Metabolic phenotyping involves the comprehensive analysis of biological fluids or tissue samples. This analysis allows biochemical classification of a person's physiological or pathological states that relate to disease diagnosis or prognosis at the individual level and to disease risk factors at the population level. These approaches are currently being implemented in hospital environments and in regional phenotyping centres worldwide. The ultimate aim of such work is to generate information on patient biology using techniques such as patient stratification to better inform clinicians on factors that will enhance diagnosis or the choice of therapy. There have been many reports of direct applications of metabolic phenotyping in a clinical setting.

Metabolic phenotyping in clinical and surgical environments

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

Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.

Exploring the human microbiome from multiple perspectives: factors altering its composition and function.

BACKGROUND: The metabolome of any given biological system contains a diverse range of low molecular weight molecules (metabolites), whose abundances can be affected by the timing and method of sample collection, storage, and handling. Thus, it is necessary to consider the requirements for preanalytical processes and biobanking in metabolomics research. Poor practice can create bias and have deleterious effects on the robustness and reproducibility of acquired data. CONTENT: This review presents both current practice and latest evidence on preanalytical processes and biobanking of samples intended for metabolomics measurement of common biofluids and tissues. It highlights areas requiring more validation and research and provides some evidence-based guidelines on best practices. SUMMARY: Although many researchers and biobanking personnel are familiar with the necessity of standardizing sample collection procedures at the axiomatic level (e.g., fasting status, time of day, “time to freezer,” sample volume), other less obvious factors can also negatively affect the validity of a study, such as vial size, material and batch, centrifuge speeds, storage temperature, time and conditions, and even environmental changes in the collection room. Any biobank or research study should establish and follow a well-defined and validated protocol for the collection of samples for metabolomics research. This protocol should be fully documented in any resulting study and should involve all stakeholders in its design. The use of samples that have been collected using standardized and validated protocols is a prerequisite to enable robust biological interpretation unhindered by unnecessary preanalytical factors that may complicate data analysis and interpretation.

/pdf/preanalytical-processing-and-biobanking-procedures-of-4g3eugu1ak.pdf

Preanalytical Processing and Biobanking Procedures of Biological Samples for Metabolomics Research: A White Paper, Community Perspective (for “Precision Medicine and Pharmacometabolomics Task Group”—The Metabolomics Society Initiative)

Metabolome analysis for investigating host-gut microbiota interactions.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1600-6143.2012.04183.x

Metabolomics of human intestinal transplant rejection.

Intestinal transplantation in children has evolved with more isolated small intestine transplants being performed compared to combined liver-intestine transplants. Consequently, surgical techniques have changed, frequently requiring the use of vascular homografts of small caliber to revascularize the isolated small intestine, the impact of which on outcomes is unknown. Among 106 pediatric intestine and multivisceral transplants performed at our center since 2003, 33 recipients of an isolated small intestine graft were included in this study. Outcome parameters were thrombotic complications, graft, and patient survival. A total of 29 of 33 (87.9%) patients required arterial and/or venous homografts from the same donor, mainly iliac or carotid artery and iliac or innominate vein, respectively (donor’s median age 1.1 years [2 months to 23 years], median weight 10 kg [14.7–48.5]). Post-transplant, there were three acute arterial homograft thromboses and one venous thrombosis resulting in two peri-operative graft salvages and two graft losses. Three of four thromboses occurred in patients with primary hypercoagulable state, including the two graft losses. Overall, at a median of 4.1 years (1–10.2) from transplant, 29 of 33 (88%) patients are alive with 26 of 33 (79%) functioning grafts. The procurement of intact, size-matched donor vessels and the management of effective post-transplant anticoagulation are critical.

The use of vascular homografts in pediatric small bowel transplantation: Single-center experience over a decade.

There continues to be debate about the lower limit of graft‐to‐recipient weight ratio (GRWR) for living donor liver transplant (LDLT).

The role of graft to recipient weight ratio on enhanced recovery of the recipient after living donor liver transplantation – A systematic review of the literature and expert panel recommendations

Does Chronic Use of Steroids Affect Outcomes After Liver Resection? Analysis of a National Database

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/lt.26500

Yong K. Kwon

Papers

Metabolomics of human intestinal transplant rejection.

The use of vascular homografts in pediatric small bowel transplantation: Single-center experience over a decade.

The role of graft to recipient weight ratio on enhanced recovery of the recipient after living donor liver transplantation – A systematic review of the literature and expert panel recommendations

Does Chronic Use of Steroids Affect Outcomes After Liver Resection? Analysis of a National Database

Pediatric acute liver failure: Reexamining key clinical features, current management, and research prospects