scholarly journals Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data

PLoS ONE ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. e0228899 ◽  
Author(s):  
Kyle D. Brumfield ◽  
Anwar Huq ◽  
Rita R. Colwell ◽  
James L. Olds ◽  
Menu B. Leddy
Keyword(s):  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Metagenomic Sequencing

scholarly journals Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Louis-Marie Bobay ◽  
Emily F. Wissel ◽  
Kasie Raymann
Keyword(s):  
Microbial Communities ◽  
Honey Bee ◽  
Deep Sequencing ◽  
Gut Microbiome ◽  
Cost Effective ◽  
Whole Genome Shotgun ◽  
Strain Level ◽  
Whole Genome ◽  
Metagenomic Sequencing ◽  
Microbiome Composition

ABSTRACT Host-associated microbiomes can be critical for the health and proper development of animals and plants. The answers to many fundamental questions regarding the modes of acquisition and microevolution of microbiome communities remain to be established. Deciphering strain-level dynamics is essential to fully understand how microbial communities evolve, but the forces shaping the strain-level dynamics of microbial communities remain largely unexplored, mostly because of methodological issues and cost. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level diversity. In fact, using this method we were able to confirm strain-level results that have been obtained from whole-genome shotgun sequencing of the honey bee gut microbiome but with a much higher resolution. Importantly, our deep sequencing approach allowed us to explore the impact of low-frequency strains (i.e., cryptic strains) on microbiome dynamics. Results show that cryptic strain diversity is not responsible for the observed variations in microbiome composition across bees. Altogether, the findings revealed new fundamental insights regarding strain dynamics of host-associated microbiomes. IMPORTANCE The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.

scholarly journals Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

2020 ◽  
Vol 6 (8) ◽  
Author(s):  
Ana Elena Pérez-Cobas ◽  
Laura Gomez-Valero ◽  
Carmen Buchrieser
Keyword(s):  
Microbial Ecology ◽  
Marker Gene ◽  
Shotgun Sequencing ◽  
Whole Genome Shotgun ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Metagenomic Sequencing ◽  
Microbial Composition ◽  
Whole Genome Shotgun Sequencing ◽  
Micro Organisms

Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.

Sa603 AUTISM-SPECIFIC MICROBIAL SIGNATURES REVEALED BY WHOLE GENOME SHOTGUN SEQUENCING

2021 ◽  
Vol 160 (6) ◽  
pp. S-569
Author(s):  
Manoj Dadlani ◽  
Kelly Moffat ◽  
Huai Li ◽  
Xin Zhou ◽  
Rita Colwell
Keyword(s):  
Shotgun Sequencing ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Whole Genome Shotgun Sequencing

scholarly journals Genomic evolution of antimicrobial resistance in Escherichia coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Markus Hans Kristofer Johansson ◽  
Patrick Munk ◽  
Burkhard Malorny ◽  
Magdalena Skarżyńska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Mobile Genetic Elements ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Fecal Samples ◽  
E Coli ◽  
Genetic Elements

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

scholarly journals Draft Genome Sequences of Six Skin Isolates of Streptococcus pyogenes

2018 ◽  
Vol 6 (26) ◽  
Author(s):  
Zhong Liang ◽  
Melissa Stephens ◽  
Victoria A. Ploplis ◽  
Shaun W. Lee ◽  
Francis J. Castellino
Keyword(s):  
Streptococcus Pyogenes ◽  
Draft Genome ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Genome Sequences ◽  
Bottom Up ◽  
Content Type

Whole-genome shotgun sequences and bottom-up assembly of contigs of six skin isolates of Streptococcus pyogenes, viz., NS88.3 (emm98.1), NS223 (emm91), NS455 (emm52), SS1448 (emm86.2), SS1572 (emm223), and SS1574 (emm224), are presented here. All contigs were annotated, and the gene arrangements and the inferred proteins were consistent with a pattern D classification.

scholarly journals Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter kashmirensis

2011 ◽  
Vol 193 (19) ◽  
pp. 5553-5554 ◽  
Author(s):  
W. Ghosh ◽  
A. George ◽  
A. Agarwal ◽  
P. Raj ◽  
M. Alam ◽  
...  
Keyword(s):  
Shotgun Sequencing ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Whole Genome Shotgun Sequencing ◽  
Sulfur Oxidizing
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