Microbal & Bacterial Genomics Services
Tailored Microbial Genomics Services and Analysis: from Genome Assembly to Genome Annotation
What is Microbial & Bacterial Genomics?
Microbial genomics (or bacterial genomics) decodes the DNA of microorganisms—whether isolated pathogens, environmental bacteria, or industrial strains. By unlocking these genomes, researchers gain critical insights into:
Strain Identification Taxonomic classification
Precisely identify species and strains
Pathway & Metabolic prediction
Map biochemical networks and metabolic potential
Antibiotic Resistance Profiling
Detect resistance genes before they become clinical problems
Comparative Microbial Genomics
Compare multiple genomes to spot evolutionary adaptations
What Can You Achieve with our Microbial Genomics Services?
Bacterial Genome Assembly
Obtain high‑quality draft or complete bacterial genomes from short or long‑read sequencing data, ready for downstream analysis.
Genome annotation
Identify coding sequences, rRNAs, tRNAs, functional domains, resistance genes, and metabolic pathways using curated databases (e.g., Prokka, RAST, PGAP).
Metabolic and Functional Profiling
Reconstruct biosynthetic, catabolic, and resistance pathways to understand organism function, ecological roles, or biotechnological potential.
Taxonomic and Phylogenomic Classification
Determine taxonomic placement and generate robust phylogenomic trees using ANI, marker genes, or GTDB-based methods.
Comparative Genomics
Compare gene content, genome organization, or metabolic traits across strains or species to identify unique features, adaptations, or virulence factors.
Data Visualization and Reporting
Get detailed genome statistics, annotation tables, heatmaps, gene presence/absence matrices, and interpretable reports ready for publication or regulatory submission.
Applications of Microbial genomics
Antimicrobial Resistance Surveillance
Detect resistance genes and mobile genetic elements to monitor emerging threats and support antibiotic stewardship efforts.
Agricultural Microbiology
Explore plant‑associated microbiomes and beneficial microbes to enhance crop health, productivity, and resilience to stress.
Biotechnology & Synthetic Biology
Identify metabolic pathways and gene clusters for enzyme discovery, biosynthesis optimization, or microbial engineering.
Environmental Microbiology
Characterize microbes in soil, water and extreme environments to understand nutrient cycling, biodegradation, or pollutant remediation.
Evolutionary & Comparative Genomics
Study microbial evolution, gene gain/loss, and genomic rearrangements to infer adaptation mechanisms and speciation.
Microbial Taxonomy & Novel Species Discovery
Use genome‑based metrics (e.g., ANI, dDDH) to classify organisms, describe new taxa, and refine microbial phylogenies.
A typical Microbial Genomics Services workflow
Our Microbial Bioinformatics Services
Quality Assessment & Preprocessing
Evaluate and filter raw sequencing data using tools like FastQC, fastp, or Trimmomatic to ensure high-quality inputs.
Custom Pipelines & Consulting
Need something specific? We offer tailored workflows, custom comparative designs, and consulting for unusual organisms, non‑standard file formats, or complex projects.
Why you should choose Tailoredomics
Adapted to Your Organism and Study Design
Whether you’re working with pathogens, symbionts, extremophiles, or environmental isolates, we tailor the pipeline to your sample’s characteristics.
Functional Insights Beyond Basic Annotation
We go beyond standard gene calling to provide insights into metabolic potential, resistance profiles, and ecological roles.
Publication‑Ready Outputs
You’ll receive structured reports, high‑resolution figures, and properly formatted data — ideal for publication, grant reporting, or collaborative projects.
Optional Multi‑Omics Integration
If your study includes transcriptomics, proteomics, or metagenomics, we can integrate these layers for deeper biological interpretation.
Customized Workflows
Each project gets a tailored pipeline—no one‑size‑fits‑all. We adapt tools and parameters to your data and goals. We can help you to design your project so you can answer your scientific questions.
Deliverables – What You’ll Receive
Every microbial genomics project with Tailoredomics comes with a clear and organized set of deliverables. We ensure all outputs are transparent, reproducible, and ready for publication, collaboration, or internal reporting.
Raw & Cleaned Data (optional)
We can provide the original raw reads and quality-filtered FASTQ files after trimming and adapter removal.
Assembled Genome Files
High‑quality genome assemblies in FASTA format, with optional polished and circularized versions (where applicable).
Annotated Genomes
GFF, GBK, and tabular annotation files including coding sequences (CDS), tRNAs, rRNAs, functional domains, and subsystem categorization.
Functional Insights
Tables with functional annotation (e.g., KEGG, COG, Pfam, eggNOG), antibiotic resistance genes (CARD), and/or virulence factors (VFDB), depending on project goals.
Phylogenomic Trees & Taxonomy
Newick-format phylogenetic trees, FastANI/GTDB output files, and visualizations (e.g., dendrograms, heatmaps) as needed.
Comparative Genomics (if included)
Core/pan‑genome matrices, Venn diagrams, synteny plots, and tables highlighting shared vs unique genes across genomes.
Summary Report (PDF)
A concise but thorough document explaining the methods used, summary statistics, key findings, and expert interpretations.
Frequently Asked Questions (F.A.Q.)
Q1. What types of microorganisms can you analyze?
We mainly work with any bacteria or archaea, but let us know if you work with microbial eukaryotes. Whether you have soil, water, gut, or industrial samples, our microbial genomics pipelines adapt to your organism of interest.
Q2. What data formats do you accept for genome assembly?
We accept raw sequencing reads (FASTQ) from Illumina, Oxford Nanopore, PacBio, or hybrid datasets. If you already have assembled contigs (FASTA), we can pick up at the annotation stage.
Q3. How long does a typical microbial genome project take?
Turnaround depends on genome size and coverage, but most bacterial genome assemblies and annotations are completed within 5–7 business days after data delivery. Complex projects (e.g. comparative genomics) may require 1–2 weeks.
Q4. Can you compare your services to the CLC Microbial Genomics Module?
While the CLC Microbial Genomics Module is a commercial GUI‑based suite, Tailoredomics offers fully customized, command‑line pipelines that:
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Use the latest open‑source tools (e.g., SPAdes, Prokka)
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Provide complete transparency (you see every parameter)
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Are more cost‑effective—no per‑sample license fees
Q5. How do I submit my sequencing data?
The most common practice is sending or sharing your FASTQ/FASTA files via a download link (e.g., Dropbox, Google Drive or educational/research institution).