Welcome to adhesiomeR, an R package for analysis of Escherichia coli adhesiome.
For adhesiome analysis, adhesiomeR uses standalone BLAST and a manually curated database of adhesins. Our database contains 525 genes comprising 102 systems of fimbriae and other adhesins; therefore adhesiomeR provides the most comprehensive collection of Escherichia coli adhesins currently available.
By using adhesiomeR web server you agree to the adhesiomeR Terms and Conditions. For software support please contact: sidorczuk.katarzyna17@gmail.com.
A) The workflow of the performed analyses. To create a pathotyped genome collection, we combined E. coli genomes available from RefSeq and performed in silico pathotyping. To extend the collection, we added APEC and ETEC genomes from other studies. Collected adhesin sequences were used to create a database for gene search, which is the main functionality of adhesiomeR. We analysed the collection of genomes using strict version of the search and we determined adhesin profiles based on the results. Then, we clustered adhesin profiles into clusters. B) Clustering based on all adhesin genes showing association of certain pathotypes with adhesiome clusters, please refer to Supplementary Information for all clustering results. C) Performance of adhesiomeR on experimentally validated adhesin systems from Von Mentzer et al., showing strong consistency (98% accuracy) between our in silico and in vitro results. See Figure S7 in the paper for more detailed comparisons. D) Functionalities implemented in adhesiomeR.
This table contains information about all adhesin genes collected in adhesiomeR database. Description of the table contents is given below:
System: indicates name of the system to which a gene belongs. For fimbrial adhesins, it is a whole operon (or multiple operons in some cases) encoding all subunits needed for assembly of given fimbriae. For nonfimbrial adhesins, it is the name of a protein product.
Gene: gene name
Accession: accession number of a sequence corresponding to a gene in our database
Function/Class: information about function or class of a gene. Annotations may include following classes: adhesion, assembly ATPase, autotransporter, chaperone, inner membrane protein, invasin, linker element, major subunit, minor subunit, nucleator, outer membrane protein, prepilin peptidase, putative nucleaotide-binding protein, regulatory, structural, termination subunit, unknown, usher.
References: reference for sequence accession source or function/class annotation (if available)
n.a. - not applicable
This table contains general information about systems collected in adhesiomeR database. Description of each column content is given below.
System: name of the system.
Alternative names: some adhesins, especially fimbrial, might have been described and known by multiple names. We note them here to provide comperehensive information about each of the systems and allow easier analysis of the results.
Type: Fimbrial for adhesins forming organelles composed of multiple subunits or Nonfimbrial for adhesins encoded by single genes, mainly autotransporters.
Morphology: Describes morphology of the fimbrial adhesins. Considered types include: fimbrial - form long, thread-like organelle structures, afimbiral - create amorphous outer-membrane associated sheaths, fibrillar - create very fine wiry structures in which some individual filaments could be rarely resolved, helical - formed by two fibrils arranged in a double helix with thinner, more flexible and more open structure than fimbriae.
Biosynthesis/Secretion pathway: indicates biosynthesis or secretion pathway leading to assembly or release of functional protein/organelle. For autotransporters, also indicates if it belongs to subfamily of self-associating autotransporters (SAAT) or family of Serine Protease Autotransporters of Enterobacteriaceae (SPATE). May include: Chaperone-usher, Nucleation/precipitation, T5aSS; SPATE, T5aSS; SAAT, T5cSS, T5eSS, T3SS; T5eSS, T2SS, T5bSS, Type IV pilus.
Description: a very short description of a system.
n.a. - not applicable
Here you can see assignment of analysed genomes to adhesin profiles.
A profile is defined as a unique pattern of adhesin gene presence/absence.
We investigated adhesin profiles using three types of gene subsets, (i) all – using all adhesin genes, (ii) fimbrial – considering only genes encoding fimbrial adhesins, (iii) nonfimbrial – based on genes encoding nonfimbrial adhesins. For each of these subsets, we define profiles as unique patterns of gene presence/absence and we number them from the most frequently occurring to the rarest ones. For profiles based on all, fimbrial and nonfimbrial subsets of genes, the profile number is preceded by ‘A-’, ‘F-’ and ‘N-’ correspondingly.
NA means that we did not identify profile matching the data.