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
1. Microbiome sample collection & preservation
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
StoolFix – Gut Microbiome Collection device:
- Swab + prefilled stab. buffer tube 2 ml
- Protects the DNA integrity & maximizes yield for months @ RT
- Combine with Isohelix DNA extraction kits
Read more from Isohelix’s DNA swabs and sample handling brochure.
2. Sample Homogenization
Powerful Bead Mill homogenizers from OMNI International, Isolate nucleic acids, proteins or living bacteria/viruses from animal and plant tissues, soil, feces.
- capacity 0,5 ml-50 ml
- Cooling unit available
Extract live bacteria/viruses from animal and plant tissues? Take a look at this poster from Omni International! Read the poster here.
3. DNA Extraction
a) MasterPure DNA Purification Kit
According to the article, where six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing were compared, 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
b) 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
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
4. 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
Analyze microbial communities using amplicon-free targeted sequencing of the total 16S rRNA gene
myBaits Expert 16S-Hyb:
- Convenient – Use the same NGS library preparation or protocol for shotgun sequencing
- Cost Effective – Identify rare taxa in metagenomic samples with less sequence depth
- Less Bias – Avoids issues associated with amplicon-based approaches
- Excellent Resolution – All constant and hypervariable regions are represented
- Open Platform – Compatible with any NGS library platform, including long-read sequencing
- Complete Solution – Kits include all necessary reagents to perform enrichment of NGS libraries Read more
For low input DNAseq
NxSeq UltraLow DNA Library Kit v2
Cost-efficient choice for inputs starting 50pg. High efficiency adaptor ligation produces complex libraries that yield improved sequencing depth uniformity and better coverage with fewer missed regions. (Lucigen/LGC Biosearch).
Interested?