The full 17-member switchgrass-rhizosphere SynCom was introduced into Brachypodium distachyon EcoFAB 2.0 devices as a standardized inoculum, then compared with axenic, SynCom16, and plant-free medium controls across five laboratories. -
+The full 17-member inoculum was applied to 10-day-old Brachypodium distachyon plants in EcoFAB 2.0 devices and compared with axenic plants, SynCom16 lacking OAS925, and plant-free medium controls in five laboratories. Its three downstream arrows represent whole-treatment effects on root composition, bulk spent-medium profiles and plant development, not a claim that protocol standardization itself is a biological mechanism or that every member facilitates colonization.
+Participating Taxa: + Paraburkholderia sp. OAS925, + Rhodococcus sp. OAS809, + + Mycobacterium sp. OAE908, + + Methylobacterium sp. OAE515, + + Variovorax sp. OAS795, + + Rhizobium sp. OAE497, + + Bosea sp. OAE506, + + Bradyrhizobium sp. OAE829, + + Lysobacter sp. OAE881, + + Arthrobacter sp. OAP107, + + Marmoricola sp. OAE513, + + Chitinophaga sp. OAE865, + + Mucilaginibacter sp. OAE612, + + Niastella sp. OAS944, + + Gottfriedia sp. OAE603, + + Brevibacillus sp. OAP136, + + Paenibacillus sp. OAE614 + +
-Biological Processes:
-The standardized SynCom17 treatment yielded root communities that reproducibly converged on high Paraburkholderia abundance across laboratories. -
+SynCom17 inoculation supplied the 17-member community from which the OAS925-dominated root profile developed by 22 DAI. The SynCom16 omission comparison supports an inoculum-composition effect, not identification of the molecular mechanism or absolute loss of the other members.
SynCom17 was one of the ring-trial treatments that drove reproducible, treatment-dependent changes in the spent EcoFAB medium metabolome. -
+SynCom17 inoculation altered the plant-microbe system and thereby changed the measured bulk spent-medium metabolite profile relative to the control treatments. This is a treatment-level effect; microbial versus plant production, uptake and extracellular enzyme activity were not separated.
The standardized SynCom17 treatment caused reproducible B. distachyon root-development decreases across laboratories and reduced shoot biomass relative to axenic plants. -
+The SynCom17 inoculation treatment reduced shoot biomass in the combined-laboratory comparison with axenic plants and reduced root development from 14 DAI onward. The experiment establishes a whole-treatment response, not OAS925-only toxicity, competition for a specific nutrient or one necessary member.
Paraburkholderia sp. OAS925 was the only SynCom17 member whose genome carried the surveyed acid-resistance systems and a type III secretion system; fluorescence microscopy also detected early root-tip and maturation-zone colonization, biofilm formation, and active swimming near B. distachyon roots. -
- - - - -Participating Taxa: +
OAS925 carried uniquely detected surveyed acid-resistance and type III secretion modules among the 17 genomes. Separate RFP-isolate plant assays showed root colonization at 1 DAI and biofilm at 3 DAI; separate culture assays showed high liquid growth and acid-tolerant motility. OAS925 was sixth, not first, in the biofilm assay. These are one-strain observations, not facilitation of another taxon. No selective gene or trait perturbation established which mechanism causes dominance in SynCom17.
- Paraburkholderia sp. OAS925 - +Source Taxon: Paraburkholderia sp. OAS925
-Biological Processes:
-Acid-resistance genes, a unique T3SS module, biofilm formation, and rapid acidic-condition motility provided candidate mechanisms for Paraburkholderia dominance in the full SynCom17 root microbiome. -
+HYPOTHESIZED - acid-tolerant motility, colonization traits and associated genomic modules may help OAS925 establish and expand on roots, contributing to its relative dominance. Separate isolate assays and gene annotation support candidate mechanisms, but none was selectively disrupted or rescued in the 17-member community.
By 22 days after inoculation, SynCom17 root microbiomes were dominated by Paraburkholderia sp. OAS925 across all five laboratories, whereas the Paraburkholderia-free SynCom16 condition produced more variable roots enriched in Rhodococcus, Mycobacterium, and Methylobacterium. -
+At 22 DAI, OAS925 accounted for about 98% of root bacterial 16S reads in SynCom17 across the five laboratories. SynCom16 lacking OAS925 had more variable relative profiles dominated by Rhodococcus, Mycobacterium and Methylobacterium. The listed participants identify the inoculum roster, not equal final abundance or proven competition. Relative read dominance does not establish extinction, absolute suppression of the other members, or mediation of the spent-medium response.
@@ -1313,37 +1300,41 @@Biological Processes:
-The Paraburkholderia-dominated SynCom17 root community modulated the rhizosphere exometabolite profile relative to axenic and SynCom16 treatments, including decreased amino-acid relative concentrations. -
-Targeted LC-MS/MS of spent EcoFAB medium resolved treatment-dependent metabolite clusters, including diverse metabolites increased in SynCom17, an amino-acid-rich cluster with lower relative concentrations in SynCom17, and a smaller nucleoside cluster increased in SynCom16 or in both SynCom treatments. -
+Bulk spent EcoFAB medium showed treatment-dependent targeted and untargeted LC-MS profiles, including an amino-acid-rich cluster depleted under SynCom17 and other clusters elevated under SynCom17 or SynCom16. This is net extracellular abundance in a plant-microbe system, not identified donor-to-recipient cross-feeding. Plant or microbial production and uptake, and extracellular enzyme activity, remain alternative contributors; OAS925-specific amino-acid flux was not isolated.
+ + + + +Participating Taxa: + + Paraburkholderia sp. OAS925, + + Rhodococcus sp. OAS809, + + Mycobacterium sp. OAE908, + + Methylobacterium sp. OAE515, + Variovorax sp. OAS795, + Rhizobium sp. OAE497, + Bosea sp. OAE506, + + Bradyrhizobium sp. OAE829, + + Lysobacter sp. OAE881, + + Arthrobacter sp. OAP107, + + Marmoricola sp. OAE513, + + Chitinophaga sp. OAE865, + + Mucilaginibacter sp. OAE612, + + Niastella sp. OAS944, + + Gottfriedia sp. OAE603, + + Brevibacillus sp. OAP136, + + Paenibacillus sp. OAE614 + +
@@ -1417,79 +1444,64 @@Compared with axenic plants, the SynCom17 treatment significantly decreased shoot fresh weight and dry weight in the combined laboratory analysis and consistently reduced root development from 14 days after inoculation onward. -
- - - - +Compared with axenic plants, SynCom17 reduced shoot fresh and dry biomass in the combined-laboratory analysis and reduced root development from 14 DAI onward. SynCom16 had a smaller shoot effect. These are whole-treatment plant outcomes with laboratory variation, not a demonstrated microbial competition mechanism, direct OAS925-only effect or reciprocal symbiosis.
-Biological Processes:
-Participating Taxa: -
Brachypodium distachyon grown in EcoFAB 2.0 altered its root-exudate metabolite profile in response to nitrate, ammonium, ammonium nitrate, and nitrogen starvation; nitrogen deficiency reduced nitrogen-containing compounds and increased shikimate-phenylpropanoid metabolites. -
+ Niastella sp. OAS944, + Gottfriedia sp. OAE603, + Brevibacillus sp. OAP136, + Paenibacillus sp. OAE614 + -Metabolites: - shikimic acid - (CHEBI:16119), - p-coumaric acid - (CHEBI:32374) -
+Biological Processes:
+The three treatment arrows are retained, the trait-to-assembly arrow remains HYPOTHESIZED, and the assembly-to-metabolome arrow is removed because a common treatment does not isolate mediation. Single-isolate assays, relative reads and net spent-medium profiles do not resolve trait necessity or cross-feeding. The removed nitrogen-status node belongs to doi:10.1126/sciadv.adg7888, whose EcoFAB plants were sterile and whose 14 bacterial bioassays were individual cultures, not the SynCom17 trial. Protocol and non-graph role/uptake claims remain under #1427; canonical Allobosea grounding is preserved.
+ +Attaches to: ecological_interactions#SynCom17 EcoFAB Ring-Trial Perturbation, ecological_interactions#Paraburkholderia Acid-Tolerant Root Colonization Traits, ecological_interactions#Paraburkholderia-Dominated SynCom17 Root Assembly, ecological_interactions#Treatment-Structured Rhizosphere Exometabolites, ecological_interactions#SynCom17 Plant Biomass and Root Development Decrease
E. coli supplies cysteine to the auxotrophic B. bifidum, facilitating cooperative degradation of 2'-fucosyllactose, the predominant human milk oligosaccharide.
+In the nutrient-limited in vitro model, E. coli K12 supplies the cysteine requirement of an infant-stool B. bifidum isolate, enabling growth and 2-fucosyllactose degradation without added cysteine or casamino acids. The delta-cysE donor control impaired coculture growth and ethanol-killed partner controls failed to support it. This supports cysteine-dependent cooperation, not a measured cysteine export rate or proof of active secretion rather than overflow or lysis.
Source Taxon: Escherichia coli
@@ -619,8 +619,7 @@Cysteine supplied by E. coli enables B. bifidum to cooperatively degrade 2'-fucosyllactose, liberating monosaccharides that return carbon to E. coli. -
+Cysteine-dependent support from E. coli permits the auxotrophic B. bifidum partner to grow and degrade 2-fucosyllactose under the tested nutrient limitation, releasing sugar substrates usable by E. coli. The mutant and killed-partner controls support the dependency; the sugar-consumption assay separately required spent-medium pH adjustment to 6.3.
Monosaccharides liberated from cooperative 2'-fucosyllactose degradation sustain E. coli growth, completing a cooperative cross-feeding loop that may help regulate E. coli abundance in the infant gut.
+B. bifidum degraded 2-fucosyllactose and left fucose and galactose that E. coli K12 subsequently consumed, measured by chromatography. E. coli grew in this spent medium only after pH readjustment from 4.3 to 6.3. This measured in vitro return of carbon does not establish that the same exchange controls E. coli abundance in infants or quantify sugar-to-cysteine flux in coculture.
Source Taxon: Bifidobacterium bifidum
@@ -680,14 +692,7 @@Monosaccharides returned from B. bifidum sustain E. coli growth and close the cooperative loop that maintains cysteine provisioning to the auxotroph. -
-Reciprocal cysteine and monosaccharide exchange completes the cooperative HMO-fed loop between E. coli and B. bifidum. -
+PARTIAL - accessible HMO-derived sugars sustain E. coli growth and can maintain the donor population supporting the cysteine-dependent partner. Reciprocal nutrient dependence is experimentally supported, but a time-resolved sugar-to-cysteine feedback gain or isotope-resolved flux was not measured; the separate spent-medium assay required pH 6.3.
E. coli cysteine provision to B. bifidum and B. bifidum monosaccharide liberation from 2'-fucosyllactose form a reciprocal, cooperative cross-feeding loop that sustains both partners in the infant-gut two-member model. -
+E. coli K12 and the infant-stool B. bifidum isolate co-grew in modified M9 with 0.5% 2-fucosyllactose and without added cysteine or casamino acids. Cysteine dependence, viable-partner controls and measured sugar utilization support reciprocal benefit in this restricted laboratory model. This node summarizes that exchange rather than adding a separate downstream outcome. Its prevalence, strength and effect on E. coli abundance in living infants remain untested.
@@ -793,6 +823,25 @@The K12 donor and infant B. bifidum isolate support nutrient-limited reciprocal cooperation, not a universal species-level interaction or demonstrated regulation of E. coli abundance in vivo. Chromatographic sugar data and a delta-cysE control do not resolve cysteine release route, export rate or isotope-resolved feedback. The pH-adjusted spent-medium assay is distinct from the live coculture. The sugar-to-mutualism summary arrow is removed as a part/whole restatement, not an independently supported causal consequence. Experimental-strain and 0.1% screening versus 0.5% coculture metadata remain under #1428.
+ +Attaches to: ecological_interactions#Cysteine provision enabling cooperative 2'-fucosyllactose degradation, ecological_interactions#Monosaccharide return sustaining E. coli growth, ecological_interactions#Cooperative Infant-Gut HMO Mutualism
GL10 and XL12 partition mixed glucose and xylose utilization as two E. coli metabolic specialists, enabling simultaneous hexose and pentose consumption and D-lactate accumulation in the synthetic consortium.
+GL10 and XL12 show partial, overlapping carbon-source specialization in the tested mixed-glucose/xylose fermentation. GL10 retains xylose metabolism in single-sugar medium, while XL12 still consumes glucose; these are not exclusive substrate users. The 1:1 consortium produced 3.76 g/L D-lactate at 36 h under the baseline conditions. NICHE_PARTITIONING denotes this engineered division of labor, not strain-resolved coculture flux, direct interstrain cross-feeding, partner-dependent growth or universal superiority across shaking speeds and inoculum ratios.
@@ -636,7 +636,7 @@The two preferred strain labels must remain distinct despite shared NCBITaxon:562. Individual-strain phenotypes and consortium-level HPLC do not resolve each strain's flux during coculture or establish an exchanged metabolite. Keep the existing direct-cross-feeding gap and zero arrows; do not restore the dangling endpoint arrows removed under #826. The abstract and 36 h xylose quantities require reconciliation against unread original supplementary data under #1429, without merging supplement text back into the article cache (#827).
+ +Attaches to: ecological_interactions#GL10-XL12 glucose-xylose niche partitioning