Characterization of microorganisms

Thanks to our expertise, we adapt our tools to identify and characterize a wide range of bacteria, yeasts and molds. We are able to work using isolated strains, nucleic acid solutions or even more complex samples such as biopsies, soil or surface samples

Identification

As a first step of a microbiological study, SMALTIS is able to accurately identify a wide variety of microorgansims, whether dealing with bacteria, yeasts or molds. At SMALTIS we offer you a wide range of identification solutions thanks to molecular biology tools. Our methods depend on the type(s) of microorganisms you wish to identify.

Methods:

MALDI-TOF de Bruker Mass Spectrometry
The mass spectometry is an analytical method allowing the identification of the gender and the species of microorganisms in just a few minutes. This fast method, dependent on databases, is well adapted to the identification of most bacteria.
At SMALTIS we are also capable of setting up databases specific to your targeted strains.

Sanger Sequencing
Sanger-Sequencing is useful for the accurate identification of unknown and/or non-cultivable strains for which mass spectrometry is not adapted (e.g. Yeast and Mold strains). Depending on the microorganism, we amplify and sequence genes specific targets. The identification is then performed by comparing the targeted sequences with international databases.

Next-Generation Sequencing (NGS)
It can be use either from an isolated microorganism or from a microbiome, i.e a well characterized environment.
To identify an isolated microorganism, whole genome sequencing is perform to obtain the raw data of the entire genome of the strain allowing both to identify the species and to obtain its genetic map.
For a microbiota (i.e all the microorganisms present in a microbiome) the useful method consists in sequencing 16S rRNA gene, a highly conserved component of the transcriptional machinery of all DNA-based life forms.

Phenotyping

After the identification, the accurate characterisation of your micro-organisms is the second step required for all your analyses. Indeed, the features of the strains used in your R&D projects will determine your results as well as your interpretation. To know better the strains you will study, we offer you at SMALTIS our services to determine their phenotypic (e.g. Morphological, Physiological, Metabolic and Resistance phenotype to antibiotics) and genotypic characteristic.

Methods:

Determination of Morphological caracteristics
The study of a micro-organism’s morphology allows us to check how pure a strain is. It is based on the study of colonies and cells’ morphology. From your strains, we at SMALTIS perform:

- The morphological study of colonies is a macroscopic study (bare eye) allowing to observe the colony’s characteristics namely:
      . The shape (round, whole, wavy, thready, …)
      . The size
      . The colour
      . The aspect (sticky, thread, …)
      . The smell

- The morphological study of cells is a microscopic study which can be perform straight or a cell coloration. It allows to observe:
      . The cell form (spherical, cylindric, spiral, wrapped or thread)
      . The gathering mode (in chain like streptococcus, in group like staphylococcus, …)
      . The size
      . The presence of spore
      . The motility

Determination of Physiological and Metabolic characteristics
Because each micro-organism has its own biochemical characteristics, at SMALTIS we offer you to identify them for each of your species by:
      . Culture on specific growth media
      . The performance of various biochemical tests (e.g. API galleries)
      . The realisation of growth curves according to different parameters (temperature, oxygen, pH)
      . The assessment of their propensity to make biofilm in a microplate

These services can be done with yeast and/or mold strains.

Genotyping
Molecular genotyping is the method used for epidemiological monitoring of pathogenic microorganisms, the production quality controls or identification of contamination sources. Thanks to various methods, SMALTIS enables you to determine the genotype of your strains and thus to verify their clonality (to verify whether or not you are dealing with the same strain).

Methods:

MLVA

Genotyping by MLVA (Multi-Locus Variable number tandem repeat Analysis) is based upon the amplification by PCR (polymerase chain reaction) of various VNTRs (Variable Number of Tandem Repeats) scattered on the bacterial genome using specific primers. The determination of the molecular size of different amplicons by electrophoresis allows to identify the number of repetitions at a specific locus. By this manner, these results reflect the number of repeated units in the amplified region as the length of repeated units is known. In some species, this method significantly increases the level of bacterial genotyping. Typing results in a numeric code, which includes the number of patterns at each locus.

Pulsed Field Gel Electrophoresis (PFGE)

Genotyping by PFGE (Pulsed Field Gel Electrophoresis) allows to analyze the macrorestriction profiles of total DNA by pulsed field gel electrophoresis. The result is a migration profile, which defines a pulsotype characteristic of a bacterial isolate. PFGE is a standard method of typing for numerous bacterial species due to its highly discriminating potential.

Measurement of virulence factors

The study of the activity and/or production of virulence factors is a key element enabling to understand bacterial pathogenicity. In this context, SMALTIS offers you to characterize your strains by:

      - Studying the activity of structural virulence factors, and more specifically the activity of determinants involved in bacterial adhesion and motility. These determinants, such as pili or flagella, may be observed in specific environments.

      - Studying the activity and/or production of secreted factors such as toxins, siderophores or enzymes involved in host colonization or infection. These secreted factors may be either enhanced through appropriate agar media, or measured out in accordance with adapted methods.