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

---

Biodegradation of PET: Current Status and Application Aspects

ACS Catalysis, Год журнала: 2019, Номер 9(5), С. 4089 - 4105

Опубликована: Апрель 8, 2019

Most petroleum-derived plastics, as exemplified by poly(ethylene terephthalate) (PET), are chemically inactive and highly resistant to microbial attack. The accumulation of plastic waste results in environmental pollution threatens ecosystems, referred the "microplastic issue". Recently, PET hydrolytic enzymes (PHEs) have been identified we reported degradation a consortium its bacterial resident, Ideonella sakaiensis. Bioremediation may thus provide an alternative solution recycling waste. mechanism into benign monomers hydrolase mono(2-hydroxyethyl) terephthalic acid (MHET) from I. sakaiensis has elucidated; nevertheless, biodegradation require additional development for commercialization owing low catalytic activity these enzymes. Here, introduce degrading microorganisms involved, along with evolution PHEs address issues that hamper enzymatic degradation. Potential applications also discussed.

Язык: Английский

---

Ecology and evolution of metabolic cross-feeding interactions in bacteria

Natural Product Reports, Год журнала: 2018, Номер 35(5), С. 455 - 488

Опубликована: Янв. 1, 2018

The causes and consequences of bacterial metabolic cross-feeding mutualisms.

Язык: Английский

---

Understanding microbial community dynamics to improve optimal microbiome selection

Microbiome, Год журнала: 2019, Номер 7(1)

Опубликована: Июнь 3, 2019

Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over decade, but the method not been systematically optimised nor mechanisms behind its success, or failure, determined. Microbial are highly dynamic and, hence, go through distinct and rapid stages community succession, consequent effect this may have on artificially selected is unknown. Using chitin as case study, we successfully with enhanced chitinase activities found continuous optimisation incubation times between selective transfers was utmost importance. The analysis composition entire revealed fundamental aspects in ecology: when were optimal, system dominated by Gammaproteobacteria (i.e. main bearers enzymes drivers degradation), before being succeeded cheating, cross-feeding grazing organisms. microbiomes to enhance widely used, though success selecting appears require optimal order avoid loss trait consequence an inevitable succession. A comprehensive understanding dynamics will improve future studies.

Язык: Английский

---

The Life of an Insect Endosymbiont from the Cradle to the Grave

Current Biology, Год журнала: 2019, Номер 29(11), С. R485 - R495

Опубликована: Июнь 1, 2019

Язык: Английский

---

Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Апрель 7, 2021

Abstract Background Microbial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria , one the most widely distributed bacterial phyla soils, are known for their ability degrade vitro. However, situ importance and specific activity across contrasting ecological environments not known. Here, we conducted three field experiments with buried straw combination microcosm 13 C-straw paddy soils under different soil fertility levels reveal ecophysiological roles residue decomposition. Results While accounting only 4.6% total abundance, encoded 16% abundance carbohydrate-active enzymes (CAZymes). The taxonomic functional compositions were, surprisingly, relatively stable during Slopes linear regression models between chemical composition Actinobacterial traits were flatter than those other groups at both local regional scales due holding genes encoding full set CAZymes, nitrogenases, antibiotic synthetases. Ecological co-occurrence network C-based metagenomic analyses indicated that degradation increased less fertile as links community members relative abundances decreasing fertility. Conclusions This study provided DNA-based evidence non-dominant plays a key role possess high proportions CAZymes group maintain presence terms roles. Their was more pronounced where possession interspecies interactions stood out more. Our work provides new angles understanding global cycling.

Язык: Английский

---

Microbial interactions for nutrient acquisition in soil: Miners, scavengers, and carriers

Soil Biology and Biochemistry, Год журнала: 2023, Номер 188, С. 109215 - 109215

Опубликована: Окт. 24, 2023

Язык: Английский

---

Dryland microbiomes reveal community adaptations to desertification and climate change

The ISME Journal, Год журнала: 2024, Номер 18(1)

Опубликована: Янв. 1, 2024

Abstract Drylands account for 45% of the Earth’s land area, supporting ~40% global population. These regions support some most extreme environments on Earth, characterized by temperatures, low and variable rainfall, soil fertility. In these biomes, microorganisms provide vital ecosystem services have evolved distinctive adaptation strategies to endure flourish in extreme. However, dryland microbiomes they are under threat due intensifying desertification climate change. this review, we a synthesis our current understanding microbial life drylands, emphasizing remarkable diversity adaptations communities. We then discuss anthropogenic threats, including influence change outline knowledge gaps. Finally, propose research priorities address those gaps safeguard sustainability fragile biomes.

Язык: Английский

---

The effect of the algal microbiome on industrial production of microalgae

Microbial Biotechnology, Год журнала: 2018, Номер 11(5), С. 806 - 818

Опубликована: Июль 5, 2018

Microbes are ubiquitously distributed, and they also present in algae production systems. The algal microbiome is a pivotal part of the alga holobiont has key role modulating populations nature. However, there lack knowledge on bacteria artificial systems ranging from laboratory flasks to industrial ponds. Coexisting microorganisms, predominantly bacteria, often regarded as contaminants research, but recent studies manifested that many symbionts not only promote growth offer advantages downstream processing. Because high expectations for microalgae bio-based economy, better understanding benefits risks algal-microbial associations important industry. Reducing cost may be through applying specific enhance at large scale well preventing broad spectrum pathogens. In this review, we highlight latest algae-microbial interactions their underlying mechanisms, discuss large-scale algal-bacterial cocultivation extend such range biotechnological applications.

Язык: Английский

---

Current Trends and Potential Applications of Microbial Interactions for Human Welfare

Frontiers in Microbiology, Год журнала: 2018, Номер 9

Опубликована: Июнь 1, 2018

For a long time, it was considered that interactions between microbes are only inhibitory in nature. However, latest developments research have demonstrated within our environment, several classes of exist which produce different products upon interaction and thus embrace wider scope useful potentially valuable aspects beyond simple antibiosis. Therefore, the current review explores types microbial describes role various physical, chemical, biological, genetic factors regulating such interactions. It further explains mechanism action biofilm formation secondary metabolites bacteria-fungi interaction. Special emphasis focus is placed on important medicine, food industry, agriculture, environment. In short, this reveals recent contributions for benefit mankind.

Язык: Английский

---