scholarly journals groEL Gene-Based Phylogenetic Analysis of Lactobacillus Species by High-Throughput Sequencing

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 530 ◽  
Author(s):  
Xie ◽  
Pan ◽  
Jiang ◽  
Liu ◽  
Lu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Hypervariable Region ◽  
Single Copy ◽  
Species Level ◽  
Gene Profiling ◽  
Lactobacillus Species ◽  
Groel Gene ◽  
Lactobacillus Mucosae

Lactobacillus is a fairly diverse genus of bacteria with more than 260 species and subspecies. Many profiling methods have been developed to carry out phylogenetic analysis of this complex and diverse genus, but limitations remain since there is still a lack of comprehensive and accurate analytical method to profile this genus at species level. To overcome these limitations, a Lactobacillus-specific primer set was developed targeting a hypervariable region in the groEL gene—a single-copy gene that has undergone rapid mutation and evolution. The results showed that this methodology could accurately perform taxonomic identification of Lactobacillus down to the species level. Its detection limit was as low as 104 colony-forming units (cfu)/mL for Lactobacillus species. The assessment of detection specificity using the Lactobacillus groEL profiling method found that Lactobacillus, Pediococcus, Weissella, and Leuconostoc genus could be distinguished, but non-Lactobacillus Genus Complex could not be detected. The groEL gene sequencing and Miseq high-throughput approach were adopted to estimate the richness and diversity of Lactobacillus species in different ecosystems. The method was tested using kurut (fermented yak milk) samples and fecal samples of human, rat, and mouse. The results indicated that Lactobacillus mucosae was the predominant gut Lactobacillus species among Chinese, and L. johnsonii accounted for the majority of lactobacilli in rat and mouse gut. Meanwhile, L. delbrueckii subsp. bulgaricus had the highest relative abundance of Lactobacillus in kurut. Thus, this groEL gene profiling method is expected to promote the application of Lactobacillus for industrial production and therapeutic purpose.

scholarly journals GenBank is a reliable resource for 21st century biodiversity research

2019 ◽  
Vol 116 (45) ◽  
pp. 22651-22656 ◽  
Author(s):  
Matthieu Leray ◽  
Nancy Knowlton ◽  
Shian-Lei Ho ◽  
Bryan N. Nguyen ◽  
Ryuji J. Machida
Keyword(s):  
Phylogenetic Analysis ◽  
Global Change ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Taxonomic Resolution ◽  
Biodiversity Research ◽  
Animal Diversity ◽  
Mitochondrial Sequences ◽  
The Many

Traditional methods of characterizing biodiversity are increasingly being supplemented and replaced by approaches based on DNA sequencing alone. These approaches commonly involve extraction and high-throughput sequencing of bulk samples from biologically complex communities or samples of environmental DNA (eDNA). In such cases, vouchers for individual organisms are rarely obtained, often unidentifiable, or unavailable. Thus, identifying these sequences typically relies on comparisons with sequences from genetic databases, particularly GenBank. While concerns have been raised about biases and inaccuracies in laboratory and analytical methods, comparatively little attention has been paid to the taxonomic reliability of GenBank itself. Here we analyze the metazoan mitochondrial sequences of GenBank using a combination of distance-based clustering and phylogenetic analysis. Because of their comparatively rapid evolutionary rates and consequent high taxonomic resolution, mitochondrial sequences represent an invaluable resource for the detection of the many small and often undescribed organisms that represent the bulk of animal diversity. We show that metazoan identifications in GenBank are surprisingly accurate, even at low taxonomic levels (likely <1% error rate at the genus level). This stands in contrast to previously voiced concerns based on limited analyses of particular groups and the fact that individual researchers currently submit annotated sequences to GenBank without significant external taxonomic validation. Our encouraging results suggest that the rapid uptake of DNA-based approaches is supported by a bioinformatic infrastructure capable of assessing both the losses to biodiversity caused by global change and the effectiveness of conservation efforts aimed at slowing or reversing these losses.

Sanger sequencing of mitochondrial hypervariable region of ancient samples for DNA authentication and screening before high-throughput sequencing

2021 ◽  
Vol 40 ◽  
pp. 103216
Author(s):  
Anna Šenovská ◽  
Eva Drozdová ◽  
Kristýna Brzobohatá ◽  
Eva Chocholová ◽  
Dana Fialová ◽  
...  
Keyword(s):  
High Throughput ◽  
Sanger Sequencing ◽  
High Throughput Sequencing ◽  
Hypervariable Region

scholarly journals Size-Fractionated Filtration Combined with Molecular Methods Reveals the Size and Diversity of Picophytoplankton

Biology ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1280
Author(s):  
Xinze Shuwang ◽  
Jun Sun ◽  
Yuqiu Wei ◽  
Congcong Guo
Keyword(s):  
Flow Cytometry ◽  
Particle Size ◽  
Vertical Distribution ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Hypervariable Region ◽  
Pcr Amplification ◽  
Euphotic Zone ◽  
Vertical Distributions ◽  
The Vertical Distribution

In this study, flow cytometry (FCM) and size-fractionated filtration, together with high-throughput molecular sequencing methods (SM), were used to investigate picophytoplankton. A particle separation filter and a higher-throughput sequencing method were used to evaluate the composition of a euphotic zone of picophytoplankton—especially picoeukaryotic phytoplankton—in the Western Pacific, and the results of flow cytometry, which is a classic way to detect picophytoplankton, were used as a standard to evaluate the reliability of the results of the SMs. Within a water column of 200 m, six water depths (5, 25, 50, 113 (DCM), 150, and 200 m) were established. In order to further study the particle size spectra of the picophytoplankton, size-fractionated filtration was used to separate water samples from each water depth into three particle size ranges: 0.2–0.6, 0.6–1.2, and 1.2–2 μm. A total of 36 (6 × 3 × 2) samples were obtained through PCR amplification of the 18S rRNA V4 hypervariable region and 16S rRNA, which were biased toward phytoplankton plastids, and then high-throughput sequencing was performed. The estimation of the picophytoplankton diameter relied on forward scattering (FSC) through FCM. The estimation of the vertical distribution and diameter of the picophytoplankton using the SM was consistent with the results with FCM; thus, we believe that the estimation of picophytoplankton composition with the SM has value as a reference, although the size-fractionated filtration seemed to cause some deviations. In addition to Prochlorococcus and Synechococcus, the SM was used to evaluate the composition of picoeukaryotic phytoplankton, which mainly included Prymnesiophycea (Haptophyta) (38.15%), Cryptophyceae (Cryptophyta) (22.36%), Dictyochophyceae (Chrysophyta) (12.22%), and Mamiellophyceae (Chlorophyta) (3.31%). In addition, the SM also detected Dinophyceae (Dinoflagellata) (11.69%) sequences and a small number of Bacillariophyceae (Diatom) (1.64%) sequences, which are generally considered to have large particle sizes. The results of the SM also showed that the picoeukaryotic phytoplankton were not evenly distributed in the euphotic layer, and the vertical distributions of the different picoeukaryotic phytoplankton were different. An analysis of correlations with environmental factors showed that temperature was the main environmental factor controlling the vertical distribution of picophytoplankton.

scholarly journals Assessment of Bifidobacterium Species Using groEL Gene on the Basis of Illumina MiSeq High-Throughput Sequencing

Genes ◽  
2017 ◽  
Vol 8 (11) ◽  
pp. 336 ◽  
Author(s):  
Lujun Hu ◽  
Wenwei Lu ◽  
Linlin Wang ◽  
Mingluo Pan ◽  
Hao Zhang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Groel Gene ◽  
Bifidobacterium Species

scholarly journals High-throughput sequencing-based gene profiling on multi-staged fruit development of date palm (Phoenix dactylifera, L.)

2012 ◽  
Vol 78 (6) ◽  
pp. 617-626 ◽  
Author(s):  
Yuxin Yin ◽  
Xiaowei Zhang ◽  
Yongjun Fang ◽  
Linlin Pan ◽  
Gaoyuan Sun ◽  
...  
Keyword(s):  
High Throughput ◽  
Fruit Development ◽  
High Throughput Sequencing ◽  
Date Palm ◽  
Phoenix Dactylifera ◽  
Gene Profiling ◽  
Phoenix Dactylifera L

scholarly journals Tracking TCRβ Sequence Clonotype Expansions during Antiviral Therapy Using High-Throughput Sequencing of the Hypervariable Region

2016 ◽  
Vol 7 ◽  
Author(s):  
Mark W. Robinson ◽  
Joseph Hughes ◽  
Gavin S. Wilkie ◽  
Rachael Swann ◽  
Stephen T. Barclay ◽  
...  
Keyword(s):  
Antiviral Therapy ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Hypervariable Region

scholarly journals Amplicon-Based High-Throughput Sequencing Method Capable of Species-Level Identification of Coagulase-Negative Staphylococci in Diverse Communities

2020 ◽  
Vol 8 (6) ◽  
pp. 897
Author(s):  
Emiel Van Reckem ◽  
Luc De Vuyst ◽  
Frédéric Leroy ◽  
Stefan Weckx
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Coagulase Negative Staphylococci ◽  
Tuf Gene ◽  
Microbial Ecosystems ◽  
Gene Database ◽  
Primer Sets ◽  
Level Identification

Coagulase-negative staphylococci (CNS) make up a diverse bacterial group, appearing in a myriad of ecosystems. To unravel the composition of staphylococcal communities in these microbial ecosystems, a reliable species-level identification is crucial. The present study aimed to design a primer set for high-throughput amplicon sequencing, amplifying a region of the tuf gene with enough discriminatory power to distinguish different CNS species. Based on 2566 tuf gene sequences present in the public European Nucleotide Archive database and saved as a custom tuf gene database in-house, three different primer sets were designed, which were able to amplify a specific region of the tuf gene for 36 strains of 18 different CNS species. In silico analysis revealed that species-level identification of closely related species was only reliable if a 100% identity cut-off was applied for matches between the amplicon sequence variants and the custom tuf gene database. From the three primer sets designed, one set (Tuf387/765) outperformed the two other primer sets for studying Staphylococcus-rich microbial communities using amplicon sequencing, as it resulted in no false positives and precise species-level identification. The method developed offers interesting potential for a rapid and robust analysis of complex staphylococcal communities in a variety of microbial ecosystems.

scholarly journals Coprolites as a source of information on the genome and diet of the cave hyena

2012 ◽  
Vol 279 (1739) ◽  
pp. 2825-2830 ◽  
Author(s):  
Céline Bon ◽  
Véronique Berthonaud ◽  
Frédéric Maksud ◽  
Karine Labadie ◽  
Julie Poulain ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
High Throughput ◽  
Cervus Elaphus ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Single Copy ◽  
Crocuta Crocuta ◽  
Spotted Hyena ◽  
Additional Species ◽  
Source Of Information

We performed high-throughput sequencing of DNA from fossilized faeces to evaluate this material as a source of information on the genome and diet of Pleistocene carnivores. We analysed coprolites derived from the extinct cave hyena ( Crocuta crocuta spelaea ), and sequenced 90 million DNA fragments from two specimens. The DNA reads enabled a reconstruction of the cave hyena mitochondrial genome with up to a 158-fold coverage. This genome, and those sequenced from extant spotted ( Crocuta crocuta ) and striped ( Hyaena hyaena ) hyena specimens, allows for the establishment of a robust phylogeny that supports a close relationship between the cave and the spotted hyena. We also demonstrate that high-throughput sequencing yields data for cave hyena multi-copy and single-copy nuclear genes, and that about 50 per cent of the coprolite DNA can be ascribed to this species. Analysing the data for additional species to indicate the cave hyena diet, we retrieved abundant sequences for the red deer ( Cervus elaphus ), and characterized its mitochondrial genome with up to a 3.8-fold coverage. In conclusion, we have demonstrated the presence of abundant ancient DNA in the coprolites surveyed. Shotgun sequencing of this material yielded a wealth of DNA sequences for a Pleistocene carnivore and allowed unbiased identification of diet.

scholarly journals Analysis of the Bacterial Communities in Two Liquors of Soy Sauce Aroma as Revealed by High-Throughput Sequencing of the 16S rRNA V4 Hypervariable Region

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Jing Tang ◽  
Xiaoxin Tang ◽  
Ming Tang ◽  
Ximin Zhang ◽  
Xiaorong Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Hypervariable Region ◽  
Soy Sauce ◽  
Alcoholic Beverages ◽  
Rrna Gene ◽  
Chinese Liquor

Chinese liquor is one of the world’s oldest distilled alcoholic beverages and an important commercial fermented product in China. The Chinese liquor fermentation process has three stages: making Daqu (the starter), stacking fermentation on the ground, and liquor fermentation in pits. We investigated the bacterial diversity of Maotai and Guotai Daqu and liquor fermentation using high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene. A total of 70,297 sequences were obtained from the Daqu samples and clustered into 17 phyla. The composition of the bacterial communities in the Daqu from these two soy sauce aroma-style Chinese liquors was the same, although some bacterial species changed in abundance. Between the Daqu and liquor fermentation samples, 12 bacterial phyla increased. The abundance of Lactobacillus and Pseudomonas increased in the liquor fermentation. This study has used high-throughput sequencing to provide new insights into the bacterial composition of the Chinese liquor Daqu and fermentation. Similarities in the distribution of bacteria in the soy sauce aroma-style Chinese liquors Daqu suggest that the abundance of bacteria might be generally concerned to other liquor.

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