scholarly journals Metagenomic Analysis of Lichen Associated Bacterial Community Profiling In Roccella Montagnei

2021 ◽  
Author(s):  
Vishnu Raja Vijayakumar ◽  
Karthikeyan Saravanan ◽  
Maharaja Somasundaram ◽  
Rajkumar Jayaraj ◽  
Panneerselvam Annamalai ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Tamil Nadu ◽  
Terrestrial Habitat ◽  
Coastal Habitat ◽  
Alpha And Beta Diversity ◽  
Community Profiling ◽  
Tree Inference ◽  
Terrestrial Environments ◽  
Similarity And Difference ◽  
Ngs Data

Abstract A lichen is a composite organism formed of algae or cyanobacteria that live in a mutually advantageous symbiotic relationship with the filaments (hyphae) of fungus. Three lichen samples were obtained from diverse sites at Kuppanasamy temple, Pollachi, a terrestrial habitat located in Coimbatore, Nithiravilai, Nagercoil, and Ramarpatham, Vedaranyam, both coastal habitats located in Kanyakumari and Nagapattinam districts of Tamil Nadu, for this study. Amplification and sequencing of 16S rRNA V3 - V4 regions were used for metagenomic study. Aside from the NGS data, distinct types of lichen microbiome profiles were clearly shown. The bacterial diversity in the lichen genera of Roccella montagnei growing in coastal and terrestrial environments was further investigated using common and unique operational taxonomic units (OTUs) and the QIIME pipeline (1.9.1). By using similarity clustering, the heat map analysis depicts the abundance information of chosen OTUs as well as the similarity and difference between OTUs and lichen samples. Using multiple methods, the Alpha and Beta diversity analysis revealed that there were differences in all of the samples. However, UPGMA tree inference of comparable bacterial community in coastal habitat lichen samples compared to terrestrial habitat validates their evolutionary lineage. As a result, the bacterial population associated with corticolous lichen is dependent on geographic locations, growth substrate, and climatic circumstances of similar lichen genera produced in different habitats and tree substrates.

Bacterial Community Profiling of Plastic Litter in the Belgian Part of the North Sea

2015 ◽  
Vol 49 (16) ◽  
pp. 9629-9638 ◽  
Author(s):  
Caroline A. De Tender ◽  
Lisa I. Devriese ◽  
Annelies Haegeman ◽  
Sara Maes ◽  
Tom Ruttink ◽  
...  
Keyword(s):  
Bacterial Community ◽  
North Sea ◽  
The North ◽  
Community Profiling ◽  
The North Sea

scholarly journals Exploring the bacterial community composition of soil from a tropical dry evergreen forest in Tamil Nadu, India

2021 ◽  
Author(s):  
Saptashwa Datta ◽  
Melvin S. Samuel ◽  
Ethiraj Selvarajan
Keyword(s):  
Bacterial Community ◽  
Tamil Nadu ◽  
Bacterial Species ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Evergreen Forest ◽  
Dry Evergreen Forest ◽  
Tropical Evergreen Forest ◽  
Tropical Dry Evergreen Forest

Abstract Metagenomics is a cutting edge omics technology that has been employed in various fields including novel product discovery, diagnostics, and pollutant monitoring. 16S metagenome amplicon sequencing is used for understanding the microbial diversity from various environments. Forest ecosystems have been known for the discovery of novel bacteria and also bacteria that produces novel compounds that are pharmaceutically and industrially relevant. In this study we try to show the bacterial community structure of the soil obtained from a tropical evergreen forest in India. We use 16s metagenomics sequencing and then follow it up with various analysis like alpha diversity analysis, to find out the dominant bacterial species found in these soils. Actinobacteria was found to be the most copmmonly found bacterial phylum followed by proteobacteria, firmicutes, chloroflexi, acidobacteria, verrucomicrobia, bacteroidetes, gemmatimonadetes, nitospirae and other unclassified organisms. Further studies can elucidate on the discovery of novel compounds from these bacteria.

scholarly journals The infant airway microbiome in health and disease impacts later asthma development

2014 ◽  
Author(s):  
Shu Mei Teo ◽  
Danny Mok ◽  
Kym Pham ◽  
Merci Kusel ◽  
Michael Serralha ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Birth Cohort ◽  
Antibiotic Usage ◽  
First Year ◽  
Respiratory Illnesses ◽  
Community Profiling ◽  
Airway Microbiome ◽  
Health And Disease ◽  
Colonization Patterns ◽  
Lower Airways

The nasopharynx (NP) is a reservoir for microbes associated with acute respiratory illnesses (ARI). The development of asthma is initiated during infancy, driven by airway inflammation associated with infections. Here, we report viral and bacterial community profiling of NP aspirates across a birth cohort, capturing all lower respiratory illnesses during their first year. Most infants were initially colonized with Staphylococcus or Corynebacterium before stable colonization with Alloiococcus or Moraxella, with transient incursions of Streptococcus, Moraxella or Haemophilus marking virus-associated ARIs. Our data identify the NP microbiome as a determinant for infection spread to the lower airways, severity of accompanying inflammatory symptoms, and risk for future asthma development. Early asymptomatic colonization with Streptococcus was a strong asthma predictor, and antibiotic usage disrupted asymptomatic colonization patterns.

scholarly journals Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

2014 ◽  
Vol 80 (24) ◽  
pp. 7583-7591 ◽  
Author(s):  
Stephen J. Salipante ◽  
Toana Kawashima ◽  
Christopher Rosenthal ◽  
Daniel R. Hoogestraat ◽  
Lisa A. Cummings ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Error Rates ◽  
Personal Genome ◽  
Rrna Gene ◽  
Ion Torrent ◽  
Community Profiling ◽  
Sequencing Platforms ◽  
Ion Torrent Platform

ABSTRACTHigh-throughput sequencing of the taxonomically informative 16S rRNA gene provides a powerful approach for exploring microbial diversity. Here we compare the performances of two common “benchtop” sequencing platforms, Illumina MiSeq and Ion Torrent Personal Genome Machine (PGM), for bacterial community profiling by 16S rRNA (V1-V2) amplicon sequencing. We benchmarked performance by using a 20-organism mock bacterial community and a collection of primary human specimens. We observed comparatively higher error rates with the Ion Torrent platform and report a pattern of premature sequence truncation specific to semiconductor sequencing. Read truncation was dependent on both the directionality of sequencing and the target species, resulting in organism-specific biases in community profiles. We found that these sequencing artifacts could be minimized by using bidirectional amplicon sequencing and an optimized flow order on the Ion Torrent platform. Results of bacterial community profiling performed on the mock community and a collection of 18 human-derived microbiological specimens were generally in good agreement for both platforms; however, in some cases, results differed significantly. Disparities could be attributed to the failure to generate full-length reads for particular organisms on the Ion Torrent platform, organism-dependent differences in sequence error rates affecting classification of certain species, or some combination of these factors. This study demonstrates the potential for differential bias in bacterial community profiles resulting from the choice of sequencing platform alone.

scholarly journals Metagenomic analysis of lichen-associated bacterial community profiling in Roccella montagnei

2021 ◽  
Vol 204 (1) ◽  
Author(s):  
Vishnu Raja Vijayakumar ◽  
Karthikeyan Saravanan ◽  
Maharaja Somasundaram ◽  
Rajkumar Jayaraj ◽  
Panneerselvam Annamalai ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Metagenomic Analysis ◽  
Community Profiling

scholarly journals Modulation of Gastrointestinal Bacterial in Chronic Atrophic Gastritis Model Rats by Chinese and West Medicine Intervention

2020 ◽  
Author(s):  
Minghan Huang ◽  
Sihan Li ◽  
Youcheng He ◽  
Cuili Lin ◽  
Yueming Sun ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Atrophic Gastritis ◽  
Close Relation ◽  
Amplicon Sequencing ◽  
Chronic Atrophic Gastritis ◽  
Bacterial Composition ◽  
Chinese Medicines ◽  
Alpha And Beta Diversity ◽  
16S Rrna Amplicon Sequencing ◽  
Pathogenic Factors

Abstract Chronic atrophic gastritis (CAG) was well-known related with multiple pathogenic factors and normally therapies comprised by western or Chinese medicines. Present study was design to identified the bacterial community characterized by 16S rRNA amplicon sequencing and determine the modulate affection of bacterial composition response western and Chinese medicine Qing huayin (QHY) as well as antibiotic on model rats. Result shown the overall structure alteration of bacterial appeared under medicine applied, antibiotic caused a marked depletion in bacterial diversity and richness, the enrichment of Firmicutes (85.1-90.7%) in antibiotic-free convert to Bacteroidetes (30.7-34.6%) in antibiotic-added model rat were demonstrated. Firmicutes was most dominant phylum and accounting for 85.1%-90.5% and significantly decreased till 21.9%-68.5% in antibiotic-added treatments. Especially QHY-treated show highest RA of Firmicutes (90.5%) and the amelioration of CAG using QHY attributed by beneficial bacterial enrichment, especially Ruminococcus, Lactobacillus and Bifidobacterium. In addition, alpha and beta diversity analysis also demonstrated the clear dispersion and aggregation that revealed the alteration and steady of bacterial community structures. In summary, QHY has potential application value in the treatment of CAG which attributed to close relation with the modulatory of internal bacterial communities.

scholarly journals Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach

2021 ◽  
Vol 37 (6) ◽  
pp. 521-532
Author(s):  
Mahesh Adhikari ◽  
Sang Woo Kim ◽  
Hyun Seung Kim ◽  
Ki Young Kim ◽  
Hyo Bin Park ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Community ◽  
South Korea ◽  
Genomic Dna ◽  
Soil Samples ◽  
Community Diversity ◽  
Next Generation ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Cultivated Soils

Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions.

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