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CommunityMech

- Showing 265 of 265 communities + Showing 295 of 295 communities
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AMD Nitrososphaerota Archaeal Community

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ANME/SRB Anaerobic Methanotrophic Syntrophic Consortia

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Marine syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) that couple the anaerobic oxidation of methane to sulfate reduction in marine sediments. Sediment-free enrichment cultures of three consortium types (ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2) exhibited high dry conductance close to that of electrogenic biofilms. Cyclic voltammetry revealed redox activity and generator-collector measurements showed electron transport over micrometer-scale distances, establishing that the symbiosis uses redox conduction (consistent with multiheme cytochrome c) for direct interspecies electron transport between the archaeal and bacterial partners.

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+ + + + + + + 6 + + STABLE +
+ SYNTROPHY +
+ + Avena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds + +

Black Soldier Fly Larvae Gut SynCom (Bacillus + Lactobacillus + Issatchenkia)

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A tripartite synthetic microbial community (SynCom) engineered from the core gut microbiota of black soldier fly larvae (BSFL) to enhance protein bioconversion from organic wastes. The SynCom combines the bacteria Bacillus and Lactobacillus with the yeast Issatchenkia and was assembled and tested in germ-free (gnotobiotic) larval hosts using multi-omics. Bacillus provides direct proteolytic activity, whereas Lactobacillus and Issatchenkia are associated with improved protein-conversion performance and amino-acid metabolic responses. The tripartite SynCom showed the highest protein conversion performance and distinct spatiotemporal distribution along the gut pH gradient, increasing final larval protein content by 63%.

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+ + + + + + + 3 + + ENGINEERED +
+ BIOTECHNOLOGY +
+ + Buchnera-Serratia Cinara cedri Endosymbiont Consortium + +

Butyrivibrio fibrisolvens + Selenomonas ruminantium + Ruminococcus albus Lignocellulolytic Rumen Consortium

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A synthetic lignocellulolytic bacterial consortium designed from six bovine rumen microbial strains to enhance lignocellulose degradation for biofuel and enzyme production. Genome-scale community metabolic models were used with flux-based parameters (pairwise metabolic assistance, PMA; growth support index, PGSI) to predict compatible, mutualistic pairs, which were validated in experimentally grown cocultures. The strongest pairwise enzymatic synergism was observed for Butyrivibrio fibrisolvens with Selenomonas ruminantium (a 41% increase in endoglucanase activity), and a three-membered community of B. fibrisolvens, S. ruminantium, and Ruminococcus albus showed synergistic activity across all lignocellulosic substrates, indicating strong metabolic interplay among compatible species.

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+ + + + + + + 3 + + ENGINEERED +
+ LIGNOCELLULOSE +
+ + Coastal Forested Wetland Seawater-Ion Microcosm Community + +

Five-member bacterial-fungal composting SynCom for lignocellulose degradation

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A rationally designed five-member bacterial-fungal synthetic microbial community (SynCom) used to bioaugment the co-composting of cattle manure and mulberry branches. Inoculation acts as an ecological engineer that elevates pile temperatures, shortens the maturation period by roughly 7 days, and enhances degradation of lignin, cellulose, and hemicellulose while boosting humus content. Metagenomics shows the SynCom restructures the native microbiome, enriching key lignocellulose-degrading functional genera such as Thermobifida and Actinomadura and increasing the abundance of carbohydrate-active enzymes (cellulases, hemicellulases, and lignin-modifying auxiliary-activity enzymes).

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+ + + + + + + 2 + + ENGINEERED +
+ LIGNOCELLULOSE +
+ + Copper Biomining Heap Leach Consortium + +

Corynebacterium glutamicum + Shewanella oneidensis Succinic-acid Co-culture

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Engineered two-member co-culture pairing the succinic-acid producer Corynebacterium glutamicum (including an ldhA-deleted, lactate-deficient strain K1) with the electroactive bacterium Shewanella oneidensis to enhance anaerobic succinic acid biosynthesis through interspecies interactions. Co-cultivation raised succinic acid yield markedly over monoculture without altering glucose consumption, and supplementation with riboflavin (the most effective of five screened redox-active additives) further improved production. Transcriptomics showed co-culture reprogrammed C. glutamicum metabolism, reinforcing its electron transport system and redistributing carbon flux toward the reductive TCA pathway.

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+ + + + + + + 2 + + ENGINEERED +
+ BIOTECHNOLOGY +
+ + Coscinodiscus Synthetic Community + +

Crucian Carp Gut Disease-resistance SynCom

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A simplified synthetic microbial community of three gut genera (Cetobacterium, Paraclostridium, and Pseudomonas) assembled from the intestinal microbiota of crucian carp (Carassius auratus). These genera were enriched in fish that displayed mild symptoms after Aeromonas hydrophila infection, and fecal microbiota transplantation from mild-symptom fish conferred enhanced resistance to the pathogen. The reconstituted SynCom significantly reduced A. hydrophila abundance by activating intestinal immune responses and reinforcing the gut barrier, supporting microbiome-based disease prevention in aquaculture.

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+ + + + + + + 3 + + ENGINEERED +
+ OTHER +
+ + Cyprus Copper Sulphide Bioleaching Consortium + +

DIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)

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Two simplified methanogenic consortia (DIETsimp) constructed by top-down selection from cow manure combined with paddy soil or marine sediment inocula for high-efficiency conversion of lignocellulose to methane via direct interspecies electron transfer (DIET). Metagenomic analysis identified Methanosarcina mazei, capable of accepting electrons via DIET, as the dominant archaeon, and the electroactive bacteria Sphaerochaeta globosa and Clostridium aceticum as the dominant bacteria. The proposed DIET-based methanogenic pathway has S. globosa and C. aceticum metabolizing intermediates (xylose, glucose, pyruvate, acetate) and transferring electrons to M. mazei for reduction of CO2 to methane. Both consortia shortened methanogenesis periods and increased methane production rates relative to conventional anaerobic digestion.

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+ + + + + + + 3 + + ENGINEERED +
+ LIGNOCELLULOSE +
+ + Dehalococcoides-Syntrophomonas TCE Dechlorination Coculture + +

Dehalococcoides mccartyi CWV2 Dechlorinating Consortium

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A native groundwater microbial consortium enriched in Dehalococcoides mccartyi (Dhc) strain CWV2, a strain capable of completely dechlorinating vinyl chloride (VC) to non-toxic ethene. The consortium remediates trichloroethene (TCE)-contaminated groundwater; amendment with biochar (BC600) derived from Zizania latifolia husks enhances microbial colonization and activity, accelerating TCE degradation and reducing VC accumulation. Community analysis indicates biochar promotes syntrophic hydrogen producers and electroactive bacteria that supply reducing equivalents and ensure long-term dechlorination stability.

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+ + + + + + + 1 + + STABLE +
+ BIOREMEDIATION +
+ + Drought-Induced Rhizosphere Iron-Enriched Actinobacteria Community + +

Dual Bacillus coagulans + Pseudomonas putida Lactic-acid Co-culture

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Engineered artificial microbial consortium for L-lactic acid (LA) fermentation directly from undetoxified lignocellulosic (corncob) hydrolysates. A dual Bacillus coagulans (Heyndrickxia coagulans) system pairs a phenolic acid decarboxylase (PAD)-overexpressing biodetoxifying strain, DSM1-25280, with a high-yield LA producer, CC17B-1, and reaches 124.72 g/L LA from undetoxified hydrolysate via a sequential-inoculation division of labor. Multidimensional analysis supports a niche-succession model transitioning from biodetoxification-mediated commensalism to competitive exclusion. A sugar-metabolism-deficient engineered Pseudomonas putida KT2440 ZL added as a heterologous aromatic scavenger reinforces the system, raising the LA titer to 146.00 g/L at 98.9% yield.

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+ + + + + + + 3 + + ENGINEERED +
+ LIGNOCELLULOSE +
+ + EcoFAB 2.0 Root Microbiome Ring Trial SynCom17 - -

Emiliania huxleyi-Phaeobacter inhibens Dynamic Interaction

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A defined marine algal-bacterial co-culture model between the coccolithophore Emiliania huxleyi CCMP3266 and the Roseobacter-group bacterium Phaeobacter inhibens DSM 17395. The interaction is dynamic: attached bacteria initially promote algal growth but later kill aging algal hosts. Evidence supports algal nutrient provisioning to the heterotrophic bacterium, bacterial attachment to naked algal cells, and indole-3-acetic acid production stimulated by algal-exuded tryptophan. -

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Escherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture

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Two-member infant-gut co-culture of Escherichia coli and Bifidobacterium bifidum. In healthy, term-born, breastfed infants these genera co-exist despite differing ecological strategies and share evolutionary adaptations for lactose acquisition. In vitro co-culture demonstrates a mutualistic cross-feeding interaction in which E. coli supplies cysteine to its auxotrophic partner B. bifidum, facilitating cooperative degradation of 2'-fucosyllactose (the predominant human milk oligosaccharide), and the liberated monosaccharides in turn sustain E. coli growth, potentially helping regulate E. coli abundance in the infant gut.

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Emiliania huxleyi-Phaeobacter inhibens Dynamic Interaction

 ENGINEERED
- PHYTOPLANKTON + DIET
- -

Engineered Gut Amino Acid Cross-Feeding Consortium

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A four-species engineered mammalian-gut consortium in which Escherichia coli, Salmonella enterica serovar Typhimurium, Bacteroides thetaiotaomicron, and Bacteroides fragilis were modified to create amino acid auxotrophies and amino acid overproduction. The design converts a consortium otherwise shaped by antagonistic interactions into one with engineered beneficial cross-feeding, increasing population evenness in anaerobic in vitro culture and in low-protein-diet gnotobiotic mice. -

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Electrostimulated Mixotrophic VFA-producing Enrichment Consortium

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A specialized mixotrophic microbial consortium enriched in a continuous electrostimulated bioreactor operated at a constant potential of 300 mV for CO2 conversion into volatile fatty acids. Decreasing hydraulic retention time (HRT) selected for a spatially organized community in which Enterococcus and Clostridium dominated the planktonic phase while Desulfovibrio and Enterococcus were enriched in the electrode biofilm. This syntrophic organization enhanced biomass-specific inorganic carbon removal and redirected carbon flux toward acetate, a key product of acetogenic pathways, with electrode-associated taxa contributing reducing equivalents that supported autotrophic CO2/HCO3- fixation.

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Engineered Gut Amino Acid Cross-Feeding Consortium

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Engineered Gut Amino Acid Cross-Feeding Consortium

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Episymbiotic CPR Bacteria and DPANN Archaea Groundwater Community

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A groundwater microbial community framework combining genome-resolved metagenomics from one agricultural and seven pristine groundwater sites, yielding 746 Candidate Phyla Radiation (CPR) bacterial and DPANN archaeal genomes. Pristine sites, which serve as local sources of drinking water, contained up to 31 percent CPR bacteria and 4 percent DPANN archaea. Little species-level overlap of metagenome-assembled genomes was observed across the sites, indicating that CPR and DPANN communities are differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy and genomic analysis identified CPR and DPANN lineages that reproducibly attach to host cells, with attachment apparently stimulating CPR bacterial growth. -

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Shewanella-Acetogen Electrosynthetic Consortia for CO2-to-Acetate

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Defined synthetic microbial electrosynthesis (MES) consortia constructed by pairing the model bidirectional electroactive bacterium Shewanella oneidensis MR-1 with either the electroactive acetogen Clostridium aceticum or the nonelectroactive acetogen Acetobacterium woodii, mimicking functional guilds of natural MES communities. Co-cultivation boosts CO2-to-acetate production by up to 88%. The two pairings use distinct interspecies electron transfer (IET) modes, namely direct interspecies electron transfer (DIET) via cytochrome c and riboflavin at the biofilm-electrode interface in the S. oneidensis-C. aceticum consortium, versus H2/formate-mediated IET in the planktonic phase for the S. oneidensis-A. woodii consortium. This metabolic stratification lets S. oneidensis act as an "ecosystem engineer" orchestrating electron flow across biofilm and suspension niches.

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Episymbiotic CPR Bacteria and DPANN Archaea Groundwater Community

3 - STABLE + ENGINEERED
- EXTREME_ENVIRONMENT + CARBON_SEQUESTRATION
- +

Emiliania huxleyi-Phaeobacter inhibens Dynamic Interaction

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A defined marine algal-bacterial co-culture model between the coccolithophore Emiliania huxleyi CCMP3266 and the Roseobacter-group bacterium Phaeobacter inhibens DSM 17395. The interaction is dynamic: attached bacteria initially promote algal growth but later kill aging algal hosts. Evidence supports algal nutrient provisioning to the heterotrophic bacterium, bacterial attachment to naked algal cells, and indole-3-acetic acid production stimulated by algal-exuded tryptophan. +

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+ + + + + + + 2 + + ENGINEERED +
+ PHYTOPLANKTON +
+ + + +

Engineered Gut Amino Acid Cross-Feeding Consortium

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A four-species engineered mammalian-gut consortium in which Escherichia coli, Salmonella enterica serovar Typhimurium, Bacteroides thetaiotaomicron, and Bacteroides fragilis were modified to create amino acid auxotrophies and amino acid overproduction. The design converts a consortium otherwise shaped by antagonistic interactions into one with engineered beneficial cross-feeding, increasing population evenness in anaerobic in vitro culture and in low-protein-diet gnotobiotic mice. +

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+ + + + + + + 4 + + ENGINEERED +
+ BIOTECHNOLOGY +
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Ensifer YF2 + Sphingobacterium Y2 Polyethylene-degrading Consortium

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Synthetic bacterial consortium for polyethylene (PE) biodegradation, built from three strains-Ensifer sp. YF2, Sphingobacterium sp. Y2, and Chryseobacterium sp. MF1-isolated from plastic-contaminated agricultural soils. A dual-strain consortium of YF2 and Y2 degraded PE more efficiently than individual strains or the full three-strain combination, using PE as the sole carbon source and inducing oxidative modifications and physical erosion of the polymer. Genomic analysis showed a complementary enzymatic division of labor - YF2 (oxidases LadA, AlkB, CYP450) performs backbone cleavage as the primary degrader, while Y2 (esterases and lipases) carries out intermediate metabolism through cross-feeding.

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+ BIOREMEDIATION +
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Episymbiotic CPR Bacteria and DPANN Archaea Groundwater Community

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A groundwater microbial community framework combining genome-resolved metagenomics from one agricultural and seven pristine groundwater sites, yielding 746 Candidate Phyla Radiation (CPR) bacterial and DPANN archaeal genomes. Pristine sites, which serve as local sources of drinking water, contained up to 31 percent CPR bacteria and 4 percent DPANN archaea. Little species-level overlap of metagenome-assembled genomes was observed across the sites, indicating that CPR and DPANN communities are differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy and genomic analysis identified CPR and DPANN lineages that reproducibly attach to host cells, with attachment apparently stimulating CPR bacterial growth. +

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+ + + + + + + 3 + + STABLE +
+ EXTREME_ENVIRONMENT +
+ + + Infant Gut DNA Phageome Succession Community + +

Infant-gut Prebiotic-response SynCom

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A defined synthetic microbial community (SynCom) modeling the early-life (infant) gut, studied alongside donor-derived infant faecal fermentations to dissect how prebiotic substrates reshape microbial and metabolic responses. Human milk oligosaccharides (HMOs) and galacto-oligosaccharides (GOS) robustly promote bifidobacterial expansion, while Bacteroides/Phocaeicola species are modulated in a feeding-mode- and substrate-dependent manner. The SynCom reveals extensive cross-feeding networks and substrate-dependent interaction rewiring, with Phocaeicola vulgatus acting as a context-dependent ecological hub that disproportionately shapes succinate and propionate production and alters Escherichia coli metabolic activity. Competitive outcomes are driven not only by acidification but by the chemical identity of fermentation products, with lactate exerting species-specific inhibition independent of bulk pH.

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+ + + + + + + 4 + + ENGINEERED +
+ DIET +
+ + Model Lignocellulose Formaldehyde Cross-Feeding Community + +

Multi-stage Anaerobic-Digestion SynCom-YSJ and SynCom-J

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Two function-driven synthetic microbial communities (SynComs) constructed for bioaugmentation of food-waste anaerobic digestion. SynCom-J is a methanogen-only consortium, whereas SynCom-YSJ is a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members. Both were introduced into semi-continuous reactors already harboring a metabolically complete native microbiome. The multi-stage SynCom-YSJ increased methane yield by 22% (vs 8% for SynCom-J), nearly eliminated the start-up lag phase, reduced propionate accumulation, and reshaped the digester microenvironment (elevated acetate, reduced propionate), upregulating genes for hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Individual member species are not named in the source abstract, so no NCBITaxon-grounded members are asserted here.

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+ + + + + + + 0 + + ENGINEERED +
+ METHANOGENESIS +
+ + Panzhihua Vanadium Titanium Tailings Community + +

Parachlorella kessleri + Saccharomyces cerevisiae Mutualistic Co-culture

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Two-member engineered co-culture of the green microalga Parachlorella kessleri and the yeast Saccharomyces cerevisiae, established to enhance microalgal lipid productivity. The partners form a mutualistic relationship based on reciprocal oxygen/carbon dioxide gas exchange. Under co-culture, biomass and lipid production increased 4-fold relative to microalgal monoculture. Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion and promoted lipid accumulation through nutrient competition, while microalgae are inferred to provide metabolic support to the yeast via exopolysaccharide (EPS)-derived molecules. Nanomechanical analyses (AFM, FluidFM) showed increased EPS production and stronger, longer microalga-yeast cell-cell interactions in co-culture.

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+ + + + + + + 2 + + ENGINEERED +
+ BIOTECHNOLOGY +
+ + Phormidium Alkaline Consortium + +

Phosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture

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An anoxic, methanogenic enrichment culture defining "lithosyntrophy," an obligate syntrophic interaction in which the electrons driving hydrogenotrophic methanogenesis originate from an inorganic compound. Candidatus Phosphitivorax anaerolimi Phox-21 oxidizes phosphite (oxidation state +3) to phosphate coupled to hydrogenogenesis, in an obligate energetic dependency on a hydrogenotrophic methanogen, Methanoculleus sp. Electrons derived from phosphite drive H2 production via an electron-confurcating hydrogenase; the methanogen consumes the H2 to keep the reaction thermodynamically favorable, establishing interspecies electron transfer that links the phosphorus and carbon redox cycles in anoxic ecosystems.

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+ + + + + + + 2 + + STABLE +
+ SYNTROPHY +
+ + Phylogenetically Diverse Denitrifying SynCom + +

Pinus armandii Endophytic Biocontrol SynCom

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A five-strain synthetic bacterial community (SynCom) assembled from endophytic bacteria isolated from multiple tissues of Pinus armandii to promote seedling growth and prime blister rust-associated defense responses. The optimized, functionally complementary SynCom comprises Pseudomonas koreensis RC1, Paenibacillus terrae RE7, Bacillus velezensis OB3 and NA3, and Bacillus subtilis NA11, selected for plant growth-promoting traits (nitrogen fixation, phosphate and potassium solubilization, IAA production) and antagonism of the rust pathogen. In pot experiments the SynCom increased seedling height and biomass and raised defense-related polyphenol oxidase and peroxidase activities relative to the control.

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+ + + + + + + 5 + + ENGINEERED +
+ RHIZOSPHERE +
+ + + +

Pleuromutilin-degrading Artificial Consortium (5-strain)

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A defined five-strain artificial microbial consortium constructed to degrade the antibiotic pleuromutilin, assembled from bacteria isolated out of a natural consortium (En4) that was itself developed by gradient enrichment and domestication under pleuromutilin stress. The consortium comprises Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis, and achieves a pleuromutilin degradation rate of 91.97%. In the parent natural community, pleuromutilin stress reduced microbial diversity and selected core taxa with functional specialization (notably Proteobacteria, and enriched pollutant-degrading genera such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Cupriavidus), and potential degradation products and metabolic pathways were proposed for the artificial consortium.

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+ + + + + + + 5 + + ENGINEERED +
+ BIOREMEDIATION +
+ + Pseudomonas-Rhodococcus Chloronitrobenzene Coculture + +

Pseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium

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Two-strain synthetic consortium of an engineered degrader (Pseudomonas putida strain Pp-TE) and a native degrader (Rhodococcus sp. strain RDK17) grown with terephthalic acid (TPA), a primary polyethylene terephthalate (PET) monomer, as the sole carbon and energy source. Although both strains utilize TPA at comparable rates in monoculture, Pp-TE consistently outcompetes RDK17 in batch and multitransfer coculture fermentations. Dominance is driven jointly by exploitative competition for TPA and by interference competition through the Pp-TE type VI secretion system, which impairs RDK17 growth via contact-dependent inhibition. Loss of TPA metabolism in Pp-TE abolishes its dominance, illustrating how interspecies interaction and metabolic capability co-determine consortium structure and overall TPA degradation.

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+ + + + + + + 2 + + ENGINEERED +
+ BIOREMEDIATION +
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Pseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium

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Two-member engineered bioremediation consortium in which genetically engineered Pseudomonas stutzeri (overexpressing nahAc and nahB) and a Rhodococcus strain (overexpressing nahH and catA) are co-anchored on S-N-doped biochar to mineralize naphthalene. Pseudomonas stutzeri acts as an oxidative bio-anode that initiates naphthalene degradation and releases electrons, while the conductive biochar matrix mediates direct interspecies electron transfer (DIET) and extracellular electron transfer (EET) to Rhodococcus, which serves as a reductive bio-cathode driving oxygenolytic ring-cleavage catalysis. The resulting bioelectrochemical syntrophic circuit achieved >98.3% naphthalene removal and 89.5% mineralization by circumventing diffusive bottlenecks.

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+ + + + + + + 2 + + ENGINEERED +
+ BIOREMEDIATION +
+ + Shewanella-Geobacter Three-Species Exoelectrogenic Biofilm Community + +

Shewanella oneidensis + Pseudomonas aeruginosa Fe0-dependent Electro-syntrophic Denitrifying Consortium

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Engineered two-member denitrifying consortium of the electroactive bacterium Shewanella oneidensis and the denitrifier Pseudomonas aeruginosa, operated in anaerobic conditions with metallic iron (Fe0) as the sole electron donor. S. oneidensis acts as a bio-engine, using its membrane-bound CymA-OmcA-MtrC complexes to harvest electrons from Fe0 biocorrosion and transfer them to P. aeruginosa. P. aeruginosa accepts these electrons for nitrate reduction, accomplishing microbial denitrification via a Fe0-S. oneidensis-P. aeruginosa electron-transfer system. This Fe0-dependent electro-syntrophy defines a metabolic window for denitrifier growth relevant to nitrate removal in water/wastewater treatment and the global nitrogen cycle.

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+ + + + + + + 2 + + ENGINEERED +
+ SYNTROPHY +
+ + Shewanella-Streptococcus Starch-Fueled Microbial Fuel Cell Coculture + +

Shewanella oneidensis MR-1 - Rhodopseudomonas palustris Electro-syntrophic Co-culture

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Engineered two-species electro-syntrophic co-culture of Shewanella oneidensis MR-1 (the electron-donating partner) and Rhodopseudomonas palustris (the electron-accepting partner) built to study and enhance artificial interspecies electron transfer (IET). In-situ polydopamine (PDA) nano-encapsulation of the S. oneidensis MR-1 surface created a conductive, adhesive cell-to-cell interface that promoted stable coaggregation of the two partners and shifted the dominant IET mode from H2-mediated MIET toward contact-dependent direct electron transfer involving outer-membrane c-type cytochromes. Nitrogenase-derived CH4, used as a quantitative indicator of IET efficiency, increased by roughly 380% in the engineered community.

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+ + + + + + + 2 + + ENGINEERED +
+ BIOTECHNOLOGY +
+ + SynComBac10 Chicken Intestinal SynCom + +

SynCom BsBv Cigar Tobacco Leaf Fermentation

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Two-species synthetic microbial community (the BsBv SynCom) of Bacillus safensis and Bacillus velezensis, screened for high extracellular cellulase, amylase and protease activities and applied to cigar tobacco leaves (cultivar QX204) during a 42-day fermentation. The consortium accelerated degradation of cellulose, protein, and starch, shifted the leaf bacterial community toward Firmicutes/Bacillus, and modulated the volatile flavor metabolite profile (e.g. phenylacetic acid, phytol, farnesol) to enhance honey, floral, and baked aromas while reducing irritancy, thereby directionally improving cigar tobacco leaf quality.

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+ + + + + + + 2 + + ENGINEERED +
+ BIOTECHNOLOGY +
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SynCom + Chlorella sorokiniana Biogas-slurry Coupling System

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A sequential synthetic microbial community (SynCom)-microalga coupling system engineered to treat livestock biogas slurry. An autochthonous microalga, Chlorella sorokiniana, isolated from the slurry is coupled with a SynCom pretreatment stage. The system operated stably for 60 days, achieving 94.41% nitrate-nitrogen removal, 81.84% total-phosphorus removal, and 6.31% chemical oxygen demand removal. SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana (by 27.15% and 488.10% vs the BG11 control), upregulating Rubisco and glutamine synthetase, providing a strategy for simultaneous pollutant abatement and resource recovery.

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+ + + + + + + 2 + + ENGINEERED +
+ BIOREMEDIATION +
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SynCom MetG2 Rhizobacteria Sugarcane Stress Resilience

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A rhizobacteria synthetic community (SynCom) named MetG2 inoculated onto sugarcane in a greenhouse experiment to enhance stress resilience through targeted modulation of plant-microbe interactions. Shotgun metagenome and metatranscriptome sequencing revealed temporal shifts in the rhizosphere microbial community, with up-regulation of genes for flagellar assembly, chemotaxis, quorum sensing, and biofilm formation (particularly within Proteobacteria), indicating active microbial movement toward root surfaces, alongside enrichment of genes for nutrient acquisition, hormone synthesis, siderophore production, and VOC synthesis. Sugarcane responded with up-regulation of hormone-related and nutrient-transporter genes and induction of stress-resistance genes, supporting MetG2 as a sustainable strategy to enhance crop productivity and resilience.

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+ RHIZOSPHERE +
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Pseudomonas-Rahnella native rhizosphere SynCom for Artemisia argyi phytoremediation

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A simplified, native rhizosphere synthetic microbial community (SynCom) pairing a Pseudomonas isolate with a Rahnella isolate, assembled by a top-down design from rhizobacteria isolated from cadmium (Cd)-contaminated agricultural soil to partner with the perennial medicinal plant Artemisia argyi. The Pseudomonas-Rahnella pair shows strong Cd tolerance (~2 mM), plant growth-promotion (PGP) traits, and carbon fixation capacity, and was chosen for functional complementarity with minimal antagonism. Under Cd stress the SynCom establishes stable endophytic colonization (10-15%) rather than rhizoplane colonization, improving root biomass, Cd uptake, soil organic carbon accumulation, and essential-oil precursors, thereby coupling phytoremediation, productivity, and carbon sequestration.

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+ BIOREMEDIATION +
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Sesame-flavor Baijiu Fuqu SynCom (13-genus)

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Thirteen-genus synthetic microbial community (SynCom) designed for Fuqu, the fermentation starter used in sesame flavor-type baijiu (Chinese liquor) production. Multi-omics analysis identified 13 core genera - the fungal/yeast genera Aspergillus, Pichia, Saccharomyces, Trichosporon, Candida, Torulaspora, Clavispora and Wickerhamomyces and the bacterial genera Bacillus, Lactobacillus, Leuconostoc, Pediococcus and Weissella - as the core microbiota driving flavor-compound formation. Assembled into a SynCom, these members yielded the highest flavor-compound diversity and 3-(methylthio)-1-propanal (a key sulfur-containing flavor compound) content in simulative fermentation, and outperformed commercial Fuqu at large scale. The community represents an engineered strategy to enhance sulfur-containing flavor compounds during baijiu fermentation.

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+ + + + + + + 13 + + ENGINEERED +
+ BIOTECHNOLOGY +
+ + + +

SynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture

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Two-species synthetic bacterial community (SynCom Y) of Agrobacterium deltaense LSQ16 and Bacillus velezensis WB, simplified from a larger biocontrol SynCom Q by stepwise strain omission. Co-cultivation synergistically enhances multispecies biofilm formation, extracellular polysaccharide production, and metabolic activity, improving suppression of watermelon Fusarium wilt. Genome-scale modeling predicts interspecies metabolite exchange (amino acids, purines, phosphates); exogenous L-ornithine and guanine enhance B. velezensis biofilm formation, consistent with cross-feeding-supported cooperation.

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+ + + + + + + 2 + + ENGINEERED +
+ RHIZOSPHERE +
+ + Thermacetogenium-Methanothermobacter Acetate Oxidation Coculture + +

Thermophilic Lignocellulose-degrading Composting SynCom

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A five-member thermophilic lignocellulose-degrading synthetic microbial community (SynCom) designed for manure composting, comprising the bacteria Bacillus cereus, Achromobacter sp., and Pseudomonas sp. together with the fungi Cladosporium sp. and Trichoderma harzianum. Inoculation drives a metabolic reprogramming from a biofilm-dependent defense-survival mode toward an active motility-metabolism mode (depleted lipopolysaccharide biosynthesis, enriched flagellar assembly), which restricts horizontal gene transfer opportunities. By intensifying thermophilic fermentation, lowering the carbon/nitrogen ratio, and enhancing humification, the SynCom attenuates antibiotic resistance genes and virulence factors, collapses high-risk ARG-mobilome interactomes, and achieves deep bio-sanitization by eliminating high-risk pathogens such as Pseudomonas aeruginosa.

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+ + + + + + + 5 + + ENGINEERED +
+ LIGNOCELLULOSE +
+ + AMD Acidophile Heterotroph Network
Community ID - CommunityMech:000001 + CommunityMech:000001
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Organic Carbon Scavenging and Remineralization

Biological Processes:

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Organic Matter Detoxification by Ferroplasma

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Biological Processes:

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Environmental Factors

var processes = []; - - processes.push("organic substance catabolic process"); - - processes.push("oxidation-reduction process"); - - var evidenceCount = 2; nodes.push({ diff --git a/docs/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.html b/docs/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.html new file mode 100644 index 00000000..c44b61d4 --- /dev/null +++ b/docs/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.html @@ -0,0 +1,1385 @@ + + + + + + ANME/SRB Anaerobic Methanotrophic Syntrophic Consortia - CommunityMech + + + +
+
+ ← Back to Communities +

ANME/SRB Anaerobic Methanotrophic Syntrophic Consortia

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+ Community ID + + CommunityMech:000276 + +
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+ Ecological State + + + STABLE + + +
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+ Environment + + marine sediment +
+ + ENVO:03000033 + + +
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+

Marine syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) that couple the anaerobic oxidation of methane to sulfate reduction in marine sediments. Sediment-free enrichment cultures of three consortium types (ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2) exhibited high dry conductance close to that of electrogenic biofilms. Cyclic voltammetry revealed redox activity and generator-collector measurements showed electron transport over micrometer-scale distances, establishing that the symbiosis uses redox conduction (consistent with multiheme cytochrome c) for direct interspecies electron transport between the archaeal and bacterial partners.

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Taxonomy

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TaxonOntology IDFunctional RolesAbundance
+ ANME-1 (anaerobic methanotrophic archaea, clade 1) + + + NCBITaxon:588814 + + + +
+ + SYNTROPHIC_PARTNER + + ELECTRON_DONOR + +
+ + 		N/A
+
    + +
  • + + PMID:40845095 + + - SUPPORT (IN_VITRO) + +
    "Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."
    + +
    • + +
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+ Desulfofervidus (sulfate-reducing bacterial partner of ANME-1) + + + NCBITaxon:1902583 + + + +
+ + SYNTROPHIC_PARTNER + + ELECTRON_ACCEPTOR + +
+ + 		N/A
+
    + +
  • + + PMID:40845095 + + - SUPPORT (IN_VITRO) + +
    "Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."
    + +
    • + +
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+ ANME-2a (anaerobic methanotrophic archaea, clade 2a) + + + NCBITaxon:588816 + + + +
+ + SYNTROPHIC_PARTNER + + ELECTRON_DONOR + +
+ + 		N/A
+
    + +
  • + + PMID:40845095 + + - SUPPORT (IN_VITRO) + +
    "Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."
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    • + +
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+ ANME-2c (anaerobic methanotrophic archaea, clade 2c) + + + NCBITaxon:3386252 + + + +
+ + SYNTROPHIC_PARTNER + + ELECTRON_DONOR + +
+ + 		N/A
+
    + +
  • + + PMID:40845095 + + - SUPPORT (IN_VITRO) + +
    "Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."
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    • + +
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+ Seep-SRB1 (sulfate-reducing bacterial partner of ANME-2a) + + + NCBITaxon:213119 + + + +
+ + SYNTROPHIC_PARTNER + + ELECTRON_ACCEPTOR + +
+ + 		N/A
+
    + +
  • + + PMID:40845095 + + - SUPPORT (IN_VITRO) + +
    "Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."
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+ Seep-SRB2 (additional sulfate-reducing bacterial partner) + + + NCBITaxon:213118 + + + +
+ + SYNTROPHIC_PARTNER + + ELECTRON_ACCEPTOR + +
+ + 		N/A
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    + +
  • + + PMID:40845095 + + - SUPPORT (IN_VITRO) + +
    "Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."
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Ecological Interactions

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+ + Ecological interaction network for ANME/SRB Anaerobic Methanotrophic Syntrophic Consortia + Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism). + +
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+ Taxon +
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+ Cross-feeding +
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+ Mutualism +
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+ Syntrophy +
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+ Competition +
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+ Commensalism +
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+ Niche partitioning +
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+ Colonization facilitation +
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+ Strain competition +
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+ Predation +
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ANME-1/Desulfofervidus syntrophy via direct interspecies electron transport

+ SYNTROPHY +
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Source Taxon: ANME-1

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Target Taxon: Desulfofervidus

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Evidence

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  • +
    + + PMID:40845095 + + - SUPPORT (IN_VITRO) +
    + +
    "Anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) form syntrophic partnerships in marine sediments to consume greenhouse gas methane."
    + +
    • + +
  • +
    + + PMID:40845095 + + - SUPPORT (IN_VITRO) +
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    "Collectively, our results establish that marine ANME/SRB symbiosis uses redox conduction, consistent with multiheme cytochrome c, for direct interspecies electron transport."
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ANME-2a/Seep-SRB1 syntrophy via direct interspecies electron transport

+ SYNTROPHY +
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Source Taxon: ANME-2a

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Target Taxon: Seep-SRB1

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Evidence

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  • +
    + + PMID:40845095 + + - SUPPORT (IN_VITRO) +
    + +
    "Generator-collector measurements further demonstrated that these redox components facilitate electron transport over micrometer-scale distances, sufficient to link archaeal and bacterial partners."
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ANME-2a+2c/Seep-SRB1+2 syntrophy via direct interspecies electron transport

+ SYNTROPHY +
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Source Taxon: ANME-2c

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Target Taxon: Seep-SRB2

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Evidence

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  • +
    + + PMID:40845095 + + - SUPPORT (IN_VITRO) +
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    "Diverse ANME/SRB consortia exhibited high dry conductance close to electrogenic biofilms."
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Growth Media

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+ anoxic artificial seawater medium (defined HEPES-buffered marine mineral medium) + +

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+ pH + 7.3 +
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+ Atmosphere + ANAEROBIC +
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+ Preparation notes: Per liter Milli-Q water: 5.67 g MgCl2·6H2O, 0.22 g CaCl2·2H2O, 26.37 g NaCl, 0.6 g KCl, 1.5 g Na2SO4, 0.174 g K2HPO4, 0.107 g NH4Cl, 25 mM HEPES; trace elements added, no vitamins. ANME-1/Desulfofervidus grown at 50°C, ANME-2a/Seep-SRB1 at 10°C, ANME-2a+2c/Seep-SRB1+2 at 20°C. +

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Evidence

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+ + + PMID:40845095 + + + + +

"grown at 50°C, ANME-2a partnered with Seep-SRB1 (ANME-2a/Seep-SRB1 consortia) grown at 10°C, and ANME-2a and ANME-2c partnered with Seep-SRB1 and Seep-SRB2 grown at 20°C"

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+ + + PMID:40845095 + + + + +

"the pH of the medium was adjusted to 7.3, filter sterilized through a 0.22-μm filter, and sparged anoxic using N 2 gas for at least 20 min"

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+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/ANME_SRB_Marine_Methane_Seep_Consortium.html b/docs/communities/ANME_SRB_Marine_Methane_Seep_Consortium.html index cd56beb4..3cc78f74 100644 --- a/docs/communities/ANME_SRB_Marine_Methane_Seep_Consortium.html +++ b/docs/communities/ANME_SRB_Marine_Methane_Seep_Consortium.html @@ -177,7 +177,8 @@ } .interaction-flow { - background: #fafafa; + background: var(--background); + color: var(--text); border-left: 3px solid var(--primary); padding: 1rem; margin: 1rem 0; @@ -199,7 +200,8 @@ } .evidence-item { - background: #fefce8; + background: var(--background); + color: var(--text); border-left: 3px solid #ca8a04; padding: 0.75rem; margin: 0.5rem 0; @@ -381,7 +383,7 @@

ANME-SRB Marine Methane Seep Consortium

Community ID - CommunityMech:000134 + CommunityMech:000134
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Environmental Factors

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Growth Media

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+ Anaerobic artificial seawater sediment/rock microcosm (methane seep AOM incubation) + +

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+ Temperature + variable by sample (4, 24, or 50 degrees C) °C +
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+ Atmosphere + ANAEROBIC +
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Composition

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ComponentConcentrationUnitCHEBI
methaneN/AN/A + + N/A + +
sulfateN/AN/A + + N/A + +
pyruvateN/AN/A + + N/A + +
+ + + +

+ Preparation notes: Samples were stored under an N2 atmosphere at 4°C prior to microcosm incubation. ANME-SRB consortia were incubated in (anaerobic) artificial seawater; sediment horizons received CH4 plus 250 μM L-Homopropargylglycine (HPG) at 4°C, and metabolic activity was confirmed by sulfide accumulation and BONCAT/HPG incorporation. Rock and push-core variants were incubated with CH4 (50°C), with pyruvate (24°C), or without added electron donor (24°C). Single active ANME:SRB aggregates were subsequently FACS-sorted for metagenomics. +

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Evidence

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+ + + PMID:37747940 + + + + +

"was incubated in anaerobic artificial sea water without electron donor at 24°C"

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"artificial sea water supplemented with pyruvate at 24°C"

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"250 μM L-Homopropargylglycine (HPG) at 4°C"

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"atmosphere at 4°C for sediment microcosm incubations"

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"Push-core samples of seafloor sediment were collected from different locations on the Costa Rica margin"

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