The Microbiome and Its Potential for Pharmacology

Chavira, Aries; Belda-Ferre, Pedro; Kościółek, Tomasz; Ali, Farhana; Dorrestein, Pieter C.; Knight, Rob

doi:10.1007/164_2019_317

Cited by 18 publications

(11 citation statements)

References 126 publications

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“…The characterization of the respiratory microenvironment will allow us to understand how dysbiosis contributes to the development, prognosis, or presentation of worse patterns of disease; this knowledge will enable us to identify new therapeutic options to improve the management of pathologies. In gastrointestinal diseases, therapies related to restoring the microbiome composition balance have been used, ranging from antibiotic modification [91] to changes in its composition through molecules, such as carbohydrates, that promote the growth of specific bacterial communities (prebiotics), as well as supplements of live bacteria to maintain the ecological balance of the microbiome (probiotics) or by direct inoculation of biota from healthy individuals [92].…”

Section: Discussionmentioning

confidence: 99%

Lung Microbiome Participation in Local Immune Response Regulation in Respiratory Diseases

et al. 2020

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The lung microbiome composition has critical implications in the regulation of innate and adaptive immune responses. Next-generation sequencing techniques have revolutionized the understanding of pulmonary physiology and pathology. Currently, it is clear that the lung is not a sterile place; therefore, the investigation of the participation of the pulmonary microbiome in the presentation, severity, and prognosis of multiple pathologies, such as asthma, chronic obstructive pulmonary disease, and interstitial lung diseases, contributes to a better understanding of the pathophysiology. Dysregulation of microbiota components in the microbiome–host interaction is associated with multiple lung pathologies, severity, and prognosis, making microbiome study a useful tool for the identification of potential therapeutic strategies. This review integrates the findings regarding the activation and regulation of the innate and adaptive immune response pathways according to the microbiome, including microbial patterns that could be characteristic of certain diseases. Further studies are required to verify whether the microbial profile and its metabolites can be used as biomarkers of disease progression or poor prognosis and to identify new therapeutic targets that restore lung dysbiosis safely and effectively.

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Section: Discussionmentioning

confidence: 99%

Lung Microbiome Participation in Local Immune Response Regulation in Respiratory Diseases

et al. 2020

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“…Metagenomics is of particular interest for the dermo-cosmetic industry, with the microbiome representing a real natural reservoir for the discovery of new molecules of interest [171][172][173].…”

Section: Expectations From Metagenomic and Data Sciencementioning

confidence: 99%

Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care

et al. 2022

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The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.

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“…Studies analyzing the composition of microbial communities are frequently used in diverse study fields, such as ecology (Galbraith et al ., 2018; Grossart et al ., 2020), agriculture (Mashiane et al ., 2017; Granjou and Phillips, 2019), human and animal health (Chen et al ., 2019; Tun et al ., 2012; Zhong et al ., 2019), and pharmacology (Chavira et al ., 2019; Wang et al ., 2019). Traditional methods used to identify the microbial agents within a biological specimen include methods such as culture (Handelsman, 2004), antigen detection (Desmonts and Remington, 1980; Lequin, 2005), and nucleic acid detection (Yang and Rothman, 2004; Driscoll, 2009) protocols.…”

Section: Introductionmentioning

confidence: 99%

Selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection

Rajeev

Salvador

2022

Preprint

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AimShotgun metagenomic sequencing analysis is widely used for microbial profiling of biological specimens and pathogen detection. However, very little is known about the technical biases caused by the choice of analysis software and databases. In this study, we evaluated shotgun metagenomics taxonomical profiling software to characterize the microbial compositions of biological samples collected from wild rodents.Method and ResultsUsing nine of the most widely used metagenomics software and four different databases, we analyzed shotgun metagenomic sequence data from three sets of wild rodent tissue samples. We demonstrated the discrepancies in results when different databases and software were used, which cause significant variation in microbial community characterizations. Our analysis also showed that these software differed in their ability to detect the presence of Leptospira, a major zoonotic pathogen of one health importance.ConclusionsSignificant differences in compositional profiles for the same dataset while using different databases and software combinations can result in confounding biological conclusions in microbial profiling.Significance and Impact of StudyThis study cautions that the selection of software and databases to analyze metagenomics data can influence the outcome and biological interpretation.

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The Microbiome and Its Potential for Pharmacology

Cited by 18 publications

References 126 publications

Lung Microbiome Participation in Local Immune Response Regulation in Respiratory Diseases

Lung Microbiome Participation in Local Immune Response Regulation in Respiratory Diseases

Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care

Selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection

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