Cross-feeding Interactions Research Articles

Lactulose Crystals Beneficially Affect Community Composition Along Entire Human Colon in Vitro, Resulting in Donor-Dependent Prebiotic Effects at Metabolic Level

A validated <i>in vitro</i> gut model (i.e. SHIME®) was used to assess the effect of repeated daily administration of lactulose on microbial metabolic activity and community composition in different colonic areas, with the focus on inter-individual differences among three human subjects. An initial rise in acetate and lactate levels was observed in the proximal colon after lactulose administration, which could be linked to an overall strong bifidogenic effect as well as higher Lactobacilli levels in donors 2 and 3. Particularly two operational taxonomic units (OTUs) related to <i>Bifidobacterium adolescentis</i> and <i>Bifidobacterium longum</i> increased with lactulose addition. The enhanced acetate and lactate production subsequently stimulated microbial species involved in cross-feeding interactions, resulting in the donor-dependent production of propionate and/or butyrate. Additionally, a reduction in markers of proteolytic fermentation was detected upon lactulose supplementation. A wide spectrum of propionate- and especially butyrate-producing microbes, such as the next-generation probiotics <i>Faecalibacterium prausnitzii</i> and <i>Akkermansia muciniphila</i>, were donor-dependently enhanced in the distal colon, which is of specific interest as many colonic diseases originate in the distal part of the colon. For the first time beneficial effects of lactulose on the microbiota as well as metabolic activity could be demonstrated over the entire colon <i>in vitro</i>.

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota.

The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit invitro. Our results revealthe type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.

An Escherichia coli Nitrogen Starvation Response Is Important for Mutualistic Coexistence with Rhodopseudomonas palustris.

Microbial mutualistic cross-feeding interactions are ubiquitous and can drive important community functions. Engaging in cross-feeding undoubtedly affects the physiology and metabolism of individual species involved. However, the nature in which an individual species' physiology is influenced by cross-feeding and the importance of those physiological changes for the mutualism have received little attention. We previously developed a genetically tractable coculture to study bacterial mutualisms. The coculture consists of fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris In this coculture, E. coli anaerobically ferments sugars into excreted organic acids as a carbon source for R. palustris In return, a genetically engineered R. palustris strain constitutively converts N2 into NH4+, providing E. coli with essential nitrogen. Using transcriptome sequencing (RNA-seq) and proteomics, we identified transcript and protein levels that differ in each partner when grown in coculture versus monoculture. When in coculture with R. palustris, E. coli gene expression changes resembled a nitrogen starvation response under the control of the transcriptional regulator NtrC. By genetically disrupting E. coli NtrC, we determined that a nitrogen starvation response is important for a stable coexistence, especially at low R. palustris NH4+ excretion levels. Destabilization of the nitrogen starvation regulatory network resulted in variable growth trends and, in some cases, extinction. Our results highlight that alternative physiological states can be important for survival within cooperative cross-feeding relationships.IMPORTANCE Mutualistic cross-feeding between microbes within multispecies communities is widespread. Studying how mutualistic interactions influence the physiology of each species involved is important for understanding how mutualisms function and persist in both natural and applied settings. Using a bacterial mutualism consisting of Rhodopseudomonas palustris and Escherichia coli growing cooperatively through bidirectional nutrient exchange, we determined that an E. coli nitrogen starvation response is important for maintaining a stable coexistence. The lack of an E. coli nitrogen starvation response ultimately destabilized the mutualism and, in some cases, led to community collapse after serial transfers. Our findings thus inform on the potential necessity of an alternative physiological state for mutualistic coexistence with another species compared to the physiology of species grown in isolation.

Broad Prebiotic Potential of Non-starch Polysaccharides from Oats (Avena sativa L.): an in vitro Study.

Prebiotics inducing the growth or activity of beneficial intestinal bacteria – probiotics producing short-chain fatty acids (SCFA) have lately received wide recognition for their beneficial influence on host intestinal microbiota and metabolic health. Some non-starch polysaccharides (NSP) are defined as prebiotics and oats being one of richest sources of NSP in grains are considered as potentially having prebiotic effect. However, information on fermentation of specific NSP of oats is limited. Moreover, bacterial cross-feeding interactions in which fermentation of prebiotics is involved is poorly characterized. Here, we report the exploration of new candidates for the syntrophic bacterial interactions and fermentability of oat non-starch polysaccharides (NSP). The results obtained by differentiating composition, viscosity and concentration of oats NSP in fermentation medium showed that Bacillus licheniformis pre-digests oat NSP, degrades high viscosity of oat β-glucan and makes hemicellulose easier to access for other bacteria. Because of fermentation, B. licheniformis produces lactic and succinic acids, which further can be used by other bacteria for cross-feeding and SCFA production.

Ecology and evolution of metabolic cross-feeding interactions in bacteria.

Literature covered: early 2000s to late 2017Bacteria frequently exchange metabolites with other micro- and macro-organisms. In these often obligate cross-feeding interactions, primary metabolites such as vitamins, amino acids, nucleotides, or growth factors are exchanged. The widespread distribution of this type of metabolic interactions, however, is at odds with evolutionary theory: why should an organism invest costly resources to benefit other individuals rather than using these metabolites to maximize its own fitness? Recent empirical work has shown that bacterial genotypes can significantly benefit from trading metabolites with other bacteria relative to cells not engaging in such interactions. Here, we will provide a comprehensive overview over the ecological factors and evolutionary mechanisms that have been identified to explain the evolution and maintenance of metabolic mutualisms among microorganisms. Furthermore, we will highlight general principles that underlie the adaptive evolution of interconnected microbial metabolic networks as well as the evolutionary consequences that result for cells living in such communities.

Disentangling metabolic functions of bacteria in the honey bee gut.

It is presently unclear how much individual community members contribute to the overall metabolic output of a gut microbiota. To address this question, we used the honey bee, which harbors a relatively simple and remarkably conserved gut microbiota with striking parallels to the mammalian system and importance for bee health. Using untargeted metabolomics, we profiled metabolic changes in gnotobiotic bees that were colonized with the complete microbiota reconstituted from cultured strains. We then determined the contribution of individual community members in mono-colonized bees and recapitulated our findings using in vitro cultures. Our results show that the honey bee gut microbiota utilizes a wide range of pollen-derived substrates, including flavonoids and outer pollen wall components, suggesting a key role for degradation of recalcitrant secondary plant metabolites and pollen digestion. In turn, multiple species were responsible for the accumulation of organic acids and aromatic compound degradation intermediates. Moreover, a specific gut symbiont, Bifidobacterium asteroides, stimulated the production of host hormones known to impact bee development. While we found evidence for cross-feeding interactions, approximately 80% of the identified metabolic changes were also observed in mono-colonized bees, with Lactobacilli being responsible for the largest share of the metabolic output. These results show that, despite prolonged evolutionary associations, honey bee gut bacteria can independently establish and metabolize a wide range of compounds in the gut. Our study reveals diverse bacterial functions that are likely to contribute to bee health and provide fundamental insights into how metabolic activities are partitioned within gut communities.

A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities

The ecology of microbes frequently involves the mixing of entire communities (community coalescence), for example, flooding events, host excretion, and soil tillage [1, 2], yet the consequences of this process for community structure and function are poorly understood [3-7]. Recent theory suggests that a community, due to coevolution between constituent species, may act as a partially cohesive unit [8-11], resulting in one community dominating after community coalescence. This dominant community is predicted to be the one that uses resources most efficiently when grown inisolation [11]. We experimentally tested these predictions using methanogenic communities, for which efficient resource use, quantified by methane production, requires coevolved cross-feeding interactions between species [12]. After propagation in laboratory-scale anaerobic digesters, community composition (determined from 16S rRNA sequencing) and methane production of mixtures of communities closely resembled that of the single most productive community grown in isolation. Analysis of each community's contribution toward the final mixture suggests that certain combinations of taxa within a community might be co-selected as a result of coevolved interactions. As a corollary of these findings, we also show that methane production increased with the number of inoculated communities. These findings are relevant to the understanding of the ecological dynamics of natural microbial communities, as well as demonstrating a simple method of predictably enhancing microbial community function in biotechnology, health, and agriculture [13].

The model of bacterial cross-feeding interactions in the bee gut

The model of bacterial cross-feeding interactions in the bee gut

Weight-loss interventions and gut microbiota changes in overweight and obese patients: a systematic review.

Imbalances in the gut microbiota, the bacteria that inhabit the intestines, are central to the pathogenesis of obesity. This systematic review assesses the association between the gut microbiota and weight loss in overweight/obese adults and its potential manipulation as a target for treating obesity. This review identified 43 studies using the keywords 'overweight' or 'obesity' and 'microbiota' and related terms; among these studies, 17 used dietary interventions, 11 used bariatric surgery and 15 used microbiota manipulation. The studies differed in their methodologies as well as their intervention lengths. Restrictive diets decreased the microbiota abundance, correlated with nutrient deficiency rather than weight loss and generally reduced the butyrate producers Firmicutes, Lactobacillus sp. and Bifidobacterium sp. The impact of surgical intervention depended on the given technique and showed a similar effect on butyrate producers, in addition to increasing the presence of the Proteobacteria phylum, which is related to changes in the intestinal absorptive surface, pH and digestion time. Probiotics differed in strain and duration with diverse effects on the microbiota, and they tended to reduce body fat. Prebiotics had a bifidogenic effect and increased butyrate producers, likely due to cross-feeding interactions, contributing to the gut barrier and improving metabolic outcomes. All of the interventions under consideration had impacts on the gut microbiota, although they did not always correlate with weight loss. These results show that restrictive diets and bariatric surgery reduce microbial abundance and promote changes in microbial composition that could have long-term detrimental effects on the colon. In contrast, prebiotics might restore a healthy microbiome and reduce body fat.

Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

BackgroundThe human gut contains approximately 1014 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides, producing short chain fatty acids and additional metabolites, e.g., vitamin K. Microbial diversity is important for colonic health: Changes in the composition of the microbiota have been associated with inflammatory bowel disease, diabetes, obesity and Crohn’s disease, and make the microbiota more vulnerable to infestation by harmful species, e.g., Clostridium difficile. To get a grip on the controlling factors of microbial diversity in the gut, we here propose a multi-scale, spatiotemporal dynamic flux-balance analysis model to study the emergence of metabolic diversity in a spatial gut-like, tubular environment. The model features genome-scale metabolic models (GEM) of microbial populations, resource sharing via extracellular metabolites, and spatial population dynamics and evolution.ResultsIn this model, cross-feeding interactions emerge readily, despite the species’ ability to metabolize sugars autonomously. Interestingly, the community requires cross-feeding for producing a realistic set of short-chain fatty acids from an input of glucose, If we let the composition of the microbial subpopulations change during invasion of adjacent space, a complex and stratified microbiota evolves, with subspecies specializing on cross-feeding interactions via a mechanism of compensated trait loss. The microbial diversity and stratification collapse if the flux through the gut is enhanced to mimic diarrhea.ConclusionsIn conclusion, this in silico model is a helpful tool in systems biology to predict and explain the controlling factors of microbial diversity in the gut. It can be extended to include, e.g., complex nutrient sources, and host-microbiota interactions via the intestinal wall.

Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification

Metabolic cross-feeding interactions between microbial strains are common in nature, and emerge during evolution experiments in the laboratory, even in homogeneous environments providing a single carbon source. In sympatry, when the environment is well-mixed, the reasons why emerging cross-feeding interactions may sometimes become stable and lead to monophyletic genotypic clusters occupying specific niches, named ecotypes, remain unclear. As an alternative to evolution experiments in the laboratory, we developed Evo2Sim, a multi-scale model of in silico experimental evolution, equipped with the whole tool case of experimental setups, competition assays, phylogenetic analysis, and, most importantly, allowing for evolvable ecological interactions. Digital organisms with an evolvable genome structure encoding an evolvable metabolic network evolved for tens of thousands of generations in environments mimicking the dynamics of real controlled environments, including chemostat or batch culture providing a single limiting resource. We show here that the evolution of stable cross-feeding interactions requires seasonal batch conditions. In this case, adaptive diversification events result in two stably co-existing ecotypes, with one feeding on the primary resource and the other on by-products. We show that the regularity of serial transfers is essential for the maintenance of the polymorphism, as it allows for at least two stable seasons and thus two temporal niches. A first season is externally generated by the transfer into fresh medium, while a second one is internally generated by niche construction as the provided nutrient is replaced by secreted by-products derived from bacterial growth. In chemostat conditions, even if cross-feeding interactions emerge, they are not stable on the long-term because fitter mutants eventually invade the whole population. We also show that the long-term evolution of the two stable ecotypes leads to character displacement, at the level of the metabolic network but also of the genome structure. This difference of genome structure between both ecotypes impacts the stability of the cross-feeding interaction, when the population is propagated in chemostat conditions. This study shows the crucial role played by seasonality in temporal niche partitioning and in promoting cross-feeding subgroups into stable ecotypes, a premise to sympatric speciation.

Stability of Cross-Feeding Polymorphisms in Microbial Communities

Cross-feeding, a relationship wherein one organism consumes metabolites excreted by another, is a ubiquitous feature of natural and clinically-relevant microbial communities and could be a key factor promoting diversity in extreme and/or nutrient-poor environments. However, it remains unclear how readily cross-feeding interactions form, and therefore our ability to predict their emergence is limited. In this paper we developed a mathematical model parameterized using data from the biochemistry and ecology of an E. coli cross-feeding laboratory system. The model accurately captures short-term dynamics of the two competitors that have been observed empirically and we use it to systematically explore the stability of cross-feeding interactions for a range of environmental conditions. We find that our simple system can display complex dynamics including multi-stable behavior separated by a critical point. Therefore whether cross-feeding interactions form depends on the complex interplay between density and frequency of the competitors as well as on the concentration of resources in the environment. Moreover, we find that subtly different environmental conditions can lead to dramatically different results regarding the establishment of cross-feeding, which could explain the apparently unpredictable between-population differences in experimental outcomes. We argue that mathematical models are essential tools for disentangling the complexities of cross-feeding interactions.

Lactate- and acetate-based cross-feeding interactions between selected strains of lactobacilli, bifidobacteria and colon bacteria in the presence of inulin-type fructans

Cross-feeding interactions were studied between selected strains of lactobacilli and/or bifidobacteria and butyrate-producing colon bacteria that consume lactate but are not able to degrade inulin-type fructans (ITF) in a medium for colon bacteria (supplemented with ITF as energy source and acetate when necessary). Degradation of oligofructose by Lactobacillus acidophilus IBB 801 and inulin by Lactobacillus paracasei 8700:2 and Bifidobacterium longum LMG 11047 resulted in the release of free fructose into the medium and the production of mainly lactate (lactobacilli) and acetate (B. longum LMG 11047). During bicultures of Lb. acidophilus IBB 801 and Anaerostipes caccae DSM 14662T on oligofructose, the latter strain converted lactate (produced by the former strain from oligofructose) into butyrate and gases, but only in the presence of acetate. During bicultures of Lb. paracasei 8700:2 and A. caccae DSM 14662T or Eubacterium hallii DSM 17630 on inulin, the butyrate-producing strains consumed low concentrations of lactate and acetate generated by inulin degradation by the Lactobacillus strain. As more acetate was produced during tricultures of Lb. paracasei 8700:2 and B. longum LMG 11047, which degraded inulin simultaneously, and A. caccae DSM 14662T or E. hallii DSM 17630, a complete conversion of lactate into butyrate and gases by these butyrate-producing strains occurred. Therefore, butyrate production by lactate-consuming, butyrate-producing colon bacterial strains incapable of ITF degradation, resulted from cross-feeding of monosaccharides and lactate by an ITF-degrading Lactobacillus strain and acetate produced by a Bifidobacterium strain.

Estimating the probability of coexistence in cross-feeding communities

The dynamics of many microbial ecosystems are driven by cross-feeding interactions, in which metabolites excreted by some species are metabolised further by others. The population dynamics of such ecosystems are governed by frequency-dependent selection, which allows for stable coexistence of two or more species. We have analysed a model of cross-feeding based on the replicator equation, with the aim of establishing criteria for coexistence in ecosystems containing three species, given the information of the three species’ ability to coexist in their three separate pairs, i.e. the long term dynamics in the three two-species component systems. The triple-system is studied statistically and the probability of coexistence in the species triplet is computed for two models of species interactions. The interaction parameters are modelled either as stochastically independent or organised in a hierarchy where any derived metabolite carries less energy than previous nutrients in the metabolic chain. We differentiate between different modes of coexistence with respect to the pair-wise dynamics of the species, and find that the probability of coexistence is close to 12 for triplet systems with three pair-wise coexistent pairs and for the so-called intransitive systems. Systems with two and one pair-wise coexistent pairs are more likely to exist for random interaction parameters, but are on the other hand much less likely to exhibit triplet coexistence. Hence we conclude that certain species triplets are, from a statistical point of view, rare, but if allowed to interact are likely to coexist. This knowledge might be helpful when constructing synthetic microbial communities for industrial purposes.

Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut.

With the increasing amount of evidence linking certain disorders of the human body to a disturbed gut microbiota, there is a growing interest for compounds that positively influence its composition and activity through diet. Besides the consumption of probiotics to stimulate favorable bacterial communities in the human gastrointestinal tract, prebiotics such as inulin-type fructans (ITF) and arabinoxylan-oligosaccharides (AXOS) can be consumed to increase the number of bifidobacteria in the colon. Several functions have been attributed to bifidobacteria, encompassing degradation of non-digestible carbohydrates, protection against pathogens, production of vitamin B, antioxidants, and conjugated linoleic acids, and stimulation of the immune system. During life, the numbers of bifidobacteria decrease from up to 90% of the total colon microbiota in vaginally delivered breast-fed infants to <5% in the colon of adults and they decrease even more in that of elderly as well as in patients with certain disorders such as antibiotic-associated diarrhea, inflammatory bowel disease, irritable bowel syndrome, obesity, allergies, and regressive autism. It has been suggested that the bifidogenic effects of ITF and AXOS are the result of strain-specific yet complementary carbohydrate degradation mechanisms within cooperating bifidobacterial consortia. Except for a bifidogenic effect, ITF and AXOS also have shown to cause a butyrogenic effect in the human colon, i.e., an enhancement of colon butyrate production. Butyrate is an essential metabolite in the human colon, as it is the preferred energy source for the colon epithelial cells, contributes to the maintenance of the gut barrier functions, and has immunomodulatory and anti-inflammatory properties. It has been shown that the butyrogenic effects of ITF and AXOS are the result of cross-feeding interactions between bifidobacteria and butyrate-producing colon bacteria, such as Faecalibacterium prausnitzii (clostridial cluster IV) and Anaerostipes, Eubacterium, and Roseburia species (clostridial cluster XIVa). These kinds of interactions possibly favor the co-existence of bifidobacterial strains with other bifidobacteria and with butyrate-producing colon bacteria in the human colon.

Bifidobacterial inulin-type fructan degradation capacity determines cross-feeding interactions between bifidobacteria and Faecalibacterium prausnitzii

Prebiotic inulin-type fructans (ITF) display a bifidogenic and butyrogenic effect. Four bifidobacterial strains (Bifidobacterium breve Yakult, Bifidobacterium adolescentis LMG 10734, Bifidobacterium angulatum LMG 11039T, and Bifidobacterium longum subsp. longum LMG 11047), displaying different ITF degradation capacities, were each grown in cocultivation with Faecalibacterium prausnitzii DSM 17677T, an ITF-degrading butyrate-producing colon bacterium, as to unravel their cross-feeding interactions. These coculture fermentations were performed in a medium for colon bacteria, whether or not including acetate (necessary for the growth of F. prausnitzii DSM 17677T and whether or not provided through cross-feeding), supplemented with oligofructose or inulin as the sole energy source. Bifidobacterium breve Yakult did not degrade oligofructose, resulting in the production of high concentrations of butyrate by F. prausnitzii DSM 17677T through oligofructose degradation. The degradation of oligofructose by B. adolescentis LMG 10734 and of oligofructose and inulin by B. angulatum LMG 11039T and B. longum LMG 11047 resulted in the production of acetate, which was cross-fed to F. prausnitzii DSM 17677T, enabling the latter strain to degrade oligofructose and inulin. Slow preferential degradation of the short chain length fractions of oligofructose (intracellularly) by B. adolescentis LMG 10734 enabled substantial oligofructose degradation by F. prausnitzii DSM 17677T. However, fast non-preferential degradation of all chain length fractions of oligofructose (extracellularly) and efficient degradation of the short chain length fractions of inulin by B. angulatum LMG 11039T and B. longum LMG 11047 made it impossible for F. prausnitzii DSM 17677T to compete for the available substrate. These results indicate that cross-feeding interactions between bifidobacteria and acetate-depending, butyrate-producing colon bacteria can be either a pure commensal or beneficial relationship between these bacteria, or can be dominated by competition, depending on the ITF degradation capacities of the bifidobacterial strains involved.

Microbiology: A division of labour combined.

The discovery of microorganisms that can oxidize ammonia all the way to nitrate refutes the century-old paradigm that this nitrification process requires the activity of two types of microbe. See Article p.504 & Letter p.555 Two groups this week report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as 'comammox' (for complete ammonia oxidation). Until now, this two-step reaction was thought to involve two organisms in a cross-feeding interaction. Phylogenetic analyses suggest that comammox Nitrospira are present in a number of diverse environments, so these findings have the potential to fundamentally change our view of the nitrogen cycle and open a new frontier in nitrification research.

Privatization of cooperative benefits stabilizes mutualistic cross-feeding interactions in spatially structured environments.

Metabolic cross-feeding interactions are ubiquitous in natural microbial communities. However, it remains generally unclear whether the production and exchange of metabolites incurs fitness costs to the producing cells and if so, which ecological mechanisms can facilitate a cooperative exchange of metabolites among unrelated individuals. We hypothesized that positive assortment within structured environments can maintain mutualistic cross-feeding. To test this, we engineered Acinetobacter baylyi and Escherichia coli to reciprocally exchange essential amino acids. Interspecific coculture experiments confirmed that non-cooperating types were selectively favoured in spatially unstructured (liquid culture), yet disfavoured in spatially structured environments (agar plates). Both an individual-based model and experiments with engineered genotypes indicated that a segregation of cross-feeders and non-cooperating auxotrophs stabilized cooperative cross-feeding in spatially structured environments. Chemical imaging confirmed that auxotrophs were spatially excluded from cooperative benefits. Together, these results demonstrate that cooperative cross-feeding between different bacterial species is favoured in structured environments such as bacterial biofilms, suggesting this type of interactions might be common in natural bacterial communities.

Gemeinsam stärker: metabolische Arbeitsteilung bei Bakterien

Microorganisms frequently engage in reciprocal cross-feeding interactions, in which two or more bacterial strains exchange essential metabolites. Benefits stemming from losing the biosynthetic capabilities to produce certain metabolites likely drive the emergence of these metabolic interdependencies. By using nanotubes, bacteria can effectively exchange nutrients with other cells and – in this way – divide metabolic functions within microbial communities.

Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides.

Arabinoxylan oligosaccharides (AXOS) are a promising class of prebiotics that have the potential to stimulate the growth of bifidobacteria and the production of butyrate in the human colon, known as the bifidogenic and butyrogenic effects, respectively. Although these dual effects of AXOS are considered beneficial for human health, their underlying mechanisms are still far from being understood. Therefore, this study investigated the metabolic interactions between Bifidobacterium longum subsp. longum NCC2705 (B. longum NCC2705), an acetate producer and arabinose substituent degrader of AXOS, and Eubacterium rectale ATCC 33656, an acetate-converting butyrate producer. Both strains belong to prevalent species of the human colon microbiota. The strains were grown on AXOS during mono- and coculture fermentations, and their growth, AXOS consumption, metabolite production, and expression of key genes were monitored. The results showed that the growth of both strains and gene expression in both strains were affected by cocultivation and that these effects could be linked to changes in carbohydrate consumption and concomitant metabolite production. The consumption of the arabinose substituents of AXOS by B. longum NCC2705 with the concomitant production of acetate allowed E. rectale ATCC 33656 to produce butyrate (by means of a butyryl coenzyme A [CoA]:acetate CoA-transferase), explaining the butyrogenic effect of AXOS. Eubacterium rectale ATCC 33656 released xylose from the AXOS substrate, which favored the B. longum NCC2705 production of acetate, explaining the bifidogenic effect of AXOS. Hence, those interactions represent mutual cross-feeding mechanisms that favor the coexistence of bifidobacterial strains and butyrate producers in the same ecological niche. In conclusion, this study provides new insights into the bifidogenic and butyrogenic effects of AXOS.