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MICROBIOMA

LaboSpace offers Microbiome Analysis by Next Generation Sequencing (NGS) on Ion Torrent ™ Personal Genome Machine® (PGM) (ThermoFisher Scientific) platform. This system is able to analyze mixed microbial populations by sequencing of hypervariable regions of the 16S rRNA bacterium.

The test is done directly on DNA extracted from biological samples such as stool, urine, saliva, skin, swabs (vaginal, buccal, rectal, cutaneous, environmental).
We can provide, to the scientist who request it, a kit for collecting and preserving the sample.
Labospace proposes two solutions of analysis:

  • Sequencing protocol of two (V3-V4) of the 9 hypervariable regions of the 16S rRNA bacterium;
  • Protocol with Ion 16S methanomeic kit (ThermoFisher Scientific), with two multiplex PCR mix  amplifying V2, V3, V4, V6-7, V8 and V9 regions, obtains the maximum coverage of the different groups of bacterial populations.

The metagenomic analysis allows to qualitatively and quantitatively assess the bacteria (family, genus and species) present in the various anatomic districts in various health and / or pathology conditions.

The raw data can be provided: 

  1. As FastQ or UBAM file
  2. Analyzed with the Ion Reporter software that useMicroseqID e Greengenes as Reference Database
  3. Analyzed with custom script

Below we report:

  • An explanatory table covering different groups of bacterial populations using the various hypervariable regions of the 16S

 

As shown in the table using V3 and V4 coverage will be 57%, while using the 7 Thermo Kit regions coverage reaches 100%.

 

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