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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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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: 20] [Impact Index Per Article: 6.7] [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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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: 4] [Impact Index Per Article: 1.3] [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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55
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van Dongen KCW, van der Zande M, Bruyneel B, Vervoort JJM, Rietjens IMCM, Belzer C, Beekmann K. An in vitro model for microbial fructoselysine degradation shows substantial interindividual differences in metabolic capacities of human fecal slurries. Toxicol In Vitro 2021; 72:105078. [PMID: 33429044 DOI: 10.1016/j.tiv.2021.105078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Fructoselysine is formed upon heating during processing of food products, and being a key intermediate in advanced glycation end product formation considered to be potentially hazardous to human health. Human gut microbes can degrade fructoselysine to yield the short chain fatty acid butyrate. However, quantitative information on these biochemical reactions is lacking, and interindividual differences therein are not well established. Anaerobic incubations with pooled and individual human fecal slurries were optimized and applied to derive quantitative kinetic information for these biochemical reactions. Of 16 individuals tested, 11 were fructoselysine metabolizers, with Vmax, Km and kcat-values varying up to 14.6-fold, 9.5-fold, and 4.4-fold, respectively. Following fructoselysine exposure, 10 of these 11 metabolizers produced significantly increased butyrate concentrations, varying up to 8.6-fold. Bacterial taxonomic profiling of the fecal samples revealed differential abundant taxa for these reactions (e.g. families Ruminococcaceae, Christenellaceae), and Ruminococcus_1 showed the strongest correlation with fructoselysine degradation and butyrate production (ρ ≥ 0.8). This study highlights substantial interindividual differences in gut microbial degradation of fructoselysine. The presented method allows for quantification of gut microbial degradation kinetics for foodborne xenobiotics, and interindividual differences therein, which can be used to refine prediction of internal exposure.
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Affiliation(s)
- Katja C W van Dongen
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands.
| | - Meike van der Zande
- Wageningen Food Safety Research (WFSR), part of Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, the Netherlands
| | - Ben Bruyneel
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands
| | - Jacques J M Vervoort
- Laboratory of Biochemistry, Wageningen University and Research, P.O. Box 8128, 6700 ET Wageningen, the Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, P.O. Box 8033, 6700 EH Wageningen, the Netherlands
| | - Karsten Beekmann
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands; Wageningen Food Safety Research (WFSR), part of Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, the Netherlands
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Abdala Asbun A, Besseling MA, Balzano S, van Bleijswijk JDL, Witte HJ, Villanueva L, Engelmann JC. Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results. Front Genet 2020; 11:489357. [PMID: 33329686 PMCID: PMC7718033 DOI: 10.3389/fgene.2020.489357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/05/2020] [Indexed: 01/04/2023] Open
Abstract
Marker gene sequencing of the rRNA operon (16S, 18S, ITS) or cytochrome c oxidase I (CO1) is a popular means to assess microbial communities of the environment, microbiomes associated with plants and animals, as well as communities of multicellular organisms via environmental DNA sequencing. Since this technique is based on sequencing a single gene, or even only parts of a single gene rather than the entire genome, the number of reads needed per sample to assess the microbial community structure is lower than that required for metagenome sequencing. This makes marker gene sequencing affordable to nearly any laboratory. Despite the relative ease and cost-efficiency of data generation, analyzing the resulting sequence data requires computational skills that may go beyond the standard repertoire of a current molecular biologist/ecologist. We have developed Cascabel, a scalable, flexible, and easy-to-use amplicon sequence data analysis pipeline, which uses Snakemake and a combination of existing and newly developed solutions for its computational steps. Cascabel takes the raw data as input and delivers a table of operational taxonomic units (OTUs) or Amplicon Sequence Variants (ASVs) in BIOM and text format and representative sequences. Cascabel is a highly versatile software that allows users to customize several steps of the pipeline, such as selecting from a set of OTU clustering methods or performing ASV analysis. In addition, we designed Cascabel to run in any linux/unix computing environment from desktop computers to computing servers making use of parallel processing if possible. The analyses and results are fully reproducible and documented in an HTML and optional pdf report. Cascabel is freely available at Github: https://github.com/AlejandroAb/CASCABEL.
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Affiliation(s)
- Alejandro Abdala Asbun
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Marc A Besseling
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Sergio Balzano
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Judith D L van Bleijswijk
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Harry J Witte
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Julia C Engelmann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, 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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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: 22] [Impact Index Per Article: 5.5] [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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van der Graaf CM, Sánchez-España J, Yusta I, Ilin A, Shetty SA, Bale NJ, Villanueva L, Stams AJM, Sánchez-Andrea I. Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes. Microorganisms 2020; 8:E1275. [PMID: 32825668 PMCID: PMC7565709 DOI: 10.3390/microorganisms8091275] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022] Open
Abstract
Acidic pit lakes are abandoned open pit mines filled with acid mine drainage (AMD)-highly acidic, metalliferous waters that pose a severe threat to the environment and are rarely properly remediated. Here, we investigated two meromictic, oligotrophic acidic mine pit lakes in the Iberian Pyrite Belt (IPB), Filón Centro (Tharsis) (FC) and La Zarza (LZ). We observed a natural attenuation of acidity and toxic metal concentrations towards the lake bottom, which was more pronounced in FC. The detection of Cu and Zn sulfides in the monimolimnion of FC suggests precipitation of dissolved metals as metal sulfides, pointing to biogenic sulfide formation. This was supported by microbial diversity analysis via 16S rRNA gene amplicon sequencing of samples from the water column, which showed the presence of sulfidogenic microbial taxa in FC and LZ. In the monimolimnion of FC, sequences affiliated with the putative sulfate-reducing genus Desulfomonile were dominant (58%), whereas in the more acidic and metal-enriched LZ, elemental sulfur-reducing Acidianus and Thermoplasma spp., and disproportionating Desulfocapsa spp. were more abundant. Furthermore, the detection of reads classified as methanogens and Desulfosporosinus spp., although at low relative abundance, represents one of the lowest pH values (2.9 in LZ) at which these taxa have been reported, to our knowledge. Analysis of potential biomarker lipids provided evidence that high levels of phosphocholine lipids with mixed acyl/ether glycerol core structures were associated with Desulfomonile, while ceramide lipids were characteristic of Microbacter in these environments. We propose that FC and LZ function as natural bioremediation reactors where metal sulfide precipitation is mediated by biosulfidogenesis starting from elemental sulfur reduction and disproportionation at an early stage (LZ), followed by sulfate reduction at a later stage (FC).
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Affiliation(s)
- Charlotte M. van der Graaf
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (S.A.S.); (A.J.M.S.)
| | - Javier Sánchez-España
- Geochemistry and Sustainable Mining Unit, Dept of Geological Resources, Spanish Geological Survey (IGME), Calera 1, Tres Cantos, 28760 Madrid, Spain;
| | - Iñaki Yusta
- Dept of Mineralogy and Petrology, University of the Basque Country (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain; (I.Y.); (A.I.)
| | - Andrey Ilin
- Dept of Mineralogy and Petrology, University of the Basque Country (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain; (I.Y.); (A.I.)
| | - Sudarshan A. Shetty
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (S.A.S.); (A.J.M.S.)
| | - Nicole J. Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Landsdiep 4, 1797 SZ ‘t Horntje, The Netherlands; (N.J.B.); (L.V.)
| | - Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Landsdiep 4, 1797 SZ ‘t Horntje, The Netherlands; (N.J.B.); (L.V.)
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (S.A.S.); (A.J.M.S.)
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (S.A.S.); (A.J.M.S.)
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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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Akkerman R, Logtenberg MJ, An R, Van Den Berg MA, de Haan BJ, Faas MM, Zoetendal E, de Vos P, Schols HA. Endo-1,3(4)-β-Glucanase-Treatment of Oat β-Glucan Enhances Fermentability by Infant Fecal Microbiota, Stimulates Dectin-1 Activation and Attenuates Inflammatory Responses in Immature Dendritic Cells. Nutrients 2020; 12:nu12061660. [PMID: 32503178 PMCID: PMC7352905 DOI: 10.3390/nu12061660] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Non-digestible carbohydrates are added to infant formula to mimic the effects of human milk oligosaccharide by acting as prebiotics and stimulating the immune system. Although not yet used in infant formulas, β-glucans are known to have beneficial health effects, and are therefore of potential interest for supplementation. Methods and results: We investigated the in vitro fermentation of native and endo-1,3(4)-β-glucanase-treated oat β-glucan using pooled fecal inocula of 2- and 8-week-old infants. While native oat β-glucan was not utilized, both inocula specifically utilized oat β-glucan oligomers containing β(1→4)-linkages formed upon enzyme treatment. The fermentation rate was highest in the fecal microbiota of 2-week-old infants, and correlated with a high lactate production. Fermentation of media supplemented with native and enzyme-treated oat β-glucans increased the relative abundance of Enterococcus and attenuated pro-inflammatory cytokine production (IL-1β, IL-6, TNFα) in immature dendritic cells. This attenuating effect was more pronounced after enzyme treatment. This attenuation might result from the enhanced ability of fermented oat β-glucan to stimulate Dectin-1 receptors. Conclusion: Our findings demonstrate that endo-1,3(4)-β-glucanase treatment enhances the fermentability of oat β-glucan and attenuates pro-inflammatory responses. Hence, this study shows that especially enzyme-treated oat β-glucans have a high potential for supplementation of infant formula.
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Affiliation(s)
- Renate Akkerman
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands; (B.J.d.H.); (M.M.F.); (P.d.V.)
- Correspondence: (R.A.); (M.J.L.)
| | - Madelon J. Logtenberg
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands;
- Correspondence: (R.A.); (M.J.L.)
| | - Ran An
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (R.A.); (E.Z.)
| | | | - Bart J. de Haan
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands; (B.J.d.H.); (M.M.F.); (P.d.V.)
| | - Marijke M. Faas
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands; (B.J.d.H.); (M.M.F.); (P.d.V.)
| | - Erwin Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (R.A.); (E.Z.)
| | - Paul de Vos
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands; (B.J.d.H.); (M.M.F.); (P.d.V.)
| | - Henk A. Schols
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands;
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Ozuolmez D, Moore EK, Hopmans EC, Sinninghe Damsté JS, Stams AJM, Plugge CM. Butyrate Conversion by Sulfate-Reducing and Methanogenic Communities from Anoxic Sediments of Aarhus Bay, Denmark. Microorganisms 2020; 8:microorganisms8040606. [PMID: 32331369 PMCID: PMC7232339 DOI: 10.3390/microorganisms8040606] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 11/29/2022] Open
Abstract
The conventional perception that the zone of sulfate reduction and methanogenesis are separated in high- and low-sulfate-containing marine sediments has recently been changed by studies demonstrating their co-occurrence in sediments. The presence of methanogens was linked to the presence of substrates that are not used by sulfate reducers. In the current study, we hypothesized that both groups can co-exist, consuming common substrates (H2 and/or acetate) in sediments. We enriched butyrate-degrading communities in sediment slurries originating from the sulfate, sulfate–methane transition, and methane zone of Aarhus Bay, Denmark. Sulfate was added at different concentrations (0, 3, 20 mM), and the slurries were incubated at 10 °C and 25 °C. During butyrate conversion, sulfate reduction and methanogenesis occurred simultaneously. The syntrophic butyrate degrader Syntrophomonas was enriched both in sulfate-amended and in sulfate-free slurries, indicating the occurrence of syntrophic conversions at both conditions. Archaeal community analysis revealed a dominance of Methanomicrobiaceae. The acetoclastic Methanosaetaceae reached high relative abundance in the absence of sulfate, while presence of acetoclastic Methanosarcinaceae was independent of the sulfate concentration, temperature, and the initial zone of the sediment. This study shows that there is no vertical separation of sulfate reducers, syntrophs, and methanogens in the sediment and that they all participate in the conversion of butyrate.
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Affiliation(s)
- Derya Ozuolmez
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
| | - Elisha K. Moore
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
- Department of Environmental Science, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| | - Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
- Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
- Correspondence: ; Tel.: +31-317-483116
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Edwards JE, Schennink A, Burden F, Long S, van Doorn DA, Pellikaan WF, Dijkstra J, Saccenti E, Smidt H. Domesticated equine species and their derived hybrids differ in their fecal microbiota. Anim Microbiome 2020; 2:8. [PMID: 33499942 PMCID: PMC7807894 DOI: 10.1186/s42523-020-00027-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/02/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Compared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the increased time available for feed to be acted upon by enzymes and the gut microbiota. However, differences in terms of microbial concentrations and/or community composition in the hindgut may also underpin the increased degradation of fiber in donkeys. Therefore, a study was conducted to assess if differences existed between the fecal microbiota of pony, donkey and hybrids derived from them (i.e. pony × donkey) when fed the same forage diet. RESULTS Fecal community composition of prokaryotes and anaerobic fungi significantly differed between equine types. The relative abundance of two bacterial genera was significantly higher in donkey compared to both pony and pony x donkey: Lachnoclostridium 10 and 'probable genus 10' from the Lachnospiraceae family. The relative abundance of Piromyces was significantly lower in donkey compared to pony × donkey, with pony not significantly differing from either of the other equine types. In contrast, the uncultivated genus SK3 was only found in donkey (4 of the 8 animals). The number of anaerobic fungal OTUs was also significantly higher in donkey than in the other two equine types, with no significant differences found between pony and pony × donkey. Equine types did not significantly differ with respect to prokaryotic alpha diversity, fecal dry matter content or fecal concentrations of bacteria, archaea and anaerobic fungi. CONCLUSIONS Donkey fecal microbiota differed from that of both pony and pony × donkey. These differences related to a higher relative abundance and diversity of taxa with known, or speculated, roles in plant material degradation. These findings are consistent with the previously reported increased fiber degradation in donkeys compared to ponies, and suggest that the hindgut microbiota plays a role. This offers novel opportunities for pony and pony × donkey to extract more energy from dietary fiber via microbial mediated strategies. This could potentially decrease the need for energy dense feeds which are a risk factor for gut-mediated disease.
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Affiliation(s)
- J. E. Edwards
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, Netherlands
| | - A. Schennink
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, Netherlands
- Present address: Micreos Human Health B.V, Bilthoven, Netherlands
| | - F. Burden
- The Donkey Sanctuary, Sidmouth, Devon EX10 ONU UK
| | - S. Long
- The Donkey Sanctuary, Sidmouth, Devon EX10 ONU UK
| | - D. A. van Doorn
- Division of Nutrition, Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, Netherlands
- Department of Equine Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, Netherlands
| | - W. F. Pellikaan
- Animal Nutrition Group, Wageningen University & Research, 6708 WD Wageningen, Netherlands
| | - J. Dijkstra
- Animal Nutrition Group, Wageningen University & Research, 6708 WD Wageningen, Netherlands
| | - E. Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - H. Smidt
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, Netherlands
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Vaidya JD, van Gastelen S, Smidt H, Plugge CM, Edwards JE. Characterization of dairy cow rumen bacterial and archaeal communities associated with grass silage and maize silage based diets. PLoS One 2020; 15:e0229887. [PMID: 32119709 PMCID: PMC7051090 DOI: 10.1371/journal.pone.0229887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/18/2020] [Indexed: 12/18/2022] Open
Abstract
The objective of the present study was to characterize the rumen bacterial and archaeal communities in dairy cows fed different ratios of maize silage (MS) and grass silage (GS), and place the findings in the context of ruminal fermentation as well as previously reported methane (CH4) emissions. Rumen fluid from 12 rumen cannulated dairy cows was collected after 10 and 17 days of feeding one of four diets, all of which had the same roughage to concentrate ratio of 80:20 based on dry matter (DM). Roughage in the four diets (GS100, GS0, GS67, GS33) consisted of either 1000 g/kg DM GS (GS100), 1000 g/kg DM MS (GS0), or a mixture of both silages in different proportions [667 g/kg DM GS and 333 g/kg DM MS (GS67); 333 g/kg DM GS and 677 g/kg DM MS (GS33)]. Total volatile fatty acid (VFA) concentrations and the molar proportions of the ruminal VFA were not affected by diet. Only the molar proportion of isovalerate was affected by time, being lower on day 17 than on day 10. Bacterial and archaeal concentrations were not affected by diet but increased from day 10 to day 17. The bacterial community composition was affected by diet, time and diet × time, whereas the archaeal community composition was only affected by diet. Several bacterial and archaeal genus level groups were associated with diet, but not with time. Analysis indicated the increased use of hydrogen by succinate and lactate producing bacteria is likely to at least partially explain the previously reported lower CH4 emissions from MS fed dairy cows. Furthermore, time had a significant effect on both bacterial and archaeal concentrations, and also bacterial community composition. This indicates that the rumen microbiota had not stabilized after 10 days of feeding the experimental diets.
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Affiliation(s)
- Jueeli D. Vaidya
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sanne van Gastelen
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Animal Nutrition Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- * E-mail:
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Joan E. Edwards
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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