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Accelerate your microbiome studies with us!

The microbiome is a fascinating and rapidly growing field of study. Complex microbial communities, whether in the air, water, soil, plants, or symbiosis with humans, are important indicators of environmental and human health. In this page we will summarize:
1. Sample collection and preservation
2. Sample homogenization
3. DNA extraction solutions
4. NGS solutions for microbial analysis

Microbiome sample collection & preservation

StoolFix – Gut Microbiome Collection device

  • Swab + prefilled stab. buffer tube 2 ml
  • Protects the DNA integrity and maximizes yield for months @ RT
  • Combine with Isohelix DNA extraction kits

GeneFiX™ Saliva DNA Microbiome Collection Device

  • Microbial DNA is perfectly preserved @ RT in the pre-filled buffer for at least 1 year
  • Patented anti-spill funnel, non-hazardous buffer & collection tube
  • Combine with Isohelix DNA extraction kits

Isohelix™ DNA/RNA Buccal Swabs (for skin, surface, tissue sampling etc.)

  • Unique swab matrix greatly improves DNA/RNA yields
  • Human and veterinary use
  • Single, twin and triple packs available + Mini Swabs
  • With stabilization pouch & buffer tubes

Read more from Isohelix’s DNA swabs and sample handling brochure.

Sample Homogenization

Powerful Bead Mill homogenizers from OMNI International, Isolate nucleic acids, proteins or living bacteria/viruses from animal and plant tissues, soil, feces.

OMNI Bead ruptor 24 elite homogenisaattori

  • capacity 0,5 ml-50 ml
  • Cooling unit available

Check the instrument details here.

Extract live bacteria/viruses from animal and plant tissues? Take a look at this poster from Omni International! Read the poster here.

What is the best kit for extracting bacterial DNA for NGS applications?

A myriad of commercial kits are available for extraction of bacterial DNA. These kits are typically tested by the kit suppliers and scientific literature comparing different commercial kits is very limited. However, there are exceptions: this article compared six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing.

Accordingly to the article, Masterpure provides the cheapest and fastest completion/hands-on-time of the kits compared.
“In cases where a differential coverage of smaller plasmids (under 5 kb in our case) may be considered negligible, the choice of DNA extraction kit can be guided largely by other factors including extraction costs, extraction time and potential for automation.” Read the article

Isolate microbial genomic DNA with Bead Mill DNA Purification kits

From soil & sediment: Bead Mill Soil DNA Purification Midi Kit (50 prep) 26-013B:

  • Effective removal of PCR inhibitors including humic compounds
  • Microbial DNA isolation from a variety of organisms including gram-positive and gram-negative bacteria
  • Isolation of pure DNA from up to 1 g soil, clay, sediment, and compost
  • Recover up to 25 µg DNA per filter
  • Includes bulk beads, spin-columns, and nontoxic reagents

From feces or urine: Bead Mill Fecal DNA Purification Mini Kit (50 prep) 26-014B:

  • Microbial DNA isolation from a variety of organisms including gram-positive and gram-negative bacteria
  • Isolation of pure DNA from up to 250 mg stool, biosolids, gut material, and urine
  • Recover up to 25 µg DNA per filter
  • Includes 2 mL tubes pre-filled with 0.5 mm glass beads

Read more about bead mill nucleic acid purification kits here.

Save time and homogenize effectively with deep well plates

  • RNase & DNase Free
  • Pre-filled 2 mL 96 deep well plates with ceramic or metal beads

 

NGS solutions for microbial analysis

Comprehensive analysis of complex microbiomes (e.g. bacteria, archaea, and fungi) is increasingly performed via next-generation sequencing (NGS) technology.

Effective bacterial ribosomal RNA depletion

For effective bacterial ribosomal RNA depletion: Lexogen RiboCop for bacteria – Stand-alone kit prior to any RNAseq solution. Read more

 

Universal Prokaryotic RNAseq

Universal Prokaryotic RNAseq: All-inclusive kit for bacterial transcriptomics, including integrated bacterial rRNA depletion. Read more

 

SWIFT NORMALASE® AMPLICON PANELS (SNAP) 16S V2 AND ITS1

Single Tube Multiplex PCR NGS Library Prep with High Throughput Workflow. Amplicon panel comprised of tiled primer pairs (=multiple overlapping amplicons) to target:

  • (a) all V1-V9 variable rRNA regions and
  • (b) ITS1 region
  • each with a single pool of multiplexed primer pairs

 

  • Short PCR1 + PCR2 workflow, ready-to-sequence libraries in 2 hours
  • Sample multiplexing on Illumina instruments: 768plex dual indices, 384plex UDIs
  • Generates robust libraries, even from low input quantities.
  • The libraries may be quantified with conventional methods such as Qubit® or Agilent Bioanalyzer and normalized by manual pooling or normalized enzymatically with the included Swift Normalase reagents.
  • Panel can be customized with additional targets including antibiotic resistance or virulence genes, allowing sub-genera level identification and functional analysis. Read more

 

For metagenomics & shotgun sequencing

Swift’s 2S® Turbo Kit and Swift’s 2S® SONIC Kit
Short, straightforward & cost-efficient 2h protocols, 2S Turbo with enzymatic fragmentation
Sample multiplexing on Illumina instruments: 768plex dual indices, 384plex UDIs. 1536plex UDIs upon request.

 

Interested?

Contact us for more information and/or demo request!

KATJA-RIIKKA LOUHI | PhD, Product Manager, Life Science

SANNA SILTANEN | PhD, Product Manager, NGS & Genomics

 

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