Microbes in the Datura Rootzone Contribute to an Antioxidant Support System of Flavonoids and Other Aromatic Compounds

The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Datura inoxia. We hypothesized that rhizospheric and endophytic microbes would be found that were capable of performing the same secondary metabolic functions of the plant rootzone they inhabited. We also hypothesized that the microbial functions would be co-operative with and supportive to plant secondary metabolite production, for example, by providing precursors to important plant bioactive molecules. The methods employed were mi-crobial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional. A few of the main bacterial genera of interest that were dis-covered in the Datura root microbiome were Flavobacterium, Chitinophaga, Pseudomonas, Strepto-myces, Rhizobium, and Bacillus. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. There was strong evidence to support the notion that synergistic production of plant de-rived secondary metabolites by microbes occurred, as well as the ability for the compounds to enter plant cells. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.

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Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia

BioTech ◽

10.3390/biotech11010001 ◽

2022 ◽

Vol 11 (1) ◽

pp. 1

Author(s):

Savanah Senn ◽

Kelly Pangell ◽

Adrianna L. Bowerman

Keyword(s):

Phenylpropanoid Pathway ◽

Bioactive Molecules ◽

Resistant Bacteria ◽

Antibiotic Resistant ◽

Metabolic Functions ◽

Agricultural Applications ◽

And Function ◽

Next Generation Sequencing Ngs ◽

Functional Analyses ◽

Datura Inoxia

The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10−5), Bradyhizobium (p = 1 × 10−8), and Paenibacillus (p = 1.46 × 10−6). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10−3) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.

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Multivariate statistical techniques for metagenomic analysis of microbial community recovered from environmental samples

Journal of Bio-Science ◽

10.3329/jbs.v24i0.37486 ◽

2018 ◽

Vol 24 ◽

pp. 45-53 ◽

Cited By ~ 1

Author(s):

Z Akond ◽

M Alam ◽

MS Ahmed ◽

MNH Mollah

Keyword(s):

Microbial Communities ◽

Microbial Mats ◽

Statistical Techniques ◽

Multivariate Statistical ◽

Linear Discriminant ◽

Metabolic Functions ◽

Metabolic Variables ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing ◽

Shed Light

High-throughput big dataset generated through next generation sequencing (NGS) of DNA samples helps identify key differences in the function and taxonomy between microbial communities as well as shed light on the diversity of microbes, cooperation and evolution in any particular ecosystem. During this study, three statistical techniques namely, Random Forest (RF), Multidimensional Scaling (MDS) and Linear Discriminant Analysis (LDA) approaches were employed for functional analysis of 212 publicly available metagenomic datasets within and between 10 environments against 27 metabolic functions. RF generates the 8 most important metabolic variables along with MDS and LDA among which Photosynthesis has the highest score (70.20); Phages, prophages has the second highest score (61.31) and Membrane Transport was found to have the eighth highest score (45.29). The MDS plot was found useful to visualize the separation of the microbes from human or animal hosts from other samples along the first dimension and the separation of the aquatic and mat communities along the second dimension. LDA analyses compared the extent of the microbial samples into three broad groups: the human and animal associated samples, the microbial mats, and the aquatic samples. RF showed that phage activity is a major difference between host-associated microbial communities and free-living. The MDS and LDA techniques suggest that mat communities were unique from both the animal associated metagenomes and the aquatic samples with differences in the vitamin and cofactor metabolism.J. bio-sci. 24: 45-53, 2016

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Fecal Microbiome and Resistome Profiling of Healthy and Diseased Pakistani Individuals Using Next-Generation Sequencing

Microorganisms ◽

10.3390/microorganisms9030616 ◽

2021 ◽

Vol 9 (3) ◽

pp. 616

Author(s):

Ome Kalsoom Afridi ◽

Johar Ali ◽

Jeong Ho Chang

Keyword(s):

Next Generation Sequencing ◽

Multidrug Resistant ◽

Next Generation ◽

Initial Screening ◽

Antibiotic Resistant ◽

Fecal Microbiome ◽

Microbial Dysbiosis ◽

Resistant Genes ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

In this paper, we aimed to characterize the fecal microbiome and its resistomes of healthy and diseased subjects infected with multidrug-resistant Escherichia coli using next-generation sequencing (NGS). After initial screening, 26 stools samples belonging to healthy (n = 13) and diseased subjects (n = 13) were selected and subjected to NGS. A total of 23 and 42 antibiotic-resistant genes (ARGs) conferring resistance to 6 and 9 classes of antibiotics were identified in the resistomes of healthy and diseased subjects, respectively. Bacteroidetes were found to be the major phylum in both healthy and diseased subjects; however, Proteobacteria was predominantly present in the diseased subjects only. Microbial dysbiosis and predominance of various ARGs in the resistome of diseased subjects reflect the excessive usage of antibiotics in Pakistan and warrants immediate attention to regulate the use of various antimicrobials.

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