The team built a synthetic gut community of 21 human commensal isolates spanning the four major phyla of the human microbiota, chosen to reflect the family-level composition of a healthy gut. Into this controlled ecosystem they introduced 94 dietary components, 79 complex glycans drawn from plant, algal, animal and microbial sources, plus 15 essential vitamins, and tracked how community structure shifted using 16S rRNA amplicon sequencing. In the base medium, Bacteroidaceae species, including Bacteroides thetaiotaomicron, Bacteroides fragilis and Phocaeicola vulgatus, predominated over Segatella copri, the key representative of the Prevotellaceae. Yet adding a single glycan or vitamin was often enough to upend that hierarchy. Strikingly, 56 of the 94 compounds, most of them of plant, algal or bacterial origin, significantly expanded S. copri, and for most of these the expansion came directly at the expense of the Bacteroidaceae. Vitamins B3 and B5 also tipped the balance toward Segatella, hinting that micronutrients, not just macronutrients, can reshape microbial power dynamics.

A central technical lesson of the study is that monoculture growth on a substrate does not predict community behavior. When each of the 21 isolates was tested individually against each of the 79 glycans as a sole carbon source, more than 1,600 bacteria–glycan pairings in total, the results were counterintuitive. Bacteroides ovatus grew on the largest number of compounds, and several Bacteroidaceae matched or exceeded S. copri in their ability to exploit individual substrates. Pectic galactan, for example, supported faster growth in B. caccae and B. thetaiotaomicron than in S. copri, yet supplementing the community with it boosted Segatella. The same paradox held for arabinan, a polysaccharide abundant in plant cell walls: B. thetaiotaomicron and P. vulgatus grew on it more rapidly than S. copri in isolation, but in the community arabinan drove a roughly 35-fold increase in S. copri relative abundance, from 1.7 percent to 59.6 percent, while overall Bacteroidaceae fell more than sixfold.

Metatranscriptomics explained part of the mechanism. In the presence of arabinan, the SusC/D-like gene pairs in the S. copri arabinan-specific polysaccharide utilization locus PUL14 were upregulated as much as 16-fold, indicating that Segatella was actively metabolizing the fiber. The causal link was confirmed genetically: deleting susC1, the key arabinan uptake gene, rendered S. copri unable to expand under arabinan supplementation. But direct utilization turned out to be necessary yet not sufficient. When the researchers assembled a stripped-down community containing only S. copri and the six Bacteroidaceae, Segatella was completely crushed, outcompeted primarily by B. thetaiotaomicron and B. fragilis even on its preferred fiber. Removing either side from the full community showed that the two families occupy the same Bacteroidales niche and compete directly. Something else in the complete 21-member community was rescuing Segatella from defeat.

That rescuer turned out to be E. coli. Using an add-in strategy, the team tested whether reintroducing individual community members into the minimal two-party competition could restore Segatella’s advantage. Lachnospiraceae species, Bifidobacteria and Collinsella had no effect. The addition of E. coli alone, however, flipped the outcome entirely, handing S. copri a decisive competitive edge over the Bacteroidaceae in the presence of arabinan. Transwell co-culture assays, which allow nutrient exchange through a porous barrier while keeping cells physically separated, showed that S. copri growth was boosted when paired with E. coli under arabinan conditions, whereas Bacteroidaceae growth was never inhibited. The interaction was mutualistic in direction: E. coli itself grew better alongside the Bacteroidales, and S. copri grew better alongside E. coli, with arabinan amplifying the benefit.

The molecular details revealed a surprising twist. Metatranscriptomic analysis of E. coli inside communities with and without S. copri showed that arabinan supplementation switched E. coli’s gene expression toward the utilization of arabinose, rhamnose, galacturonate and galactose, the simple sugars released when complex arabinan is degraded, and away from maltose metabolism. This suggested classic cross-feeding, with E. coli scavenging monosaccharides shed by the polysaccharide degraders. Yet when the researchers supplemented the competitions directly with those simple sugars, S. copri expanded only when E. coli was present. Even more strikingly, a quadruple E. coli Nissle mutant engineered to be unable to metabolize arabinose, rhamnose, galactose and galacturonate still promoted S. copri just as effectively as the wild type. The presence of the sugars, rather than their consumption by E. coli, appears to be what matters, pointing to a signalling-based interaction rather than a purely nutritional one, in which polysaccharide-derived sugars act as interbacterial signals that reconfigure community dynamics.

The synergy proved remarkably broad. All eight additional plant-derived polysaccharides tested, including the starch derivatives amylose and amylopectin, promoted S. copri over Bacteroidaceae in an E. coli-dependent manner, as did vitamins B3 and B5. Multiple S. copri strains and closely related Segatella species, including S. brasiliensis, S. sinensis and S. sinica, retained the E. coli-dependent advantage, while more distantly related species such as S. brunsvicensis and S. hominis did not, mapping the interaction onto the phylogeny of the genus. On the Enterobacteriaceae side, the effect was not confined to E. coli: commensal and laboratory E. coli strains, pathogenic isolates including UTI89, and other family members such as Klebsiella oxytoca, Klebsiella pneumoniae and Salmonella enterica all boosted Segatella under arabinan conditions. The mechanism, in other words, is a conserved family-level partnership rather than a quirk of one laboratory strain.

Critically, the phenomenon survived the leap to realistic ecosystems. When S. copri and E. coli were introduced into stabilized human faecal communities derived from eight healthy donors, arabinan supplementation consistently drove a marked expansion of Segatella, recapitulating the synthetic community results. In caecal communities from specific pathogen-free mice, which naturally lack Enterobacteriaceae, the researchers could cleanly attribute the effect: S. copri expanded only when both E. coli and arabinan were supplied. Finally, the team turned to global metagenomic data from roughly 1,000 healthy adults. Non-industrialized individuals harbored not only more S. copri, as expected, but also significantly higher prevalence, diversity and abundance of Enterobacteriaceae, and S. copri abundance correlated positively with the number of Enterobacteriaceae species in these populations. An analysis of more than 3,300 food metagenomes from the curatedFoodMetagenomicData database reinforced the ecological story: plant-based foods carried the highest Enterobacteriaceae loads, and Enterobacteriaceae enriched in plant foods were also enriched in the stools of non-industrialized individuals, suggesting that diet and environmental exposure deliver both the fiber and the bacterial partners together.

The study reframes what determines the two great gut microbiota signatures. Dominance by Bacteroidaceae or Prevotellaceae is not a simple function of dietary fiber intake; it emerges from an ecosystem-level interplay in which dietary glycans and vitamins act synergistically with commensal Enterobacteriaceae to favor Segatella, through a combination of direct polysaccharide utilization, cross-feeding and sugar-dependent signalling. The findings may help explain why Prevotellaceae-dominated configurations emerge early in life in non-industrialized settings, where Enterobacteriaceae prevalence rises in step with Segatella as children reach two to three years of age. They also carry practical implications: prebiotic or vitamin interventions aimed at reshaping the microbiome may succeed or fail depending on the baseline presence of Enterobacteriaceae and the existing community composition, underscoring the case for personalized, combinatorial strategies rather than one-size-fits-all fiber supplementation. For a field long focused on pairwise battles over nutrients, the message is that the decisive alliances in the gut are often three-way, involving the food on the plate, the dominant degraders and the quiet facilitators standing between them.

Subject of Research: Diet- and Enterobacteriaceae-dependent competition between dominant Bacteroidales families in the human gut microbiome

Article Title: Synergy between Enterobacteriaceae and diet mediates competition between dominant Bacteroidales in the human gut

Article References: Tawk, C., El Mouali, Y., Huang, K. D., Valkiers, S., Heidrich, V., Gronow, A., Osbelt, L., Rapp, J., Link, H., Segata, N., Typas, A., & Strowig, T. (2026). Synergy between Enterobacteriaceae and diet mediates competition between dominant Bacteroidales in the human gut. Nature Microbiology. https://doi.org/10.1038/s41564-026-02500-6

Image Credits: AI Generated

DOI: 10.1038/s41564-026-02500-6

Keywords: gut microbiome, Segatella copri, Bacteroidaceae, Prevotellaceae, Enterobacteriaceae, dietary fiber, arabinan, cross-feeding, synthetic microbial communities, metatranscriptomics, microbial ecology, enterotypes

The study, published in Nature Microbiology, focused on a long-standing puzzle in human microbiome research. Across the globe, human gut communities fall into recognizable patterns. In industrialized populations, members of the bacterial family Bacteroidaceae tend to dominate. In many non-industrialized populations, by contrast, bacteria of the family Prevotellaceae are far more common, including the species Segatella copri, formerly known as Prevotella copri. A plant-rich diet has long been discussed as a possible explanation for these regional differences, since Prevotellaceae are often associated with the consumption of complex plant carbohydrates. But diet alone, the new work suggests, cannot account for the pattern.

“We wanted to understand which factors actually influence the competition between these bacteria in the gut,” says Dr Caroline Tawk, one of the first authors of the study and, until recently, a researcher in Strowig’s department. Supported by a joint fellowship from the HZI and EMBL, she spent several months at EMBL in Heidelberg, where she developed a highly parallelized experimental setup capable of testing a wide range of dietary components at once. This high-throughput approach allowed the team to move beyond single-species, single-substrate experiments and instead examine how nutrients play out within a realistic bacterial community.

The experimental design was deliberately rigorous. The researchers first assembled a defined community of 21 human gut bacteria, a simplified but reproducible stand-in for the far more complex ecosystem of the human intestine. Against this community, they tested 94 dietary components, with a particular focus on complex carbohydrates and vitamins, the classes of molecules most likely to shape competition among fiber-degrading microbes. The outcome was striking: more than half of the tested components promoted the growth of S. copri within the community. On the surface, this seemed to confirm the idea that plant carbohydrates directly favor Prevotellaceae over their Bacteroidaceae rivals.

A closer look at one carbohydrate, however, overturned that assumption. The team examined arabinan, a complex sugar found in plant cell walls, in particular detail. S. copri can directly utilize arabinan, but so can other members of the Bacteroidaceae. That meant a direct nutritional benefit could not explain why S. copri expanded in the community while its competitors did not. Something other than simple access to the substrate was tipping the balance, and the researchers set out to identify what it was.

The answer emerged when the team simplified the system. “When we brought S. copri and Bacteroidaceae together without the other members of the gut community, S. copri did not prevail despite the presence of arabinan,” Tawk explains. “Only when we added Escherichia coli to the mix, the competitive balance shifted in favor of S. copri.” This was a pivotal observation. E. coli, a member of the family Enterobacteriaceae, was not merely a passive bystander; its presence was required for S. copri to gain the upper hand. Other Enterobacteriaceae tested, including Klebsiella and Salmonella, also supported S. copri under certain conditions, indicating that the effect is a family-level trait rather than a quirk of a single strain.

Even more intriguing was what happened when the researchers used strains of E. coli that cannot metabolize the monosaccharides released during arabinan breakdown. These metabolically impaired strains still supported the growth of S. copri. “We therefore assume that the presence of the sugars—as signal molecules, rather than their consumption by E. coli—may be sufficient to explain the observed supportive effect,” says Dr Youssef El Mouali, the other first author of the study. The exact molecular mechanism, however, remains unknown. The finding hints at a form of cross-species communication in which sugars liberated from dietary fiber act as signals that reconfigure competitive interactions, rather than simply serving as food. Untangling that signaling pathway is now a priority for the group.

Laboratory models, however convincing, always leave open the question of whether the phenomenon operates in real people. To address this, the HZI team partnered with researchers from the University of Trento to analyze publicly available microbiome data from approximately 1,000 healthy adults. As expected, S. copri and Enterobacteriaceae were both more common and more diverse in datasets from non-industrialized populations. Crucially, within that group, a higher number of different Enterobacteriaceae species was associated with a higher proportion of S. copri. This correlation mirrors the laboratory experiments and suggests that the supportive relationship between Enterobacteriaceae and S. copri is not an artifact of defined communities in a flask, but a dynamic that also plays out in the human gut.

The broader implications reach into one of the most debated questions in microbiome science: why do interventions such as fiber supplementation or probiotics produce such variable results from person to person? The new findings offer a mechanistic explanation. A dietary component cannot be evaluated in isolation from the existing bacterial community, because its impact is mediated by the ecological web in which it lands. The same arabinan that helps S. copri flourish in one microbial context leaves it outcompeted in another. For clinicians and nutrition scientists, this means that predicting the outcome of a dietary change may require knowing not just what a person eats, but who else lives in their intestine.

“Our results show that the effect of a dietary component should not be considered in isolation from the existing bacterial community,” Strowig summarizes. “We need to clarify in further studies whether this knowledge can be used for personalized dietary or microbiome approaches.” If the underlying mechanisms can be pinned down, the ecological logic revealed by this study could inform strategies for deliberately reshaping gut communities, whether to establish bacteria associated with healthier metabolic profiles or to limit the expansion of unwanted ones. The work was supported by grants from the German Research Foundation (DFG), the RESIST Cluster of Excellence, and the program Amplifying Funds in Infection Biology. For now, the message is clear: in the gut, context is everything, and even the humblest fiber is only as influential as the microbes that surround it.

Subject of Research: How dietary fiber and Enterobacteriaceae jointly shape competition between dominant gut bacterial groups

Article Title: Dietary fiber does not act alone in the microbiome

Article References: Dietary fiber does not act alone in the microbiome. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: gut microbiome, dietary fiber, Segatella copri, Bacteroidaceae, Prevotellaceae, Enterobacteriaceae, Escherichia coli, arabinan, microbiome competition, personalized nutrition, Nature Microbiology, Helholtz Centre for Infection Research