Search#
Simple Search#
Simple search bars
The Simple Search allows users to easily find strains by searching with BacDive-IDs, taxon names, culture collection numbers, NCBI Tax-IDs or sequence accession numbers.
Simple Search examples
The Simple Search bar is supplemented with a Smart Search function. When the user starts typing into the search bar, the Smart Search function makes suggestions based on precalculated Advanced Search queries.
Smart Search suggestions
Advanced Search#
The BacDive Advanced Search enables large-scale queries that can combine several data fields for comparative analyses of a multitude of strains.
The Advanced Search input mask
Search Field Types#
Text Fields#
Text based data fields can be queried using the operators contains, exact, begins with, and ends with, as well as the negated forms NOT contains, NOT exact, NOT begins with, and NOT ends with.
The Advanced Search operators for text fields
All filled
Search a field with an asterisk * to find all strains for which this field is filled.
Numeric Fields#
Numeric data fields can be queried using the operators = (equal), < (lower), > (higher) with a number, or the between min-max operator with a number range (e.g. 1-3), as well as the negated forms NOT = (equal), NOT < (lower), NOT > (higher), and NOT between min-max.
The Advanced Search operators for numeric fields
Enumerated and Boolean Fields#
For fields that can only take on one of a defined set values, the query can be chosen from a dropdown menu.
An Advanced Search enumerated field
Combining Search Fields#
By combining several of the available search fields, users can compile complex search queries.
Conditional statements, like Genus exact Escherichia (the genus name is an exact match to 'Escherichia') or Genome seq. accession number contains * (a genome sequence accession number is present) can be combined using the logical operators AND and OR. The BacDive Advanced Search allows user to create up to three groups (combined by AND or OR) of up to five conditional statements (combined by AND).
The following example search query returns strains that fulfill all three conditional statements: are of genus Escherichia, are human pathogens, and have a genome sequence accession number.
Example for an advanced search combining unrelated fields
In some cases several fields are related to each other and can (or should) be used together in search queries. In the search fields overview, these are connected by a soft border line. In the following example the first field Metabolite (utilization) stands for the metabolite strains are to be queried for, while the second field Utilization activity indicates whether utilization for this metabolite was observed or not. Additionally the kind of test which was performed to make this observation can be specified using the third field.
Example for related Advanced Search fields
Metabolite utilization search example showing combinations of related fields and OR combination of two condition groups
The metabolite utilization example above queries the database for strains which utilize glucose or fructose or both as carbon source. Since the AND operator has precedence over the OR operator, two separate conditional groups for the two metabolites, with three conditional statements each, are needed for this query.
Operator precedence
The AND operator has higher precedence than the OR operator. In the Advanced Search it is not possible to override precedence.
List of Search Fields#
Name and taxonomic classification#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| Domain | The name of a taxonomic domain | free text | E.g. Bacteria |
| Phylum | The name of a taxonomic phylum | free text | E.g. Bacillota |
| Class | The name of a taxonomic class | free text | E.g. Bacilli |
| Order | The name of a taxonomic order | free text | E.g. Caryophanales |
| Family | The name of a taxonomic family | free text | E.g. Bacillaceae |
| Genus | The name of a taxonomic genus | free text | E.g. Bacillus |
| Species epithet | The second part of a taxonomic species name | free text | E.g. subtilis |
| Subspecies epithet | The third part of a taxonomic subspecies name | free text | E.g. inaquosorum |
| Species name | The name of a taxonomic species, including genus name and species epithet | free text | E.g. Bacillus subtilis |
| Full scientific name | The full scientific name of a taxonomic species, including genus name, species epithet, author name(s), and year of valid publication | free text | E.g. Bacillus subtilis (Ehrenberg 1835) Cohn 1872 (Approved Lists 1980) |
| Strain designation | The name of a strain as given in a publication or public database that is not a culture collection number | free text | E.g. Marburg, D5 |
| Variant | The name of a distinct variation within a microbiological species or strain, such as serotype, biovar, or isotype | free text | E.g. genomospecies 14 |
| Type strain | Whether a strain is the type strain of a species | yes/no | yes, no |
Morphology#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| Gram stain | Gram staining behavior | enumeration | positive, negative, variable |
| Cell length | The length of a cell in µm | floating-point number | E.g. 2.1 |
| Cell width | The width of a cell in µm | floating-point number | E.g. 0.5 |
| Cell shape | The shape of a cell | enumeration | rod-shape, coocus-shaped, ring-shaped, etc. |
| Motility | Whether a strain has the ability to move | yes/no | yes, no |
| Flagellum arrangement | A description of the flagellum or flagella of a bacterium | enumeration | monotrichous, peritrichous, polar, etc. |
| Hemolysis | Whether a strain is capable of hemolysis | enumeration | alpha, beta, gamma, alpha/beta, CAMP test |
| Colony size | The diameter of a colony in mm, when grown on a distinct medium and temperature after a certain time of cultivation | floating-point number | E.g. 1.1 |
| Incubation period | Incubation period, in days, for growth on agar plates | integer | E.g. 3 |
| Pigment production | Whether a strain produces a pigment. To be used together with field 'Pigment name'. | yes/no | yes, no |
| Pigment color | The name of a color. The color of the pigment produced by a strain. The color of colonies of the strain. | free text | E.g. orange, Beige (1001) |
| Pigment name | The name of a pigment | free text | E.g. carotenoid pigment, bacteriochlorophyll a |
| Multicellular complex forming ability | Whether a strain has the ability to form multicellular complexes (aggregations) | yes/no | yes, no |
Culture and growth conditions#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| Culture medium | The name of a culture medium | free text | E.g. Tryptic soy agar |
| Culture medium growth | Whether a strain grows on a specific culture medium. To be used with the 'Culture medium' or 'Culture medium composition' field. | yes/no | yes, no |
| Culture medium composition | The composition of a culture medium. This field can be used to search for strains growing on media containing a specific ingredient when it is used together with the 'Culture medium growth' field. | free text | E.g. Glucose |
| Temperature | A temperature in °C | floating-point number | E.g. 37.0 |
| Temperature type | The type of temperature tested. To be used together with field 'Temperature'. | enumeration | maximum, minimum, optimum, growth, other |
| Temperature test result | The result of a growth test at a certain temperature. To be used together with fields 'Temperature' and 'Temperature type'='growth'. | enumeration | positive, no, inconsistent |
| pH | A pH value | floating-point number | E.g. 6.5 |
| pH type | The type of pH tested. To be used together with field 'pH'. | enumeration | maximum, minimum, optimum, growth, other |
| pH test result | The result of a growth test at a certain pH. To be used together with field 'pH' and 'pH type'='growth'. | enumeration | positive, no, inconsistent |
| pH growth range | Whether a strain grows in a certain pH range. Acidophile (growth positive <4) or alkaliphile (growth positive >8.5). | enumeration | acidophile, alkaliphile |
Physiology and metabolism#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| Spore formation ability | Whether a strain has the ability to form spores | yes/no | yes, no |
| Produced compound | The name of a compound (e.g. secondary metabolite) produced by a strain | free text | E.g. Ethanol |
| Salt | The type of salt tested. To be used together with fields 'Salt concentration' and 'Salt concentration unit'. | free text | NaCl, marine salts, Na+ |
| Salt concentration | A salt concentration (usually in %). To be used together with fields 'Salt' and 'Salt concentration unit'. | floating-point number | E.g. 6.6 |
| Salt concentration unit | The unit of a queried salt concentration. To be used together with fields 'Salt' and 'Salt type concentration'. | enumeration | %(w/v), %, g/L, M |
| Salt relation | The type of relation a strain has to the tested salt. To be used together with fields 'Salt', 'Salt concentration', and 'Salt concentration unit'. | enumeration | growth, minimum, maximum, optimum, resistant, other |
| Salt test result | The result of a growth test at a certain salt concentration. To be used together with fields 'Salt', 'Salt concentration', 'Salt concentration unit', and 'Salt relation'='growth'. | enumeration | positive, no, inconsistent |
| Peptidoglycan (short) | The short form for a Peptidoglycan nomenclature after Schumann (2011). See https://www.dsmz.de/collection/catalogue/microorganisms/special-groups-of-organisms/peptidoglycans | free text | E.g. A11 |
| Peptidoglycan | The name of a peptidoglycan | free text | E.g. A1gamma m-Dpm-direct |
| Oxygen tolerance | The oxygen tolerance of a strain | enumeration | aerobe, anaerobe, etc. |
| Nutrition type | The nutrition type of a strain, by energy, electron, and/or carbon source | enumeration | autotroph, phototroph, etc. |
| Utilized metabolite | The name of a metabolite that a strain utilizes, for example a substrate, an electron acceptor, or a metabolite that is being degraded. | free text | E.g. D-fructose |
| Metabolite utilization ability | Whether a strain is able to utilize a specific metabolite. To be used together with field 'Utilized metabolite'. | enumeration | -, +, +/- |
| Metabolite utilization type | The type of metabolite utilization. To be used together with fields 'Utilized metabolite' and 'Metabolite utilization ability'. | enumeration | assimilation, growth, fermentation, etc. |
| Antibiotic | The name of an antibiotic | free text | E.g. chloramphenicol, ampicillin |
| Sensitivity against antibiotic | Whether a strain is sensitive against a specific antibiotic. To be used together with 'Antibiotic'. | yes/no | yes, no |
| Antibiotic sensitivity concentration | integer | E.g. 10, 30, 100 | |
| Resistance against antibiotic | Whether a strain is resistant against a specific antibiotic. To be used together with 'Antibiotic'. | yes/no | yes, no |
| Antibiotic resistance concentration | integer | E.g. 10, 30, 100 | |
| Produced metabolite | The name of a metabolite that a strain produces | free text | E.g. Indole |
| Metabolite production | Whether a strain produces a specific metabolite. To be used together with field 'Produced metabolite'. | yes/no | yes, no |
| Voges-Proskauer test (acetoin) | Whether a strain produces acetoin | enumeration | -, +, +/- |
| Methyl Red test (glucose) | Whether a strain performs mixed acid fermentation of glucose | enumeration | -, +, +/- |
| Indole test | Whether a strain has the ability to convert tryptophan to indole | enumeration | -, +, +/- |
| Citrate test | Whether a strain has the ability to use citrate as sole carbon source enumeration | -, +, +/- | |
| Enzyme | The name of an enzyme. To be used with 'Enzyme activity'. | free text | E.g. Catalase |
| Enzyme activity | Whether a specific enzyme is active in a strain. To be used together with field 'Enzyme'. | enumeration | -, +, +/- |
| EC number | The EC number of an enzyme. Can be used instead of an enzyme name. To be used with 'Enzyme activity'. | free text | E.g. 1.11.1.6 |
| API test | The name of an Analytical Profile Index (API) test. Whether results of a specific API test are available for a strain. | enumeration | API_20A, API_20E, etc. |
| EnzymeDetector Pathway | The name of a BRENDA EnzymeDetector pathway | free text | E.g. Glycolysis |
| EnzymeDetector enzyme coverage | BRENDA EnzymeDetector coverage of a specific pathway in percent. To be used together with 'EnzymeDetector pathway'. | floating-point number | E.g. 70.59 |
Isolation, sampling and environmental information#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| Sample type/Isolated from | A description of the sample or environment a strain was isolated from | free text | E.g. human blood, soil |
| Host species | The name of a taxonomic species | free text | E.g. Acanthopleura japonica, Halictus ligatus |
| Geographic location | The name or description of the geographic region. For example, a city, country, sea, or region. | free text | E.g. South Sea near Geoje Island |
| Country | The name of a country | enumeration | Afghanistan, Algeria, Angola, etc. |
| Continent | The name of a continent | enumeration | Africa, Asia, etc. |
Safety information#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| Pathogenicity (human) | Whether a strain has the ability to cause pathological conditions in humans | enumeration | yes, yes in single cases |
| Pathogenicity (animal) | Whether a strain has the ability to cause pathological conditions in animals | enumeration | yes, yes in single cases |
| Pathogenicity (plant) | Whether a strain has the ability to cause pathological conditions in plants | enumeration | yes, yes in single cases |
| Biosafety level | The biosafety level defined for a strain by a national authority | integer | E.g. 1 |
Sequence information#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| INSDC 16S rRNA accession | The INSDC (GenBank, ENA, DDBJ) sequence accession number of a 16S rRNA gene | free text | E.g. KY386500 |
| INSDC genome accession | An INSDC (GenBank, ENA, DDBJ) genome assembly accession number | free text | E.g. GCA_000160075 |
| BV-BRC genome accession | A BV-BRC genome assembly accession number | free text | E.g. 592010.4 |
| IMG genome accession | A JGI IMG genome assembly accession number | free text | E.g. 2562617177 |
| GC content | A DNA guanine-cytosine content in % | floating-point number | E.g. 54.27 |
Literature / External links#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| Culture collection number | The unique identifier given to a strain by a public culture collection or bioresource center | free text | E.g. DSM 105287, LMG 29911 |
| StrainInfo SI-ID | The identifier of a strain in the StrainInfo database | integer | E.g. 404846 |
| Infecting phage | The name of a phage that is able to infect a strain | free text | E.g. Acinetobacter phage vB_AbaM-Bhz15 |
| Special collection | The name of a BacDive special collection | enumeration | DZIF, Mouse-Microbiome, etc. |
Antibiotic susceptibility testing#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| [Antibiotic (concentration)] | An inhibition zone diameter in mm | integer | E.g. 10 |
Fatty acid profile#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| Fatty acid | The short notation designation for a fatty acid | free text | E.g. C16:0 |
| ECL | The equivalent chain length of a fatty acid | floating-point number | E.g. 13.85 |
| FA percent-share | The percent-share (%) of an individual fatty acid in the fatty acids profile | floating-point number | E.g. 11.2 |
| FA analysis culture medium | The name of a culture medium | free text | E.g. TSA |
| FA analysis medium type | Whether the FA analysis culture medium is solid or liquid | enumeration | Agar, liquid |
| FA analysis incubation temperature | The FA analysis incubation temperature, in °C | integer | E.g. 37 |
| FA analysis incubation period | The FA analysis incubation period, in days | integer | E.g. 3 |
| FA analysis incubation pH | The FA analysis incubation pH | floating-point number | E.g. 7.5 |
| FA analysis incubation oxygen condition | The FA analysis incubation oxygen condition | free text | E.g. aerobic |
| FA analysis software | The software version used for FA analysis | enumeration | Sherlock 2.11, Sherlock 4.0, etc. |
| FA analysis reference table | The reference peak naming table used for FA analysis | enumeration | ACTIN 6, TSBA 4.0, etc. |
| FA analysis instrument | The instrument used for FA analysis | free text | E.g. Agilent 6850 , Hewlett Packard 5890A gas chromatograph |
| FA analysis protocol | The protocol (or method) used for FA analysis | enumeration | Sasser 1990, Collins 1980, etc. |
Reference#
| Search field | Description | Input format | Expected input |
|---|---|---|---|
| Title | The title of a reference | free text | E.g. deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |
| Author(s) | The author(s) of a reference | free text | E.g. Isabel Schober, Julia Koblitz |
| Journal | The name of a scientific journal | enumeration | IJSEM, Nucleic Acicds, Res., etc. |
| DOI | The Digital Object Identifier (DOI) of a publication | free text | E.g. 10.1093/database/baaf059 |
| ID_reference | A BacDive reference ID number | integer | E.g. 20215 |
Export of Search Results#
Advanced Search results can be downloaded as csv files. The downloaded csv files contain each hit as a row with the default columns (BacDive) ID, designation, strain_number, is_type_strain, and species. The searched fields are present as additional columns.
Button to download Advanced Search results
API Test Finder#
API®-Tests#
Analytical Profile Index or API tests are defined series of micro-format physiological tests on easy-to-use test strips, that are used for the identification of microorganisms and can easily be performed in any laboratory without the need of expensive devices. Developed in the 1970s and sold by biomérieux, these tests are still routinely used in medical laboratories as well as in culture collections.
API test strip of type 'rapid ID 32 Strep' after incubation
Every cupule on the test strip represents a physiological reaction, for example the activity of an enzyme or the utilization of a metabolite. After incolulation of the cupules with a bacterial suspension and incubation, the tests are interpreted by color change or turbidity and recorded as positive (+), negative (-) or weak (+/-).
Example record of API test results
Test results are typically recorded on paper forms. Using the BacDive API test finder, this data can easily be compared to the world wide largest API data collection.
BacDive displays raw API observations
All API data in BacDive are raw observations. No statistics were applied to this data and results for reactions can differ between tests for the same strain, as can be seen for sorbitol in the screenshot below.
In the strain detail view, API data are displayed in tables. Extended descriptions for the single reactions can be displayed with the mouse-over function.
Example API test result table for DSM 20523
Searching Strains by API Data#
The API Test Finder allows a live search of the API test data stored in BacDive.
The API test type can be chosen in the dropdown menu
After choosing the API test type, API tests can be searched by entering "+" or "-" in the respective test fields.
By choosing the desired observation for each field, the user can find strains that match a specific API test result pattern
The search can be further refined by entering information into the fields "BacDive_ID", "species" or "Collection_numbers". A click on the species name brings the user to the strain detail view of the respective strain.
The complete search mask can be reset by selecting another API test type or by clicking the "reset filter" button.
Reset to start a new search
Isolation Source Search#
The Microbial Isolation Source Search is a tool to query bacterial strains by their isolation sources.
Isolation Source Tags#
Isolation source tags describe the original isolation source entry of a bacterial strain using a controlled vocabulary, the Microbial Isolation Source Ontology (MISO). This ontology is hierarchically ordered into three levels, e.g. #Environmental (Level 1), #Aquatic (Level 2), #Marine (Level 3).
Examples for Isolation Source Tags with MISO categories in three levels
Apply filters#
Click the Filter button (see below) to start applying isolation source filters to the strain list.
The Filter button opens the isolation source category selection mask
Open the Isolation categories tab to see the filter mask (see screenshot below) choose and apply isolation source filters. Do not forget to click the submit filter button.
Isolation source category selection
It is possible to submit more than one isolation source filter. The result can be further specified by adding additional filters for isolation, sampling, name and taxonomic classification.
From the result list, single strains can be accessed directly or strains can be added to the download selection for custom export.
Microbial Isolation Source Search results
Show Map#
Click the Open Map button (see below) to see the geographic origins of the strains in the filtered or unfiltered strain list.
The Open Map button opens a map showing origin countries of the filtered strains
The map shows origin countries of the listed strains by coloring countries from light yellow (few strains) to dark red (many strains).
The Open Map button opens a map showing origin countries of the filtered strains
Open Chart (Krona Chart)#
Click the Open Chart button to see a Krona Chart of the isolation sources in the filtered or unfiltered strain list.
The Open Chart button opens a Krona Chart showing the isolation sources of the filtered strains
Krona Chart for strains with isolation source #Environmental, #Aquatic, #Marine
TAXplorer#
The TAXplorer offers users the opportunity to browser through prokaryotic taxonomy and filter all available strains by their taxonomic classification.
The TAXplorer filters are set through dropwdown menus
The search can be started on any taxonomic level, starting on the domain level is not necessary.
The result list to the right of the dropdown menus shows all strains found for the chosen taxonomy (see below). Single strains can be chosen for addition to the download selection by clicking the respective checkboxes and confirming with the red Add selection button.
The TAXplorer result lists, checkboxes for strain selection, and Add selection button