Microbiome definition re-visited: old concepts and new challenges

Microbiome, Journal Year: 2020, Volume and Issue: 8(1)

Published: June 30, 2020

The field of microbiome research has evolved rapidly over the past few decades and become a topic great scientific public interest. As result this rapid growth in interest covering different fields, we are lacking clear commonly agreed definition term "microbiome." Moreover, consensus on best practices is missing. Recently, panel international experts discussed current gaps frame European-funded MicrobiomeSupport project. meeting brought together about 40 leaders from diverse areas, while more than hundred all world took part an online survey accompanying workshop. This article excerpts outcomes workshop corresponding embedded short historical introduction future outlook. We propose based compact, clear, comprehensive description provided by Whipps et al. 1988, amended with set novel recommendations considering latest technological developments findings. clearly separate terms microbiota provide discussion composition microbiota, heterogeneity dynamics microbiomes time space, stability resilience microbial networks, core microbiomes, functionally relevant keystone species as well co-evolutionary principles microbe-host inter-species interactions within microbiome. These broad definitions suggested unifying concepts will help to improve standardization studies future, could be starting point for integrated assessment data resulting transfer knowledge basic science into practice. Furthermore, standards important solving new challenges associated anthropogenic-driven changes planetary health, which understanding might play key role. Video Abstract.

Language: Английский

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Current challenges and best-practice protocols for microbiome analysis

Briefings in Bioinformatics, Journal Year: 2019, Volume and Issue: 22(1), P. 178 - 193

Published: Nov. 7, 2019

Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological ecological roles environmental microorganisms. However, analysis is affected by experimental conditions (e.g. errors genomic repeats) computationally intensive cumbersome downstream quality control, assembly, binning statistical analyses). Moreover, introduction new technologies protocols led to a flood methodologies, which also have an immediate effect results analyses. The aim this work review most important workflows for 16S rRNA shotgun long-read metagenomics, as well provide best-practice design, sample processing, sequencing, binning, annotation visualization. To simplify standardize computational analysis, we set metagenomic data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).

Language: Английский

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Disease-induced changes in plant microbiome assembly and functional adaptation

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: Sept. 15, 2021

The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in growth health. Increasing evidence indicates that rhizosphere recruits beneficial microbes to suppress soil-borne pathogens. However, ecological processes govern assembly functions below- aboveground compartments under pathogen invasion are not fully understood. Here, we studied bacterial fungal communities associated with 12 (e.g., soils, roots, stems, fruits) chili pepper (Capsicum annuum L.) using amplicons (16S ITS) metagenomics approaches at main production sites China investigated how Fusarium wilt disease (FWD) affects assembly, co-occurrence patterns, plant-associated microbiomes.The amplicon data analyses revealed FWD affected less on reproductive organs (fruit) than vegetative (root stem), strongest impact upper stem epidermis. Fungal intra-kingdom networks were stable their more sensitive communities. analysis microbial interkingdom network further indicated destabilized induced importance taxa. Although diseased plants susceptible colonization by other pathogenic fungi, can also recruit potential bacteria. Some taxa enriched identified core for microbiomes hub networks. On hand, metagenomic significant enrichment several functional genes involved detoxification, biofilm formation, plant-microbiome signaling pathways (i.e., chemotaxis) plants.Together, demonstrate a could bacteria mitigate changes organ facilitate or its offspring survival. may attract through modulation pathways. These findings significantly advance our understanding interactions provide important harnessing sustainable agriculture. Video abstract.

Language: Английский

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Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection

mBio, Journal Year: 2020, Volume and Issue: 11(2)

Published: April 27, 2020

Recent advances in the analysis of microbial communities colonizing human body have identified a resident community urinary tract (UT). Compared to many other niches, UT harbors relatively low biomass. Studies genera and species that may constitute core microbiome. However, contribution microbiome infection (UTI) recurrent UTI (rUTI) pathobiology is not yet clearly understood. Evidence suggests commensal within urogenital (UGT) microbiomes, such as Lactobacillus crispatus, act protect against colonization with uropathogens. mechanisms fundamental biology microbiome-host relationship are The ability measure characterize has been enabled through development next-generation sequencing bioinformatic platforms allow for unbiased detection DNA. Translating technological into clinical insight will require further study genomic ecology both health disease. Future diagnostic, prognostic, therapeutic options management soon incorporate efforts measure, restore, and/or preserve native, healthy microbiomes.

Language: Английский

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Lichens redefined as complex ecosystems

New Phytologist, Journal Year: 2020, Volume and Issue: 227(5), P. 1281 - 1283

Published: June 2, 2020

This article is a Commentary on Mark et al . (2020), 227 : 1362–1375

Language: Английский

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PGPR in Agriculture: A Sustainable Approach to Increasing Climate Change Resilience

Frontiers in Sustainable Food Systems, Journal Year: 2021, Volume and Issue: 5

Published: July 6, 2021

Growing environmental concerns are potentially narrowing global yield capacity of agricultural systems. Climate change is the most significant problem world currently facing. To meet food demand, production must be doubled by 2050; over exploitation arable lands using unsustainable techniques might resolve demand issues, but they have negative effects. Current crop systems a major reason for changing climate through diminishing biodiversity, physical and chemical soil degradation, water pollution. The application fertilizers pesticides contribute to greenhouse gas emissions (GHG) toxic depositions. At this crucial time, there pressing need transition more sustainable practices, ones that concentrate on promoting mechanisms, which enable crops grow well in resource limited environmentally challenging environments, also develop with greater use efficiency optimum yields across wider array conditions. phytomicrobiome considered as one best strategies; better alternative agriculture, viable solution twin challenges security stability. Use phytomicrobiome, due its friendly mechanisms plant growth promotion, becoming widespread industry. Therefore, review, we emphasize contribution beneficial members, particularly rhizobacteria (PGPR), strategy improvement face change. Also, roles dwelling microbes stress amelioration, nutrient supply (nitrogen fixation, phosphorus solubilization), phytohormone along factors could affect their been discussed extensively. Lastly, limitations expansion biobased techniques, instance, perspective producers, indigenous microbial competition regulatory approval discussed. This review largely focusses importance approaches such biobased/PGPR-based our systems, especially context current conditions, almost certain worsen near future.

Language: Английский

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Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies

Chemical Reviews, Journal Year: 2022, Volume and Issue: 123(1), P. 31 - 72

Published: Nov. 1, 2022

The human microbiome is composed of a collection dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, coevolution with host has resulted these playing profound role promoting health. Consequently, perturbations can cause or exacerbate several diseases. In this Review, we present our current understanding relationship between health and disease development, focusing on microbiomes found across digestive, respiratory, urinary, reproductive systems as well skin. We further discuss strategies by which composition function be modulated to exert therapeutic effect host. Finally, examine technologies such multiomics approaches cellular reprogramming microbes enable significant advancements research engineering.

Language: Английский

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Endometrial microbiota composition is associated with reproductive outcome in infertile patients

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: Jan. 4, 2022

Abstract Background Previous evidence indicates associations between the female reproductive tract microbiome composition and outcome in infertile patients undergoing assisted reproduction. We aimed to determine whether endometrial microbiota is associated with outcomes of live birth, biochemical pregnancy, clinical miscarriage or no pregnancy. Methods Here, we present a multicentre prospective observational study using 16S rRNA gene sequencing analyse fluid biopsy samples before embryo transfer cohort 342 asymptomatic for infection treatments. Results A dysbiotic profile composed Atopobium , Bifidobacterium Chryseobacterium Gardnerella Haemophilus Klebsiella Neisseria Staphylococcus Streptococcus was unsuccessful outcomes. In contrast, Lactobacillus consistently enriched birth Conclusions Our findings indicate that useful biomarker predict outcome, offering an opportunity further improve diagnosis treatment strategies.

Language: Английский

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The Essentials of Marine Biotechnology

Frontiers in Marine Science, Journal Year: 2021, Volume and Issue: 8

Published: March 16, 2021

Coastal countries have traditionally relied on the existing marine resources (e.g., fishing, food, transport, recreation, and tourism) as well tried to support new economic endeavors (ocean energy, desalination for water supply, seabed mining). Modern societies lifestyle resulted in an increased demand dietary diversity, better health well-being, biomedicines, natural cosmeceuticals, environmental conservation, sustainable energy sources. These societal needs stimulated interest of researchers diverse underexplored environments promising sources biomolecules biomass, they are addressed by emerging field (blue) biotechnology. Blue biotechnology provides opportunities a wide range initiatives commercial pharmaceutical, biomedical, cosmetic, nutraceutical, feed, agricultural, related industries. This article synthesizes essence, opportunities, responsibilities, challenges encountered outlines attainment valorization directly derived or bio-inspired products from organisms. First, concept bioeconomy is introduced. Then, diversity bioresources including overview most prominent organisms their potential biotechnological uses described. followed introducing methodologies exploration these main use case scenarios food agronomy, bioremediation climate change, materials, healthcare, well-being sectors. The key aspects fields legislation funding provided, with emphasis importance communication stakeholder engagement at all levels development. Finally, vital overarching concepts, such quadruple helix Responsible Research Innovation principle highlighted important follow within field. authors this review collaborating under European Commission-funded Cooperation Science Technology (COST) Action Ocean4Biotech – transdisciplinary networking platform focus study state affairs.

Language: Английский

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Viral Infections, the Microbiome, and Probiotics

Frontiers in Cellular and Infection Microbiology, Journal Year: 2021, Volume and Issue: 10

Published: Feb. 12, 2021

Viral infections continue to cause considerable morbidity and mortality around the world. Recent rises in these are likely due complex multifactorial external drivers, including climate change, increased mobility of people goods rapid demographic change name but a few. In parallel with factors, we gaining better understanding internal factors associated viral immunity. Increasingly gastrointestinal (GI) microbiome has been shown be significant player host immune system, acting as key regulator immunity defense mechanisms. An increasing body evidence indicates that disruption homeostasis between GI system can adversely impact This review aims shed light on our how host-microbiota interactions shape early life antibiotic exposure, immunosenescence, diet inflammatory diseases. We also discuss base for commensal organisms therapeutics prevention and/or treatment infections, such gastroenteritis, hepatitis, human immunodeficiency virus (HIV), papilloma (HPV), upper respiratory tract (URTI), influenza SARS CoV-2. The interplay microbiome, invasive viruses physiology is yet fully characterized, increasingly shows have an disease outcomes. While current informative, further well designed clinical trials will needed understand array immunological mechanisms underlying this intricate relationship.

Language: Английский

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