Comparison of bacterial communities in roots of selected trees with and without summer truffle (Tuber aestivum) ectomycorrhiza

Abstract In this study, we examined the effect of the presence of mycorrhiza and ascomata of summer truffle (Tuber aestivum) on the bacterial composition of roots from small trees growing in selected sites of the Nida Basin. Qualitative DNA sequencing methods such as Sanger and next-generation sequencing (NGS) were used. The Sanger method revealed different bacterial species compositions between the samples where summer truffle ascomata was recorded and control samples. Five genera of bacteria could be distinguished: Bacillus, Erwinia, Pseudomonas, Rahnella and Serratia, among which the most numerous were Pseudomonas (Gammmaproteobacteria class) at 32.9%. The results obtained by the NGS method also showed differences in species composition of the bacteria depending on the study sample. Seven genera of bacteria were distinguished: Rhizorhabdus, Methylotenera, Sphingomonas, Nitrosospira, Streptomyces, Methyloceanibacter and Niastella, which dominated in roots from the truffle sites. Telmatobacter, Roseiarcus, Granulicella, Paludibaculum, Acidipila, Acidisphaera and Aliidongia dominated in roots from the control sites. With the NGS method, it is possible to identify the microbiome of a whole root, while only a root fragment can be analysed by the Sanger method. These results extend the scope of knowledge on the preferences of certain groups of bacteria associated with truffles and their influence on the formation of ascomata in summer truffles. Our results may also be useful in selecting and monitoring sites that promote ascomata of Tuber aestivum.

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Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing

Scientific Reports ◽

10.1038/s41598-021-98985-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hiroaki Ikegami ◽

Shingo Noguchi ◽

Kazumasa Fukuda ◽

Kentaro Akata ◽

Kei Yamasaki ◽

...

Keyword(s):

Next Generation Sequencing ◽

Respiratory Infections ◽

Statistical Significance ◽

Bacterial Species ◽

Bacterial Flora ◽

Lung Abscess ◽

Next Generation ◽

Causative Agents ◽

Sanger Method ◽

Generation Sequencing

AbstractNext-generation sequencing (NGS) technologies have been applied in bacterial flora analysis. However, there is no standardized protocol, and the optimal clustering threshold for estimating bacterial species in respiratory infection specimens is unknown. This study was conducted to investigate the optimal threshold for clustering 16S ribosomal RNA gene sequences into operational taxonomic units (OTUs) by comparing the results of NGS technology with those of the Sanger method, which has a higher accuracy of sequence per single read than NGS technology. This study included 45 patients with pneumonia with aspiration risks and 35 patients with lung abscess. Compared to Sanger method, the concordance rates of NGS technology (clustered at 100%, 99%, and 97% homology) with the predominant phylotype were 78.8%, 71.3%, and 65.0%, respectively. With respect to the specimens dominated by the Streptococcus mitis group, containing several important causative agents of pneumonia, Bray Curtis dissimilarity revealed that the OTUs obtained at 100% clustering threshold (versus those obtained at 99% and 97% thresholds; medians of 0.35, 0.69, and 0.71, respectively) were more similar to those obtained by the Sanger method, with statistical significance (p < 0.05). Clustering with 100% sequence identity is necessary when analyzing the microbiota of respiratory infections using NGS technology.

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Next Generation Sequencing (NGS) for the Determination of Fish Flesh Microbiota

Journal of Food Research ◽

10.5539/jfr.v8n4p101 ◽

2019 ◽

Vol 8 (4) ◽

pp. 101 ◽

Cited By ~ 1

Author(s):

Theofania Tsironi ◽

Vladimiros Lougovois ◽

Vassiliki Nefeli Simou ◽

Afrodite Mexi ◽

Stamatios Koussissis ◽

...

Keyword(s):

Next Generation Sequencing ◽

Bacterial Species ◽

Microbial Flora ◽

Next Generation ◽

Fish Flesh ◽

Fish Samples ◽

Freshwater Habitats ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

The objective of the study is the assessment of the microbial ecology and safety of fish in Greece using next-generation sequencing (NGS) and the correlation of the species of microbial flora with the production of histamine. Fourteen different fish species were obtained from local fish stores (Greece) within 1 day from capture. The initial microbiota in fish flesh was determined using NGS. The main pathogenic bacterial species identified in the tested fish samples included Vibrio spp., Clostridium spp., Staphylococcus, Flavobacterium and Janthinobacterium representing both native freshwater habitats and contaminants arising from different sources, including sewage and direct contamination by wild animals, livestock, and feed. The initial spoilage microbiota of fish consisted of several psychrotrophic Gram-negative bacteria, such as Pseudomonas, Acinetobacter, Moraxella, Shewanella, Psychrobacter, Lactobacillus, Brochothrix and Photobacterium. The results of the study show the potential of the application and the usefulness of NGS for the determination of microbial flora associated with food-borne diseases and spoilage in fish products. Histamine formation correlated with the valid reads (concentration and number of bacteria) and slightly with the genus of the identified microorganisms.

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

Online Journal of Public Health Informatics ◽

10.5210/ojphi.v7i1.5682 ◽

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.

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Metagenomic Analysis of the Gut Bacteriome of Usherhopper, Poekilocerus bufonius (Klug) from Hadda, Saudi Arabia

10.21203/rs.3.rs-583183/v1 ◽

2021 ◽

Author(s):

Nabih A. Baeshen ◽

Mazen A. Majeed ◽

Mohammed Abdullah T Alotaibi ◽

Mohamed Hamed Alnefai ◽

Aala A. Abulfaraj ◽

...

Keyword(s):

Saudi Arabia ◽

Next Generation Sequencing ◽

Pest Management ◽

Bacterial Communities ◽

The Other ◽

Economic Losses ◽

Plant Fibers ◽

Next Generation Sequencing Ngs ◽

Effective Conservation ◽

Generation Sequencing

Abstract Background:Microbial communities that colonize insect guts contribute positively to the absorption of nutrients, immunity and the overall health of the host. Recent studies have been tapered towards only economically important arthropods, particularly honeybees. On the other hand, arthropods such as grasshoppers are considered as pests because they create havoc leading to economic losses. Grasshoppers are considered phytophagous pests that have a large appetite for plant fibers, whose digestion depend largely on the bacterial communities in their guts. This study characterises the gut microbiome in Usherhopper, Poekilocerus bufonius using the metagenomics methods through the next generation sequencing (NGS). Results:A total of 59,072,222 bacterial reads were recorded which were classified into phylum and genus levels. Proteobacteria were the most shared at the phylum-level whereas Wolbachia were the most dominant genera based on the total reads. Conclusions: The host-microbiome interactions and their perceived influence on the ecosystem are yet to be fully explained, therefore a detailed study is pivotal in order to enforce effective conservation and pest management.

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Bacterial Diversity in Soil Surround Subterranean Termites-Damaged Wooden Buildings in Seonamsa Temple and Effect of the Termites on Bacterial Diversity in Humus Soil

Journal of Conservation Science ◽

10.12654/jcs.2021.37.4.04 ◽

2021 ◽

Vol 37 (4) ◽

pp. 357-361

Author(s):

Young Hee Kim ◽

Boa Lim ◽

Jeung Min Lee ◽

Jin Young Hong ◽

Soo Ji Kim ◽

...

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Soil Microorganisms ◽

Operational Taxonomic Unit ◽

Illumina Miseq ◽

Subterranean Termites ◽

Bacterial Composition ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing ◽

Humus Soil

In order to determine the changes in microbial community due to termites, soil microorganisms surrounding the termites were investigated. First, bacterial communities from soil with termites collected at Seonamsa temple, Suncheon city, Korea were compared by next-generation sequencing (NGS, Illumina Miseq). The bacterial composition of soil from Daeungjeon without termites and the soil from Josadang, Palsangjeon, and Samjeon with termites were compared. Next, the bacterial composition of these soils was also compared with that of humus soil cultured with termites. A total high-quality sequences of 71,942 and 72,429 reads were identified in Seonamsa temple’s soil and humus soil, respectively. The dominant phyla in the collected Seonamsa temple’s soil were Proteobacteria (27%), Firmicutes (24%) and Actinobacteria (21%), whereas those in the humus soil were Bacteriodetes (56%) and Proteobacteria (37%). Using a two-dimensional plot to explain the principal coordinate analysis of operational taxonomic unit compositions of the soil samples, it was confirmed that the samples were divided into soil with and without termites, and it was especially confirmed that the Proteobacteria phylum was increased in humus soil with termites than in humus soil without termites.

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