Journal: Frontiers in Microbiology

Article Title: Effect of dietary supplementation with Brevibacillus laterosporus on broiler growth performance, meat quality and gut microbiome

doi: 10.3389/fmicb.2025.1608076

Figure Lengend Snippet: Relative abundance of the top phyla (A) and genus (B) in the samples. Sankey diagram of species composition at phylum and genus levels (C) .

Article Snippet: The cecum microbial composition analysis showed that compared with the CON group, the Shannon, Chao1, and observed species indexes in the MBL group were significantly higher ( P < 0.05; ).

Techniques:

Journal: PLoS ONE

Article Title: Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

doi: 10.1371/journal.pone.0026624

Figure Lengend Snippet: 1. CloVR-16S supports analysis of pyrotagged amplicon pool sequence data as well as individual samples sequence data, using components from the Mothur package for preprocessing, alignment, operational taxonomic unit (OTU) assignment and alpha diversity estimation. QIIME components are used for sequence clustering, alignment, phylogenetic inference and beta diversity estimation. Sequence reads are assigned to taxonomies using the RDP classifier . Additional visualizations are generated with R script implemented in CloVR. Differentially abundant taxa determined with Metastats . 2. CloVR-Metagenomics supports functional and taxonomic assignments of non-redundant whole-genome shotgun (WGS) sequence data from metagenomic samples. Reads are classified based on BLASTX and BLASTN searches against functional (COG , optionally KEGG , eggNOG ) and taxonomic (RefSeq ) reference databases, respectively. The results are statistically evaluated using Metastats and visualized using R scripts implemented in CloVR. 3. CloVR-Microbe supports microbial whole-genome sequencing projects, including Illumina and 454 or Sanger sequence assembly with Velvet and Celera assembler (CA) , respectively. Gene predictions and annotations are performed using the complex IGS standard operating procedure for automated prokaryotic annotation (IGS) .

Article Snippet: CloVR supports a broad variety of small to large-scale microbial genomics applications of current and next-generation sequencing platforms with four automated pipelines: (i) 16S rRNA-based microbial community composition analysis of Sanger and 454 sequence data (CloVR-16S) ; (ii) taxonomic and functional community composition analysis of metagenomic whole-genome shotgun (WGS) sequence data (CloVR-Metagenomics) ; (iii) bacterial single-genome WGS Sanger, 454 or Illumina sequence assembly and annotation using the IGS Annotation Engine (CloVR-Microbe) ; and (iv) large-scale BLAST searches of Sanger, 454 or Illumina sequence data (CloVR-Search).

Techniques: Amplification, Sequencing, Generated, Functional Assay

Journal: PLoS ONE

Article Title: Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

doi: 10.1371/journal.pone.0026624

Figure Lengend Snippet: Example datasets used for CloVR pipeline benchmarking.

Article Snippet: CloVR supports a broad variety of small to large-scale microbial genomics applications of current and next-generation sequencing platforms with four automated pipelines: (i) 16S rRNA-based microbial community composition analysis of Sanger and 454 sequence data (CloVR-16S) ; (ii) taxonomic and functional community composition analysis of metagenomic whole-genome shotgun (WGS) sequence data (CloVR-Metagenomics) ; (iii) bacterial single-genome WGS Sanger, 454 or Illumina sequence assembly and annotation using the IGS Annotation Engine (CloVR-Microbe) ; and (iv) large-scale BLAST searches of Sanger, 454 or Illumina sequence data (CloVR-Search).

Techniques: Amplification

Journal: PLoS ONE

Article Title: Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

doi: 10.1371/journal.pone.0026624

Figure Lengend Snippet: Cost and runtime parameters of CloVR pipeline runs on example datasets.

Article Snippet: CloVR supports a broad variety of small to large-scale microbial genomics applications of current and next-generation sequencing platforms with four automated pipelines: (i) 16S rRNA-based microbial community composition analysis of Sanger and 454 sequence data (CloVR-16S) ; (ii) taxonomic and functional community composition analysis of metagenomic whole-genome shotgun (WGS) sequence data (CloVR-Metagenomics) ; (iii) bacterial single-genome WGS Sanger, 454 or Illumina sequence assembly and annotation using the IGS Annotation Engine (CloVR-Microbe) ; and (iv) large-scale BLAST searches of Sanger, 454 or Illumina sequence data (CloVR-Search).

Techniques:

Journal: PLoS ONE

Article Title: Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

doi: 10.1371/journal.pone.0026624

Figure Lengend Snippet: Costs for single CloVR-16S (blue), CloVR-Metagenomics (red) and CloVR-Microbe (black) runs of comparable datasets (∼500 K 454 GS FLX or GS FLX Titanium reads, see ) on Amazon EC2 were extrapolated to calculate the number of runs that are obtainable for a given dollar value. The black dashed line represents the average annual cost ($130 K) to set up and maintain a local cluster of 240 CPUs for a three years from Dudley et al . . Numbers in boxes show how many runs of CloVR-16S, -Metagenomics, and -Microbe can be afforded for the same cost. As an example, approximately three 454 GS FLX Titanium sequencers (two genomes per sequencing plate and one run per day, adding up to 2,190 datasets) or one Illumina GAIIx sequencer (five genomes per lane, eight lanes per sequencing flow cell and one run per week, adding up to 2,080 datasets) can be processed with CloVR-Microbe on Amazon EC2 annually for the same cost as estimated to set up and maintain the 240 CPU local cluster. The local cluster would, however, provide resources exceeding those required for each of the projected analysis protocols.

Article Snippet: CloVR supports a broad variety of small to large-scale microbial genomics applications of current and next-generation sequencing platforms with four automated pipelines: (i) 16S rRNA-based microbial community composition analysis of Sanger and 454 sequence data (CloVR-16S) ; (ii) taxonomic and functional community composition analysis of metagenomic whole-genome shotgun (WGS) sequence data (CloVR-Metagenomics) ; (iii) bacterial single-genome WGS Sanger, 454 or Illumina sequence assembly and annotation using the IGS Annotation Engine (CloVR-Microbe) ; and (iv) large-scale BLAST searches of Sanger, 454 or Illumina sequence data (CloVR-Search).

Techniques: Sequencing