Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis

Aguiar‐Pulido, Vanessa; Huang, Wenrui; Suárez-Ulloa, Victoria; Cickovski, Trevor; Mathee, Kalai; Narasimhan, Giri

doi:10.4137/ebo.s36436

Cited by 273 publications

(236 citation statements)

References 167 publications

(187 reference statements)

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“…It is complemented by metatranscriptomics, which defines the collection of genes expressed by a particular microbial community, and by metaproteomics and metabolomics, which define the proteins and metabolites (such as short and medium chain fatty acids) collectively produced (or metabolized) by the microorganisms (table 1). 2122 Whole genome shotgun sequencing is used to infer the functional or enzymatic capabilities of the identified microorganisms 20…”

Section: Introduction Definitions and Nomenclaturementioning

confidence: 99%

The role of the gut microbiome in systemic inflammatory disease

Clemente

Manasson

Scher

2018

BMJ

410

337

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The role of the gut microbiome in models of inflammatory and autoimmune disease is now well characterized. Renewed interest in the human microbiome and its metabolites, as well as notable advances in host mucosal immunology, has opened multiple avenues of research to potentially modulate inflammatory responses. The complexity and interdependence of these diet-microbe-metabolite-host interactions are rapidly being unraveled. Importantly, most of the progress in the field comes from new knowledge about the functional properties of these microorganisms in physiology and their effect in mucosal immunity and distal inflammation. This review summarizes the preclinical and clinical evidence on how dietary, probiotic, prebiotic, and microbiome based therapeutics affect our understanding of wellness and disease, particularly in autoimmunity.

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Section: Introduction Definitions and Nomenclaturementioning

confidence: 99%

The role of the gut microbiome in systemic inflammatory disease

Clemente

Manasson

Scher

2018

BMJ

410

337

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“…We share an optimistic view on the basis of the metatranscriptomic, metaproteomic and metabonomic studies being reported (Lim et al, 2013; Aguiar-Pulido et al, 2016; Yu et al, 2016). The NIH-sponsored Human Microbiome Project has been established to comprehensively characterize human microbiota from multiple body sites and analyze their impact in human health and disease (Peterson et al, 2009; Proctor, 2016).…”

Section: “Which Entities Are Active?”mentioning

confidence: 97%

Pharmacometabolomics Informs Viromics toward Precision Medicine

Balasopoulou¹,

Patrinos²,

Κάτσιλα³

2016

Front. Pharmacol.

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Nowadays, we are experiencing the big data era with the emerging challenge of single data interpretation. Although the advent of high-throughput technologies as well as chemo- and bio-informatics tools presents pan-omics data as the way forward to precision medicine, personalized health care and tailored-made therapeutics can be only envisaged when interindividual variability in response to/toxicity of xenobiotics can be interpreted and thus, predicted. We know that such variability is the net outcome of genetics (host and microbiota) and environmental factors (diet, lifestyle, polypharmacy, and microbiota) and for this, tremendous efforts have been made to clarify key-molecules from correlation to causality to clinical significance. Herein, we focus on the host–microbiome interplay and its direct and indirect impact on efficacy and toxicity of xenobiotics and we inevitably wonder about the role of viruses, as the least acknowledged ones. We present the emerging discipline of pharmacometabolomics-informed viromics, in which pre-dose metabotypes can assist modeling and prediction of interindividual response to/toxicity of xenobiotics. Such features, either alone or in combination with host genetics, can power biomarker discovery so long as the features are variable among patients, stable enough to be of predictive value, and better than pre-existing tools for predicting therapeutic efficacy/toxicity.

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“…Объединение подходов метагеномики, метатранскриптомики и метаметаболомики даёт более полное представление о микробиоме [9]. Использование вместе ко-ассоциативных и метаболических сетей позволит глубже понимать скрытые механизмы, обеспечивающие стабильность и динамику мик-робных сообществ [16].…”

Section: метаметаболомunclassified

Современные Тенденции Развития Биологии Водных Экосистем

Likhoshvai

2017

mbj

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Охарактеризованы новые направления океанологии, сформированные в последние несколько лет бла-годаря внедрению в практику современных методов получения и обработки данных. Это методы мас-сового секвенирования, «омики» и биоинформационные методы хранения и анализа данных. Выяв-ление биологически активных веществ в водной среде и результаты лабораторных экспериментов по-казывают, что существует молекулярное взаимодействие (сигналинг) как на уровне популяционных и межвидовых отношений между микроорганизмами, так и на уровне их трофических связей. «От мо-лекул к экосистеме» -так охарактеризовано актуальное направление биологии морских экосистем. Объединение и анализ огромных массивов данных, включая полученные с помощью космических съё-мок и «облачных» технологий, сформировали новое направление экоинформатики, которое примени-тельно к водным экосистемам позволяет приблизиться к пониманию их структурно-функциональной организации в целом.Ключевые слова: биология водных экосистем, «омики», большие данные, сигналинг

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Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis

Cited by 273 publications

References 167 publications

The role of the gut microbiome in systemic inflammatory disease

The role of the gut microbiome in systemic inflammatory disease

Pharmacometabolomics Informs Viromics toward Precision Medicine

Современные Тенденции Развития Биологии Водных Экосистем

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