Backfill related_ingredients via full-text re-fetch (Kombucha, Lotus, OMM12) (#30)

kb/communities/Kombucha_KMC_IMBG1_Fermentation_Community.yaml

@@ -234,4 +234,56 @@ related_ingredients:
     evidence_source: IN_VITRO
     snippet: cellulose-based pellicles created by the cellulose-producing bacteria
     explanation: Names cellulose as the pellicle material produced by community bacteria.
+- preferred_term: glucose
+  chebi_term:
+    id: CHEBI:17234
+    label: glucose
+  relevance: >
+    Glucose is the monosaccharide that acetobacteria polymerize into the cellulose pellicle, linking
+    the sugar substrate to the structural biofilm of the kombucha community.
+  evidence:
+  - reference: PMID:26061774
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: polymerizing glucose to cellulose
+    explanation: Names glucose as the substrate polymerized into cellulose by the acetobacteria.
+- preferred_term: acetic acid
+  chebi_term:
+    id: CHEBI:15366
+    label: acetic acid
+  relevance: >
+    Acetic acid is a fermentation product formed from carbohydrate metabolism in the kombucha and
+    associated lactobacilli, contributing to the acidic character of the beverage.
+  evidence:
+  - reference: PMID:26061774
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: cabbage carbohydrates to the lactic acid or acetic acid
+    explanation: Names acetic acid as a fermentation product of carbohydrate metabolism in the culture.
+- preferred_term: lactic acid
+  chebi_term:
+    id: CHEBI:28358
+    label: rac-lactic acid
+  relevance: >
+    Lactic acid is produced when recruited lactobacilli ferment carbohydrates in the kombucha culture,
+    contributing to the fermentative capacity of the probiotic drink.
+  evidence:
+  - reference: PMID:26061774
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: cabbage carbohydrates to the lactic acid or acetic acid
+    explanation: Names lactic acid as a fermentation product of carbohydrate metabolism in the culture.
+- preferred_term: lactose
+  chebi_term:
+    id: CHEBI:17716
+    label: lactose
+  relevance: >
+    Lactose is the dairy sugar that kombucha lacks, making the non-dairy beverage suitable for people
+    with lactose intolerance.
+  evidence:
+  - reference: PMID:26061774
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: for people with lactose intolerance
+    explanation: Names lactose in the context of kombucha as a non-dairy substitute for the intolerant.
 metal_relevance: NOT_APPLICABLE

kb/communities/Lotus_LjSC3.yaml

@@ -467,6 +467,125 @@ ecological_interactions:
     snippet: japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system
       and detected signatures of host preference among commensal bacteria in a community
       context, but not in mono-associations
+related_ingredients:
+- preferred_term: glucose
+  chebi_term:
+    id: CHEBI:17234
+    label: glucose
+  relevance: >
+    Glucose is a primary sugar in the artificial root exudate used to grow the
+    Lj-SC3 community in vitro, mimicking the carbon sources Lotus roots secrete
+    to shape rhizosphere bacterial colonization.
+  evidence:
+  - reference: PMID:34312531
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: 'Artificial root exudates (modified from ref. 45 ) were composed of 0.9 mM glucose'
+    explanation: Glucose listed as a defined component of the artificial root exudate medium.
+- preferred_term: fructose
+  chebi_term:
+    id: CHEBI:28757
+    label: fructose
+  relevance: >
+    Fructose is a root-exudate sugar supplied in the artificial exudate that supports
+    growth of the synthetic community during host-preference and colonization assays.
+  evidence:
+  - reference: PMID:34312531
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: '0.9 mM glucose, 0.9 mM fructose'
+    explanation: Fructose listed as a defined component of the artificial root exudate.
+- preferred_term: sucrose
+  chebi_term:
+    id: CHEBI:17992
+    label: sucrose
+  relevance: >
+    Sucrose is a plant-derived disaccharide included in the artificial root exudate
+    representing the photosynthate-derived carbon legume roots release to microbes.
+  evidence:
+  - reference: PMID:34312531
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: '0.9 mM fructose, 0.2 mM sucrose'
+    explanation: Sucrose listed as a defined component of the artificial root exudate.
+- preferred_term: succinic acid
+  chebi_term:
+    id: CHEBI:15741
+    label: succinic acid
+  relevance: >
+    Succinic acid is an organic acid in the artificial root exudate; such dicarboxylic
+    acids are common rhizosphere carbon sources favored by root-associated bacteria.
+  evidence:
+  - reference: PMID:34312531
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: '0.2 mM sucrose, 0.8 mM succinic acid'
+    explanation: Succinic acid listed as a defined component of the artificial root exudate.
+- preferred_term: sodium lactate
+  chebi_term:
+    id: CHEBI:75228
+    label: sodium lactate
+  relevance: >
+    Sodium lactate provides a lactate carbon source in the artificial root exudate
+    used to culture the Lj-SC3 community under defined rhizosphere-mimicking conditions.
+  evidence:
+  - reference: PMID:34312531
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: '0.8 mM succinic acid, 0.6 mM sodium lactate'
+    explanation: Sodium lactate listed as a defined component of the artificial root exudate.
+- preferred_term: citric acid
+  chebi_term:
+    id: CHEBI:30769
+    label: citric acid
+  relevance: >
+    Citric acid is a tricarboxylic acid in the artificial root exudate, mimicking
+    the organic acids legume roots exude to recruit and feed rhizosphere bacteria.
+  evidence:
+  - reference: PMID:34312531
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: '0.6 mM sodium lactate, 0.3 mM citric acid'
+    explanation: Citric acid listed as a defined component of the artificial root exudate.
+- preferred_term: serine
+  chebi_term:
+    id: CHEBI:17822
+    label: serine
+  relevance: >
+    Serine is an amino acid component of the artificial root exudate, representing
+    the nitrogen-containing exudate compounds that influence community assembly.
+  evidence:
+  - reference: PMID:34312531
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: '0.3 mM citric acid, 0.9 mM serine'
+    explanation: Serine listed as a defined amino-acid component of the artificial root exudate.
+- preferred_term: alanine
+  chebi_term:
+    id: CHEBI:16449
+    label: alanine
+  relevance: >
+    Alanine is an amino acid supplied in the artificial root exudate, contributing
+    to the nitrogen and carbon resources available to the synthetic community.
+  evidence:
+  - reference: PMID:34312531
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: '0.9 mM serine, 0.9 mM alanine'
+    explanation: Alanine listed as a defined amino-acid component of the artificial root exudate.
+- preferred_term: glutamic acid
+  chebi_term:
+    id: CHEBI:18237
+    label: glutamic acid
+  relevance: >
+    Glutamic acid is an amino acid in the artificial root exudate, among the exuded
+    compounds that root-associated bacteria use during colonization assays.
+  evidence:
+  - reference: PMID:34312531
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: 0.9 mM alanine and 0.5 mM glutamic acid
+    explanation: Glutamic acid listed as a defined amino-acid component of the artificial root exudate.
 growth_media:
 - name: Tryptic Soy Agar (TSA) for bacterial isolation
   ph: '7.0'

kb/communities/OMM12_Gnotobiotic_Mouse_Gut_Community.yaml

@@ -122,6 +122,18 @@ environmental_factors:
     evidence_source: IN_VIVO
     snippet: established in several germ-free mouse facilities world-wide
     explanation: Supports facility-to-facility use of OMM12.
+related_ingredients:
+- preferred_term: complex carbohydrates
+  relevance: >
+    The OMM12 member Muribaculum intestinale YL27 is predicted from its genome to degrade complex
+    carbohydrates, identifying dietary/host-derived polysaccharides as substrates utilized within the
+    community.
+  evidence:
+  - reference: PMID:31998276
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: genome-based prediction indicates the potential to degrade complex carbohydrates
+    explanation: Names complex carbohydrates as substrates degraded by OMM12 member M. intestinale YL27.
 associated_datasets:
 - name: Oligo-MM12 whole-genome sequence resource
   dataset_type: GENOME

references_cache/PMID_29051233.md

@@ -12,3 +12,8 @@ Quoted snippets used in curated records:
 
 URL: https://pubmed.ncbi.nlm.nih.gov/29051233/
 
+
+
+Full text (re-fetched 2026-06-15 via Europe PMC fullTextXML):
+
+ Genome Announc Genome Announc 1979 genann GA Genome Announcements 2169-8287 American Society for Microbiology (ASM) PMC5646386 PMC5646386.1 5646386 5646386 29051233 10.1128/genomeA.00758-17 genomeA00758-17 1 Prokaryotes High-Quality Whole-Genome Sequences of the Oligo-Mouse-Microbiota Bacterial Community Genome Announcement Garzetti et al. Garzetti Debora a b Brugiroux Sandrine a Bunk Boyke c Pukall Rüdiger c McCoy Kathy D. d Macpherson Andrew J. d Stecher Bärbel a b a Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, Munich, Germany b German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany c Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany d Maurice Müller Laboratories, Department of Clinical Research (DKF), UVCM, University Hospital, Bern, Switzerland Address correspondence to Debora Garzetti, garzetti@mvp.uni-muenchen.de . 19 10 2017 10 2017 5 42 300104 e00758-17 20 6 2017 11 8 2017 19 10 2017 24 10 2017 24 10 2017 Copyright © 2017 Garzetti et al. 2017 Garzetti et al. https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license . ABSTRACT The Oligo-Mouse-Microbiota (Oligo-MM 12 ) is a community of 12 mouse intestinal bacteria to be used for microbiome research in gnotobiotic mice. We present here the high-quality whole genome sequences of the Oligo-MM 12 strains, which were obtained by combining the accuracy of the Illumina platforms with the long reads of the PacBio technology. Deutsches Zentrum für Infektionsforschung (DZIF) https://doi.org/10.13039/100009139 Debora Garzetti Sandrine Brugiroux Bärbel Stecher pmc-status-qastatus 0 pmc-status-live yes pmc-status-embargo no pmc-status-released yes pmc-prop-open-access yes pmc-prop-olf no pmc-prop-manuscript no pmc-prop-legally-suppressed no pmc-prop-has-pdf yes pmc-prop-has-supplement no pmc-prop-pdf-only no pmc-prop-suppress-copyright no pmc-prop-is-real-version no pmc-prop-is-scanned-article no pmc-prop-preprint no pmc-prop-in-epmc yes pmc-license-ref CC BY cover-date October 2017 GENOME ANNOUNCEMENT In a recent study, we described a defined intestinal community of 12 murine strains, termed Oligo-Mouse-Microbiota (Oligo-MM 12 ), which permanently colonize gnotobiotic mice over several generations and provide colonization resistance against Salmonella enterica serovar Typhimurium ( 1 ). This bacterial consortium has been thoroughly characterized by biochemical and molecular methods, and the individual strains have been deposited at the German Culture Collection of Microorganisms and Cell Cultures (DSMZ) ( Table 1 ). The genomes of the 12 bacteria were previously sequenced and assembled via different techniques and algorithms ( 1 – 3 ). Since the Oligo-MM 12 strains are being used by an increasing number of research groups ( 1 , 3 – 5 ), the multitude of genome sequences precludes the possibility of a meaningful exchange of data within the scientific community. Thus, there is a strong need for availability and constant update of the Oligo-MM 12 reference genomes. TABLE 1 Assembly information and accession numbers of the Oligo-MM 12 genomes Oligo-MM strain Total length (bp) No. of contigs No. of genes DSM no. Accession no. [ Clostridium ] innocuum I46 4,468,984 1 4,629 26113 CP022722 Bacteroides caecimuris I48 4,800,416 19 4,225 26085 NHMU00000000 Lactobacillus reuteri I49 2,063,604 3 2,006 32035 NHMT00000000 Enterococcus faecalis KB1 3,025,555 1 2,942 32036 CP022712 Acutalibacter muris KB18 3,802,813 1 3,990 26090 CP021422 Bifidobacterium animalis subsp. animalis YL2 2,021,926 2 1,732 26074 NHMR00000000 Muribaculum intestinale YL27 3,306,969 1 2,786 28989 CP021421 Flavonifractor plautii YL31 3,813,655 5 3,924 26117 NHMQ00000000 [ Clostridium ] clostridioforme YL32 7,157,460 16 7,735 26114 NHTR00000000 Akkermansia muciniphila YL44 2,737,167 1 2,731 26127 CP021420 Turicimonas muris YL45 2,887,709 20 2,754 26109 NHMP00000000 Blautia coccoides YL58 5,128,482 1 5,230 26115 CP022713 It is well recognized that sequences from the Illumina platforms have low error rates, with systematic errors being mainly situated at the end of the reads, but are too short for an efficient complete genome assembly ( 6 ). On the contrary, the long reads generated by PacBio sequencing are less accurate and contain random errors ( 6 ). Aiming to create a set of reference genomes, in this study we present the high-quality genome sequences of the Oligo-MM 12 bacteria, which were assembled by a hybrid approach combining Illumina and PacBio sequences ( Table 1 ). As previously described ( 1 ), the complete genome sequence of Acutalibacter muris KB18 was obtained on the PacBio RSII platform and assembled using the RS_HGAP_Assembly.3 protocol (default parameters). Error correction was then performed by mapping Illumina reads onto the finished genome with the Burrows–Wheeler Alignment tool ( 7 ), with subsequent variant calling using CLC Genomics Workbench version 7.0.4. Here, Illumina MiSeq reads ( 1 ) of the remaining 11 bacterial genomes were assembled onto their respective PacBio complete genomes ( 2 ) by applying a reference-guided approach using SPAdes ( 8 ), with a minimum contig length of 500 bp. Assemblies were evaluated with QUAST (Quality Assessment Tool for genome assemblies) ( 9 ), and the final genomes were automatically annotated using RAST (Rapid Annotations using Subsystems Technology) ( 10 ). In future studies, genetic variation, genome evolution, and functional genomics, among other research applications, of the Oligo-MM 12 community can be assessed by high-quality analyses. Accession number(s). The assembled whole-genome sequences of the Oligo-MM 12 strains have been deposited in DDBJ/ENA/GenBank under the accession numbers given in Table 1 . Citation Garzetti D, Brugiroux S, Bunk B, Pukall R, McCoy KD, Macpherson AJ, Stecher B. 2017. High-quality whole-genome sequences of the Oligo-Mouse-Microbiota bacterial community. Genome Announc 5:e00758-17. https://doi.org/10.1128/genomeA.00758-17 . ACKNOWLEDGMENTS We thank Cathrin Spröer, Nicole Heyer, and Simone Severitt for sequencing of the KB18 PacBio genome. This work was supported by the German Center for Infection Research (DZIF), the Center for Gastrointestinal Microbiome Research (CEGIMIR), and the German Research Foundation (DFG). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. REFERENCES 1. Brugiroux S , Beutler M , Pfann C , Garzetti D , Ruscheweyh HJ , Ring D , Diehl M , Herp S , Lötscher Y , Hussain S , Bunk B , Pukall R , Huson DH , Münch PC , McHardy AC , McCoy KD , Macpherson AJ , Loy A , Clavel T , Berry D , Stecher B 2016 Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium . Nat Microbiol 2 : 16215 . doi: 10.1038/nmicrobiol.2016.215 . 27869789 2. Uchimura Y , Wyss M , Brugiroux S , Limenitakis JP , Stecher B , McCoy KD , Macpherson AJ 2016 Complete genome sequences of 12 species of stable defined moderately diverse mouse microbiota 2 . Genome Announc 4 ( 5 ): e00951-16 . doi: 10.1128/genomeA.00951-16 . 27634994 PMC5026434 3. Lagkouvardos I , Pukall R , Abt B , Foesel BU , Meier-Kolthoff JP , Kumar N , Bresciani A , Martínez I , Just S , Ziegler C , Brugiroux S , Garzetti D , Wenning M , Bui TP , Wang J , Hugenholtz F , Plugge CM , Peterson DA , Hornef MW , Baines JF , Smidt H , Walter J , Kristiansen K , Nielsen HB , Haller D , Overmann J , Stecher B , Clavel T 2016 The Mouse intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota . Nat Microbiol 1 : 16131 . doi: 10.1038/nmicrobiol.2016.131 . 27670113 4. Studer N , Desharnais L , Beutler M , Brugiroux S , Terrazos MA , Menin L , Schürch CM , McCoy KD , Kuehne SA , Minton NP , Stecher B , Bernier-Latmani R , Hapfelmeier S 2016 Functional intestinal bile acid 7α-dehydroxylation by Clostridium scindens associated with protection from Clostridium difficile infection in a gnotobiotic mouse model . Front Cell Infect Microbiol 6 : 191 . doi: 10.3389/fcimb.2016.00191 . 28066726 PMC5168579 5. Li H , Limenitakis JP , Fuhrer T , Geuking MB , Lawson MA , Wyss M , Brugiroux S , Keller I , Macpherson JA , Rupp S , Stolp B , Stein JV , Stecher B , Sauer U , McCoy KD , Macpherson AJ 2015 The outer mucus layer hosts a distinct intestinal microbial niche . Nat Commun 6 : 8292 . doi: 10.1038/ncomms9292 . 26392213 PMC4595636 6. Loman NJ , Pallen MJ 2015 Twenty years of bacterial genome sequencing . Nat Rev Microbiol 13 : 787 – 794 . doi: 10.1038/nrmicro3565 . 26548914 7. Li H , Durbin R 2009 Fast and accurate short read alignment with Burrows-Wheeler transform . Bioinformatics 25 : 1754 – 1760 . doi: 10.1093/bioinformatics/btp324 . 19451168 PMC2705234 8. Bankevich A , Nurk S , Antipov D , Gurevich AA , Dvorkin M , Kulikov AS , Lesin VM , Nikolenko SI , Pham S , Prjibelski AD , Pyshkin AV , Sirotkin AV , Vyahhi N , Tesler G , Alekseyev MA , Pevzner PA 2012 SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing . J Comput Biol 19 : 455 – 477 . doi: 10.1089/cmb.2012.0021 . 22506599 PMC3342519 9. Gurevich A , Saveliev V , Vyahhi N , Tesler G 2013 QUAST: quality assessment tool for genome assemblies . Bioinformatics 29 : 1072 – 1075 . doi: 10.1093/bioinformatics/btt086 . 23422339 PMC3624806 10. Aziz RK , Bartels D , Best AA , DeJongh M , Disz T , Edwards RA , Formsma K , Gerdes S , Glass EM , Kubal M , Meyer F , Olsen GJ , Olson R , Osterman AL , Overbeek RA , McNeil LK , Paarmann D , Paczian T , Parrello B , Pusch GD , Reich C , Stevens R , Vassieva O , Vonstein V , Wilke A , Zagnitko O 2008 The RAST server: rapid annotations using subsystems technology . BMC Genomics 9 : 75 . doi: 10.1186/1471-2164-9-75 . 18261238 PMC2265698