Microbiome definition re-visited: old concepts and new challenges

Microbiome, Год журнала: 2020, Номер 8(1)

Опубликована: Июнь 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.

Язык: Английский

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The gut–liver axis and the intersection with the microbiome

Nature Reviews Gastroenterology & Hepatology, Год журнала: 2018, Номер 15(7), С. 397 - 411

Опубликована: Май 10, 2018

Язык: Английский

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The gut microbiota at the intersection of diet and human health

Science, Год журнала: 2018, Номер 362(6416), С. 776 - 780

Опубликована: Ноя. 15, 2018

Diet affects multiple facets of human health and is inextricably linked to chronic metabolic conditions such as obesity, type 2 diabetes, cardiovascular disease. Dietary nutrients are essential not only for but also the survival trillions microbes that reside within intestines. a key component relationship between humans their microbial residents; gut use ingested fundamental biological processes, outputs those processes may have important impacts on physiology. Studies in animal models beginning unravel underpinnings this relationship, increasing evidence suggests it underlie some broader effects diet

Язык: Английский

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Environmental stress destabilizes microbial networks

The ISME Journal, Год журнала: 2021, Номер 15(6), С. 1722 - 1734

Опубликована: Янв. 15, 2021

Язык: Английский

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Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

Nature Communications, Год журнала: 2017, Номер 8(1)

Опубликована: Ноя. 21, 2017

Abstract Hundreds of clinical studies have demonstrated associations between the human microbiome and disease, yet fundamental questions remain on how we can generalize this knowledge. Results from individual be inconsistent, comparing published data is further complicated by a lack standard processing analysis methods. Here introduce MicrobiomeHD database, which includes 28 case–control gut spanning ten diseases. We perform cross-disease meta-analysis these using standardized find consistent patterns characterizing disease-associated changes. Some diseases are associated with over 50 genera, while most show only 10–15 genus-level marked presence potentially pathogenic microbes, whereas others characterized depletion health-associated bacteria. Furthermore, that about half genera bacteria respond to more than one disease. Thus, many found in likely not disease-specific but rather part non-specific, shared response health

Язык: Английский

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The Human Gut Microbiome: From Association to Modulation

Cell, Год журнала: 2018, Номер 172(6), С. 1198 - 1215

Опубликована: Март 1, 2018

Язык: Английский

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Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries

Gut, Год журнала: 2020, Номер 69(7), С. 1218 - 1228

Опубликована: Фев. 17, 2020

Objective Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We others have shown that frailty co-varies with alterations in the gut microbiota a manner accelerated consumption restricted diversity diet. The Mediterranean diet (MedDiet) associated health. In NU-AGE project, we investigated if 1-year MedDiet intervention could alter reduce Design profiled 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy Poland) before after administration 12-month long tailored elderly (NU-AGE diet). Results Adherence was specific microbiome alterations. Taxa enriched adherence were positively several markers lower improved cognitive function, negatively inflammatory including C-reactive protein interleukin-17. Analysis inferred microbial metabolite profiles indicated diet-modulated change an increase short/branch chained fatty acid production secondary bile acids, p-cresols, ethanol carbon dioxide. Microbiome ecosystem network analysis showed bacterial taxa responded occupy keystone interaction positions, whereas frailty-associated are peripheral networks. Conclusion Collectively, our findings support feasibility improving habitual modulate turn has potential promote healthier ageing.

Язык: Английский

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Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

Cell Host & Microbe, Год журнала: 2019, Номер 25(6), С. 789 - 802.e5

Опубликована: Июнь 1, 2019

Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and composition remain unexplored. Here, we used multivariate methods to integrate 24-h records fecal shotgun metagenomes from 34 healthy subjects collected over 17 days. Microbiome depended on multiple days dietary history was more strongly associated with than conventional nutrient profiles, microbial responses diet were highly personalized. Data two consuming only meal replacement beverages suggest that monotonous does not induce stability in humans, instead, overall diversity associates stability. Our work provides methodological insights for future diet-microbiome studies suggests food-based interventions seeking modulate microbiota may need be tailored individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477.

Язык: Английский

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The sponge holobiont in a changing ocean: from microbes to ecosystems

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Март 9, 2018

The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, microbiota, interactions among them. Accordingly, ecological concepts can be applied to understand host-derived processes govern dynamics interactive networks within holobiont. In marine systems, holobionts further integrated into larger more ecosystems, concept referred as "nested ecosystems." this review, we discuss dynamic interact at multiple scales respond environmental change. We focus on symbiosis sponges their communities—a resulted one most diverse environment. recent years, sponge microbiology remarkably advanced terms curated databases, standardized protocols, information functions microbiota. Like Russian doll, these translated holobiont impact surrounding ecosystem. For example, sponge-associated metabolisms, fueled by high filtering capacity substantially affect biogeochemical cycling key nutrients like carbon, nitrogen, phosphorous. Since increasingly threatened anthropogenic stressors jeopardize stability ecosystem, link between perturbations, dysbiosis, diseases. Experimental studies suggest community composition is tightly linked health, but whether dysbiosis cause or consequence collapse remains unresolved. Moreover, potential role microbiome mediating for acclimate adapt change unknown. Future should aim identify mechanisms underlying scales, from develop management strategies preserve provided our present future oceans.

Язык: Английский

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From hairballs to hypotheses–biological insights from microbial networks

FEMS Microbiology Reviews, Год журнала: 2018, Номер 42(6), С. 761 - 780

Опубликована: Июль 25, 2018

Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these is not straightforward, the biological implications network properties unclear. Analysis allows researchers predict hub species interactions. Additionally, such analyses can help identify alternative states niches. Here, we review factors that result in spurious predictions address emergent be meaningful context microbiome. We also give overview studies analyse new hypotheses. Moreover, show a simulation how affected by choice environmental factors. For example, consistent across tools, heterogeneity induces modularity. highlight need for robust inference suggest strategies infer more reliably.

Язык: Английский

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