A toddler SHIME® model to study microbiota of young children

2020 ◽  
Vol 367 (16) ◽  
Author(s):  
Pauline Bondue ◽  
Sarah Lebrun ◽  
Bernard Taminiau ◽  
Nadia Everaert ◽  
Gisele LaPointe ◽  
...  
Keyword(s):  
Young Children ◽  
Short Chain Fatty Acid ◽  
Amplicon Sequencing ◽  
Bacterial Populations ◽  
16S Rrna Amplicon Sequencing ◽  
Biofilm Development ◽  
Stabilization Period ◽  
Gut Microbiota Composition

ABSTRACT The ‘first 1000 days of life’ determine the gut microbiota composition and can have long-term health consequences. In this study, the simulator of the human intestinal microbial ecosystem (SHIME®) model, which represents the main functional sections of the digestive tract, was chosen to study the microbiota of young children. The aim of this study was to reproduce the digestive process of toddlers and their specific colonic environment. The ascending, transverse and descending colons of SHIME® model were inoculated with feces from three donors aged between 1 and 2 years-old, in three separate runs. For each run, samples from colon vessels were collected at days 14, 21 and 28 after microbiota stabilization period. Short chain fatty acid concentrations determined by HPLC showed that microbiota obtained in SHIME® model shared characteristics between adults and infants. In addition, microbial diversity and bacterial populations determined by 16S rRNA amplicon sequencing were specific to each colon vessel. In conclusion, the SHIME® model developed in this study seemed well adapted to evaluate prebiotic and probiotic impact on the specific microbiota of toddlers, or medicine and endocrine disruptor metabolism. Moreover, this study is the first to highlight some biofilm development in in vitro gastrointestinal modelling systems.

scholarly journals Framework as a Service, FaaS: Personalized Prebiotic Development for Infants with the Elements of Time and Parametric Modelling of In Vitro Fermentation

2020 ◽  
Vol 8 (5) ◽  
pp. 623
Author(s):  
Ka-Lung Lam ◽  
Wai-Yin Cheng ◽  
Fan Yang ◽  
Shaoling Lin ◽  
Lijun You ◽  
...  
Keyword(s):  
Amplicon Sequencing ◽  
Parametric Modeling ◽  
Lag Phase ◽  
Parametric Modelling ◽  
Maximum Increase ◽  
In Vitro Fermentation ◽  
16S Rrna Amplicon Sequencing ◽  
Beta Glucans ◽  
Increase Rate

We proposed a framework with parametric modeling to obtain biological relevant parameters from the total probiotic growth pattern and metabolite production curves. The lag phase, maximum increase rate, and maximum capacity were obtained via a 205-h exploratory In vitro fermentation of a library of 13 structural-characterized prebiotic candidates against an exclusively breastfed infant fecal inoculum. We also conducted 16S rRNA amplicon sequencing of the infant fecal inoculum. Moreover, we introduce a robust composite metabolite-based indicator that reflects the eubiosis/dysbiosis of microbiota to complement the conventional microbial markers. In terms of short-chain fatty acid, we discovered that polymeric beta-glucans from barley demonstrated potential as prebiotic candidates, while alpha-glucans as glycogen showed the least dissolved ammonia production. In terms of total probiotic, beta-glucans from oat and mushroom sclerotia of Pleurotus tuber-regium showed comparable sustainability when compared to alpha-glucans after 48 h. Being classical prebiotic, galacto-oligosaccharides gave the second-highest metabolite-based indicator, followed by lactose. While limited improvement could be made to lactose and oligosaccharides, polymeric beta-glucans from barley avails more capacity for novel prebiotic development, such as structural modification. We anticipate that more similar parallel screening with the element of time and parametric modeling will provide more novel insights.

scholarly journals DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Julia Franzen ◽  
Theodoros Georgomanolis ◽  
Anton Selich ◽  
Chao-Chung Kuo ◽  
Reinhard Stöger ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Amplicon Sequencing ◽  
Cell Types ◽  
Ctcf Binding ◽  
Long Term Culture ◽  
Pattern Development ◽  
Genomic Regions ◽  
Cg Dinucleotides

AbstractCulture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated during long-term culture of mesenchymal stem cells (MSCs) and other cell types. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpopulations. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no enriched interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results support the notion that DNAm changes during culture-expansion are not directly regulated by a targeted mechanism but rather resemble epigenetic drift.

scholarly journals The Bordetella Bps Polysaccharide Is Critical for Biofilm Development in the Mouse Respiratory Tract

2007 ◽  
Vol 189 (22) ◽  
pp. 8270-8276 ◽  
Author(s):  
Gina Parise Sloan ◽  
Cheraton F. Love ◽  
Neelima Sukumar ◽  
Meenu Mishra ◽  
Rajendar Deora
Keyword(s):  
Whooping Cough ◽  
Three Dimensional ◽  
Respiratory Pathogens ◽  
Adolescents And Adults ◽  
The Stability ◽  
Inert Surfaces ◽  
Biofilm Development

ABSTRACT Bordetellae are respiratory pathogens that infect both humans and animals. Bordetella bronchiseptica establishes asymptomatic and long-term to life-long infections of animal nasopharynges. While the human pathogen Bordetella pertussis is the etiological agent of the acute disease whooping cough in infants and young children, it is now being increasingly isolated from the nasopharynges of vaccinated adolescents and adults who sometimes show milder symptoms, such as prolonged cough illness. Although it has been shown that Bordetella can form biofilms in vitro, nothing is known about its biofilm mode of existence in mammalian hosts. Using indirect immunofluorescence and scanning electron microscopy, we examined nasal tissues from mice infected with B. bronchiseptica. Our results demonstrate that a wild-type strain formed robust biofilms that were adherent to the nasal epithelium and displayed architectural attributes characteristic of a number of bacterial biofilms formed on inert surfaces. We have previously shown that the Bordetella Bps polysaccharide encoded by the bpsABCD locus is critical for the stability and maintenance of three-dimensional structures of biofilms. We show here that Bps is essential for the formation of efficient nasal biofilms and is required for the colonization of the nose. Our results document a biofilm lifestyle for Bordetella in mammalian respiratory tracts and highlight the essential role of the Bps polysaccharide in this process and in persistence of the nares.

scholarly journals Toxoflavin secreted by Pseudomonas alcaliphila inhibits growth of Legionella pneumophila and its host Vermamoeba vermiformis

2022 ◽  
Author(s):  
Sebastien P. Faucher ◽  
Sara Matthews ◽  
Arvin Nickzad ◽  
Passoret Vounba ◽  
Deeksha Shetty ◽  
...  
Keyword(s):  
Legionella Pneumophila ◽  
Severe Pneumonia ◽  
Amplicon Sequencing ◽  
Inhibitory Effect ◽  
Water Systems ◽  
Bulk Water ◽  
Cooling Towers ◽  
High Concentration ◽  
16S Rrna Amplicon Sequencing

Legionella pneumophila is a natural inhabitant of water systems. From there, it can be transmitted to humans by aerosolization resulting in severe pneumonia. Most large outbreaks are caused by cooling towers contaminated with L. pneumophila. The resident microbiota of the cooling tower is a key determinant for the colonization and growth of L. pneumophila. The genus Pseudomonas correlates negatively with the presence of L. pneumophila, but it is not clear which species is responsible. Therefore, we identified the Pseudomonas species inhabiting 14 cooling towers using a Pseudomonas-specific 16S rRNA amplicon sequencing strategy. Cooling towers free of L. pneumophila contained a high relative abundance of members from the Pseudomonas alcaliphila/oleovorans phylogenetic cluster. In vitro, P. alcaliphila JCM 10630 inhibited the growth of L. pneumophila on agar plates. Analysis of the P. alcaliphila genome revealed the presence of a genes cluster predicted to produce toxoflavin. L. pneumophila growth was inhibited by pure toxoflavin and by extract from P. alcaliphila culture found to contain toxoflavin by LC-ESI-MS. In addition, toxoflavin inhibits growth of Vermameoba vermiformis, a host cell of L. pneumophila. Our study indicates that P. alcaliphila may be important to restrict growth of L. pneumophila in water systems through the production of toxoflavin. A sufficiently high concentration is likely not achieved in the bulk water but might have a local inhibitory effect such as in biofilm.

scholarly journals Interaction of intestinal bacteria with human rotavirus during infection in children

2020 ◽  
Author(s):  
Roberto Gozalbo-Rovira ◽  
Antonio Rubio-del-Campo ◽  
Cristina Santiso-Bellón ◽  
Susana Vila-Vicent ◽  
Javier Buesa ◽  
...  
Keyword(s):  
Intestinal Bacteria ◽  
Amplicon Sequencing ◽  
Blood Group Antigens ◽  
16S Rrna Amplicon Sequencing ◽  
Human Rotavirus ◽  
Key Factor ◽  
Antibody Titers ◽  
Microscopy Analysis ◽  
Stool Samples

AbstractThe gut microbiota has emerged as a key factor in the pathogenesis of intestinal viruses, including enteroviruses, noroviruses and rotaviruses (RV), where stimulatory and inhibitory effects on infectivity have been reported. With the aim of determining whether members of the microbiota interact with RV during infection, a combination of anti-RV antibody labelling, fluorescence-activated cell sorting and 16S rRNA amplicon sequencing was used to characterize the interaction between specific bacteria and RV in stool samples of children suffering diarrhea produced by G1P[8] RV. The genera Ruminococcus and Oxalobacter were identified as RV binders in stools, displaying enrichments between 4.8 to 5.4-fold compared to samples non-labelled with anti-RV antibodies. In vitro binding of the G1P[8] Wa human RV strain to two Ruminococcus gauvreauii human isolates was confirmed by fluorescence microscopy. Analysis in R. gauvreauii with antibodies directed to several histo-blood group antigens (HBGA) indicated that these bacteria express HBGA-like substances at their surfaces that can be the target for RV binding. Furthermore, in vitro infection of Wa strain in differentiated Caco-2 cells was significantly reduced by incubation with R. gauvreauii. These data, together with previous findings that had shown a negative correlation between Ruminococcus levels and antibody titers to RV in healthy individuals, suggest a pivotal interaction between this bacterial group and human RV. These results reveal likely mechanisms on how specific bacterial taxa of the intestinal microbiota could negatively affect RV infection and open new possibilities for anti-viral strategies.

scholarly journals Coffee Consumption Modulates Amoxicillin-Induced Dysbiosis in the Murine Gut Microbiome

2021 ◽  
Vol 12 ◽  
Author(s):  
Emma Diamond ◽  
Katharine Hewlett ◽  
Swathi Penumutchu ◽  
Alexei Belenky ◽  
Peter Belenky
Keyword(s):  
Gut Microbiome ◽  
Burkholderia Cepacia ◽  
Coffee Consumption ◽  
Amplicon Sequencing ◽  
Antibiotic Use ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Caffeinated Coffee

The microbiome is essential for host health, and perturbations resulting from antibiotic use can lead to dysbiosis and disease. Diet can be a powerful modulator of microbiome composition and function, with the potential to mitigate the negative effects of antibiotic use. Thus, it is necessary to study the impacts of diet and drug interactions on the gut microbiome. Coffee is a commonly consumed beverage containing many compounds that have the potential to affect the microbiome, including caffeine, polyphenols, and fiber. We supplemented mice with caffeinated and decaffeinated coffee in conjunction with amoxicillin, and used 16S rRNA amplicon sequencing of fecal samples to investigate changes in diversity and composition of the murine fecal microbiome. We found that antibiotics, regardless of coffee supplementation, caused significant disruption to the murine fecal microbiome, enriching for Proteobacteria, Verrucomicrobia, and Bacteroidetes, but reducing Firmicutes. While we found that coffee alone did not have a significant impact on the composition of the fecal microbiome, coffee supplementation did significantly affect relative abundance metrics in mice treated with amoxicillin. After caffeinated coffee supplementation, mice treated with amoxicillin showed a smaller increase in Proteobacteria, specifically of the family Burkholderiaceae. Correspondingly we found that in vitro, Burkholderia cepacia was highly resistant to amoxicillin, and that it was inhibited by concentrations of caffeine and caffeinated coffee comparable to levels of caffeine in murine ceca. Overall, this work shows that coffee, and possibly the caffeine component, can impact both the microbiome and microbiome members during antibiotic exposure.

scholarly journals Can Physical Activity Influence Human Gut Microbiota Composition Independently of Diet? A Systematic Review

Nutrients ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1890
Author(s):  
Barbara Dorelli ◽  
Francesca Gallè ◽  
Corrado De Vito ◽  
Guglielmo Duranti ◽  
Matteo Iachini ◽  
...  
Keyword(s):  
Physical Activity ◽  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Microbiota Composition ◽  
Human Gut ◽  
Exercise Interventions ◽  
Human Gut Microbiota ◽  
16S Rrna Amplicon Sequencing ◽  
New Perspective ◽  
Gut Microbiota Composition

Evidence suggests that physical activity (PA) influences the human gut microbiota composition, but its role is unclear because of dietary interference. The aim of this review is to clarify this issue from this new perspective in healthy individuals. Articles analyzing intestinal microbiota from fecal samples by 16S rRNA amplicon sequencing were selected by searching the electronic databases PubMed, Scopus, and Web of Science until December 2020. For each study, methodological quality was assessed, and results about microbiota biodiversity indices, phylum and genus composition, and information on PA and diet were considered. From 997 potentially relevant articles, 10 met the inclusion criteria and were analyzed. Five studies involved athletes, three were performed on active people classified on the basis of habitual PA level, and two among sedentary subjects undergoing exercise interventions. The majority of the studies reported higher variability and prevalence of the phylum Firmicutes (genera Ruminococcaceae or Fecalibacteria) in active compared to inactive individuals, especially in athletes. The assessment of diet as a possible confounder of PA/exercise effects was completed only in four studies. They reported a similar abundance of Lachnospiraceae, Paraprevotellaceae, Ruminococcaceae, and Veillonellaceae, which are involved in metabolic, protective, structural, and histological functions. Further studies are needed to confirm these findings.

scholarly journals Curcumin Supplementation (Meriva®) Modulates Inflammation, Lipid Peroxidation and Gut Microbiota Composition in Chronic Kidney Disease

Nutrients ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 231
Author(s):  
Francesca Pivari ◽  
Alessandra Mingione ◽  
Giada Piazzini ◽  
Camilla Ceccarani ◽  
Emerenziana Ottaviano ◽  
...  
Keyword(s):  
Chronic Kidney Disease ◽  
Lipid Peroxidation ◽  
Kidney Disease ◽  
Gut Microbiota ◽  
Term Administration ◽  
Inflammatory State ◽  
Gut Microbiota Composition

Chronic kidney disease (CKD) subjects suffer from high risk of cardiovascular mortality, and any intervention preventing the progression of CKD may have an enormous impact on public health. In the last decade, there has been growing awareness that the gut microbiota (GM) can play a pivotal role in controlling the pathogenesis of systemic inflammatory state and CKD progression. To ameliorate the quality of life in CKD subjects, the use of dietary supplements has increased over time. Among those, curcumin has demonstrated significant in vitro anti-inflammatory properties. In this pilot study, 24 CKD patients and 20 healthy volunteers were recruited. CKD patients followed nutritional counselling and were supplemented with curcumin (Meriva®) for six months. Different parameters were evaluated at baseline and after 3–6 months: uremic toxins, metagenomic of GM, and nutritional, inflammatory, and oxidative status. Curcumin significantly reduced plasma pro-inflammatory mediators (CCL-2, IFN-γ, and IL-4) and lipid peroxidation. Regarding GM, after 6 months of curcumin supplementation, Escherichia-Shigella was significantly lower, while Lachnoclostridium was significant higher. Notably, at family level, Lactobacillaceae spp. were found significantly higher in the last 3 months of supplementation. No adverse events were observed in the supplemented group, confirming the good safety profile of curcumin phytosome after long-term administration.

scholarly journals Epigenetic drift during long-term culture of cells in vitro

2018 ◽  
Author(s):  
Julia Franzen ◽  
Theodoros Georgomanolis ◽  
Anton Selich ◽  
Chao-Chung Kuo ◽  
Reinhard Stöger ◽  
...  
Keyword(s):  
Stem Cells ◽  
Amplicon Sequencing ◽  
Cell Types ◽  
Ctcf Binding ◽  
Chromatin Conformation ◽  
Long Term Culture ◽  
Induced Pluripotent ◽  
Genomic Regions

AbstractCulture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes at specific sites in the genome. These changes might be due to an directly regulated epigenetic process, or to gradual deregulation of the epigenetic state, which is often referred to as “epigenetic drift”. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated in the course of culture expansion of mesenchymal stem cells (MSCs) and other cell types. During reprogramming into induced pluripotent stem cells (iPSCs) particularly the culture-associated hypomethylation is reversed simultaneously with age-associated and pluripotency-associated DNAm changes. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that upon passaging the DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpolulations of MSCs at later passages. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no preferential interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results indicate that DNAm changes during culture-expansion resembles epigenetic drift, which seems to occur in relation to chromatin conformation.

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