From b12eb113c11c998e122eda9f833a78263464e666 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Thu, 5 Mar 2026 07:05:41 -0800 Subject: [PATCH] Add GLBRC UFMP fermentation community (closes #17) New community YAML for the GLBRC ultra-filtered milk permeate fermentation bioreactor (PMID:37324413). 282-day continuous reactor converting dairy coproducts to renewable chemicals via carboxylate platform. 10 MAG-resolved taxa with Actinobacteriota-Firmicutes cross-feeding network (lactose -> organic acids -> medium-chain fatty acids). Co-Authored-By: Claude Opus 4.6 --- .../GLBRC_UFMP_Fermentation_Community.yaml | 438 ++++++++++++++++++ 1 file changed, 438 insertions(+) create mode 100644 kb/communities/GLBRC_UFMP_Fermentation_Community.yaml diff --git a/kb/communities/GLBRC_UFMP_Fermentation_Community.yaml b/kb/communities/GLBRC_UFMP_Fermentation_Community.yaml new file mode 100644 index 00000000..3720b11f --- /dev/null +++ b/kb/communities/GLBRC_UFMP_Fermentation_Community.yaml @@ -0,0 +1,438 @@ +name: GLBRC Ultra-Filtered Milk Permeate Fermentation Community +description: > + A fermentative microbial community maintained in a 282-day continuous bioreactor experiment + fed ultra-filtered milk permeate (UFMP), a low-value dairy coproduct. Originally inoculated + from an acid-phase digester at the Nine Springs Wastewater Treatment Plant (Madison, WI). + Metagenome-assembled genomes (MAGs) revealed functional partitioning between phyla: + Actinobacteriota members (Olsenella, Bifidobacterium, Pauljensenia) degrade lactose via the + Leloir pathway and bifid shunt, producing acetic, lactic, and succinic acids. Firmicutes + members (Clostridium, Agathobacter) perform chain elongation via reverse beta-oxidation, + converting lactic acid, ethanol, or lactose into butyric, hexanoic, and octanoic acids. + This cross-feeding between Actinobacteriota (acid producers) and Firmicutes (chain elongators) + forms the core metabolic network enabling conversion of dairy waste into renewable chemicals + via the carboxylate platform. +ecological_state: STABLE +community_origin: NATURAL +community_category: BIOTECHNOLOGY +engineering_design: + objective: > + Characterize the microbial community converting dairy coproducts (ultra-filtered milk + permeate) into renewable chemicals via carboxylate platform fermentation. + assembly_strategy: > + Inoculated from an acid-phase digester; enriched through continuous bioreactor operation + over 282 days. + perturbation_design: > + Continuous feed of UFMP at 0.5 L/day, pH 5.5, 35 degrees C, 6-day hydraulic retention time. + measurement_endpoints: + - Metagenome sequencing and MAG reconstruction + - Metabolic pathway analysis from genome annotations + - Product quantification (organic acids, medium-chain fatty acids) + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + Fermentative microbial communities have the potential to serve as biocatalysts for + the conversion of low-value dairy coproducts into renewable chemicals + explanation: Describes the engineering objective of the bioreactor community +environment_term: + preferred_term: Anaerobic bioreactor (35C, pH 5.5, 6-day retention time) + term: + id: ENVO:01001405 + label: laboratory bioreactor + notes: > + Anaerobic continuous stirred-tank reactor fed ultra-filtered milk permeate (UFMP) at + 0.5 L/day. Operated at 35 degrees C, pH controlled at 5.5, with a 6-day hydraulic + retention time. Total operation period was 282 days. +taxonomy: +- taxon_term: + preferred_term: Olsenella_B sp. (MAG ATO3) + term: + id: NCBITaxon:133926 + label: Olsenella + notes: > + Dominant Actinobacteriota member (up to 61.5% relative abundance). Degrades lactose + via the Leloir pathway, producing acetic and lactic acids. + strain_designation: + strain_name: MAG ATO3 + isolation_source: UFMP bioreactor metagenome + functional_role: + - PRIMARY_DEGRADER + abundance_level: DOMINANT + abundance_value: up to 61.5% relative abundance + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Actinobacteriota phylum are important in the degradation of lactose, + via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, + and succinic acids + explanation: Olsenella_B sp. ATO3 is the most abundant Actinobacteriota performing lactose degradation +- taxon_term: + preferred_term: Clostridium_B sp. (MAG CLOS1) + term: + id: NCBITaxon:1485 + label: Clostridium + notes: > + Dominant Firmicutes member (up to 45.6% relative abundance). Performs chain elongation + from lactic acid to butyric, hexanoic, and octanoic acids via reverse beta-oxidation. + strain_designation: + strain_name: MAG CLOS1 + isolation_source: UFMP bioreactor metagenome + functional_role: + - SECONDARY_FERMENTER + abundance_level: DOMINANT + abundance_value: up to 45.6% relative abundance + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Firmicutes phylum contribute to the chain-elongation-mediated production + of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, + ethanol, or lactic acid as the growth substrate + explanation: Clostridium_B sp. CLOS1 is the dominant chain elongator using lactic acid +- taxon_term: + preferred_term: Pauljensenia sp. (MAG ACT2) + term: + id: NCBITaxon:2767049 + label: Pauljensenia + notes: > + Actinobacteriota member (up to 29.6% relative abundance). Produces succinic acid + from lactose. + strain_designation: + strain_name: MAG ACT2 + isolation_source: UFMP bioreactor metagenome + functional_role: + - PRIMARY_DEGRADER + abundance_level: DOMINANT + abundance_value: up to 29.6% relative abundance + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Actinobacteriota phylum are important in the degradation of lactose, + via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, + and succinic acids + explanation: Pauljensenia sp. ACT2 is an Actinobacteriota member producing succinic acid +- taxon_term: + preferred_term: Agathobacter rectalis (MAG LCO1) + term: + id: NCBITaxon:1851376 + label: Agathobacter + notes: > + Firmicutes member (up to 18.7% relative abundance). Performs lactose-based chain + elongation to medium-chain fatty acids. + strain_designation: + strain_name: MAG LCO1 + isolation_source: UFMP bioreactor metagenome + functional_role: + - SECONDARY_FERMENTER + abundance_level: DOMINANT + abundance_value: up to 18.7% relative abundance + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Firmicutes phylum contribute to the chain-elongation-mediated production + of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, + ethanol, or lactic acid as the growth substrate + explanation: Agathobacter rectalis LCO1 performs lactose-based chain elongation +- taxon_term: + preferred_term: Bifidobacterium tibiigranuli (MAG BIF2) + term: + id: NCBITaxon:1678 + label: Bifidobacterium + notes: > + Actinobacteriota member (up to 17.4% relative abundance). Ferments lactose via the + bifid shunt pathway. + strain_designation: + strain_name: MAG BIF2 + isolation_source: UFMP bioreactor metagenome + functional_role: + - PRIMARY_DEGRADER + abundance_level: DOMINANT + abundance_value: up to 17.4% relative abundance + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Actinobacteriota phylum are important in the degradation of lactose, + via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, + and succinic acids + explanation: Bifidobacterium tibiigranuli BIF2 ferments lactose via the bifid shunt +- taxon_term: + preferred_term: RUG023 sp. (MAG SPH2) + term: + id: NCBITaxon:203691 + label: Spirochaetota + notes: > + Spirochaetota member (up to 16.1% relative abundance). Produces ethanol which serves + as substrate for chain elongation by Firmicutes. + strain_designation: + strain_name: MAG SPH2 + isolation_source: UFMP bioreactor metagenome + functional_role: + - CROSS_FEEDER + abundance_level: DOMINANT + abundance_value: up to 16.1% relative abundance + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Firmicutes phylum contribute to the chain-elongation-mediated production + of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, + ethanol, or lactic acid as the growth substrate + explanation: RUG023 sp. SPH2 produces ethanol used as chain elongation substrate +- taxon_term: + preferred_term: Bifidobacterium sp. (MAG BIF11) + term: + id: NCBITaxon:1678 + label: Bifidobacterium + notes: > + Second Bifidobacterium MAG (up to 15.3% relative abundance). Lactose fermentation + via bifid shunt. + strain_designation: + strain_name: MAG BIF11 + isolation_source: UFMP bioreactor metagenome + functional_role: + - PRIMARY_DEGRADER + abundance_level: DOMINANT + abundance_value: up to 15.3% relative abundance + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Actinobacteriota phylum are important in the degradation of lactose, + via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, + and succinic acids + explanation: Bifidobacterium BIF11 contributes to lactose degradation via bifid shunt +- taxon_term: + preferred_term: Olsenella_B sp900119625 (MAG ATO6) + term: + id: NCBITaxon:133926 + label: Olsenella + notes: > + Second Olsenella MAG (up to 13.9% relative abundance). Lactose degradation via + Leloir pathway. + strain_designation: + strain_name: MAG ATO6 + isolation_source: UFMP bioreactor metagenome + functional_role: + - PRIMARY_DEGRADER + abundance_level: DOMINANT + abundance_value: up to 13.9% relative abundance + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Actinobacteriota phylum are important in the degradation of lactose, + via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, + and succinic acids + explanation: Olsenella_B ATO6 contributes to lactose degradation via Leloir pathway +- taxon_term: + preferred_term: Bifidobacterium thermophilum (MAG BIF18) + term: + id: NCBITaxon:1682 + label: Bifidobacterium thermophilum + notes: > + Third Bifidobacterium MAG (up to 11.4% relative abundance). Lactose fermentation. + strain_designation: + strain_name: MAG BIF18 + isolation_source: UFMP bioreactor metagenome + functional_role: + - PRIMARY_DEGRADER + abundance_level: DOMINANT + abundance_value: up to 11.4% relative abundance + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Actinobacteriota phylum are important in the degradation of lactose, + via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, + and succinic acids + explanation: Bifidobacterium thermophilum BIF18 contributes to lactose fermentation +- taxon_term: + preferred_term: Acidaminococcus sp. (MAG ACID1) + term: + id: NCBITaxon:904 + label: Acidaminococcus + notes: > + Firmicutes member (up to 10.2% relative abundance). Possible ethanol-based chain + elongation. + strain_designation: + strain_name: MAG ACID1 + isolation_source: UFMP bioreactor metagenome + functional_role: + - SECONDARY_FERMENTER + abundance_level: DOMINANT + abundance_value: up to 10.2% relative abundance + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Firmicutes phylum contribute to the chain-elongation-mediated production + of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, + ethanol, or lactic acid as the growth substrate + explanation: Acidaminococcus sp. ACID1 may perform ethanol-based chain elongation +ecological_interactions: +- name: Lactose Degradation to Organic Acids + description: > + Actinobacteriota members (Olsenella, Bifidobacterium, Pauljensenia) degrade lactose + via the Leloir pathway and the bifid shunt, producing acetic, lactic, and succinic + acids as primary fermentation products. These short-chain acids serve as substrates + for downstream chain elongation by Firmicutes. + interaction_type: CROSS_FEEDING + metabolites: + - preferred_term: lactose + term: + id: CHEBI:17716 + label: lactose + notes: Primary substrate from ultra-filtered milk permeate + - preferred_term: acetic acid + term: + id: CHEBI:15366 + label: acetate + notes: Product of Leloir pathway and bifid shunt + - preferred_term: lactic acid + term: + id: CHEBI:422 + label: lactate + notes: Product of lactose fermentation; substrate for chain elongation + - preferred_term: succinic acid + term: + id: CHEBI:30031 + label: succinate + notes: Produced primarily by Pauljensenia sp. + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Actinobacteriota phylum are important in the degradation of lactose, + via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, + and succinic acids + explanation: Documents lactose degradation pathways of Actinobacteriota members +- name: Chain Elongation to Medium-Chain Fatty Acids + description: > + Firmicutes members (Clostridium, Agathobacter) perform reverse beta-oxidation (chain + elongation) using lactic acid, ethanol, or lactose as electron donors and carbon sources + to produce butyric (C4), hexanoic (C6), and octanoic (C8) acids. This represents + a key cross-feeding interaction where Actinobacteriota-produced lactic acid fuels + Firmicutes chain elongation. + interaction_type: CROSS_FEEDING + metabolites: + - preferred_term: lactic acid + term: + id: CHEBI:422 + label: lactate + notes: Electron donor and carbon source for chain elongation + - preferred_term: ethanol + term: + id: CHEBI:16236 + label: ethanol + notes: Alternative electron donor for chain elongation + - preferred_term: butyric acid + term: + id: CHEBI:30772 + label: butyrate + notes: C4 chain elongation product + - preferred_term: hexanoic acid + term: + id: CHEBI:30776 + label: hexanoate + notes: C6 chain elongation product + - preferred_term: octanoic acid + term: + id: CHEBI:28837 + label: octanoate + notes: C8 chain elongation product + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Firmicutes phylum contribute to the chain-elongation-mediated production + of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, + ethanol, or lactic acid as the growth substrate + explanation: Documents chain elongation by Firmicutes using multiple substrates +- name: Actinobacteriota-Firmicutes Cross-Feeding Network + description: > + The core metabolic interaction in the community is cross-feeding between Actinobacteriota + (which produce lactic acid from lactose) and Firmicutes (which consume lactic acid + for chain elongation). This syntrophic relationship enables the full conversion of + lactose into medium-chain fatty acids via a two-step metabolic cascade. + interaction_type: CROSS_FEEDING + source_taxon: + preferred_term: Olsenella (Actinobacteriota) + term: + id: NCBITaxon:133926 + label: Olsenella + notes: Representative of Actinobacteriota acid producers + target_taxon: + preferred_term: Clostridium (Firmicutes) + term: + id: NCBITaxon:1485 + label: Clostridium + notes: Representative of Firmicutes chain elongators + metabolites: + - preferred_term: lactic acid + term: + id: CHEBI:422 + label: lactate + notes: Key cross-feeding metabolite between Actinobacteriota and Firmicutes + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + members of the Actinobacteriota phylum are important in the degradation of lactose, + via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, + and succinic acids + explanation: Actinobacteriota produce lactic acid consumed by Firmicutes chain elongators +environmental_factors: +- name: Temperature + value: '35' + unit: degrees C + description: Bioreactor maintained at mesophilic temperature. +- name: pH + value: '5.5' + description: Controlled at acidic pH optimal for carboxylate platform fermentation. +- name: Hydraulic Retention Time + value: '6' + unit: days + description: 6-day retention time with 0.5 L/day feed rate. +- name: Feed Substrate + value: Ultra-filtered milk permeate (UFMP) + description: > + Low-value dairy coproduct used as primary carbon source. Contains lactose as the + main fermentable sugar. +- name: Atmosphere + value: Anaerobic + description: Anaerobic conditions maintained throughout the 282-day operation. +associated_datasets: +- name: Metagenome Sequencing + dataset_type: METAGENOME + repository: NCBI_BIOPROJECT + accession: PRJNA768492 + url: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA768492 + description: > + Shotgun metagenome sequencing data from the UFMP fermentation bioreactor used for + MAG reconstruction and metabolic pathway analysis. + evidence: + - reference: PMID:37324413 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + Fermentative microbial communities have the potential to serve as biocatalysts for + the conversion of low-value dairy coproducts into renewable chemicals + explanation: Links the metagenome dataset to the UFMP fermentation community study