Rauf Salamzade
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View article: Complex multicellularity linked with expanded chemical arsenals in microbes
Complex multicellularity linked with expanded chemical arsenals in microbes Open
Single-celled microorganisms evolving to form cooperative multicellular units represents a key innovation in the history of life. Multicellularity is required for cell differentiation and, as such, is critical to the emergence of biologica…
View article: skDER and CiDDER: two scalable approaches for microbial genome dereplication
skDER and CiDDER: two scalable approaches for microbial genome dereplication Open
An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping the pangenome of a species or broader …
View article: Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution
Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution Open
Encoded within many microbial genomes, biosynthetic gene clusters (BGCs) underlie the synthesis of various secondary metabolites that often mediate ecologically important functions. Several studies and bioinformatics methods developed over…
View article: zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters
zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters Open
Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic el…
View article: Large-scale investigation for antimicrobial activity reveals novel defensive species across the healthy skin microbiome
Large-scale investigation for antimicrobial activity reveals novel defensive species across the healthy skin microbiome Open
The human skin microbiome constitutes a dynamic barrier that can impede pathogen invasion by producing antimicrobial natural products. Gene clusters encoding for production of secondary metabolites, biosynthetic gene clusters (BGCs), that …
View article: The porcine skin microbiome exhibits broad fungal antagonism
The porcine skin microbiome exhibits broad fungal antagonism Open
View article: Combined metagenomic- and culture-based approaches to investigate bacterial strain–level associations with medication-controlled mild-moderate atopic dermatitis
Combined metagenomic- and culture-based approaches to investigate bacterial strain–level associations with medication-controlled mild-moderate atopic dermatitis Open
Strain-level differences in toxin genes from Staphylococcus strains may explain varying effects on HK, with S aureus and non-aureus strains negatively affecting viability and barrier function. These differences are lik…
View article: Global diversity of enterococci and description of 18 previously unknown species
Global diversity of enterococci and description of 18 previously unknown species Open
Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococca…
View article: The Porcine Skin Microbiome Exhibits Broad Fungal Antagonism
The Porcine Skin Microbiome Exhibits Broad Fungal Antagonism Open
The skin and its microbiome function to protect the host from pathogen colonization and environmental stressors. In this study, using the Wisconsin Miniature Swine™ model, we characterize the porcine skin fungal and bacterial microbiomes, …
View article: Datasets for "Micromonosporaceae Biosynthetic Gene Cluster Diversity Highlights the Need for Broad Spectrum Investigation"
Datasets for "Micromonosporaceae Biosynthetic Gene Cluster Diversity Highlights the Need for Broad Spectrum Investigation" Open
In this data collection is:Data S1: A folder with all the fasta files, representing the 42 strains (41 Micromonosporaceae, 1 Streptomycetaceae).Data S2: A folder with all the .gbk files for the BGC regions predicted by antiSMASH v5.1.1. Th…
View article: Micromonosporaceae biosynthetic gene cluster diversity highlights the need for broad-spectrum investigations
Micromonosporaceae biosynthetic gene cluster diversity highlights the need for broad-spectrum investigations Open
Investigations of the bacterial family Micromonosporaceae have enabled the development of secondary metabolites critical to human health. Historical investigation of bacterial families for natural product discovery has focused on terrestri…
View article: <i>Micromonosporaceae</i> biosynthetic gene cluster diversity highlights the need for broad-spectrum investigations
<i>Micromonosporaceae</i> biosynthetic gene cluster diversity highlights the need for broad-spectrum investigations Open
Supplementary material for 'Micromonosporaceae biosynthetic gene cluster diversity highlights the need for broad-spectrum investigations', as described in Microbial Genomics.Data S13: A folder containing the files pertaining …
View article: zol: prepTG Databases for BGC-Rich Taxa (Comprehensive)
zol: prepTG Databases for BGC-Rich Taxa (Comprehensive) Open
<p>Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring most*<i> </i>genomes from GTDB-R214 belonging to a select bacteria genus which is a common source of natural …
View article: zol: prepTG Databases for BGC-Rich Taxa (Comprehensive)
zol: prepTG Databases for BGC-Rich Taxa (Comprehensive) Open
Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring most* genomes from GTDB-R214 belonging to a select bacteria genus which is a common source of natural products. * A handful of genomes …
View article: zol: prepTG Databases for BGC-rich Taxa
zol: prepTG Databases for BGC-rich Taxa Open
<p>Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring distinct, representative genomes for bacterial taxa which are common sources of natural products. Representative genomes …
View article: zol: prepTG Databases for BGC-rich Taxa
zol: prepTG Databases for BGC-rich Taxa Open
Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring distinct, representative genomes for bacterial taxa which are common sources of natural products. Representative genomes for each genus…
View article: skDER Representative Genomes for Select Bacterial Taxa
skDER Representative Genomes for Select Bacterial Taxa Open
<p>Genomes belonging to a single genus or order were gathered using a loose search of taxonomic classifications in GTDB R214. By loose we required the string 'g__{GENUSNAME}' to be found in taxonomic info column by GTDB, thus allowin…
View article: zol: prepTG Databases for ESKAPE Pathogens
zol: prepTG Databases for ESKAPE Pathogens Open
Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring distinct, representative genomes for one of the six genera containing ESKAPE pathogens. Representative genomes for each genus/taxon wer…
View article: zol: prepTG Databases for Other Bacterial Taxa
zol: prepTG Databases for Other Bacterial Taxa Open
Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring distinct, representative genomes for some well studied taxa/genera. Representative genomes for each genus/taxon were selected using skD…
View article: zol: prepTG Databases for ESKAPE Pathogens
zol: prepTG Databases for ESKAPE Pathogens Open
Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring distinct, representative genomes for one of the six genera containing ESKAPE pathogens. Representative genomes for each genus/taxon wer…
View article: skDER Representative Genomes for Select Bacterial Taxa
skDER Representative Genomes for Select Bacterial Taxa Open
Genomes belonging to a single genus or order were gathered using a loose search of taxonomic classifications in GTDB R214. By loose we required the string 'g__{GENUSNAME}' to be found in taxonomic info column by GTDB, thus allowing gatheri…
View article: zol: prepTG Databases for Other Bacterial Taxa
zol: prepTG Databases for Other Bacterial Taxa Open
Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring distinct, representative genomes for some well studied taxa/genera. Representative genomes for each genus/taxon were selected using skD…
View article: skDER & CiDDER: two scalable approaches for microbial genome dereplication
skDER & CiDDER: two scalable approaches for microbial genome dereplication Open
An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping the pangenome of a species, it is ofte…
View article: zol: prepTG Databases for Other Bacterial Taxa
zol: prepTG Databases for Other Bacterial Taxa Open
Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring distinct, representative genomes for one of the ten well studied taxa/genera. Representative genomes for each genus/taxon were selected…
View article: zol: prepTG Databases for Genera of 7 ESKAPEE Pathogens
zol: prepTG Databases for Genera of 7 ESKAPEE Pathogens Open
Each of the tar.gz compressed directories corresponds to prepTG databases (for the zol suite) featuring distinct, representative genomes for one of the six genera containing ESKAPE pathogens + Escherichia (ESKAPEE). Representative genomes …
View article: skDER Representative Genomes for 17 Bacterial Taxa
skDER Representative Genomes for 17 Bacterial Taxa Open
Genomes belonging to a single genus or order were gathered using a loose search of taxonomic classifications in GTDB R214. By loose we required the string 'g__{GENUSNAME}' to be found in taxonomic info column by GTDB, thus allowing gatheri…
View article: Genomic epidemiology and antibiotic susceptibility profiling of uropathogenic <i>Escherichia coli</i> among children in the United States
Genomic epidemiology and antibiotic susceptibility profiling of uropathogenic <i>Escherichia coli</i> among children in the United States Open
Escherichia coli is the most common cause of urinary tract infections (UTIs) in children, and yet the underlying mechanisms of virulence and antibiotic resistance and the overall population structure of the species is poorly understood wit…
View article: Datasets for "Micromonosporaceae Biosynthetic Gene Cluster Diversity Highlights the Need for Broad Spectrum Investigation"
Datasets for "Micromonosporaceae Biosynthetic Gene Cluster Diversity Highlights the Need for Broad Spectrum Investigation" Open
In this data collection is: Data S1: A folder with all the fasta files, representing the 42 strains (41 Micromonosporaceae, 1 Streptomycetaceae). Data S2: A folder with all the .gbk files…
View article: Datasets for "Micromonosporaceae Biosynthetic Gene Cluster Diversity Highlights the Need for Broad Spectrum Investigation"
Datasets for "Micromonosporaceae Biosynthetic Gene Cluster Diversity Highlights the Need for Broad Spectrum Investigation" Open
In this data collection is: Data S1: A folder with all the fasta files, representing the 42 strains (41 Micromonosporaceae, 1 Streptomycetaceae). Data S2: A folder with all the .gbk files…
View article: zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters
zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters Open
Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic el…