Tracking Human Gut Microbiome Changes Resulting from a Colonoscopy

Smarr, Larry; Hyde, Embriette R.; McDonald, Daniel; Sandborn, William J.; Knight, Rob

doi:10.3414/me17-01-0036

Cited by 7 publications

(9 citation statements)

References 15 publications

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“…This largely comes down to what question you are trying to answer. Remarkable changes have been observed between one day and the next, especially in the times surrounding colonoscopy and surgery, 25,39 as well as during clinical situations such as IBD flares. These changes would be missed entirely with a less-frequent study design.…”

Section: What Is the Best Way To Collect A Sample For Microbiome Analmentioning

confidence: 99%

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians

Allaband

McDonald

Vázquez-Baeza

et al. 2019

Clinical Gastroenterology and Hepatology

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221

208

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Advances in technical capabilities for reading complex human microbiomes are leading to an explosion of microbiome research, leading in turn to intense interest among clinicians in applying these techniques to their patients. In this review, we discuss the content of the human microbiome, including intersubject and intrasubject variability, considerations of study design including important confounding factors, and different methods in the laboratory and on the computer to read the microbiome and its resulting gene products and metabolites. We highlight several common pitfalls for clinicians, including the expectation that an individual's microbiome will be stable, that diet can induce rapid changes that are large compared with the differences among subjects, that everyone has essentially the same core stool microbiome, and that different laboratory and computational methods will yield essentially the same results. We also highlight the current limitations and future promise of these techniques, with the expectation that an understanding of these considerations will help accelerate the path toward routine clinical application of these techniques developed in research settings.

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Section: What Is the Best Way To Collect A Sample For Microbiome Analmentioning

confidence: 99%

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians

Allaband

McDonald

Vázquez-Baeza

et al. 2019

Clinical Gastroenterology and Hepatology

Self Cite

221

208

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“…Examples of scientifically published personal science include Larry Smarr's self-diagnosis of inflammatory bowel disease from gut microbiome analyses [12] and Dana Lewis' work in type 1 diabetes, aiming to help both herself and the wider community by developing tools and methods to achieve improved blood glucose control [13]. It has been suggested that patients using personal science in collaboration with clinicians are in a better position to sustain a behavioural change [14].…”

Section: Personal Sciencementioning

confidence: 99%

Ethical Aspects of Personal Science for Persons with Parkinson’s Disease: What Happens When Self-Tracking Goes from Selfcare to Publication?

Riggare

Hägglund

Bredenoord

et al. 2021

JPD

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Using Parkinson’s disease as an exemplary chronic condition, this Commentary discusses ethical aspects of using self-tracking for personal science, as compared to using self-tracking in the context of conducting clinical research on groups of study participants. Conventional group-based clinical research aims to find generalisable answers to clinical or public health questions. The aim of personal science is different: to find meaningful answers that matter first and foremost to an individual with a particular health challenge. In the case of personal science, the researcher and the participant are one and the same, which means that specific ethical issues may arise, such as the need to protect the participant against self-harm. To allow patient-led research in the form of personal science in the Parkinson field to evolve further, the development of a specific ethical framework for self-tracking for personal science is needed.

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“…The metagenomic data for these seven time points have been previously compared 11,28 with a set of metagenomic data from healthy individuals drawn from the NIH Human Microbiome Project 29 , as well as selected metagenomic data from patients with ICD and with UC. It has been shown 30 that LS’s gut microbiome taxonomic profile deviated a great deal from the healthy individuals and furthermore, that his gut microbiome exhibited major taxonomic shifts over time.…”

Section: Introductionmentioning

confidence: 99%

Longitudinal flux balance analyses of a patient with Crohn’s disease highlight microbiome metabolic alterations

Basile

Heinken

Hertel

et al. 2022

Preprint

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Inflammatory bowel diseases (IBD) are characterised by episodic inflammation of the gastrointestinal tract. Gut microbial dysbiosis characterises the pathoetiology, but its role remains understudied. We report the first use of constraint-based microbial community modelling on a single individual with IBD, covering seven dates over 16 months, enabling us to identify a number of time-correlated microbial species and metabolites. We find that the individual's dynamical microbial ecology in the disease state drives time-varying in silico overproduction, compared to healthy controls, of more than 24 biologically important metabolites, including oxygen, methane, thiamine, formaldehyde, trimethylamine N-oxide, folic acid, serotonin, histamine, and tryptamine. A number of these metabolites may yield new biomarkers of disease progression. The microbe-metabolite contribution analysis revealed that some genus Dialister species changed metabolic pathways according to the disease phases. At the first time point, characterised by the highest levels of blood and faecal inflammation biomarkers, they produced L-serine or formate. The production of the compounds, through a cascade effect, was mediated by the interaction with pathogenic Escherichia coli strains and Desulfovibrio piger. We integrated the microbial community metabolic models of each time point with a male whole-body, organ-resolved model of human metabolism to track the metabolic consequences of dysbiosis at different body sites. The presence of D. piger in the gut microbiome influenced the sulphur metabolism with a domino effect affecting the liver. These results underline the importance of tracking an individual's gut microbiome along a time course, creating a new analysis framework for self-quantified medicine.

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Tracking Human Gut Microbiome Changes Resulting from a Colonoscopy

Cited by 7 publications

References 15 publications

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians

Ethical Aspects of Personal Science for Persons with Parkinson’s Disease: What Happens When Self-Tracking Goes from Selfcare to Publication?

Longitudinal flux balance analyses of a patient with Crohn’s disease highlight microbiome metabolic alterations

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