Set up of a new in vitro model to study dietary fructans fermentation in formula-fed babies

Microbiota-dependent influence of prebiotics on the resilience of infant gut microbiota to amoxicillin/clavulanate perturbation in an in vitro colon model

Antibiotic exposure disturbs the developing infant gut microbiota. The capacity of the gut microbiota to recover from this disturbance (resilience) depends on the type of antibiotic. In this study, infant gut microbiota was exposed to a combination of amoxicillin and clavulanate (amoxicillin/clavulanate) in an in vitro colon model (TIM-2) with fecal-derived microbiota from 1-month-old (1-M; a mixed-taxa community type) as well as 3-month-old (3-M; Bifidobacterium dominated community type) breastfed infants. We investigated the effect of two common infant prebiotics, 2'-fucosyllactose (2'-FL) or galacto-oligosaccharides (GOS), on the resilience of infant gut microbiota to amoxicillin/clavulanate-induced changes in microbiota composition and activity. Amoxicillin/clavulanate treatment decreased alpha diversity and induced a temporary shift of microbiota to a community dominated by enterobacteria. Moreover, antibiotic treatment increased succinate and lactate in both 1- and 3-M colon models, while decreasing the production of short-chain (SCFA) and branched-chain fatty acids (BFCA). The prebiotic effect on the microbiota recovery depended on the fermenting capacity of antibiotic-exposed microbiota. In the 1-M colon model, the supplementation of 2'-FL supported the recovery of microbiota and restored the production of propionate and butyrate. In the 3-M colon model, GOS supplementation supported the recovery of microbiota and increased the production of acetate and butyrate.

Infant Fecal Fermentations with Galacto-Oligosaccharides and 2′-Fucosyllactose Show Differential Bifidobacterium longum Stimulation at Subspecies Level

The objective of the current study was to evaluate the potential of 2′-FL and GOS, individually and combined, in beneficially modulating the microbial composition of infant and toddler (12–18 months) feces using the micro-Matrix bioreactor. In addition, the impacts of GOS and 2′-FL, individually and combined, on the outgrowth of fecal bifidobacteria at (sub)species level was investigated using the baby M-SHIME® model. For young toddlers, significant increases in the genera Bifidobacterium, Veillonella, and Streptococcus, and decreases in Enterobacteriaceae, Clostridium XIVa, and Roseburia were observed in all supplemented fermentations. In addition, GOS, and combinations of GOS and 2′-FL, increased Collinsella and decreased Salmonella, whereas 2′-FL, and combined GOS and 2′-FL, decreased Dorea. Alpha diversity increased significantly in infants with GOS and/or 2′-FL, as well as the relative abundances of the genera Veillonella and Akkermansia with 2′-FL, and Lactobacillus with GOS. Combinations of GOS and 2′-FL significantly stimulated Veillonella, Lactobacillus, Bifidobacterium, and Streptococcus. In all supplemented fermentations, Proteobacteria decreased, with the most profound decreases accomplished by the combination of GOS and 2′-FL. When zooming in on the different (sub)species of Bifidobacterium, GOS and 2’-FL were shown to be complementary in stimulating breast-fed infant-associated subspecies of Bifidobacterium longum in a dose-dependent manner: GOS stimulated Bifidobacterium longum subsp. longum, whereas 2′-FL supported outgrowth of Bifidobacterium longum subsp. infantis.

In vitro human gut microbiota fermentation models: opportunities, challenges, and pitfalls

The human gut microbiota (HGM) plays a pivotal role in health and disease. Consequently, nutritional and medical research focusing on HGM modulation strategies as a means of improving host health is steadily increasing. In vitro HGM fermentation models offer a valid complement to human and animal studies when it comes to the mechanistic exploration of novel modulation approaches and their direct effects on HGM composition and activity, while excluding interfering host effects. However, in vitro cultivation of HGM can be challenging due to its high oxygen sensitivity and the difficulties of accurately modeling the physio-chemical complexity of the gut environment. Despite the increased use of in vitro HGM models, there is no consensus about appropriate model selection and operation, sometimes leading to major deficiencies in study design and result interpretation. In this review paper, we aim to analyze crucial aspects of the application, setup and operation, data validation and result interpretation of in vitro HGM models. When carefully designed and implemented, in vitro HGM modeling is a powerful strategy for isolating and investigating biotic and abiotic factors in the HGM, as well as evaluating their effects in a controlled environment akin to the gut. Furthermore, complementary approaches combining different in vitro and in vivo models can strengthen the design and interpretation of human studies.

Comparative analysis of prebiotic effects of four oligosaccharides using in vitro gut model: digestibility, microbiome, and metabolome changes

Fructooligosaccharides (FOS), Ad-fructooligosaccharides (Ad-FOS), resistant maltodextrin (RMD), and maltooligosaccharides (MOS) are commercially available prebiotic oligosaccharides. In this study, the effects of prebiotics on the human gut microbial ecosystem were evaluated using an in vitro gut model. FOS and Ad-FOS showed tolerance to digestion, whereas RMD and MOS showed moderate digestion by digestive enzymes. In in vitro fecal fermentation, Bifidobacterium spp. increased in the following order: FOS, Ad-FOS, MOS, and RMD, whereas Bacteroides spp. increased in RMD medium. Bacteroides xylanisolvens exhibited cross-feeding by enabling the growth of other beneficial bacteria during co-culture in RMD medium. In metabolome analysis, total short-chain fatty acids (SCFAs) were highly produced in the following order: RMD, FOS, MOS, and Ad-FOS; acetate in the order of FOS, MOS/RMD, and Ad-FOS; butyrate in the order of RMD, MOS, FOS, and Ad-FOS; and propionate only in RMD. In addition, the conversion of betaine to trimethylamine was rarely affected in the following order: MOS, RMD, FOS, and Ad-FOS. Lastly, the four oligosaccharides inhibited the adhesion of pathogenic Escherichia coli to human epithelial cells to a similar extent. The comparative analysis results obtained in this study will provide comprehensive information of these substances to manufacturers and customers.

Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach

The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.

Structure and function of non-digestible carbohydrates in the gut microbiome

Together with proteins and fats, carbohydrates are one of the macronutrients in the human diet. Digestible carbohydrates, such as starch, starch-based products, sucrose, lactose, glucose and some sugar alcohols and unusual (and fairly rare) α-linked glucans, directly provide us with energy while other carbohydrates including high molecular weight polysaccharides, mainly from plant cell walls, provide us with dietary fibre. Carbohydrates which are efficiently digested in the small intestine are not available in appreciable quantities to act as substrates for gut bacteria. Some oligo- and polysaccharides, many of which are also dietary fibres, are resistant to digestion in the small intestines and enter the colon where they provide substrates for the complex bacterial ecosystem that resides there. This review will focus on these non-digestible carbohydrates (NDC) and examine their impact on the gut microbiota and their physiological impact. Of particular focus will be the potential of non-digestible carbohydrates to act as prebiotics, but the review will also evaluate direct effects of NDC on human cells and systems.

Technological tools and strategies for culturing human gut microbiota in engineered in vitro models

The gut microbiota directly impacts the pathophysiology of different human body districts. Consequently, microbiota investigation is an hot topic of research and its in vitro culture has gained extreme interest in different fields. However, the high sensitivity of microbiota to external stimuli, such as sampling procedure, and the physicochemical complexity of the gut environment make its in vitro culture a challenging task. New engineered microfluidic gut-on-a-chip devices have the potential to model some important features of the intestinal structure, but they are usually unable to sustain culture of microbiota over an extended period of time. The integration of gut-on-a-chip devices with bioreactors for continuous bacterial culture would lead to fast advances in the study of microbiota-host crosstalk. In this review, we summarize the main technologies for the continuous culture of microbiota as upstream systems to be coupled with microfluidic devices to study bacteria-host cells communication. The engineering of integrated microfluidic platforms, capable of sustaining both anaerobic and aerobic cultures, would be the starting point to unveil complex biological phenomena proper of the microbiota-host crosstalks, paving to way to multiple research and technological applications.

In vitro models of gut digestion across childhood: current developments, challenges and future trends

The human digestion is a multi-step and multi-compartment process essential for human health, at the heart of many issues raised by academics, the medical world and industrials from the food, nutrition and pharma fields. In the first years of life, major dietary changes occur and are concomitant with an evolution of the whole child digestive tract anatomy and physiology, including colonization of gut microbiota. All these phenomena are influenced by child exposure to environmental compounds, such as drugs (especially antibiotics) and food pollutants, but also childhood infections. Due to obvious ethical, regulatory and technical limitations, in vivo approaches in animal and human are more and more restricted to favor complementary in vitro approaches. This review summarizes current knowledge on the evolution of child gut physiology from birth to 3 years old regarding physicochemical, mechanical and microbial parameters. Then, all the available in vitro models of the child digestive tract are described, ranging from the simplest static mono-compartmental systems to the most sophisticated dynamic and multi-compartmental models, and mimicking from the oral phase to the colon compartment. Lastly, we detail the main applications of child gut models in nutritional, pharmaceutical and microbiological studies and discuss the limitations and challenges facing this field of research.

Intestinal fermentation in vitro models to study food-induced gut microbiota shift: an updated review

In vitro gut fermentation models were firstly introduced in nutrition and applied microbiology research back in the 1990s. These models have improved greatly during time, mainly over the resemblance to the complexity of digestion stages, the replication of experimental conditions, the multitude of ecological parameters to assay. The state of the science is that the most competitive models shall include a complex gut microbiota, small working volumes, distinct interconnected compartments and rigorous bio-chemical and ecological settings, controlled by a computer, as well as a free-hands accessibility, not to contaminate the mock microbiota. These models are a useful tool to study the impact of a given diet compound, e.g. prebiotics, on the human gut microbiota. The principal application is to focus on the shift of the core microbial groups and selected species together with their metabolites, assaying their diversity, richness and abundance in the community over time. Besides, it is possible to study how a compound is digested, which metabolic pathways are triggered, and the type and quantity of microbial metabolites produced. Further prospective should focus on challenges with pathogens as well as on ecology of gut syndromes. In this minireview an updated presentation of the most used intestinal models is presented, basing on their concept, technical features, as well as on research applications.

In vitro gastrointestinal digestion and fermentation models and their applications in food carbohydrates

Food nutrients plays a crucial role in human health, especially in gastrointestinal (GI) health. The effect of food nutrients on human health mainly depends on the digestion and fermentation process in the GI tract. In vitro GI digestion and fermentation models had the advantages of reproducibility, simplicity, universality, and could integrally simulate the in vivo conditions to mimic oral, gastric, small intestinal and large intestinal digestive processes. They could not only predict the relationship among material composition, structure and digestive characteristics, but also evaluate the bioavailability of material components and the impact of digestive metabolites on GI health. This review systematicly summarized the current state of the in vitro simulation models, and made detailed descriptions for their applications, advantages and disadvantages, and specially their applications in food carbohydrates. In addition, it also provided the suggestions for the improvement of in vitro models and firstly proposed to establish a set of standardized methods of in vitro dynamic digestion and fermentation conditions for food carbohydrates, which were in order to further evaluate more effects of the nutrients on human health in future.

In Vitro Fermentation of Sheep and Cow Milk Using Infant Fecal Bacteria

While human milk is the optimal food for infants, formulas that contain ruminant milk can have an important role where breastfeeding is not possible. In this regard, cow milk is most commonly used. However, recent years have brought interest in other ruminant milk. While many similarities exist between ruminant milk, there are likely enough compositional differences to promote different effects in the infant. This may include effects on different bacteria in the large bowel, leading to different metabolites in the gut. In this study sheep and cow milk were digested using an in vitro infant digestive model, followed by fecal fermentation using cultures inoculated with fecal material from two infants of one month and five months of age. The effects of the cow and sheep milk on the fecal microbiota, short-chain fatty acids (SCFA), and other metabolites were investigated. Significant differences in microbial, SCFA, and metabolite composition were observed between fermentation of sheep and cow milk using fecal inoculum from a one-month-old infant, but comparatively minimal differences using fecal inoculum from a five-month-old infant. These results show that sheep milk and cow milk can have differential effects on the gut microbiota, while demonstrating the individuality of the gut microbiome.

Lactate Metabolism Is Strongly Modulated by Fecal Inoculum, pH, and Retention Time in PolyFermS Continuous Colonic Fermentation Models Mimicking Young Infant Proximal Colon

The metabolism of lactate impacts infant gut health and may lead to acute accumulation of lactate and/or H₂ associated with pain and crying of colicky infants. Because gut microbiota studies are limited due to ethical and safety concerns, in vitro fermentation models were developed as powerful tools to assess effects of environmental conditions on the gut microbiota. In this study, we established a continuous colonic fermentation model (PolyFermS), inoculated with immobilized fecal microbiota and mimicking the proximal colon of 2-month-old infants. We investigated the effects of pH and retention time (RT) on lactate metabolism and of lactate-utilizing bacteria (LUB) exhibiting little or no H₂ production. We observed that a drop in pH from 6.0 to 5.0 increased the number of lactate-producing bacteria (LPB) and decreased LUB concomitantly with lactate accumulation. Increasing RT from 5 to 10 h at pH 5.0 resulted in complete lactate consumption associated with increased LUB. Supplementation with dl-lactate (60 mM) to mimic lactate accumulation promoted propionate and butyrate production with no effect on acetate production. We further demonstrated that lactate-utilizing Propionibacterium avidum was able to colonize the reactors 4 days after spiking, suggesting its ability to compete with other lactate-utilizing bacteria producing H₂ In conclusion, we showed that PolyFermS is a suitable model for mimicking young infant colonic microbiota. We report for the first time pH and RT as strong drivers for composition and metabolic activity of infant gut microbiota, especially for the metabolism of lactate, which is a key intermediate product for ecology and infant health.IMPORTANCE The metabolism of lactate is important for infant gut health and may lead to acute lactate and/or H₂ accumulation, pain, and crying as observed in colicky infants. Functional human studies often faced ethical challenges due to invasive medical procedures; thus, in this study, we implemented PolyFermS fermentation models to mimic the infant proximal colon, which were inoculated with immobilized fecal microbiota of two 2-month-old infants. We investigated the impact of pH, retention time, and accumulation of dl-lactate on microbiota composition and metabolic activity. We found that a drop in pH from 6.0 to 5.0 led to increased LPB and decreased LUB concomitantly with lactate accumulation. Increasing the RT resulted in complete lactate consumption associated with increased LUB. Our data highlight for the first time the impact of key abiotic factors on the metabolism of lactate, which is an important intermediate product for ecology and infant health.

Inulin-Type Fructan Supplementation of 3- to 6-Year-Old Children Is Associated with Higher Fecal Bifidobacterium Concentrations and Fewer Febrile Episodes Requiring Medical Attention

Background

Inulin-type fructans used in formula have been shown to promote microbiota composition and stool consistency closer to those of breastfed infants and to have beneficial effects on fever occurrence, diarrhea, and incidence of infections requiring antibiotic treatment in infants.

Objectives

The primary study aim was to explore whether prophylactic supplementation with prebiotic fructans is able to influence the frequency of infectious diseases in kindergarten children during a winter period. A secondary objective was to ascertain the effect on the intestinal microbiota.

Methods

142 boys and 128 girls aged 3-6 y were randomly allocated to consume 6 g/d fructans or maltodextrin for 24 wk. At baseline, stool samples were collected for microbiota analysis and anthropometric measurements were made. During the intervention period diagnoses were recorded by physicians, whereas disease symptoms, kindergarten absenteeism, dietary habits, and stool consistency were recorded by parents. Baseline measurements were repeated at wk 24.

Results

In total 219 children finished the study. Both the relative abundance of Bifidobacterium (P < 0.001) and that of Lactobacillus (P = 0.014) were 19.9% and 7.8% higher, respectively, post data normalization, in stool samples of children receiving fructans as compared with those of controls at wk 24. This was accompanied by significantly softer stools within the normal range in the prebiotic group from wk 12 onwards. The incidence of febrile episodes requiring medical attention [0.65 ± 1.09 compared with 0.9 ± 1.11 infections/(24 wk × child), P = 0.04] and that of sinusitis (0.01 ± 0.1 compared with 0.06 ± 0.25, P = 0.03) were significantly lower in the prebiotic group. The number of infectious episodes and their duration reported by parents did not differ significantly between the 2 intervention groups.

Conclusions

Prebiotic supplementation modified the composition of the intestinal microbiota and resulted in softer stools in kindergarten-aged children. The reduction in febrile episodes requiring medical attention supports the concept of further studies on prebiotics in young children. This trial was registered at clinicaltrials.gov as NCT03241355.

The application of in vitro human intestinal models on the screening and development of pre- and probiotics

The importance of the gut microbiota community on host's health and disease has long been recognised and is well documented. The development of pro- and prebiotic interventions offers an opportunity for the modulation of the gut microbiota towards long lasting health. In vitro fermentation models were developed as a powerful tool to study the impact of pro- and prebiotics on the gut microbiota under tightly controlled conditions, which allow dynamic sampling over time in reactors mimicking different colon regions. These models have been further evolved to suit specific experimental purposes, e.g. including immobilised faecal microbiota, peristaltic movement, mucin microcosm and the ability to perform treatments in parallel. In this review we discuss the advantages, disadvantages and technical considerations of the most frequently used models. We further focus on recent advances in the application of these models in prebiotics and probiotics research and outline their predictability for clinical research.

Effect of dietary nucleosides and yeast extracts on composition and metabolic activity of infant gut microbiota in PolyFermS colonic fermentation models

Nucleotides (NT) and nucleosides (NS) are added to infant formula to mimic the content of breast milk, but little is known about their impact on infant gut microbiota. In this study, we tested the effect of NS and of yeast extracts (YE) with different NT content using PolyFermS continuous fermentation models mimicking formula-fed, healthy and enteropathogen-contaminated infant gut microbiota. Microbiota composition, short-chain fatty acid (SCFA) formation and gene expression were determined. NS, and to a larger extend YE modulated microbiota composition and increased metabolic activity in both models. Anaerococcus, Peptoniphilus, Fusobacterium, Lactobacillus/Pediococcus/Leuconostoc and Veillonella were enhanced when YE and/or NS were added. The production of SCFA increased with the level of supplied NT equivalents. Addition of NS and YE reduced colonization of Salmonella compared to control periods. Gene expression analysis confirmed taxonomical changes and indicated functional responses to YE. Transcripts related to NT and sulfur metabolism and iron acquisition increased while biosynthesis of co-factors and vitamins decreased after YE addition. Elevated butyrate formation correlated with increased transcripts encoding key enzymes of the two major butyrate synthesis pathways. Our results uncover a strong dose-dependent modulation of NS and YE on infant gut microbiota composition and metabolic activity.

Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro

The introduction of different nutrient and energy sources during weaning leads to significant changes in the infant gut microbiota. We used an in vitro infant digestive and gut microbiota model system to investigate the effect of four commercially available cereal products based on either wheat, sorghum, rice or oats, on the gut microbiota of six infants. Our results indicated cereal additions induced numerous changes in the gut microbiota composition. The relative abundance of bacterial families associated with fibre degradation, Bacteroidaceae, Bifidobacteriaceae, Lactobacillaceae, Prevotellaceae, Ruminococcaceae and Veillonellaceae increased, whilst the abundance of Enterobacteriaceae decreased with cereal additions. Corresponding changes in the production of SCFAs showed higher concentrations of acetate following all cereal additions, whilst, propionate and butyrate varied between specific cereal additions. These cereal-specific variations in the concentrations of SCFAs showed a moderate correlation with the relative abundance of potential SCFA-producing bacterial families. Overall, our results demonstrated clear shifts in the abundance of bacterial groups associated with weaning and an increase in the production of SCFAs following cereal additions.

Iron Fortification of Foods for Infants and Children in Low-Income Countries: Effects on the Gut Microbiome, Gut Inflammation, and Diarrhea

Iron deficiency anemia (IDA) is common among infants and children in Sub-Saharan Africa and is a leading contributor to the global burden of disease, as well as a hindrance to national development. In-home iron fortification of complementary foods using micronutrient powders (MNPs) effectively reduces the risk for IDA by ensuring that the iron needs of infants and young children are met without changing their traditional diet. However, the iron dose delivered by MNPs is high, and comparable on a mg iron per kg body weight to the supplemental doses (2 mg/kg) typically given to older children, which increases diarrhea risk. In controlled studies, iron-containing MNPs modestly increase risk for diarrhea in infants; in some cases, the diarrhea is severe and may require hospitalization. Recent in vitro and in vivo studies provide insights into the mechanism of this effect. Provision of iron fortificants to school-age children and iron-containing MNPs to weaning infants decreases the number of beneficial ‘barrier’ commensal gut bacteria (e.g., bifidobacteria), increases the enterobacteria to bifidobacteria ratio and abundances of opportunistic pathogens (e.g., pathogenic Escherichia coli), and induces gut inflammation. Thus, although iron-containing MNPs are highly effective in reducing IDA, they may increase gastrointestinal morbidity in infants, and safer formulations are needed.

Application of in vitro gut fermentation models to food components: A review

In vitro fermentation models have been developed for study of relationships between gut microbiota and food components. In vitro fermentation gut models involve use of pure cultures, mixed cultures, and human feces, and range from simple batch style fermentations performed in serum bottles to sophisticated pH-controlled multistage continuous culture systems. These models are increasingly used as an alternative to in vivo assays not only for disclosure of physiological activities of food components in the human intestine, but also for development of novel health functional foods. The purpose of this review is to introduce the present status and challenges of use of in vitro gut fermentation models in food studies.

Production of immune response mediators by HT-29 intestinal cell-lines in the presence of Bifidobacterium-treated infant microbiota

The colonisation and establishment of the intestinal microbiota starts immediately at birth and is essential for the development of the intestine and the immune system. This microbial community gradually increases in number and diversity until the age of two or three years when it becomes a stable ecosystem resembling that of adults. This period constitutes a unique window of opportunity to modulate it through probiotic action, with a potential impact in later health. In the present work we have investigated how putative bifidobacterial probiotics modify the metabolic profiles and immune-modulatory properties of faecal microbiotas. An in vitro pH-controlled single-stage continuous-culture system (CCS) inoculated with infant faeces was employed to characterise the effects of two Bifidobacterium species on the intestinal microbiotas in three children, together with the effects of these modified microbiotas on cytokine production by HT-29 cells. Intestinal bacterial communities, production of short-chain fatty acids and lactate were determined by quantitative PCR and gas chromatography, respectively. Cytokines production by HT-29 cells was measured by ELISA. The combination of CCS with infant faeces and human intestinal cells provided a suitable model to evaluate the specific modulation of the intestinal microbiota and immune system by probiotics. In the CCS, infant faecal microbiotas were influenced by the addition of bifidobacteria, resulting in changes in their ability to induce the production of immune mediators by HT-29 cells. The different metabolic and immunological responses induced by the bifidobacterial species tested indicate the need to assess potential probiotics in model systems including complex intestinal microbiotas. Potential probiotic bifidobacteria can modulate the infant microbiota and its ability to induce the production of mediators of the immune response by intestinal cells.

Synergistic effects of Bifidobacterium thermophilum RBL67 and selected prebiotics on inhibition of Salmonella colonization in the swine proximal colon PolyFermS model

Background

Probiotics and prebiotics are promising strategies to counteract Salmonella prevalence in swine. In the present study, we investigated the effects of prebiotics (fructo- (FOS), galacto- (GOS) and mannan- (MOS) oligosaccharides) and the bacteriocinogenic Bifidobacterium thermophilum RBL67 (RBL67) on Salmonella enterica subsp. enterica serovar Typhimurium N-15 (N-15) colonization using the PolyFermS in vitro continuous fermentation model simulating the swine proximal colon.

Material and methods

The PolyFermS model was designed with a first-stage reactor containing immobilized fecal pig microbiota. This reactor continuously inoculated five parallel second-stage reactors, a control and four treatment reactors, all operated with proximal colon conditions. FOS and GOS (5.2 g/day), and MOS (half dosage) and RBL67 (10⁸ copy numbers/mL applied daily) were tested on the ability of N-15 to colonize reactors, inoculated with the same microbiota. Reactor effluents were collected daily and analyzed for microbial composition (quantitative PCR and 454 pyrosequencing of 16S rRNA gene pool) and main metabolites (HPLC).

Results

RBL67 and N-15 were shown to stably colonize the system. Colonization of N-15 was strongly inhibited by FOS and GOS, whereas addition of RBL67 alone or combined with MOS showed intermediate results. However, the effect of FOS and GOS was enhanced when prebiotics were combined with a daily addition of RBL67. FOS and GOS increased the total short chain fatty acid production, especially acetate and propionate. RBL67 combined with FOS additionally stimulated butyrate production.

Conclusions

Our study demonstrates the suitability of the porcine PolyFermS in vitro model to study nutritional effects of pro- and prebiotics on gut microbiota composition and activity. It can further be used to monitor Salmonella colonization. The inhibition effects of FOS and GOS on N-15 colonization are partly due to an increased acetate production, while further antimicrobial mechanisms may contribute to an enhanced inhibition with prebiotic-RBL67 combinations. A future direction of this work could be to understand the anti-Salmonella effects of Bifidobacterium thermophilum RBL67 in the presence of prebiotics to unravel the mechanism of this probiotic:pathogen interaction.

Electronic supplementary material

The online version of this article (doi:10.1186/s13099-014-0044-y) contains supplementary material, which is available to authorized users.

In vitro continuous fermentation model (PolyFermS) of the swine proximal colon for simultaneous testing on the same gut microbiota

In vitro gut modeling provides a useful platform for a fast and reproducible assessment of treatment-related changes. Currently, pig intestinal fermentation models are mainly batch models with important inherent limitations. In this study we developed a novel in vitro continuous fermentation model, mimicking the porcine proximal colon, which we validated during 54 days of fermentation. This model, based on our recent PolyFermS design, allows comparing different treatment effects on the same microbiota. It is composed of a first-stage inoculum reactor seeded with immobilized fecal swine microbiota and used to constantly inoculate (10% v/v) five second-stage reactors, with all reactors fed with fresh nutritive chyme medium and set to mimic the swine proximal colon. Reactor effluents were analyzed for metabolite concentrations and bacterial composition by HPLC and quantitative PCR, and microbial diversity was assessed by 454 pyrosequencing. The novel PolyFermS featured stable microbial composition, diversity and metabolite production, consistent with bacterial activity reported for swine proximal colon in vivo. The constant inoculation provided by the inoculum reactor generated reproducible microbial ecosystems in all second-stage reactors, allowing the simultaneous investigation and direct comparison of different treatments on the same porcine gut microbiota. Our data demonstrate the unique features of this novel PolyFermS design for the swine proximal colon. The model provides a tool for efficient, reproducible and cost-effective screening of environmental factors, such as dietary additives, on pig colonic fermentation.

Novel Polyfermentor intestinal model (PolyFermS) for controlled ecological studies: validation and effect of pH

In vitro gut fermentation modeling offers a useful platform for ecological studies of the intestinal microbiota. In this study we describe a novel Polyfermentor Intestinal Model (PolyFermS) designed to compare the effects of different treatments on the same complex gut microbiota. The model operated in conditions of the proximal colon is composed of a first reactor containing fecal microbiota immobilized in gel beads, and used to continuously inoculate a set of parallel second-stage reactors. The PolyFermS model was validated with three independent intestinal fermentations conducted for 38 days with immobilized human fecal microbiota obtained from three child donors. The microbial diversity of reactor effluents was compared to donor feces using the HITChip, a high-density phylogenetic microarray targeting small subunit rRNA sequences of over 1100 phylotypes of the human gastrointestinal tract. Furthermore, the metabolic response to a decrease of pH from 5.7 to 5.5, applied to balance the high fermentative activity in inoculum reactors, was studied. We observed a reproducible development of stable intestinal communities representing major taxonomic bacterial groups at ratios similar to these in feces of healthy donors, a high similarity of microbiota composition produced in second-stage reactors within a model, and a high time stability of microbiota composition and metabolic activity over 38 day culture. For all tested models, the pH-drop of 0.2 units in inoculum reactors enhanced butyrate production at the expense of acetate, but was accompanied by a donor-specific reorganization of the reactor community, suggesting a concerted metabolic adaptation and trigger of community-specific lactate or acetate cross-feeding pathways in response to varying pH. Our data showed that the PolyFermS model allows the stable cultivation of complex intestinal microbiota akin to the fecal donor and can be developed for the direct comparison of different experimental conditions in parallel reactors continuously inoculated with the exact same microbiota.

Experimental models of the gut microbiome

The human gut contains a diverse microbiota with large potential to influence health. Given the difficulty to access the main sites of the gut, in vitro models have been developed to dynamically monitor microbial processes at the site of metabolic activity. These models range from simple batch fermentations to complex multi-compartmental continuous systems. The latter include different models, focussing on similar but each also on distinct digestive parameters. The most intensively used include the three-stage continuous culture system, SHIME(®), EnteroMix, Lacroix model and TIM-2. Especially after inclusion of surface-attached mucosal microbes (M-SHIME), such models have been shown representative of the in vivo situation in terms of microbial composition and activity. They have even been shown to maintain the interpersonal variation among different human fecal inocula. Novel developments, such as the incorporation of host cells, will further broaden the potential of in vitro models to unravel the importance of gut microbes for human health and disease.

Protective effect of probiotics on Salmonella infectivity assessed with combined in vitro gut fermentation-cellular models

Background

Accurate assessment of probiotics with targeted anti-Salmonella activity requires suitable models accounting for both, microbe-microbe and host-microbe interactions in gut environments. Here we report the combination of two original in vitro intestinal models closely mimicking the complex in vivo conditions of the large intestine. Effluents from continuous in vitro three-stage fermentation colonic models of Salmonella Typhimurium infection inoculated with immobilized child microbiota and Salmonella were directly applied to confluent mucus-secreting HT29-MTX cell layers. The effects of Salmonella, addition of two bacteriocinogenic strains, Bifidobacterium thermophilum RBL67 (thermophilicin B67) and Escherichia coli L1000 (microcin B17), and inulin were tested on Salmonella growth and interactions with epithelial cell layers. Salmonella adhesion and invasion were investigated and epithelial integrity assessed by transepithelial electrical resistance (TER) measurements and confocal microscopy observation. Data from complex effluents were compared with pure Salmonella cultures.

Results

Salmonella in effluents of all reactors of the colonic fermentation model stabilized at mean values of 5.3 ± 0.8 log₁₀ cfu/ml effluent. Invasion of cell-associated Salmonella was up to 50-fold lower in complex reactor samples compared to pure Salmonella cultures. It further depended on environmental factors, with 0.2 ± 0.1% being measured with proximal, 0.6 ± 0.2% with transverse and 1.3 ± 0.7% with distal reactor effluents, accompanied by a similar high decrease of TER across cell monolayers (minus 45%) and disruption of tight junctions. Subsequent addition of E. coli L1000 stimulated Salmonella growth (6.4 ± 0.6 log₁₀ cfu/ml effluent of all 3 reactors) and further decreased TER, but led to 10-fold decreased invasion efficiency when tested with distal reactor samples. In contrast, presence of B. thermophilum RBL67 revealed a protective effect on epithelial integrity compared to previous E. coli L1000 periods, as reflected by a significant mean increase of TER by 58% in all reactors. Inulin addition enhanced Salmonella growth and invasion when tested with distal and proximal reactor samples, respectively, but induced a limited decrease of TER (minus 18%) in all reactors.

Conclusions

Our results highlight the benefits of combining suitable cellular and colonic fermentation models to assess strain-specific first-level host protection properties of probiotics during Salmonella infection, providing an efficient system biology tool for preclinical development of new antimicrobials.

How beneficial is the use of probiotic supplements for the aging gut?

The specific health benefits of probiotic supplementation in aging populations remain relatively undefined. Although some probiotic research performed to date has focused on specific populations – particular disease groups or those in dynamic life stages such as the very young and older adults – dedicated studies of older subjects with a typical range of age-related conditions are few. Published studies also feature a narrow range of probiotic strains. Exploitation of strain specificity to modulate the composition and function of the microbiota is crucial to maximize the potential benefit of probiotics. A combination of prebiotic (dietary) and probiotic agents may prove most effective in targeted modulation of the microbiota. The efficacy of specific probiotic strains in modulating the microbiota of older populations is worth pursuing, although the role of antibiotics and polypharmacy (use of multiple medications) in influencing the potential benefits of probiotic intervention requires more dedicated study.