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 21 Profiling sow vaginal and fecal and piglet gastrointestinal microbiome and the passage of sow microbiome to their progeny from birth to weaning

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 21-21
Author(s):  
Huyen Tran ◽  
Brenda de Rodas ◽  
Manohar M Lahoti ◽  
Timothy J Johnson
Keyword(s):  
Alpha Diversity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Gastrointestinal Microbiome ◽  
Core Microbiome ◽  
Linear Discriminant ◽  
Fecal Microbiome ◽  
The Core ◽  
Vaginal Swabs ◽  
Sampling Points

Abstract The objectives of this study were 1) to profile the sow vaginal and fecal microbiome and the corresponding piglet gastrointestinal microbiome from birth to weaning, and 2) to identify the core microbiome shared between sows and piglets. A total of 226 samples collected from sows (vaginal swabs pre-farrow; fecal samples at farrow, d 3, 7, 10, 17 post-farrow) and their progenies (stomach, ileum, and colon digesta at birth, d 2, and 14 after birth) were used for the analyses of microbial community structure using 16S rRNA V4 amplicon sequencing with Illumina MiSeq. Our data indicated that the piglet and sow microbiome were quite distinct. Piglets had lower bacterial alpha diversity (chao1, richness, Shannon, Simpson indices; P < 0.01) than sows across all timepoints. Beta diversity of piglets by sample types was significantly different (P < 0.001) than sows by sample types when averaged across all timepoints or separation by timepoints. Feature selection by the Linear discriminant analysis effect size (LEfSe) indicated that the genera associated with piglets included those classified as Lactobacillus, unclassified Micrococcaceae, and Rothia when averaged across sampling points and sample types. Genera associated with sows included those classified as Treponema, YRC22, Unclassified RF39, Unclassified Christensenellaceae, Turicibacter, Unclassified RFP12, Unclassified F16, Collinsella, Coprococcus, Unclassified Coriobacteriaceae, and Unclassified Mogibacteriaceae. The genera shared between sow vaginal samples and piglets included those classified as Bacteroides, Fusobacterium, Haemophilus, Prevotella, Veillonella, and unclassified Clostridiadiaceae. The genera shared between sow fecal and piglet samples included those classified as Bacteroides, Lactobacillus, unclassified Clostridiadiaceae, unclassified Ruminococceae, and Prevotella. Overall, there are evidences that bacterial genera were passed from sows to piglets and influenced the microbial communities of piglets later in life.

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 Rolling a mycobiome down a hill: endophytes in the Taiwanese Cloud Forest

2017 ◽  
Author(s):  
Dan Thomas ◽  
Roo Vandegrift ◽  
Yu-Ming Ju ◽  
Monica Hsieh ◽  
Bitty Roy
Keyword(s):  
Tree Species ◽  
Spatial Scales ◽  
Cloud Forest ◽  
Fungal Endophytes ◽  
Amplicon Sequencing ◽  
Fungal Endophyte ◽  
Core Microbiome ◽  
The Core ◽  
Host Tree Species ◽  
Ecological Importance

AbstractFungal endophytes of plants are ubiquitous and important to host plant health. Despite their ecological importance, landscape-level patterns of microbial communities in plant hosts are not well-characterized. Fungal wood-inhabiting and foliar endophyte communities from multiple tree hosts were sampled at multiple spatial scales across a 25 ha subtropical research plot in northern Taiwan, using culture-free, community DNA amplicon sequencing methods. Fungal endophyte communities were distinct between leaves and wood, but the mycobiomes were highly variable across and within tree species. Of the variance that could be explained, host tree species was the most important driver of mycobiome community-composition. Within a single tree species, “core” mycobiomes were characterized using cooccurrence analysis. These core groups of endophytes in leaves and wood show divergent spatial patterns. For wood endophytes, a more consistent, “minimal” core mycobiome coexisted with the host across the extent of the study. For leaf endophytes, the core fungi resembled a more dynamic, “gradient” model of the core microbiome, changing across the topography and distance of the study.

scholarly journals Bacterial and Fungal Endophytic Microbiomes of Salicornia europaea

2019 ◽  
Vol 85 (13) ◽  
Author(s):  
Bliss Ursula Furtado ◽  
Marcin Gołębiewski ◽  
Monika Skorupa ◽  
Piotr Hulisz ◽  
Katarzyna Hrynkiewicz
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Community Composition ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Salicornia Europaea ◽  
Core Microbiome ◽  
Plant Organs ◽  
Content Type ◽  
Microbial Groups

ABSTRACT We examined Salicornia europaea, a nonmycorrhizal halophyte associated with specific and unique endophytic bacteria and fungi. The microbial community structure was analyzed at two sites differing in salinization history (anthropogenic and naturally saline site), in contrasting seasons (spring and fall) and in two plant organs (shoots and roots) via 16S rRNA and internal transcribed spacer amplicon sequencing. We observed distinct communities at the two sites, and in shoots and roots, while the season was of no importance. The bacterial community was less diverse in shoot libraries than in roots, regardless of the site and season, whereas no significant differences were observed for the fungal community. Proteobacteria and Bacteroidetes dominated bacterial assemblages, and Ascomycetes were the most frequent fungi. A root core microbiome operational taxonomic unit belonging to the genus Marinimicrobium was identified. We detected a significant influence of the Salicornia bacterial community on the fungal one by means of cocorrespondence analysis. In addition, pathways and potential functions of the bacterial community in Salicornia europaea were inferred and discussed. We can conclude that bacterial and fungal microbiomes of S. europaea are determined by the origin of salinity at the sites. Bacterial communities seemed to influence fungal ones, but not the other way around, which takes us closer to understanding of interactions between the two microbial groups. In addition, the plant organs of the halophyte filter the microbial community composition. IMPORTANCE Endophytes are particularly fascinating because of their multifaceted lifestyle, i.e., they may exist as either free-living soil microbes or saprobic ones or pathogens. Endophytic communities of halophytes may be different than those in other plants because salinity acts as an environmental filter. At the same time, they may contribute to the host’s adaptation to adverse environmental conditions, which may be of importance in agriculture.

scholarly journals Core of the saliva microbiome: an analysis of the MG-RAST data

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Simone G. Oliveira ◽  
Rafaela R. Nishiyama ◽  
Claudio A. C. Trigo ◽  
Ana Luiza Mattos-Guaraldi ◽  
Alberto M. R. Dávila ◽  
...  
Keyword(s):  
Statistical Tests ◽  
Principal Component ◽  
Amplicon Sequencing ◽  
Health Condition ◽  
Oral Microbiota ◽  
Oral Diseases ◽  
Core Microbiome ◽  
Shotgun Metagenomics ◽  
The Core ◽  
Spearman’S Correlation

Abstract Background Oral microbiota is considered as the second most complex in the human body and its dysbiosis can be responsible for oral diseases. Interactions between the microorganism communities and the host allow establishing the microbiological proles. Identifying the core microbiome is essential to predicting diseases and changes in environmental behavior from microorganisms. Methods Projects containing the term “SALIVA”, deposited between 2014 and 2019 were recovered on the MG-RAST portal. Quality (Failed), taxonomic prediction (Unknown and Predicted), species richness (Rarefaction), and species diversity (Alpha) were analyzed according to sequencing approaches (Amplicon sequencing and Shotgun metagenomics). All data were checked for normality and homoscedasticity. Metagenomic projects were compared using the Mann–Whitney U test and Spearman's correlation. Microbiome cores were inferred by Principal Component Analysis. For all statistical tests, p < 0.05 was used. Results The study was performed with 3 projects, involving 245 Amplicon and 164 Shotgun metagenome datasets. All comparisons of variables, according to the type of sequencing, showed significant differences, except for the Predicted. In Shotgun metagenomics datasets the highest correlation was between Rarefaction and Failed (r =  − 0.78) and the lowest between Alpha and Unknown (r =  − 0.12). In Amplicon sequencing datasets, the variables Rarefaction and Unknown (r = 0.63) had the highest correlation and the lowest was between Alpha and Predicted (r =  − 0.03). Shotgun metagenomics datasets showed a greater number of genera than Amplicon. Propionibacterium, Lactobacillus, and Prevotella were the most representative genera in Amplicon sequencing. In Shotgun metagenomics, the most representative genera were Escherichia, Chitinophaga, and Acinetobacter. Conclusions Core of the salivary microbiome and genera diversity are dependent on the sequencing approaches. Available data suggest that Shotgun metagenomics and Amplicon sequencing have similar sensitivities to detect the taxonomic level investigated, although Shotgun metagenomics allows a deeper analysis of the microorganism diversity. Microbiome studies must consider characteristics and limitations of the sequencing approaches. Were identified 20 genera in the core of saliva microbiome, regardless of the health condition of the host. Some bacteria of the core need further study to better understand their role in the oral cavity.

THE CORE AND PERIPHERY OF THE CURRENT CULTURE OF ARTISTIC CREATION ABOUT THE GREAT PATRIOTIC WAR IN THE STUDENTS’ VIEWS

2020 ◽  
Vol 6 (3) ◽  
pp. 130-149
Author(s):  
Elena N. NARKHOVA ◽  
Dmitry Yu. NARKHOV
Keyword(s):  
Historical Memory ◽  
Soviet Period ◽  
Russian Society ◽  
Student Culture ◽  
The Core ◽  
Musical Works ◽  
Great Patriotic War ◽  
History Of ◽  
Current Student ◽  
Historical Periods

This article analyzes the degree of demand for works of art (films and television films and series, literary and musical works, works of monumental art) associated with the history of the Great Patriotic War among contemporary students. This research is based on the combination of two theories, which study the dynamics and statics of culture in the society — the theory of the nucleus and periphery by Yu. M. Lotman and the theory of actual culture by L. N. Kogan. The four waves of research (2005, 2010, 2015, 2020) by the Russian Society of Socio¬logists (ROS) have revealed a series of works in various genres on this topic in the core structure and on the periphery of the current student culture; this has also allowed tracing the dynamics of demand and the “movement” of these works in the sociocultural space. The authors introduce the concept of the archetype of the echo of war. The high student recognition of works of all historical periods (from wartime to the present day) is shown. A significant complex of works has been identified, forming two contours of the periphery. Attention is drawn to the artistic work of contemporary students as a way to preserve the historical memory of the Great Patriotic War. This article explains the necessity of preserving the layer of national culture in order to reproduce the national identity in the conditions of informational and ideological pluralism of the post-Soviet period. The authors note the differentiation of youth due to the conditions and specifics of socialization in the polysemantic sociocultural space.

Indexicality of Grammar: The Case of Japanese Transgender Speakers

2019 ◽  
Author(s):  
Hideko Abe
Keyword(s):  
Gender Identity ◽  
Gender Identity Disorder ◽  
Grammatical Gender ◽  
Core Structure ◽  
Subject Positions ◽  
Transgender Identity ◽  
The Core ◽  
History Of ◽  
History Of Scholarship ◽  
Grammatical Structures

This article discusses how the intersection of grammatical gender and social gender, entwined in the core structure of language, can be analyzed to understand the dynamic status of selfhood. After reviewing a history of scholarship that demonstrates this claim, the discussion analyzes the language practices of transgender individuals in Japan, where transgender identity is currently understood in terms of sei-dōitsusei-shōgai (gender identity disorder). Based on fieldwork conducted between 2011 and 2017, the analysis reveals how individuals identifying with sei-dōitsusei-shōgai negotiate subject positions by manipulating the specific indexical meanings attached to grammatical structures.

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 18S rRNA Analysis Reveals High Diversity of Phytoplankton with Emphasis on a Naked Dinoflagellate Gymnodinium sp. at the Han River (Korea)

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 73
Author(s):  
Buhari Lawan Muhammad ◽  
Taehee Kim ◽  
Jang-Seu Ki
Keyword(s):  
Water Quality ◽  
Quality Management ◽  
18S Rrna ◽  
Water Quality Management ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Freshwater Ecosystems ◽  
Reservoir Area ◽  
Han River ◽  
Phytoplankton Communities

Biomonitoring of phytoplankton communities in freshwater ecosystems is imperative for efficient water quality management. In the present study, we present the seasonal diversity of phytoplankton from the non-reservoir area of the Han River (Korea), assessed using the 18S rRNA amplicon sequencing. Our results uncovered a considerably high eukaryotic diversity, which was predominantly represented by phytoplankton in all the seasons (38–63%). Of these, the diatoms, Cyclostephanos tholiformis, Stephanodiscus hantzschii, and Stephanodiscus sp., were frequently detected in spring and winter. Interestingly, for the first time in the Han River, we detected a large number of operational taxonomic unit (OTU) reads belonging to the naked dinoflagellate Gymnodinium sp., which dominated in autumn (15.8%) and was observed only in that season. Molecular cloning and quantitative real-time polymerase chain reaction (PCR) confirmed the presence of Gymnodinium sp. in the samples collected in 2012 and 2019. Moreover, a comparison of the present data with our previous data from a reservoir area (Paldang Dam) revealed similar patterns of phytoplankton communities. This molecular approach revealed a prospective toxic species that was not detected through microscopy. Collectively, resolving phytoplankton communities at a level relevant for water quality management will provide a valuable reference for future studies on phytoplankton for environmental monitoring.

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