Sample pre-treatment procedures for the omics analysis of human gut microbiota: Turning points, tips and tricks for gene sequencing and metabolomics

Zubeldia‐Varela, Elisa; Barber, Domingo; Barbas, Coral; Pérez‐Gordo, Marina; Rojo, David

doi:10.1016/j.jpba.2020.113592

Cited by 15 publications

(26 citation statements)

References 86 publications

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“…Therefore, imaging is only useful for "appearance" stage. Advances in metabolomics allow immediate internal display of the organization of tissues [25]; however, its process is tedious and costly [26]; therefore, it is not widely used. This study used NMR metabolomics combined with mass spectrometry metabolomics to explore the metabolic profile of IVD and further performed quantitative and qualitative analysis of spectrograms to establish an in vivo metabolism model of noninvasive detection of degeneration.…”

Section: Discussionmentioning

confidence: 99%

Glycine‐Serine‐Threonine Metabolic Axis Delays Intervertebral Disc Degeneration through Antioxidant Effects: An Imaging and Metabonomics Study

Liu

Yang

et al. 2021

Oxidative Medicine and Cellular Longevity

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Although intervertebral disc degeneration (IDD) can be described as different stages of change through biological methods, this long and complex process cannot be defined in stages by single or simple combination of biological techniques. Under the background of the development of nuclear magnetic resonance (NMR) technology and the emerging metabonomics, we based on animal models and expanded to the study of clinical human degeneration models. The characteristics of different stages of IDD were analyzed by omics. Omics imaging combined with histology, cytology, and proteomics was used for screening of the intervertebral disc (IVD) of research subjects. Furthermore, mass spectrometry nontargeted metabolomics was used to explore profile of metabolites at different stages of the IDD process, to determine differential metabolic pathways and metabolites. NMR spectroscopy was used to qualitatively and quantitatively identify markers of degeneration. NMR was combined with mass spectrometry metabolomics to explore metabolic pathways. Metabolic pathways were determined through protein molecular biology and histocytology of the different groups. Distinguishing advantages of magnetic resonance spectroscopy (MRS) for analysis of metabolites and effective reflection of structural integrity and water molecule metabolism through diffusion tensor imaging (DTI) were further used to verify the macrometabolism profile during degeneration. A corresponding model of in vitro metabolomics and in vivo omics imaging was established. The findings of this study show that a series of metabolic pathways associated with the glycine-serine-threonine (Gly-Ser-Thr) metabolic axis affects carbohydrate patterns and energy utilization efficiency and ultimately delays disc degeneration through antioxidant effects.

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Section: Discussionmentioning

confidence: 99%

Glycine‐Serine‐Threonine Metabolic Axis Delays Intervertebral Disc Degeneration through Antioxidant Effects: An Imaging and Metabonomics Study

Liu

Yang

et al. 2021

Oxidative Medicine and Cellular Longevity

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“…As for possible limitations, the use of this metabolomic approach will not allow the discovery of new compounds that may be relevant in host–microbiota physiology. Even if they state that their method is “customizable and expandable,” an untargeted metabolomic approach is still fundamental to overcome this drawback 2 . Another key point that is not tackled in‐depth is the importance of quorum sensing.…”

Section: Figurementioning

confidence: 99%

A step closer to understanding the relationship between host and gut microbiota metabolism

Barker-Tejeda

Zubeldia‐Varela

Obeso

2022

Allergy

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“…For the in-depth study of non-IgE-GI-FA, feces are the sample of choice. This is due to the fact that the main system affected is the gastrointestinal tract and to their non-invasive collection [33]. There are fecal biomarkers, such as immune cell derived proteins and/or gut microbiota metabolites, defined as biological entities capable of predicting an individual's physiological state or pathological condition.…”

Section: Approaches For the Study Of Non-ige-gi-famentioning

confidence: 99%

“…sive collection [33]. There are fecal biomarkers, such as immune cell derived proteins and/or gut microbiota metabolites, defined as biological entities capable of predicting an individual's physiological state or pathological condition.…”

Section: Approaches For the Study Of Non-ige-gi-famentioning

confidence: 99%

“…Approximately 70% of the primary colonization of the gut microbiota of newborns is vertically transmitted, occurring directly from mother to offspring. However, the composition of the gut microbiota is dynamic and changes throughout life due to factors such as delivery mode, age, diet, antibiotic consumption, ethnicity, lifestyle, environmental factors, and diseases and disorders, among others [33,[55][56][57].…”

Section: Gut Microbiota and Omics Techniquesmentioning

confidence: 99%

See 1 more Smart Citation

Non-IgE-Mediated Gastrointestinal Food Protein-Induced Allergic Disorders. Clinical Perspectives and Analytical Approaches

Zubeldia‐Varela

Barker-Tejeda

Blanco-Pérez

et al. 2021

Foods

Self Cite

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Non-IgE-mediated gastrointestinal food allergy (non-IgE-GI-FA) is the name given to a series of pathologies whose main entities are food protein-induced allergic proctocolitis (FPIAP), food protein-induced enteropathy (FPE), and food protein-induced enterocolitis syndrome (FPIES). These are more uncommon than IgE-mediated food allergies, their mechanisms remain largely unknown, and their diagnosis is mainly done by clinical history, due to the lack of specific biomarkers. In this review, we present the latest advances found in the literature about clinical aspects, the current diagnosis, and treatment options of non-IgE-GI-FAs. We discuss the use of animal models, the analysis of gut microbiota, omics techniques, and fecal proteins with a focus on understanding the pathophysiological mechanisms of these pathologies and obtaining possible diagnostic and/or prognostic biomarkers. Finally, we discuss the unmet needs that researchers should tackle to advance in the knowledge of these barely explored pathologies.

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Sample pre-treatment procedures for the omics analysis of human gut microbiota: Turning points, tips and tricks for gene sequencing and metabolomics

Cited by 15 publications

References 86 publications

Glycine‐Serine‐Threonine Metabolic Axis Delays Intervertebral Disc Degeneration through Antioxidant Effects: An Imaging and Metabonomics Study

Glycine‐Serine‐Threonine Metabolic Axis Delays Intervertebral Disc Degeneration through Antioxidant Effects: An Imaging and Metabonomics Study

A step closer to understanding the relationship between host and gut microbiota metabolism

Non-IgE-Mediated Gastrointestinal Food Protein-Induced Allergic Disorders. Clinical Perspectives and Analytical Approaches

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