Microbial Community Analysis (MCA)

High-resolution microbiome profiling and rapid insights powered by long-read sequencing and advanced bioinformatic workflows.

Why Choose Biocracy for MCA?

  • Long-Read Accuracy — Oxford Nanopore reads span thousands of bases, delivering species- and strain-level resolution that short-read platforms rarely achieve.
  • Complete Service — Marker-based (16S rRNA, ITS) and whole-metagenome options, free taxonomic classification, abundance tables, and optional advanced analytics.
  • Absolute Quantification — Use qPCR to convert relative read counts into copy numbers for truly actionable data.
  • Easy Logistics — Our proprietary sampling kits streamline sample collection and shipping; no cold chain required.
  • Flexible Turnaround — Standard and rapid turnaround times to suit your needs. 

Our Sequencing Options

Targeted (16S / ITS) Whole Metagenome
What is sequenced? Full-length 16S or ITS genes amplified by PCR All DNA extracted from the sample
Depth & breadth Focused on bacteria/archaea (16S) or fungi (ITS) Captures bacteria, archaea, fungi, viruses, plasmids
Typical questions “Who is present?” community comparisons “Who is present and what can they do?” genes & pathways
Pros
  • Highly sensitive (PCR enrichment)
  • Excellent for low-biomass swabs
  • Lower cost & data volume
  • Functional insight (genes, AMR, metabolism)
  • Detects novel organisms
  • Enables genome recovery (MAGs)
Cons
  • Limited functional information
  • Primer bias can skew taxa
  • Needs more DNA & depth
  • Database gaps / poor annotation can hinder calls
  • Larger files, higher cost

In practice: Shotgun metagenomics sequences everything, but interpretation can be limited by incomplete or poorly annotated reference databases. Many projects benefit from a hybrid strategy—targeted profiling for community structure plus shotgun or targeted qPCR for key functions.

Relative vs Absolute Abundance

Sequencing alone provides relative abundances (percent of reads per taxon). To determine real population shifts, you need absolute abundances.

Our integrated qPCR service measures total microbial load or specific targets, and converts sequencing proportions into copy numbers (e.g., 1 × 106 cells g-1). Absolute quantification is essential for:

  • Tracking pathogen or probiotic load over time
  • Comparing samples with different biomasses
  • Meeting regulatory or QC thresholds

DNA Input: Will a Swab Work for Metagenomics?

  • Targeted 16S/ITS: PCR enrichment means sub-nanogram yields are usually sufficient.
  • Shotgun Metagenomics: Optimal libraries need ≥ 100 ng high-molecular-weight DNA (1 µg ideal). Swabs may yield 1 – 20 ng, which is often too low.

If DNA is limited, we recommend:

  1. Using marker-based sequencing (most low-biomass swabs)
  2. Applying whole-genome amplification (can introduce bias)
  3. Collecting a higher-biomass sample when feasible

What You Receive

  1. Interactive taxonomic tables (relative & absolute if qPCR added)
  2. Species/strain-level profiles with quality metrics
  3. Optional add-ons: assembly, functional annotation, strain tracking, statistical analysis

Simple Workflow

  1. Optional: Purchase Kit – Swab or bulk-sample kit shipped to you. Preservative stabilizes DNA at ambient temperature. DNA extraction and return shipping included in price.
  2. Collect & Return – Collect your sample and ship to us.
  3. Sequence & Analyze – Choose sequencing service(s) with standard or rapid turnaround.
  4. Review Results – Download reports; schedule optional consultation.

Ready to Profile Your Microbiome?

From quick community snapshots to absolute quantification and full functional metagenomic insights, Biocracy’s MCA service delivers fast, accurate, and tailored results.