Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar

Pe poke is a naturally fermented sticky soybean food of Myanmar. The present study was aimed to profile the whole microbial community structure and their predictive gene functionality of pe poke samples prepared in different fermentation periods viz. 3 day (3ds), 4 days (4ds), 5 days (5ds) and sun-dried sample (Sds). The pH of samples was 7.6 to 8.7, microbial load was 2.1–3.9 x 108 cfu/g with dynamic viscosity of 4.0±1.0 to 8.0±1.0cP. Metataxonomic profile of pe poke samples showed different domains viz. bacteria (99.08%), viruses (0.65%), eukaryota (0.08%), archaea (0.03%) and unclassified sequences (0.16%). Firmicutes (63.78%) was the most abundant phylum followed by Proteobacteria (29.54%) and Bacteroidetes (5.44%). Bacillus thermoamylovorans was significantly abundant in 3ds and 4ds (p<0.05); Ignatzschineria larvae was significantly abundant in 5ds (p<0.05), whereas, Bacillus subtilis was significantly abundant in Sds (p <0.05). A total of 172 species of Bacillus was detected. In minor abundance, the existence of bacteriophages, archaea, and eukaryotes were also detected. Alpha diversity analysis showed the highest Simpson’s diversity index in Sds comparable to other samples. Similarly, a non-parametric Shannon’s diversity index was also highest in Sds. Good’s coverage of 0.99 was observed in all samples. Beta diversity analysis using PCoA showed no significant clustering. Several species were shared between samples and many species were unique to each sample. In KEGG database, a total number of 33 super-pathways and 173 metabolic sub-pathways were annotated from the metagenomic Open Reading Frames. Predictive functional features of pe poke metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including various essential amino acids, different vitamins, and enzymes. Spearman’s correlation was inferred between the abundant species and functional features.

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A checklist of gilled mushrooms (Basidiomycota: Agaricomycetes) with diversity analysis in Hollongapar Gibbon Wildlife Sanctuary, Assam, India

Journal of Threatened Taxa ◽

10.11609/jott.1770.7.15.8272-8287 ◽

2015 ◽

Vol 7 (15) ◽

pp. 8272 ◽

Cited By ~ 1

Author(s):

Girish Gogoi ◽

Vipin Parkash

Keyword(s):

Species Richness ◽

Diversity Index ◽

Abundant Species ◽

Shannon Diversity Index ◽

Diversity Analysis ◽

Wildlife Sanctuary ◽

Shannon Diversity ◽

Number Of Species ◽

Simpson Diversity Index ◽

Richness Index

Hollongapar Gibbon Wildlife Sanctuary is comprised of five distinct compartments. A total of 138 species of gilled mushrooms belonging to 48 genera, 23 families, five orders of the class Agaricomycetes, division Basidiomycota, have been collected and analyzed. The order Agaricales was was found with the highest number of species (113), followed by Russulales (14), Polyporales (5), Cantharellales (4) and Boletales (2). The species Coprinellus disseminatus and Megacollybia rodmani have shown the highest (8.26) and the lowest density (0.05), respectively. A total of 24 species, e.g., Termitomyces albuminosus, Marasmius curreyi, Marasmiellus candidus, Leucocoprinus medioflavus, Mycena leaiana, Hygrocybe miniata, Collybia chrysoropha, Gymnopus confluens were common with frequency percentage of 11.9, whereas Megacollybia rodmani with less frequency percentage (2.4) was found only in few quadrates of the sanctuary. The highly abundant species were Termitomyces medius (91.7) and Coprinellus disseminatus (86.8), and less abundant species were Psilocybe wayanadensis (1.0) and Lepiota sp. (1.0) in the study site. The order of the species richness index (R) compartment wise was 2>3>4>5>1. Both the Shannon diversity index and Simpson diversity index of agarics was maximum (1.88, 0.98) in compartment 2, whereas minimum (1.72, 0.95) in compartment 1 and 5, respectively. Moreover, the compartment 2 was found very much similar with compartment 3 and very less similar with compartment 1.<div> </div>

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Study on the Diversity of Epiphytic Bacteria on Corn and Alfalfa using Illumina MiSeq/NovaSeq High-throughput Sequencing System

10.21203/rs.3.rs-561736/v1 ◽

2021 ◽

Author(s):

Mei-Xiao Wu ◽

hui Tang

Keyword(s):

High Throughput ◽

Beta Diversity ◽

High Throughput Sequencing ◽

Raw Materials ◽

Diversity Index ◽

Alpha Diversity ◽

Illumina Miseq ◽

Diversity Analysis ◽

Epiphytic Bacteria ◽

Paired End Sequencing

Abstract PurposeTo investigate the diversity of the epiphytic bacteria on corn and alfalfa collected in Hengshui city and Xingtai city, hebei province, China.MethodsIllumina MiSeq/NovaSeq High-throughput sequencing systerm was used to conduct Paired-end sequencing of community DNA fragments from surface of corn and alfalfa in Hengshui and Xingtai. QIIME2 and R language were employed to sort and calculate the number of sequences and taxonomic units for each sample. Thereafter, the abundance, distribution, alpha diversity index of species, beta diversity and the differences of abundance among the samples were analyzed. ResultAt phylum level, the advantage bacterium group are Proteobacteria (70%), Firmicutes (13%), Actinobacteria (9%) and Bacteroidetes (7%). The dominant genera are Pseudomonas (8%), Acinetobacter (4%), Chryseobacterium (3%), Hymenobacter (1%). Enterobacteriaceae (24%) are the most predominant bacteria on both corn and alfalfa samples. Alpha diversity analysis and beta diversity analysis showed that the diversity of epiphytic microbial community was significantly affected by plant species, but not by region. The diversity and richness of epiphytic bacterial community of alfalfa were significantly higher than that of corn, yet corn had more LAB than alfalfa samples. ConclusionThis study contributes to expanding our understanding of the diversity of epiphytic microorganisms in corn and alfalfa silage and provide a basis for the selection of raw materials.

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Health Benefits of Uses and Applications of Moringa oleifera in Bakery Products

Plants ◽

10.3390/plants10020318 ◽

2021 ◽

Vol 10 (2) ◽

pp. 318

Author(s):

Paula García Milla ◽

Rocío Peñalver ◽

Gema Nieto

Keyword(s):

Moringa Oleifera ◽

Essential Amino Acids ◽

Bakery Products ◽

Unani Medicine ◽

Functional Value ◽

Organoleptic Characteristics ◽

Wide Range ◽

Potential Applications ◽

Medicinal Properties ◽

Excellent Source

Moringa oleifera belongs to the Moringaceae family and is the best known of the native Moringa oleifera genus. For centuries, it has been used as a system of Ayurvedic and Unani medicine and has a wide range of nutritional and bioactive compounds, including proteins, essential amino acids, carbohydrates, lipids, fibre, vitamins, minerals, phenolic compounds, phytosterols and others. These characteristics allow it to have pharmacological properties, including anti-diabetic, anti-inflammatory, anticarcinogenic, antioxidant, cardioprotective, antimicrobial and hepatoprotective properties. The entire Moringa oleifera plant is edible, including its flowers, however, it is not entirely safe, because of compounds that have been found mainly in the root and bark, so the leaf was identified as the safest. Moringa oleifera is recognised as an excellent source of phytochemicals, with potential applications in functional and medicinal food preparations due to its nutritional and medicinal properties; many authors have experimented with incorporating it mainly in biscuits, cakes, brownies, meats, juices and sandwiches. The results are fascinating, as the products increase their nutritional value; however, the concentrations cannot be high, as this affects the organoleptic characteristics of the supplemented products. The aim of this study is to review the application of Moringa oleifera in bakery products, which will allow the creation of new products that improve their nutritional and functional value.

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Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽

10.1093/genetics/159.3.1103 ◽

2001 ◽

Vol 159 (3) ◽

pp. 1103-1115 ◽

Cited By ~ 1

Author(s):

Hongguang Shao ◽

Zhijian Tu

Keyword(s):

Phylogenetic Analyses ◽

Mosquito Species ◽

Open Reading Frames ◽

Inverted Repeats ◽

Sequence Comparisons ◽

Wide Range ◽

Multiple Copies ◽

Catalytic Motif ◽

Open The Doors ◽

Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

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Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds

Parasites & Vectors ◽

10.1186/s13071-021-04602-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Peter Halvarsson ◽

Johan Höglund

Keyword(s):

Species Richness ◽

Diversity Index ◽

Nematode Species ◽

Abundant Species ◽

Anthelmintic Treatment ◽

Host Age ◽

Larval Culture ◽

Nematode Parasites ◽

South Central ◽

Nematode Diversity

Abstract Background A novel way to study the species composition and diversity of nematode parasites in livestock is to perform deep sequencing on composite samples containing a mixture of different species. Herein we describe for the first time the nematode community structures (nemabiomes) inhabiting Swedish sheep and how these are/were affected by host age and recent anthelmintic treatments. Methods A total of 158 fecal samples were collected (n = 35 in 2007 and n = 123 in 2013–2016) and cultured from groups of sheep on 61 commercial farms in the south-central part of the country where most animals are grazed. Among the samples, 2 × 44 (56%) were paired collections from the same groups pre- and post-treatment with anthelmintics such as macrocyclic lactones, benzimidazoles or levamisole. Samples were analyzed for their nemabiome using the PacBio platform followed by bioinformatic sequence analysis with SCATA. Species richness and diversity were calculated and analyzed in R. Results Nematode ITS2 sequences were found in all larval culture samples except two, even though the fecal egg counts were below the McMaster threshold in 20 samples. Sequencing yielded, on average, 1008 sequences per sample. In total, 16 operational taxonomical units (OTU), all with ≥ 98 % identity to sequences in the NCBI database, were recognized. The OTUs found represented nematode species of which ten are commonly associated with sheep. Multiple species were identified in all pre-anthelmintic treatment larval culture samples. No effects on nematode diversity were found in relation to host age. On the other hand, recent anthelmintic treatment lowered species richness, especially after use of ivermectin and albendazole. Interestingly, despite zero egg counts after use of levamisole, these samples still contained nematode DNA and especially H. contortus. Conclusions Our findings provide evidence that nemabiome analysis combined with diversity index analysis provides an objective methodology in the study of the efficacy of anthelmintic treatment as both high and low abundant species were detected.

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Molecular markers and antioxidant activity in berry crops: Genetic diversity analysis

Canadian Journal of Plant Science ◽

10.4141/cjps2011-240 ◽

2012 ◽

Vol 92 (6) ◽

pp. 1121-1133 ◽

Cited By ~ 9

Author(s):

S. C. Debnath ◽

Y. L. Siow ◽

J. Petkau ◽

D. An ◽

N. V. Bykova

Keyword(s):

Genetic Diversity ◽

Antioxidant Activity ◽

Molecular Markers ◽

Molecular Techniques ◽

Diversity Analysis ◽

Full Potential ◽

Genetic Diversity Analysis ◽

Wide Range ◽

Berry Crops ◽

Improvement Programs

Debnath, S. C., Siow, Y. L., Petkau, J., An, D. and Bykova, N. V. 2012. Molecular markers and antioxidant activity in berry crops: Genetic diversity analysis. Can. J. Plant Sci. 92: 1121–1133. An improved understanding of important roles of dietary fruits in maintaining human health has led to a dramatic increase of global berry crop production. Berry fruits contain relatively high levels of vitamin C, cellulose and pectin, and produce anthocyanins, which have important therapeutic values, including antitumor, antiulcer, antioxidant and anti-inflammatory activities. There is a need to develop reliable methods to identify berry germplasm and assess genetic diversity/relatedness for dietary properties in berry genotypes for practical breeding purposes through genotype selection in a breeding program for cultivar development, and proprietary-rights protection. The introduction of molecular biology techniques, such as DNA-based markers, allows direct comparison of different genetic materials independent of environmental influences. Significant progress has been made in diversity analysis of wild cranberry, lowbush blueberry, lingonberry and cloudberry germplasm, and in strawberry and raspberry cultivars and advanced breeding lines developed in Canada. Inter simple sequence repeat (ISSR) markers detected an adequate degree of polymorphism to differentiate among berry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in the current berry improvement programs. Although multiple factors affect antioxidant activity, a wide range of genetic diversity has been reported in wild and cultivated berry crops. Diversity analysis based on molecular markers did not agree with those from antioxidant activity. The paper also discusses the issues that still need to be addressed to utilize the full potential of molecular techniques including expressed sequence tag-polymerase chain reaction (EST-PCR) analysis to develop improved environment-friendly berry cultivars suited to the changing needs of growers and consumers.

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Temporal and spatial variability in the community structure of the fauna of four sandy beaches in south-eastern New South Wales.

Marine and Freshwater Research ◽

10.1071/mf9840663 ◽

1984 ◽

Vol 35 (6) ◽

pp. 663 ◽

Cited By ~ 46

Author(s):

DM Dexter

Keyword(s):

Community Structure ◽

Diversity Index ◽

Abundant Species ◽

Sandy Beaches ◽

Sampling Procedure ◽

Wave Action ◽

Physical Factors ◽

Faunal Composition ◽

South Wales ◽

Temporal And Spatial

Four intertidal sandy beaches with different exposures, La Perouse, Ocean Beach, Dolls Point, and Towra Point, were studied for temporal and spatial changes in faunal composition and community structure. Each of these beaches was sampled from 6 to 12 times between July 1980 and July 1981 using a 500 �m sieve. A stratified random sampling procedure across the intertidal zone isolated 40 660 individuals representing 85 species. Distribution and abundance of species were strongly influenced by tidal level. Densities changed during the year but no seasonal changes in intertidal zonation patterns were found. Changes in density were correlated with the reproductive activities of the abundant species, especially Pseudolana concinna and Exoediceros maculosus at La Perouse, and Spio pacifica at Dolls Point and Towra Point. The number of species increased from high to low tide, and also increased with decreasing exposure to wave action. Crustaceans dominated the fauna in the most exposed site and decreased in abundance with increasing protection. Ocean Beach experienced the least fluctuation in physical factors such as wave action, salinity, and temperature, and its fauna exhibited the highest diversity index (H') and evenness (J'), the most stable density, and the greatest stability in faunal composition through time. The highest densities and the most species were found at Towra Point, which also was the most protected site.

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Obtaining Various Shapes of Machined Surface Using a Tool with a Multi-Insert Cutting Edge

Applied Sciences ◽

10.3390/app9050880 ◽

2019 ◽

Vol 9 (5) ◽

pp. 880 ◽

Cited By ~ 1

Author(s):

Tadeusz Mikolajczyk ◽

Danil Pimenov ◽

Catalin Pruncu ◽

Karali Patra ◽

Hubert Latos ◽

...

Keyword(s):

Cutting Edge ◽

Machined Surface ◽

Wide Range ◽

Complex Shapes ◽

Functional Features ◽

Tool Set ◽

The Individual ◽

Milling Tools ◽

Novel Design ◽

Positive Results

A novel design of a universal form tool is presented for machining complex planar and axisymmetric surfaces. The geometric and kinematic flexibility (GKF) of this tool type means that it can machine a wide range of profiles using a single setup. The operating principle of this multi-insert tool is its combination of single cutting edges, each of which form the individual details of the machined surface. The structure and application of both turning and milling multi-insert tools with combinations of single edges are described in the paper. Complex shapes and forms can be machined by changing the cutting-edge positions. The number of combinations of a given tool set can be determined by using the relations detailed in this study. Both turning and milling tools are utilized in a unique tool holder that clamps the inserts into position and allows their adjustment that is facilitated by special prepared analytical software to the desired object profiles. It is possible to use these tools in machining both wood and aluminum alloys. Finally, the design of the multi-insert tools for turning and milling and its functional features were experimentally verified with positive results.

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FLORISTIC, STRUCTURE AND ECOLOGICAL GROUPS OF A TREE COMMUNITY IN THE ATLANTIC RAINFOREST AT SERRA DO MAR, SP, BRAZIL

Nativa ◽

10.31413/nativa.v6i0.6351 ◽

2018 ◽

Vol 6 ◽

pp. 706

Author(s):

Vitor De Andrade Kamimura ◽

Rodrigo Ferreira Morais ◽

Carlos Alfredo Joly ◽

Marco Antonio Assis

Keyword(s):

Species Distribution ◽

Diversity Index ◽

Abundant Species ◽

Atlantic Rainforest ◽

Ecological Groups ◽

Serra Do Mar ◽

Palm Trees ◽

Dispersal Syndromes ◽

Tree Community ◽

Euterpe Edulis

FLORÍSTICA, ESTRUTURA E GRUPOS ECOLÓGICOS DE UMA COMUNIDADE ARBÓREA NA FLORESTA ATLÂNTICA, SERRA DO MAR, SP, BRASIL Neste trabalho, avaliamos a composição florística e estrutural de uma comunidade arbórea em um contínuo da Floresta Atlântica das Terras Baixas no sudeste brasileiro, acessando a distribuição das espécies entre grupos ecológicos. Para tanto, foram amostrados todos os indivíduos arbóreos com PAP≥15 cm, incluindo palmeiras e samambaias arborescentes, em um hectare, dividido em sub-parcelas de 10x10 m. A comunidade foi analisada por meio do índice de diversidade de Shannon e equabilidade de Pielou, e distribuição de suas espécies entre síndromes de dispersão e classes sucessionais. Registramos 1.120 indivíduos vivos distribuídos em 133 espécies de 41 famílias. As famílias mais ricas em espécies foram Myrtaceae (32 espécies), Fabaceae (12) e Rubiaceae (11), e Euterpe edulis a espécie mais abundante (11,1% do total). Na área de estudo, foram encontradas quatro espécies na lista espécies ameaçadas do Livro Vermelho da Flora do Brasil, e registrada uma dominância de espécies Zoocóricas (86,7% das espécies classificadas) e Não Pioneiras (73,5%). Os resultados gerais da estrutura e composição de espécies da comunidade foram similares à de outros levantamentos realizados na mesma região deste estudo. Por fim, nossos resultados corroboram a grande diversidade arbórea e uma dominância de espécies Zoocóricas e Não-Pioneiras em contínuos de Floresta Atlântica.Palavras-chave: classe sucessional, floresta ombrófila densa, diversidade, síndrome de dispersão. ABSTRACT:The present study evaluated the floristic and structural composition of a tree community in a Lowland Atlantic Rainforest along a forest continuum in Brazilian southeast, assessing the species distribution among ecological groups. For this purpose, we sampled all trees with PBH≥15 cm, including palm trees and tree ferns, in a total area of one hectare, divided into subplots of 10x10 m. The studied community was also analyzed through the Shannon diversity index and Pielou equability, and its species distribution among dispersal syndromes and successional classes. We recorded 1,120 living individuals distributed in 131 species of 40 families. The richest families were Myrtaceae (32 species), Fabaceae (12) and Rubiaceae (11), and Euterpe edulis was the most abundant species (11.1% of the total). In the study area, there were found four species on the Livro Vermelho da Flora do Brasil and recorded a dominance of zoochoric species (86.7% of species classified) and non-pioneers (71.6%). The general results of the community structure and species composition were similar with other surveys carried out in the same region of this study. Finally, our results corroborate the great diversity of trees and a dominance of zoochoric and non-pioneer species in the Atlantic Rainforest continuous.Keywords: dispersal syndromes, diversity, ombrophilous dense forest, successional groups.

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hPSC-Derived Enteric Ganglioids Model Human ENS Development and Function

10.1101/2022.01.04.474746 ◽

2022 ◽

Author(s):

Homa Majd ◽

Ryan M Samuel ◽

Jonathan T Ramirez ◽

Ali Kalantari ◽

Kevin Barber ◽

...

Keyword(s):

Ex Vivo ◽

Xenograft Model ◽

Developmental Relationships ◽

Drug Candidates ◽

Effective Strategies ◽

Wide Range ◽

Functional Features ◽

And Function

The enteric nervous system (ENS) plays a central role in gut physiology and mediating the crosstalk between the gastrointestinal (GI) tract and other organs. The human ENS has remained elusive, highlighting the need for an in vitro modeling and mapping blueprint. Here we map out the developmental and functional features of the human ENS, by establishing robust and scalable 2D ENS cultures and 3D enteric ganglioids from human pluripotent stem cells (hPSCs). These models recapitulate the remarkable neuronal and glial diversity found in primary tissue and enable comprehensive molecular analyses that uncover functional and developmental relationships within these lineages. As a salient example of the power of this system, we performed in-depth characterization of enteric nitrergic neurons (NO neurons) which are implicated in a wide range of GI motility disorders. We conducted an unbiased screen and identified drug candidates that modulate the activity of NO neurons and demonstrated their potential in promoting motility in mouse colonic tissue ex vivo. We established a high-throughput strategy to define the developmental programs involved in NO neuron specification and discovered that PDGFR inhibition boosts the induction of NO neurons in enteric ganglioids. Transplantation of these ganglioids in the colon of NO neuron-deficient mice results in extensive tissue engraftment, providing a xenograft model for the study of human ENS in vivo and the development of cell-based therapies for neurodegenerative GI disorders. These studies provide a framework for deciphering fundamental features of the human ENS and designing effective strategies to treat enteric neuropathies.

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