A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database

Karu, Naama; Deng, Lu; Slae, Mordechai; Guo, An Chi; Sajed, Tanvir; Huynh, Hien Q.; Wine, Eytan; Wishart, David S.

doi:10.1016/j.aca.2018.05.031

Cited by 209 publications

(240 citation statements)

References 163 publications

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“…Over the past decade, our team, as part of the Human Metabolome Project (HMP), has been systematically characterizing human biofluids using a combination of quantitative metabolomic techniques and literature analyses. During that time, we have characterized human (adult) serum [13], cerebrospinal fluid [14], urine [12], saliva [15] and stool samples [16]. Other groups have also analyzed the metabolomes for human breath [17], breast milk [18], bile fluids [19] and hair [20].…”

Section: Discussionmentioning

confidence: 99%

The Urinary Metabolome of Healthy Newborns

et al. 2020

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The knowledge of normal metabolite values for neonates is key to establishing robust cut-off values to diagnose diseases, to predict the occurrence of new diseases, to monitor a neonate's metabolism, or to assess their general health status. For full term-newborns, many reference biochemical values are available for blood, serum, plasma and cerebrospinal fluid. However, there is a surprising lack of information about normal urine concentration values for a large number of important metabolites in neonates. In the present work, we used targeted tandem mass spectrometry (MS/MS)-based metabolomic assays to identify and quantify 136 metabolites of biomedical interest in the urine from 48 healthy, full-term term neonates, collected in the first 24 h of life. In addition to this experimental study, we performed a literature review (covering the past eight years and over 500 papers) to update the references values in the Human Metabolome Database/Urine Metabolome Database (HMDB/UMDB). Notably, 86 of the experimentally measured urinary metabolites are being reported in neonates/infants for the first time and another 20 metabolites are being reported in human urine for the first time ever. Sex differences were found for 15 metabolites. The literature review allowed us to identify another 78 urinary metabolites with concentration data. As a result, reference concentration values and ranges for 378 neonatal urinary metabolites are now publicly accessible via the HMDB.

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Section: Discussionmentioning

confidence: 99%

The Urinary Metabolome of Healthy Newborns

et al. 2020

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“…Various estimates of distinct human metabolomes have been reported that were derived using multiple analytical platforms to gain maximum metabolite coverage. The human cerebrospinal fluid metabolome (308 metabolites) [20], the human serum metabolome (4229 "highly probable" metabolites) [21], the human urine metabolome (2651 "confirmed" metabolites) [22], and the human fecal metabolome (>6000 identified metabolites) [23] have all been described. The culmination of these efforts is the human metabolome database (HMDB 4.0) that comprises 114,100 total metabolites that encompass "the complete collection of small molecules found in the human body including peptides, lipids, amino acids, nucleic acids, carbohydrates, organic acids, biogenic amines, vitamins, minerals, food additives, drugs, cosmetics, contaminants, pollutants, and just about any other chemical that humans ingest, metabolize, catabolize or come into contact with" [24].…”

Section: The Need For Biomarkers Of Premalignant Liver Diseasementioning

confidence: 99%

Metabolomic and Lipidomic Biomarkers for Premalignant Liver Disease Diagnosis and Therapy

Beyoğlu

Idle

2020

Metabolites

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In recent years, there has been a plethora of attempts to discover biomarkers that are more reliable than α-fetoprotein for the early prediction and prognosis of hepatocellular carcinoma (HCC). Efforts have involved such fields as genomics, transcriptomics, epigenetics, microRNA, exosomes, proteomics, glycoproteomics, and metabolomics. HCC arises against a background of inflammation, steatosis, and cirrhosis, due mainly to hepatic insults caused by alcohol abuse, hepatitis B and C virus infection, adiposity, and diabetes. Metabolomics offers an opportunity, without recourse to liver biopsy, to discover biomarkers for premalignant liver disease, thereby alerting the potential of impending HCC. We have reviewed metabolomic studies in alcoholic liver disease (ALD), cholestasis, fibrosis, cirrhosis, nonalcoholic fatty liver (NAFL), and nonalcoholic steatohepatitis (NASH). Specificity was our major criterion in proposing clinical evaluation of indole-3-lactic acid, phenyllactic acid, N-lauroylglycine, decatrienoate, N-acetyltaurine for ALD, urinary sulfated bile acids for cholestasis, cervonoyl ethanolamide for fibrosis, 16α-hydroxyestrone for cirrhosis, and the pattern of acyl carnitines for NAFL and NASH. These examples derive from a large body of published metabolomic observations in various liver diseases in adults, adolescents, and children, together with animal models. Many other options have been tabulated. Metabolomic biomarkers for premalignant liver disease may help reduce the incidence of HCC.

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“…Human fecal metabolome database (HFMDB) is a freely available database containing manually curated >6000 identified human fecal metabolites with their extensive chemical information, metabolite descriptions, and reference data in the same format as that of the human metabolome database (HMDB) .…”

Section: Tools For Analytical Platformsmentioning

confidence: 99%

Tools and resources for metabolomics research community: A 2017–2018 update

Misra¹,

Mohapatra

2018

Electrophoresis

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The scale at which MS‐ and NMR‐based platforms generate metabolomics datasets for both research, core, and clinical facilities to address challenges in the various sciences—ranging from biomedical to agricultural—is underappreciated. Thus, metabolomics efforts spanning microbe, environment, plant, animal, and human systems have led to continual and concomitant growth of in silico resources for analysis and interpretation of these datasets. These software tools, resources, and databases drive the field forward to help keep pace with the amount of data being generated and the sophisticated and diverse analytical platforms that are being used to generate these metabolomics datasets. To address challenges in data preprocessing, metabolite annotation, statistical interrogation, visualization, interpretation, and integration, the metabolomics and informatics research community comes up with hundreds of tools every year. The purpose of the present review is to provide a brief and useful summary of more than 95 metabolomics tools, software, and databases that were either developed or significantly improved during 2017–2018. We hope to see this review help readers, developers, and researchers to obtain informed access to these thorough lists of resources for further improvisation, implementation, and application in due course of time.

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A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database

Cited by 209 publications

References 163 publications

The Urinary Metabolome of Healthy Newborns

The Urinary Metabolome of Healthy Newborns

Metabolomic and Lipidomic Biomarkers for Premalignant Liver Disease Diagnosis and Therapy

Tools and resources for metabolomics research community: A 2017–2018 update

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