, and impairments in social behavior and cognition in mice. Overall, our research provides valuable insights into the gut-brain axis involvement in ASD development. In addition, dietary interventions might correct the disbalance in gut microbiota and immune responses and, ultimately, might improve detrimental behavioral outcomes in ASD.
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Affiliation(s)
- Naika Prince
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Lucia N Peralta Marzal
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Anastasia Markidi
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
- Division of Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Sabbir Ahmed
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Youri Adolfs
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Himanshu Kumar
- Danone Nutricia Research, 3584 CT, Utrecht, The Netherlands
| | - Guus Roeselers
- Danone Nutricia Research, 3584 CT, Utrecht, The Netherlands
| | - Johan Garssen
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
- Danone Nutricia Research, 3584 CT, Utrecht, The Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
- Department of Neuroscience, Faculty of Science, VU university, 1081 HV, Amsterdam, The Netherlands
| | - Paula Perez-Pardo
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands.
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Mikulic N, Uyoga MA, Stoffel NU, Derrien M, Nyilima S, Kostopoulos I, Roeselers G, Chenoll E, Mwasi E, Pironaci G, Karanja S, Bourdet-Sicard R, Zimmermann MB. Prebiotics increase iron absorption and reduce the adverse effects of iron on the gut microbiome and inflammation: a randomized controlled trial using iron stable isotopes in Kenyan infants. Am J Clin Nutr 2024; 119:456-469. [PMID: 38042412 PMCID: PMC10884607 DOI: 10.1016/j.ajcnut.2023.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/18/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
BACKGROUND Iron fortificants tend to be poorly absorbed and may adversely affect the gut, especially in African children. OBJECTIVE We assessed the effects of prebiotic galacto-oligosaccharides/fructo-oligosaccharides (GOS/FOS) on iron absorption and gut health when added to iron-fortified infant cereal. METHODS We randomly assigned Kenyan infants (n = 191) to receive daily for 3 wk a cereal containing iron and 7.5 g GOS/FOS (7.5 g+iron group), 3 g (3-g+iron group) GOS/FOS, or no prebiotics (iron group). A subset of infants in the 2 prebiotic+iron groups (n = 66) consumed 4 stable iron isotope-labeled test meals without and with prebiotics, both before and after the intervention. Primary outcome was fractional iron absorption (FIA) from the cereal with or without prebiotics regardless of dose, before and after 3 wk of consumption. Secondary outcomes included fecal gut microbiota, iron and inflammation status, and effects of prebiotic dose. RESULTS Median (25th-75th percentiles) FIAs from meals before intervention were as follows: 16.3% (8.0%-27.6%) without prebiotics compared with 20.5% (10.4%-33.4%) with prebiotics (Cohen d = 0.53; P < 0.001). FIA from the meal consumed without prebiotics after intervention was 22.9% (8.5%-32.4%), 41% higher than from the meal without prebiotics before intervention (Cohen d = 0.36; P = 0.002). FIA from the meal consumed with prebiotics after intervention was 26.0% (12.2%-36.1%), 60% higher than from the meal without prebiotics before intervention (Cohen d = 0.45; P = 0.007). After 3 wk, compared with the iron group, the following results were observed: 1) Lactobacillus sp. abundances were higher in both prebiotic+iron groups (P < 0.05); 2) Enterobacteriaceae sp. abundances (P = 0.022) and the sum of pathogens (P < 0.001) were lower in the 7.5-g+iron group; 3) the abundance of bacterial toxin-encoding genes was lower in the 3-g+iron group (false discovery rate < 0.05); 4) fecal pH (P < 0.001) and calprotectin (P = 0.033) were lower in the 7.5-g+iron group. CONCLUSIONS Adding prebiotics to iron-fortified infant cereal increases iron absorption and reduces the adverse effects of iron on the gut microbiome and inflammation in Kenyan infants. This trial was registered at clinicaltrials.gov as NCT03894358.
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Affiliation(s)
- Nadja Mikulic
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | - Mary A Uyoga
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | - Nicole U Stoffel
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | | | - Suzane Nyilima
- Public and Community Health Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | | | | | - Edith Mwasi
- Paediatrics Department, Msambweni County Referral Hospital, Msambweni, Kenya
| | - Giulia Pironaci
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | - Simon Karanja
- Public and Community Health Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | - Michael B Zimmermann
- Medical Research Council Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford, United Kingdom.
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Cianci D, Tims S, Roeselers G, El Galta R, Swinkels S. Multi-part strategy for testing differential taxa abundance in sequencing data: A simulation study with an application to a microbiome study. J Microbiol Methods 2023; 212:106810. [PMID: 37607610 DOI: 10.1016/j.mimet.2023.106810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
Comparing the microbiome across study arms is a recurrent goal in many studies. Standard statistical methods are often used for this purpose, however, they do not always represent the best choice in this context given the characteristics of microbiota sequencing data, e.g., non-negative, highly skewed counts with a large number of zeros. A multi-part strategy, that combines a two-part test (as described by Wagner et al., 2011), a Wilcoxon sum-rank test, a Chi-square and a Barnard's test was explored to compare the taxa abundance between study arms. The choice of the test is based on the data structure. The type I error of the multi-part strategy was evaluated by using a simulation study and the method was applied to real data. The script to perform the analysis with the multi-part approach is provided in the statistical software SAS. Several scenarios were simulated and in all of them the type I error was not inflated. Based on the statistical differences resulting from the two-part test (as described by Wagner et al., 2011) and the multi-part strategy (as proposed in this article), different biological implications can be extracted from the same comparison in the same data set. In the comparison of taxa abundance between study arms, we showed that careful attention needs to be paid on the data structure, in order to be able to choose an appropriate analysis method. Our approach selects the most suitable test according to the type of data observed, maintains a good type I error and is easily applicable by using the SAS macro provided.
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Affiliation(s)
- Daniela Cianci
- Julius Center for Health Sciences and Primary Care, Department of Data Science & Biostatistics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | | | | | - Rachid El Galta
- Former employee of Danone Nutricia Research, Utrecht, The Netherlands
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Tims S, Marsaux C, Pinto A, Daly A, Karall D, Kuhn M, Santra S, Roeselers G, Knol J, MacDonald A, Scholl-Bürgi S. Altered gut microbiome diversity and function in patients with propionic acidemia. Mol Genet Metab 2022; 137:308-322. [PMID: 36274442 DOI: 10.1016/j.ymgme.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022]
Abstract
Propionic acidemia (PA) is an inherited metabolic disorder of propionate metabolism, where the gut microbiota may play a role in pathophysiology and therefore, represent a relevant therapeutic target. Little is known about the gut microbiota composition and activity in patients with PA. Although clinical practice varies between metabolic treatment centers, management of PA requires combined dietary and pharmaceutical treatments, both known to affect the gut microbiota. This study aimed to characterize the gut microbiota and its metabolites in fecal samples of patients with PA compared with healthy controls from the same household. Eight patients (aged 3-14y) and 8 controls (4-31y) were recruited from Center 1 (UK) and 7 patients (11-33y) and 6 controls (15-54y) from Center 2 (Austria). Stool samples were collected 4 times over 3 months, alongside data on dietary intakes and medication usage. Several microbial taxa differed between patients with PA and controls, particularly for Center 1, e.g., Proteobacteria levels were increased, whereas butyrate-producing genera, such as Roseburia and Faecalibacterium, were decreased. Most measured microbial metabolites were lower in patients with PA, and butyrate was particularly depleted in patients from Center 1. Furthermore, microbiota profile of these patients showed the lowest compositional and functional diversity, and lowest stability over 3 months. As the first study to map the gut microbiota of patients with PA, this work represents an important step forward for developing new therapeutic strategies to further improve PA clinical status. New dietary strategies should consider microbial propionate production as well as butyrate production and microbiota stability.
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Affiliation(s)
- Sebastian Tims
- Danone Nutricia Research, Uppsalalaan 12, 3584CT Utrecht, the Netherlands.
| | - Cyril Marsaux
- Danone Nutricia Research, Uppsalalaan 12, 3584CT Utrecht, the Netherlands.
| | - Alex Pinto
- Department of Dietetics, Birmingham Women's and Children's NHS Foundation Trust, Steelhouse Lane, Birmingham B4 6NH, UK.
| | - Anne Daly
- Department of Dietetics, Birmingham Women's and Children's NHS Foundation Trust, Steelhouse Lane, Birmingham B4 6NH, UK.
| | - Daniela Karall
- Department of Pediatrics I, Inherited Metabolic Disorders, Medical University of Innsbruck, Anichstr. 35, 6020 Innsbruck, Austria.
| | - Mirjam Kuhn
- Danone Nutricia Research, Uppsalalaan 12, 3584CT Utrecht, the Netherlands.
| | - Saikat Santra
- Department of Clinical Inherited Metabolic Disorders, Birmingham Women's and Children's NHS Foundation Trust, Steelhouse Lane, Birmingham B4 6NH, UK.
| | - Guus Roeselers
- Danone Nutricia Research, Uppsalalaan 12, 3584CT Utrecht, the Netherlands.
| | - Jan Knol
- Danone Nutricia Research, Uppsalalaan 12, 3584CT Utrecht, the Netherlands; Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708WE Wageningen, the Netherlands.
| | - Anita MacDonald
- Department of Dietetics, Birmingham Women's and Children's NHS Foundation Trust, Steelhouse Lane, Birmingham B4 6NH, UK.
| | - Sabine Scholl-Bürgi
- Department of Pediatrics I, Inherited Metabolic Disorders, Medical University of Innsbruck, Anichstr. 35, 6020 Innsbruck, Austria.
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Dierikx T, Berkhout D, Eck A, Tims S, van Limbergen J, Visser D, de Boer M, de Boer N, Touw D, Benninga M, Schierbeek N, Visser L, Knol J, Roeselers G, de Vries J, de Meij T. Influence of timing of maternal antibiotic administration during caesarean section on infant microbial colonisation: a randomised controlled trial. Gut 2022; 71:1803-1811. [PMID: 34803023 PMCID: PMC9380480 DOI: 10.1136/gutjnl-2021-324767] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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] [Received: 03/26/2021] [Accepted: 11/02/2021] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Revised guidelines for caesarean section (CS) advise maternal antibiotic administration prior to skin incision instead of after umbilical cord clamping, unintentionally exposing the infant to antibiotics antenatally. We aimed to investigate if timing of intrapartum antibiotics contributes to the impairment of microbiota colonisation in CS born infants. DESIGN In this randomised controlled trial, women delivering via CS received antibiotics prior to skin incision (n=20) or after umbilical cord clamping (n=20). A third control group of vaginally delivering women (n=23) was included. Faecal microbiota was determined from all infants at 1, 7 and 28 days after birth and at 3 years by 16S rRNA gene sequencing and whole-metagenome shotgun sequencing. RESULTS Compared with vaginally born infants, profound differences were found in microbial diversity and composition in both CS groups in the first month of life. A decreased abundance in species belonging to the genera Bacteroides and Bifidobacterium was found with a concurrent increase in members belonging to the phylum Proteobacteria. These differences could not be observed at 3 years of age. No statistically significant differences were observed in taxonomic and functional composition of the microbiome between both CS groups at any of the time points. CONCLUSION We confirmed that microbiome colonisation is strongly affected by CS delivery. Our findings suggest that maternal antibiotic administration prior to CS does not result in a second hit on the compromised microbiome. Future, larger studies should confirm that antenatal antibiotic exposure in CS born infants does not aggravate colonisation impairment and impact long-term health.
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Affiliation(s)
- Thomas Dierikx
- Department of Paediatric Gastroenterology, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands .,Department of Paediatric Gastroenterology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Daniel Berkhout
- Department of Paediatric Gastroenterology, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands,Department of Paediatric Gastroenterology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Anat Eck
- Nutricia Research Center, Utrecht, The Netherlands
| | | | - Johan van Limbergen
- Department of Paediatric Gastroenterology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands,Department of Paediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Douwe Visser
- Department of Neonatology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Marjon de Boer
- Department of Obstetrics and Gynaecology, Reproduction and Development, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Nanne de Boer
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Daan Touw
- Department of Pharmaceutical Analysis, University of Groningen Groningen Research Institute of Pharmacy, Groningen, The Netherlands,Department of Clinical Pharmacy and Pharmacology, University Medical Centre Groningen, Groningen, The Netherlands
| | - Marc Benninga
- Department of Paediatric Gastroenterology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Nine Schierbeek
- Department of Paediatric Gastroenterology, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Laura Visser
- Department of Obstetrics and Gynaecology, Reproduction and Development, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Jan Knol
- Nutricia Research Center, Utrecht, The Netherlands,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Johanna de Vries
- Department of Obstetrics and Gynaecology, Reproduction and Development, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Tim de Meij
- Department of Paediatric Gastroenterology, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands,Department of Paediatric Gastroenterology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
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Rodriguez-Herrera A, Tims S, Polman J, Porcel Rubio R, Muñoz Hoyos A, Agosti M, Lista G, Corvaglia LT, Knol J, Roeselers G, Pérez Navero JL. Early-life fecal microbiome and metabolome dynamics in response to an intervention with infant formula containing specific prebiotics and postbiotics. Am J Physiol Gastrointest Liver Physiol 2022; 322:G571-G582. [PMID: 35348015 PMCID: PMC9109790 DOI: 10.1152/ajpgi.00079.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This study examined fecal metabolome dynamics to gain greater functional insights into the interactions between nutrition and the activity of the developing gut microbiota in healthy term-born infants. The fecal samples used here originate from a randomized, controlled, double-blind clinical study that assessed the efficacy of infant formula with prebiotics and postbiotics (experimental arm) compared with a standard infant formula (control arm). A group of exclusively breast-fed term infants was used as a reference arm. First, conventional targeted physiological and microbial measurements were performed, which showed differences in fecal Bifidobacterium levels and corresponding activity (e.g., lactate levels). Next, the overall fecal microbiota composition was determined by 16S rRNA gene amplicon sequencing. The microbiota composition profiles showed several bacterial groups in the experimental arm to be significantly different from the control arm and mostly closer to the levels observed in the reference arm. Finally, we applied an untargeted UPLC-MS/MS approach to examine changes in the fecal metabolome. Fecal metabolome profiles showed the most distinct separation, up to 404 significantly different metabolites, between the study arms. Our data reveal that infant formula with specific prebiotics and postbiotics may trigger responses in the intestinal microbiota composition that brings the ensuing fecal metabolite profile of formula-fed infants closer toward those observed in breast-fed infants. Furthermore, our results demonstrate a clear need for establishing an infant gut metabolome reference database to translate these metabolite profile dynamics into functional and physiologically relevant responses.NEW & NOTEWORTHY Untargeted metabolomics techniques can provide a "snapshot" of an ecosystem in response to environmental stimuli, such as nutritional interventions. Our analyses of fecal samples from infants demonstrate the potential of phenotyping by metabolomics while deciphering the complex interactions of early-life nutrition and gut microbiome development.
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Affiliation(s)
| | | | - Jan Polman
- 2Danone Nutricia Research, Utrecht, The Netherlands
| | | | - Antonio Muñoz Hoyos
- 4Department of Pediatrics, Hospital Clínico Universitario San Cecilio, Granada, Spain
| | - Massimo Agosti
- 5Neonatologia e Terapia Intensiva Neonatale, Polo
Universitario F. Del Ponte, Varese, Italy
| | - Gianluca Lista
- 6Terapia Intensiva Neonatale, Ospedale dei Bambini
Vittore Buzzi, ASST-FBF-Sacco, Milano, Italy
| | | | - Jan Knol
- 2Danone Nutricia Research, Utrecht, The Netherlands,8Department of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | - Juan L. Pérez Navero
- 9Pediatrics Department, Reina Sofia University Hospital, Maimonides Institute for Biomedical Research, CIBERER, Cordoba, Spain
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Gala AAD, Kumar H, Sedani S, Openshaw-Lawrence N, Verkuijl JM, Glogowski N, Steingold A, Ponnusamy V, Ekitzidou G, Yip P, Nessel I, Michael-Titus AT, Roeselers G, Shah DK. Alterations in the Stool Microbiome in Newborns undergoing Mild Therapeutic Hypothermia after Hypoxic-Ischemic Encephalopathy. Dev Neurosci 2022; 44:373-383. [PMID: 35139510 DOI: 10.1159/000522523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/02/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Hypoxic-ischemic encephalopathy (HIE) is associated with brain injury in newborns, and may lead to disability or death. Mild therapeutic hypothermia (TH) is an effective neuroprotective intervention and an established standard of care in western countries. The gut microbiome, the genomic and physico-chemical contribution of the gut microbiota, serves important functions and is increasingly recognised as a major influencer on development. The impact of HIE and TH on the evolving gut microbiota of the newborn remains to be elucidated. OBJECTIVE To carry out an exploratory study on the effects of HIE and TH on the gut microbiome in term neonates. METHODS AND RESULTS Stool samples were obtained from 28 newborns with HIE (median age 68 h) undergoing TH on the neonatal unit (HIE TH group), with a follow-on stool sample available for 20 of these babies (median age 151 h). For comparison, a single stool specimen was obtained from 19 healthy newborns on the postnatal ward (median age 34 h). The microbiota composition was determined using established microbial DNA extraction and 16S rRNA gene sequencing methodology. There was no difference in the mode of delivery or the method of feeding the newborns, once established, between the two groups. All the infants in the HIE TH group had received antibiotics compared to only one of the controls. A lower -diversity, quantified by the Shannon diversity index, was noted in the microbiota of the HIE TH group in comparison to the control group. The HIE TH group had a higher mean relative abundance (MRA) of facultative anaerobes and aerobes such as Staphylococcus species and a lower MRA of strict anaerobes, such as members of the Bacteroides genus, compared to the control. Also, there was a significant reduction in the MRA of the genus Bifidobacterium in the HIE TH group. Although the mode of delivery exerts a profound influence on the gut microbiota of the newborn, distance-based redundancy analysis showed that TH may exert an independent influence. This study could not determine the independent contribution of the use of antibiotics or the NICU environment. CONCLUSION In this study we demonstrate an alteration in the microbiota composition in newborns undergoing TH for HIE. (359 words).
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Affiliation(s)
- Ammee A D Gala
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | | | - Sagar Sedani
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | | | | | - Nicola Glogowski
- Royal London Hospital (Barts Health NHS Trust), London, United Kingdom
| | - Adam Steingold
- Royal London Hospital (Barts Health NHS Trust), London, United Kingdom
| | | | | | - Ping Yip
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Isabell Nessel
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Adina T Michael-Titus
- Danone Nutricia Research, Utrecht, The Netherlands
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | | | - Divyen K Shah
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Royal London Hospital (Barts Health NHS Trust), London, United Kingdom
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8
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Lay C, Chu CW, Purbojati RW, Acerbi E, Drautz-Moses DI, de Sessions PF, Jie S, Ho E, Kok YJ, Bi X, Chen S, Mak SY, Chua MC, Goh AEN, Chiang WC, Rao R, Chaithongwongwatthana S, Khemapech N, Chongsrisawat V, Martin R, Roeselers G, Ho YS, Hibberd ML, Schuster SC, Knol J. A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants. BMC Microbiol 2021; 21:191. [PMID: 34172012 PMCID: PMC8229302 DOI: 10.1186/s12866-021-02230-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 04/09/2020] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 153 infants born by elective C-section received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented from birth until 4 months old. Vaginally born infants were included as a reference group. Stool samples were collected from day 3 till week 22. Multi-omics were deployed to investigate the impact of mode of delivery and nutrition on the development of the infant gut microbiome, and uncover putative biological mechanisms underlying the role of a compromised microbiome as a risk factor for NCD. RESULTS As early as day 3, infants born vaginally presented a hypoxic and acidic gut environment characterized by an enrichment of strict anaerobes (Bifidobacteriaceae). Infants born by C-section presented the hallmark of a compromised microbiome driven by an enrichment of Enterobacteriaceae. This was associated with meta-omics signatures characteristic of a microbiome adapted to a more oxygen-rich gut environment, enriched with genes associated with reactive oxygen species metabolism and lipopolysaccharide biosynthesis, and depleted in genes involved in the metabolism of milk carbohydrates. The synbiotic formula modulated expression of microbial genes involved in (oligo)saccharide metabolism, which emulates the eco-physiological gut environment observed in vaginally born infants. The resulting hypoxic and acidic milieu prevented the establishment of a compromised microbiome. CONCLUSIONS This study deciphers the putative functional hallmarks of a compromised microbiome acquired during C-section birth, and the impact of nutrition that may counteract disturbed microbiome development. TRIAL REGISTRATION The study was registered in the Dutch Trial Register (Number: 2838 ) on 4th April 2011.
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Affiliation(s)
| | | | - Rikky Wenang Purbojati
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Enzo Acerbi
- Danone Nutricia Research, Singapore, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | | | - Song Jie
- Genome Institute of Singapore, Singapore, Singapore
| | - Eliza Ho
- Genome Institute of Singapore, Singapore, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Shi Ya Mak
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Mei Chien Chua
- KK Women's and Children's Hospital, Singapore, Singapore
| | - Anne E N Goh
- KK Women's and Children's Hospital, Singapore, Singapore
| | | | - Rajeshwar Rao
- KK Women's and Children's Hospital, Singapore, Singapore
| | | | - Nipon Khemapech
- King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Voranush Chongsrisawat
- King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rocio Martin
- Danone Nutricia Research, Utrecht, The Netherlands
| | | | - Ying Swan Ho
- Bioprocessing Technology Institute, Singapore, Singapore
| | - Martin L Hibberd
- Genome Institute of Singapore, Singapore, Singapore
- London School of Hygiene and Tropical Medicine, London, UK
| | - Stephan C Schuster
- Singapore Centre For Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
| | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands.
- Wageningen University, Wageningen, The Netherlands.
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9
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Phavichitr N, Wang S, Chomto S, Tantibhaedhyangkul R, Kakourou A, Intarakhao S, Jongpiputvanich S, Roeselers G, Knol J. Impact of synbiotics on gut microbiota during early life: a randomized, double-blind study. Sci Rep 2021; 11:3534. [PMID: 33574421 PMCID: PMC7878856 DOI: 10.1038/s41598-021-83009-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/08/2021] [Indexed: 12/24/2022] Open
Abstract
Human milk is considered the optimal nutrition for infants and found to contain significant numbers of viable bacteria. The aim of the study was to assess the effects of a specific synbiotic combination at doses closer to the bacterial cells present in human milk, on intestinal bifidobacteria proportions (relative abundance), reduction of potential pathogens and gut physiological conditions. A clinical study was conducted in 290 healthy infants aged from 6 to 19 weeks. Infants received either a control infant formula or one of the two investigational infant formulas (control formula with 0.8 g/100 ml scGOS/lcFOS and Bifidobacterium breve M-16V at either 1 × 104 cfu/ml or 1 × 106 cfu/ml). Exclusively breastfed infants were included as a reference. Analyses were performed on intention-to-treat groups and all-subjects-treated groups. After 6 weeks of intervention, the synbiotics at two different doses significantly increased the bifidobacteria proportions in healthy infants. The synbiotic supplementation also decreased the prevalence (infants with detectable levels) and the abundance of C. difficile. Closer to the levels in the breastfed reference group, fecal pH was significantly lower while l-lactate concentrations and acetate proportions were significantly higher in the synbiotic groups. All formulas were well tolerated and all groups showed a comparable safety profile based on the number and severity of adverse events and growth. In healthy infants, supplementation of infant-type bifidobacterial strain B. breve M-16V, at a dose close to bacterial numbers found in human milk, with scGOS/lcFOS (9:1) created a gut environment closer to the breastfed reference group. This specific synbiotic mixture may also support gut microbiota resilience during early life. Clinical Trial Registration This clinical study named Color Synbiotics Study, was registered in ClinicalTrials.gov on 18 March 2013. Registration number is NCT01813175. https://clinicaltrials.gov/ct2/show/NCT01813175.
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Affiliation(s)
| | - Shugui Wang
- Danone Nutricia Research, Singapore, Singapore
| | - Sirinuch Chomto
- Nutritional Unit, Department of Pediatrics, King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Sukkrawan Intarakhao
- Department of Pediatrics, Thammasat Hospital, Faculty of Medicine, Thammasat University, Bangkok, Thailand
| | - Sungkom Jongpiputvanich
- Department of Pediatrics, Thammasat Hospital, Faculty of Medicine, Thammasat University, Bangkok, Thailand
| | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands.,Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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10
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Kumar H, Collado MC, Wopereis H, Salminen S, Knol J, Roeselers G. The Bifidogenic Effect Revisited-Ecology and Health Perspectives of Bifidobacterial Colonization in Early Life. Microorganisms 2020; 8:E1855. [PMID: 33255636 PMCID: PMC7760687 DOI: 10.3390/microorganisms8121855] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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] [Received: 10/22/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Extensive microbial colonization of the infant gastrointestinal tract starts after parturition. There are several parallel mechanisms by which early life microbiome acquisition may proceed, including early exposure to maternal vaginal and fecal microbiota, transmission of skin associated microbes, and ingestion of microorganisms present in breast milk. The crucial role of vertical transmission from the maternal microbial reservoir during vaginal delivery is supported by the shared microbial strains observed among mothers and their babies and the distinctly different gut microbiome composition of caesarean-section born infants. The healthy infant colon is often dominated by members of the keystone genus Bifidobacterium that have evolved complex genetic pathways to metabolize different glycans present in human milk. In exchange for these host-derived nutrients, bifidobacteria's saccharolytic activity results in an anaerobic and acidic gut environment that is protective against enteropathogenic infection. Interference with early-life microbiota acquisition and development could result in adverse health outcomes. Compromised microbiota development, often characterized by decreased abundance of Bifidobacterium species has been reported in infants delivered prematurely, delivered by caesarean section, early life antibiotic exposure and in the case of early life allergies. Various microbiome modulation strategies such as probiotic, prebiotics, synbiotics and postbiotics have been developed that are able to generate a bifidogenic shift and help to restore the microbiota development. This review explores the evolutionary ecology of early-life type Bifidobacterium strains and their symbiotic relationship with humans and discusses examples of compromised microbiota development in which stimulating the abundance and activity of Bifidobacterium has demonstrated beneficial associations with health.
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Affiliation(s)
- Himanshu Kumar
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (H.K.); (H.W.); (J.K.)
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-Spanish National Research Council (IATA-CSIC), Paterna, 46980 Valencia, Spain;
- Functional Foods Forum, Faculty of Medicine, University of Turku, 20500 Turku, Finland;
| | - Harm Wopereis
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (H.K.); (H.W.); (J.K.)
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, 20500 Turku, Finland;
| | - Jan Knol
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (H.K.); (H.W.); (J.K.)
- Laboratory for Microbiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Guus Roeselers
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (H.K.); (H.W.); (J.K.)
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11
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Troisi J, Autio R, Beopoulos T, Bravaccio C, Carraturo F, Corrivetti G, Cunningham S, Devane S, Fallin D, Fetissov S, Gea M, Giorgi A, Iris F, Joshi L, Kadzielski S, Kraneveld A, Kumar H, Ladd-Acosta C, Leader G, Mannion A, Maximin E, Mezzelani A, Milanesi L, Naudon L, Peralta Marzal LN, Perez Pardo P, Prince NZ, Rabot S, Roeselers G, Roos C, Roussin L, Scala G, Tuccinardi FP, Fasano A. Genome, Environment, Microbiome and Metabolome in Autism (GEMMA) Study Design: Biomarkers Identification for Precision Treatment and Primary Prevention of Autism Spectrum Disorders by an Integrated Multi-Omics Systems Biology Approach. Brain Sci 2020; 10:E743. [PMID: 33081368 PMCID: PMC7603049 DOI: 10.3390/brainsci10100743] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/07/2020] [Accepted: 10/14/2020] [Indexed: 12/26/2022] Open
Abstract
Autism Spectrum Disorder (ASD) affects approximately 1 child in 54, with a 35-fold increase since 1960. Selected studies suggest that part of the recent increase in prevalence is likely attributable to an improved awareness and recognition, and changes in clinical practice or service availability. However, this is not sufficient to explain this epidemiological phenomenon. Research points to a possible link between ASD and intestinal microbiota because many children with ASD display gastro-intestinal problems. Current large-scale datasets of ASD are limited in their ability to provide mechanistic insight into ASD because they are predominantly cross-sectional studies that do not allow evaluation of perspective associations between early life microbiota composition/function and later ASD diagnoses. Here we describe GEMMA (Genome, Environment, Microbiome and Metabolome in Autism), a prospective study supported by the European Commission, that follows at-risk infants from birth to identify potential biomarker predictors of ASD development followed by validation on large multi-omics datasets. The project includes clinical (observational and interventional trials) and pre-clinical studies in humanized murine models (fecal transfer from ASD probands) and in vitro colon models. This will support the progress of a microbiome-wide association study (of human participants) to identify prognostic microbiome signatures and metabolic pathways underlying mechanisms for ASD progression and severity and potential treatment response.
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Affiliation(s)
- Jacopo Troisi
- Theoreo srl spin off company of the University of Salerno, Via degli Ulivi, 3, 84090 Montecorvino Pugliano (SA), Italy;
| | - Reija Autio
- Faculty of Social Sciences, Health Sciences Unit, Tampere University, Arvo Ylpön Katu 34, 33014 Tampere, Finland;
| | - Thanos Beopoulos
- Bio-Modeling System, 3, Rue De L’arrivee. 75015 Paris, France; (T.B.); (M.G.); (F.I.)
| | - Carmela Bravaccio
- Department of science medicine translational, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy;
| | | | - Giulio Corrivetti
- Azienda Sanitaria Locale (ASL) Salerno, Via Nizza, 146, 84125 Salerno (SA), Italy;
| | - Stephen Cunningham
- National University of Ireland Galaway, University Road, Galaway, Ireland; (S.C.); (L.J.); (G.L.); (A.M.)
| | - Samantha Devane
- Massachusetts General Hospital, Fruit Street, 55, Boston, MA 02114, USA; (S.D.); (S.K.)
| | - Daniele Fallin
- John Hopkins School of Public Health and the Wendy Klag Center for Autism and Developmental Disabilities, 615 N. Wolfe St, Baltimore, MD 21205, USA; (D.F.); (C.L.-A.)
| | - Serguei Fetissov
- Laboratory of Neuronal and Neuroendocrine Differentiation and Communication, Inserm UMR 1239, Rouen University of Normandy, 25 rue Tesnière, 76130 Mont-Saint-Aignan, France;
| | - Manuel Gea
- Bio-Modeling System, 3, Rue De L’arrivee. 75015 Paris, France; (T.B.); (M.G.); (F.I.)
| | | | - François Iris
- Bio-Modeling System, 3, Rue De L’arrivee. 75015 Paris, France; (T.B.); (M.G.); (F.I.)
| | - Lokesh Joshi
- National University of Ireland Galaway, University Road, Galaway, Ireland; (S.C.); (L.J.); (G.L.); (A.M.)
| | - Sarah Kadzielski
- Massachusetts General Hospital, Fruit Street, 55, Boston, MA 02114, USA; (S.D.); (S.K.)
| | - Aletta Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3508 TB Utrecht, The Netherlands; (A.K.); (L.N.P.M.); (P.P.P.); (N.Z.P.)
| | - Himanshu Kumar
- Danone Nutricia Research, Uppsalalaan, 12, 3584 CT Utrecht, The Netherlands; (H.K.); (R.G.)
| | - Christine Ladd-Acosta
- John Hopkins School of Public Health and the Wendy Klag Center for Autism and Developmental Disabilities, 615 N. Wolfe St, Baltimore, MD 21205, USA; (D.F.); (C.L.-A.)
| | - Geraldine Leader
- National University of Ireland Galaway, University Road, Galaway, Ireland; (S.C.); (L.J.); (G.L.); (A.M.)
| | - Arlene Mannion
- National University of Ireland Galaway, University Road, Galaway, Ireland; (S.C.); (L.J.); (G.L.); (A.M.)
| | - Elise Maximin
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (E.M.); (L.N.); (S.R.); (L.R.)
| | - Alessandra Mezzelani
- Consiglio Nazionale delle Ricerche (CNR), Piazzale Aldo Moro, 7, 00185 Roma, Italy; (A.M.); (L.M.)
| | - Luciano Milanesi
- Consiglio Nazionale delle Ricerche (CNR), Piazzale Aldo Moro, 7, 00185 Roma, Italy; (A.M.); (L.M.)
| | - Laurent Naudon
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (E.M.); (L.N.); (S.R.); (L.R.)
| | - Lucia N. Peralta Marzal
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3508 TB Utrecht, The Netherlands; (A.K.); (L.N.P.M.); (P.P.P.); (N.Z.P.)
| | - Paula Perez Pardo
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3508 TB Utrecht, The Netherlands; (A.K.); (L.N.P.M.); (P.P.P.); (N.Z.P.)
| | - Naika Z. Prince
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3508 TB Utrecht, The Netherlands; (A.K.); (L.N.P.M.); (P.P.P.); (N.Z.P.)
| | - Sylvie Rabot
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (E.M.); (L.N.); (S.R.); (L.R.)
| | - Guus Roeselers
- Danone Nutricia Research, Uppsalalaan, 12, 3584 CT Utrecht, The Netherlands; (H.K.); (R.G.)
| | | | - Lea Roussin
- Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (E.M.); (L.N.); (S.R.); (L.R.)
| | - Giovanni Scala
- Theoreo srl spin off company of the University of Salerno, Via degli Ulivi, 3, 84090 Montecorvino Pugliano (SA), Italy;
| | | | - Alessio Fasano
- European Biomedical Research Institute of Salerno (EBRIS), Via S. de Renzi, 3, 84125 Salerno (SA), Italy;
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12
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Béghin L, Tims S, Roelofs M, Rougé C, Oozeer R, Rakza T, Chirico G, Roeselers G, Knol J, Rozé JC, Turck D. Fermented infant formula (with Bifidobacterium breve C50 and Streptococcus thermophilus O65) with prebiotic oligosaccharides is safe and modulates the gut microbiota towards a microbiota closer to that of breastfed infants. Clin Nutr 2020; 40:778-787. [PMID: 32893049 DOI: 10.1016/j.clnu.2020.07.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 11/25/2019] [Revised: 05/28/2020] [Accepted: 07/17/2020] [Indexed: 01/15/2023]
Abstract
BACKGROUND & AIMS Microbiome-modulators can help positively steer early-life microbiota development but their effects on microbiome functionality and associated safety and tolerance need to be demonstrated. We investigated the microbiome impact of a new combination of bioactive compounds, produced by the food-grade microorganisms Bifidobacterium breve C50 and Streptococcus thermophilus ST065 during a fermentation process, and prebiotics in an infant formula. Tolerance and safety were also assessed. METHODS An exploratory prospective, randomized, double-blind, controlled, multi-centre study was designed to investigate the effect of bioactive compounds and prebiotics (short-chain galacto-oligosaccharides (scGOS)/long-chain fructo-oligosaccharides (lcFOS) 9:1). Experimental formulas containing these bioactive compounds and prebiotics (FERM/scGOS/lcFOS), prebiotics (scGOS/lcFOS), or bioactive compounds (FERM), were compared to a standard cow's milk-based control formula (Control). Exclusively breastfed infants were included as a reference arm since exclusive breastfeeding is considered as the optimal feeding for infants. The study lasted six months and included visits to health care professionals at baseline, two, four and six months of age. Stool SIgA concentration was the primary study outcome parameter. RESULTS There were 280 infants randomized over the experimental arms and 70 infants entered the breastfed-reference arm. Demographics were balanced, growth and tolerance parameters were according to expectation and adverse events were limited. At four months of age the median SIgA concentration in the FERM/scGOS/lcFOS group was significantly higher compared to the Control group (p = 0.03) and was more similar to the concentrations found in the breastfed-reference group. Bifidobacterium increased over time in all groups. The FERM/scGOS/lcFOS combination resulted in a microbiota composition and metabolic activity closer to the breastfed infants' microbiome. CONCLUSION The FERM/scGOS/lcFOS combination showed a significant positive effect on SIgA levels. All formulas tested were associated with normal growth and were well-tolerated. Additionally, at four months of age the FERM/scGOS/lcFOS formula brought the microbiome composition and metabolic activity closer towards that of breastfed infants. CLINICAL TRIAL REGISTRY Registration number NTR2726 (Netherlands Trial Register; www.trialregister.nl/).
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Affiliation(s)
- Laurent Béghin
- Univ. Lille, CHU Lille, Clinical Investigation Center, CIC-1403-Inserm-CHU and U1286 - INFINITE - Institute for Translational Research in Inflammation, F-59000, Lille, France
| | | | | | | | - Raish Oozeer
- Danone Nutricia Research, Utrecht, the Netherlands
| | - Thameur Rakza
- Department of Neonatology, Lille University Jeanne de Flandre Children's Hospital and Faculty of Medicine, University of Lille, F-59000, Lille, France
| | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, the Netherlands; Laboratory of Microbiology, Wageningen University, the Netherlands
| | | | - Dominique Turck
- Univ. Lille, CHU Lille, Clinical Investigation Center, CIC-1403-Inserm-CHU and U1286 - INFINITE - Institute for Translational Research in Inflammation, F-59000, Lille, France; Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Lille University Jeanne de Flandre Children's Hospital and Faculty of Medicine, University of Lille, F-59000, Lille, France
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13
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Chew C, Barros KV, Weffort VRS, Maranhão HDS, Laranjeira M, Knol J, Roeselers G, de Morais MB. Gut Microbiota of Young Children Living in Four Brazilian Cities. Front Pediatr 2020; 8:573815. [PMID: 33365290 PMCID: PMC7751462 DOI: 10.3389/fped.2020.573815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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] [Received: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022] Open
Abstract
Recent studies have demonstrated that gut microbiota development is influenced by human biogeographic factors such as race, ethnicity, diet, lifestyle or culture-specific variations, and other environmental influences. However, biogeographic variation in gut microbiota assembly remains largely unexplored in Latin America. In this paper, we compared food recall information and microbiota composition of toddlers living in geographically separated urban populations within four states of Brazil. 16S RNA gene sequencing revealed that alpha diversity was similar between the four different populations. Gut microbiota compositions were dominated by members of the phyla Firmicutes and Bacteroidetes, resembling a more adult-like microbiota as compared with those of Western European toddlers of similar age. These findings suggest that inter-individual and nutrition-induced differences were apparent in the fecal microbiota. We conclude that urban dietary pattern plays a larger role in influencing the gut microbiota composition than do biogeographic factors.
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Affiliation(s)
- Charmaine Chew
- Danone Nutricia Research, Singapore, Singapore.,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | | | | | | | | | - Jan Knol
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands.,Danone Nutricia Research, Utrecht, Netherlands
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14
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Wegh CAM, Geerlings SY, Knol J, Roeselers G, Belzer C. Postbiotics and Their Potential Applications in Early Life Nutrition and Beyond. Int J Mol Sci 2019; 20:E4673. [PMID: 31547172 PMCID: PMC6801921 DOI: 10.3390/ijms20194673] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [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: 09/04/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/15/2022] Open
Abstract
Postbiotics are functional bioactive compounds, generated in a matrix during fermentation, which may be used to promote health. The term postbiotics can be regarded as an umbrella term for all synonyms and related terms of these microbial fermentation components. Therefore, postbiotics can include many different constituents including metabolites, short-chain fatty acids (SCFAs), microbial cell fractions, functional proteins, extracellular polysaccharides (EPS), cell lysates, teichoic acid, peptidoglycan-derived muropeptides and pili-type structures. Postbiotics is also a rather new term in the '-biotics' field. Where consensus exists for the definitions of pre- and probiotics, this is not yet the case for postbiotics. Here we propose a working definition and review currently known postbiotic compounds, their proposed mechanisms, clinical evidence and potential applications. Research to date indicates that postbiotics can have direct immunomodulatory and clinically relevant effects and evidence can be found for the use of postbiotics in healthy individuals to improve overall health and to relief symptoms in a range of diseases such as infant colic and in adults atopic dermatitis and different causes of diarrhea.
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Affiliation(s)
- Carrie A M Wegh
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands.
| | - Sharon Y Geerlings
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands.
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands.
- Danone-Nutricia Research, 3584 CT Utrecht, The Netherlands.
| | - Guus Roeselers
- Danone-Nutricia Research, 3584 CT Utrecht, The Netherlands.
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands.
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15
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Dierikx TH, Berkhout DJC, Visser L, Benninga MA, Roeselers G, de Boer NKH, de Vries JIP, de Meij TGJ. The influence of timing of Maternal administration of Antibiotics during cesarean section on the intestinal Microbial colonization in Infants (MAMI-trial): study protocol for a randomised controlled trial. Trials 2019; 20:479. [PMID: 31382981 PMCID: PMC6683546 DOI: 10.1186/s13063-019-3552-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/02/2019] [Indexed: 02/08/2023] Open
Abstract
Background A disturbance in the early colonisation of the gut by microorganisms is associated with an aberrant innate immune system and a variety of clinical conditions later in life. Several factors are considered to influence this initial colonisation, including maternally administered antibiotics during pregnancy and delivery. Recent revisions to international obstetric guidelines have resulted in the exposure of all infants born by caesarean section (CS) to broad-spectrum antibiotics perinatally. To date, the consequences of these new guidelines on neonatal gut colonisation and the associated short- and long-term health implications have not yet been addressed. The aim of this study is to investigate the influence of the timing of antibiotic administration during CS to the mother on the course of neonatal intestinal colonisation up to 2 years of age. Methods/design This single-centre randomised controlled trial will recruit 40 women scheduled for an elective CS. The subjects will be randomised to receive 1500 mg of cefuroxime intravenously either prior to the skin incision (n = 20) or after clamping of the umbilical cord (n = 20). Levels of cefuroxime in cord blood will be determined for exposed neonates. Faecal samples from the children will be collected on days 1, 7 and 28 days and at 2 years old and analysed by 16S sequencing. Shannon-diversity indices, absolute and relative abundances, and unsupervised and supervised classification methods will be used to evaluate the effect of the timing of intrapartum cefuroxime administration on the composition of the microbiota. The outcomes for both study groups will be compared to the intestinal microbiota of vaginally born infants (n = 20). To detect possible effects on health state, a questionnaire on health-related issues will be taken at the age of 2 years. Discussion In the proposed study, changes in the intestinal microbiota of 40 children born by CS will be followed until the age of 2 years. Research on this topic is necessary since significant effects relating to the timing of antibiotic administration on microbial colonisation may conflict with the current guidelines, as this may have health consequences later in life. Trial registration Netherlands Clinical Trial Registry, NTR6000. Retrospectively registered on 25 July 2016. Electronic supplementary material The online version of this article (10.1186/s13063-019-3552-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas H Dierikx
- Department of Paediatric Gastroenterology, Amsterdam UMC, location VUmc, 1081 HV, Amsterdam, The Netherlands.
| | - Daniel J C Berkhout
- Department of Paediatric Gastroenterology, Amsterdam UMC, location VUmc, 1081 HV, Amsterdam, The Netherlands
| | - Laura Visser
- Department of Gynaecology and Obstetrics, Amsterdam UMC, location VUmc, 1081 HV, Amsterdam, The Netherlands
| | - Marc A Benninga
- Department of Paediatric Gastroenterology, Amsterdam UMC, location AMC, 1105 AZ, Amsterdam, The Netherlands
| | | | - Nanne K H de Boer
- Department of Gastroenterology and Hepatology, Amsterdam UMC, location VUmc, AG&M Research Institute, 1081 HV, Amsterdam, The Netherlands
| | - Johanna I P de Vries
- Department of Gynaecology and Obstetrics, Amsterdam UMC, location VUmc, 1081 HV, Amsterdam, The Netherlands
| | - Tim G J de Meij
- Department of Paediatric Gastroenterology, Amsterdam UMC, location VUmc, 1081 HV, Amsterdam, The Netherlands
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Wopereis H, van Ampting MTJ, Cetinyurek-Yavuz A, Slump R, Candy DCA, Butt AM, Peroni DG, Vandenplas Y, Fox AT, Shah N, Roeselers G, Harthoorn LF, Michaelis LJ, Knol J, West CE. A specific synbiotic-containing amino acid-based formula restores gut microbiota in non-IgE mediated cow's milk allergic infants: a randomized controlled trial. Clin Transl Allergy 2019; 9:27. [PMID: 31164972 PMCID: PMC6543596 DOI: 10.1186/s13601-019-0267-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Altered gut microbiota is implicated in cow's milk allergy (CMA) and differs markedly from healthy, breastfed infants. Infants who suffer from severe CMA often rely on cow's milk protein avoidance and, when breastfeeding is not possible, on specialised infant formulas such as amino-acid based formulas (AAF). Herein, we report the effects of an AAF including specific synbiotics on oral and gastrointestinal microbiota of infants with non-IgE mediated CMA with reference to healthy, breastfed infants. METHODS In this prospective, randomized, double-blind controlled study, infants with suspected non-IgE mediated CMA received test or control formula. Test formula was AAF with synbiotics (prebiotic fructo-oligosaccharides and probiotic Bifidobacterium breve M-16V). Control formula was AAF without synbiotics. Healthy, breastfed infants were used as a separate reference group (HBR). Bacterial compositions of faecal and salivary samples were analysed by 16S rRNA-gene sequencing. Faecal analysis was complemented with the analysis of pH, short-chain fatty acids (SCFAs) and lactic acids. RESULTS The trial included 35 test subjects, 36 controls, and 51 HBR. The 16S rRNA-gene sequencing revealed moderate effects of test formula on oral microbiota. In contrast, the gut microbiota was substantially affected across time comparing test with control. In both groups bacterial diversity increased over time but was characterised by a more gradual increment in test compared to control. Compositionally this reflected an enhancement of Bifidobacterium spp. and Veillonella sp. in the test group. In contrast, the control-fed infants showed increased abundance of adult-like species, mainly within the Lachnospiraceae family, as well as within the Ruminococcus and Alistipes genus. The effects on Bifidobacterium spp. and Lachnospiraceae spp. were previously confirmed through enumeration by fluorescent in situ hybridization and were shown for test to approximate the proportions observed in the HBR. Additionally, microbial activity was affected as evidenced by an increase of l-lactate, a decrease of valerate, and reduced concentrations of branched-chain SCFAs in test versus control. CONCLUSIONS The AAF including specific synbiotics effectively modulates the gut microbiota and its metabolic activity in non-IgE mediated CMA infants bringing it close to a healthy breastfed profile.Trial registration Registered on 1 May 2013 with Netherlands Trial Register Number NTR3979.
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Affiliation(s)
- Harm Wopereis
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | | | | | - Rob Slump
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, The Netherlands
| | | | | | - Diego G. Peroni
- University Hospital Verona, Verona, Italy
- Present Address: Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Yvan Vandenplas
- KidZ Health Castle, UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Adam T. Fox
- Guy’s and St Thomas’ Hospitals NHS Foundation Trust, London, UK
| | - Neil Shah
- Great Ormond Street Hospital, London, UK
| | - Guus Roeselers
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, The Netherlands
| | | | - Louise J. Michaelis
- Great North Children’s Hospital, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Jan Knol
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | | | - the ASSIGN study group
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Royal Alexandra Children’s Hospital, Brighton, UK
- University Hospital Verona, Verona, Italy
- Present Address: Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
- KidZ Health Castle, UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Guy’s and St Thomas’ Hospitals NHS Foundation Trust, London, UK
- Great Ormond Street Hospital, London, UK
- Great North Children’s Hospital, Royal Victoria Infirmary, Newcastle upon Tyne, UK
- Umeå University, Umeå, Sweden
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Fiamoncini J, Yiorkas AM, Gedrich K, Rundle M, Alsters SI, Roeselers G, van den Broek TJ, Clavel T, Lagkouvardos I, Wopereis S, Frost G, van Ommen B, Blakemore AI, Daniel H. Determinants of postprandial plasma bile acid kinetics in human volunteers. Am J Physiol Gastrointest Liver Physiol 2017; 313:G300-G312. [PMID: 28663304 DOI: 10.1152/ajpgi.00157.2017] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 05/17/2017] [Revised: 06/21/2017] [Accepted: 06/26/2017] [Indexed: 01/31/2023]
Abstract
Bile acids (BA) are signaling molecules with a wide range of biological effects, also identified among the most responsive plasma metabolites in the postprandial state. We here describe this response to different dietary challenges and report on key determinants linked to its interindividual variability. Healthy men and women (n = 72, 62 ± 8 yr, mean ± SE) were enrolled into a 12-wk weight loss intervention. All subjects underwent an oral glucose tolerance test and a mixed-meal tolerance test before and after the intervention. BA were quantified in plasma by liquid chromatography-tandem mass spectrometry combined with whole genome exome sequencing and fecal microbiota profiling. Considering the average response of all 72 subjects, no effect of the successful weight loss intervention was found on plasma BA profiles. Fasting and postprandial BA profiles revealed high interindividual variability, and three main patterns in postprandial BA response were identified using multivariate analysis. Although the women enrolled were postmenopausal, effects of sex difference in BA response were evident. Exome data revealed the contribution of preselected genes to the observed interindividual variability. In particular, a variant in the SLCO1A2 gene, encoding the small intestinal BA transporter organic anion-transporting polypeptide-1A2 (OATP1A2), was associated with delayed postprandial BA increases. Fecal microbiota analysis did not reveal evidence for a significant influence of bacterial diversity and/or composition on plasma BA profiles. The analysis of plasma BA profiles in response to two different dietary challenges revealed a high interindividual variability, which was mainly determined by genetics and sex difference of host with minimal effects of the microbiota.NEW & NOTEWORTHY Considering the average response of all 72 subjects, no effect of the successful weight loss intervention was found on plasma bile acid (BA) profiles. Despite high interindividual variability, three main patterns in postprandial BA response were identified using multivariate analysis. A variant in the SLCO1A2 gene, encoding the small intestinal BA transporter organic anion-transporting polypeptide-1A2 (OATP1A2), was associated with delayed postprandial BA increases in response to both the oral glucose tolerance test and the mixed-meal tolerance test.
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Affiliation(s)
- Jarlei Fiamoncini
- Nutrition and Food Sciences, Technische Universität München, Freising-Weihenstephan, Germany;
| | - Andrianos M Yiorkas
- Section of Investigative Medicine, Imperial College London, London, United Kingdom.,Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom; and
| | - Kurt Gedrich
- Nutrition and Food Sciences, Technische Universität München, Freising-Weihenstephan, Germany
| | - Milena Rundle
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Sanne I Alsters
- Section of Investigative Medicine, Imperial College London, London, United Kingdom.,Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom; and
| | - Guus Roeselers
- Microbiology & Systems Biology Group, The Netherlands Organisation for Applied Scientific Research, Zeist, The Netherlands.,Danone-Nutricia Research, Utrecht, The Netherlands
| | - Tim J van den Broek
- Microbiology & Systems Biology Group, The Netherlands Organisation for Applied Scientific Research, Zeist, The Netherlands
| | - Thomas Clavel
- Institute of Medical Microbiology, Rheinisch-Westfaelische Technische Hochschule Aachen University Hospital, Aachen, Germany
| | - Ilias Lagkouvardos
- Core Facility Microbiome/Next Generation Sequencing, Institute for Food & Health, Technische Universität München, Freising-Weihenstephan, Germany
| | - Suzan Wopereis
- Microbiology & Systems Biology Group, The Netherlands Organisation for Applied Scientific Research, Zeist, The Netherlands
| | - Gary Frost
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Ben van Ommen
- Microbiology & Systems Biology Group, The Netherlands Organisation for Applied Scientific Research, Zeist, The Netherlands
| | - Alexandra I Blakemore
- Section of Investigative Medicine, Imperial College London, London, United Kingdom.,Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom; and
| | - Hannelore Daniel
- Nutrition and Food Sciences, Technische Universität München, Freising-Weihenstephan, Germany
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18
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Botschuijver S, Roeselers G, Levin E, Jonkers DM, Welting O, Heinsbroek SEM, de Weerd HH, Boekhout T, Fornai M, Masclee AA, Schuren FHJ, de Jonge WJ, Seppen J, van den Wijngaard RM. Intestinal Fungal Dysbiosis Is Associated With Visceral Hypersensitivity in Patients With Irritable Bowel Syndrome and Rats. Gastroenterology 2017. [PMID: 28624575 DOI: 10.1053/j.gastro.2017.06.004] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Visceral hypersensitivity is one feature of irritable bowel syndrome (IBS). Bacterial dysbiosis might be involved in the activation of nociceptive sensory pathways, but there have been few studies of the role of the mycobiome (the fungal microbiome) in the development of IBS. We analyzed intestinal mycobiomes of patients with IBS and a rat model of visceral hypersensitivity. METHODS We used internal transcribed spacer 1-based metabarcoding to compare fecal mycobiomes of 18 healthy volunteers with those of 39 patients with IBS (with visceral hypersensitivity or normal levels of sensitivity). We also compared the mycobiomes of Long-Evans rats separated from their mothers (hypersensitive) with non-handled (normally sensitive) rats. We investigated whether fungi can cause visceral hypersensitivity using rats exposed to fungicide (fluconazole and nystatin). The functional relevance of the gut mycobiome was confirmed in fecal transplantation experiments: adult maternally separated rats were subjected to water avoidance stress (to induce visceral hypersensitivity), then given fungicide and donor cecum content via oral gavage. Other rats subjected to water avoidance stress were given soluble β-glucans, which antagonize C-type lectin domain family 7 member A (CLEC7A or DECTIN1) signaling via spleen-associated tyrosine kinase (SYK), a SYK inhibitor to reduce visceral hypersensitivity, or vehicle (control). The sensitivity of mast cells to fungi was tested with mesenteric windows (ex vivo) and the human mast cell line HMC-1. RESULTS α diversity (Shannon index) and mycobiome signature (stability selection) of both groups of IBS patients differed from healthy volunteers, and the mycobiome signature of hypersensitive patients differed from that of normally sensitive patients. We observed mycobiome dysbiosis in rats that had been separated from their mothers compared with non-handled rats. Administration of fungicide to hypersensitive rats reduced their visceral hypersensitivity to normal levels of sensitivity. Administration of cecal mycobiomes from rats that had been separated from their mothers (but not non-handled mycobiome) restored hypersensitivity to distension. Administration of soluble β-glucans or a SYK inhibitor reduced visceral hypersensitivity, compared with controls. Particulate β-glucan (a DECTIN-1 agonist) induced mast cell degranulation in mesenteric windows and HMC-1 cells responded to fungal antigens by release of histamine. CONCLUSIONS In an analysis of patients with IBS and controls, we associated fungal dysbiosis with IBS. In studies of rats, we found fungi to promote visceral hypersensitivity, which could be reduced by administration of fungicides, soluble β-glucans, or a SYK inhibitor. The intestinal fungi might therefore be manipulated for treatment of IBS-related visceral hypersensitivity.
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Affiliation(s)
- Sara Botschuijver
- Tytgat Institute for Liver and Intestinal Research, Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Guus Roeselers
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, The Netherlands
| | - Evgeni Levin
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, The Netherlands
| | - Daisy M Jonkers
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Olaf Welting
- Tytgat Institute for Liver and Intestinal Research, Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Sigrid E M Heinsbroek
- Tytgat Institute for Liver and Intestinal Research, Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Heleen H de Weerd
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, The Netherlands
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Institute for Biodiversity and Ecosystems Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Matteo Fornai
- Tytgat Institute for Liver and Intestinal Research, Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands; Division of Pharmacology, Department of Clinical & Experimental Medicine, University of Pisa, Pisa, Italy
| | - Ad A Masclee
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Frank H J Schuren
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, The Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - Jurgen Seppen
- Tytgat Institute for Liver and Intestinal Research, Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - René M van den Wijngaard
- Tytgat Institute for Liver and Intestinal Research, Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands.
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19
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van Nieuwenhuijzen EJ, Houbraken JAMP, Punt PJ, Roeselers G, Adan OCG, Samson RA. The fungal composition of natural biofinishes on oil-treated wood. Fungal Biol Biotechnol 2017; 4:2. [PMID: 28955471 PMCID: PMC5611603 DOI: 10.1186/s40694-017-0030-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/07/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Biofinished wood is considered to be a decorative and protective material for outdoor constructions, showing advantages compared to traditional treated wood in terms of sustainability and self-repair. Natural dark wood staining fungi are essential to biofinish formation on wood. Although all sorts of outdoor situated timber are subjected to fungal staining, the homogenous dark staining called biofinish has only been detected on specific vegetable oil-treated substrates. Revealing the fungal composition of various natural biofinishes on wood is a first step to understand and control biofinish formation for industrial application. RESULTS A culture-based survey of fungi in natural biofinishes on oil-treated wood samples showed the common wood stain fungus Aureobasidium and the recently described genus Superstratomyces to be predominant constituents. A culture-independent approach, based on amplification of the internal transcribed spacer regions, cloning and Sanger sequencing, resulted in clone libraries of two types of biofinishes. Aureobasidium was present in both biofinish types, but was only predominant in biofinishes on pine sapwood treated with raw linseed oil. Most cloned sequences of the other biofinish type (pine sapwood treated with olive oil) could not be identified. In addition, a more in-depth overview of the fungal composition of biofinishes was obtained with Illumina amplicon sequencing that targeted the internal transcribed spacer region 1. All investigated samples, that varied in wood species, (oil) treatments and exposure times, contained Aureobasidium and this genus was predominant in the biofinishes on pine sapwood treated with raw linseed oil. Lapidomyces was the predominant genus in most of the other biofinishes and present in all other samples. Surprisingly, Superstratomyces, which was predominantly detected by the cultivation-based approach, could not be found with the Illumina sequencing approach, while Lapidomyces was not detected in the culture-based approach. CONCLUSIONS Overall, the culture-based approach and two culture-independent methods that were used in this study revealed that natural biofinishes were composed of multiple fungal genera always containing the common wood staining mould Aureobasidium. Besides Aureobasidium, the use of other fungal genera for the production of biofinished wood has to be considered.
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Affiliation(s)
| | - Jos A. M. P. Houbraken
- Applied and Industrial Mycology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Peter J. Punt
- TNO, Microbiology and Systems Biology, Zeist, The Netherlands
- Dutch DNA Biotech BV, Zeist, The Netherlands
| | - Guus Roeselers
- TNO, Microbiology and Systems Biology, Zeist, The Netherlands
- Present Address: Danone Nutricia Research, Utrecht, The Netherlands
| | - Olaf C. G. Adan
- Department of Applied Physics, Section Transport in Permeable Media, University of Technology Eindhoven, Eindhoven, The Netherlands
| | - Robert A. Samson
- Applied and Industrial Mycology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
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20
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Goverse G, Molenaar R, Macia L, Tan J, Erkelens MN, Konijn T, Knippenberg M, Cook ECL, Hanekamp D, Veldhoen M, Hartog A, Roeselers G, Mackay CR, Mebius RE. Diet-Derived Short Chain Fatty Acids Stimulate Intestinal Epithelial Cells To Induce Mucosal Tolerogenic Dendritic Cells. J I 2017; 198:2172-2181. [DOI: 10.4049/jimmunol.1600165] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 12/16/2016] [Indexed: 12/27/2022]
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22
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de Boer P, Caspers M, Sanders JW, Kemperman R, Wijman J, Lommerse G, Roeselers G, Montijn R, Abee T, Kort R. Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores. Microbiome 2015; 3:30. [PMID: 26217487 PMCID: PMC4515881 DOI: 10.1186/s40168-015-0096-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 07/14/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Spoilage of food products is frequently caused by bacterial spores and lactic acid bacteria. Identification of these organisms by classic cultivation methods is limited by their ability to form colonies on nutrient agar plates. In this study, we adapted and optimized 16S rRNA amplicon sequencing for quantification of bacterial spores in a canned food matrix and for monitoring the outgrowth of spoilage microbiota in a ready-to-eat food matrix. RESULTS The detection limit of bar-coded 16S rRNA amplicon sequencing was determined for the number of bacterial spores in a canned food matrix. Analysis of samples from a canned food matrix spiked with a mixture of equinumerous spores from the thermophiles, Geobacillus stearothermophilus and Geobacillus thermoglucosidans, and the mesophiles, Bacillus sporothermodurans, Bacillus cereus, and Bacillus subtilis, led to the detection of these spores with an average limit of 2 × 10(2) spores ml(-1). The data were normalized by setting the number of sequences resulting from DNA of an inactivated bacterial species, present in the matrix at the same concentration in all samples, to a fixed value for quantitative sample-to-sample comparisons. The 16S rRNA amplicon sequencing method was also employed to monitor population dynamics in a ready-to-eat rice meal, incubated over a period of 12 days at 7 °C. The most predominant outgrowth was observed by the genera Leuconostoc, Bacillus, and Paenibacillus. Analysis of meals pre-treated with weak acids showed inhibition of outgrowth of these three genera. The specificity of the amplicon synthesis was improved by the design of oligonucleotides that minimize the amplification of 16S rRNA genes from chloroplasts originating from plant-based material present in the food. CONCLUSION This study shows that the composition of complex spoilage populations, including bacterial spores, can be monitored in complex food matrices by bar-coded amplicon sequencing in a quantitative manner. In order to allow sample-to-sample comparisons, normalizations based on background DNA are described. This method offers a solution for the identification and quantification of spoilage microbiota, which cannot be cultivated under standard laboratory conditions. The study indicates variable detection limits among species of bacterial spores resulting from differences in DNA extraction efficiencies.
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Affiliation(s)
- Paulo de Boer
- />TI Food and Nutrition, Wageningen, The Netherlands
- />TNO Microbiology and Systems Biology, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Martien Caspers
- />TI Food and Nutrition, Wageningen, The Netherlands
- />TNO Microbiology and Systems Biology, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | | | | | | | | | - Guus Roeselers
- />TI Food and Nutrition, Wageningen, The Netherlands
- />TNO Microbiology and Systems Biology, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Roy Montijn
- />TI Food and Nutrition, Wageningen, The Netherlands
| | - Tjakko Abee
- />TI Food and Nutrition, Wageningen, The Netherlands
- />Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Remco Kort
- />TI Food and Nutrition, Wageningen, The Netherlands
- />TNO Microbiology and Systems Biology, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
- />Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands
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Paauw A, Jonker D, Roeselers G, Heng JME, Mars-Groenendijk RH, Trip H, Molhoek EM, Jansen HJ, van der Plas J, de Jong AL, Majchrzykiewicz-Koehorst JA, Speksnijder AGCL. Rapid and reliable discrimination between Shigella species and Escherichia coli using MALDI-TOF mass spectrometry. Int J Med Microbiol 2015; 305:446-52. [PMID: 25912807 DOI: 10.1016/j.ijmm.2015.04.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [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: 11/27/2014] [Revised: 03/11/2015] [Accepted: 04/06/2015] [Indexed: 11/24/2022] Open
Abstract
E. coli-Shigella species are a cryptic group of bacteria in which the Shigella species are distributed within the phylogenetic tree of E. coli. The nomenclature is historically based and the discrimination of these genera developed as a result of the epidemiological need to identify the cause of shigellosis, a severe disease caused by Shigella species. For these reasons, this incorrect classification of shigellae persists to date, and the ability to rapidly characterize E. coli and Shigella species remains highly desirable. Until recently, existing matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) assays used to identify bacteria could not discriminate between E. coli and Shigella species. Here we present a rapid classification method for the E. coli-Shigella phylogroup based on MALDI-TOF MS which is supported by genetic analysis. E. coli and Shigella isolates were collected and genetically characterized by MLVA. A custom reference library for MALDI-TOF MS that represents the genetic diversity of E. coli and Shigella strains was developed. Characterization of E. coli and Shigella species is based on an approach with Biotyper software. Using this reference library it was possible to distinguish between Shigella species and E. coli. Of the 180 isolates tested, 94.4% were correctly classified as E. coli or shigellae. The results of four (2.2%) isolates could not be interpreted and six (3.3%) isolates were classified incorrectly. The custom library extends the existing MALDI-TOF MS method for species determination by enabling rapid and accurate discrimination between Shigella species and E. coli.
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Affiliation(s)
- Armand Paauw
- Department of CBRN Protection, TNO, PO Box 45, 2280 AA Rijswijk, The Netherlands.
| | - Debby Jonker
- Cluster of Infectious Diseases, Public Health Service Amsterdam, PO Box 2200, 1000 CE Amsterdam, The Netherlands
| | - Guus Roeselers
- Department of CBRN Protection, TNO, PO Box 45, 2280 AA Rijswijk, The Netherlands
| | - Jonathan M E Heng
- Department of CBRN Protection, TNO, PO Box 45, 2280 AA Rijswijk, The Netherlands
| | | | - Hein Trip
- Department of CBRN Protection, TNO, PO Box 45, 2280 AA Rijswijk, The Netherlands
| | - E Margo Molhoek
- Department of CBRN Protection, TNO, PO Box 45, 2280 AA Rijswijk, The Netherlands
| | - Hugo-Jan Jansen
- Expert Centre Force Health Protection, Ministry of Defence, PO Box 185, MPC 56A, 3940 AD, Doorn, The Netherlands
| | - Jan van der Plas
- Expert Centre Force Health Protection, Ministry of Defence, PO Box 185, MPC 56A, 3940 AD, Doorn, The Netherlands
| | - Ad L de Jong
- Department of CBRN Protection, TNO, PO Box 45, 2280 AA Rijswijk, The Netherlands
| | | | - Arjen G C L Speksnijder
- Cluster of Infectious Diseases, Public Health Service Amsterdam, PO Box 2200, 1000 CE Amsterdam, The Netherlands; Naturalis Biodiversity Centre, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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Roeselers G, Coolen J, van der Wielen PWJJ, Jaspers MC, Atsma A, de Graaf B, Schuren F. Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time. Environ Microbiol 2015; 17:2505-14. [DOI: 10.1111/1462-2920.12739] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 12/01/2014] [Accepted: 12/01/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Guus Roeselers
- Microbiology and Systems Biology Group; TNO; Zeist The Netherlands
| | - Jordy Coolen
- Microbiology and Systems Biology Group; TNO; Zeist The Netherlands
| | | | - Marco C. Jaspers
- Microbiology and Systems Biology Group; TNO; Zeist The Netherlands
| | | | | | - Frank Schuren
- Microbiology and Systems Biology Group; TNO; Zeist The Netherlands
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25
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de Souza CB, Roeselers G, Troost F, Jonkers D, Koenen M, Venema K. Corrigendum to “Prebiotic effects of cassava bagasse in TNO's in vitro model of the colon in lean versus obese microbiota” [Journal of Functional Foods 11 (2014) 210–220]. J Funct Foods 2015. [DOI: 10.1016/j.jff.2015.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Aguirre M, Jonkers DMAE, Troost FJ, Roeselers G, Venema K. In vitro characterization of the impact of different substrates on metabolite production, energy extraction and composition of gut microbiota from lean and obese subjects. PLoS One 2014; 9:e113864. [PMID: 25426858 PMCID: PMC4245234 DOI: 10.1371/journal.pone.0113864] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to investigate the effect of galacto-oligosaccharides, lactulose, apple fiber and sugar beet pectin on the composition and activity of human colonic microbiota of lean and obese healthy subjects using an in vitro model of the proximal colon: TIM-2. Substrate fermentation was assessed by measuring the production of short-chain and branched-chain fatty acids, lactate and ammonia and by studying the composition of the bacterial communities over time. The results suggest that energy harvest (in terms of metabolites) of lean and obese microbiotas is different and may depend on the fermentable substrate. For galacto-oligosaccharides and lactulose, the cumulative amount of short-chain fatty acids plus lactate produced in TIM-2 was lower in the fermentation experiments with the lean microbiota (123 and 155 mmol, respectively) compared to the obese (162 and 173 mmol, respectively). This was reversed for the pectin and the fiber. The absolute amount produced of short-chain fatty acids including lactate was higher after 72 h in the fermentation experiments with apple fiber-L (108 mmol) than with apple fiber-O (92 mmol). Sugar beet-L was also higher (130 mmol) compared to sugar beet-O (103 mmol). Galacto-oligosaccharides and lactulose boosted the balance of health-promoting over toxic metabolites produced by the microbiota from obese subjects. Firmicutes were more predominant in the inoculum prepared from feces of obese subjects compared to lean subjects. The average abundance at time zero was 92% and 74%, respectively. On the other hand, Bacteroidetes were more dominant in the microbiota prepared with homogenates from lean subjects with an average abundance of 22% compared with the microbiota prepared with homogenates from obese subjects (3.6%). This study brings evidence that different fermentable carbohydrates are fermented differently by lean and obese microbiotas, which contributes to the understanding of the role of diet and the microbiota in tackling obesity.
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Affiliation(s)
- Marisol Aguirre
- Top Institute of Food & Nutrition, Wageningen, Gelderland, The Netherlands
- Department of Human Biology, Maastricht University, Maastricht, Limburg, The Netherlands
- Department of Microbiology & Systems Biology, The Netherlands Organization for Applied Scientific Research, Zeist, Utrecht, The Netherlands
| | - Daisy M. A. E. Jonkers
- Department of Human Biology, Maastricht University, Maastricht, Limburg, The Netherlands
| | - Freddy J. Troost
- Department of Human Biology, Maastricht University, Maastricht, Limburg, The Netherlands
| | - Guus Roeselers
- Department of Microbiology & Systems Biology, The Netherlands Organization for Applied Scientific Research, Zeist, Utrecht, The Netherlands
| | - Koen Venema
- Top Institute of Food & Nutrition, Wageningen, Gelderland, The Netherlands
- Department of Microbiology & Systems Biology, The Netherlands Organization for Applied Scientific Research, Zeist, Utrecht, The Netherlands
- * E-mail:
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Bussolo de Souza C, Roeselers G, Troost F, Jonkers D, Koenen M, Venema K. Prebiotic effects of cassava bagasse in TNO's in vitro model of the colon in lean versus obese microbiota. J Funct Foods 2014. [DOI: 10.1016/j.jff.2014.09.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton ILG, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 2014; 15:924. [PMID: 25342549 PMCID: PMC4287430 DOI: 10.1186/1471-2164-15-924] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. RESULTS Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. CONCLUSIONS The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Jonathan A Eisen
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, 4081 Biological Laboratories, Cambridge, MA 02138, USA.
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Kelder T, Stroeve JHM, Bijlsma S, Radonjic M, Roeselers G. Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health. Nutr Diabetes 2014; 4:e122. [PMID: 24979151 PMCID: PMC4079927 DOI: 10.1038/nutd.2014.18] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 05/20/2014] [Accepted: 05/30/2014] [Indexed: 02/06/2023] Open
Abstract
Background: Recent evidence suggests that the gut microbiota plays an important role in human metabolism and energy homeostasis and is therefore a relevant factor in the assessment of metabolic health and flexibility. Understanding of these host–microbiome interactions aids the design of nutritional strategies that act via modulation of the microbiota. Nevertheless, relating gut microbiota composition to host health states remains challenging because of the sheer complexity of these ecosystems and the large degrees of interindividual variation in human microbiota composition. Methods: We assessed fecal microbiota composition and host response patterns of metabolic and inflammatory markers in 10 apparently healthy men subjected to a high-fat high-caloric diet (HFHC, 1300 kcal/day extra) for 4 weeks. DNA was isolated from stool and barcoded 16S rRNA gene amplicons were sequenced. Metabolic health parameters, including anthropomorphic and blood parameters, where determined at t=0 and t=4 weeks. Results: A correlation network approach revealed diet-induced changes in Bacteroides levels related to changes in carbohydrate oxidation rates, whereas the change in Firmicutes correlates with changes in fat oxidation. These results were confirmed by multivariate models. We identified correlations between microbial diversity indices and several inflammation-related host parameters that suggest a relation between diet-induced changes in gut microbiota diversity and inflammatory processes. Conclusions: This approach allowed us to identify significant correlations between abundances of microbial taxa and diet-induced shifts in several metabolic health parameters. Constructed correlation networks provide an overview of these relations, revealing groups of correlations that are of particular interest for explaining host health aspects through changes in the gut microbiota.
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Affiliation(s)
- T Kelder
- Microbiology and Systems Biology, TNO, Zeist, The Netherlands
| | - J H M Stroeve
- Microbiology and Systems Biology, TNO, Zeist, The Netherlands
| | - S Bijlsma
- Microbiology and Systems Biology, TNO, Zeist, The Netherlands
| | - M Radonjic
- Microbiology and Systems Biology, TNO, Zeist, The Netherlands
| | - G Roeselers
- Microbiology and Systems Biology, TNO, Zeist, The Netherlands
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Kort R, Caspers M, van de Graaf A, van Egmond W, Keijser B, Roeselers G. Shaping the oral microbiota through intimate kissing. Microbiome 2014; 2:41. [PMID: 25408893 PMCID: PMC4233210 DOI: 10.1186/2049-2618-2-41] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/20/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND The variation of microbial communities associated with the human body can be the cause of many factors, including the human genetic makeup, diet, age, surroundings, and sexual behavior. In this study, we investigated the effects of intimate kissing on the oral microbiota of 21 couples by self-administered questionnaires about their past kissing behavior and by the evaluation of tongue and salivary microbiota samples in a controlled kissing experiment. In addition, we quantified the number of bacteria exchanged during intimate kissing by the use of marker bacteria introduced through the intake of a probiotic yoghurt drink by one of the partners prior to a second intimate kiss. RESULTS Similarity indices of microbial communities show that average partners have a more similar oral microbiota composition compared to unrelated individuals, with by far most pronounced similarity for communities associated with the tongue surface. An intimate kiss did not lead to a significant additional increase of the average similarity of the oral microbiota between partners. However, clear correlations were observed between the similarity indices of the salivary microbiota of couples and self-reported kiss frequencies, and the reported time passed after the latest kiss. In control experiments for bacterial transfer, we identified the probiotic Lactobacillus and Bifidobacterium marker bacteria in most kiss receivers, corresponding to an average total bacterial transfer of 80 million bacteria per intimate kiss of 10 s. CONCLUSIONS This study indicates that a shared salivary microbiota requires a frequent and recent bacterial exchange and is therefore most pronounced in couples with relatively high intimate kiss frequencies. The microbiota on the dorsal surface of the tongue is more similar among partners than unrelated individuals, but its similarity does not clearly correlate to kissing behavior, suggesting an important role for specific selection mechanisms resulting from a shared lifestyle, environment, or genetic factors from the host. Furthermore, our findings imply that some of the collective bacteria among partners are only transiently present, while others have found a true niche on the tongue's surface allowing long-term colonization.
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Affiliation(s)
- Remco Kort
- TNO Microbiology and Systems Biology, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
- Micropia, Natura Artis Magistra, Plantage Kerklaan 38-40, 1018 CZ Amsterdam, The Netherlands
- VU University Amsterdam, Molecular Cell Physiology, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Martien Caspers
- TNO Microbiology and Systems Biology, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Astrid van de Graaf
- Micropia, Natura Artis Magistra, Plantage Kerklaan 38-40, 1018 CZ Amsterdam, The Netherlands
| | - Wim van Egmond
- Micropia, Natura Artis Magistra, Plantage Kerklaan 38-40, 1018 CZ Amsterdam, The Netherlands
| | - Bart Keijser
- TNO Microbiology and Systems Biology, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Guus Roeselers
- TNO Microbiology and Systems Biology, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
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Coolen JPM, Sjödin A, Maraha B, Hajer GF, Forsman M, Verspui E, Frenay HME, Notermans DW, de Vries MC, Reubsaet FAG, Paauw A, Roeselers G. Draft genome sequence of Francisella tularensis subsp. holarctica BD11-00177. Stand Genomic Sci 2013; 8:539-47. [PMID: 24501637 PMCID: PMC3910693 DOI: 10.4056/sigs.4217923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Francisella tularensis is a facultative intracellular bacterium in the class Gammaproteobacteria. This strain is of interest because it is the etiologic agent of tularemia and a highly virulent category A biothreat agent. Here we describe the draft genome sequence and annotation of Francisella tularensis subsp. holarctica BD11-00177, isolated from the first case of indigenous tularemia detected in The Netherlands since 1953. Whole genome DNA sequence analysis assigned this isolate to the genomic group B.FTNF002–00, which previously has been exclusively reported from Spain, France, Italy, Switzerland and Germany. Automatic annotation of the 1,813,372 bp draft genome revealed 2,103 protein-coding and 46 RNA genes.
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Affiliation(s)
| | - Andreas Sjödin
- Division for CBRN Defence and Security, FOI - Swedish Defence Research Agency, Umeå, Sweden
| | - Boulos Maraha
- Department of Medical Microbiology, Beatrix Hospital, Gorinchem and Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | - Gerard F Hajer
- Department of Surgery, Beatrix Hospital, Gorinchem, The Netherlands
| | - Mats Forsman
- Division for CBRN Defence and Security, FOI - Swedish Defence Research Agency, Umeå, Sweden
| | - Ellen Verspui
- Public Health Service Zuid Holland Zuid, Dordrecht, The Netherlands
| | - Hendrina M E Frenay
- Department of Medical Microbiology, Beatrix Hospital, Gorinchem and Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | - Daan W Notermans
- Diagnostic Laboratory for Infectious Diseases and Perinatal Screening (LIS), Center for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Maaike C de Vries
- Diagnostic Laboratory for Infectious Diseases and Perinatal Screening (LIS), Center for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Frans A G Reubsaet
- Diagnostic Laboratory for Infectious Diseases and Perinatal Screening (LIS), Center for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJCT, Dutilh BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Gloerich J, Geerts W, van der Biezen E, Pluk W, Francoijs KJ, Russ L, Lam P, Malfatti SA, Tringe SG, Haaijer SCM, Op den Camp HJM, Stunnenberg HG, Amann R, Kuypers MMM, Jetten MSM. The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium. Environ Microbiol 2013; 15:1275-89. [PMID: 22568606 PMCID: PMC3655542 DOI: 10.1111/j.1462-2920.2012.02774.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/11/2012] [Accepted: 04/12/2012] [Indexed: 11/28/2022]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the 'Candidatus Scalindua' species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by 'Candidatus Scalindua profunda' to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater 'Candidatus Kuenenia stuttgartiensis'. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K.stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.
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Affiliation(s)
- Jack van de Vossenberg
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Dagmar Woebken
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Wouter J Maalcke
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Hans J C T Wessels
- Nijmegen Centre for Mitochondrial Disorders, Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Bas E Dutilh
- CMBI, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Boran Kartal
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Eva M Janssen-Megens
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Guus Roeselers
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Jia Yan
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Daan Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Jolein Gloerich
- Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Wim Geerts
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Erwin van der Biezen
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Wendy Pluk
- Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Kees-Jan Francoijs
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Lina Russ
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Phyllis Lam
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | | | | | - Suzanne C M Haaijer
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Henk G Stunnenberg
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Rudi Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of TechnologyDelft, the Netherlands
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Roeselers G, Ponomarenko M, Lukovac S, Wortelboer HM. Ex vivo systems to study host-microbiota interactions in the gastrointestinal tract. Best Pract Res Clin Gastroenterol 2013; 27:101-13. [PMID: 23768556 DOI: 10.1016/j.bpg.2013.03.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/18/2013] [Accepted: 03/26/2013] [Indexed: 01/31/2023]
Abstract
It is increasingly apparent that the microbial ecosystems in the mammalian gastrointestinal tract play an intricate role in health and disease. There is a growing interest in the development of targeted strategies for modulating health through the modification of these microbiota. Ecologists are faced with the challenge of understanding the structure and function of ecosystems, the component parts of which interact with each other in complex and diffuse ways. The human gut microbiota, with its high species richness and diversity (up to 1000 bacterial species per individual) including members of all three domains of life, situated in the dynamic environment of the gastrointestinal tract, is probably among the most complex ecosystems on this planet. In order to elucidate the mechanistic foundations, and physiological significance, of beneficial or pathogenic relationships between the gut microbiota and their hosts, researchers require tractable model ecosystems that allow to recapitulate and investigate host-microbe and microbe-microbe interactions. This review discusses ex vivo gastrointestinal models systems that can be used to gain mechanistic insights into the emergent properties of the host-microbial superorganism.
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Affiliation(s)
- Guus Roeselers
- TNO, Utrechtseweg 48, Zeist, 3704 HE Utrecht, The Netherlands.
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Newton ILG, Roeselers G. The effect of training set on the classification of honey bee gut microbiota using the Naïve Bayesian Classifier. BMC Microbiol 2012; 12:221. [PMID: 23013113 PMCID: PMC3520854 DOI: 10.1186/1471-2180-12-221] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 09/23/2012] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Microbial ecologists now routinely utilize next-generation sequencing methods to assess microbial diversity in the environment. One tool heavily utilized by many groups is the Naïve Bayesian Classifier developed by the Ribosomal Database Project (RDP-NBC). However, the consistency and confidence of classifications provided by the RDP-NBC is dependent on the training set utilized. RESULTS We explored the stability of classification of honey bee gut microbiota sequences by the RDP-NBC utilizing three publically available ribosomal RNA sequence databases as training sets: ARB-SILVA, Greengenes and RDP. We found that the inclusion of previously published, high-quality, full-length sequences from 16S rRNA clone libraries improved the precision in classification of novel bee-associated sequences. Specifically, by including bee-specific 16S rRNA gene sequences a larger fraction of sequences were classified at a higher confidence by the RDP-NBC (based on bootstrap scores). CONCLUSIONS Results from the analysis of these bee-associated sequences have ramifications for other environments represented by few sequences in the public databases or few bacterial isolates. We conclude that for the exploration of relatively novel habitats, the inclusion of high-quality, full-length 16S rRNA gene sequences allows for a more confident taxonomic classification.
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Affiliation(s)
- Irene L G Newton
- Department of Biology, 1001 E 3rd Street, Bloomington, IN 47405, USA.
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Mattila HR, Rios D, Walker-Sperling VE, Roeselers G, Newton ILG. Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse. PLoS One 2012; 7:e32962. [PMID: 22427917 PMCID: PMC3299707 DOI: 10.1371/journal.pone.0032962] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 02/07/2012] [Indexed: 01/25/2023] Open
Abstract
Recent losses of honey bee colonies have led to increased interest in the microbial communities that are associated with these important pollinators. A critical function that bacteria perform for their honey bee hosts, but one that is poorly understood, is the transformation of worker-collected pollen into bee bread, a nutritious food product that can be stored for long periods in colonies. We used 16S rRNA pyrosequencing to comprehensively characterize in genetically diverse and genetically uniform colonies the active bacterial communities that are found on honey bees, in their digestive tracts, and in bee bread. This method provided insights that have not been revealed by past studies into the content and benefits of honey bee-associated microbial communities. Colony microbiotas differed substantially between sampling environments and were dominated by several anaerobic bacterial genera never before associated with honey bees, but renowned for their use by humans to ferment food. Colonies with genetically diverse populations of workers, a result of the highly promiscuous mating behavior of queens, benefited from greater microbial diversity, reduced pathogen loads, and increased abundance of putatively helpful bacteria, particularly species from the potentially probiotic genus Bifidobacterium. Across all colonies, Bifidobacterium activity was negatively correlated with the activity of genera that include pathogenic microbes; this relationship suggests a possible target for understanding whether microbes provide protective benefits to honey bees. Within-colony diversity shapes microbiotas associated with honey bees in ways that may have important repercussions for colony function and health. Our findings illuminate the importance of honey bee-bacteria symbioses and examine their intersection with nutrition, pathogen load, and genetic diversity, factors that are considered key to understanding honey bee decline.
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Affiliation(s)
- Heather R. Mattila
- Department of Biological Sciences, Wellesley College, Wellesley, Massachussetts, United States of America
| | - Daniela Rios
- Department of Biological Sciences, Wellesley College, Wellesley, Massachussetts, United States of America
| | | | - Guus Roeselers
- Microbiology & Systems Biology group, TNO, Utrechtseweg, Zeist, The Netherlands
| | - Irene L. G. Newton
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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Biesbroek G, Sanders EAM, Roeselers G, Wang X, Caspers MPM, Trzciński K, Bogaert D, Keijser BJF. Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection. PLoS One 2012; 7:e32942. [PMID: 22412957 PMCID: PMC3295791 DOI: 10.1371/journal.pone.0032942] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 02/02/2012] [Indexed: 02/07/2023] Open
Abstract
Introduction Accurate analyses of microbiota composition of low-density communities (103–104 bacteria/sample) can be challenging. Background DNA from chemicals and consumables, extraction biases as well as differences in PCR efficiency can significantly interfere with microbiota assessment. This study was aiming to establish protocols for accurate microbiota analysis at low microbial density. Methods To examine possible effects of bacterial density on microbiota analyses we compared microbiota profiles of serial diluted saliva and low (nares, nasopharynx) and high-density (oropharynx) upper airway communities in four healthy individuals. DNA was extracted with four different extraction methods (Epicentre Masterpure, Qiagen DNeasy, Mobio Powersoil and a phenol bead-beating protocol combined with Agowa-Mag-mini). Bacterial DNA recovery was analysed by 16S qPCR and microbiota profiles through GS-FLX-Titanium-Sequencing of 16S rRNA gene amplicons spanning the V5–V7 regions. Results Lower template concentrations significantly impacted microbiota profiling results. With higher dilutions, low abundant species were overrepresented. In samples of <105 bacteria per ml, e.g. DNA <1 pg/µl, microbiota profiling deviated from the original sample and other dilutions showing a significant increase in the taxa Proteobacteria and decrease in Bacteroidetes. In similar low density samples, DNA extraction method determined if DNA levels were below or above 1 pg/µl and, together with lysis preferences per method, had profound impact on microbiota analyses in both relative abundance as well as representation of species. Conclusion This study aimed to interpret microbiota analyses of low-density communities. Bacterial density seemed to interfere with microbiota analyses at < than 106 bacteria per ml or DNA <1 pg/µl. We therefore recommend this threshold for working with low density materials. This study underlines that bias reduction is crucial for adequate profiling of especially low-density bacterial communities.
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Affiliation(s)
- Giske Biesbroek
- Department of Pediatric Infectious Diseases and Immunity UMC Utrecht, Utrecht, The Netherlands
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Roeselers G, Newton ILG. On the evolutionary ecology of symbioses between chemosynthetic bacteria and bivalves. Appl Microbiol Biotechnol 2012; 94:1-10. [PMID: 22354364 PMCID: PMC3304057 DOI: 10.1007/s00253-011-3819-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [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: 09/21/2011] [Revised: 12/03/2011] [Accepted: 12/05/2011] [Indexed: 11/28/2022]
Abstract
Mutualistic associations between bacteria and eukaryotes occur ubiquitously in nature, forming the basis for key ecological and evolutionary innovations. Some of the most prominent examples of these symbioses are chemosynthetic bacteria and marine invertebrates living in the absence of sunlight at deep-sea hydrothermal vents and in sediments rich in reduced sulfur compounds. Here, chemosynthetic bacteria living in close association with their hosts convert CO2 or CH4 into organic compounds and provide the host with necessary nutrients. The dominant macrofauna of hydrothermal vent and cold seep ecosystems all depend on the metabolic activity of chemosynthetic bacteria, which accounts for almost all primary production in these complex ecosystems. Many of these enigmatic mutualistic associations are found within the molluscan class Bivalvia. Currently, chemosynthetic symbioses have been reported from five distinct bivalve families (Lucinidae, Mytilidae, Solemyidae, Thyasiridae, and Vesicomyidae). This brief review aims to provide an overview of the diverse physiological and genetic adaptations of symbiotic chemosynthetic bacteria and their bivalve hosts.
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Affiliation(s)
- Guus Roeselers
- Microbiology and Systems Biology Group, TNO, Utrechtseweg 48, 3700 AJ Zeist, The Netherlands.
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Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF. Evidence for a core gut microbiota in the zebrafish. ISME J 2011; 5:1595-608. [PMID: 21472014 DOI: 10.1038/ismej.2011.38] [Citation(s) in RCA: 639] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Experimental analysis of gut microbial communities and their interactions with vertebrate hosts is conducted predominantly in domesticated animals that have been maintained in laboratory facilities for many generations. These animal models are useful for studying coevolved relationships between host and microbiota only if the microbial communities that occur in animals in lab facilities are representative of those that occur in nature. We performed 16S rRNA gene sequence-based comparisons of gut bacterial communities in zebrafish collected recently from their natural habitat and those reared for generations in lab facilities in different geographic locations. Patterns of gut microbiota structure in domesticated zebrafish varied across different lab facilities in correlation with historical connections between those facilities. However, gut microbiota membership in domesticated and recently caught zebrafish was strikingly similar, with a shared core gut microbiota. The zebrafish intestinal habitat therefore selects for specific bacterial taxa despite radical differences in host provenance and domestication status.
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Affiliation(s)
- Guus Roeselers
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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Bates AE, Harmer TL, Roeselers G, Cavanaugh CM. Phylogenetic characterization of episymbiotic bacteria hosted by a hydrothermal vent limpet (lepetodrilidae, vetigastropoda). Biol Bull 2011; 220:118-127. [PMID: 21551448 DOI: 10.1086/bblv220n2p118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Marine invertebrates hosting chemosynthetic bacterial symbionts are known from multiple phyla and represent remarkable diversity in form and function. The deep-sea hydrothermal vent limpet Lepetodrilus fucensis from the Juan de Fuca Ridge complex hosts a gill symbiosis of particular interest because it displays a morphology unique among molluscs: filamentous bacteria are found partially embedded in the host's gill epithelium and extend into the fluids circulating across the lamellae. Our objective was to investigate the phylogenetic affiliation of the limpet's primary gill symbionts for comparison with previously characterized bacteria. Comparative 16S rRNA sequence analysis identified one γ- and three ε-Proteobacteria as candidate symbionts. We used fluorescence in situ hybridization (FISH) to test which of these four candidates occur with the limpet's symbiotic gill bacteria. The γ-proteobacterial probes consistently hybridized to the entire area where symbiotic bacteria were found, but fluorescence signal from the ε-proteobacterial probes was generally absent. Amplification of the γ-proteobacterial 16S rRNA gene using a specific forward primer yielded a sequence similar to that of limpets collected from different ridge sections. In total, direct amplification or FISH identified a single γ-proteobacterial lineage from the gills of 23 specimens from vents separated by a distance up to about 200 km and collected over the course of 2 years, suggesting a highly specific and widespread symbiosis. Thus, we report the first filamentous γ-proteobacterial gill symbiont hosted by a mollusc.
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Affiliation(s)
- Amanda E Bates
- Department of Biology, University of Victoria, British Columbia, Canada.
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Roeselers G, Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. Complete genome sequence of Candidatus Ruthia magnifica. Stand Genomic Sci 2010; 3:163-73. [PMID: 21304746 PMCID: PMC3035367 DOI: 10.4056/sigs.1103048] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [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: 11/30/2022] Open
Abstract
The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Mollusca) is a member of the Vesicomyidae. Species within this family form symbioses with chemosynthetic Gammaproteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a rudimentary gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. The C. magnifica symbiont, Candidatus Ruthia magnifica, was the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced (Newton et al. 2007). Here we expand upon the original report and provide additional details complying with the emerging MIGS/MIMS standards. The complete genome exposed the genetic blueprint of the metabolic capabilities of the symbiont. Genes which were predicted to encode the proteins required for all the metabolic pathways typical of free-living chemoautotrophs were detected in the symbiont genome. These include major pathways including carbon fixation, sulfur oxidation, nitrogen assimilation, as well as amino acid and cofactor/vitamin biosynthesis. This genome sequence is invaluable in the study of these enigmatic associations and provides insights into the origin and evolution of autotrophic endosymbiosis.
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Affiliation(s)
- Guus Roeselers
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
- Radboud University, Department of Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Irene L. G. Newton
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
- Department of Biological Sciences, 106 Central St, Wellesley, MA 02482, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Thomas A. Auchtung
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Geoffrey F. Dilly
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Rachel J. Dutton
- Harvard Medical School, Department of Microbiology and Molecular Genetics, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Meredith C. Fisher
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Kristina M. Fontanez
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Evan Lau
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Frank J. Stewart
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Paul M. Richardson
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kerrie W. Barry
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Elizabeth Saunders
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - John C. Detter
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Dongying Wu
- University of California, Davis Genome Center, Genome and Biomedical Sciences Facility, Room 5311, 451 East Health Sciences Drive, Davis, CA 95616–8816, USA
| | - Jonathan A. Eisen
- University of California, Davis Genome Center, Genome and Biomedical Sciences Facility, Room 5311, 451 East Health Sciences Drive, Davis, CA 95616–8816, USA
| | - Colleen M. Cavanaugh
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
- Corresponding author
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Roeselers G, Loosdrecht MCMV, Muyzer G. Phototrophic biofilms and their potential applications. J Appl Phycol 2008; 20:227-235. [PMID: 19396356 PMCID: PMC2668646 DOI: 10.1007/s10811-007-9223-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 06/19/2007] [Accepted: 06/19/2007] [Indexed: 05/11/2023]
Abstract
Phototrophic biofilms occur on surfaces exposed to light in a range of terrestrial and aquatic environments. Oxygenic phototrophs like diatoms, green algae, and cyanobacteria are the major primary producers that generate energy and reduce carbon dioxide, providing the system with organic substrates and oxygen. Photosynthesis fuels processes and conversions in the total biofilm community, including the metabolism of heterotrophic organisms. A matrix of polymeric substances secreted by phototrophs and heterotrophs enhances the attachment of the biofilm community. This review discusses the actual and potential applications of phototrophic biofilms in wastewater treatment, bioremediation, fish-feed production, biohydrogen production, and soil improvement.
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Affiliation(s)
- G. Roeselers
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - M. C. M. van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - G. Muyzer
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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Roeselers G, Huisjes EH, Van Loosdrecht MC, Muyzer G. Diversity and expression of cyanobacterial hupS genes in pure cultures and in a nitrogen-limited phototrophic biofilm. FEMS Microbiol Ecol 2008; 63:292-300. [DOI: 10.1111/j.1574-6941.2008.00435.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Roeselers G, van Loosdrecht MCM, Muyzer G. Heterotrophic pioneers facilitate phototrophic biofilm development. Microb Ecol 2007; 54:578-85. [PMID: 17370028 DOI: 10.1007/s00248-007-9238-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 02/26/2007] [Indexed: 05/14/2023]
Abstract
Phototrophic biofilms are matrix-enclosed microbial communities, mainly driven by light energy. In this study, the successional changes in community composition of freshwater phototrophic biofilms growing on polycarbonate slides under different light intensities were investigated. The sequential changes in community composition during different developmental stages were examined by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments in conjugation with sequencing and phylogenetic analysis. Biofilm development was monitored with subsurface light sensors. The development of these biofilms was clearly light dependent. It was shown that under high light conditions the initial colonizers of the substratum predominantly consisted of green algae, whereas at low light intensities, heterotrophic bacteria were the initial colonizers. Cluster analysis of DGGE banding patterns revealed a clear correlation in the community structure with the developmental phases of the biofilms. At all light intensities, filamentous cyanobacteria affiliated to Microcoleus vaginatus became dominant as the biofilms matured. It was shown that the initial colonization phase of the phototrophic biofilms is shorter on polycarbonate surfaces precolonized by heterotrophic bacteria.
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Affiliation(s)
- G Roeselers
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, The Netherlands
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Roeselers G, Stal LJ, van Loosdrecht MCM, Muyzer G. Development of a PCR for the detection and identification of cyanobacterial nifD genes. J Microbiol Methods 2007; 70:550-6. [PMID: 17681622 DOI: 10.1016/j.mimet.2007.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 06/08/2007] [Accepted: 06/20/2007] [Indexed: 11/23/2022]
Abstract
In this study we have designed degenerate primers after comparative analysis of nifD gene sequences from public databases, and developed a PCR protocol for the amplification of nifD sequences from cyanobacteria. The primers were tested on a variety of nitrogenase-containing and nitrogenase-lacking bacteria. By using this protocol, we amplified nifD sequences from DNA that was isolated from three phototrophic microbial communities. Denaturing gradient gel electrophoresis (DGGE) and clone library analysis of the nifD amplicons showed the presence of distinct groups of diazotrophic cyanobacteria in each of the investigated microbial communities. Phylogenetic trees constructed from the sequences of nifD gene fragments are congruent with those based on ribosomal RNA gene sequences.
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Affiliation(s)
- Guus Roeselers
- Department of Biotechnology, Delft University of Technology, NL-2628 BC Delft, The Netherlands
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Roeselers G, Zippel B, Staal M, van Loosdrecht M, Muyzer G. On the reproducibility of microcosm experiments - different community composition in parallel phototrophic biofilm microcosms. FEMS Microbiol Ecol 2007; 58:169-78. [PMID: 17064259 DOI: 10.1111/j.1574-6941.2006.00172.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Phototrophic biofilms were cultivated simultaneously using the same inoculum in three identical flow-lane microcosms located in different laboratories. The growth rates of the biofilms were similar in the different microcosms, but denaturing gradient gel electrophoresis (DGGE) analysis of both 16S and 18S rRNA gene fragments showed that the communities developed differently in terms of species richness and community composition. One microcosm was dominated by Microcoleus and Phormidium species, the second microcosm was dominated by Synechocystis and Phormidium species, and the third microcosm was dominated by Microcoleus- and Planktothrix- affiliated species. No clear effect of light intensity on the cyanobacterial community composition was observed. In addition, DGGE profiles obtained from the cultivated biofilms showed a low resemblance with the profiles derived from the inoculum. These findings demonstrate that validation of reproducibility is essential for the use of microcosm systems in microbial ecology studies.
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Affiliation(s)
- Guus Roeselers
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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Roeselers G, Norris TB, Castenholz RW, Rysgaard S, Glud RN, Kühl M, Muyzer G. Diversity of phototrophic bacteria in microbial mats from Arctic hot springs (Greenland). Environ Microbiol 2007; 9:26-38. [PMID: 17227409 DOI: 10.1111/j.1462-2920.2006.01103.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the genotypic diversity of oxygenic and anoxygenic phototrophic microorganisms in microbial mat samples collected from three hot spring localities on the east coast of Greenland. These hot springs harbour unique Arctic microbial ecosystems that have never been studied in detail before. Specific oligonucleotide primers for cyanobacteria, purple sulfur bacteria, green sulfur bacteria and Choroflexus/Roseiflexus-like green non-sulfur bacteria were used for the selective amplification of 16S rRNA gene fragments. Amplification products were separated by denaturing gradient gel electrophoresis (DGGE) and sequenced. In addition, several cyanobacteria were isolated from the mat samples, and classified morphologically and by 16S rRNA-based methods. The cyanobacterial 16S rRNA sequences obtained from DGGE represented a diverse, polyphyletic collection of cyanobacteria. The microbial mat communities were dominated by heterocystous and non-heterocystous filamentous cyanobacteria. Our results indicate that the cyanobacterial community composition in the samples were different for each sampling site. Different layers of the same heterogeneous mat often contained distinct and different communities of cyanobacteria. We observed a relationship between the cyanobacterial community composition and the in situ temperatures of different mat parts. The Greenland mats exhibited a low diversity of anoxygenic phototrophs as compared with other hot spring mats which is possibly related to the photochemical conditions within the mats resulting from the Arctic light regime.
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Affiliation(s)
- Guus Roeselers
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, NL-2628 BC Delft, the Netherlands
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