16S Metagenomics & Microbiome Sequencing
16S Metagenomics & Microbiome Sequencing Services in Hyderabad — Soil, Gut, Food, Water & Environmental Profiling
Plan a microbiome study around the matrix, comparison and biological question. Manna Biotech scopes full-length 16S rRNA, targeted V3–V4, fungal ITS and shotgun metagenomics workflows with sample preparation, controls, sequencing and documented bioinformatics for research and industrial R&D.
- Scientist-guided, founder-led
- Research and industrial R&D
- Nacharam, Hyderabad · India-wide sample enquiries
Choose the sequencing strategy
Marker profiling and shotgun sequencing provide different evidence.
The term “16S metagenomics” commonly refers to bacterial marker-gene profiling. It does not sequence every gene in a community. Select the assay and executing platform before comparing datasets or interpreting functions.
Full-length 16S V1–V9
Oxford Nanopore full-length 16S can improve discrimination over a short variable region and support species-level calls where read quality, the organism and the reference database permit. It does not reliably distinguish every species or strain.
Targeted 16S V3–V4
Short-read or targeted 16S workflows can fit established study designs and reference datasets. We confirm platform, primers, library preparation and executing facility before acceptance; V3–V4 results are not directly interchangeable with full-length profiles.
ITS fungal profiling
Fungal marker analysis uses an appropriate ITS target, primers and curated references. Taxon recovery and resolution depend on primer bias, extraction and database coverage; ITS and bacterial 16S answer complementary questions.
Shotgun metagenomics
Community DNA sequencing can support taxonomic and gene-content analysis beyond a marker assay. Depth, host DNA, expected abundance and computational scope determine what can be observed; DNA findings do not establish gene expression.
Sample matrices
Extraction and controls must fit the material.
Agricultural soil and rhizosphere
Compare soil compartments, crop stages or bio-input interventions using an agreed sampling design. Soil heterogeneity and inhibitors require appropriate extraction, blank controls and replicate planning.
Aquaculture pond water and sediment
Study pond microbial communities across sites or management conditions. Water filtration, sediment subsampling, preservation and extraction are matrix-specific and are confirmed before dispatch.
Fermented foods and dairy
Profile research batches, starter communities or product-development samples. DNA from dead cells may be detected, so abundance estimates do not replace viable counts, shelf-life validation or statutory food testing.
Preclinical and research gut or fecal samples
Plan ethically approved, de-identified research sampling with documented provenance and appropriate handling. Human or animal materials require institutional, consent and biosafety review before acceptance; this is not a consumer gut-health diagnosis.
Industrial effluents
Investigate microbial composition in approved treatment or process studies. Chemical hazards, sample containment, inhibitors and receiving-facility capability must be reviewed before material is sent.
Biofilms and environmental surfaces
Compare defined surface communities or process locations with consistent sampling area, negative controls and handling. Low biomass and contamination can dominate results without a careful design.
Study design before sequencing
Make the comparison interpretable from the first sample.
- 01
Define groups, replicates and metadata
Agree the biological question, sample units, controls, covariates and intended comparisons. A large number of reads cannot repair missing biological replication or an uncontrolled sampling design.
- 02
Confirm collection and preservation
Use matrix-specific instructions for containers, stabilization, temperatures and transport times. Obtain acceptance before shipment and keep batch, site, condition and collection-time records consistent.
- 03
Extract, sequence and review QC
Document the extraction and library approach, assay controls, read yield and filtering. Report samples that fail criteria, low-biomass concerns and potential batch effects before downstream conclusions.
- 04
Analyse the agreed comparisons
Record filtering, reference versions, taxonomy thresholds, statistical assumptions and correction for multiple comparisons. Deliver data and figures with enough methods detail for review and reproducibility.
Bioinformatics deliverables
From quality-controlled reads to comparisons with stated limitations.
Alpha diversity
Agreed richness and within-sample diversity summaries, including Shannon and Simpson indices, with the normalization, depth and sample-exclusion decisions recorded.
Beta diversity and ordination
Between-sample distances with PCoA or NMDS where appropriate, linked to the sample metadata and study design. Statistical group comparisons require suitable replication and assumption checks.
Taxonomic bar plots and tables
Abundance tables and figures from phylum to the finest supported rank, including species only where the assay/reference evidence permits. Unclassified taxa and ambiguity remain visible.
Differential abundance
Appropriate compositional-data methods for predefined comparisons, with covariate handling, effect estimates and multiple-testing correction. Exploratory findings are separated from confirmatory claims.
Functional pathway prediction
PICRUSt2 may support inferred functional profiles for compatible, quality-controlled 16S datasets. Predictions are labelled as inference, checked for reference coverage and not represented as measured gene content, metabolic activity or an ITS result.
Raw files, methods and NCBI SRA support
Receive agreed reads, QC, taxonomy/diversity outputs, publication-grade plots and methods. NCBI SRA upload preparation includes sample metadata and file support after owner approval; public release timing and repository acceptance remain separate decisions.
Turnaround and quotation
A defined study scope, not an unexplained per-sample number.
A typical accepted microbiome work package is planned for 2–4 weeks after satisfactory sample QC and scope confirmation. Matrix complexity, extraction problems, sequencing capacity and extra statistical comparisons can change the timeline. The quote separates sample preparation, sequencing and analysis.
Share the planned groups, sample count, matrix, available metadata, required assay and intended use. If you already have raw reads, request analysis-only support rather than sending new biological samples. A confidentiality agreement can be arranged before proprietary process information is exchanged.
Research-grade scope and clear reporting boundaries.
These are research-grade microbiome services for non-clinical investigation and industrial R&D, not NABL-accredited or GLP reports, clinical gut-health testing or statutory food/water certification. A microbiome profile does not diagnose disease, prove safety or directly measure the viability or function of detected organisms.
Sample suitability, the executing facility, method availability, biosafety, acceptance criteria and deliverables are confirmed in writing before work begins. We do not guarantee a particular result, publication, regulatory approval or commercial outcome.
Scientific leadership
Dr Chathyushya K B
Founder, MD & CEO — PhD Microbiology, ICMR-NIN; PGDM Bioinformatics; Advanced Diploma in Patent Law, NALSAR; 15+ years' scientific experience.
The scientific team reviews the question, sample plan and interpretation so that the report explains what the evidence supports and where further work is needed.
Read the founder's scientific profile →Request a service quotation
Start with the question your data must answer.
Describe the sample matrix, 16S/ITS/shotgun question, study groups and replicates, sample count, available metadata, required analyses, intended use and timeline.
Send a non-confidential outline first. Do not include patient identifiers or upload proprietary sequence data in this enquiry. Ask for an NDA and an approved transfer route when needed.
Nacharam, Hyderabad laboratory — approximately a 12-minute walk from Habsiguda Metro. Contact us before dispatching samples; collection, preservation and transport instructions depend on the approved assay.
Contract and bulk enquiries: +91 8977681985 · Technical scope: +91 8978792215
Related services
Choose the service that matches the scientific question.
Nanopore platform service options
Compare long-read marker, isolate WGS, plasmid and shotgun sequencing scopes.
Soil and bio-input research
Connect microbiome comparisons to rhizosphere study design, strain identity and agriculture R&D.
Targeted aquaculture PCR
Use a pathogen-specific assay alongside a community profile when the research question needs both.
Food authenticity and research testing
Discuss a focused DNA identity, contamination or product-development question.
India-wide microbiome scope
Coordinate remote project planning and sample review from institutions across India.
Questions
Frequently asked questions
Should I choose full-length 16S V1–V9, V3–V4, ITS or shotgun metagenomics?
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Full-length 16S and V3–V4 target bacterial marker genes; their resolution and biases differ. ITS targets fungi. Shotgun sequencing samples broader community DNA and may support gene-content analysis at sufficient depth. Choose based on the organisms, matrix, comparison and existing datasets, then confirm primers, platform and execution scope. A bacterial marker assay is not a direct measurement of all community genes.
Does full-length Nanopore 16S guarantee species-level identification?
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No. Full-length V1–V9 can improve resolution over a shorter region, but some species share very similar 16S sequences and databases may be incomplete. Read accuracy, classifier settings and reference quality also matter. Reports use the finest rank supported by the evidence and retain ambiguous or unclassified assignments rather than forcing every read to a species.
Can soil, pond water, food and gut samples use the same preservation method?
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No. Collection, stabilization, inhibitors, biomass and transport conditions differ across matrices. Ask for a written, assay-specific sampling and shipping plan before collecting or dispatching material. Research gut or fecal samples require the relevant institutional, consent and biosafety approvals and de-identification; do not include patient identifiers in the enquiry.
What diversity, statistical and functional outputs can I request?
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A defined scope can include Shannon/Simpson alpha diversity, beta-diversity distances and PCoA/NMDS, taxonomic plots, and differential abundance with suitable replication and multiple-testing correction. PICRUSt2 predictions may be appropriate for compatible 16S data and are reported as inferred function, not measured activity. Shotgun-derived gene tables and ITS profiling have different analysis requirements.
What is the turnaround and can you help with NCBI SRA deposition?
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A typical accepted sequencing and analysis project is planned for 2–4 weeks after QC and written scope confirmation; complex matrices or additional comparisons may need longer. The quotation lists raw reads, reports and analysis files. SRA support can cover metadata and upload preparation with the owner’s approval, without guaranteeing repository or journal acceptance.