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

2018 ◽  
Vol 24 ◽  
pp. 45-53 ◽  
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

scholarly journals Cyanobacterial Mats in Calcite-Precipitating Serpentinite-Hosted Alkaline Springs of the Voltri Massif, Italy

2020 ◽  
Vol 9 (1) ◽  
pp. 62
Author(s):  
Aysha Kamran ◽  
Kathrin Sauter ◽  
Andreas Reimer ◽  
Theresa Wacker ◽  
Joachim Reitner ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbial Mats ◽  
Environmental Dna ◽  
Cyanobacterial Mats ◽  
Cyanobacterial Community ◽  
Mineral Precipitation ◽  
Community Based ◽  
Specific Adaptation ◽  
Carbonate Buildups ◽  
Generation Sequencing

(1) Background: Microbial communities in terrestrial, calcifying high-alkaline springs are not well understood. In this study, we investigate the structure and composition of microbial mats in ultrabasic (pH 10–12) serpentinite springs of the Voltri Massif (Italy). (2) Methods: Along with analysis of chemical and mineralogical parameters, environmental DNA was extracted and subjected to analysis of microbial communities based upon next-generation sequencing. (3) Results: Mineral precipitation and microbialite formation occurred, along with mat formation. Analysis of the serpentinite spring microbial community, based on Illumina sequencing of 16S rRNA amplicons, point to the relevance of alkaliphilic cyanobacteria, colonizing carbonate buildups. Cyanobacterial groups accounted for up to 45% of all retrieved sequences; 3–4 taxa were dominant, belonging to the filamentous groups of Leptolyngbyaceae, Oscillatoriales, and Pseudanabaenaceae. The cyanobacterial community found at these sites is clearly distinct from creek water sediment, highlighting their specific adaptation to these environments.

scholarly journals Structure of Microbial Communities When Complementary Effluents Are Anaerobically Digested

2021 ◽  
Vol 11 (3) ◽  
pp. 1293
Author(s):  
Ana Eusébio ◽  
André Neves ◽  
Isabel Paula Marques
Keyword(s):  
Anaerobic Digestion ◽  
Microbial Communities ◽  
Volatile Fatty Acids ◽  
Olive Mill Wastewater ◽  
Organic Load ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Olive Mill

Olive oil and pig productions are important industries in Portugal that generate large volumes of wastewater with high organic load and toxicity, raising environmental concerns. The principal objective of this study is to energetically valorize these organic effluents—piggery effluent and olive mill wastewater—through the anaerobic digestion to the biogas/methane production, by means of the effluent complementarity concept. Several mixtures of piggery effluent were tested, with an increasing percentage of olive mill wastewater. The best performance was obtained for samples of piggery effluent alone and in admixture with 30% of OMW, which provided the same volume of biogas (0.8 L, 70% CH4), 63/75% COD removal, and 434/489 L CH4/kg SVin, respectively. The validation of the process was assessed by molecular evaluation through Next Generation Sequencing (NGS) of the 16S rRNA gene. The structure of the microbial communities for both samples, throughout the anaerobic process, was characterized by the predominance of bacterial populations belonging to the phylum Firmicutes, mainly Clostridiales, with Bacteroidetes being the subdominant populations. Archaea populations belonging to the genus Methanosarcina became predominant throughout anaerobic digestion, confirming the formation of methane mainly from acetate, in line with the greatest removal of volatile fatty acids (VFAs) in these samples.

Characterization of Balsamic Vinegar by Multivariate Statistical Analysis of Trace Element Content

1998 ◽  
Vol 81 (5) ◽  
pp. 1087-1095 ◽  
Author(s):  
Antonella Del Signore ◽  
Barbara Campisi ◽  
Franco Di Giacomo
Keyword(s):  
Principal Component Analysis ◽  
Principal Component ◽  
Trace Element Content ◽  
The Other ◽  
Statistical Techniques ◽  
Multivariate Statistical ◽  
Linear Discriminant ◽  
Balsamic Vinegar ◽  
And Cluster Analysis

Abstract To characterize vinegars according to the types prescribed by Italian regulations, 8 trace elements (Cr, Mn, Co, Ni, Cu, Zn, Cd, and Pb) were determined. The data collected were successively elaborated by 3 statistical techniques: linear principal component analysis (LPCA), linear discriminant analysis (LDA), and cluster analysis (CA). LDA and LPCA best classified and discriminated the 3 types of vinegar under study, separating traditional balsamic vinegars from the other 2 types, nontraditionally aged balsamic vinegars and common vinegars. The latter 2 types were appreciably distinguished only by LDA through bidimensional analysis of discriminant scores

Multivariate statistic for researchers

2016 ◽  
Author(s):  
Shamshuritawati Sharif ◽  
Hazlina Ali ◽  
Sharipah Soaad Syed Yahaya
Keyword(s):  
Discriminant Analysis ◽  
Linear Discriminant Analysis ◽  
Statistical Techniques ◽  
Multivariate Statistical Techniques ◽  
Valuable Resource ◽  
Multivariate Statistical ◽  
Multivariate Statistic ◽  
Linear Discriminant ◽  
New Ideas ◽  
Young Researchers

This book is a valuable resource for those engaged in multivariate statistical techniques. Most chapters include a set of problems and solution that enable readers to overcome the drawback of the classical techniques.It covers a theoretical disadvantage of correlation and covariance test, Hotellings T2 statistic, local influence, and linear discriminant analysis to inspire new or young researchers with new ideas for theoretical improvement.This book is also worthy for people who want to learn multivariate statistics extensively.

scholarly journals Metagenomic Profiling and Identification of Antimicrobial Resistance Genes from Airborne Microbial Communities

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Tamar Dickerson ◽  
Jonathan L. Jacobs ◽  
Nicole Waybright ◽  
Danielle Swales ◽  
Peggy Lowary ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Temporal Dynamics ◽  
Animal Health ◽  
Functional Metagenomics ◽  
Antimicrobial Resistance Genes ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Antimicrobial resistance (AMR) is recognized as a severe threat to human and animal health worldwide, yet relatively little is known regarding the bioavailability of AMR genes in airborne microbial communities. Hence, the objective of our study is to use next generation sequencing (NGS) to assess the temporal dynamics of airborne bacterial communities as well as functional metagenomics to investigate the dispersion of AMR genes present within them.

Changes of Cardiopulmonary and Metabolic Functions during Jogging with and without Breast Supports: a randomized controlled trial

2020 ◽  
Author(s):  
Rungchai Chaunchaiyakul ◽  
Kunanya Masodsai
Keyword(s):  
Controlled Trial ◽  
Forced Expiratory Volume ◽  
Exercise Intolerance ◽  
Metabolic Functions ◽  
Respiratory Flow ◽  
Metabolic Variables ◽  
Late Recovery ◽  
Shed Light ◽  
Healthy Females ◽  
Cardiovascular Functions

Abstract Background:To shed light on the physiologic reasons behind exercise intolerance in active females, we investigated the physiological changes of cardiopulmonary and metabolic functions during jogging with and without breast supports.Methods/Design:Thirteen healthy females participated in three randomized jogging trials of no bra (NB, served as control), and two breast supports of casual bra (CB), and jogging bra (JB). Immediate effects of bras on static and dynamic lung functions were identified by using the standard pulmonary function test. Metabolic changes and cardiovascular functions were continuously determined at rest, during jogging and recovery.Results:Results showed the only immediate effect of donning jogging bra on temporary reductions in resting respiratory flow rates (forced expiratory volume in 1 second and maximum voluntary ventilation) (P<0.05) compared with pre-bras values, while static lung function remained unchanged. Theabove immediate effects of breast support on respiratory flow reductions regained during exercise. All cardiorespiratory and metabolic variables were similar among conditions (P>0.05) of either at rest, during or after jogging. Only casual bra showed significant late recovery in tidal volume, oxygen consumption and energy expenditure compared with resting values.Conclusions: Any types of breast support exhibit no limitation on cardiorespiratory and metabolic functions during jogging. Jogging with breast support is recommended during exercise for health promotion and wellbeing in adolescent girls and women.Trial registration: The current study was retrospectively registered. Clinicaltrials.in.th TCTR20200311002. Registered 11 March 2020.

scholarly journals Metataxonomic analysis of tissue-associated microbiota in grooved carpet-shell (Ruditapes decussatus) and Manila (Ruditapes philippinarum) clams

2021 ◽  
Author(s):  
Diego Gerpe ◽  
Aide Lasa ◽  
Alberto Lema ◽  
Jesús L. Romalde
Keyword(s):  
Ruditapes Philippinarum ◽  
Ruditapes Decussatus ◽  
Microbial World ◽  
General Picture ◽  
Specific Tissue ◽  
Next Generation Sequencing Ngs ◽  
Tissue Origin ◽  
Generation Sequencing ◽  
Shed Light ◽  
Selection Of

AbstractCulture-dependent techniques only permit the study of a low percentage of the microbiota diversity in the environment. The introduction of next generation sequencing (NGS) technologies shed light into this hidden microbial world, providing a better knowledge on the general microbiota and, specifically, on the microbial populations of clams. Tissue-associated microbiota of Ruditapes decussatus and Ruditapes philippinarum (mantle, gills, gonad and hepatopancreas) was analysed in two different locations of Galicia (northwest of Spain) during Spring (April) and Autumn (October), employing a metataxonomic approach. High bacterial diversity and richness were found in all samples where a total of 22,044 OTUs were obtained. In most samples, phylum Proteobacteria was most frequently retrieved, although other phyla as Actinobacteria, Bacteroidetes, Tenericutes, Firmicutes or Chlamydiae also appeared at high relative abundances in the samples. At genus level, great variation was found across tissues and sampling periods. A Nonmetric Multidimensional Scaling (NMDS) and a hierarchical clustering analysis allowed to further analyse the factors responsible for the differences among groups of samples in the different sites. Results showed sample ordination based on tissue origin and sampling periods, pointing out that the microbiota was influenced by these factors. Indeed, predominance of certain genera was observed, such as Endozoicomonas or Methylobacterium in gills and gonads, respectively, suggesting that selection of specific bacterial taxa is likely to occur. So far, this study provided a general picture of the tissue associated microbial population structure in R. decussatus and R. philippinarum clams, which, ultimately, allowed the identification of specific tissue-related taxa.

scholarly journals 5-Methylcytosine and 5-Hydroxymethylcytosine Signatures Underlying Pediatric Cancers

Epigenomes ◽  
2019 ◽  
Vol 3 (2) ◽  
pp. 9 ◽  
Author(s):  
Shalu Jhanwar ◽  
Ajinkya Deogade
Keyword(s):  
Pediatric Cancer ◽  
Therapeutic Potential ◽  
The Past ◽  
Pediatric Cancers ◽  
Genome Wide ◽  
Recent Developments ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Shed Light

In addition to the genetic variations, recent evidence has shown that DNA methylation of both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) underlies the pathogenesis of pediatric cancer. Given the high mortality rate, there is an urgent need to study the mechanisms contributing to the pathogenicity of pediatric cancer. Over the past decades, next-generation sequencing (NGS) has enabled us to perform genome-wide screening to study the complex regulatory mechanisms of 5mC and 5hmC underlying pediatric tumorigenesis. To shed light on recent developments on pediatric cancer predisposition and tumor progression, here we discuss the role of both genome-wide and locus-specific dysregulation of 5mC and 5hmC in hematopoiesis malignancy and neuroblastoma, the most common types of pediatric cancer, together with their therapeutic potential.

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

2021 ◽  
Author(s):  
Savanah Senn ◽  
Kelly Pangell ◽  
Adrianna L. Bowerman
Keyword(s):  
Phenylpropanoid Pathway ◽  
Bioactive Molecules ◽  
Plant Secondary Metabolite ◽  
Resistant Bacteria ◽  
Antibiotic Resistant ◽  
Metabolic Functions ◽  
Agricultural Applications ◽  
Next Generation Sequencing Ngs ◽  
Datura Inoxia ◽  
Generation Sequencing

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.

scholarly journals Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques—validity and compatibility in ecological studies

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5289 ◽  
Author(s):  
Stafva Lindström ◽  
Owen Rowe ◽  
Sari Timonen ◽  
Liselotte Sundström ◽  
Helena Johansson
Keyword(s):  
Next Generation Sequencing ◽  
Restriction Fragment Length Polymorphism ◽  
Microbial Communities ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Illumina Miseq ◽  
Fungal Communities ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Restriction Fragment Length

Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) with a Next Generation Sequencing (NGS) method (Illumina MiSeq), offers a solid alternative for comprehensive assessment of microbial communities. Here, these two methods were combined in a study of complex bacterial and fungal communities in the nest mounds of the antFormica exsecta, with the aim to assess the degree to which these methods can be used to complement each other. The results show that these methodologies capture similar spatiotemporal variations, as well as corresponding functional and taxonomical detail, of the microbial communities in a challenging medium consisting of soil, decomposing plant litter and an insect inhabitant. Both methods are suitable for the analysis of complex environmental microbial communities, but when combined, they complement each other well and can provide even more robust results. T-RFLP can be trusted to show similar general community patterns as Illumina MiSeq and remains a good option if resources for NGS methods are lacking.

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