Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe

Lamichhane, Santosh; Sen, Partho; Dickens, Alex M.; Orešič, Matej; Bertram, Hanne Christine

doi:10.1016/j.ymeth.2018.04.029

Cited by 147 publications

(104 citation statements)

References 130 publications

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“…However, human microbiome research requires integration with other omic approaches to advance microbiome-based interventions for health and disease management. Pairing metabolomics with metagenomics is now becoming a very promising approach for the identification of complex bacterial metabolic functions, leading towards the development of therapeutic strategies for manipulation of the microbial metabolism in those at risk of disease development [20][21][22]. Taxonomic shifts triggered by different physiological and pathological conditions could modify interactions between microbial community members.…”

Section: Discussionmentioning

confidence: 99%

“…Given that many metabolites and metabolic pathways are relatively conserved across species, the coupling of two omics approaches provides insights into the association of the human microbiome with health status and risk of disease development [19]. Much work has been done to explore a complex interplay between host-microbiome and metabolome in the gut [20], cervix [21], and saliva [22]. Indeed a recent multi-omic integration study revealed that mainly amino acids and amino acid degradation products, such as polyamines, were well-predicted to be modulated by cervical microorganisms [21].…”

Section: Introductionmentioning

confidence: 99%

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Cervicovaginal Microbiome and Urine Metabolome Paired Analysis Reveals Niche Partitioning of the Microbiota in Patients with Human Papilloma Virus Infections

2020

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In this study, we evaluate the association between vaginal and cervical human papillomavirus infections high-risk types (HPV+H), negative controls (HPV−), the bacterial biota, and urinary metabolites via integration of metagenomics, metabolomics, and bioinformatics analysis. We recently proposed that testing urine as a biofluid could be a non-invasive method for the detection of cervical HPV+H infections by evaluating the association between cervical HPV types and a total of 24 urinary metabolites identified in the samples. As a follow-up study, we expanded the analysis by pairing the urine metabolome data with vaginal and cervical microbiota in selected samples from 19 Puerto Rican women diagnosed with HPV+H infections and HPV− controls, using a novel comprehensive framework, Model-based Integration of Metabolite Observations and Species Abundances 2 (MIMOSA2). This approach enabled us to estimate the functional activities of the cervicovaginal microbiome associated with HPV+H infections. Our results suggest that HPV+H infections could induce changes in physicochemical properties of the genital tract through which niche partitioning may occur. As a result, Lactobacillus sp. enrichment coincided with the depletion of L. iners and Shuttleworthia, which dominate under normal physiological conditions. Changes in the diversity of microbial species in HPV+H groups influence the capacity of new community members to produce or consume metabolites. In particular, the functionalities of four metabolic enzymes were predicted to be associated with the microbiota, including acylphosphatase, prolyl aminopeptidase, prolyl-tRNA synthetase, and threonyl-tRNA synthetase. Such metabolic changes may influence systemic health effects in women at risk of developing cervical cancer. Overall, even assuming the limitation of the power due to the small sample number, our study adds to current knowledge by suggesting how microbial taxonomic and metabolic shifts induced by HPV infections may influence the maintenance of microbial homeostasis and indicate that HPV+H infections may alter the ecological balance of the cervicovaginal microbiota, resulting in higher bacterial diversity.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Cervicovaginal Microbiome and Urine Metabolome Paired Analysis Reveals Niche Partitioning of the Microbiota in Patients with Human Papilloma Virus Infections

2020

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“…Research is currently required to translate microbiome investigation into targeted practical outcomes that benefit the human host (Schmidt et al ., ). However, the interaction between host and the gut microbiota is highly dynamic and complex (Lamichhane et al ., ) and can be significantly influenced by overall health status, diet, genetic factors, age, response of the immune system, inflammatory status, drug interaction and composition of the diet. These factors are modulators of the microbiome, therefore dietary intervention strategies aim to alter the diversity of organisms in the gut (Sharma et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Ensuring the future of functional foods

Birch

Bonwick

2018

Int J of Food Sci Tech

129

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Consumption of functional foods suggests a strategy to reduce the incidence of chronic health disorders. This message has resonated with consumers and driven market growth. Functional food research has significantly increased over the last decade but few studies have addressed the bioavailability of active ingredients for clinical efficacy. Baked goods such as bread, biscuits and cake are popular categories for innovation due to their widespread consumption. These new developments have often impacted on organoleptic properties of the finished products and thus consumer acceptance. Blending of bioactive ingredients may overcome this deficit. However, an understanding of the role of the microbiome in health has indicated that the efficacy of functional foods is unlikely to be uniform within the population. Further growth in the functional foods market, is likely to require greater evidence of the bioavailability of active ingredients, clinical effect and support for health claims by regulators especially in the EU.

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“…Akkermansia, Christensenellaceae, Tenericutes, Eggerthella, Pasteurellaceae, and Butyricimonas are associated with body mass index in patients with metabolic syndrome as well as levels of triglycerides and high-density lipoproteins. [14][15][16][17][18] With regards to protein metabolism, the microbiota-derived metabolites produced from aromatic amino acids (tyrosine, tryptophan, and phenylalanine) affect host signaling pathways interacting with host immunity. Bacteroides thetaiotaomicron, Proteus vulgaris, and Escherichia coli act through tryptophanase activity, producing indole which is sulfated in the liver and resulting in the production of 3-indoxyl sulfate and related compounds which promote systemic inflammation through transcription of IL-6.…”

Section: Identification and Study Of The Gut Microbiota (Gm)mentioning

confidence: 99%

Modulating the Intestinal Microbiota: Therapeutic Opportunities in Liver Disease

Philips¹,

Augustine²,

Yerol³

et al. 2019

Journal of Clinical and Translational Hepatology

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Gut microbiota has been demonstrated to have a significant impact on the initiation, progression and development of complications associated with multiple liver diseases. Notably, nonalcoholic fatty liver diseases, including nonalcoholic steatohepatitis and cirrhosis, severe alcoholic hepatitis, primary sclerosing cholangitis and hepatic encephalopathy, have strong links to dysbiosisor a pathobiological change in the microbiota. In this review, we provide clear and concise discussions on the human gut microbiota, methods of identifying gut microbiota and its functionality, liver diseases that are affected by the gut microbiota, including novel associations under research, and provide current evidence on the modulation of gut microbiota and its effects on specific liver disease conditions.

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Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe

Cited by 147 publications

References 130 publications

Cervicovaginal Microbiome and Urine Metabolome Paired Analysis Reveals Niche Partitioning of the Microbiota in Patients with Human Papilloma Virus Infections

Cervicovaginal Microbiome and Urine Metabolome Paired Analysis Reveals Niche Partitioning of the Microbiota in Patients with Human Papilloma Virus Infections

Ensuring the future of functional foods

Modulating the Intestinal Microbiota: Therapeutic Opportunities in Liver Disease

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