1
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Mehra P, Kumar A. Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology. Cell Biochem Funct 2024; 42:e4063. [PMID: 38961596 DOI: 10.1002/cbf.4063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/12/2024] [Accepted: 05/18/2024] [Indexed: 07/05/2024]
Abstract
The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.
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Affiliation(s)
- Parul Mehra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
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2
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Chang DYH, Yong SB, Yii CY, Lin CH. Correspondence "Validation of fermentation techniques for prebiotic impact on gut microbiota". Pharmacol Res 2024; 206:107270. [PMID: 38885781 DOI: 10.1016/j.phrs.2024.107270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Affiliation(s)
| | - Su-Boon Yong
- Department of Allergy and Immunology, China Medical University Children's Hospital, Taichung, Taiwan; Department of Medicine, College of Medicine, China Medical University, Taichung, Taiwan; Center for Allergy, Immunology, and Microbiome (A.I.M.), China Medical University Hospital, Taichung, Taiwan.
| | - Chin-Yuan Yii
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Landseed International Hospital, Taoyuan, Taiwan.
| | - Chien-Heng Lin
- Division of Pediatric Pulmonology, China Medical University Children's Hospital, Taichung, Taiwan; Department of Biomedical Imaging and Radiological Science, College of Health Care, China Medical University, Taichung, Taiwan.
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3
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Isokääntä H, Pinto da Silva L, Karu N, Kallonen T, Aatsinki AK, Hankemeier T, Schimmel L, Diaz E, Hyötyläinen T, Dorrestein PC, Knight R, Orešič M, Kaddurah-Daouk R, Dickens AM, Lamichhane S. Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization. Anal Chem 2024; 96:8893-8904. [PMID: 38782403 PMCID: PMC11154662 DOI: 10.1021/acs.analchem.3c04436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Metabolites from feces provide important insights into the functionality of the gut microbiome. As immediate freezing is not always feasible in gut microbiome studies, there is a need for sampling protocols that provide the stability of the fecal metabolome and microbiome at room temperature (RT). Here, we investigated the stability of various metabolites and the microbiome (16S rRNA) in feces collected in 95% ethanol (EtOH) and commercially available sample collection kits with specific preservatives OMNImet•GUT/OMNIgene•GUT. To simulate field-collection scenarios, the samples were stored at different temperatures at varying durations (24 h + 4 °C, 24 h RT, 36 h RT, 48 h RT, and 7 days RT) and compared to aliquots immediately frozen at -80 °C. We applied several targeted and untargeted metabolomics platforms to measure lipids, polar metabolites, endocannabinoids, short-chain fatty acids (SCFAs), and bile acids (BAs). We found that SCFAs in the nonstabilized samples increased over time, while a stable profile was recorded in sample aliquots stored in 95% EtOH and OMNImet•GUT. When comparing the metabolite levels between aliquots stored at room temperature and at +4 °C, we detected several changes in microbial metabolites, including multiple BAs and SCFAs. Taken together, we found that storing samples at RT and stabilizing them in 95% EtOH yielded metabolomic results comparable to those from flash freezing. We also found that the overall composition of the microbiome did not vary significantly between different storage types. However, notable differences were observed in the α diversity. Altogether, the stability of the metabolome and microbiome in 95% EtOH provided results similar to those of the validated commercial collection kits OMNImet•GUT and OMNIgene•GUT, respectively.
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Affiliation(s)
- Heidi Isokääntä
- Research
Center for Infections and Immunity, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Lucas Pinto da Silva
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
| | - Naama Karu
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Teemu Kallonen
- Department
of Clinical Microbiology, Laboratory Division, Turku University Hospital, Kiinamyllynkatu 10 D, 20520 Turku, Finland
- Clinical
Microbiome Bank, Microbe Center, University
Hospital and University of Turku, 20520 Turku, Finland
| | - Anna-Katariina Aatsinki
- Centre
for
Population Health Research, University of
Turku, Kiinamyllynkatu
10A, 20520 Turku, Finland
| | - Thomas Hankemeier
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Leyla Schimmel
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Edgar Diaz
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Tuulia Hyötyläinen
- School
of Science and Technology, Örebro
University, 70281 Örebro, Sweden
| | - Pieter C. Dorrestein
- Center
for Microbiome Innovation, University of
California, San Diego, La Jolla, California 92093-6607, United States
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California,
San Diego, 9500 Gilman, La Jolla, California 92093-0657, United States
| | - Rob Knight
- Center
for Microbiome Innovation, University of
California, San Diego, La Jolla, California 92093-6607, United States
| | - Matej Orešič
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden
| | - Rima Kaddurah-Daouk
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Alex M. Dickens
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
- Department of Chemistry, University of
Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Santosh Lamichhane
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
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4
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Roach J, Mital R, Haffner JJ, Colwell N, Coats R, Palacios HM, Liu Z, Godinho JLP, Ness M, Peramuna T, McCall LI. Microbiome metabolite quantification methods enabling insights into human health and disease. Methods 2024; 222:81-99. [PMID: 38185226 DOI: 10.1016/j.ymeth.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Many of the health-associated impacts of the microbiome are mediated by its chemical activity, producing and modifying small molecules (metabolites). Thus, microbiome metabolite quantification has a central role in efforts to elucidate and measure microbiome function. In this review, we cover general considerations when designing experiments to quantify microbiome metabolites, including sample preparation, data acquisition and data processing, since these are critical to downstream data quality. We then discuss data analysis and experimental steps to demonstrate that a given metabolite feature is of microbial origin. We further discuss techniques used to quantify common microbial metabolites, including short-chain fatty acids (SCFA), secondary bile acids (BAs), tryptophan derivatives, N-acyl amides and trimethylamine N-oxide (TMAO). Lastly, we conclude with challenges and future directions for the field.
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Affiliation(s)
- Jarrod Roach
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Rohit Mital
- Department of Biology, University of Oklahoma
| | - Jacob J Haffner
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Nathan Colwell
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Randy Coats
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Horvey M Palacios
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Zongyuan Liu
- Department of Chemistry and Biochemistry, University of Oklahoma
| | | | - Monica Ness
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Thilini Peramuna
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma; Department of Chemistry and Biochemistry, San Diego State University.
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5
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Alexander JL, Wyatt NJ, Camuzeaux S, Chekmeneva E, Jimenez B, Sands CJ, Fuller H, Takis P, Ahmad T, Doyle JA, Hart A, Irving PM, Kennedy NA, Lees CW, Lindsay JO, McIntyre RE, Parkes M, Prescott NJ, Raine T, Satsangi J, Speight RA, Jostins-Dean L, Powell N, Marchesi JR, Stewart CJ, Lamb CA. Considerations for peripheral blood transport and storage during large-scale multicentre metabolome research. Gut 2024; 73:379-383. [PMID: 36754608 PMCID: PMC10850673 DOI: 10.1136/gutjnl-2022-329297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/13/2023] [Indexed: 02/10/2023]
Affiliation(s)
- James L Alexander
- Department of Gastroenterology, Imperial College Healthcare NHS Trust, London, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Nicola J Wyatt
- Department of Gastroenterology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Stephane Camuzeaux
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Elena Chekmeneva
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Beatriz Jimenez
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Caroline J Sands
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Hannah Fuller
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Panteleimon Takis
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Tariq Ahmad
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, Devon, UK
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Jennifer A Doyle
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ailsa Hart
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Gastroenterology, St Mark's Hospital and Academic Institute, London, UK
| | - Peter M Irving
- Department of Gastroenterology, Guy's and St Thomas' Hospitals NHS Trust, London, UK
- School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Nicholas A Kennedy
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, Devon, UK
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Charlie W Lees
- Edinburgh IBD Unit, Western General Hospital, Edinburgh, UK
- Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - James O Lindsay
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine, Queen Mary University of London, London, UK
- Department of Gastroenterology, Barts Health NHS Trust, London, UK
| | - Rebecca E McIntyre
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, UK
| | - Natalie J Prescott
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Tim Raine
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, UK
| | - Jack Satsangi
- Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Richard Alexander Speight
- Department of Gastroenterology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Luke Jostins-Dean
- Kennedy Institute of Rheumatology, Oxford University, Oxford, Oxfordshire, UK
| | - Nick Powell
- Department of Gastroenterology, Imperial College Healthcare NHS Trust, London, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher A Lamb
- Department of Gastroenterology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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6
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Hussan H, Clinton SK, Grainger EM, Webb M, Wang C, Webb A, Needleman B, Noria S, Zhu J, Choueiry F, Pietrzak M, Bailey MT. Distinctive patterns of sulfide- and butyrate-metabolizing bacteria after bariatric surgery: potential implications for colorectal cancer risk. Gut Microbes 2023; 15:2255345. [PMID: 37702461 PMCID: PMC10501170 DOI: 10.1080/19490976.2023.2255345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/09/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023] Open
Abstract
Despite improved cardiometabolic outcomes following bariatric surgery, its long-term impact on colorectal cancer (CRC) risk remains uncertain. In parallel, the influence of bariatric surgery on the host microbiome and relationships with disease outcomes is beginning to be appreciated. Therefore, we investigated the impact of Roux-en-Y gastric bypass (RYGB) and vertical sleeve gastrectomy (VSG) on the patterns of sulfide-reducing and butyrate-producing bacteria, which are hypothesized to modulate CRC risk after bariatric surgery. In this single-center, cross-sectional study, we included 15 pre-surgery subjects with severe obesity and patients who are at a median (range) of 25.6 (9.9-46.5) months after RYGB (n = 16) or VSG (n = 10). The DNA abundance of fecal bacteria and enzymes involved in butyrate and sulfide metabolism were identified using metagenomic sequencing. Differences between pre-surgery and post-RYGB or post-VSG cohorts were quantified using the linear discriminant analysis (LDA) effect size (LEfSe) method. Our sample was predominantly female (87%) with a median (range) age of 46 (23-71) years. Post-RYGB and post-VSG patients had a higher DNA abundance of fecal sulfide-reducing bacteria than pre-surgery controls (LDA = 1.3-4.4, p < .05). The most significant enrichments were for fecal E. coli, Acidaminococcus and A. finegoldii after RYGB, and for A. finegoldii, S. vestibularis, V. parvula after VSG. As for butyrate-producing bacteria, R. faecis was more abundant, whereas B. dentium and A. hardus were lower post-RYGB vs. pre-surgery. B. dentium was also lower in post-VSG vs. pre-surgery. Consistent with these findings, our analysis showed a greater enrichment of sulfide-reducing enzymes after bariatric surgery, especially RYGB, vs. pre-surgery. The DNA abundance of butyrate-producing enzymes was lower post-RYGB. In conclusion, the two most used bariatric surgeries, RYGB and VSG, are associated with microbiome patterns that are potentially implicated in CRC risk. Future studies are needed to validate and understand the impact of these microbiome changes on CRC risk after bariatric surgery.
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Affiliation(s)
- Hisham Hussan
- Division of Gastroenterology, Department of Internal Medicine, University of California, Davis; Sacramento, CA, USA
- The UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Steven K. Clinton
- Division of Medical Oncology; Department of Internal Medicine, The Ohio StateUniversity, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Elizabeth M. Grainger
- Division of Medical Oncology; Department of Internal Medicine, The Ohio StateUniversity, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Maxine Webb
- Division of Medical Oncology; Department of Internal Medicine, The Ohio StateUniversity, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Cankun Wang
- Division of Biomedical Informatics, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Amy Webb
- Division of Biomedical Informatics, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Bradley Needleman
- Center for Minimally Invasive Surgery; Department of General Surgery, The Ohio State University, Columbus, OH, USA
| | - Sabrena Noria
- Center for Minimally Invasive Surgery; Department of General Surgery, The Ohio State University, Columbus, OH, USA
| | - Jiangjiang Zhu
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Department of Human Sciences, The Ohio State University, Columbus, OH, USA
| | - Fouad Choueiry
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Department of Human Sciences, The Ohio State University, Columbus, OH, USA
| | - Maciej Pietrzak
- Division of Biomedical Informatics, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Michael T. Bailey
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children’s Hospital and Department of Pediatrics, Columbus, OH, USA
- The Oral and Gastrointestinal Microbiology Research Affinity Group, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
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7
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Nam SL, Tarazona Carrillo K, de la Mata AP, Harynuk JJ. Untargeted Metabolomic Profiling of Aqueous and Lyophilized Pooled Human Feces from Two Diet Cohorts Using Two-Dimensional Gas Chromatography Coupled with Time-of-Flight Mass Spectrometry. Metabolites 2023; 13:828. [PMID: 37512535 PMCID: PMC10383202 DOI: 10.3390/metabo13070828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
The metabolic profiles of human feces are influenced by various genetic and environmental factors, which makes feces an attractive biosample for numerous applications, including the early detection of gut diseases. However, feces is complex, heterogeneous, and dynamic with a significant live bacterial biomass. With such challenges, stool metabolomics has been understudied compared to other biospecimens, and there is a current lack of consensus on methods to collect, prepare, and analyze feces. One of the critical steps required to accelerate the field is having a metabolomics stool reference material available. Fecal samples are generally presented in two major forms: fecal water and lyophilized feces. In this study, two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-TOFMS) was used as an analytical platform to characterize pooled human feces, provided by the National Institute of Standards and Technology (NIST) as Research-Grade Test Materials. The collected fecal samples were derived from eight healthy individuals with two different diets: vegans and omnivores, matched by age, sex, and body mass index (BMI), and stored as fecal water and lyophilized feces. Various data analysis strategies were presented to determine the differences in the fecal metabolomic profiles. The results indicate that the sample storage condition has a major influence on the metabolic profiles of feces such that the impact from storage surpasses the metabolic differences from the diet types. The findings of the current study would contribute towards the development of a stool reference material.
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Affiliation(s)
- Seo Lin Nam
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | | | | | - James J Harynuk
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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8
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Sidebottom AM. A Brief History of Microbial Study and Techniques for Exploring the Gastrointestinal Microbiome. Clin Colon Rectal Surg 2023; 36:98-104. [PMID: 36844714 PMCID: PMC9946713 DOI: 10.1055/s-0042-1760678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Over the past 20 years, the study of microbial communities has benefited from simultaneous advancements across several fields resulting in a high-resolution view of human consortia. Although the first bacterium was described in the mid-1600s, the interest in community membership and function has not been a focus or feasible until recent decades. With strategies such as shotgun sequencing, microbes can be taxonomically profiled without culturing and their unique variants defined and compared across phenotypes. Approaches such as metatranscriptomics, metaproteomics, and metabolomics can define the current functional state of a population through the identification of bioactive compounds and significant pathways. Prior to sample collection in microbiome-based studies it is critical to evaluate the requirements of downstream analyses to ensure accurate processing and storage for generation of high data quality. A common pipeline for the analysis of human samples includes approval of collection protocols and method finalization, patient sample collection, sample processing, data analysis, and visualization. Human-based microbiome studies are inherently challenging but with the application of complementary multi-omic strategies there is an unbounded potential for discovery.
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9
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Moutinho TJ, Powers DA, Hanson GF, Levy S, Baveja R, Hefner I, Mohamed M, Abdelghani A, Baker RL, Papin JA, Moore SR, Hourigan SK. Fecal sphingolipids predict parenteral nutrition-associated cholestasis in the neonatal intensive care unit. JPEN J Parenter Enteral Nutr 2022; 46:1903-1913. [PMID: 35285019 PMCID: PMC9468188 DOI: 10.1002/jpen.2374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/23/2022] [Accepted: 03/06/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND Parenteral nutrition-associated cholestasis (PNAC) in the neonatal intensive care unit (NICU) causes significant morbidity and associated healthcare costs. Laboratory detection of PNAC currently relies on elevated serum conjugated bilirubin levels in the aftermath of impaired bile flow. Here, we sought to identify fecal biomarkers, which when integrated with clinical data, would better predict risk for developing PNAC. METHODS Using untargeted metabolomics in 200 serial stool samples from 60 infants, we applied statistical and machine learning approaches to identify clinical features and metabolic biomarkers with the greatest associative potential for risk of developing PNAC. Stools were collected prospectively from infants receiving PN with soybean oil-based lipid emulsion at a level IV NICU. RESULTS Low birth weight, extreme prematurity, longer duration of PN, and greater number of antibiotic courses were all risk factors for PNAC (P < 0.05). We identified 78 stool biomarkers with early predictive potential (P < 0.05). From these 78 biomarkers, we further identified 12 sphingomyelin lipids with high association for the development of PNAC in precholestasis stool samples when combined with birth anthropometry. CONCLUSION We demonstrate the potential for stool metabolomics to enhance early identification of PNAC risk. Earlier detection of high-risk infants would empower proactive mitigation with alterations to PN for at-risk infants and optimization of energy nutrition with PN for infants at lower risk.
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Affiliation(s)
- Thomas J. Moutinho
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Deborah A. Powers
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Gabriel F. Hanson
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Shira Levy
- Inova Children's HospitalFalls ChurchVirginiaUSA
| | - Rajiv Baveja
- Fairfax Neonatal AssociatesFalls ChurchVirginiaUSA
| | | | | | | | | | - Jason A. Papin
- Department of Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Sean R. Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of PediatricsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Suchitra K. Hourigan
- Inova Children's HospitalFalls ChurchVirginiaUSA,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of PediatricsUniversity of VirginiaCharlottesvilleVirginiaUSA,Division of Pediatric GastroenterologyPediatric Specialists of VirginiaFairfaxVirginiaUSA,Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
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10
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Pettersen VK, Antunes LCM, Dufour A, Arrieta MC. Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics. Comput Struct Biotechnol J 2021; 20:274-286. [PMID: 35024099 PMCID: PMC8718658 DOI: 10.1016/j.csbj.2021.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022] Open
Abstract
Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography-mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.
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Affiliation(s)
- Veronika Kuchařová Pettersen
- Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Pediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Centre for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Luis Caetano Martha Antunes
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
- National Institute of Science and Technology of Innovation on Diseases of Neglected Populations, Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - Marie-Claire Arrieta
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
- International Microbiome Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Petrov ME, Jiao N, Panchanathan SS, Reifsnider E, Coonrod DV, Liu L, Krajmalnik-Brown R, Gu H, Davidson LA, Chapkin RS, Whisner CM. Protocol of the Snuggle Bug/Acurrucadito Study: a longitudinal study investigating the influences of sleep-wake patterns and gut microbiome development in infancy on rapid weight gain, an early risk factor for obesity. BMC Pediatr 2021; 21:374. [PMID: 34465311 PMCID: PMC8405858 DOI: 10.1186/s12887-021-02832-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/09/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Overweight, obesity, and associated comorbidities are a pressing global issue among children of all ages, particularly among low-income populations. Rapid weight gain (RWG) in the first 6 months of infancy contributes to childhood obesity. Suboptimal sleep-wake patterns and gut microbiota (GM) have also been associated with childhood obesity, but little is known about their influences on early infant RWG. Sleep may alter the GM and infant metabolism, and ultimately impact obesity; however, data on the interaction between sleep-wake patterns and GM development on infant growth are scarce. In this study, we aim to investigate associations of infant sleep-wake patterns and GM development with RWG at 6 months and weight gain at 12 months. We also aim to evaluate whether temporal interactions exist between infant sleep-wake patterns and GM, and if these relations influence RWG. METHODS The Snuggle Bug/ Acurrucadito study is an observational, longitudinal study investigating whether 24-h, actigraphy-assessed, sleep-wake patterns and GM development are associated with RWG among infants in their first year. Based on the Ecological Model of Growth, we propose a novel conceptual framework to incorporate sleep-wake patterns and the GM as metabolic contributors for RWG in the context of maternal-infant interactions, and familial and socio-physical environments. In total, 192 mother-infant pairs will be recruited, and sleep-wake patterns and GM development assessed at 3 and 8 weeks, and 3, 6, 9, and 12 months postpartum. Covariates including maternal and child characteristics, family and environmental factors, feeding practices and dietary intake of infants and mothers, and stool-derived metabolome and exfoliome data will be assessed. The study will apply machine learning techniques combined with logistic time-varying effect models to capture infant growth and aid in elucidating the dynamic associations between study variables and RWG. DISCUSSION Repeated, valid, and objective assessment at clinically and developmentally meaningful intervals will provide robust measures of longitudinal sleep, GM, and growth. Project findings will provide evidence for future interventions to prevent RWG in infancy and subsequent obesity. The work also may spur the development of evidence-based guidelines to address modifiable factors that influence sleep-wake and GM development and prevent childhood obesity.
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Affiliation(s)
- Megan E Petrov
- Edson College of Nursing and Health Innovation, Arizona State University, 550 N. 3rd Street, Suite 301, Phoenix, AZ, 85004, USA
| | - Nana Jiao
- Edson College of Nursing and Health Innovation, Arizona State University, 550 N. 3rd Street, Suite 301, Phoenix, AZ, 85004, USA
| | - Sarada S Panchanathan
- Valleywise Comprehensive Health Center - Phoenix (Pediatric Clinic), 2525 E. Roosevelt St., Phoenix, AZ, 85008, USA
- College of Medicine Phoenix, University of Arizona, Phoenix, AZ, 85007, USA
| | - Elizabeth Reifsnider
- Edson College of Nursing and Health Innovation, Arizona State University, 550 N. 3rd Street, Suite 301, Phoenix, AZ, 85004, USA
| | - Dean V Coonrod
- Valleywise Health, Department of Obstetrics and Gynecology, 2525 E. Roosevelt St., Phoenix, AZ, 85008, USA
| | - Li Liu
- Biodesign Institute, Arizona State University, 1001 S. McAllister Ave BDA230B, Tempe, AZ, 85287, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S. McAllister Ave, PO Box 875701, Tempe, AZ, 85287, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, 550 N. 3rd. Street, Suite 501, Phoenix, AZ, 85004, USA
| | - Laurie A Davidson
- Department of Nutrition and Food Science, Program in Integrative Nutrition and Complex Diseases, Texas A&M University, 2253 TAMU, 112 Cater-Mattil, College Station, TX, 77843, USA
| | - Robert S Chapkin
- Department of Nutrition and Food Science, Program in Integrative Nutrition and Complex Diseases, Texas A&M University, 2253 TAMU, 112 Cater-Mattil, College Station, TX, 77843, USA
| | - Corrie M Whisner
- College of Health Solutions, Arizona State University, 550 N. 3rd. Street, Suite 501, Phoenix, AZ, 85004, USA.
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