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Aboshady HM, Gavriilidou A, Ghanem N, Radwan MA, Elnahas A, Agamy R, Fahim NH, Elsawy MH, Shaarawy AMBM, Abdel-Hafeez AM, Kantanen J, Ginja C, Makgahlela ML, Kugonza DR, Gonzalez-Prendes R, Crooijmans RPMA. Gut Microbiota Diversity of Local Egyptian Cattle Managed in Different Ecosystems. Animals (Basel) 2024; 14:2752. [PMID: 39335341 PMCID: PMC11428623 DOI: 10.3390/ani14182752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 09/16/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
The animal gastrointestinal tract contains a complex microbiome whose composition ultimately reflects the co-evolution of microorganisms with their animal host and their host's environment. This study aimed to gain insights into the adaptation of the microbiota of local Egyptian cattle to three different ecosystems (Upper Egypt, Middle Egypt, and Lower Egypt) distributed across 11 governorates (with an average of 12 animals per governorate) using amplicon sequencing. We analyzed the microbiota from 136 fecal samples of local Egyptian cattle through a 16S rRNA gene sequencing approach to better understand the fecal microbial diversity of this breed which developed under different ecosystems. An alpha diversity analysis showed that the fecal microbiota of the Egyptian cattle was not significantly diverse across areas, seasons, sexes, or farm types. Meanwhile, microbiota data revealed significant differences in richness among age groups (p = 0.0018). The microbial community differed significantly in the distribution of its relative abundance rather than in richness across different ecosystems. The taxonomic analysis of the reads identified Firmicutes and Actinobacteriota as the dominant phyla, accounting for over 93% of the total bacterial community in Egyptian cattle. Middle Egypt exhibited a different microbial community composition compared to Upper and Lower Egypt, with a significantly higher abundance of Firmicutes and Euryarchaeota and a lower abundance of Actinobacteriota in this region than the other two ecosystems. Additionally, Middle Egypt had a significantly higher relative abundance of the Methanobacteriaceae family and the Methanobrevibacter genera than Lower and Upper Egypt. These results suggest a difference in the adaptation of the fecal microbial communities of Egyptian cattle raised in Middle Egypt. At the genus level, eleven genera were significantly different among the three ecosystems including Bacillus, DNF00809, Kandleria, Lachnospiraceae_NK3A20_group, Methanobrevibacter, Mogibacterium, Olsenella, Paeniclostridium, Romboutsia, Turicibacter, and UCG-005. These significant differences in microbiota composition may impact the animal's adaptation to varied environments.
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Affiliation(s)
- Hadeer M. Aboshady
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt (M.A.R.); (R.A.); (N.H.F.)
| | - Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
| | - Nasser Ghanem
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt (M.A.R.); (R.A.); (N.H.F.)
| | - Mohamed A. Radwan
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt (M.A.R.); (R.A.); (N.H.F.)
| | - Ahmed Elnahas
- Animal Production Department, Faculty of Agriculture, Sohag University, Sohag 82524, Egypt;
| | - Rania Agamy
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt (M.A.R.); (R.A.); (N.H.F.)
| | - Nadia H. Fahim
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt (M.A.R.); (R.A.); (N.H.F.)
| | - Mohamed H. Elsawy
- Department of Cattle, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt; (M.H.E.); (A.-M.B.M.S.); (A.M.A.-H.)
| | - Al-Moataz Bellah M. Shaarawy
- Department of Cattle, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt; (M.H.E.); (A.-M.B.M.S.); (A.M.A.-H.)
| | - Ahmed M. Abdel-Hafeez
- Department of Cattle, Animal Production Research Institute, Agriculture Research Center, Dokki, Giza 12618, Egypt; (M.H.E.); (A.-M.B.M.S.); (A.M.A.-H.)
| | - Juha Kantanen
- Natural Resources Institute Finland, 31600 Jokioinen, Finland;
| | - Catarina Ginja
- CIISA, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisboa, Portugal
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Associate Laboratory, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, University of Porto, 4485-661 Vairão, Portugal
| | - Mahlako L. Makgahlela
- Agricultural Research Council, Animal Production, Private Bag X2, Irene 0062, South Africa;
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9301, South Africa
| | - Donald R. Kugonza
- School of Agricultural Sciences, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Rayner Gonzalez-Prendes
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands; (R.G.-P.); (R.P.M.A.C.)
| | - Richard P. M. A. Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands; (R.G.-P.); (R.P.M.A.C.)
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2
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Paulo LM, Liu YC, Castilla-Archilla J, Ramiro-Garcia J, Hughes D, Mahony T, Holohan BC, Wilmes P, O'Flaherty V. Full-scale study on high-rate low-temperature anaerobic digestion of agro-food wastewater: process performances and microbial community. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 90:1239-1249. [PMID: 39215735 DOI: 10.2166/wst.2024.272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024]
Abstract
The fast-growing global population has led to a substantial increase in food production, which generates large volumes of wastewater during the process. Despite most industrial wastewater being discharged at lower ambient temperatures (<20 °C), majority of the high-rate anaerobic reactors are operated at mesophilic temperatures (>30 °C). High-rate low-temperature anaerobic digestion (LtAD) has proven successful in treating industrial wastewater both at laboratory and pilot scales, boasting efficient organic removal and biogas production. In this study, we demonstrated the feasibility of two full-scale high-rate LtAD bioreactors treating meat processing and dairy wastewater, and the microbial communities in both reactors were examined. Both reactors exhibited rapid start-up, achieving considerable chemical oxygen demand (COD) removal efficiencies (total COD removal >80%) and generating high-quality biogas (CH4% in biogas >75%). Long-term operations (6-12 months) underscored the robustness of LtAD bioreactors even during winter periods (average temperature <12 °C), as evidenced by sustained high COD removal rates (total COD removal >80%). The stable performance was underpinned by a resilient microbial community comprising active acetoclastic methanogens, hydrolytic, and fermentative bacteria. These findings underscore the feasibility of high-rate low-temperature anaerobic wastewater treatment, offering promising solutions to the zero-emission wastewater treatment challenge.
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Affiliation(s)
- Lara M Paulo
- Microbial Ecology Laboratory, School of Biological and Chemical Sciences and Ryan Institute, University of Galway, Galway, H91 TK33, Ireland; Dairy Processing Technology Centre, University of Limerick, Analog Devices Building, Limerick V94 T9PX, Ireland
| | - Yu-Chen Liu
- Microbial Ecology Laboratory, School of Biological and Chemical Sciences and Ryan Institute, University of Galway, Galway, H91 TK33, Ireland
| | - Juan Castilla-Archilla
- Microbial Ecology Laboratory, School of Biological and Chemical Sciences and Ryan Institute, University of Galway, Galway, H91 TK33, Ireland; Dairy Processing Technology Centre, University of Limerick, Analog Devices Building, Limerick V94 T9PX, Ireland
| | - Javier Ramiro-Garcia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dermot Hughes
- Dairy Processing Technology Centre, University of Limerick, Analog Devices Building, Limerick V94 T9PX, Ireland; NVP Energy, Galway Technology Centre, Mervue Business Park, Galway, Ireland
| | - Thérèse Mahony
- Microbial Ecology Laboratory, School of Biological and Chemical Sciences and Ryan Institute, University of Galway, Galway, H91 TK33, Ireland; Dairy Processing Technology Centre, University of Limerick, Analog Devices Building, Limerick V94 T9PX, Ireland
| | - B Conall Holohan
- Microbial Ecology Laboratory, School of Biological and Chemical Sciences and Ryan Institute, University of Galway, Galway, H91 TK33, Ireland; NVP Energy, Galway Technology Centre, Mervue Business Park, Galway, Ireland; Department of Microbiology, Huygensgebouw, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, School of Biological and Chemical Sciences and Ryan Institute, University of Galway, Galway, H91 TK33, Ireland; Dairy Processing Technology Centre, University of Limerick, Analog Devices Building, Limerick V94 T9PX, Ireland E-mail:
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3
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Aldas-Vargas A, Kers JG, Smidt H, Rijnaarts HHM, Sutton NB. Bioaugmentation has temporary effect on anaerobic pesticide biodegradation in simulated groundwater systems. Biodegradation 2024; 35:281-297. [PMID: 37439919 PMCID: PMC10951022 DOI: 10.1007/s10532-023-10039-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/30/2023] [Indexed: 07/14/2023]
Abstract
Groundwater is the most important source for drinking water in The Netherlands. Groundwater quality is threatened by the presence of pesticides, and biodegradation is a natural process that can contribute to pesticide removal. Groundwater conditions are oligotrophic and thus biodegradation can be limited by the presence and development of microbial communities capable of biodegrading pesticides. For that reason, bioremediation technologies such as bioaugmentation (BA) can help to enhance pesticide biodegradation. We studied the effect of BA using enriched mixed inocula in two column bioreactors that simulate groundwater systems at naturally occurring redox conditions (iron and sulfate-reducing conditions). Columns were operated for around 800 days, and two BA inoculations (BA1 and BA2) were conducted in each column. Inocula were enriched from different wastewater treatment plants (WWTPs) under different redox-conditions. We observed a temporary effect of BA1, reaching 100% removal efficiency of the pesticide 2,4-D after 100 days in both columns. In the iron-reducing column, 2,4-D removal was in general higher than under sulfate-reducing conditions demonstrating the influence of redox conditions on overall biodegradation. We observed a temporary shift in microbial communities after BA1 that is relatable to the increase in 2,4-D removal efficiency. After BA2 under sulfate-reducing conditions, 2,4-D removal efficiency decreased, but no change in the column microbial communities was observed. The present study demonstrates that BA with a mixed inoculum can be a valuable technique for improving biodegradation in anoxic groundwater systems at different redox-conditions.
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Affiliation(s)
- Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Jannigje G Kers
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
| | - Huub H M Rijnaarts
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands.
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van Trijp MPH, Rios-Morales M, Witteman B, Abegaz F, Gerding A, An R, Koehorst M, Evers B, van Dongen KCV, Zoetendal EG, Schols H, Afman LA, Reijngoud DJ, Bakker BM, Hooiveld GJ. Intraintestinal fermentation of fructo- and galacto-oligosaccharides and the fate of short-chain fatty acids in humans. iScience 2024; 27:109208. [PMID: 38420581 PMCID: PMC10901090 DOI: 10.1016/j.isci.2024.109208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/21/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Consumption of fructo- (FOS) and galacto-oligosaccharides (GOS) has health benefits which have been linked in part to short-chain fatty acids (SCFA) production by the gut microbiota. However, detailed knowledge of this process in the human intestine is lacking. We aimed to determine the acute fermentation kinetics of a FOS:GOS mixture in healthy males using a naso-intestinal catheter for sampling directly in the ileum or colon. We studied the fate of SCFA as substrates for glucose and lipid metabolism by the host after infusion of 13C-SCFA. In the human distal ileum, no fermentation of FOS:GOS, nor SCFA production, or bacterial cross-feeding was observed. The relative composition of intestinal microbiota changed rapidly during the test day, which demonstrates the relevance of postprandial intestinal sampling to track acute responses of the microbial community toward interventions. SCFA were vividly taken up and metabolized by the host as shown by incorporation of 13C in various host metabolites.
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Affiliation(s)
- Mara P H van Trijp
- Division of Human Nutrition and Health, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Melany Rios-Morales
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Ben Witteman
- Division of Human Nutrition and Health, Wageningen University, Wageningen 6708 WE, the Netherlands
- Hospital Gelderse Vallei, Department of Gastroenterology and Hepatology, Ede 6716 RP, the Netherlands
| | - Fentaw Abegaz
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
- Statistics and Probability Unit, University of Groningen, Groningen 9747 AG, the Netherlands
| | - Albert Gerding
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Ran An
- Laboratory of Microbiology, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Martijn Koehorst
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Bernard Evers
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Katja C V van Dongen
- Division of Toxicology, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Henk Schols
- Laboratory of Food Chemistry, Wageningen University, Wageningen 6708 WG, the Netherlands
| | - Lydia A Afman
- Division of Human Nutrition and Health, Wageningen University, Wageningen 6708 WE, the Netherlands
| | - Dirk-Jan Reijngoud
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Barbara M Bakker
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Guido J Hooiveld
- Division of Human Nutrition and Health, Wageningen University, Wageningen 6708 WE, the Netherlands
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5
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Ou Y, Belzer C, Smidt H, de Weerth C. Development of the gut microbiota in the first 14 years of life and its relations to internalizing and externalizing difficulties and social anxiety during puberty. Eur Child Adolesc Psychiatry 2024; 33:847-860. [PMID: 37071196 PMCID: PMC10894087 DOI: 10.1007/s00787-023-02205-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/03/2023] [Indexed: 04/19/2023]
Abstract
Relations between the gut microbiota and host mental health have been suggested by a growing number of case-control and cross-sectional studies, while supporting evidence is limited in large community samples followed during an extended period. Therefore, the current preregistered study ( https://osf.io/8ymav , September 7, 2022) described child gut microbiota development in the first 14 years of life and explored its relations to internalizing and externalizing difficulties and social anxiety in puberty, a period of high relevance for the development of mental health problems. Fecal microbiota composition was analysed by 16S ribosomal RNA gene amplicon sequencing in a total of 1003 samples from 193 children. Through a clustering method, four distinct microbial clusters were newly identified in puberty. Most children within three of these clusters remained in the same clusters from the age of 12 to 14 years, suggesting stability in microbial development and transition during this period. These three clusters were compositionally similar to enterotypes (i.e., a robust classification of the gut microbiota based on its composition across different populations) enriched in Bacteroides, Prevotella, and Ruminococcus, respectively. Two Prevotella 9-predominated clusters, including one reported by us earlier in middle childhood and the other one in puberty, were associated with more externalizing behavior at age 14. One Faecalibacterium-depleted pubertal cluster was related to more social anxiety at age 14. This finding was confirmed by a negative cross-sectional relation between Faecalibacterium and social anxiety in the 14-year-olds. The findings of this study continue to map gut microbiota development in a relatively large community sample followed from birth onwards, importantly extending our knowledge to puberty. Results indicate that Prevotella 9 and Faecalibacterium may be relevant microbial taxa in relation to externalizing behavior and social anxiety, respectively. These correlational findings need validations from other similar cohort studies, as well as well-designed mechanistic pre-clinical investigations before inferring cause and effect.
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Affiliation(s)
- Yangwenshan Ou
- Laboratory of Microbiology, Wageningen University and Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Center, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands.
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
| | - Carolina de Weerth
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Center, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands
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Eckermann HA, Meijer J, Cooijmans K, Lahti L, de Weerth C. Daily skin-to-skin contact alters microbiota development in healthy full-term infants. Gut Microbes 2024; 16:2295403. [PMID: 38197254 PMCID: PMC10793693 DOI: 10.1080/19490976.2023.2295403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
The gut microbiota is vital for human body development and function. Its development in early life is influenced by various environmental factors. In this randomized controlled trial, the gut microbiota was obtained as a secondary outcome measure in a study on the effects of one hour of daily skin-to-skin contact (SSC) for five weeks in healthy full-term infants. Specifically, we studied the effects on alpha/beta diversity, volatility, microbiota maturation, and bacterial and gut-brain-axis-related functional abundances in microbiota assessed thrice in the first year. Pregnant Dutch women (n = 116) were randomly assigned to the SSC or care-as-usual groups. The SSC group participants engaged in one hour of daily SSC from birth to five weeks of age. Stool samples were collected at two, five, and 52 weeks and the V4 region was sequenced. We observed significant differences in the microbiota composition, bacterial abundances, and predicted functional pathways between the groups. The SSC group exhibited lower microbiota volatility during early infancy. Microbiota maturation was slower in the SSC group during the first year and our results suggested that breastfeeding duration may have partially mediated this relation. Our findings provide evidence that postpartum SSC may influence microbiota development. Replication is necessary to validate and generalize these results. Future studies should include direct stress measurements and extend microbiota sampling beyond the first year to investigate stress as a mechanism and research SSC's impact on long-term microbiota maturation trajectories.
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Affiliation(s)
- Henrik Andreas Eckermann
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
| | - Jennifer Meijer
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
| | - Kelly Cooijmans
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Carolina de Weerth
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
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7
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Ou Y, Rots E, Belzer C, Smidt H, de Weerth C. Gut microbiota and child behavior in early puberty: does child sex play a role? Gut Microbes 2023; 15:2278222. [PMID: 37943628 PMCID: PMC10731618 DOI: 10.1080/19490976.2023.2278222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
A growing number of studies have indicated relations between the gut microbiota and mental health. However, to date, there is a scarcity of microbiota studies in community samples in early puberty. The current preregistered study (https://osf.io/wu2vt) investigated gut microbiota composition in relation to sex in low-risk children and explored behavioral associations with gut microbiota composition and metabolites in the same samples, together with the potential role of sex. Fecal microbiota composition was analyzed in 12-year-old children (N = 137) by 16S rRNA gene sequencing and quantitative PCR. Modest sex differences were observed in beta diversity. Generalized linear models showed consistent behavioral relations to both relative and absolute abundances of individual taxa, including positive associations between Parasutterella and mother-reported internalizing behavior, and negative associations between Odoribacter and mother-reported externalizing behavior. Additionally, Prevotella 9 was positively related to mother-reported externalizing behavior, confirming earlier findings on the same cohort at 5 years of age. Sex-related differences were found in behavioral relations to Ruminiclostridium 5, Alistipes, Streptococcus, Ruminiclostridium 9, Ruminococcaceae UCG-5, and Dialister, for relative abundances, as well as to Family XIII AD3011 group and an unidentified bacterium within the Tenericutes, for absolute abundances. Limited behavioral relations were observed regarding alpha diversity and fecal metabolites. Our findings describe links between the gut microbiota and child behavior, together with differences between child sexes in these relations, in low-risk early pubertal children. Importantly, this study confirmed earlier findings in this cohort of positive relations between Prevotella 9 and externalizing behavior at age 10 years. Results also show the merit of including absolute abundances in microbiota studies.
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Affiliation(s)
- Yangwenshan Ou
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eline Rots
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Carolina de Weerth
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
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8
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Willemsen Y, Ou Y, Belzer C, Arias Vásquez A, Smidt H, Beijers R, de Weerth C. A longitudinal study of the gut microbiota during the first three years of life: Links with problem behavior and executive functions at preschool age. Dev Psychopathol 2023:1-17. [PMID: 37994488 DOI: 10.1017/s0954579423001402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Early life is a sensitive period when microbiota-gut-brain interactions may have important impact on development. This study investigated the associations of the gut microbiota in the first three years of life (two, six, and 12 weeks, and one and three years) with problem behavior and executive functions in N = 64 three-year-old children. Higher relative abundance of Streptococcus at the age of two weeks, as well as its trajectory over time (including ages two, six and 12 weeks, and one and three years), was related to worse executive functions. Higher relative abundance of [Ruminococcus] torques group at the age of three years, as well as its trajectory from one to three years, was associated with less internalizing behavior. Besides, several robust age-specific associations were identified: higher Bifidobacterium relative abundance (age three years) was associated with more internalizing and externalizing issues; higher Blautia relative abundance (age three years) was linked to less internalizing behavior; and increased relative abundance of an unidentified Enterobacteriaceae genus (age two weeks) was related to more externalizing behavior. Our findings provide important longitudinal evidence that early-life gut microbiota may be linked to behavioral and cognitive development in low-risk children.
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Affiliation(s)
- Yvonne Willemsen
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yangwenshan Ou
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Alejandro Arias Vásquez
- Department of Psychiatry and Human Genetics, Donders Center for Medical Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Roseriet Beijers
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- Behavioral Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Carolina de Weerth
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
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Hesp K, van der Heijden JME, Munroe S, Sipkema D, Martens DE, Wijffels RH, Pomponi SA. First continuous marine sponge cell line established. Sci Rep 2023; 13:5766. [PMID: 37031251 PMCID: PMC10082835 DOI: 10.1038/s41598-023-32394-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/27/2023] [Indexed: 04/10/2023] Open
Abstract
The potential of sponge-derived chemicals for pharmaceutical applications remains largely unexploited due to limited available biomass. Although many have attempted to culture marine sponge cells in vitro to create a scalable production platform for such biopharmaceuticals, these efforts have been mostly unsuccessful. We recently showed that Geodia barretti sponge cells could divide rapidly in M1 medium. In this study we established the first continuous marine sponge cell line, originating from G. barretti. G. barretti cells cultured in OpM1 medium, a modification of M1, grew more rapidly and to a higher density than in M1. Cells in OpM1 reached 1.74 population doublings after 30 min, more than twofold higher than the already rapid growth rate of 0.74 population doublings in 30 min in M1. The maximum number of population doublings increased from 5 doublings in M1 to at least 98 doublings in OpM1. Subcultured cells could be cryopreserved and used to inoculate new cultures. With these results, we have overcome a major obstacle that has blocked the path to producing biopharmaceuticals with sponge cells at industrial scale for decades.
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Affiliation(s)
- Kylie Hesp
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands.
| | | | - Stephanie Munroe
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Dirk E Martens
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
| | - Rene H Wijffels
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Shirley A Pomponi
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
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10
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López Nadal A, Boekhorst J, Lute C, van den Berg F, Schorn MA, Bergen Eriksen T, Peggs D, McGurk C, Sipkema D, Kleerebezem M, Wiegertjes GF, Brugman S. Omics and imaging combinatorial approach reveals butyrate-induced inflammatory effects in the zebrafish gut. Anim Microbiome 2023; 5:15. [PMID: 36869372 PMCID: PMC9985269 DOI: 10.1186/s42523-023-00230-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/01/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Prebiotic feed additives aim to improve gut health by influencing the microbiota and the gut barrier. Most studies on feed additives concentrate on one or two (monodisciplinary) outcome parameters, such as immunity, growth, microbiota or intestinal architecture. A combinatorial and comprehensive approach to disclose the complex and multifaceted effects of feed additives is needed to understand their underlying mechanisms before making health benefit claims. Here, we used juvenile zebrafish as a model species to study effects of feed additives by integrating gut microbiota composition data and host gut transcriptomics with high-throughput quantitative histological analysis. Zebrafish received either control, sodium butyrate or saponin-supplemented feed. Butyrate-derived components such as butyric acid or sodium butyrate have been widely used in animal feeds due to their immunostimulant properties, thereby supporting intestinal health. Soy saponin is an antinutritional factor from soybean meal that promotes inflammation due to its amphipathic nature. RESULTS We observed distinct microbial profiles associated with each diet, discovering that butyrate (and saponin to a lesser extent) affected gut microbial composition by reducing the degree of community-structure (co-occurrence network analysis) compared to controls. Analogously, butyrate and saponin supplementation impacted the transcription of numerous canonical pathways compared to control-fed fish. For example, both butyrate and saponin increased the expression of genes associated with immune response and inflammatory response, as well as oxidoreductase activity, compared to controls. Furthermore, butyrate decreased the expression of genes associated with histone modification, mitotic processes and G-coupled receptor activity. High-throughput quantitative histological analysis depicted an increase of eosinophils and rodlet cells in the gut tissue of fish receiving butyrate after one week of feeding and a depletion of mucus-producing cells after 3 weeks of feeding this diet. Combination of all datasets indicated that in juvenile zebrafish, butyrate supplementation increases the immune and the inflammatory response to a greater extent than the established inflammation-inducing anti-nutritional factor saponin. Such comprehensive analysis was supplemented by in vivo imaging of neutrophil and macrophage transgenic reporter zebrafish (mpeg1:mCherry/mpx:eGFPi114) larvae. Upon exposure to butyrate and saponin, these larvae displayed a dose-dependent increase of neutrophils and macrophages in the gut area. CONCLUSION The omics and imaging combinatorial approach provided an integrated evaluation of the effect of butyrate on fish gut health and unraveled inflammatory-like features not previously reported that question the usage of butyrate supplementation to enhance fish gut health under basal conditions. The zebrafish model, due to its unique advantages, provides researchers with an invaluable tool to investigate effects of feed components on fish gut health throughout life.
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Affiliation(s)
- Adrià López Nadal
- grid.4818.50000 0001 0791 5666Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Host-Microbe Interactomics, Wageningen University and Research, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Jos Boekhorst
- grid.4818.50000 0001 0791 5666Host-Microbe Interactomics, Wageningen University and Research, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Carolien Lute
- grid.4818.50000 0001 0791 5666Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Frank van den Berg
- grid.4818.50000 0001 0791 5666Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Michelle A. Schorn
- grid.4818.50000 0001 0791 5666Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | | | - David Peggs
- Skretting Aquaculture Innovation, Stavanger, Norway
| | | | - Detmer Sipkema
- grid.4818.50000 0001 0791 5666Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Michiel Kleerebezem
- grid.4818.50000 0001 0791 5666Host-Microbe Interactomics, Wageningen University and Research, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Geert F. Wiegertjes
- grid.4818.50000 0001 0791 5666Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Sylvia Brugman
- Host-Microbe Interactomics, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands.
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11
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Atzeni A, Martínez MÁ, Babio N, Konstanti P, Tinahones FJ, Vioque J, Corella D, Fitó M, Vidal J, Moreno-Indias I, Pertusa-Martinez S, Álvarez-Sala A, Castañer O, Goday A, Damas-Fuentes M, Belzer C, Martínez-Gonzalez MÁ, Hu FB, Salas-Salvadó J. Association between ultra-processed food consumption and gut microbiota in senior subjects with overweight/obesity and metabolic syndrome. Front Nutr 2022; 9:976547. [PMID: 36299993 PMCID: PMC9589409 DOI: 10.3389/fnut.2022.976547] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022] Open
Abstract
The production and consumption of ultra-processed foods (UPF) has increased considerably during the last years worldwide. Collective evidence shows the association between UPF consumption and adverse health outcomes, including inflammatory gastro-intestinal disorders and obesity. The gut microbiota has been suggested as potential mediator of the effects of UPF consumption on metabolism and health. However, few studies have been conducted in order to elucidate these aspects. Therefore, the aim of the present study was to assess the cross-sectional associations between UPF consumption and gut microbiota in a population of senior subjects (n = 645) within the frame of the PREDIMED-Plus trial. Eligible participants were men and women (aged 55-75 years), without documented history of cardiovascular disease at enrollment, with overweight/obesity (body mass index ≤ 27 and <40 kg/m2) and metabolic syndrome. Using the information of food frequency questionnaires, the consumption of UPF, expressed as a percentage of total dietary energy intake in kcal/day, was calculated considering those food items classified in group 4 of NOVA system. Population was categorized according to tertiles of UPF consumption. Taxonomic fecal microbiota information, along with blood biochemical parameters, anthropometric measurements and clinical data were obtained. Bioinformatics analysis was performed to study the association between fecal microbiota composition and UPF consumption. We observed that subjects allocated in the highest tertile of UPF consumption (21.4 ± 5.0 % kcal/day) presented lower adherence to MedDiet (p < 0.001) and higher total energy intake (p < 0.001). The taxonomic analysis of the fecal microbiota revealed a significant (Benjamini-Hochberg adjusted p < 0.2) positive association between specific taxa and tertiles (T) of UPF consumption: Alloprevotella (p = 0.041 vs. T2; p = 0.065 vs. T3), Negativibacillus (p = 0.096 vs. T3), Prevotella (p = 0.116 vs. T3), and Sutterella (p = 0.116 vs. T2). UPF consumption was positively associated with lower adherence to MedDiet and higher total energy intake in senior subjects with overweight obesity and metabolic syndrome. In addition, positive association with specific fecal microbiota taxa related to inflammatory gastro-intestinal diseases and low consumption of fruits and vegetables, was observed.
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Affiliation(s)
- Alessandro Atzeni
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Universitat Rovira i Virgili, Department de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - María Ágeles Martínez
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Universitat Rovira i Virgili, Department de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - Nancy Babio
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Universitat Rovira i Virgili, Department de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - Prokopis Konstanti
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Francisco J Tinahones
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica de Málaga - IBIMA, Hospital Universitario Virgen de la Vic, Málaga, Spain
| | - Jesús Vioque
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigación Sanitaria y Biomédica de Alicante, Universidad Miguel Hernández (ISABIAL-UMH), Alicante, Spain
| | - Dolores Corella
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | - Montserrat Fitó
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Unit of Cardiovascular Risk and Nutrition, Institut Hospital del Mar de Investigaciones Médicas Municipal d'Investigació Médica (IMIM), Barcelona, Spain
| | - Josep Vidal
- CIBER Diabetes y Enfermedades Metabólicas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Department of Endocrinology, Institut d'Investigacions Biomédiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Isabel Moreno-Indias
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica de Málaga - IBIMA, Hospital Universitario Virgen de la Vic, Málaga, Spain
| | | | - Andrea Álvarez-Sala
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Preventive Medicine, University of Valencia, Valencia, Spain
| | - Olga Castañer
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Unit of Cardiovascular Risk and Nutrition, Institut Hospital del Mar de Investigaciones Médicas Municipal d'Investigació Médica (IMIM), Barcelona, Spain
| | - Albert Goday
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain.,IMIM, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Miguel Damas-Fuentes
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica de Málaga - IBIMA, Hospital Universitario Virgen de la Vic, Málaga, Spain
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Miguel Á Martínez-Gonzalez
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain.,Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Frank B Hu
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, United States.,Channing Division for Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Jordi Salas-Salvadó
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain.,Universitat Rovira i Virgili, Department de Bioquímica i Biotecnologia, Unitat de Nutrició, Reus, Spain.,Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
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12
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Transplantation of maternal intestinal flora to the newborn after elective cesarean section (SECFLOR): study protocol for a double blinded randomized controlled trial. BMC Pediatr 2022; 22:565. [PMID: 36175995 PMCID: PMC9521560 DOI: 10.1186/s12887-022-03609-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
Background A complication of elective cesarean section (CS) delivery is its interference with the normal intestinal colonization of the infant, affecting the immune and metabolic signaling in early life— a process that has been associated with long-term morbidity, such as allergy and diabetes. We evaluate, in CS-delivered infants, whether the normal intestinal microbiome and its early life development can be restored by immediate postnatal transfer of maternal fecal microbiota (FMT) to the newborn, and how this procedure influences the maturation of the immune system. Methods Sixty healthy mothers with planned elective CS are recruited and screened thoroughly for infections. A maternal fecal sample is taken prior to delivery and processed according to a transplantation protocol. After double blinded randomization, half of the newborns will receive a diluted aliquot of their own mother’s stool orally administered in breast milk during the first feeding while the other half will be similarly treated with a placebo. The infants are clinically followed, and fecal samples are gathered weekly until the age of 4 weeks, then at the ages of 8 weeks, 3, 6, 12 and 24 months. The parents fill in questionnaires until the age of 24 months. Blood samples are taken at the age of 2–3 days and 3, 6, 12 and 24 months to assess development of major immune cell populations and plasma proteins throughout the first years of life. Discussion This is the first study to assess long-time effects on the intestinal microbiome and the development of immune system of a maternal fecal transplant given to term infants born by CS. Trial registration ClinicalTrials.gov NCT04173208, registration date 21.11.2019. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-022-03609-3.
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13
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Influence of 1-Methylcyclopropene (1-MCP) on the Processing and Microbial Communities of Spanish-Style and Directly Brined Green Table Olive Fermentations. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8090441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This work evaluates the effect of 1-methylcyclopropene (1-MCP) on postharvest and fermentation of Manzanilla cultivar, processed as Spanish-style or directly brined table olives. During postharvest handling, 1-MCP (2.85 µL/L) reduced the number of colour-turning olives by 18.42% over the untreated fruits. In Spanish-style and directly brined fermentation, the 1-MCP treatment led to lower pH levels, higher titratable acidities, improved firmness and colour olives than untreated fruits. A panel of expert testers also gave higher scores, and overall acceptability to the 1-MCP treated fruits, especially in the case of Spanish-style fermented olives. Metagenomic analysis of olive biofilms at the end of the fermentation process (176 days) revealed that Lactiplantibacillus was the most abundant bacterial genus in both Spanish-style and directly brined olives (>72%). However, fungal biodiversity was higher than bacterial in all treatments. Saccharomyces was the predominant yeast genus associated with directly brined olives (>97%), whilst Wickerhamomyces (>37%) and Zygoascus (>18%) were with Spanish-style fermentations. The 1-MCP treatment doubled the presence of Wickerhamomyces in Spanish-style fruits (74%) whilst reducing the presence of Zygoascus and allowing the growth of Enterobacter (15%) in directly brined olives. Thus, the postharvesting treatment of table olives with 1-MCP could help reduce the maturation progress of olives and improve the organoleptic and quality characteristics of the products without affecting the microbiological evolution of the fermentations.
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14
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Zhang C, Atashgahi S, Bosma TNP, Peng P, Smidt H. Organohalide respiration potential in marine sediments from Aarhus Bay. FEMS Microbiol Ecol 2022; 98:fiac073. [PMID: 35689665 PMCID: PMC9303371 DOI: 10.1093/femsec/fiac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/09/2022] [Accepted: 06/08/2022] [Indexed: 11/14/2022] Open
Abstract
Organohalide respiration (OHR), catalysed by reductive dehalogenases (RDases), plays an important role in halogen cycling. Natural organohalides and putative RDase-encoding genes have been reported in Aarhus Bay sediments, however, OHR has not been experimentally verified. Here we show that sediments of Aarhus Bay can dehalogenate a range of organohalides, and different organohalides differentially affected microbial community compositions. PCE-dechlorinating cultures were further examined by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing. Known organohalide-respiring bacteria (OHRB) including Dehalococcoides, Dehalobacter and Desulfitobacterium decreased in abundance during transfers and serial dilutions, suggesting the importance of yet uncharacterized OHRB in these cultures. Switching from PCE to 2,6-DBP led to its complete debromination to phenol in cultures with and without sulfate. 2,6-DBP debrominating cultures differed in microbial composition from PCE-dechlorinating cultures. Desulfobacterota genera recently verified to include OHRB, including Desulfovibrio and Desulfuromusa, were enriched in all microcosms, whereas Halodesulfovibrio was only enriched in cultures without sulfate. Hydrogen and methane were detected in cultures without sulfate. Hydrogen likely served as electron donor for OHR and methanogenesis. This study shows that OHR can occur in marine environments mediated by yet unknown OHRB, suggesting their role in natural halogen cycling.
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Affiliation(s)
- Chen Zhang
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom N P Bosma
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peng Peng
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109-2125, United States
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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15
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Black Soldier Fly Larvae Influence Internal and Substrate Bacterial Community Composition Depending on Substrate Type and Larval Density. Appl Environ Microbiol 2022; 88:e0008422. [PMID: 35532232 PMCID: PMC9128521 DOI: 10.1128/aem.00084-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Saprophagous fly larvae interact with a rich community of bacteria in decomposing organic matter. Larvae of some species, such as the black soldier fly, can process a wide range of organic residual streams into edible insect biomass and thus produce protein as a sustainable component of livestock feed. The microbiological safety of the insects and substrates remains a point of concern. Substrate-associated bacteria can dominate the larval gut microbiota, but the larvae can also alter the bacterial community in the substrate. However, the relative importance of substrate type and larval density in bacterial community dynamics is unknown. We investigated four larval densities (0 [control], 50, 100, or 200 larvae per container [520 mL; diameter, 75 mm]) and three feed substrates (chicken feed, chicken manure, and camelina substrate [50% chicken feed, 50% camelina oilseed press cake]) and sampled the bacterial communities of the substrates and larvae at three time points over 15 days. Although feed substrate was the strongest driver of microbiota composition over time, larval density significantly altered the relative abundances of several common bacterial genera, including potential pathogens, in each substrate and in larvae fed chicken feed. Bacterial communities of the larvae and substrate differed to a higher degree in chicken manure and camelina than in chicken feed. This supports the substrate-dependent impact of black soldier fly larvae on bacteria both within the larvae and in the substrate. This study indicates that substrate composition and larval density can alter bacterial community composition and might be used to improve insect microbiological safety. IMPORTANCE Black soldier fly larvae can process organic side streams into nutritious insect biomass, yielding a sustainable ingredient of animal feed. In processing such organic residues, the larvae impact the substrate and its microbiota. However, their role relative to the feed substrate in shaping the bacterial community is unknown. This may be important for the waste management industry to determine whether pathogens can be controlled by manipulating the larval density and the timing of harvest. We investigated how the type of feed substrate and the larval density (number of larvae per container) interacted to influence bacterial community composition in the substrates and larvae over time. Substrate type was the strongest driver of bacterial community composition, and the magnitude of the impact of the larvae depended on the substrate type and larval density. Thus, both substrate composition and larval density may be used to improve the microbiological safety of the larvae as animal feed.
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16
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Kers JG, Saccenti E. The Power of Microbiome Studies: Some Considerations on Which Alpha and Beta Metrics to Use and How to Report Results. Front Microbiol 2022; 12:796025. [PMID: 35310396 PMCID: PMC8928147 DOI: 10.3389/fmicb.2021.796025] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/28/2021] [Indexed: 01/04/2023] Open
Abstract
Background Since sequencing techniques have become less expensive, larger sample sizes are applicable for microbiota studies. The aim of this study is to show how, and to what extent, different diversity metrics and different compositions of the microbiota influence the needed sample size to observe dissimilar groups. Empirical 16S rRNA amplicon sequence data obtained from animal experiments, observational human data, and simulated data were used to perform retrospective power calculations. A wide variation of alpha diversity and beta diversity metrics were used to compare the different microbiota datasets and the effect on the sample size. Results Our data showed that beta diversity metrics are the most sensitive to observe differences as compared with alpha diversity metrics. The structure of the data influenced which alpha metrics are the most sensitive. Regarding beta diversity, the Bray–Curtis metric is in general the most sensitive to observe differences between groups, resulting in lower sample size and potential publication bias. Conclusion We recommend performing power calculations and to use multiple diversity metrics as an outcome measure. To improve microbiota studies, awareness needs to be raised on the sensitivity and bias for microbiota research outcomes created by the used metrics rather than biological differences. We have seen that different alpha and beta diversity metrics lead to different study power: because of this, one could be naturally tempted to try all possible metrics until one or more are found that give a statistically significant test result, i.e., p-value < α. This way of proceeding is one of the many forms of the so-called p-value hacking. To this end, in our opinion, the only way to protect ourselves from (the temptation of) p-hacking would be to publish a statistical plan before experiments are initiated, describing the outcomes of interest and the corresponding statistical analyses to be performed.
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Affiliation(s)
- Jannigje Gerdien Kers
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
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17
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Eckermann HA, Ou Y, Lahti L, Weerth C. Can gut microbiota throughout the first 10 years of life predict executive functioning in childhood? Dev Psychobiol 2022; 64:e22226. [DOI: 10.1002/dev.22226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Henrik Andreas Eckermann
- Department of Cognitive Neuroscience Cognition and Behavior Radboud University Medical Center Donders Institute for Brain Nijmegen The Netherlands
| | - Yangwenshan Ou
- Laboratory of Microbiology Wageningen University Wageningen The Netherlands
| | - Leo Lahti
- Department of Computing University of Turku Turku Finland
| | - Carolina Weerth
- Department of Cognitive Neuroscience Cognition and Behavior Radboud University Medical Center Donders Institute for Brain Nijmegen The Netherlands
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18
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Oceanographic setting influences the prokaryotic community and metabolome in deep-sea sponges. Sci Rep 2022; 12:3356. [PMID: 35233042 PMCID: PMC8888554 DOI: 10.1038/s41598-022-07292-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/16/2022] [Indexed: 11/09/2022] Open
Abstract
Marine sponges (phylum Porifera) are leading organisms for the discovery of bioactive compounds from nature. Their often rich and species-specific microbiota is hypothesised to be producing many of these compounds. Yet, environmental influences on the sponge-associated microbiota and bioactive compound production remain elusive. Here, we investigated the changes of microbiota and metabolomes in sponges along a depth range of 1232 m. Using 16S rRNA gene amplicon sequencing and untargeted metabolomics, we assessed prokaryotic and chemical diversities in three deep-sea sponge species: Geodia barretti, Stryphnus fortis, and Weberella bursa. Both prokaryotic communities and metabolome varied significantly with depth, which we hypothesized to be the effect of different water masses. Up to 35.5% of microbial ASVs (amplicon sequence variants) showed significant changes with depth while phylum-level composition of host microbiome remained unchanged. The metabolome varied with depth, with relative quantities of known bioactive compounds increasing or decreasing strongly. Other metabolites varying with depth were compatible solutes regulating osmolarity of the cells. Correlations between prokaryotic community and the bioactive compounds in G. barretti suggested members of Acidobacteria, Proteobacteria, Chloroflexi, or an unclassified prokaryote as potential producers.
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Houtman TA, Eckermann HA, Smidt H, de Weerth C. Gut microbiota and BMI throughout childhood: the role of firmicutes, bacteroidetes, and short-chain fatty acid producers. Sci Rep 2022; 12:3140. [PMID: 35210542 PMCID: PMC8873392 DOI: 10.1038/s41598-022-07176-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/14/2022] [Indexed: 02/06/2023] Open
Abstract
Childhood obesity is a risk factor for numerous health conditions. A critical factor in the etiology of obesity appears to be the gut microbiota, which is the microbial community that resides in the human gut. The ratio of the phyla Firmicutes and Bacteroidetes (F/B) and gut bacterial genera that produce short-chain fatty acids (SCFA) have been suggested to contribute to obesity. The current study investigated (1) whether differences in F/B ratio can be observed in infancy and childhood in relation to zBMI in healthy children, and (2) whether an innovative proxy measure adds evidence to a relationship between SCFA producers and the etiology of obesity. Stool samples were collected at five time points, and zBMI was assessed at eight time points throughout the first 12 years of life. Our confirmatory analyses with Bayesian multilevel models showed no relationship between the F/B ratio and zBMI. Also, a proxy measure constructed from known SCFA producers was unrelated to zBMI throughout the first 12 years of life. Exploratory analyses using multilevel and random forest models suggest that the relative abundances of Firmicutes and Bacteroidetes were independently negatively associated with zBMI from infancy through childhood, and the SCFA producing genera Subdoligranulum and Alistipes were negatively related to future BMI in childhood.
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Affiliation(s)
- Timothy A Houtman
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Henrik A Eckermann
- Donders Institute for Brain, Cognition and Behavior, Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Carolina de Weerth
- Donders Institute for Brain, Cognition and Behavior, Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
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Lian J, Steinert G, de Vree J, Meijer S, Heryanto C, Bosma R, Wijffels RH, Barbosa MJ, Smidt H, Sipkema D. Bacterial diversity in different outdoor pilot plant photobioreactor types during production of the microalga Nannochloropsis sp. CCAP211/78. Appl Microbiol Biotechnol 2022; 106:2235-2248. [PMID: 35166894 PMCID: PMC8930801 DOI: 10.1007/s00253-022-11815-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 12/22/2021] [Accepted: 01/29/2022] [Indexed: 11/25/2022]
Abstract
As large-scale outdoor production cannot be done in complete containment, cultures are (more) open for bacteria, which may affect the productivity and stability of the algae production process. We investigated the bacterial diversity in two indoor reactors and four pilot-scale outdoor reactors for the production of Nannochloropsis sp. CCAP211/78 spanning four months of operation from July to October. Illumina sequencing of 16S rRNA gene amplicons demonstrated that a wide variety of bacteria were present in all reactor types, with predominance of Bacteroidetes and Alphaproteobacteria. Bacterial communities were significantly different between all reactor types (except between the horizontal tubular reactor and the vertical tubular reactor) and also between runs in each reactor. Bacteria common to the majority of samples included one member of the Saprospiraceae family and one of the NS11-12_marine group (both Bacteroidetes). Hierarchical clustering analysis revealed two phases during the cultivation period separated by a major shift in bacterial community composition in the horizontal tubular reactor, the vertical tubular reactor and the raceway pond with a strong decrease of the Saprospiraceae and NS11-12_marine group that initially dominated the bacterial communities. Furthermore, we observed a less consistent pattern of bacterial taxa appearing in different reactors and runs, most of which belonging to the classes Deltaproteobacteria and Flavobacteriia. In addition, canonical correspondence analysis showed that the bacterial community composition was significantly correlated with the nitrate concentration. This study contributes to our understanding of bacterial diversity and composition in different types of outdoor reactors exposed to a range of dynamic biotic and abiotic factors. Key points • Reactor types had significantly different bacterial communities except HT and VT • The inoculum source and physiochemical factors together affect bacterial community • The bacterial family Saprospiraceae is positively correlated to microalgal growth.
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Affiliation(s)
- Jie Lian
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jeroen de Vree
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Sven Meijer
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christa Heryanto
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Rouke Bosma
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, N8049, Bodø, Norway
| | - Maria J Barbosa
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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Ou Y, Belzer C, Smidt H, de Weerth C. Development of the gut microbiota in healthy children in the first ten years of life: associations with internalizing and externalizing behavior. Gut Microbes 2022; 14:2038853. [PMID: 35188073 PMCID: PMC8865293 DOI: 10.1080/19490976.2022.2038853] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Increasing evidence indicates that psychopathological disorders are associated with the gut microbiota. However, data are largely lacking from long-term longitudinal birth cohorts, especially those comprising low-risk healthy individuals. Therefore, this study aims to describe gut microbiota development in healthy children from birth till age 10 years, as well as to investigate potential associations with internalizing and externalizing behavior. RESULTS Fecal microbial composition of participants in an ongoing longitudinal study (N = 193) was analyzed at 1, 3 and 4 months, and 6 and 10 years of age by 16S ribosomal RNA gene sequencing. Based on these data, three clusters were identified in infancy, two of which were predominated by Bifidobacterium. In childhood, four clusters were observed, two of which increased in prevalence with age. One of the childhood clusters, similar to an enterotype, was highly enriched in genus-level taxon Prevotella_9. Breastfeeding had marked associations with microbiota composition up till age 10, implying an extended role in shaping gut microbial ecology. Microbial clusters were not associated with behavior. However, Prevotella_9 in childhood was positively related to mother-reported externalizing behavior at age 10; this was validated in child reports. CONCLUSIONS This study validated previous findings on Bifidobacterium-enriched and -depleted clusters in infancy. Importantly, it also mapped continued development of gut microbiota in middle childhood. Novel associations between gut microbial composition in the first 10 years of life (especially Prevotella_9), and externalizing behavior at age 10 were found. Replications in other cohorts, as well as follow-up assessments, will help determine the significance of these findings.
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Affiliation(s)
- Yangwenshan Ou
- Department of Agrotechnology and Food Sciences, Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, EH Wageningen, 6700Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Center, P.O. Box 9010, 6500GL Nijmegen, Netherlands
| | - Clara Belzer
- Department of Agrotechnology and Food Sciences, Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, EH Wageningen, 6700Netherlands
| | - Hauke Smidt
- Department of Agrotechnology and Food Sciences, Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, EH Wageningen, 6700Netherlands
| | - Carolina de Weerth
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Center, P.O. Box 9010, 6500GL Nijmegen, Netherlands
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Fecal Microbiota Signatures Are Not Consistently Related to Symptom Severity in Irritable Bowel Syndrome. Dig Dis Sci 2022; 67:5137-5148. [PMID: 35624331 PMCID: PMC9587953 DOI: 10.1007/s10620-022-07543-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/01/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is the most prevalent functional bowel disorder, but its pathophysiology is still unknown. Although a microbial signature associated with IBS severity has been suggested, its association with IBS severity still remains largely unknown. AIMS This study aims to assess longitudinal dynamics of fecal microbiota and short-chain fatty acids (SCFAs) in different IBS severity groups and study the association with stool pattern, diet, depression, anxiety, and quality of life (QoL). METHODS A longitudinal study was performed, including n = 91 IBS patients and n = 28 matched controls. All participants collected fecal samples for microbiota composition and SCFA analysis and completed validated questionnaires regarding IBS severity, stool pattern, depression, anxiety, and IBS-QoL at two timepoints with four weeks in-between. Diet was assessed at the first timepoint. RESULTS Over time, 36% of IBS patients changed in severity group, and 53% changed in predominant stool pattern. The largest proportion of microbiota variation was explained by the individual (R2 = 70.07%). Microbiota alpha diversity and composition, and SCFAs did not differ between IBS severity groups, nor between IBS and controls. Relative abundances of Bifidobacterium, Terrisporobacter, and Turicibacter consistently differed between IBS and controls, but not between IBS severity groups. Large dynamics over time were observed in the association of microbiota composition with questionnaire data where IBS symptom severity was associated at T1 but not at T2. CONCLUSIONS Fecal microbiota and SCFA signatures were not consistently associated with IBS severity over time, indicating the importance of repeated sampling in IBS research.
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Lingbeek MM, Borewicz K, Febery E, Han Y, Doelman J, van Kuijk SJA. Short-chain fatty acid administration via water acidifier improves feed efficiency and modulates fecal microbiota in weaned piglets. J Anim Sci 2021; 99:6408630. [PMID: 34679178 PMCID: PMC8599185 DOI: 10.1093/jas/skab307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022] Open
Abstract
This study examined the effect of a water acidifier containing free and buffered short-chain fatty acids (SCFA-WA) on growth performance and microbiota of weaned piglets. In total, 192 male piglets, approximately 4 wk of age, were allocated to 24 pens (12 per treatment) with 8 piglets per pen. The piglets received either regular drinking water (negative control) or drinking water with the acidifier supplied at 2 L/1,000 L. Body weight and feed intake were measured weekly on pen level. During the first 2 wk, daily visual assessment and scoring of the feces was conducted. Fecal samples of three piglets per pen were collected on days 14 and 42 for high-throughput sequencing analysis of the microbiota. Piglets offered SCFA-WA had significantly improved feed efficiency in the third week (P = 0.025) and over the whole study period (days 0 to 42, P = 0.042) compared with piglets in the negative control group, with a strong tendency observed during the first feeding phase (days 0 to 21, P = 0.055). Furthermore, the water acidifier group had a higher water intake than piglets provided with control water during the second feeding phase (days 21 to 42, P = 0.028) and over the whole study period (days 0 to 42, P = 0.043). There was no significant difference in body weight, average daily gain, or average daily feed intake (days 0 to 21, 21 to 42, 0 to 42). Furthermore, there was no overall significant difference in fecal scoring between the treatments. In terms of the fecal microbiota response, piglets offered the water acidifier showed a significantly higher relative abundance (RA) of genus Clostridium sensu stricto 1 and a lower RA of genus Streptococcus compared to the control. Furthermore, the redundancy analysis showed a positive association between improved feed efficiency and daily weight gain and RA of Butyricicoccus and Faecalibacterium. In conclusion, consumption of the water acidifier containing free and buffered SCFA modulated the microbiota and improved feed efficiency in piglets.
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Affiliation(s)
- Mandy M Lingbeek
- Trouw Nutrition R&D, P.O. Box 299, 3800 AG, Amersfoort, The Netherlands
| | - Klaudyna Borewicz
- Trouw Nutrition R&D, P.O. Box 299, 3800 AG, Amersfoort, The Netherlands
| | - Erica Febery
- Drayton Animal Health Ltd, Alcester Road, Stratford-on-Avon, Warwickshire CV37 9RQ, UK
| | - Yanming Han
- Trouw Nutrition R&D, P.O. Box 299, 3800 AG, Amersfoort, The Netherlands
| | - John Doelman
- Trouw Nutrition R&D, P.O. Box 299, 3800 AG, Amersfoort, The Netherlands
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Lam SY, Ioannou A, Konstanti P, Visseren T, Doukas M, Peppelenbosch MP, Belzer C, Fuhler GM. Technical challenges regarding the use of formalin-fixed paraffin embedded (FFPE) tissue specimens for the detection of bacterial alterations in colorectal cancer. BMC Microbiol 2021; 21:297. [PMID: 34715774 PMCID: PMC8555202 DOI: 10.1186/s12866-021-02359-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Background Formalin-fixed paraffin embedded (FFPE) tissues may provide an exciting resource to study microbial associations in human disease, but the use of these low biomass specimens remains challenging. We aimed to reduce unintentional bacterial interference in molecular analysis of FFPE tissues and investigated the feasibility of conducting quantitative polymerase chain reaction (qPCR) and 16S rRNA amplicon sequencing using 14 colorectal cancer, 14 normal adjacent and 13 healthy control tissues. Results Bacterial contaminants from the laboratory environment and the co-extraction of human DNA can affect bacterial analysis. The application of undiluted template improves bacterial DNA amplification, allowing the detection of specific bacterial markers (Escherichia coli and Faecalibacterium prausnitzii) by qPCR. Nested and non-nested PCR-based 16S rRNA amplicon sequencing approaches were employed, showing that bacterial communities of tissues and paired paraffin controls cluster separately at genus level on weighted Unifrac in both non-nested (R2 = 0.045; Pr(> F) = 0.053) and nested (R2 = 0.299; Pr(> F) = 0.001) PCR datasets. Nevertheless, considerable overlap of bacterial genera within tissues was seen with paraffin, DNA extraction negatives (non-nested PCR) or PCR negatives (nested PCR). Following mathematical decontamination, no differences in α- and β diversity were found between tumor, normal adjacent and control tissues. Conclusions Bacterial marker analysis by qPCR seems feasible using non-normalized template, but 16S rRNA amplicon sequencing remains challenging. Critical evaluation of laboratory procedures and incorporation of positive and negative controls for bacterial analysis of FFPE tissues are essential for quality control and to account for bacterial contaminants. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02359-z.
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Affiliation(s)
- Suk Yee Lam
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Athanasia Ioannou
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH , Wageningen, The Netherlands
| | - Prokopis Konstanti
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH , Wageningen, The Netherlands
| | - Thijmen Visseren
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Maikel Petrus Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH , Wageningen, The Netherlands
| | - Gwenny Manel Fuhler
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
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Verheggen RJHM, Konstanti P, Smidt H, Hermus ARMM, Thijssen DHJ, Hopman MTE. Eight-week exercise training in humans with obesity: Marked improvements in insulin sensitivity and modest changes in gut microbiome. Obesity (Silver Spring) 2021; 29:1615-1624. [PMID: 34467673 PMCID: PMC9291576 DOI: 10.1002/oby.23252] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/15/2021] [Accepted: 06/06/2021] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Obesity is associated with impaired gut microbiota diversity, which has been linked to the development of type 2 diabetes. This study aims to examine the effects of an 8-week aerobic exercise intervention on insulin sensitivity, visceral adiposity, and gut microbiota diversity and composition in participants with obesity. METHODS Fourteen participants (mean [SD], age 51 [11] years; BMI 34.9 [4.9] kg/m2 ) performed an 8-week exercise intervention (2 to 4 times/week on 65% to 85% of heart rate reserve). Insulin sensitivity (hyperinsulemic euglycemic clamp), cardiorespiratory fitness (maximal oxygen uptake), visceral adiposity (dual-energy X-ray absorptiometry scan) and gut microbiota composition (16S rRNA gene sequencing) were measured before and after the intervention. RESULTS Insulin sensitivity showed a significant increase (pre: 3.8 [1.9] mg/min/kg; post: 4.5 [1.7] mg/min/kg; p = 0.007) after training, whereas visceral adiposity decreased (pre: 959 [361] cm3 ; post: 897 [364] cm3 ; p = 0.02). No change in gut microbiota α- or β-diversity was found. At the genus level, the abundance of Ruminococcus gauvreauii (p = 0.02); Lachnospiraceae FCS020 group (p = 0.04), and Anaerostipes (p = 0.04) significantly increased after exercise training. Significant positive correlations were present for M-value (R. gauvreauii) and VO2 max (R. gauvreauii and Anaerostipes). CONCLUSIONS Eight-week exercise training in humans with obesity leads to marked improvements in insulin sensitivity and body composition and is accompanied by modest changes in 3 gut microbiome genera, all belonging to the Firmicutes phylum.
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Affiliation(s)
- Rebecca J. H. M. Verheggen
- Department of PhysiologyRadboud University Medical CenterRadboud Institute for Health SciencesNijmegenthe Netherlands
| | - Prokopis Konstanti
- Laboratory of MicrobiologyWageningen UniversityWageningenthe Netherlands
| | - Hauke Smidt
- Laboratory of MicrobiologyWageningen UniversityWageningenthe Netherlands
| | - Ad R. M. M. Hermus
- Department of Internal MedicineDivision of EndocrinologyRadboud University Medical CenterRadboud Institute for Health SciencesNijmegenthe Netherlands
| | - Dick H. J. Thijssen
- Department of PhysiologyRadboud University Medical CenterRadboud Institute for Health SciencesNijmegenthe Netherlands
- Research Institute for Sport and Exercise SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Maria T. E. Hopman
- Department of PhysiologyRadboud University Medical CenterRadboud Institute for Health SciencesNijmegenthe Netherlands
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Free Faecal Water: Analysis of Horse Faecal Microbiota and the Impact of Faecal Microbial Transplantation on Symptom Severity. Animals (Basel) 2021; 11:ani11102776. [PMID: 34679798 PMCID: PMC8533009 DOI: 10.3390/ani11102776] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Free faecal water (FFW) in equines causes soiling of the hindquarters and tail and may also include additional symptoms. The cause of FFW is unknown. In this study it was investigated whether the microbes present in the last part of the gut (i.e., the hindgut microbiota) may be involved. From the analysis of faecal samples, it was found that horses suffering from FFW had no differences in their hindgut microbiota compared to healthy horses stabled at the same location. However, subsequent treatment of the FFW horses with a faecal microbiota transplantation (FMT) from a healthy donor animal resulted in a decrease in FFW symptom severity. Nevertheless, animals did not respond uniformly to this treatment, with some only having temporary decreases in FFW symptom severity. No lasting changes in the hindgut microbiota of the FFW horses occurred as a result of the faecal transplant. The practical implication of these findings is that FMT can potentially be used to temporarily alleviate FFW symptom severity in horses, although future studies using controls are needed to confirm the effectiveness of FMT to treat FFW. Abstract Free faecal water (FFW) in equines results in pollution of the hindquarters and tail and can also involve clinical signs. Though the cause of FFW is unknown, it was hypothesized that it may involve the gut microbiota. This hypothesis was addressed as follows. First, the faecal prokaryotic community composition of horses suffering from FFW relative to healthy controls (n = 10) was compared. Second, FFW horses were treated with a standardised faecal microbiota transplantation (FMT) protocol (n = 10), followed by assessment of FFW symptom severity and faecal prokaryotic community composition over a follow-up period of 168 days. No significant differences were found in the faecal microbiota composition of FFW horses compared to healthy controls (p > 0.05). Relative to before FMT, FFW symptom severity decreased in affected horses 14 days after FMT (p = 0.02) and remained decreased for the remainder of the study (p < 0.02). However, individual animal responses to FMT varied. FMT had no effect on FFW horse faecal prokaryotic community composition in terms of alpha or beta diversity. Alpha diversity of the donor inocula used in the FMT was always lower than that of the faecal microbiota of the FFW treated horses (p < 0.001). In conclusion, whilst findings indicate FFW horses do not have an altered hindgut microbiota, some horses that received FMT had a temporary alleviation of FFW symptom severity without causing changes in the faecal microbiota. Future studies using controls are now needed to confirm the effectiveness of FMT to treat FFW.
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Chagas JC, Ramin M, Exposito RG, Smidt H, Krizsan SJ. Effect of a Low-Methane Diet on Performance and Microbiome in Lactating Dairy Cows Accounting for Individual Pre-Trial Methane Emissions. Animals (Basel) 2021; 11:ani11092597. [PMID: 34573563 PMCID: PMC8468840 DOI: 10.3390/ani11092597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022] Open
Abstract
This study examined the effects of partly replacing grass silage (GS) with maize silage (MS), with or without rapeseed oil (RSO) supplementation, on methane (CH4) emissions, production performance, and rumen microbiome in the diets of lactating dairy cows. The effect of individual pre-trial CH4-emitting characteristics on dietary emissions mitigation was also examined. Twenty Nordic Red cows at 71 ± 37.2 (mean ± SD) days in milk were assigned to a replicated 4 × 4 Latin square design with four dietary treatments (GS, GS supplemented with RSO, GS plus MS, GS plus MS supplemented with RSO) applied in a 2 × 2 factorial arrangement. Partial replacement of GS with MS decreased the intake of dry matter (DM) and nutrients, milk production, yield of milk components, and general nutrient digestibility. Supplementation with RSO decreased the intake of DM and nutrients, energy-corrected milk yield, composition and yield of milk fat and protein, and general digestibility of nutrients, except for crude protein. Individual cow pre-trial measurements of CH4-emitting characteristics had a significant influence on gas emissions but did not alter the magnitude of CH4 emissions. Dietary RSO decreased daily CH4, yield, and intensity. It also increased the relative abundance of rumen Methanosphaera and Succinivibrionaceae and decreased that of Bifidobacteriaceae. There were no effects of dietary MS on CH4 emissions in this study, but supplementation with 41 g RSO/kg of DM reduced daily CH4 emissions from lactating dairy cows by 22.5%.
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Affiliation(s)
- Juana C. Chagas
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences (SLU), Skogsmarksgränd, 90183 Umeå, Sweden;
- Correspondence: (J.C.C.); (S.J.K.); Tel.: +46-90-7868748 (J.C.C.)
| | - Mohammad Ramin
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences (SLU), Skogsmarksgränd, 90183 Umeå, Sweden;
| | - Ruth Gomez Exposito
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (R.G.E.); (H.S.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (R.G.E.); (H.S.)
| | - Sophie J. Krizsan
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences (SLU), Skogsmarksgränd, 90183 Umeå, Sweden;
- Correspondence: (J.C.C.); (S.J.K.); Tel.: +46-90-7868748 (J.C.C.)
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Brucha G, Aldas-Vargas A, Ross Z, Peng P, Atashgahi S, Smidt H, Langenhoff A, Sutton NB. 2,4-Dichlorophenoxyacetic acid degradation in methanogenic mixed cultures obtained from Brazilian Amazonian soil samples. Biodegradation 2021; 32:419-433. [PMID: 33877512 PMCID: PMC8260542 DOI: 10.1007/s10532-021-09940-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 03/31/2021] [Indexed: 01/23/2023]
Abstract
2,4-Dichlorophenoxyacetic acid (2,4-D) is the third most applied pesticide in Brazil to control broadleaf weeds in crop cultivation and pastures. Due to 2,4-D's high mobility and long half-life under anoxic conditions, this herbicide has high probability for groundwater contamination. Bioremediation is an attractive solution for 2,4-D contaminated anoxic environments, but there is limited understanding of anaerobic 2,4-D biodegradation. In this study, methanogenic enrichment cultures were obtained from Amazonian top soil (0-40 cm) and deep soil (50 -80 cm below ground) that biotransform 2,4-D (5 µM) to 4-chlorophenol and phenol. When these cultures were transferred (10% v/v) to fresh medium containing 40 µM or 160 µM 2,4-D, the rate of 2,4-D degradation decreased, and biotransformation did not proceed beyond 4-chlorophenol and 2,4-dichlorophenol in the top and deep soil cultures, respectively. 16S rRNA gene sequencing and qPCR of a selection of microbes revealed no significant enrichment of known organohalide-respiring bacteria. Furthermore, a member of the genus Cryptanaerobacter was identified as possibly responsible for phenol conversion to benzoate in the top soil inoculated culture. Overall, these results demonstrate the effect of 2,4-D concentration on biodegradation and microbial community composition, which are both important factors when developing pesticide bioremediation technologies.
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Affiliation(s)
- Gunther Brucha
- Environmental Technology, Wageningen University & Research, PO BOX 17, 6700 EV, Wageningen, The Netherlands
- Institute of Science and Technology, Universidade Federal de Alfenas, Alfenas, Brazil
| | - Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, PO BOX 17, 6700 EV, Wageningen, The Netherlands
| | - Zacchariah Ross
- Environmental Technology, Wageningen University & Research, PO BOX 17, 6700 EV, Wageningen, The Netherlands
| | - Peng Peng
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Alette Langenhoff
- Environmental Technology, Wageningen University & Research, PO BOX 17, 6700 EV, Wageningen, The Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, PO BOX 17, 6700 EV, Wageningen, The Netherlands.
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Wen C, van Dixhoorn I, Schokker D, Woelders H, Stockhofe-Zurwieden N, Rebel JMJ, Smidt H. Environmentally enriched housing conditions affect pig welfare, immune system and gut microbiota in early life. Anim Microbiome 2021; 3:52. [PMID: 34321110 PMCID: PMC8320228 DOI: 10.1186/s42523-021-00115-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/16/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Conventional pig housing and management conditions are associated with gastrointestinal pathophysiology and disease susceptibility in early life. Developing new strategies to reduce both therapeutic and prophylactic antibiotic use is urgent for the sustainable swine production globally. To this end, housing methodology providing effective environmental enrichment could be a promising alternative approach to reduce antibiotic usage, as it has been proven to positively influence pig welfare and immune status and reduce susceptibility to infections. It is, however, poorly understood how this enriched housing affects systemic and local pulmonary immune status and gut microbiota colonization during early life. In the present study, we compared the effects of two housing conditions, i.e., conventional housing: (CH) versus enriched housing (EH), on immune status and gut microbiota from birth until 61 days of age. RESULTS The expected benefits of enrichment on pig welfare were confirmed as EH pigs showed more positive behaviour, less aggression behaviour during the weaning transition and better human animal relation during the post weaning phase. Regarding the pigs' immune status, EH pigs had higher values of haemoglobin and mean corpuscular volume in haematological profiles and higher percentages of T cells and cytotoxic T cells in peripheral blood. Furthermore, EH pigs showed higher ex vivo secretion of IL1ß and TNF-α after lipopolysaccharide stimulation of whole blood than CH pigs. The structure of the developing faecal microbiota of CH and EH pigs significantly differed as early as day 12 with an increase in the relative abundance of several bacterial groups known to be involved in the production of short chain fatty acids, such as Prevotella_2, Christensenellaceae_R_7_group and Ruminococcus gauvreauii group. Furthermore, the main difference between both housing conditions post weaning was that on day 61, CH pigs had significantly larger inter-individual variation of ileal and colonic microbiota than EH pigs. In addition to housing, other intrinsic factors (e.g., sex) were associated with gut microbiota development and immune competence. CONCLUSIONS In addition to the known welfare benefits for pigs, environmentally enriched housing also positively drives important aspects of the development of the immune system and the establishment of gut microbiota in early life. Consequently, EH may contribute to increasing productivity of pigs and reducing antibiotic use.
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Affiliation(s)
- Caifang Wen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ingrid van Dixhoorn
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Dirkjan Schokker
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Henri Woelders
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Johanna M. J. Rebel
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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30
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de Vries HJ, Kleibusch E, Hermes GDA, van den Brink P, Plugge CM. Biofouling control: the impact of biofilm dispersal and membrane flushing. WATER RESEARCH 2021; 198:117163. [PMID: 33951583 DOI: 10.1016/j.watres.2021.117163] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 05/26/2023]
Abstract
Pure culture studies have shown that biofilm dispersal can be triggered if the nutrient supply is discontinued by stopping the flow. Stimulating biofilm dispersal in this manner would provide a sustainable manner to control unwanted biofilm growth in industrial settings, for instance on synthetic membranes used to purify water. The response of multispecies biofilms to nutrient limitation has not been thoroughly studied. To assess biomass dispersal during nutrient limitation it is common practise to flush the biofilm after a stop-period. Hence, flow-stop-induced biomass removal could occur as a response to nutrient limitation followed by mechanical removal due to biofilm flushing (e.g. biofilm detachment). Here, we investigated the feasibility to reduce membrane biofouling by stopping the flow and flushing the membrane. Using a membrane fouling simulator, biomass removal from synthetic membranes after different stop-periods was determined, as well as biomass removal at different cross flow velocities. Biomass removal from membrane surfaces depended on the nutrient limiting period and on the flow velocity during the biofilm flush. When flushed at a low flow velocity (0.1 m.s-1), the duration of the stop-period had a large effect on the biomass removal rate, but when the flow velocity was increased to 0.2 m.s-1, the length of the stop period became less considerable. The flow velocity during membrane flushing has an effect on the bacterial community that colonized the membranes afterwards. Repetition of the stop-period and biofilm flushing after three repetitive biofouling cycles led to a stable bacterial community. The increase in bacterial community stability coincided with a decrease in cleaning effectivity to restore membrane performance. This shows that membrane cleaning comes at the costs of a more stable bacterial community that is increasingly difficult to remove.
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Affiliation(s)
- Hendrik J de Vries
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Eva Kleibusch
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Gerben D A Hermes
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Paula van den Brink
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands.
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31
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Bloemendaal M, Szopinska-Tokov J, Belzer C, Boverhoff D, Papalini S, Michels F, van Hemert S, Arias Vasquez A, Aarts E. Probiotics-induced changes in gut microbial composition and its effects on cognitive performance after stress: exploratory analyses. Transl Psychiatry 2021; 11:300. [PMID: 34016947 PMCID: PMC8137885 DOI: 10.1038/s41398-021-01404-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 03/24/2021] [Accepted: 04/21/2021] [Indexed: 02/04/2023] Open
Abstract
Stress negatively affects cognitive performance. Probiotics remediate somatic and behavioral stress responses, hypothetically by acting on the gut microbiota. Here, in exploratory analyses, we assessed gut microbial alterations after 28-days supplementation of multi-strain probiotics (EcologicBarrier consisting of Lactobacilli, Lactococci, and Bifidobacteria in healthy, female subjects (probiotics group n = 27, placebo group n = 29). In an identical pre-session and post-session, subjects performed a working memory task before and after an acute stress intervention. Global gut microbial beta diversity changed over time, but we were not able to detect differences between intervention groups. At the taxonomic level, Time by Intervention interactions were not significant after multiple comparison correction; the relative abundance of eight genera in the probiotics group was higher (uncorrected) relative to the placebo group: Butyricimonas, Parabacteroides, Alistipes, Christensenellaceae_R-7_group, Family_XIII_AD3011_group, Ruminococcaceae_UCG-003, Ruminococcaceae_UCG-005, and Ruminococcaceae_UCG-010. In a second analysis step, association analyses were done only within this selection of microbial genera, revealing the probiotics-induced change in genus Ruminococcaceae_UCG-003 was significantly associated with probiotics' effect on stress-induced working memory changes (rspearman(27) = 0.565; pFDR = 0.014) in the probiotics group only and independent of potential confounders (i.e., age, BMI, and baseline dietary fiber intake). That is subjects with a higher increase in Ruminococcaceae_UCG-003 abundance after probiotics were also more protected from negative effects of stress on working memory after probiotic supplementation. The bacterial taxa showing an increase in relative abundance in the probiotics group are plant fiber degrading bacteria and produce short-chain fatty acids that are known for their beneficial effect on gut and brain health, e.g., maintaining intestinal-barrier and blood-brain-barrier integrity. This study shows that gut microbial alterations, modulated through probiotics use, are related to improved cognitive performance in acute stress circumstances.
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Affiliation(s)
- Mirjam Bloemendaal
- Departments of Psychiatry and Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Joanna Szopinska-Tokov
- Departments of Psychiatry and Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - David Boverhoff
- Donders Institute for Brain Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, the Netherlands
| | - Silvia Papalini
- Donders Institute for Brain Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, the Netherlands
- Laboratory for Biological Psychology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Franziska Michels
- Donders Institute for Brain Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, the Netherlands
| | | | - Alejandro Arias Vasquez
- Departments of Psychiatry and Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Esther Aarts
- Donders Institute for Brain Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, the Netherlands
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32
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Enteric and Fecal Methane Emissions from Dairy Cows Fed Grass or Corn Silage Diets Supplemented with Rapeseed Oil. Animals (Basel) 2021; 11:ani11051322. [PMID: 34063117 PMCID: PMC8148109 DOI: 10.3390/ani11051322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary In this study, we evaluated methane emissions from dairy cows fed grass or corn silage diets supplemented with rapeseed oil. Enteric methane emissions decreased on adding rapeseed oil to the diet, but methane emissions from feces of dairy cows fed diets supplemented with rapeseed oil did not differ. Thus, no trade-offs were observed between enteric and fecal methane emissions due to forage type or addition of rapeseed oil to diets fed to Swedish dairy cows. Abstract This study evaluated potential trade-offs between enteric methane (CH4) emissions and CH4 emissions from feces of dairy cows fed grass silage or partial replacement of grass silage with corn silage, both with and without supplementation of rapeseed oil. Measured data for eight dairy cows (two blocks) included in a production trial were analyzed. Dietary treatments were grass silage (GS), GS supplemented with rapeseed oil (GS-RSO), GS plus corn silage (GSCS), and GSCS supplemented with rapeseed oil (GSCS-RSO). Feces samples were collected after each period and incubated for nine weeks to estimate fecal CH4 emissions. Including RSO (0.5 kg/d) in the diet decreased dry matter intake (DMI) by 1.75 kg/d. Enteric CH4 emissions were reduced by inclusion of RSO in the diet (on average 473 vs. 607 L/d). In 9-week incubations, there was a trend for lower CH4 emissions from feces of cows fed diets supplemented with RSO (on average 3.45 L/kg DM) than cows with diets not supplemented with RSO (3.84 L/kg DM). Total CH4 emissions (enteric + feces, L/d) were significantly lower for the cows fed diets supplemented with RSO. Total fecal CH4 emissions were similar between treatments, indicating no trade-offs between enteric and fecal CH4 emissions.
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33
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Lian J, Schimmel P, Sanchez‐Garcia S, Wijffels RH, Smidt H, Sipkema D. Different co-occurring bacteria enhance or decrease the growth of the microalga Nannochloropsis sp. CCAP211/78. Microb Biotechnol 2021; 14:1159-1170. [PMID: 33683803 PMCID: PMC8085966 DOI: 10.1111/1751-7915.13784] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 11/29/2022] Open
Abstract
Marine photosynthetic microalgae are ubiquitously associated with bacteria in nature. However, the influence of these bacteria on algal cultures in bioreactors is still largely unknown. In this study, eighteen different bacterial strains were isolated from cultures of Nannochloropsis sp. CCAP211/78 in two outdoor pilot-scale tubular photobioreactors. The majority of isolates was affiliated with the classes Alphaproteobacteria and Flavobacteriia. To assess the impact of the eighteen strains on the growth of Nannochloropsis sp. CCAP211/78, 24-well plates coupled with custom-made LED boxes were used to simultaneously compare replicate axenic microalgal cultures with addition of individual bacterial isolates. Co-culturing of Nannochloropsis sp. CCAP211/78 with these strains demonstrated distinct responses, which shows that the technique we developed is an efficient method for screening the influence of harmful/beneficial bacteria. Two of the tested strains, namely a strain of Maritalea porphyrae (DMSP31) and a Labrenzia aggregata strain (YP26), significantly enhanced microalgal growth with a 14% and 12% increase of the chlorophyll concentration, respectively, whereas flavobacterial strain YP206 greatly inhibited the growth of the microalga with 28% reduction of the chlorophyll concentration. Our study suggests that algal production systems represent a 'natural' source to isolate and study microorganisms that can either benefit or harm algal cultures.
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Affiliation(s)
- Jie Lian
- Laboratory of MicrobiologyWageningen University & ResearchStippeneng 4Wageningen6708 WEThe Netherlands
| | - Patrick Schimmel
- Laboratory of MicrobiologyWageningen University & ResearchStippeneng 4Wageningen6708 WEThe Netherlands
| | - Selene Sanchez‐Garcia
- Laboratory of MicrobiologyWageningen University & ResearchStippeneng 4Wageningen6708 WEThe Netherlands
| | - Rene H. Wijffels
- Bioprocess Engineering Group, AlgaePARCWageningen University & ResearchPO Box 16Wageningen6700 AAThe Netherlands
- Faculty of Biosciences and AquacultureNord UniversityBodøN‐8049Norway
| | - Hauke Smidt
- Laboratory of MicrobiologyWageningen University & ResearchStippeneng 4Wageningen6708 WEThe Netherlands
| | - Detmer Sipkema
- Laboratory of MicrobiologyWageningen University & ResearchStippeneng 4Wageningen6708 WEThe Netherlands
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Habes QL, Konstanti P, Kiers HD, Koch RM, Stolk RF, Belzer C, Kox M, Pickkers P. No interplay between gut microbiota composition and the lipopolysaccharide-induced innate immune response in humans in vivo. Clin Transl Immunology 2021; 10:e1278. [PMID: 33968408 PMCID: PMC8082703 DOI: 10.1002/cti2.1278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/04/2021] [Accepted: 03/26/2021] [Indexed: 12/21/2022] Open
Abstract
Objective Animal studies have demonstrated the extensive interplay between the gut microbiota and immunity. Moreover, in critically ill patients, who almost invariably suffer from a pronounced immune response, a shift in gut microbiota composition is associated with infectious complications and mortality. We examined the relationship between interindividual differences in gut microbiota composition and variation in the in vivo cytokine response induced by bacterial lipopolysaccharide (LPS). Furthermore, we evaluated whether an LPS challenge alters the composition of the gut microbiota. Methods Healthy male volunteers received an intravenous bolus of 2 ng kg−1 LPS (n = 70) or placebo (n = 8). Serial plasma concentrations of tumor necrosis factor‐α, interleukin (IL)‐6, IL‐8 and IL‐10 were measured, and subjects were divided into high and low cytokine responders. Gut microbiota composition was determined using 16s RNA gene sequencing of faecal samples obtained 1 day before (baseline) and 1 day and 7 days following the LPS challenge. Results Baseline microbiota composition, analysed by principal coordinate analysis and random forest analysis, did not differ between high and low responders for any of the four measured cytokines. Furthermore, baseline microbiota diversity (Shannon and Chao indices) was similar in high and low responders. No changes in microbiota composition or diversity were observed at 1 and 7 days following the LPS challenge. Conclusion Our results indicate that existing variation in gut microbiota composition does not explain the observed variability in the LPS‐induced innate immune response. These findings strongly argue against the interplay between the gut microbiota composition and the innate immune response in humans.
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Affiliation(s)
- Quirine Lm Habes
- Department of Intensive Care Medicine Radboud University Medical Center Nijmegen The Netherlands.,Radboud Center for Infectious Diseases Radboud University Medical Center Nijmegen The Netherlands.,Department of Anesthesiology, Pain and Palliative Medicine Radboud University Medical Center Nijmegen The Netherlands
| | - Prokopis Konstanti
- Laboratory of Microbiology Wageningen University Wageningen The Netherlands
| | - Harmke D Kiers
- Department of Intensive Care Medicine Radboud University Medical Center Nijmegen The Netherlands.,Radboud Center for Infectious Diseases Radboud University Medical Center Nijmegen The Netherlands
| | - Rebecca M Koch
- Department of Intensive Care Medicine Radboud University Medical Center Nijmegen The Netherlands.,Radboud Center for Infectious Diseases Radboud University Medical Center Nijmegen The Netherlands.,Department of Anesthesiology, Pain and Palliative Medicine Radboud University Medical Center Nijmegen The Netherlands
| | - Roeland F Stolk
- Department of Intensive Care Medicine Radboud University Medical Center Nijmegen The Netherlands.,Radboud Center for Infectious Diseases Radboud University Medical Center Nijmegen The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology Wageningen University Wageningen The Netherlands
| | - Matthijs Kox
- Department of Intensive Care Medicine Radboud University Medical Center Nijmegen The Netherlands.,Radboud Center for Infectious Diseases Radboud University Medical Center Nijmegen The Netherlands
| | - Peter Pickkers
- Department of Intensive Care Medicine Radboud University Medical Center Nijmegen The Netherlands.,Radboud Center for Infectious Diseases Radboud University Medical Center Nijmegen The Netherlands
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J J Schreven S, de Vries H, D A Hermes G, Smidt H, Dicke M, J A van Loon J. Relative contributions of egg-associated and substrate-associated microorganisms to black soldier fly larval performance and microbiota. FEMS Microbiol Ecol 2021; 97:6204668. [PMID: 33784380 PMCID: PMC8044291 DOI: 10.1093/femsec/fiab054] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/26/2021] [Indexed: 11/23/2022] Open
Abstract
Larvae of the black soldier fly (BSF) can be used to convert organic waste into insect biomass for animal feed. In this process, they interact with microorganisms originating from the substrate, the insect and the environment. The substrate is the main determinant of the larval gut microbiota composition, but inoculation of the substrate with egg-associated bacteria can improve larval performance. We aimed to quantify the relative importance of substrate-associated and egg-associated microorganisms in BSF larval performance, bacterial abundance and bacterial community composition, when larvae were fed with chicken feed or chicken manure. For this, we inactivated substrate-associated microorganisms by autoclaving, or disinfected BSF eggs. Larval survival, weight and proportion of prepupae were determined on day 15. We collected substrate and larval samples on days 0 and 15 and performed 16S rRNA gene-targeted qPCR and amplicon sequencing. In both chicken feed and chicken manure, egg disinfection did not cause any difference in larval performance or overall microbiota composition. In contrast, in chicken manure, substrate-associated microorganisms increased larval biomass and sterilizing the substrate caused major shifts in microbiota. Thus, substrate-associated microorganisms impact not only larval microbiota but also larval performance, whereas egg-associated microorganisms have a minor role in the densities present.
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Affiliation(s)
- Stijn J J Schreven
- Laboratory of Entomology, Plant Sciences Group, Wageningen University & Research, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Hugo de Vries
- Laboratory of Microbiology, Agrotechnology & Food Sciences Group, Wageningen University & Research, PO Box 8033, 6700 EH Wageningen, The Netherlands
| | - Gerben D A Hermes
- Laboratory of Microbiology, Agrotechnology & Food Sciences Group, Wageningen University & Research, PO Box 8033, 6700 EH Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Agrotechnology & Food Sciences Group, Wageningen University & Research, PO Box 8033, 6700 EH Wageningen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Plant Sciences Group, Wageningen University & Research, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Joop J A van Loon
- Laboratory of Entomology, Plant Sciences Group, Wageningen University & Research, PO Box 16, 6700 AA Wageningen, The Netherlands
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A toolbox for the comprehensive analysis of small volume human intestinal samples that can be used with gastrointestinal sampling capsules. Sci Rep 2021; 11:8133. [PMID: 33854074 PMCID: PMC8046781 DOI: 10.1038/s41598-021-86980-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/25/2021] [Indexed: 02/02/2023] Open
Abstract
Detailed knowledge on the fate of dietary components inside the human intestinal tract is lacking. Access to this inner world of digestion is now possible through novel human gastrointestinal sampling capsules. Due to the novelty of such devices, no methodology has been published to stabilise and analyse the resulting samples. A complicating factor is that excretion of such capsules in faeces may take days, while degradation of the dietary components continues. Therefore a stabilising reagent should be pre-loaded in the capsule to ensure the measurement of a representative sample. Considering the small volume of recovered samples, analytical methods must be optimized to collect as many data as possible from little material. We present a complete workflow for stabilising and analysing the fermentation status of dietary fibres in such samples, including microbiota, fibre degradation, and short chain fatty acids. The final quenching reagent was designed based on safety and effectiveness to inhibit fructo- and galacto-oligosaccharides degradation and short chain fatty acids production by human ileostomy microbiota, and subsequently validated in faecal samples. The final composition of the stock quenching reagent is 175 mM Tris, 525 mM NaCl, 35 mM EDTA, 12% SDS, and 8 M urea at pH 8.5.
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37
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Ducarmon QR, Terveer EM, Nooij S, Bloem MN, Vendrik KEW, Caljouw MAA, Sanders IMJG, van Dorp SM, Wong MC, Zwittink RD, Kuijper EJ. Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home. Genome Med 2021; 13:54. [PMID: 33827686 PMCID: PMC8028076 DOI: 10.1186/s13073-021-00869-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical risk factors for MDRO colonisation and investigated the role of the gut microbiota in providing colonisation resistance against MDROs. Methods We conducted a prospective cohort study in a Dutch nursing home. Demographical, epidemiological and clinical data were collected at four time points with 2-month intervals (October 2016–April 2017). To obtain longitudinal data, faecal samples from residents were collected for at least two time points. Ultimately, twenty-seven residents were included in the study and 93 faecal samples were analysed, of which 27 (29.0%) were MDRO-positive. Twelve residents (44.4%) were colonised with an MDRO at at least one time point throughout the 6-month study. Results Univariable generalised estimating equation logistic regression indicated that antibiotic use in the previous 2 months and hospital admittance in the previous year were associated with MDRO colonisation. Characterisation of MDRO isolates through whole-genome sequencing revealed Escherichia coli sequence type (ST)131 to be the most prevalent MDRO and ward-specific clusters of E. coli ST131 were identified. Microbiota analysis by 16S rRNA gene amplicon sequencing revealed no differences in alpha or beta diversity between MDRO-positive and negative samples, nor between residents who were ever or never colonised. Three bacterial taxa (Dorea, Atopobiaceae and Lachnospiraceae ND3007 group) were more abundant in residents never colonised with an MDRO throughout the 6-month study. An unexpectedly high abundance of Bifidobacterium was observed in several residents. Further investigation of a subset of samples with metagenomics showed that various Bifidobacterium species were highly abundant, of which B. longum strains remained identical within residents over time, but were different between residents. Conclusions Our study provides new evidence for the role of the gut microbiota in colonisation resistance against MDROs in the elderly living in a nursing home setting. Dorea, Atopobiaceae and Lachnospiraceae ND3007 group may be associated with protection against MDRO colonisation. Furthermore, we report a uniquely high abundance of several Bifidobacterium species in multiple residents and excluded the possibility that this was due to probiotic supplementation. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00869-z.
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Affiliation(s)
- Quinten R Ducarmon
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands. .,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Elisabeth M Terveer
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michelle N Bloem
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Karuna E W Vendrik
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Monique A A Caljouw
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Ingrid M J G Sanders
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sofie M van Dorp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Internal Medicine and Geriatrics, Onze Lieve Vrouwe Gasthuis (OLVG Hospital), Amsterdam, The Netherlands
| | - Man C Wong
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Romy D Zwittink
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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van Trijp MPH, Schutte S, Esser D, Wopereis S, Hoevenaars FPM, Hooiveld GJEJ, Afman LA. Minor Changes in the Composition and Function of the Gut Microbiota During a 12-Week Whole Grain Wheat or Refined Wheat Intervention Correlate with Liver Fat in Overweight and Obese Adults. J Nutr 2021; 151:491-502. [PMID: 33188417 PMCID: PMC7948209 DOI: 10.1093/jn/nxaa312] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/27/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Whole grain wheat (WGW) products are advocated as a healthy choice when compared with refined wheat (RW). One proposed mechanism for these health benefits is via the microbiota, because WGW contains multiple fibers. WGW consumption has been proposed to ameliorate nonalcoholic fatty liver disease, in which microbiota might play a role. OBJECTIVES We investigated the effect of WGW compared with RW intervention on the fecal microbiota composition and functionality, and correlated intervention-induced changes in bacteria with changes in liver health parameters in adults with overweight or obesity. METHODS We used data of a 12-wk double-blind, randomized, controlled, parallel trial to examine the effects of a WGW (98 g/d) or RW (98 g/d) intervention on the secondary outcomes fecal microbiota composition, predicted microbiota functionality, and stool consistency in 37 women and men (aged 45-70 y, BMI 25-35 kg/m2). The changes in microbiota composition, measured using 16S ribosomal RNA gene sequencing, after a 12-wk intervention were analyzed with nonparametric tests, and correlated with changes in liver fat and circulating concentrations of liver enzymes including alanine transaminase, aspartate transaminase, γ-glutamyltransferase, and serum amyloid A. RESULTS The WGW intervention increased the mean (± SD) relative abundances of Ruminococcaceae_UCG-014 (baseline: 2.2 ± 4.6%, differential change over time (Δ) 0.51 ± 4.2%), Ruminiclostridium_9 (baseline: 0.065 ± 0.11%, Δ 0.054 ± 0.14%), and Ruminococcaceae_NK4A214_group (baseline: 0.37 ± 0.56%, Δ 0.17 ± 0.83%), and also the predicted pathway acetyl-CoA fermentation to butyrate II (baseline: 0.23 ± 0.062%, Δ 0.035 ± 0.059%), compared with the RW intervention (P values <0.05). A change in Ruminococcaceae_NK4A214_group was positively correlated with the change in liver fat, in both the WGW (ρ = 0.54; P = 0.026) and RW (ρ = 0.67; P = 0.024) groups. CONCLUSIONS In middle-aged overweight and obese adults, a 12-wk WGW intervention increased the relative abundance of a number of bacterial taxa from the family Ruminococcaceae and increased predicted fermentation pathways when compared with an RW intervention. Potential protective health effects of replacement of RW by WGW on metabolic organs, such as the liver, via modulation of the microbiota, deserve further investigation.This trial was registered at clinicaltrials.gov as NCT02385149.
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Affiliation(s)
- Mara P H van Trijp
- Nutrition, Metabolism & Genomics Group, Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
| | - Sophie Schutte
- Nutrition, Metabolism & Genomics Group, Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
| | - Diederik Esser
- Nutrition, Metabolism & Genomics Group, Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
| | - Suzan Wopereis
- TNO, Netherlands Organization for Applied Scientific Research, Zeist, The Netherlands
| | - Femke P M Hoevenaars
- TNO, Netherlands Organization for Applied Scientific Research, Zeist, The Netherlands
| | - Guido J E J Hooiveld
- Nutrition, Metabolism & Genomics Group, Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
| | - Lydia A Afman
- Nutrition, Metabolism & Genomics Group, Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
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New Insights into Microbial Diversity of the Traditional Packed Table Olives Aloreña de Málaga through Metataxonomic Analysis. Microorganisms 2021; 9:microorganisms9030561. [PMID: 33803149 PMCID: PMC8000080 DOI: 10.3390/microorganisms9030561] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/25/2022] Open
Abstract
Aloreña de Málaga is a table olive especially characterised by its natural freshness and short shelf-life. In this work, we applied a metataxonomic approach to unravel the microbial diversity of bacterial and fungi populations through the shelf-life of traditionally packed Aloreña de Málaga. A significant increase in lactic acid bacteria and mesophilic aerobic populations was observed during shelf-life, reaching the maximum population levels (4-5 log10 CFU) at the end of the study (260 days). On the contrary, a rapid reduction in yeast and mould populations was reported. The use of a metataxonomic analysis based on the amplification of 16S (bacteria) and internal transcribed spacer (ITS) region (fungi) regions revealed a low diversity for both microbial groups. Lactiplantibacillus (65.05 ± 8.65% in brine vs. 58.70 ± 15.70% in fruit), Pediococcus (28.17 ± 7.36% in brine vs. 27.20 ± 15.95% in fruit), and Celerinatantimonas (4.64 ± 1.08% in brine vs. 11.82 ± 18.17% in fruit) were the main genera found among bacteria, and an increase in Lactiplantibacillus and a reduction in Celerinatantimonas populations during the shelf-life were observed. On the other hand, Citeromyces was the dominant fungi genus (54.11 ± 2.00% in brine vs. 50.91 ± 16.14% in fruit), followed by Candida (8.80 ± 2.57% in brine vs. 12.32 ± 8.61% in fruit) and Penicillium (6.48 ± 1.87% vs. 8.48 ± 4.43% in fruit). No food-borne pathogen genera were detected in any of the samples analysed, indicating the high level of food safety found in this ready-to-eat fermented vegetable. Data obtained in this work will help in the design of new strategies for the control of microbial populations during the shelf-life of Aloreña de Málaga.
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40
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Morales D, Shetty SA, López-Plaza B, Gómez-Candela C, Smidt H, Marín FR, Soler-Rivas C. Modulation of human intestinal microbiota in a clinical trial by consumption of a β-D-glucan-enriched extract obtained from Lentinula edodes. Eur J Nutr 2021; 60:3249-3265. [PMID: 33580297 DOI: 10.1007/s00394-021-02504-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/28/2021] [Indexed: 12/23/2022]
Abstract
PURPOSE The aim of this study was to evaluate the hypocholesterolemic, immune- and microbiota-modulatory effect of a mushroom extract in hypercholesterolemic subjects. METHODS A randomized, controlled, double-blind, and parallel clinical trial was carried out with subjects from 18 to 65 years old (n = 52) with untreated mild hypercholesterolemia. Volunteers consumed a β-D-glucan-enriched (BGE) mixture (10.4 g/day) obtained from shiitake mushrooms (Lentinula edodes) ensuring a 3.5 g/day of fungal β-D-glucans or a placebo incorporated in three different commercial creams. RESULTS This mixture showed hypocholesterolemic activities in vitro and in animal studies. After eight weeks intervention, no significant differences in lipid- or cholesterol-related parameters were found compared to placebo subjects as well as before and after the BGE mixture administration. No inflammatory or immunomodulatory responses were noticed and no changes in IL-1β, IL-6, TNF-α or oxLDL were recorded. However, consumption of the BGE mixture was safe and managed to achieve the dietary fibre intake recommended as cardiovascular protective diet. Moreover, the BGE mixture modulated the colonic microbiota differently compared to placebo. Microbial community composition varied from before to after the intervention with several genera being positively or negatively correlated with some biomarkers related to cholesterol metabolism. CONCLUSION These results suggested a relation between cholesterol metabolism, microbiota and BGE administration. Nevertheless, the precise significance of this differential modulation was not fully elucidated and requires further studies.
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Affiliation(s)
- Diego Morales
- Department of Production and Characterization of Novel Foods, Institute of Food Science Research - CIAL (UAM+CSIC), Universidad Autónoma de Madrid, C/ Nicolas Cabrera 9, Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Sudarshan A Shetty
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Bricia López-Plaza
- Nutrition Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), 28046, Madrid, Spain
| | - Carmen Gómez-Candela
- Nutrition Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), 28046, Madrid, Spain
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Francisco Ramón Marín
- Department of Production and Characterization of Novel Foods, Institute of Food Science Research - CIAL (UAM+CSIC), Universidad Autónoma de Madrid, C/ Nicolas Cabrera 9, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Cristina Soler-Rivas
- Department of Production and Characterization of Novel Foods, Institute of Food Science Research - CIAL (UAM+CSIC), Universidad Autónoma de Madrid, C/ Nicolas Cabrera 9, Campus de Cantoblanco, 28049, Madrid, Spain
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Kohn N, Szopinska-Tokov J, Llera Arenas A, Beckmann C, Arias-Vasquez A, Aarts E. Multivariate associative patterns between the gut microbiota and large-scale brain network connectivity. Gut Microbes 2021; 13:2006586. [PMID: 34856861 PMCID: PMC8726725 DOI: 10.1080/19490976.2021.2006586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/21/2021] [Accepted: 11/02/2021] [Indexed: 02/04/2023] Open
Abstract
Research on the gut-brain axis has accelerated substantially over the course of the last years. Many reviews have outlined the important implications of understanding the relation of the gut microbiota with human brain function and behavior. One substantial drawback in integrating gut microbiome and brain data is the lack of integrative multivariate approaches that enable capturing variance in both modalities simultaneously. To address this issue, we applied a linked independent component analysis (LICA) to microbiota and brain connectivity data.We analyzed data from 58 healthy females (mean age = 21.5 years). Magnetic Resonance Imaging data were acquired using resting state functional imaging data. The assessment of gut microbial composition from feces was based on sequencing of the V4 16S rRNA gene region. We used the LICA model to simultaneously factorize the subjects' large-scale brain networks and microbiome relative abundance data into 10 independent components of spatial and abundance variation.LICA decomposition resulted in four components with non-marginal contribution of the microbiota data. The default mode network featured strongly in three components, whereas the two-lateralized fronto-parietal attention networks contributed to one component. The executive-control (with the default mode) network was associated to another component. We found that the abundance of Prevotella genus was associated with the strength of expression of all networks, whereas Bifidobacterium was associated with the default mode and frontoparietal-attention networks.We provide the first exploratory evidence for multivariate associative patterns between the gut microbiota and brain network connectivity in healthy humans considering the complexity of both systems.
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Affiliation(s)
- N. Kohn
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - J. Szopinska-Tokov
- Department of Psychiatry, Donders Institute for Brain, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Institute for Brain, Nijmegen, The Netherlands
| | - A. Llera Arenas
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - C.F. Beckmann
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - A. Arias-Vasquez
- Department of Psychiatry, Donders Institute for Brain, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Institute for Brain, Nijmegen, The Netherlands
| | - E Aarts
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
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Meijerink N, Kers JG, Velkers FC, van Haarlem DA, Lamot DM, de Oliveira JE, Smidt H, Stegeman JA, Rutten VPMG, Jansen CA. Early Life Inoculation With Adult-Derived Microbiota Accelerates Maturation of Intestinal Microbiota and Enhances NK Cell Activation in Broiler Chickens. Front Vet Sci 2020; 7:584561. [PMID: 33330708 PMCID: PMC7710667 DOI: 10.3389/fvets.2020.584561] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023] Open
Abstract
Studies in mammals, including chickens, have shown that the development of the immune system is affected by interactions with intestinal microbiota. Early life microbial colonization may affect the development of innate and adaptive immunity and may contribute to lasting effects on health and resilience of broiler chickens. We inoculated broiler chickens with adult-derived-microbiota (AM) to investigate their effects on intestinal microbiota composition and natural killer (NK) cells, amongst other immune cells. We hypothesized that AM inoculation directly upon hatch (day 0) would induce an alteration in microbiota composition shortly after hatch, and subsequently affect (subsets of) intestinal NK cells and their activation. Microbiota composition of caecal and ileal content of chickens of 1, 3, 7, 14, 21, and 35 days of age was assessed by sequencing of 16S ribosomal RNA gene amplicons. In parallel, subsets and activation of intestinal NK cells were analyzed by flow cytometry. In caecal content of 1- and 3-day-old AM chickens, a higher alpha-diversity (Faith's phylogenetic diversity) was observed compared to control chickens, whereas ileal microbiota were unaffected. Regarding beta-diversity, caecal microbiota profiles could be clustered into three distinct community types. Cluster A represented caecal microbiota of 1-day-old AM chickens and 1- and 3-day-old control chickens. Cluster B included microbiota of seven of eight 3- and 7-day-old AM and 7-day-old control chickens, and cluster C comprised microbiota of all chickens of 14-days and older, independent of inoculation. In 3-day-old AM chickens an increase in the percentages of intestinal IL-2Rα+NK cells and activated NK cells was observed compared to control chickens of the same age. In addition, an increase in relative numbers of intestinal cytotoxic CD8αα+T cells was observed in 14- and 21-day-old AM chickens. Taken together, these results indicate that early exposure to AM shapes and accelerates the maturation of caecal microbiota, which is paralleled by an increase in IL-2Rα+NK cells and enhanced NK cell activation. The observed association between early life development of intestinal microbiota and immune system indicates possibilities to apply microbiota-targeted strategies that can accelerate maturation of intestinal microbiota and strengthen the immune system, thereby improving the health and resilience of broiler chickens.
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Affiliation(s)
- Nathalie Meijerink
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Jannigje G. Kers
- Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Francisca C. Velkers
- Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Daphne A. van Haarlem
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - David M. Lamot
- Cargill Animal Nutrition and Health Innovation Center, Velddriel, Netherlands
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - J. Arjan Stegeman
- Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Victor P. M. G. Rutten
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Christine A. Jansen
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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Chiariotti A, Edwards JE, Hermes GDA, Catillo G, Meo Zilio D, Di Giovanni S, Smidt H, Buttazzoni L. Increasing the Sustainability of Maize Grain Production by Using Arbuscular Mycorrhizal Fungi Does Not Affect the Rumen of Dairy Cattle ( Bos taurus) and Buffalo ( Bubalus bubalis). Front Vet Sci 2020; 7:556764. [PMID: 33195529 PMCID: PMC7593576 DOI: 10.3389/fvets.2020.556764] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/31/2020] [Indexed: 11/29/2022] Open
Abstract
New approaches are needed to improve the sustainability of feed production and utilization by ruminants. Promising approaches include increased use of buffaloes for more sustainable milk production, and arbuscular mycorrhizal fungi (AMF) to reduce crop production input needs. However, studies assessing the effect of crops grown in the presence of AMF on rumen microbial utilization are limited. Based on current knowledge, we hypothesized that maize grain grown on AMF-inoculated soil affected ruminal fermentation and microbiota, and that this effect differed between buffalo and cattle. A dietary cross-over study (four weeks per diet) was conducted using rumen-cannulated cattle (n = 5) and buffalo (n = 6) to assess the effect of maize grain (3.9% (w/v) of diet) grown on soil with or without AMF (15 kg/ha) on ruminal fermentation and microbiota. Production of maize on AMF-treated soil did not affect any of the assessed ruminal fermentation parameters, microbial concentrations, or prokaryotic community composition (using prokaryotic 16S rRNA gene sequence analysis). In contrast, host type had numerous effects. Protozoal counts, lactate, total VFA and isobutyrate, were significantly higher in buffaloes compared to cattle. Conversely, butyrate was significantly lower in buffaloes than in cattle. Host type explained 9.3% of the total variation in prokaryotic community composition, and relative abundance of nine amplicon sequence variants significantly differed between host types. These findings indicate that AMF treatment of maize crops has no detrimental impact on the value of the resulting maize grains as a ruminant feed, and provides additional insight into rumen-based differences between cattle and buffalo.
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Affiliation(s)
- Antonella Chiariotti
- Council for Agricultural Research and Economics (CREA), Research Center for Animal Production and Aquaculture, Monterotondo, Italy
| | - Joan E Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Gerben D A Hermes
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Gennaro Catillo
- Council for Agricultural Research and Economics (CREA), Research Center for Animal Production and Aquaculture, Monterotondo, Italy
| | - David Meo Zilio
- Council for Agricultural Research and Economics (CREA), Research Center for Animal Production and Aquaculture, Monterotondo, Italy
| | - Sabrina Di Giovanni
- Council for Agricultural Research and Economics (CREA), Research Center for Animal Production and Aquaculture, Monterotondo, Italy
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Luca Buttazzoni
- Council for Agricultural Research and Economics (CREA), Research Center for Animal Production and Aquaculture, Monterotondo, Italy
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Dame-Korevaar A, Kers JG, van der Goot J, Velkers FC, Ceccarelli D, Mevius DJ, Stegeman A, Fischer EAJ. Competitive Exclusion Prevents Colonization and Compartmentalization Reduces Transmission of ESBL-Producing Escherichia coli in Broilers. Front Microbiol 2020; 11:566619. [PMID: 33304325 PMCID: PMC7693455 DOI: 10.3389/fmicb.2020.566619] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/21/2020] [Indexed: 11/13/2022] Open
Abstract
Extended spectrum beta-lactamase (ESBL)-producing bacteria are resistant to extended-spectrum cephalosporins and are common in broilers. Interventions are needed to reduce the prevalence of ESBL-producing bacteria in the broiler production pyramid. This study investigated two different interventions. The effect of a prolonged supply of competitive exclusion (CE) product and compartmentalization on colonization and transmission, after challenge with a low dose of ESBL-producing Escherichia coli, in broilers kept under semi-field conditions, were examined. One-day-old broilers (Ross 308) (n = 400) were housed in four experimental rooms, subdivided in one seeder (S/C1)-pen and eight contact (C2)-pens. In two rooms, CE product was supplied from day 0 to 7. At day 5, seeder-broilers were inoculated with E. coli strain carrying bla CTX-M- 1 on plasmid IncI1 (CTX-M-1-E. coli). Presence of CTX-M-1-E. coli was determined using cloacal swabs (day 5-21 daily) and cecal samples (day 21). Time until colonization and cecal excretion (log10 CFU/g) were analyzed using survival analysis and linear regression. Transmission coefficients within and between pens were estimated using maximum likelihood. The microbiota composition was assessed by 16S ribosomal RNA gene amplicon sequencing in cecal content of broilers on days 5 and 21. None of the CE broilers was CTX-M-1-E. coli positive. In contrast, in the untreated rooms 187/200 of the broilers were CTX-M-1-E. coli positive at day 21. Broilers in C2-pens were colonized later than seeder-broilers (Time to event Ratio 3.53, 95% CI 3.14 to 3.93). The transmission coefficient between pens was lower than within pens (3.28 × 10-4 day-2, 95% CI 2.41 × 10-4 to 4.32 × 10-4 vs. 6.12 × 10-2 day-2, 95% CI 4.78 × 10-2 to 7.64 × 10-2). The alpha diversity of the cecal microbiota content was higher in CE broilers than in control broilers at days 5 and 21. The supply of a CE product from day 0 to 7 prevented colonization of CTX-M-1-E. coli after challenge at day 5, likely as a result of CE induced effects on the microbiota composition. Furthermore, compartmentalization reduced transmission rate between broilers. Therefore, a combination of compartmentalization and supply of a CE product may be a useful intervention to reduce transmission and prevent colonization of ESBL/pAmpC-producing bacteria in the broiler production pyramid.
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Affiliation(s)
- Anita Dame-Korevaar
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Jannigje G. Kers
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Jeanet van der Goot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Francisca C. Velkers
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Dik J. Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Arjan Stegeman
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Egil A. J. Fischer
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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Müller M, Hermes GDA, Emanuel E. C, Holst JJ, Zoetendal EG, Smidt H, Troost F, Schaap FG, Damink SO, Jocken JWE, Lenaerts K, Masclee AAM, Blaak EE. Effect of wheat bran derived prebiotic supplementation on gastrointestinal transit, gut microbiota, and metabolic health: a randomized controlled trial in healthy adults with a slow gut transit. Gut Microbes 2020; 12:1704141. [PMID: 31983281 PMCID: PMC7524158 DOI: 10.1080/19490976.2019.1704141] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Acute intake of the wheat bran extract Arabinoxylan-Oligosaccharide (AXOS) modulates the gut microbiota, improves stool characteristics and postprandial glycemia in healthy humans. Yet, little is known on how long-term AXOS intake influences gastrointestinal (GI) functioning, gut microbiota, and metabolic health. In this randomized, placebo-controlled, double-blind study, we evaluated the effects of AXOS intake on GI function and metabolic health in adults with slow GI transit without constipation. Forty-eight normoglycemic adults were included with whole-gut transit time (WGTT) of >35 h receiving either 15 g/day AXOS or placebo (maltodextrin) for 12-wks. The primary outcome was WGTT, and secondary outcomes included stool parameters, gut permeability, short-chain fatty acids (SCFA), microbiota composition, energy expenditure, substrate oxidation, glucose, insulin, lipids, gut hormones, and adipose tissue (AT) function. WGTT was unchanged, but stool consistency softened after AXOS. 12-wks of AXOS intake significantly changed the microbiota by increasing Bifidobacterium and decreasing microbial alpha-diversity. With a good classification accuracy, overall microbiota composition classified responders with decreased WGTT after AXOS. The incretin hormone Glucagon-like protein 1 was reduced after AXOS compared to placebo. Energy expenditure, plasma metabolites, AT parameters, SCFA, and gut permeability were unchanged. In conclusion, intake of wheat bran extract increases fecal Bifidobacterium and softens stool consistency without major effects on energy metabolism in healthy humans with a slow GI transit. We show that overall gut microbiota classified responders with decreased WGTT after AXOS highlighting that GI transit and change thereof were associated with gut microbiota independent of Bifidobacterium. NCT02491125.
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Affiliation(s)
- Mattea Müller
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Gerben D. A. Hermes
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Canfora Emanuel E.
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Jens J. Holst
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Erwin G. Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Freddy Troost
- Division of Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands,Food Innovation and Health Research, Centre for Healthy Eating and Food Innovation, Maastricht University, Venlo, The Netherlands
| | - Frank G. Schaap
- Division of Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Steven Olde Damink
- Division of Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Johan W. E. Jocken
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Kaatje Lenaerts
- Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Ad A. M. Masclee
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Ellen E. Blaak
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands,CONTACT Ellen E. Blaak Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, P.O. Box 616, Maastricht6200, The Netherlands
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46
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Ducarmon QR, Hoogerwerf MA, Janse JJ, Geelen AR, Koopman JPR, Zwittink RD, Goeman JJ, Kuijper EJ, Roestenberg M. Dynamics of the bacterial gut microbiota during controlled human infection with Necator americanus larvae. Gut Microbes 2020; 12:1-15. [PMID: 33222610 PMCID: PMC7714523 DOI: 10.1080/19490976.2020.1840764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Hookworms are soil-transmitted helminths that use immune-evasive strategies to persist in the human duodenum where they are responsible for anemia and protein loss. Given their location and immune regulatory effects, hookworms likely impact the bacterial microbiota. However, microbiota studies struggle to deconvolute the effect of hookworms from confounders such as coinfections and malnutrition. We thus used an experimental human hookworm infection model to explore temporal changes in the gut microbiota before and during hookworm infection. Volunteers were dermally exposed to cumulative dosages of 50, 100 or 150 L3 Necator americanus larvae. Fecal samples were collected for microbiota profiling through 16S rRNA gene amplicon sequencing at weeks zero, four, eight, fourteen and twenty. During the acute infection phase (trial week zero to eight) no changes in bacterial diversity were detected. During the established infection phase (trial week eight to twenty), bacterial richness (Chao1, p = .0174) increased significantly over all volunteers. No relation was found between larval dosage and diversity, stability or relative abundance of individual bacterial taxa. GI symptoms were associated with an unstable microbiota during the first eight weeks and rapid recovery at week twenty. Barnesiella, amongst other taxa, was more abundant in volunteers with more GI symptoms throughout the study. In conclusion, this study showed that clinical GI symptoms following N. americanus infection are associated with temporary microbiota instability and relative abundance of specific bacterial taxa. These results suggest a possible role of hookworm-induced enteritis on microbiota stability.
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Affiliation(s)
- Q. R. Ducarmon
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands,Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands,CONTACT Meta Roestenberg Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands; Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - M. A. Hoogerwerf
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - J. J. Janse
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - A. R. Geelen
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands,Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - J. P. R. Koopman
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - R. D. Zwittink
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands,Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - J. J. Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - E. J. Kuijper
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands,Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - M. Roestenberg
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands,Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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47
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Kers JG, de Oliveira JE, Fischer EAJ, Tersteeg‐Zijderveld MHG, Konstanti P, Stegeman JA(A, Smidt H, Velkers FC. Associations between phenotypic characteristics and clinical parameters of broilers and intestinal microbial development throughout a production cycle: A field study. Microbiologyopen 2020; 9:e1114. [PMID: 33068065 PMCID: PMC7658455 DOI: 10.1002/mbo3.1114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/09/2020] [Accepted: 08/18/2020] [Indexed: 01/09/2023] Open
Abstract
Disturbances in intestinal health are a common problem affecting commercial broiler chickens worldwide. Several studies have revealed associations between health, production performance, and intestinal microbiota. This study aimed to describe the development of the intestinal microbiota of broilers within a production cycle to evaluate to what extent clinical parameters and phenotypic characteristics can explain the intestinal microbiota variation. Of four well-performing flocks within two farms, the cecal content was collected of nine broilers at 0, 2, 4, or 5, 7, 11, or 12, 14, 21, 28, 35, and 40 days of the production cycle. In total, 342 samples were analyzed using 16S ribosomal RNA gene amplicon sequencing. Variables as macroscopic gut abnormalities, gut lesions, age, individual body weight, sex, footpad integrity, the color of ceca, and foam in cecal content were determined. Ileum tissue was collected for histological quantification of villus length and crypt depth. Flock infection levels of the intestinal disease coccidiosis were measured in pooled feces from the poultry house. Increases in phylogenetic diversity were observed from hatch until day 21 of age. Constrained multivariate analysis indicated that age, farm, body weight, ileum crypt depth, cecal color, and the coccidiosis lesion score were important variables to describe the variation in cecal microbiota. These results contribute to determining relevant variables in flocks that may be indicative of the intestinal microbiota composition. Moreover, this knowledge increases the awareness of interactions between the intestinal microbiota and broiler health as well as their relative importance.
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Affiliation(s)
- Jannigje G. Kers
- Department of Population Health SciencesDivision of Farm Animal HealthFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Jean E. de Oliveira
- Cargill Animal Nutrition and HealthInnovation Center VelddrielVelddrielThe Netherlands
| | - Egil A. J. Fischer
- Department of Population Health SciencesDivision of Farm Animal HealthFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Monique H. G. Tersteeg‐Zijderveld
- Department of Population Health SciencesInstitute for Risk Assessment SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Prokopis Konstanti
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Jan Arend (Arjan) Stegeman
- Department of Population Health SciencesDivision of Farm Animal HealthFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Hauke Smidt
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Francisca C. Velkers
- Department of Population Health SciencesDivision of Farm Animal HealthFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
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de Vries H, Geervliet M, Jansen CA, Rutten VPMG, van Hees H, Groothuis N, Wells JM, Savelkoul HFJ, Tijhaar E, Smidt H. Impact of Yeast-Derived β-Glucans on the Porcine Gut Microbiota and Immune System in Early Life. Microorganisms 2020; 8:microorganisms8101573. [PMID: 33066115 PMCID: PMC7601942 DOI: 10.3390/microorganisms8101573] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 01/10/2023] Open
Abstract
Piglets are susceptible to infections in early life and around weaning due to rapid environmental and dietary changes. A compelling target to improve pig health in early life is diet, as it constitutes a pivotal determinant of gut microbial colonization and maturation of the host’s immune system. In the present study, we investigated how supplementation of yeast-derived β-glucans affects the gut microbiota and immune function pre- and post-weaning, and how these complex systems develop over time. From day two after birth until two weeks after weaning, piglets received yeast-derived β-glucans or a control treatment orally and were subsequently vaccinated against Salmonella Typhimurium. Faeces, digesta, blood, and tissue samples were collected to study gut microbiota composition and immune function. Overall, yeast-derived β-glucans did not affect the vaccination response, and only modest effects on faecal microbiota composition and immune parameters were observed, primarily before weaning. This study demonstrates that the pre-weaning period offers a ‘window of opportunity’ to alter the gut microbiota and immune system through diet. However, the observed changes were modest, and any long-lasting effects of yeast-derived β-glucans remain to be elucidated.
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Affiliation(s)
- Hugo de Vries
- Laboratory of Microbiology, Wageningen University, 6700 EH Wageningen, The Netherlands;
- Host-Microbe Interactomics Group, Wageningen University, 6700 AH Wageningen, The Netherlands;
| | - Mirelle Geervliet
- Cell Biology and Immunology Group, Wageningen University, 6700 AH Wageningen, The Netherlands; (M.G.); (N.G.); (H.F.J.S.); (E.T.)
| | - Christine A. Jansen
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (C.A.J.); (V.P.M.G.R.)
| | - Victor P. M. G. Rutten
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (C.A.J.); (V.P.M.G.R.)
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Hubèrt van Hees
- Research and Development, Trouw Nutrition, 3800 AG Amersfoort, The Netherlands;
| | - Natalie Groothuis
- Cell Biology and Immunology Group, Wageningen University, 6700 AH Wageningen, The Netherlands; (M.G.); (N.G.); (H.F.J.S.); (E.T.)
| | - Jerry M. Wells
- Host-Microbe Interactomics Group, Wageningen University, 6700 AH Wageningen, The Netherlands;
| | - Huub F. J. Savelkoul
- Cell Biology and Immunology Group, Wageningen University, 6700 AH Wageningen, The Netherlands; (M.G.); (N.G.); (H.F.J.S.); (E.T.)
| | - Edwin Tijhaar
- Cell Biology and Immunology Group, Wageningen University, 6700 AH Wageningen, The Netherlands; (M.G.); (N.G.); (H.F.J.S.); (E.T.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, 6700 EH Wageningen, The Netherlands;
- Correspondence:
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van Trijp MPH, Rösch C, An R, Keshtkar S, Logtenberg MJ, Hermes GDA, Zoetendal EG, Schols HA, Hooiveld GJEJ. Fermentation Kinetics of Selected Dietary Fibers by Human Small Intestinal Microbiota Depend on the Type of Fiber and Subject. Mol Nutr Food Res 2020; 64:e2000455. [PMID: 32918522 PMCID: PMC7685165 DOI: 10.1002/mnfr.202000455] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/23/2020] [Indexed: 12/25/2022]
Abstract
SCOPE An underexplored topic is the investigation of health effects of dietary fibers via modulation of human small intestine (SI) microbiota. A few previous studies hint at fermentation of some dietary fibers in the distal SI of humans and pigs. Here the potential of human SI microbiota to degrade dietary fibers and produce metabolites in vitro is investigated. METHODS AND RESULTS Fructans, galacto-oligosaccharides, lemon pectins, and isomalto/malto-polysaccharides are subjected to in vitro batch fermentations inoculated with ileostomy effluent from five subjects. Fiber degradation products, formation of bacterial metabolites, and microbiota composition are determined over time. Galacto- and fructo-oligosaccharides are rapidly utilized by the SI microbiota of all subjects. At 5h of fermentation, 31%-82% of galacto-oligosaccharides and 29%-89% fructo-oligosaccharides (degree of polymerization DP4-8) are utilized. Breakdown of fructo-oligosaccharides/inulin DP ≥ 10, lemon pectin, and iso-malto/maltopolysaccharides only started after 7h incubation. Degradation of different fibers result in production of mainly acetate, and changed microbiota composition over time. CONCLUSION Human SI microbiota have hydrolytic potential for prebiotic galacto- and fructo-oligosaccharides. In contrast, the higher molecular weight fibers inulin, lemon pectin, and iso-malto/maltopolysaccharides show slow fermentation rate. Fiber degradation kinetics and microbiota responses are subject dependent, therefore personalized nutritional fiber based strategies are required.
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Affiliation(s)
- Mara P. H. van Trijp
- Nutrition, Metabolism and Genomics GroupDivision of Human Nutrition and HealthWageningen UniversityStippeneng 4WageningenWG 6708The Netherlands
| | - Christiane Rösch
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9WageningenWG 6708The Netherlands
| | - Ran An
- Laboratory of MicrobiologyWageningen UniversityStippeneng 4WageningenWG 6708The Netherlands
| | - Shohreh Keshtkar
- Nutrition, Metabolism and Genomics GroupDivision of Human Nutrition and HealthWageningen UniversityStippeneng 4WageningenWG 6708The Netherlands
| | - Madelon J. Logtenberg
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9WageningenWG 6708The Netherlands
| | - Gerben D. A. Hermes
- Laboratory of MicrobiologyWageningen UniversityStippeneng 4WageningenWG 6708The Netherlands
| | - Erwin G. Zoetendal
- Laboratory of MicrobiologyWageningen UniversityStippeneng 4WageningenWG 6708The Netherlands
| | - Henk A. Schols
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9WageningenWG 6708The Netherlands
| | - Guido J. E. J. Hooiveld
- Nutrition, Metabolism and Genomics GroupDivision of Human Nutrition and HealthWageningen UniversityStippeneng 4WageningenWG 6708The Netherlands
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50
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Logtenberg MJ, Akkerman R, An R, Hermes GDA, de Haan BJ, Faas MM, Zoetendal EG, Schols HA, de Vos P. Fermentation of Chicory Fructo-Oligosaccharides and Native Inulin by Infant Fecal Microbiota Attenuates Pro-Inflammatory Responses in Immature Dendritic Cells in an Infant-Age-Dependent and Fructan-Specific Way. Mol Nutr Food Res 2020; 64:e2000068. [PMID: 32420676 PMCID: PMC7378940 DOI: 10.1002/mnfr.202000068] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/09/2020] [Indexed: 12/19/2022]
Abstract
SCOPE Inulin-type fructans are commonly applied in infant formula to support development of gut microbiota and immunity. These inulin-type fructans are considered to be fermented by gut microbiota, but it is unknown how fermentation impacts immune modulating capacity and whether the process of fermentation is dependent on the infant's age. METHODS AND RESULTS The in vitro fermentation of chicory fructo-oligosaccharides (FOS) and native inulin are investigated using pooled fecal inocula of two- and eight-week-old infants. Both inocula primarily utilize the trisaccharides in FOS, while they almost completely utilize native inulin with degree of polymerization (DP) 3-8. Fecal microbiota of eight-week-old infants degrades longer chains of native inulin up to DP 16. This correlates with a higher abundance of Bifidobacterium and higher production of acetate and lactate after 26 h of fermentation. Fermented FOS and native inulin attenuate pro-inflammatory cytokines produced by immature dendritic cells (DCs), but profiles and magnitude of attenuation are stronger with native inulin than with FOS. CONCLUSION The findings demonstrate that fermentation of FOS and native inulin is dependent on the infant's age and fructan structure. Fermentation enhances attenuating effects of pro-inflammatory responses in DCs, which depend mainly on microbial metabolites formed during fermentation.
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Affiliation(s)
- Madelon J. Logtenberg
- Laboratory of Food ChemistryWageningen University and ResearchBornse Weilanden 9, 6708 WGWageningenThe Netherlands
| | - Renate Akkerman
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical BiologyUniversity of Groningen and University Medical Centre GroningenHanzeplein 1, 9700 RBGroningenThe Netherlands
| | - Ran An
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 4, 6708 WEWageningenThe Netherlands
| | - Gerben D. A. Hermes
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 4, 6708 WEWageningenThe Netherlands
| | - Bart J. de Haan
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical BiologyUniversity of Groningen and University Medical Centre GroningenHanzeplein 1, 9700 RBGroningenThe Netherlands
| | - Marijke M. Faas
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical BiologyUniversity of Groningen and University Medical Centre GroningenHanzeplein 1, 9700 RBGroningenThe Netherlands
| | - Erwin G. Zoetendal
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 4, 6708 WEWageningenThe Netherlands
| | - Henk A. Schols
- Laboratory of Food ChemistryWageningen University and ResearchBornse Weilanden 9, 6708 WGWageningenThe Netherlands
| | - Paul de Vos
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical BiologyUniversity of Groningen and University Medical Centre GroningenHanzeplein 1, 9700 RBGroningenThe Netherlands
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