Microbial Diversity Analysis

Microbial Diversity Analysis

Nowadays the analysis of amplified sequences is considered one of the most important approaches for microbial identification and diversity analysis.

Next Generation Sequencing (NGS) techniques allow for sequencing millions of reads and many samples in a single run through multiplexing strategies.

The data produced can then be compared with validated public microbial sequences databases in order to investigate the taxonomic diversity of the samples reaching genus or even species level.Amplicon analysis includes sequencing of housekeeping genes (16S or 18S) for Bacteria and Eukaryotes but other genes could be also used.

Some our basic assays include:

  • Bacteria 16S
  • Fungi (18S, SSU, ITS1-4)
  • Archaea 16s
  • Algae
  • Cyanobacteria

Areas of Control

The areas in which the modern SMALLOMICS laboratory offers solutions through microbial diversity studies are:

Microbiological analysis in water is crucial for testing safety. There are several law prerequisites that differentiate between drinking water and swimming waters (swimming pools, natural bodies). Although these prerequisites cover a wide range of pathogenic microorganisms in water they might miss pathogenic microorganisms that cannot be captured by conventional techniques and might be responsible for low water quality.We can provide microbial diversity and function analysis using Next Generation Sequencing (NGS) in different water samples including:
• Drinking Water
• Swimming Pools
• Environment (sea, rivers, lakes)
• Special aquatic ecosystems (aquaculture, reservoirs, etc.)

Microbial diversity in soils is huge.Exploring microbial diversity using NGS techniques can allow for the investigation of the majority of soil microbes taxonomy and function.

This might allow for the investigation of pathways including decomposition of complex or toxic organic compounds providing hints for soil quality.

Microbiological food and beverages testing is critical for ensuring safety for the consumers and avoiding losses for the producers.

• Accurate identification of microbial groups.
• Identification of all genes and metabolic pathways identified in a product.
• Detection of undesirable microbes along production lines that can cause changes in quality.
• Accurately determining and extending the end of shelf life of a product.
• Authenticity, traceability and safety of food and raw materials.
• Quantification of targeted micro-organisms of technological importance in fermentation products
• Screening for undesirable genetic modification (for cotton, maize or soya)

Wastewater treatment plants and sewage systems are designed in order to treat and return wastewater to ecosystems (usually water bodies) through complex tube systems. Therefore these systems represent sources of urban or rural microbial communities that finally end up in natural environments.

The monitoring of such microorganisms can be easily performed using NGS technologies assisting in the better performance of WWTPs.

Monitoring microbial diversity along production lines (from source to final product in industry) and at different sampling points (temporally or spatially in environmental studies) could follow changes in the abundance of microorganisms of interest. The importance of monitoring is based on the fast changes in microbial community composition due to the:

• the coupling of microbial metabolisms
• the competition between microbes for energy sources and
• the changes in optimal growth conditions

Areas of Application

Our analyzes can be applied in the following areas.



All Smallomics staff have a high scientific background with many publications and conferences presentations.


For each data analysis we offer detailed reports and suggest actions that can be taken.


Smallomics collaborates with universities in Greece and abroad on data analysis and research.