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 In Vitro Infant Faecal Fermentation of Low Viscosity Barley β-Glucan and Its Acid Hydrolyzed Derivatives: Evaluation of Their Potential as Novel Prebiotics

Molecules ◽  
2019 ◽  
Vol 24 (5) ◽  
pp. 828 ◽  
Author(s):  
Ka-Lung Lam ◽  
Kin-Chun Ko ◽  
Xiaojie Li ◽  
Xinxin Ke ◽  
Wai-Yin Cheng ◽  
...  
Keyword(s):  
Anaerobic Fermentation ◽  
Amplicon Sequencing ◽  
Short Chain Fatty Acids ◽  
In Vitro Fermentation ◽  
Deep Well ◽  
Low Viscosity ◽  
16S Amplicon Sequencing ◽  
High Level ◽  
Faecal Microbiome

Barley contains high level of β-1,3-1,4-glucans (BBGs) which can be fermented by microbes and are a potential prebiotic. In the present study, native BBG with low viscosity and a MW of 319 kDa was depolymerized by acid hydrolysis to produce a series of four structurally characterized fragments with MWs ranging from 6–104 kDa. In vitro fermentation of these BBG samples by infant faecal microbiome was evaluated using a validated deep-well plate protocol as parallel miniature bioreactors. Microbial taxa were identified using 16S amplicon sequencing after 40 h of anaerobic fermentation. Bioinformatics analysis including diversity indexes, predicted metagenomic KEGG functions and predicted phenotypes were performed on the sequenced data. Short chain fatty acids and dissolved ammonia were quantified and the SCFAs/NH3 ratio was used to evaluate the eubiosis/dysbiosis potential. Correlation analysis showed that most of the parameters investigated showed a parabolic function instead of a monotonous function with the BBG samples having different MWs. Among the five BBGs, it was concluded that BBG with an intermediate MW of 28 kDa is the most promising candidate to be developed as a novel prebiotic.

scholarly journals Cut-Lengths of Perennial Ryegrass Leaf-Blades Influences In Vitro Fermentation by the Anaerobic Fungus Neocallimastix frontalis

2020 ◽  
Vol 8 (11) ◽  
pp. 1774
Author(s):  
Hugo R. Jimenez ◽  
Joan E. Edwards ◽  
Ruth Sanderson ◽  
Alison H. Kingston-Smith ◽  
Neil R. McEwan ◽  
...  
Keyword(s):  
Perennial Ryegrass ◽  
Leaf Blade ◽  
Plant Biomass ◽  
Gas Production ◽  
Lag Phase ◽  
Anaerobic Fungi ◽  
In Vitro Fermentation ◽  
Batch Cultures ◽  
Neocallimastix Frontalis

Anaerobic fungi in the gut of domesticated and wild mammalian herbivores play a key role in the host’s ability to utilize plant biomass. Due to their highly effective ability to enzymatically degrade lignocellulose, anaerobic fungi are biotechnologically interesting. Numerous factors have been shown to affect the ability of anaerobic fungi to break down plant biomass. However, methods to reduce the non-productive lag time in batch cultures and the effect of leaf-blade cut-length and condition on the fungal fermentation are not known. Therefore, experimentation using a novel gas production approach with pre-grown, axenic cultures of Neocallimastix frontalis was performed using both fresh and air-dried perennial ryegrass leaf-blades of different cut-lengths. The methodology adopted removed the lag-phase and demonstrated the digestion of un-autoclaved leaf-blades. Fermentation of leaf-blades of 4.0 cm cut-length produced 18.4% more gas yet retained 11.2% more apparent DM relative to 0.5 cm cut-length leaf-blades. Drying did not affect fermentation by N. frontalis, although an interaction between drying and leaf-blade cut-length was noted. Removal of the lag phase and the use of un-autoclaved substrates are important when considering the biotechnological potential of anaerobic fungi. A hypothesis based upon sporulation at cut surfaces is proposed to describe the experimental results.

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 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 Gut microbiota and phytoestrogen-associated infertility in southern white rhinoceros

2018 ◽  
Author(s):  
Candace L. Williams ◽  
Alexis R. Ybarra ◽  
Ashley N. Meredith ◽  
Barbara S. Durrant ◽  
Christopher W. Tubbs
Keyword(s):  
Estrogen Receptor ◽  
Negative Relationship ◽  
Amplicon Sequencing ◽  
Receptor Activation ◽  
Fecal Microbiota ◽  
16S Rrna Amplicon Sequencing ◽  
Activation Assay ◽  
White Rhinoceros ◽  
Southern White Rhinoceros

AbstractWith recent poaching of southern white rhinoceros (Ceratotherium simum simum; SWR) reaching record levels, the need for a robust assurance population is urgent. However, the global captive SWR population is not currently self-sustaining due to the reproductive failure of captive-born females. Dietary phytoestrogens have been proposed to play a role in this phenomenon, and recent work has demonstrated a negative relationship between diet estrogenicity and fertility of captive-born female SWR. To further examine this relationship, we compared gut microbial communities, fecal phytoestrogens, and fertility of SWR to another rhinoceros species–the greater one-horned rhinoceros (Rhinoceros unicornis; GOHR), which consumes a similar diet but exhibits high levels of fertility in captivity. Using 16S rRNA amplicon sequencing and mass spectrometry, we identified a species-specific fecal microbiota and three dominant fecal phytoestrogen profiles. These profiles exhibited varying levels of estrogenicity when tested in an in vitro estrogen receptor activation assay for both rhinoceros species, with profiles dominated by the microbial metabolite, equol, stimulating the highest levels of receptor activation. Finally, we found that SWR fertility varies significantly with respect to phytoestrogen profile, but also with the abundance of several bacterial taxa and microbially-derived phytoestrogen metabolites. Taken together, these data suggest that in addition to species differences in estrogen receptor sensitivity to phytoestrogens, reproductive outcomes may be driven by gut microbiota’s transformation of dietary phytoestrogens in captive SWR females.

scholarly journals Association between Oral Candida and Bacteriome in Children with Severe ECC

2018 ◽  
Vol 97 (13) ◽  
pp. 1468-1476 ◽  
Author(s):  
J. Xiao ◽  
A. Grier ◽  
R.C. Faustoferri ◽  
S. Alzoubi ◽  
A.L. Gill ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Oral Microbiota ◽  
16S Rrna Amplicon Sequencing ◽  
Acid Tolerant ◽  
Oral Candida

Candida albicans is an opportunistic fungal organism frequently detected in the oral cavity of children with severe early childhood caries (S-ECC). Previous studies suggested the cariogenic potential of C. albicans, in vitro and in vivo, and further demonstrated its synergistic interactions with Streptococcus mutans. In combination, the 2 organisms are associated with higher caries severity in a rodent model. However, it remains unknown whether C. albicans influences the composition and diversity of the entire oral bacterial community to promote S-ECC onset. With 16s rRNA amplicon sequencing, this study analyzed the microbiota of saliva and supragingival plaque from 39 children (21 S-ECC and 18 caries-free [CF]) and 33 mothers (17 S-ECC and 16 CF). The results revealed that the presence of oral C. albicans is associated with a highly acidogenic and acid-tolerant bacterial community in S-ECC, with an increased abundance of plaque Streptococcus (particularly S. mutans) and certain Lactobacillus/Scardovia species and salivary/plaque Veillonella and Prevotella, as well as decreased levels of salivary/plaque Actinomyces. Concurrent with this microbial community assembly, the activity of glucosyltransferases (cariogenic virulence factors secreted by S. mutans) in plaque was significantly elevated when C. albicans was present. Moreover, the oral microbial community composition and diversity differed significantly by disease group (CF vs. S-ECC) and sample source (saliva vs. plaque). Children and mothers within the CF and S-ECC groups shared microbiota composition and diversity, suggesting a strong maternal influence on children’s oral microbiota. Altogether, this study underscores the importance of C. albicans in association with the oral bacteriome in the context of S-ECC etiopathogenesis. Further longitudinal studies are warranted to examine how fungal-bacterial interactions modulate the onset and severity of S-ECC, potentially leading to novel anticaries treatments that address fungal contributions.

scholarly journals Interaction of Intestinal Bacteria with Human Rotavirus during Infection in Children

2021 ◽  
Vol 22 (3) ◽  
pp. 1010
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 ◽  
Vitro Binding ◽  
Key Factor ◽  
Antibody Titers ◽  
Microscopy Analysis ◽  
Antibody Labeling

The gut microbiota has emerged as a key factor in the pathogenesis of intestinal viruses, including enteroviruses, noroviruses and rotaviruses (RVs), where stimulatory and inhibitory effects on infectivity have been reported. With the aim of determining whether members of the microbiota interact with RVs during infection, a combination of anti-RV antibody labeling, 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 from diarrhea produced by G1P[8] RV. The genera Ruminococcus and Oxalobacter were identified as RV binders in stools, displaying enrichments between 4.8- and 5.4-fold compared to samples nonlabeled 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 (HBGAs) indicated that these bacteria express HBGA-like substances on their surfaces, which can be the target for RV binding. Furthermore, in vitro infection of the Wa strain in differentiated Caco-2 cells was significantly reduced by incubation with R. gauvreauii. These data, together with previous findings showing 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 of how specific bacterial taxa of the intestinal microbiota could negatively affect RV infection and open new possibilities for antiviral strategies.

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