Bio-DX
Microbiome & Functional Analysis of Environmental Microorganisms
We analyze the structure and function of microbial communities, from 16S rRNA and ITS amplicons to shotgun metagenomics and MAG construction, for uses such as gut microbiome research, wastewater treatment, and environmental monitoring.
Service Overview
We combine sequencing with bioinformatics analysis to study the composition and functions of microbial communities. From bacteria and fungi to uncultured microorganisms, we choose the method that fits your goal.
1. 16S rRNA amplicon analysis
We characterize bacterial communities in environmental, food, and gut samples.
Ideal for:
- Characterizing the microbial composition of fermentation or treatment tanks
- Comparing changes in the gut microbiome between treated and control groups
- Assessing the microorganisms in environmental samples such as soil and water
Key analyses: community profiling (tables of operational taxonomic units [OTUs] or amplicon sequence variants [ASVs], composition plots) and diversity analysis (alpha and beta diversity, non-metric multidimensional scaling [NMDS])
Options: group comparison (principal coordinates analysis [PCoA] plots, permutational multivariate analysis of variance [PERMANOVA] tests, and LEfSe to identify differential taxa), correlation with environmental factors, and time-series analysis
2. ITS region analysis
We read the internal transcribed spacer (ITS) region between rRNA genes to characterize fungal (mold and yeast) communities.
Ideal for:
- Characterizing the yeasts and molds in your samples
- Assessing the diversity of soil fungal communities
- Combining ITS analysis of fungi with 16S rRNA analysis of bacteria from the same samples
Key analyses: fungal community profiling, diversity analysis, and joint analysis with bacteria when combined with 16S rRNA analysis
Options: correlation with environmental factors and time-series analysis
3. Shotgun metagenomics and MAG construction
Rather than amplifying a single marker gene, we use shotgun sequencing on community DNA and analyze both taxonomic composition and functional potential.
Ideal for:
- Learning not only which taxa are present but also what they can do, such as metabolic pathways
- Reconstructing the genomes of microorganisms that cannot be cultured
- Exploring unknown microorganisms and functions in an environment
Key analyses: taxonomic and functional profiling, metabolic pathway analysis, de novo gene prediction, and construction and functional inference of metagenome-assembled genomes (MAGs)
Options: correlation with environmental factors and time-series analysis
The PtBio Approach
Industrial microbiome analysis raises questions a standard report cannot answer. Whether the job is managing a wastewater treatment process, characterizing the gut microbiome, or environmental monitoring, the work does not end with a community profile.
We tailor the sampling design, choice of method, and interpretation to your application, and work with you throughout the project.
What we resolve in the initial consultation
| Your challenge | What PtBio proposes |
|---|---|
| Not sure which samples or time points to collect | A sampling design based on your goal |
| Unsure what the detected microbes mean | Functional interpretation in the industrial context, with a literature review |
| Groups differ, but which taxa matter? | Identification and prioritization of key taxa with LEfSe and other methods |
| Want to apply the results to product development or quality control | Action-oriented reports and ongoing support |
Why PtBio
| Strength | What it means for you |
|---|---|
| Collaborative custom analysis | End-to-end design from sampling to interpretation, tailored to your application |
| GTDB taxonomy | We use GTDB (Genome Taxonomy Database), a genome-based taxonomy, as the reference system |
| Full-length 16S | Identification down to species level, where the sequence data allow, by reading the full-length 16S rRNA gene with long reads (PacBio HiFi) |
| From amplicons to metagenomes | 16S, ITS, shotgun metagenomics, and MAG construction, chosen to fit your goal |
| Joint research lab at Hiroshima University | We apply methods developed in joint research with the Laboratory of Bio-DX (Professor Hidemasa Bono, Graduate School of Integrated Sciences for Life) |
Why We Use GTDB
Bacteria and archaea can be classified with a name-based system such as NCBI Taxonomy, or with GTDB (Genome Taxonomy Database), which defines taxa from genome phylogeny. The table compares named genera and species in NCBI Taxonomy with all genera and species in GTDB, including taxa with placeholder names, so the two counts use different criteria.
| Rank | NCBI Taxonomy (named taxa, September 2026) | GTDB R232 |
|---|---|---|
| Genera | 6,284 | 37,503 |
| Species | 30,438 | 199,923 |
For NCBI Taxonomy we count only species with a binomial name. Roughly 530,000 entries with provisional names such as “Bacillus sp.” are excluded.
Named microbes are heavily skewed toward those that grow in culture. Most environmental microbes are hard to culture and carry no formal name. Because GTDB derives its taxa from genome sequences, microbes without a name are part of the reference system too.
Sources: GTDB Release 232 statistics / NCBI Taxonomy statistics
Supported Samples
| Category | Samples we have analyzed |
|---|---|
| Human | Feces, saliva, intestinal mucosa, intestinal fluid, vaginal swabs |
| Environmental | Soil, environmental water, sewage and wastewater treatment tanks |
| Industrial processes and cultures | Methane fermentation tanks, microbial enrichment cultures |
We may also be able to handle sample types not listed here. Please contact us to discuss.
Technologies
| Method | Sequencing platform | Read type | Identification level | Main use |
|---|---|---|---|---|
| Full-length 16S rRNA amplicon (V1–V9) | PacBio (HiFi) | Long reads | Up to species | Species-level comparison |
| Full-length 16S rRNA amplicon (V1–V9) | Oxford Nanopore | Long reads | Up to species | Cost-effective mid-scale projects |
| 16S rRNA amplicon (V3–V4) | Illumina | Short reads | Genus | Large-scale screening |
| ITS amplicon | Illumina | Short reads | Genus | Fungal (mold and yeast) communities |
| Shotgun metagenomics | Illumina | Short reads | Taxonomy and gene function | Taxonomic and functional profiling |
| Shotgun metagenomics | PacBio (HiFi) | Long reads | Taxonomy and gene function | MAG construction |
Process
- Contact us — We propose an analysis method that fits your goal.
- Sampling & DNA extraction (approx. 1–2 weeks) — Development of a sampling strategy, collection of environmental samples, high-quality DNA extraction and quality assessment
- Sequencing data acquisition (approx. 2–3 weeks) — Choice of full-length 16S rRNA amplicon sequencing or shotgun metagenomics (short or long reads)
- Data analysis & microbiome profiling (approx. 3–4 weeks) — Taxonomic and functional profiling, MAG (Metagenome-Assembled Genome) construction, integrated analysis with environmental factors
- Result interpretation & report preparation (approx. 2–3 weeks) — Interpretation of microbial community structure and function, ecological discussion, custom report preparation, proposals for future research strategy
In the initial consultation we ask about your sample type, analysis goal, and budget, and propose a method and analysis plan.
Plans & Pricing
16S rRNA amplicon analysis (short reads)
From ¥30K (excluding tax, per sample) / Delivery: 1 month
We sequence the V3–V4 region to profile many samples to genus level at low cost.
Full-length 16S rRNA amplicon analysis (long reads)
From ¥35K (excluding tax, per sample) / Delivery: 1 month
We read the full-length 16S rRNA gene to profile the microbiome, down to species level where the data allow.
Shotgun metagenomic analysis (short reads)
From ¥56K (excluding tax, per sample) / Delivery: 1 month
We identify the microbes and also profile the functions of their genes.
Shotgun metagenomic analysis (long reads)
From ¥65K (excluding tax, per sample) / Delivery: 1–2 months
We sequence community DNA with long reads. MAG construction is quoted separately depending on the scope.
Cost Examples
Costs vary by project. Use these examples as a guide and contact us for a quote.
| Analysis | Example | Sample size | Cost (excl. tax) |
|---|---|---|---|
| Microbiome analysis (full-length 16S) | Time-series microbiome monitoring of environmental samples | About 90 samples | From approx. ¥2.1M |
| Microbiome analysis (full-length 16S) | Group comparison of the human gut microbiome | About 60 samples | From approx. ¥1.8M |
Note: Prices include sequencing and vary with sample count, analysis scope, and options.
Related project: Next-generation human-waste treatment through metagenomic analysis (a field trial at a human-waste treatment facility in Higashihiroshima)
Deliverables
You receive an analysis report that summarizes the results, and the full set of data behind it. We organize the data by analysis step in folders and deliver it on a hard drive or through cloud storage, in a form your team can reanalyze or hand to another provider.
Analysis report (PDF and HTML)
One document covers how we sequenced, what data we obtained, how we analyzed it, and what we found. You can view the results on screen and switch between sample groups and taxonomic levels.
Included in every project
- Raw sequencer output, with checksums so you can confirm the files are intact (how to verify them, in Japanese)
- Data volume and quality checks
- A list of the software and databases we used, so the analysis can be reproduced later
When we profile which microbes are present and in what proportions (16S rRNA and ITS amplicon analysis)
- A table of which microbes are present in each sample and in what proportion, at each taxonomic level from order down to species, as far as the data allow
- Figures for comparing proportions at a glance (stacked bar charts, pie charts per sample)
- Numbers for the diversity within each sample and the similarity between samples (Excel)
- For bacteria and archaea, results classified two ways on request: with named taxa only, and with the genome-based GTDB taxonomy
When we also examine what the microbes can do (shotgun metagenomics, MAG construction)
- A list of the genes and metabolic functions present, in addition to the taxa
- Reconstructed genome sequences of microbes that cannot be cultured, with an assessment of their completeness
On request
- A comparison table arranged by sampling site or time point (Excel), for tracking changes over time or between sites
- A shortlist of microbes that differ significantly between conditions (LEfSe), and tests of overall community differences (PERMANOVA)
- Functions predicted from community composition (PICRUSt2 and others)
- Phylogenetic trees and correlation analysis with environmental measurements
FAQ
Q: What are the advantages of GTDB?
A: GTDB defines taxa from genome sequences, so uncultured microorganisms without a formal name are part of the reference system. This makes it well suited to samples such as soil and treatment tanks, where uncultured microorganisms are common.
Q: How much sample do you need?
A: As a guide, about 0.5 g of soil, 0.2 g of feces, or 10 mL of liquid. Requirements vary with the sample condition and the analysis goal, so please consult us.
Q: Can you analyze fungi?
A: Yes. ITS region sequencing covers mold and yeast communities. Combined with 16S rRNA analysis, we can analyze bacteria and fungi in the same samples.
Q: What is the difference between full-length 16S and V3–V4?
A: Full-length 16S (long reads) can identify down to species level but costs more. V3–V4 (short reads) identifies to genus level but processes large numbers of samples at low cost. We propose whichever fits your goal.
Q: When do you recommend amplicon analysis, and when shotgun metagenomics?
A: Amplicon analysis suits questions about community composition. Shotgun metagenomics suits questions about which genes and metabolic pathways are present, or about reconstructing the genomes of uncultured microorganisms. We propose an approach that fits your goal and budget.
Q: Do you offer volume discounts?
A: Large projects are priced individually by sample count and analysis scope. Please contact us.
Q: We have no bioinformatics specialist in house. Is that a problem?
A: No. We support you from interpreting the results to applying them in product development and quality control.
Q: Can you run additional analyses after delivery?
A: Yes. We handle additional analyses, visualizations, and comparisons with other samples.
Q: What is the typical timeline?
A: The timeline depends on the method, sample count, and analysis scope. We give a project-specific estimate in the initial consultation.
Q: Can we get a cost estimate first?
A: Yes. We provide a rough estimate in the initial consultation.
Contact Us
For microbiome and metagenomic analysis inquiries and quotes, please use our inquiry form.