monarch-initiative · caufieldjh · Feb 21, 2026
diff --git a/kb/disorders/Diabetes_Mellitus.yaml b/kb/disorders/Diabetes_Mellitus.yaml
diff --git a/references_cache/DOI_10.1038_s41587-022-01628-0.md b/references_cache/DOI_10.1038_s41587-022-01628-0.md
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+---
+reference_id: "DOI:10.1038/s41587-022-01628-0"
+title: "Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine"
+authors:
+- Almut Heinken
+- Johannes Hertel
+- Geeta Acharya
+- Dmitry A. Ravcheev
+- Malgorzata Nyga
+- Onyedika Emmanuel Okpala
+- Marcus Hogan
+- Stefanía Magnúsdóttir
+- Filippo Martinelli
+- Bram Nap
+- German Preciat
+- Janaka N. Edirisinghe
+- Christopher S. Henry
+- Ronan M. T. Fleming
+- Ines Thiele
+journal: Nature Biotechnology
+year: '2023'
+doi: 10.1038/s41587-022-01628-0
+content_type: abstract_only
+---
+
+# Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
+**Authors:** Almut Heinken, Johannes Hertel, Geeta Acharya, Dmitry A. Ravcheev, Malgorzata Nyga, Onyedika Emmanuel Okpala, Marcus Hogan, Stefanía Magnúsdóttir, Filippo Martinelli, Bram Nap, German Preciat, Janaka N. Edirisinghe, Christopher S. Henry, Ronan M. T. Fleming, Ines Thiele
+**Journal:** Nature Biotechnology (2023)
+**DOI:** [10.1038/s41587-022-01628-0](https://doi.org/10.1038/s41587-022-01628-0)
+
+## Content
+
+AbstractThe human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- and molecule-resolved, scalable computational modeling. Here, we extend our previous resource of genome-scale metabolic reconstructions of human gut microorganisms with a greatly expanded version. AGORA2 (assembly of gut organisms through reconstruction and analysis, version 2) accounts for 7,302 strains, includes strain-resolved drug degradation and biotransformation capabilities for 98 drugs, and was extensively curated based on comparative genomics and literature searches. The microbial reconstructions performed very well against three independently assembled experimental datasets with an accuracy of 0.72 to 0.84, surpassing other reconstruction resources and predicted known microbial drug transformations with an accuracy of 0.81. We demonstrate that AGORA2 enables personalized, strain-resolved modeling by predicting the drug conversion potential of the gut microbiomes from 616 patients with colorectal cancer and controls, which greatly varied between individuals and correlated with age, sex, body mass index and disease stages. AGORA2 serves as a knowledge base for the human microbiome and paves the way to personalized, predictive analysis of host–microbiome metabolic interactions.
diff --git a/references_cache/DOI_10.1080_19490976.2022.2142009.md b/references_cache/DOI_10.1080_19490976.2022.2142009.md
@@ -0,0 +1,26 @@
+---
+reference_id: "DOI:10.1080/19490976.2022.2142009"
+title: Unique Pakistani gut microbiota highlights population-specific microbiota signatures of type 2 diabetes mellitus
+authors:
+- Afshan Saleem
+- Aamer Ikram
+- Evgenia Dikareva
+- Emilia Lahtinen
+- Dollwin Matharu
+- Anne-Maria Pajari
+- Willem M. de Vos
+- Fariha Hasan
+- Anne Salonen
+- Ching Jian
+journal: Gut Microbes
+year: '2022'
+doi: 10.1080/19490976.2022.2142009
+content_type: unavailable
+---
+
+# Unique Pakistani gut microbiota highlights population-specific microbiota signatures of type 2 diabetes mellitus
+**Authors:** Afshan Saleem, Aamer Ikram, Evgenia Dikareva, Emilia Lahtinen, Dollwin Matharu, Anne-Maria Pajari, Willem M. de Vos, Fariha Hasan, Anne Salonen, Ching Jian
+**Journal:** Gut Microbes (2022)
+**DOI:** [10.1080/19490976.2022.2142009](https://doi.org/10.1080/19490976.2022.2142009)
+
+## Content
diff --git a/references_cache/DOI_10.1371_journal.pone.0226372.md b/references_cache/DOI_10.1371_journal.pone.0226372.md
@@ -0,0 +1,25 @@
+---
+reference_id: "DOI:10.1371/journal.pone.0226372"
+title: Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals
+authors:
+- Aftab Ahmad
+- Wanwei Yang
+- Guofang Chen
+- Muhammad Shafiq
+- Sundus Javed
+- Syed Shujaat Ali Zaidi
+- Ramla Shahid
+- Chao Liu
+- Habib Bokhari
+journal: PLOS ONE
+year: '2019'
+doi: 10.1371/journal.pone.0226372
+content_type: unavailable
+---
+
+# Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals
+**Authors:** Aftab Ahmad, Wanwei Yang, Guofang Chen, Muhammad Shafiq, Sundus Javed, Syed Shujaat Ali Zaidi, Ramla Shahid, Chao Liu, Habib Bokhari
+**Journal:** PLOS ONE (2019)
+**DOI:** [10.1371/journal.pone.0226372](https://doi.org/10.1371/journal.pone.0226372)
+
+## Content
diff --git a/references_cache/DOI_10.15252_msb.20198982.md b/references_cache/DOI_10.15252_msb.20198982.md
@@ -0,0 +1,23 @@
+---
+reference_id: "DOI:10.15252/msb.20198982"
+title: "Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome"
+authors:
+- Ines Thiele
+- Swagatika Sahoo
+- Almut Heinken
+- Johannes Hertel
+- Laurent Heirendt
+- Maike K Aurich
+- Ronan MT Fleming
+journal: Molecular Systems Biology
+year: '2020'
+doi: 10.15252/msb.20198982
+content_type: unavailable
+---
+
+# Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome
+**Authors:** Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike K Aurich, Ronan MT Fleming
+**Journal:** Molecular Systems Biology (2020)
+**DOI:** [10.15252/msb.20198982](https://doi.org/10.15252/msb.20198982)
+
+## Content
diff --git a/references_cache/GEO_GSE1124.md b/references_cache/GEO_GSE1124.md
@@ -1,5 +1,5 @@
 ---
-reference_id: GEO:GSE1124
+reference_id: "GEO:GSE1124"
 title: Whole blood transcriptome of childhood malaria
 content_type: summary
 ---

diff --git a/references_cache/GEO_GSE116306.md b/references_cache/GEO_GSE116306.md
@@ -1,5 +1,5 @@
 ---
-reference_id: GEO:GSE116306
+reference_id: "GEO:GSE116306"
 title: Blood transcriptional profiles discriminates cerebral and mild malaria patient living in Senegal
 content_type: summary
 ---

diff --git a/references_cache/GEO_GSE117613.md b/references_cache/GEO_GSE117613.md
@@ -1,5 +1,5 @@
 ---
-reference_id: GEO:GSE117613
+reference_id: "GEO:GSE117613"
 title: Whole-blood transcriptional signatures composed of erythropoietic and Nrf2-regulated genes differ between cerebral malaria and severe malarial anemia
 content_type: summary
 ---

diff --git a/references_cache/PMID_15832489.md b/references_cache/PMID_15832489.md
@@ -0,0 +1,59 @@
+---
+reference_id: "PMID:15832489"
+title: "Pathophysiology of type 2 diabetes mellitus in children and adolescents: treatment implications."
+authors:
+- Gungor N
+- Arslanian S
+journal: Treat Endocrinol
+year: '2002'
+doi: 10.2165/00024677-200201060-00002
+content_type: abstract_only
+---
+
+# Pathophysiology of type 2 diabetes mellitus in children and adolescents: treatment implications.
+**Authors:** Gungor N, Arslanian S
+**Journal:** Treat Endocrinol (2002)
+**DOI:** [10.2165/00024677-200201060-00002](https://doi.org/10.2165/00024677-200201060-00002)
+
+## Content
+
+1. Treat Endocrinol. 2002;1(6):359-71. doi: 10.2165/00024677-200201060-00002.
+
+Pathophysiology of type 2 diabetes mellitus in children and adolescents: 
+treatment implications.
+
+Gungor N(1), Arslanian S.
+
+Author information:
+(1)Division of Pediatric Endocrinology, Metabolism, and Diabetes Mellitus, 
+Children's Hospital, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, 
+USA.
+
+Erratum in
+    Treat Endocrinol. 2003;2(2):143.
+
+Type 2 diabetes mellitus was considered an exclusive disease of adulthood until 
+the late 1970s, when reports of an increased prevalence in the pediatric age 
+group emerged in the literature. The concerning upswing in the rate of diagnosis 
+of type 2 diabetes mellitus in children and adolescents has continued, parallel 
+to the increasing rates of obesity. The disease is not specific to the U.S.; it 
+has proven to be a global problem. The current information on type 2 diabetes 
+mellitus in children and adolescents is mostly extrapolated from studies in 
+adults with type 2 diabetes mellitus, due to the paucity of studies conducted in 
+youth. Obesity, family history of type 2 diabetes mellitus, minority ethnicity 
+and race, polycystic ovary syndrome, maternal diabetes mellitus or impaired 
+glucose tolerance during gestation, and acanthosis nigricans are the major risk 
+factors and markers of youth-onset type 2 diabetes mellitus. The 
+pathophysiology, which involves both an insulin secretion defect and resistance 
+to insulin, needs further clarification in pediatric studies. Current management 
+approaches involve lifestyle modification (nutritional and exercise) along with 
+pharmacologic agents, such as insulin and oral antihyperglycemic medications, as 
+indicated. A recent study on the use of metformin in childhood-onset type 2 
+diabetes mellitus demonstrated the drug to be effective and to have a good 
+safety profile in this population. However, the outcomes of ongoing studies and 
+future studies focusing on type 2 diabetes mellitus in the pediatric age group 
+will be crucial in terms of fine-tuning management plans and setting up 
+appropriate prevention strategies.
+
+DOI: 10.2165/00024677-200201060-00002
+PMID: 15832489 [Indexed for MEDLINE]