Defining and quantifying the core microbiome: Challenges and prospects

2021 ◽  
Vol 118 (51) ◽  
pp. e2104429118
Author(s):  
Alexander T. Neu ◽  
Eric E. Allen ◽  
Kaustuv Roy
Keyword(s):  
Microbial Ecology ◽  
Representative Sample ◽  
Sequence Variants ◽  
Core Microbiome ◽  
The Core ◽  
Taxonomic Level ◽  
Functional Attributes ◽  
Wide Range ◽  
Ecological Roles ◽  
History Of

The term “core microbiome” has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.

scholarly journals Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Marine Drugs ◽  
2020 ◽  
Vol 18 (6) ◽  
pp. 298
Author(s):  
Alison E. Murray ◽  
Nicole E. Avalon ◽  
Lucas Bishop ◽  
Karen W. Davenport ◽  
Erwan Delage ◽  
...  
Keyword(s):  
Marine Invertebrate ◽  
Bioactive Compound ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Specific Sequence ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
The Core ◽  
Synoicum Adareanum ◽  
Palmerolide A

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

scholarly journals Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling

mSystems ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Shuo Jiao ◽  
Yiqin Xu ◽  
Jie Zhang ◽  
Xin Hao ◽  
Yahai Lu
Keyword(s):  
Nutrient Cycling ◽  
Microbial Ecology ◽  
Eastern China ◽  
Habitat Preferences ◽  
Soil Nutrient ◽  
Rice Soils ◽  
Core Microbiota ◽  
Continental Scale ◽  
The Core ◽  
Ecological Roles

ABSTRACT Revealing the ecological roles of the core microbiota in community maintaining and soil nutrient cycling is crucial for understanding ecosystem function, yet there is a dearth of continental-scale studies on this fundamental topic in microbial ecology. Here, we collected 251 soil samples from adjacent pairs of maize and rice fields at a continental scale in eastern China. We revealed the major ecological roles of the core microbiota in maintaining complex connections between bacterial taxa and their associations with belowground multinutrient cycling. By identifying the habitat preferences of the core microbiota, we built a continental atlas for mapping the spatial distributions of bacteria in agro-soils, which helps forecast the responses of agricultural ecosystems to anthropogenic disturbance. The multinutrient cycling index for maize and rice soils was related to bacterial α-diversity and β-diversity, respectively. Rice soils exhibited higher bacterial diversity and closer bacterial cooccurrence relationships than maize soils. In contrast to the macro- or microecological latitudinal richness patterns in natural terrestrial ecosystems, the bacteria in maize soils showed higher richness at high latitudes; however, this trend was not observed in rice soils. This study provides a new perspective on the distinct bacterial biogeographic patterns to predict the ecological roles of the core microbiota in agro-soils and thus helps manage soil bacterial communities for better provisioning of key ecosystem services. IMPORTANCE Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services—the ultimate goal of microbial ecology.

Partitioning experiments in the laser-heated diamond anvil cell: volatile content in the Earth's core

2008 ◽  
Vol 366 (1883) ◽  
pp. 4295-4314 ◽  
Author(s):  
Andrew P Jephcoat ◽  
M. Ali Bouhifd ◽  
Don Porcelli
Keyword(s):  
Trace Elements ◽  
Diamond Anvil Cell ◽  
The Core ◽  
The Earth ◽  
Wide Range ◽  
Recent Developments ◽  
Mantle Reservoir ◽  
History Of ◽  
Diamond Anvil ◽  
Laser Heated

The present state of the Earth evolved from energetic events that were determined early in the history of the Solar System. A key process in reconciling this state and the observable mantle composition with models of the original formation relies on understanding the planetary processing that has taken place over the past 4.5 Ga. Planetary size plays a key role and ultimately determines the pressure and temperature conditions at which the materials of the early solar nebular segregated. We summarize recent developments with the laser-heated diamond anvil cell that have made possible extension of the conventional pressure limit for partitioning experiments as well as the study of volatile trace elements. In particular, we discuss liquid–liquid, metal–silicate (M–Sil) partitioning results for several elements in a synthetic chondritic mixture, spanning a wide range of atomic number—helium to iodine. We examine the role of the core as a possible host of both siderophile and trace elements and the implications that early segregation processes at deep magma ocean conditions have for current mantle signatures, both compositional and isotopic. The results provide some of the first experimental evidence that the core is the obvious replacement for the long-sought, deep mantle reservoir. If so, they also indicate the need to understand the detailed nature and scale of core–mantle exchange processes, from atomic to macroscopic, throughout the age of the Earth to the present day.

scholarly journals Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions

Animals ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 4
Author(s):  
Giulietta Minozzi ◽  
Filippo Biscarini ◽  
Emanuela Dalla Costa ◽  
Matteo Chincarini ◽  
Nicola Ferri ◽  
...  
Keyword(s):  
Animal Health ◽  
Control Group ◽  
P Value ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Core Microbiome ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
The Core ◽  
Wide Range

The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated with management and housing of animals increases the hypothalamic–pituitary axis activity, with growing evidence that the microbiome composition can be modified. Therefore, the purpose of the present study was to describe the core microbiome in sheep, characterized using 16S rRNA gene sequencing, and to explore whether exposure to stressful husbandry conditions changed sheep hindgut microbiome composition. Sheep (n = 10) were divided in two groups: isolated group (individually separated for 3 h/day) and control group (housed in the home pen for the entire trial period). Sheep core microbiome was dominated by Firmicutes (43.6%), Bacteroidetes (30.38%), Proteobacteria (10.14%), and Verrucomicrobia (7.55%). Comparative results revealed few operational taxonomic units (OTUs) with significantly different relative abundance between groups. Chao1, abundance-based coverage estimator (ACE), and Fisher’s alpha indices did not show differences between groups. OTU-based Bray–Curtis distances between groups were not significant (p-value = 0.07). In conclusion, these results describing the core microbiome of sheep do not suggest a strong effect of stressful husbandry conditions on microbial composition.

scholarly journals Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7744 ◽  
Author(s):  
Gian Maria Niccolò Benucci ◽  
Reid Longley ◽  
Peng Zhang ◽  
Qi Zhao ◽  
Gregory Bonito ◽  
...  
Keyword(s):  
16S Rdna ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Human Consumption ◽  
Fruiting Bodies ◽  
Core Microbiome ◽  
Microbial Indicators ◽  
The Core ◽  
History Of ◽  
Body Production

Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.

scholarly journals Uncovering the core microbiome and distributions of palmerolide in Synoicum adareanum across the Anvers Island archipelago, Antarctica

2020 ◽  
Author(s):  
Alison Murray ◽  
Nicole Avalon ◽  
Lucas Bishop ◽  
Karen W. Davenport ◽  
Erwan Delage ◽  
...  
Keyword(s):  
Specific Activity ◽  
Marine Invertebrate ◽  
Bioactive Compound ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Specific Sequence ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
The Core ◽  
Synoicum Adareanum

AbstractPolar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganismal diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which the bioactive macrolide that has specific activity to melanoma, palmerolide A (PalA), was found. PalA bears structural resemblance to a combined nonribosomal peptide polyketide, that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64° 46'S, 64° 03'W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island archipelago. The microbiome composition (V3-V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacteria, 20 of which were distinct from regional bacterioplankton. Co-occurrence analysis yielded several potentially interacting subsystems and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. Taking these results together with an analysis of biosynthetic potential of related microbiome taxa indicates a core microbiome with substantial promise for natural product biosynthesis that likely interact with the host and with each other.

Project WAGR: The UK Demonstration Project for Power Reactor Decommissioning - The Core and Beyond

2003 ◽  
Author(s):  
Terry Benest
Keyword(s):  
Pressure Vessel ◽  
Reactor Core ◽  
Processing Route ◽  
Nuclear Facilities ◽  
The Core ◽  
Research Activities ◽  
Wide Range ◽  
Cutting Equipment ◽  
History Of ◽  
The Uk

The United Kingdom Atomic Energy Authority (UKAEA) has built and operated a wide range of nuclear facilities since the late 1940s. UKAEA’s present mission is to restore the environment of these facilities in a safe and secure manner. This restoration includes the decommissioning of a number of redundant research and power reactors. The Windscale Advanced Gas-cooled Reactor (WAGR) operated at an output of 33 MW (e) from 1963–1981 and comprised a carbon dioxide cooled, graphite moderated reactor using uranium dioxide fuel in stainless steel cans. WAGR was the prototype reactor used to develop technologies for the family of full-scale commercial AGRs that followed. Following shutdown, UKAEA decided to continue their research activities into the decommissioning phase to develop dismantling techniques and establish waste routes. The initial phases of the project involved the construction of the waste handling route and the design and construction of a remote dismantling machine and an interim ILW store. The reactor core and pressure vessel is now being dismantled in a programme of 10 campaigns. This paper will summarise the history of the reactor, the operation of the waste-processing route, the installed dismantling equipment and the successful completion of the first seven campaigns. The rapid completion of Campaign 6, “the reactor core and restraint structures”, will be described in detail. The paper will also describe work to develop remotely operated oxy-propane cutting equipment to dismantle the core support structures and the pressure vessel and due to be used in 2003/2004. Special attention will be given in this paper to the recent rapid progress in the remote dismantling campaigns and the low radiation doses incurred by operators.

Non-disruptive Disruptions: Cleantech and the New Green Spirit of Capitalism

2018 ◽  
pp. 17-36
Author(s):  
Jesse Goldstein
Keyword(s):  
Agricultural Practices ◽  
Agricultural Improvement ◽  
Industrial Economy ◽  
Disruptive Technologies ◽  
The Core ◽  
Wide Range ◽  
Land Grabs ◽  
History Of ◽  
Spirit Of Capitalism ◽  
Potential Improvement

After overviewing the history of cleantech, Chapter One introduces the core contradiction investigated throughout the text: while the professionals I met were excited about “disruptive” technologies that might radically transform society, when it came to actually finding (and funding) commercially viable projects, disruption quickly gave way to incremental gains in already established markets. Building off of Boltanski and Chiappello’s New Spirit of Capitalism, I argue that planetary improvement represents a new, green spirit of capitalism that mobilizes a seemingly radical, anti-systemic critique of capitalism in order to provide moral legitimacy for proposals to create a better, greener version of the modern industrial economy. As a term, planetary improvement references the discourse of agricultural improvement that helped legitimize enclosure and colonial land grabs in the first centuries of capitalism’s ascent. Agricultural improvement targeted ‘inefficient’ forms of agricultural production – from those practiced by European commoners to a wide range of indigenous agricultural practices throughout the colonized world. In a similar way, planetary improvement recasts ‘dirty’ or ‘wasteful’ forms of industrial production and consumer-driven lifestyles as a terrain of potential improvement. Instead of inefficient commoners or inefficient laborers, here it is capital itself that is guilty of being wasteful.

Filosofie jako životní cesta

2019 ◽  
Keyword(s):  
Final Part ◽  
The Core ◽  
Wide Range ◽  
University Life ◽  
History Of ◽  
Curriculum Vitae ◽  
Life Journey ◽  
Selection Of

The collection of papers Philosophy as a Life Journey was published in honour of Jan Zouhar, a distinguished professor, an expert in the history of Czech philosophy and an organizer of university life. The volume begins with an interview in which Professor Zouhar outlines his philosophical creed. The core of the collection comprises six personal contributions (Laudationes) and sixteen original scientific works that focus on a wide range of issues related to philosophy, history, literature, language, ethnography and culture. The final part of the volume (Appendices) contains a brief curriculum vitae of Professor Zouhar and a selection of his works and photographs followed by a list of volume contributors.

Group Experiences and Individual Differences in Stuttering

2019 ◽  
Vol 62 (12) ◽  
pp. 4335-4350 ◽  
Author(s):  
Seth E. Tichenor ◽  
J. Scott Yaruss
Keyword(s):  
Individual Differences ◽  
Support Groups ◽  
Support Group ◽  
Affective States ◽  
Life Outcomes ◽  
Self Help ◽  
Wide Range ◽  
Group Experiences ◽  
History Of ◽  
Adults Who Stutter

Purpose This study explored group experiences and individual differences in the behaviors, thoughts, and feelings perceived by adults who stutter. Respondents' goals when speaking and prior participation in self-help/support groups were used to predict individual differences in reported behaviors, thoughts, and feelings. Method In this study, 502 adults who stutter completed a survey examining their behaviors, thoughts, and feelings in and around moments of stuttering. Data were analyzed to determine distributions of group and individual experiences. Results Speakers reported experiencing a wide range of both overt behaviors (e.g., repetitions) and covert behaviors (e.g., remaining silent, choosing not to speak). Having the goal of not stuttering when speaking was significantly associated with more covert behaviors and more negative cognitive and affective states, whereas a history of self-help/support group participation was significantly associated with a decreased probability of these behaviors and states. Conclusion Data from this survey suggest that participating in self-help/support groups and having a goal of communicating freely (as opposed to trying not to stutter) are associated with less negative life outcomes due to stuttering. Results further indicate that the behaviors, thoughts, and experiences most commonly reported by speakers may not be those that are most readily observed by listeners.

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