Comparative methods for fecal sample storage to preserve gut microbial structure and function in an in vitro model of the human colon

Large intestinal nutritional and physicochemical parameters from different dog sizes reshape canine microbiota structure and functions in vitro

Different dog sizes are associated with variations in large intestinal physiology including gut microbiota, which plays a key role in animal health. This study aims to evaluate, using the CANIM-ARCOL (Canine Mucosal Artificial Colon), the relative importance of gut microbes versus physicochemical and nutritional parameters of the canine colonic environment in shaping microbiota structure and functions. CANIM-ARCOL was set up to reproduce nutrient availability, bile acid profiles, colonic pH, and transit time from small, medium, or large dogs according to in vivo data, while bioreactors were all inoculated with a fecal sample collected from medium size dogs (n = 2). Applying different dog size parameters resulted in a positive association between size and gas or SCFA production, as well as distinct microbiota profiles as revealed by 16S Metabarcoding. Comparisons with in vivo data from canine stools and previous in vitro results obtained when CANIM-ARCOL was inoculated with fecal samples from three dog sizes revealed that environmental colonic parameters were sufficient to drive microbiota functions. However, size-related fecal microbes were necessary to accurately reproduce in vitro the colonic ecosystem of small, medium, and large dogs. For the first time, this study provides mechanistic insights on which parameters from colonic ecosystem mainly drive canine microbiota in relation to dog size. The CANIM-ARCOL can be used as a relevant in vitro platform to unravel interactions between food or pharma compounds and canine colonic microbiota, under different dog size conditions. The potential of the model will be extended soon to diseased situations (e.g. chronic enteropathies or obesity).

Assessment of fecal bacterial viability and diversity in fresh and frozen fecal microbiota transplant (FMT) product in horses

BACKGROUND

Currently, lack of standardization for fecal microbiota transplantation (FMT) in equine practice has resulted in highly variable techniques, and there is no data on the bacterial metabolic activity or viability of the administered product. The objectives of this study were to compare the total and potentially metabolically active bacterial populations in equine FMT, and assess the effect of different frozen storage times, buffers, and temperatures on an equine FMT product. Fresh feces collected from three healthy adult horses was subjected to different storage methods. This included different preservation solutions (saline plus glycerol or saline only), temperature (-20 °C or -80 °C), and time (fresh, 30, 60, or 90 days). Samples underwent DNA extraction to assess total bacterial populations (both live and dead combined) and RNA extraction followed by reverse transcription to cDNA as a proxy to assess viable bacteria, then 16s rRNA gene amplicon sequencing using the V1-V2 region.

RESULTS

The largest difference in population indices and taxonomic composition at the genus level was seen when evaluating the results of DNA-based (total) and cDNA-based (potentially metabolically active) extraction method. At the community level, alpha diversity (observed species, Shannon diversity) was significantly decreased in frozen samples for DNA-based analysis (P < 0.05), with less difference seen for cDNA-based sequencing. Using DNA-based analysis, length of storage had a significant impact (P < 0.05) on the bacterial community profiles. For potentially metabolically active populations, storage overall had less of an effect on the bacterial community composition, with a significant effect of buffer (P < 0.05). Individual horse had the most significant effect within both DNA and cDNA bacterial communities.

CONCLUSIONS

Frozen storage of equine FMT material can preserve potentially metabolically active bacteria of the equine fecal microbiome, with saline plus glycerol preservation more effective than saline alone. Larger studies are needed to determine if these findings apply to other individual horses. The ability to freeze FMT material for use in equine patients could allow for easier clinical use of fecal transplant in horses with disturbances in their intestinal microbiome.

Impact of Western Diet on Enterohemorrhagic Escherichia coli Colonization in the Human In Vitro Mucosal Artificial Colon as Mediated by Gut Microbiota

Enterohemorrhagic Escherichia coli (EHEC) is a major food-borne pathogen that causes human disease ranging from diarrhea to life-threatening complications. Accumulating evidence demonstrates that the Western diet enhances the susceptibility to enteric infection in mice, but the effect of diet on EHEC colonization and the role of human gut microbiota remains unknown. Our research aimed to investigate the effects of a Standard versus a Western diet on EHEC colonization in the human in vitro Mucosal ARtificial COLon (M-ARCOL) and the associated changes in the gut microbiota composition and activities. After donor selection using simplified fecal batch experiments, two M-ARCOL bioreactors were inoculated with a human fecal sample (n = 4) and were run in parallel, one receiving a Standard diet, the other a Western diet and infected with EHEC O157:H7 strain EDL933. EHEC colonization was dependent on the donor and diet in the luminal samples, but was maintained in the mucosal compartment without elimination, suggesting a favorable niche for the pathogen, and may act as a reservoir. The Western diet also impacted the bacterial short-chain fatty acid and bile acid profiles, with a possible link between high butyrate concentrations and prolonged EHEC colonization. The work demonstrates the application of a complex in vitro model to provide insights into diet, microbiota, and pathogen interactions in the human gut.

Impact of cryoprotective agents on human gut microbes and in vitro stabilized artificial gut microbiota communities

The availability of microbial biobanks for the storage of individual gut microbiota members or their derived and artificially assembled consortia has become fundamental for in vitro investigation of the molecular mechanisms behind microbe-microbe and/or microbe-host interactions. However, to preserve bacterial viability, adequate storage and processing technologies are required. In this study, the effects on cell viability of seven different combinations of cryoprotective agents were evaluated by flow cytometry for 53 bacterial species representing key members of the human gut microbiota after one and 3 months of cryopreservation at -80°C. The obtained results highlighted that no universal cryoprotectant was identified capable of guaranteeing effective recovery of intact cells after cryopreservation for all tested bacteria. However, the presence of inulin or skimmed milk provided high levels of viability protection during cryoexposure. These results were further corroborated by cryopreserving 10 artificial gut microbiota produced through in vitro continuous fermentation system technology. Indeed, in this case, the inclusion of inulin or skimmed milk resulted in a high recovery of viable cells, while also allowing consistent and reliable preservation of the artificial gut microbiota biodiversity. Overall, these results suggest that, although the efficacy of various cryoprotective agents is species-specific, some cryoprotectants based on glycerol and the addition of inulin or skimmed milk are preferable to retain viability and biodiversity for both single bacterial species and artificial gut microbiota.

Development of a new antibiotic-induced dysbiosis model of the canine colonic microbiota

As in humans, antibiotics are widely used in dogs to treat gastrointestinal infections, contributing to the global burden of antimicrobial resistance on both human and animal health. Close contact between pets and their owners can lead to horizontal transfer of gut microbes, including transmission of antibiotic resistance. Nevertheless, until now, the impact of antibiotics on the canine gut microbiota has been poorly described. The aim of this study was to adapt the canine mucosal artificial colon (CANIM-ARCOL) model, reproducing the main nutritional, physicochemical and microbial parameters found in the large intestine of the dog to simulate an antibiotic-induced perturbation. Following initial investigation of five antibiotic cocktails at in-field doses, a 5-day regimen of metronidazole/enrofloxacin (ME) was selected for further model development. Two CANIM-ARCOL bioreactors were inoculated with a faecal sample (n=2 donors) and run in parallel for 26 days under control or antibiotic conditions. ME reduced microbial diversity and induced major shifts in bacterial populations, leading to a state of dysbiosis characterized by an increase in the relative abundance of Streptococcaceae, Lactobacillaceae and Enterobacteriaceae, and a decrease in the relative abundance of Bacteroidaceae, Fusobacteriota and Clostridiaceae. Overall, mucus-associated microbiota were less impacted by antibiotics than luminal microbes. Microbial alterations were associated with drastic decreases in gas production and short-chain fatty acid concentrations. Finally, the model was well validated through in-vitro-in-vivo comparisons in a study in dogs. The CANIM-ARCOL model provides a relevant platform as an alternative to in-vivo assays for an in-depth understanding of antibiotic-microbiota interactions and further testing of restoration strategies at individual level.

Gut Microbiome Integration in Drug Discovery and Development of Small Molecules

Human microbiomes, particularly in the gut, could have a major impact on the efficacy and toxicity of drugs. However, gut microbial metabolism is often neglected in the drug discovery and development process. Medicen, a Paris-based human health innovation cluster, has gathered more than 30 international leading experts from pharma, academia, biotech, clinical research organizations, and regulatory science to develop proposals to facilitate the integration of microbiome science into drug discovery and development. Seven subteams were formed to cover the complementary expertise areas of 1) pharma experience and case studies, 2) in silico microbiome-drug interaction, 3) in vitro microbial stability screening, 4) gut fermentation models, 5) animal models, 6) microbiome integration in clinical and regulatory aspects, and 7) microbiome ecosystems and models. Each expert team produced a state-of-the-art report of their respective field highlighting existing microbiome-related tools at every stage of drug discovery and development. The most critical limitations are the growing, but still limited, drug-microbiome interaction data to produce predictive models and the lack of agreed-upon standards despite recent progress. In this paper we will report on and share proposals covering 1) how microbiome tools can support moving a compound from drug discovery to clinical proof-of-concept studies and alert early on potential undesired properties stemming from microbiome-induced drug metabolism and 2) how microbiome data can be generated and integrated in pharmacokinetic models that are predictive of the human situation. Examples of drugs metabolized by the microbiome will be discussed in detail to support recommendations from the working group. SIGNIFICANCE STATEMENT: Gut microbial metabolism is often neglected in the drug discovery and development process despite growing evidence of drugs' efficacy and safety impacted by their interaction with the microbiome. This paper will detail existing microbiome-related tools covering every stage of drug discovery and development, current progress, and limitations, as well as recommendations to integrate them into the drug discovery and development process.

Canine Mucosal Artificial Colon: development of a new colonic in vitro model adapted to dog sizes

Differences in dog breed sizes are an important determinant of variations in digestive physiology, mainly related to the large intestine. In vitro gut models are increasingly used as alternatives to animal experiments for technical, cost, societal, and regulatory reasons. Up to now, only one in vitro model of the canine colon incorporates the dynamics of different canine gut regions, yet no adaptations exist to reproduce size-related digestive parameters. To address this limitation, we developed a new model of the canine colon, the CANIne Mucosal ARtificial COLon (CANIM-ARCOL), simulating main physiochemical (pH, transit time, anaerobiosis), nutritional (ileal effluent composition), and microbial (lumen and mucus-associated microbiota) parameters of this ecosystem and adapted to three dog sizes (i.e., small under 10 kg, medium 10-30 kg, and large over 30 kg). To validate the new model regarding microbiota composition and activities, in vitro fermentations were performed in bioreactors inoculated with stools from 13 dogs (4 small, 5 medium, and 4 large). After a stabilization period, microbiota profiles clearly clustered depending on dog size. Bacteroidota and Firmicutes abundances were positively correlated with dog size both in vitro and in vivo, while opposite trends were observed for Actinobacteria and Proteobacteria. As observed in vivo, microbial activity also increased with dog size in vitro, as evidenced from gas production, short-chain fatty acids, ammonia, and bile acid dehydroxylation. In line with the 3R regulation, CANIM-ARCOL could be a relevant platform to assess bilateral interactions between food and pharma compounds and gut microbiota, capturing inter-individual or breed variabilities. KEY POINTS: • CANIM-ARCOL integrates main canine physicochemical and microbial colonic parameters • Gut microbiota associated to different dog sizes is accurately maintained in vitro • The model can help to move toward personalized approach considering dog body weight.

Colon-targeted delivery of polyphenols: construction principles, targeting mechanisms and evaluation methods

Polyphenols have received considerable attention for their promotive effects on colonic health. However, polyphenols are mostly sensitive to harsh gastrointestinal environments, thus, must be protected. It is necessary to design and develop a colon-targeted delivery system to improve the stability, colon-targeting and bioavailability of polyphenols. This paper mainly introduces research on colon-targeted controlled release of polyphenols. The physiological features affecting the dissolution, release and absorption of polyphenol-loaded delivery systems in the colon are first discussed. Simultaneously, the types of colon-targeted carriers with different release mechanisms are described, and colon-targeting assessment models that have been studied so far and their advantages and limitations are summarized. Based on the current research on polyphenols colon-targeting, outlook and reflections are proposed, with the goal of inspiring strategic development of new colon-targeted therapeutics to ensure that the polyphenols reach the colon with complete bioactivity.

Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem

Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.

Effect of Operational Parameters on the Cultivation of the Gut Microbiome in Continuous Bioreactors Inoculated with Feces: A Systematic Review

Since the early 1980s, multiple researchers have contributed to the development of in vitro models of the human gastrointestinal system for the mechanistic interrogation of the gut microbiome ecology. Using a bioreactor for simulating all the features and conditions of the gastrointestinal system is a massive challenge. Some conditions, such as temperature and pH, are readily controlled, but a more challenging feature to simulate is that both may vary in different regions of the gastrointestinal tract. Promising solutions have been developed for simulating other functionalities, such as dialysis capabilities, peristaltic movements, and biofilm growth. This research field is under constant development, and further efforts are needed to drive these models closer to in vivo conditions, thereby increasing their usefulness for studying the gut microbiome impact on human health. Therefore, understanding the influence of key operational parameters is fundamental for the refinement of the current bioreactors and for guiding the development of more complex models. In this review, we performed a systematic search for operational parameters in 229 papers that used continuous bioreactors seeded with human feces. Despite the reporting of operational parameters for the various bioreactor models being variable, as a result of a lack of standardization, the impact of specific operational parameters on gut microbial ecology is discussed, highlighting the advantages and limitations of the current bioreactor systems.

In Vitro Modelling of Oral Microbial Invasion in the Human Colon

Recent advances in the human microbiome characterization have revealed significant oral microbial detection in stools of dysbiotic patients. However, little is known about the potential interactions of these invasive oral microorganisms with commensal intestinal microbiota and the host. In this proof-of-concept study, we proposed a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Oral invasion of the intestinal microbiota was simulated by injection of enriched saliva in the in vitro colon model inoculated with a fecal sample from the same healthy adult donor. The mucosal compartment of M-ARCOL was able to retain the highest species richness levels over time, while species richness levels decreased in the luminal compartment. This study also showed that oral microorganisms preferably colonized the mucosal microenvironment, suggesting potential oral-to-intestinal mucosal competitions. This new model of oral-to-gut invasion can provide useful mechanistic insights into the role of oral microbiome in various disease processes. IMPORTANCE Here, we propose a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Our study revealed the importance of integrating the mucus compartment, which retained higher microbial richness during fermentation, showed the preference of oral microbial invaders for the mucosal resources, and indicated potential oral-to-intestinal mucosal competitions. It also underlined promising opportunities to further understand mechanisms of oral invasion into the human gut microbiome, define microbe-microbe and mucus-microbe interactions in a compartmentalized fashion, and help to better characterize the potential of oral microbial invasion and their persistence in the gut.

Application of Nucleic Acid-Based Strategies to Detect Infectious Pathogens in Orthopaedic Implant-Related Infection

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Implant-associated infection in orthopaedic surgery remains an enormous and largely unsolved clinical problem with a high rate of persistent or recurrent infection. This may be due, at least in part, to the potential for underdiagnosis by traditional microbial culture or the potential for culture to incompletely identify the microbial species present.

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Nucleic acid-based diagnostic techniques, focused on using the diagnostic information contained in DNA or RNA to identify microbial species, have been developing rapidly and have garnered escalating interest for both clinical and research applications.

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Commonly applied techniques include end-point polymerase chain reaction (PCR), quantitative PCR, Sanger sequencing, and next-generation sequencing. Understanding the specific strengths and weaknesses of each technique is critical to understanding their utility, applying the correct assessment strategy, and critically understanding and interpreting research.

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The best practices for interpreting nucleic acid-based diagnostic techniques include considering positive and negative controls, reads per sample, detection thresholds (for differentiating contaminants from positive results), and the primer set or targeted regions.

Exposure to polyethylene microplastics alters immature gut microbiome in an infant in vitro gut model

Infants are characterized by an immaturity of the gut ecosystem and a high exposure to microplastics (MPs) through diet, dust and suckling. However, the bidirectional interactions between MPs and the immature infant intestinal microbiota remain unknown. Our study aims to investigate the impact of chronic exposure to polyethylene (PE) MPs on the gut microbiota and intestinal barrier of infants, using the new Toddler mucosal Artificial Colon coupled with a co-culture of epithelial and mucus-secreting cells. Gut microbiota composition was determined by 16S metabarcoding and microbial activities were evaluated by gas, short chain fatty acid and volatolomics analyses. Gut barrier integrity was assessed via evaluation of intestinal permeability, inflammation and mucus synthesis. Exposure to PE MPs induced gut microbial shifts increasing α-diversity and abundance of potentially harmful pathobionts, such as Dethiosulfovibrionaceae and Enterobacteriaceae. Those changes were associated to butyrate production decrease and major changes in volatile organic compounds profiles. In contrast, no significant impact of PE MPs on the gut barrier, as mediated by microbial metabolites, was reported. For the first time, this study indicates that ingestion of PE MPs can induce perturbations in the gut microbiome of infants. Next step would be to further investigate the potential vector effect of MPs.

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.

Microplastics: What happens in the human digestive tract? First evidences in adults using in vitro gut models

Microplastics (MPs) are ubiquitous in the environment and humans are inevitably exposed to them. However, the effects of MPs in the human digestive environment are largely unknown. The aim of our study was to investigate the impact of repeated exposure to polyethylene (PE) MPs on the human gut microbiota and intestinal barrier using, under adult conditions, the Mucosal Artificial Colon (M-ARCOL) model, coupled with a co-culture of intestinal epithelial and mucus-secreting cells. The composition of the luminal and mucosal gut microbiota was determined by 16S metabarcoding and microbial activities were characterized by gas, short chain fatty acid, volatolomic and AhR activity analyses. Gut barrier integrity was assessed via intestinal permeability, inflammation and mucin synthesis. First, exposure to PE MPs induced donor-dependent effects. Second, an increase in abundances of potentially harmful pathobionts, Desulfovibrionaceae and Enterobacteriaceae, and a decrease in beneficial bacteria such as Christensenellaceae and Akkermansiaceae were observed. These bacterial shifts were associated with changes in volatile organic compounds profiles, notably characterized by increased indole 3-methyl- production. Finally, no significant impact of PE MPs mediated by changes in gut microbial metabolites was reported on the intestinal barrier. Given these adverse effects of repeated ingestion of PE MPs on the human gut microbiota, studying at-risk populations like infants would be a valuable advance.

Role of mucus-bacteria interactions in Enterotoxigenic Escherichia coli (ETEC) H10407 virulence and interplay with human microbiome

The intestinal mucus layer has a dual role in human health constituting a well-known microbial niche that supports gut microbiota maintenance but also acting as a physical barrier against enteric pathogens. Enterotoxigenic Escherichia coli (ETEC), the major agent responsible for traveler's diarrhea, is able to bind and degrade intestinal mucins, representing an important but understudied virulent trait of the pathogen. Using a set of complementary in vitro approaches simulating the human digestive environment, this study aimed to describe how the mucus microenvironment could shape different aspects of the human ETEC strain H10407 pathophysiology, namely its survival, adhesion, virulence gene expression, interleukin-8 induction and interactions with human fecal microbiota. Using the TNO gastrointestinal model (TIM-1) simulating the physicochemical conditions of the human upper gastrointestinal (GI) tract, we reported that mucus secretion and physical surface sustained ETEC survival, probably by helping it to face GI stresses. When integrating the host part in Caco2/HT29-MTX co-culture model, we demonstrated that mucus secreting-cells favored ETEC adhesion and virulence gene expression, but did not impede ETEC Interleukin-8 (IL-8) induction. Furthermore, we proved that mucosal surface did not favor ETEC colonization in a complex gut microbial background simulated in batch fecal experiments. However, the mucus-specific microbiota was widely modified upon the ETEC challenge suggesting its role in the pathogen infectious cycle. Using multi-targeted in vitro approaches, this study supports the major role played by mucus in ETEC pathophysiology, opening avenues in the design of new treatment strategies.

A child is not an adult: development of a new in vitro model of the toddler colon

Early life is a critical period where gut ecosystem and functions are being established with significant impact on health. For regulatory, technical, and cost reasons, in vitro gut models can be used as a relevant alternative to in vivo assays. An exhaustive literature review was conducted to adapt the Mucosal Artificial Colon (M-ARCOL) to specific physicochemical (pH, transit time, and nutritional composition of ileal effluents) and microbial parameters from toddlers in the age range of 6 months-3 years, resulting in the Tm-ARCOL. In vitro fermentations were performed to validate this newly developed colonic model compared to in vivo toddler data. Results were also compared to those obtained with the classical adult configuration. Fecal samples from 5 toddlers and 4 adults were used to inoculate bioreactors, and continuous fermentations were performed for 8 days. Gut microbiota structure (lumen and mucus-associated microbiota) and functions (gas and short-chain fatty acids) were monitored. Clearly distinct microbial signatures were obtained between the two in vitro conditions, with lower α-diversity indices and higher abundances of infant-related microbial populations (e.g., Bifidobacteriaceae, Enterobacteriaceae) in toddler versus adult conditions. In accordance with in vivo data, methane was found only in adult bioreactors, while higher percentage of acetate but lower proportions of propionate and butyrate was measured in toddlers compared to adults. This new in vitro model will provide a powerful platform for gut microbiome mechanistic studies in a pediatric context, both in nutritional- (e.g., nutrients, probiotics, prebiotics) and health-related (e.g., drugs, enteric pathogens) studies. KEY POINTS: • Development of a novel in vitro colonic model recapitulating the toddler environment. • Specific toddler versus adult digestive conditions are preserved in vitro. • The new model provides a powerful platform for microbiome mechanistic studies.

Role, Relevance, and Possibilities of In vitro fermentation models in human dietary, and gut-microbial studies

Dietary studies play a crucial role in determining the health-benefiting effects of most food substances, including prebiotics, probiotics, functional foods, and bioactive compounds. Such studies involve gastrointestinal digestion and colonic fermentation of dietary substances. In colonic fermentation, any digested food is further metabolized in the gut by the residing colonic microbiota, causing a shift in the gut microenvironment and production of various metabolites, such as short-chain fatty acids (SCFA). These diet-induced shifts in the microbial community and metabolite production, which can be assessed through in vitro fermentation models using a donor's fecal microbiota, are well known to impact the health of the host. Although in vivo or animal experiments are the gold standard in dietary studies, recent advancements using different in vitro systems, like artificial colon (ARCOL), mini bioreactor array (MBRA), TNO in vitro model of the colon (TIM), Simulator of the Human Intestinal Microbial Ecosystem (SHIME), M-SHIME, CoMiniGut, and Dynamic Gastrointestinal Simulator (SIMGI) make it easy to study the dietary impact in terms of the gut microbiota and metabolites. Such a continuous in vitro system can have multiple compartments corresponding to different parts of the colon, i.e., proximal, transverse, and distal colon, making the findings physiologically more significant. Further, post-fermentation samples can be analyzed using metagenomic, metabolomic, qPCR and flow cytometry approaches. Moreover, studies have shown that in vitro results are in accordance with the in vivo findings, supporting their relevance in dietary studies and giving confidence that shifts in metabolites are only due to microbes. This review meticulously describes the recent advancements in various fermentation models and their relevance in dietary studies. This article is protected by copyright. All rights reserved.

Lentils and Yeast Fibers: A New Strategy to Mitigate Enterotoxigenic Escherichia coli (ETEC) Strain H10407 Virulence?

Dietary fibers exhibit well-known beneficial effects on human health, but their anti-infectious properties against enteric pathogens have been poorly investigated. Enterotoxigenic Escherichia coli (ETEC) is a major food-borne pathogen that causes acute traveler’s diarrhea. Its virulence traits mainly rely on adhesion to an epithelial surface, mucus degradation, and the secretion of two enterotoxins associated with intestinal inflammation. With the increasing burden of antibiotic resistance worldwide, there is an imperious need to develop novel alternative strategies to control ETEC infections. This study aimed to investigate, using complementary in vitro approaches, the inhibitory potential of two dietary-fiber-containing products (a lentil extract and yeast cell walls) against the human ETEC reference strain H10407. We showed that the lentil extract decreased toxin production in a dose-dependent manner, reduced pro-inflammatory interleukin-8 production, and modulated mucus-related gene induction in ETEC-infected mucus-secreting intestinal cells. We also report that the yeast product reduced ETEC adhesion to mucin and Caco-2/HT29-MTX cells. Both fiber-containing products strengthened intestinal barrier function and modulated toxin-related gene expression. In a complex human gut microbial background, both products did not elicit a significant effect on ETEC colonization. These pioneering data demonstrate the promising role of dietary fibers in controlling different stages of the ETEC infection process.

Effect of Intramuscularly Administered Oxytetracycline or Enrofloxacin on Vancomycin-Resistant Enterococci, Extended Spectrum Beta-Lactamase- and Carbapenemase-Producing Enterobacteriaceae in Pigs

Simple Summary

Nowadays, there is great concern about the prevalence of multidrug resistant bacteria in food-producing animals since they are potential sources of transmission to humans. The aim of this work was to evaluate the effect of two antibiotics (oxytetracycline and enrofloxacin) treatments in pigs on resistant bacteria that are considered a threat to public health. This study highlights that the use of oxytetracycline or enrofloxacin in food-producing animals could select resistant bacteria in pig faeces. Special care should be taken to avoid faecal contamination of carcasses during slaughter.

Abstract

Nowadays, there is a great concern about the prevalence of multidrug resistant Enterococcus spp. and Enterobacteriaceae in food-producing animals. The aim of this work was to evaluate the effect of oxytetracycline or enrofloxacin treatment on vancomycin-resistant enterococci (VRE), extended spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae in pigs. A total of 26 piglets were received and distributed in three groups. Group 1 was treated with enrofloxacin (N = 12), group 2 with oxytetracycline (N = 10) and group 3 did not receive any treatment (control group) (N = 4). A higher number of vancomycin-resistant E. faecium were recovered compared to E. faecalis. In the pigs treated with enrofloxacin, vancomycin resistant E. faecium was found in a higher percentage of animals than in the control group. ESBL-producing E. coli was not detected in rectal samples from control animals. However, it was detected in 17–20% of animals treated with oxytetracycline on days 6 to 17 and in 17–50% of the animals treated with enrofloxacin. Carbapenemase-producing E. coli was isolated in animals treated with oxytetracycline, but not in animals treated with enrofloxacin or in the control group. This study highlights that the use of oxytetracycline or enrofloxacin in food-producing animals could select ESBL and carbapenemase-producing E. coli. Further studies shall be needed to validate the results obtained, considering a more robust and extended experimental design.

Storage of soil microbiome for application in sustainable agriculture: prospects and challenges

Soil microbiome is a dynamic micro-ecosystem driving and fine-tuning several biological processes in the global macro-ecosystems. Its tremendous potential towards mediating sustainability in the ecosystem necessitates the urgent need to store it optimally and efficiently as "next-generation biologicals" for future applications via soil transplantation. The challenge, therefore, is to devise a strategy for the storage of soil microbiome such that its "functionality" is preserved for later application. This review discusses the current endeavours made towards storage of the soil microbiome. The methods for assessing the integrity of soil microbiome by targeting the structural diversity and functional potential of the preserved microbiomes have also been discussed. Further, the success stories related to the storage of fecal microbiome for application in transplants have also been highlighted. This is done primarily with the objective of learning lessons, and parallel application of the knowledge gained, in bringing about improvement in the research domain of soil microbiome storage. Subsequently, the limitations of current techniques of preservation have also been delineated. Further, the open questions in the area have been critically discussed. In conclusion, possible alternatives for storage, comprehensive analyses of the composition of the stored microbiome and their potential have been presented.

The final fate of food: On the establishment of in vitro colon models

The search for life/health quality has driven the search for a better understanding of food components on the overall individual health, which turns to be intrinsically related to the digestive system. In vitro digestion models are considered an alternative for the in vivo studies for a variety of practical reasons, but further research is still needed concerning the colon model establishment. An effective in vitro colon model should consider all unit operations and transport phenomena, together with chemical and biochemical reactions, material handling and reactor design. Due to the different techniques and dependence on the donor microbiota, it is difficult to obtain a standard protocol with results reproductible in time and space. Furthermore, the colon model should be fed with a representative substrate, thus what happens in upper digestion tract and absorption prior to colon is also of crucial importance. Essentially, there are two ways to think about how to achieve a good and useful in vitro colon model: a complex biomimetic system that provides results comparable with the in vivo studies or a simple system, that despite the fact it could not give physiologically relevant data, it is sufficient to understand the fate of some specific components.

Nitric Oxide Impacts Human Gut Microbiota Diversity and Functionalities

The disruption of gut microbiota homeostasis has been associated with numerous diseases and with a disproportionate inflammatory response, including overproduction of nitric oxide (NO) in the intestinal lumen. However, the influence of NO on the human gut microbiota has not been well characterized yet. We used in vitro fermentation systems inoculated with human fecal samples to monitor the effect of repetitive NO pulses on the gut microbiota. NO exposure increased the redox potential and modified the fermentation profile and gas production. The overall metabolome was modified, reflecting less strict anaerobic conditions and shifts in amino acid and nitrogen metabolism. NO exposure led to a microbial shift in diversity with a decrease in Clostridium leptum group and Faecalibacterium prausnitzii biomass and an increased abundance of the Dialister genus. Escherichia coli, Enterococcus faecalis, and Proteus mirabilis operational taxonomic unit abundance increased, and strains from those species isolated after NO stress showed resistance to high NO concentrations. As a whole, NO quickly changed microbial fermentations, functions, and composition in a pulse- and dose-dependent manner. NO could shift, over time, the trophic chain to conditions that are unfavorable for strict anaerobic microbial processes, implying that a prolonged or uncontrolled inflammation has detrimental and irreversible consequences on the human microbiome.

IMPORTANCE Gut microbiota dysbiosis has been associated with inflammatory diseases. The human inflammatory response leads to an overproduction of nitric oxide (NO) in the gut. However, so far, the influence of NO on the human gut microbiota has not been characterized. In this study, we used in vitro fermentation systems with human fecal samples to understand the effect of NO on the microbiota: NO modified the microbial composition and its functionality. High NO concentration depleted the microbiota of beneficial butyrate-producing species and favored potentially deleterious species (E. coli, E. faecalis, and P. mirabilis), which we showed can sustain high NO concentrations. Our work shows that NO may participate in the vicious circle of inflammation, leading to detrimental and irreversible consequences on human health.

In Vitro Evaluation of Dietary Fiber Anti-Infectious Properties against Food-Borne Enterotoxigenic Escherichia coli

Dietary fibers have well-known beneficial effects on human health, but their anti-infectious properties against human enteric pathogens have been poorly investigated. Enterotoxigenic Escherichia coli (ETEC) is the main agent of travelers’ diarrhea, against which targeted preventive strategies are currently lacking. ETEC pathogenesis relies on multiple virulence factors allowing interactions with the intestinal mucosal layer and toxins triggering the onset of diarrheal symptoms. Here, we used complementary in vitro assays to study the antagonistic properties of eight fiber-containing products from cereals, legumes or microbes against the prototypical human ETEC strain H10407. Inhibitory effects of these products on the pathogen were tested through growth, toxin production and mucus/cell adhesion inhibition assays. None of the tested compounds inhibited ETEC strain H10407 growth, while lentil extract was able to decrease heat labile toxin (LT) concentration in culture media. Lentil extract and specific yeast cell walls also interfered with ETEC strain H10407 adhesion to mucin beads and human intestinal cells. These results constitute a first step in the use of dietary fibers as a nutritional strategy to prevent ETEC infection. Further work will be dedicated to the study of fiber/ETEC interactions within a complex gut microbial background.

Understanding protein digestion in infants and the elderly: Current in vitro digestion models

The last decades have witnessed a surge of interest in the fate of dietary proteins during gastrointestinal (GI) digestion. Although several in vitro digestion models are available as alternatives to clinical experiments, most of them focus on the digestive conditions of healthy young adults. This study investigates the static/dynamic models used to simulate digestion in infants and the elderly and considers the related in vivo conditions. The in vitro digestive protocols targeting these two groups are summarized, and the challenges associated with the further development of in vitro digestion models are discussed. Static models rely on several factors (e.g., enzyme concentration, pH, reaction time, and rotation speed) to differentiate digestive conditions depending on age. Dynamic models can more accurately simulate the complex digestion process and allow the inclusion of further parameters (sequential secretion of digestive fluids, gradual changes in pH, peristaltic mixing, GI emptying, and the inoculation of luminal microbiota). In the case of infants, age or growth stage clarification and the differentiation of digestive protocols between full-term and preterm infants are required, whereas protocols dealing with various health statuses are required in the case of the elderly, as this group is prone to oral cavity and GI function deterioration.

Microplastics in the human digestive environment: A focus on the potential and challenges facing in vitro gut model development

Plastic pollution is a major issue worldwide, generating massive amounts of smaller plastic particles, including microplastics (MPs). Their ubiquitous nature in the environment but also in foodstuff and consumer packaged goods has revealed potential threats to humans who can be contaminated mainly through air, food and water consumption. In this review, the current literature on human exposure to MPs is summarized with a focus on the gastrointestinal tract as portal of entry. Then, we discuss the vector effect of MPs, in their pristine versus weathered forms, with well-known contaminants as heavy metals and chemicals, or more emerging ones as antibiotics or microbial pathogens, like Pseudomonas spp., Vibrio spp., Campylobacter spp. and Escherichia coli. Comprehensive knowledge on MP fate in the gastrointestinal tract and their potential impact on gut homeostasis disruption, including gut microbiota, mucus and epithelial barrier, is reported in vitro and in vivo in mammals. Special emphasis is given on the crucial need of developing robust in vitro gut models to adequately simulate human digestive physiology and absorption processes. Finally, this review points out future research directions on MPs in human intestinal health.

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.

Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments

The gut microbiota has a profound effect on human health and is modulated by food and bioactive compounds. To study such interaction, in vitro batch fermentations are performed with fecal material, and some experimental designs may require that such fermentations be performed with previously frozen stools. Although it is known that freezing fecal material does not alter the composition of the microbial community in 16S rRNA gene amplicon and metagenomic sequencing studies, it is not known whether the microbial community in frozen samples could still be used for in vitro fermentations. To explore this, we undertook a pilot study in which in vitro fermentations were performed with fecal material from celiac, cow’s milk allergic, obese, or lean children that was frozen (or not) with 20% glycerol. Before fermentation, the fecal material was incubated in a nutritious medium for 6 days, with the aim of giving the microbial community time to recover from the effects of freezing. An aliquot was taken daily from the stabilization vessel and used for the in vitro batch fermentation of lentils. The microbial community structure was significantly different between fresh and frozen samples, but the variation introduced by freezing a sample was always smaller than the variation among individuals, both before and after fermentation. Moreover, the potential functionality (as determined in silico by a genome-scaled metabolic reconstruction) did not differ significantly, possibly due to functional redundancy. The most affected genus was Bacteroides, a fiber degrader. In conclusion, if frozen fecal material is to be used for in vitro fermentation purposes, our preliminary analyses indicate that the functionality of microbial communities can be preserved after stabilization.

Assessment of stool collection and storage conditions for in vitro human gut model studies

BACKGROUND

The role of the gut microbiota in health and disease is becoming increasingly apparent. Faeces is the most accessible sample to collect from human volunteers for studying the gut microbiota. However, the impact of stool collection and storage conditions on microbial and metabolic profiles have not been fully evaluated. By understanding the effect of different stool collection and storage conditions on microbial and metabolic composition, we can consider these parameters in the design of in vitro fermentation studies.

METHODS

Stool samples from 3 volunteers were stored under 5 different conditions to mimic methods that researchers may use to collect and store stool samples for study of the gut microbiota, including: fresh sample used within 10 min; stored on wet ice (4 °C) for 60 min; stored in an anaerobic chamber in a temperature-controlled bag (4 °C) for 60 min; freezing at -20 °C for 60 min and freezing at -20 °C for 60 min and then at -80 °C for 2 weeks. The stored samples were added to basal medium in batch culture fermenters alone (negative control) or with 5 g 2'-Fucosyllactose (2'FL) Human Milk Oligosaccharide (HMO) (as a positive fermentation control). Samples were collected at 3 timepoints (0, 12 and 24 h) for analysis by Flow Cytometry-Fluorescent In Situ Hybridisation (FC-FISH) and ¹H-Nuclear Magnetic Resonance (NMR) spectroscopy to assess the impact on microbial and metabolic profiles, respectively.

RESULTS

Freezing stool significantly impacted microbial numbers and activity during in vitro fermentations, whereas storing the stool on wet ice (4 °C) or in an anaerobic chamber at 4 °C for 60 min had minimal effects on microbial and metabolic profiles throughout the 24 h batch culture fermentation experiments.

DISCUSSION

For in vitro batch culture fermentation studies where it may not be practical or possible to use fresh stool, either storing the stool on wet ice (4 °C) or in an anaerobic chamber at 4 °C for 60 min could be plausible alternatives to maintain microbial and metabolic profiles for analysis.

An Oral FMT Capsule as Efficient as an Enema for Microbiota Reconstruction Following Disruption by Antibiotics, as Assessed in an In Vitro Human Gut Model

Fecal microbiota transplantation (FMT) is an innovative therapy already used in humans to treat Clostridioides difficile infections associated with massive use of antibiotics. Clinical studies are obviously the gold standard to evaluate FMT efficiency but remain limited by regulatory, ethics, and cost constraints. In the present study, an in vitro model of the human colon reproducing medically relevant perturbation of the colonic ecosystem by antibiotherapy was used to compare the efficiency of traditional FMT enema formulations and a new oral capsule in restoring gut microbiota composition and activity. Loss of microbial diversity, shift in bacterial populations, and sharp decrease in fermentation activities induced in vivo by antibiotherapy were efficiently reproduced in the in vitro model, while capturing inter-individual variability of gut microbiome. Oral capsule was as efficient as enema to decrease the number of disturbed days and bacterial load had no effect on enema performance. This study shows the relevance of human colon models as an alternative approach to in vivo assays during preclinical studies for evaluating FMT efficiency. The potential of this in vitro approach could be extended to FMT testing in the management of many digestive or extra-intestinal pathologies where gut microbial dysbiosis has been evidenced such as inflammatory bowel diseases, obesity or cancers.