Metabolic Modeling and Bidirectional Culturing of Two Gut Microbes Reveal Cross-Feeding Interactions and Protective Effects on Intestinal Cells

MetaFlowTrain: a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions

Metabolic fluxes between cells, organisms, or communities drive ecosystem assembly and functioning and explain higher-level biological organization. Exometabolite-mediated inter-organismal interactions, however, remain poorly described due to technical challenges in measuring these interactions. Here, we present MetaFlowTrain, an easy-to-assemble, cheap, semi-high-throughput, and modular fluidic system in which multiple media can be flushed at adjustable flow rates into gnotobiotic microchambers accommodating diverse micro-organisms, ranging from bacteria to small eukaryotes. These microchambers can be used alone or connected in series to create microchamber trains within which metabolites, but not organisms, directionally travel between microchambers to modulate organismal growth. Using MetaFlowTrain, we uncover soil conditioning effects on synthetic community structure and plant growth, and reveal microbial antagonism mediated by exometabolite production. Our study highlights MetaFlowTrain as a versatile system for investigating plant-microbe-microbe metabolic interactions. We also discuss the system´s potential to discover metabolites that function as signaling molecules, drugs, or antimicrobials across various systems.

Genome-Scale Community Model-Guided Development of Bacterial Coculture for Lignocellulose Bioconversion

Microbial communities have shown promising potential in degrading complex biopolymers, producing value-added products through collaborative metabolic functionality. Hence, developing synthetic microbial consortia has become a predominant technique for various biotechnological applications. However, diverse microbial entities in a consortium can engage in distinct biochemical interactions that pose challenges in developing mutualistic communities. Therefore, a systems-level understanding of the inter-microbial metabolic interactions, growth compatibility, and metabolic synergisms is essential for developing effective synthetic consortia. This study demonstrated a genome-scale community modeling approach to assess the inter-microbial interaction pattern and screen metabolically compatible bacterial pairs for designing the lignocellulolytic coculture system. Here, we have investigated the pairwise growth and biochemical synergisms among six termite gut bacterial isolates by implementing flux-based parameters, i.e., pairwise growth support index (PGSI) and metabolic assistance (PMA). Assessment of the PGSI and PMA helps screen nine beneficial bacterial pairs that were validated by designing a coculture experiment with lignocellulosic substrates. For the cocultured bacterial pairs, the experimentally measured enzymatic synergisms (DES) showed good coherence with model-derived biochemical compatibility (PMA), which explains the fidelity of the in silico predictions. The highest degree of enzymatic synergisms has been observed in C. denverensis P3 and Brevibacterium sp P5 coculture, where the total cellulase activity has been increased by 53%. Hence, the flux-based assessment of inter-microbial interactions and metabolic compatibility helps select the best bacterial coculture system with enhanced lignocellulolytic functionality. The flux-based parameters (PGSI and PMA) in the proposed community modeling strategy will help optimize the composition of microbial consortia for developing synthetic microcosms for bioremediation, bioengineering, and biomedical applications.

Mode of Action of Psyllium in Reducing Gas Production from Inulin and its Interaction with Colonic Microbiota: A 24-hour, Randomized, Placebo-Controlled Trial in Healthy Human Volunteers

BACKGROUND

Recent studies show that the increase in breath hydrogen (BH2) and symptoms after ingestion of inulin are reduced by coadministering psyllium (PI).

OBJECTIVES

To determine if slowing delivery of inulin to the colon by administering it in divided doses would mimic the effect of PI. Primary endpoint was the BH2 area under the curve AUC0-24 h. Secondary endpoints included BH2 AUC0-6 h, 6-12 h, and 12-24 h. Exploratory endpoints included the correlation of BH2 AUC0-24 h with dietary fermentable oligo-, di-, monosaccharides, and polyols (FODMAPs) intake and in vitro fermentation results.

METHODS

A total of 17 healthy adults were randomly assigned to a single-blind, 3-arm, crossover trial. All consumed 20 g inulin (I) powder dissolved in 500 mL water and mixed with either 20 g maltodextrin (control) or 20 g PI consumed as a single dose or 20 g inulin given in divided doses (DDI), 62.5 mL every 45 min over 6 h. Twenty-four-hour BH2, dietary FODMAP intake, stool microbiota, and gas production in vitro were measured. Responders were defined as those whose AUC0-24 h BH2 was reduced by PI, whereas nonresponders showed no reduction.

RESULTS

Compared with control, PI did not reduce mean BH2 AUC0-24 h, whereas DDI increased it, P < 0.0002. DDI and PI both significantly reduced BH2 AUC0-6 h compared with the control, P < 0.0001. However, subsequently, DDI significantly increased BH2 from 6 to 12 h (P < 0.0001) and overnight (12-24 h) (P < 0.0001), whereas PI did so only overnight (P = 0.0002). Nonresponders showed greater release of arabinose during in vitro fermentation and higher abundance of 2 species, Clostridium spp. AM22_11AC and Phocaeicola dorei, which also correlated with BH2 production on PI. Dietary FODMAP intake tended to correlate inversely with BH2 AUC0-24 h (r = -0.42, P = 0.09) and correlated with microbiome community composition.

CONCLUSIONS

DDI, like PI, reduces early BH2 production. PI acts by delaying transit to the colon but not reducing colonic fermentation over 24 h. Dietary FODMAP intake correlates with BH2 response to inulin and the microbiome. This trial was registered at www.

CLINICALTRIALS

gov as NCT05619341.

Food colorant brilliant blue causes persistent functional and structural changes in an in vitro simplified microbiota model system

The human gut microbiota plays a vital role in maintaining host health by acting as a barrier against pathogens, supporting the immune system, and metabolizing complex carbon sources into beneficial compounds such as short-chain fatty acids. Brilliant blue E-133 (BB), is a common food dye that is not absorbed or metabolized by the body, leading to substantial exposure of the gut microbiota. Despite this, its effects on the microbiota are not well-documented. In this study, we cultivated the Simplified Human Microbiota Model (SIHUMIx) in a three-stage in vitro approach (stabilization, exposure, and recovery). Using metaproteomic and metabolomic approaches, we observed significant shifts in microbial composition, including an increase in the relative abundance of Bacteroides thetaiotaomicron and a decrease in beneficial species such as Bifidobacterium longum and Clostridium butyricum. We observed lower protein abundance in energy metabolism, metabolic end products, and particularly lactate and butyrate. Disturbance in key metabolic pathways related to energy production, stress response, and amino acid metabolism were also observed, with some pathways affected independently of bacterial abundance. These functional changes persisted during the recovery phase, indicating that the microbiota did not fully return to its pre-exposure state. Our findings suggest that BB has a lasting impact on gut microbiota structure and function, raising concerns about its widespread use in the food industry. This study underscores the need for further research into the long-term effects of food colorants on the gut microbiota and their potential health implications.

Comparison of Fecal Microbiota and Metabolites Between Captive and Grazing Male Reindeer

The reindeer (Rangifer tarandus) is a circumpolar member of the Cervidae family, and has adapted to a harsh environment. Summer is a critical period for reindeer, with peak digestibility facilitating body fat accumulation. The gut microbiota plays a pivotal role in nutrient metabolism, and is affected by captivity. However, differences in the composition of the gut microbiota and metabolites between captive and grazing reindeer during summer remain poorly understood. Here, we conducted a comparative study of the fecal microbiota and metabolites between captive (n = 6) and grazing (n = 6) male reindeer, using full-length 16S rRNA gene sequencing and gas chromatography-time-of-flight mass spectrometry, respectively. Our results indicated that Prevotella, Phocaeicola, Papillibacter, Muribaculum, and Bacteroides were the predominant genera in the feces of reindeer. However, microbial diversity was significantly higher in captive reindeer compared to their grazing counterparts. Principal coordinate analysis revealed significant differences in the fecal microbiota between captive and grazing reindeer. In captive reindeer, the relative abundances of the genera Clostridium, Paraprevotella, Alistipes, Paludibacter, Lentimicrobium, Paraclostridium, and Anaerovibrio were significantly higher, while those of the genera Prevotella, Phocaeicola, Pseudoflavonifractor, and Lactonifactor were significantly lower. A comparison of predicted functions indicated that pathways involved in fat digestion and absorption, histidine metabolism, lysine biosynthesis, and secondary bile acid biosynthesis were more abundant in captive reindeer, whereas the pathways of fructose and mannose metabolism and propanoate metabolism were less abundant. An untargeted metabolomic analysis revealed that 624 metabolites (e.g., amino acids, lipids, fatty acids, and bile acids) and 645 metabolites (e.g., carbohydrates and purines) were significantly increased in the feces of captive and grazing reindeer, respectively. In conclusion, we unveiled significant differences in fecal microbiota and metabolites between captive and grazing male reindeer, with the results suggesting a potentially enhanced ability to utilize plant fibers in grazing reindeer.

Engineering Gut Symbionts: A Way to Promote Bee Growth?

Bees play a crucial role as pollinators, contributing significantly to ecosystems. However, the honeybee population faces challenges such as global warming, pesticide use, and pathogenic microorganisms. Promoting bee growth using several approaches is therefore crucial for maintaining their roles. To this end, the bacterial microbiota is well-known for its native role in supporting bee growth in several respects. Maximizing the capabilities of these microorganisms holds the theoretical potential to promote the growth of bees. Recent advancements have made it feasible to achieve this enhancement through the application of genetic engineering. In this review, we present the roles of gut symbionts in promoting bee growth and collectively summarize the engineering approaches that would be needed for future applications. Particularly, as the engineering of bee gut symbionts has not been advanced, the dominant gut symbiotic bacteria Snodgrassella alvi and Gilliamella apicola are the main focus of the paper, along with other dominant species. Moreover, we propose engineering strategies that will allow for the improvement in bee growth with listed gene targets for modification to further encourage the use of engineered gut symbionts to promote bee growth.

LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models

BACKGROUND

Uniform random sampling of mass-balanced flux solutions offers an unbiased appraisal of the capabilities of metabolic networks. Unfortunately, it is impossible to avoid thermodynamically infeasible loops in flux samples when using convex samplers on large metabolic models. Current strategies for randomly sampling the non-convex loopless flux space display limited efficiency and lack theoretical guarantees.

RESULTS

Here, we present LooplessFluxSampler, an efficient algorithm for exploring the loopless mass-balanced flux solution space of metabolic models, based on an Adaptive Directions Sampling on a Box (ADSB) algorithm. ADSB is rooted in the general Adaptive Direction Sampling (ADS) framework, specifically the Parallel ADS, for which theoretical convergence and irreducibility results are available for sampling from arbitrary distributions. By sampling directions that adapt to the target distribution, ADSB traverses more efficiently the sample space achieving faster mixing than other methods. Importantly, the presented algorithm is guaranteed to target the uniform distribution over convex regions, and it provably converges on the latter distribution over more general (non-convex) regions provided the sample can have full support.

CONCLUSIONS

LooplessFluxSampler enables scalable statistical inference of the loopless mass-balanced solution space of large metabolic models. Grounded in a theoretically sound framework, this toolbox provides not only efficient but also reliable results for exploring the properties of the almost surely non-convex loopless flux space. Finally, LooplessFluxSampler includes a Markov Chain diagnostics suite for assessing the quality of the final sample and the performance of the algorithm.

Gut microbiota bridges dietary nutrients and host immunity

Dietary nutrients and the gut microbiota are increasingly recognized to cross-regulate and entrain each other, and thus affect host health and immune-mediated diseases. Here, we systematically review the current understanding linking dietary nutrients to gut microbiota-host immune interactions, emphasizing how this axis might influence host immunity in health and diseases. Of relevance, we highlight that the implications of gut microbiota-targeted dietary intervention could be harnessed in orchestrating a spectrum of immune-associated diseases.

Unveiling abundance-dependent metabolic phenotypes of microbial communities

IMPORTANCE

In nature, organisms live in communities and not as isolated species, and their interactions provide a source of resilience to environmental disturbances. Despite their importance in ecology, human health, and industry, understanding how organisms interact in different environments remains an open question. In this work, we provide a novel approach that, only using genomic information, studies the metabolic phenotype exhibited by communities, where the exploration of suboptimal growth flux distributions and the composition of a community allows to unveil its capacity to respond to environmental changes, shedding light of the degrees of metabolic plasticity inherent to the community.

Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community

A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.

Proteomic analyses of Bacteroides ovatus and Bifidobacterium longum in xylan bidirectional culture shows sugar cross-feeding interactions

The intestinal microbiome is a community of anaerobic microorganisms whose activities significantly impact human health. Its composition can be modulated by consuming foods rich in dietary fiber, such as xylan, a complex polysaccharide that can be considered an emerging prebiotic. In this work, we evaluated how certain gut bacteria acted as primary degraders, fermenting dietary fibers, and releasing metabolites that other bacteria can further use. Different bacterial strains of Lactobacillus, Bifidobacterium, and Bacteroides were evaluated for their ability to consume xylan and interact with one another. Results from unidirectional assays gave indications of possible cross-feeding between bacteria using xylan as a carbon source. Bidirectional assays showed that Bifidobacterium longum PT4 increased its growth in the presence of Bacteroides ovatus HM222. Proteomic analyses indicated that B. ovatus HM222 synthesizes enzymes facilitating xylan degradation, such as β-xylanase, arabinosidase, L-arabinose isomerase, and xylosidase. Interestingly, the relative abundance of these proteins remains largely unaffected in the presence of Bifidobacterium longum PT4. In the presence of B. ovatus, B. longum PT4 increased the production of enzymes such as α-L-arabinosidase, L-arabinose isomerase, xylulose kinase, xylose isomerase, and sugar transporters. These results show an example of positive interaction between bacteria mediated by xylan consumption. Bacteroides degraded this substrate to release xylooligosaccharides, or monosaccharides (xylose, arabinose), which might support the growth of secondary degraders such as B. longum.

Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium

The human gut is home to trillions of microorganisms that influence several aspects of our health. This dense microbial community targets almost all dietary polysaccharides and releases multiple metabolites, some of which have physiological effects on the host. A healthy equilibrium between members of the gut microbiota, its microbial diversity, and their metabolites is required for intestinal health, promoting regulatory or anti-inflammatory immune responses. In contrast, the loss of this equilibrium due to antibiotics, low fiber intake, or other conditions results in alterations in gut microbiota composition, a term known as gut dysbiosis. This dysbiosis can be characterized by a reduction in health-associated microorganisms, such as butyrate-producing bacteria, enrichment of a small number of opportunistic pathogens, or a reduction in microbial diversity. Bifidobacterium species are key species in the gut microbiome, serving as primary degraders and contributing to a balanced gut environment in various ways. Colonization resistance is a fundamental property of gut microbiota for the prevention and control of infections. This community competes strongly with foreign microorganisms, such as gastrointestinal pathogens, antibiotic-resistant bacteria, or even probiotics. Resistance to colonization is based on microbial interactions such as metabolic cross-feeding, competition for nutrients, or antimicrobial-based inhibition. These interactions are mediated by metabolites and metabolic pathways, representing the inner workings of the gut microbiota, and play a protective role through colonization resistance. This review presents a rationale for how microbial interactions provide resistance to colonization and gut dysbiosis, highlighting the protective role of Bifidobacterium species.

Gut-on-a-Chip for the Analysis of Bacteria-Bacteria Interactions in Gut Microbial Community: What Would Be Needed for Bacterial Co-Culture Study to Explore the Diet-Microbiota Relationship?

Bacterial co-culture studies using synthetic gut microbiomes have reported novel research designs to understand the underlying role of bacterial interaction in the metabolism of dietary resources and community assembly of complex microflora. Since lab-on-a-chip mimicking the gut (hereafter "gut-on-a-chip") is one of the most advanced platforms for the simulative research regarding the correlation between host health and microbiota, the co-culture of the synthetic bacterial community in gut-on-a-chip is expected to reveal the diet-microbiota relationship. This critical review analyzed recent research on bacterial co-culture with perspectives on the ecological niche of commensals, probiotics, and pathogens to categorize the experimental approaches for diet-mediated management of gut health as the compositional and/or metabolic modulation of the microbiota and the control of pathogens. Meanwhile, the aim of previous research on bacterial culture in gut-on-a-chip has been mainly limited to the maintenance of the viability of host cells. Thus, the integration of study designs established for the co-culture of synthetic gut consortia with various nutritional resources into gut-on-a-chip is expected to reveal bacterial interspecies interactions related to specific dietary patterns. This critical review suggests novel research topics for co-culturing bacterial communities in gut-on-a-chip to realize an ideal experimental platform mimicking a complex intestinal environment.

Cross-Feeding and Enzymatic Catabolism for Mannan-Oligosaccharide Utilization by the Butyrate-Producing Gut Bacterium Roseburia hominis A2-183

β-Mannan is abundant in the human diet and in hemicellulose derived from softwood. Linear or galactose-substituted β-mannan-oligosaccharides (MOS/GMOSs) derived from β-mannan are considered emerging prebiotics that could stimulate health-associated gut microbiota. However, the underlying mechanisms are not yet resolved. Therefore, this study investigated the cross-feeding and metabolic interactions between Bifidobacterium adolescentis ATCC 15703, an acetate producer, and Roseburia hominis A2-183 DSMZ 16839, a butyrate producer, during utilization of MOS/GMOSs. Cocultivation studies suggest that both strains coexist due to differential MOS/GMOS utilization, along with the cross-feeding of acetate from B. adolescentis E194a to R. hominis A2-183. The data suggest that R. hominis A2-183 efficiently utilizes MOS/GMOS in mono- and cocultivation. Notably, we observed the transcriptional upregulation of certain genes within a dedicated MOS/GMOS utilization locus (RhMosUL), and an exo-oligomannosidase (RhMan113A) gene located distally in the R. hominis A2-183 genome. Significantly, biochemical analysis of β-1,4 mannan-oligosaccharide phosphorylase (RhMOP130A), α-galactosidase (RhGal36A), and exo-oligomannosidase (RhMan113A) suggested their potential synergistic role in the initial utilization of MOS/GMOSs. Thus, our results enhance the understanding of MOS/GMOS utilization by potential health-promoting human gut microbiota and highlight the role of cross-feeding and metabolic interactions between two secondary mannan degraders inhabiting the same ecological niche in the gut.