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

---

From hairballs to hypotheses–biological insights from microbial networks

FEMS Microbiology Reviews, Journal Year: 2018, Volume and Issue: 42(6), P. 761 - 780

Published: July 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.

Language: Английский

---

Gut Microbiota, Muscle Mass and Function in Aging: A Focus on Physical Frailty and Sarcopenia

Nutrients, Journal Year: 2019, Volume and Issue: 11(7), P. 1633 - 1633

Published: July 17, 2019

Human gut microbiota is able to influence the host physiology by regulating multiple processes, including nutrient absorption, inflammation, oxidative stress, immune function, and anabolic balance. Aging associated with reduced biodiversity, increased inter-individual variability, over-representation of pathobionts, these phenomena may have great relevance for skeletal muscle mass function. For this reason, presence a gut-muscle axis onset progression age-related physical frailty sarcopenia has been recently hypothesized. In narrative review, we summarize studies supporting possible association between microbiota-related parameters measures mass, performance in animal models humans. Reduced distinct composition fermentative capacity mice, administration probiotics or butyrate mouse wasting improved mass. However, no targeted human microbiome sarcopenia. Limited evidence from shows an composition, involving key taxa such as Faecalibacterium Bifidobacterium, grip strength. Similarly, few conducted on patients parkinsonism showed trend towards different those gait speed. No assessed fecal other performance. several studies, mainly cross-sectional design, suggest frailty, mostly according deficit accumulation model. Namely, was lower representation butyrate-producing bacteria. Therefore, conclude that causal link fitness still uncertain due lack large number covariates, diet, exercise, multimorbidity, polypharmacy, both function older age. relationship remains very promising area research future.

Language: Английский

---

The microbiome extends host evolutionary potential

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Aug. 26, 2021

Abstract The microbiome shapes many host traits, yet the biology of microbiomes challenges traditional evolutionary models. Here, we illustrate how integrating into quantitative genetics can help untangle complexities host-microbiome evolution. We describe two general ways in which may affect potential: by shifting mean phenotype and changing variance population. synthesize literature across diverse taxa discuss these scenarios could shape response to selection. conclude outlining key avenues research improve our understanding complex interplay between hosts microbiomes.

Language: Английский

---

Gut microbiota in ulcerative colitis: insights on pathogenesis and treatment

Journal of Digestive Diseases, Journal Year: 2020, Volume and Issue: 21(3), P. 147 - 159

Published: Feb. 10, 2020

Gut microbiota constitute the largest reservoir of human microbiome and are an abundant stable ecosystem-based on its diversity, complexity, redundancy, host interactions This ecosystem is indispensable for development health. The integrity intestinal mucosal barrier depends with gut microbiota. commensal bacterial community implicated in pathogenesis inflammatory bowel disease (IBD), including ulcerative colitis (UC). dysbiosis microbes characterized by reduced biodiversity, abnormal composition microbiota, altered spatial distribution, as well among between different strains host. defects microecology, related metabolic pathways molecular mechanisms, play a critical role innate immunity mucosa UC. Fecal transplantation (FMT) has been used to treat many diseases most promising outcome reported antibiotic-associated diarrhea, followed IBD. review evaluated results various reports FMT efficacy remains highly controversial, needs be regularized integrated management, standardization procedures, individualization treatment.

Language: Английский

---

Emerging strategies for precision microbiome management in diverse agroecosystems

Nature Plants, Journal Year: 2021, Volume and Issue: 7(3), P. 256 - 267

Published: March 8, 2021

Language: Английский

---

The Effects of Temperature on Animal Gut Microbiomes

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: March 10, 2020

Temperature is a prominent abiotic environmental variable that drives the adaptive trajectories of animal lineages and structures composition communities. Global temperature regimes are expected to undergo rapid shifts in next century, yet for many taxa we lack an understanding consequences these predicted populations. In this review, synthesize recent evidence variation shapes function gut microbiomes, key regulators host physiology, with potential population responses climate change. Several studies spanning range taxa, including Chordata, Arthropoda, Mollusca, have reported repeatable associations between community microbiome. several cases, same microbiome been observed across distantly related suggesting existence conserved mechanisms underlying temperature-induced plasticity. Extreme temperatures can disrupt stability alpha-diversity within microbiomes individual hosts generate beta-diversity among Microbiome states resulting from extreme associated, some cases causally linked, both beneficial deleterious effects on phenotypes. We propose routes by which changes may impact fitness, colonization resistance gut, energy nutrient assimilation, life history traits. Cumulatively, available data indicate disruption be mechanism changing will fitness wild-living

Language: Английский

---

The Structure of Ecological Networks Across Levels of Organization

Annual Review of Ecology Evolution and Systematics, Journal Year: 2020, Volume and Issue: 51(1), P. 433 - 460

Published: Sept. 1, 2020

Interactions connect the units of ecological systems, forming networks. Individual-based networks characterize variation in niches among individuals within populations. These individual-based merge with each other, species-based and food webs that describe architecture communities. Networks at broader spatiotemporal scales portray structure interactions across landscapes over macroevolutionary time. Here, I review patterns observed multiple levels biological organization. A fundamental challenge is to understand amount interdependence as we move from beyond. Despite uneven distribution studies, regularities network emerge due architectural shared by complex interplay between traits numerical effects. illustrate integration these organizational exploring consequences emergence highly connected species for structures scales.

Language: Английский

---

Simple animal models for microbiome research

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(12), P. 764 - 775

Published: Aug. 15, 2019

Language: Английский

---

Bacterial species rarely work together

Science, Journal Year: 2022, Volume and Issue: 376(6593), P. 581 - 582

Published: May 5, 2022

Competition is prevalent and could be harnessed as an alternative to antibiotics.

Language: Английский

---