Single-Cell to Million-Scale Discovery

High-Throughput Screening Service

Convert library diversity into lead strains — from 1536-well plate assays to picoliter droplet sorting and biosensor-guided single-cell isolation. Part of our Microbial Strain Engineering & Fermentation Optimization Platform.

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Explore Platform
pL Droplets
microfluidic encapsulation
FACS + Flow
fluorescence-activated sorting
7 modalities
plate · cell · droplet · biosensor
Schematic of a high-throughput screening workflow spanning plate-based, cell-based, ultra-high-throughput droplet, and biosensor-coupled screening converging into validated and isolated lead strains.
Resolution On Demand
plate to single cell
Plate to droplet, one pipeline — 96/384/1536-well to pL drops
Phenotype-matched resolution from bulk reads to single cells
Hit-ready for immediate downstream evolution
Overview

Seven Modalities, One Screening Engine

A library is only as valuable as the screen that reads it. We let the phenotype choose the platform.

Every strain-improvement program eventually hits the same bottleneck: generating genetic diversity is fast, but measuring it is slow. Creative BioMart Microbe delivers a full-spectrum High-Throughput Screening (HTS) service that matches the screening modality to your phenotype — from dense microplate assays for characterizing thousands of clones, to flow cytometry and FACS for sorting fluorescent populations, and droplet microfluidics for single-cell resolution at ultra-high throughput.

Conventional plate-based screening uses standard 96/384/1536-well formats with automated liquid handling for reproducible, high-density characterization. Cell-based methods leverage flow cytometry, fluorescence and luminescence reporters, and droplet sorting to isolate rare high-performers. Ultra-high-throughput droplet microfluidics compartmentalizes single cells in picoliter volumes for fluorescence-activated droplet sorting and biosensor-coupled selection.

Functional biosensor screening converts intracellular metabolite levels into optical signals, enabling enrichment without fluorophore-modified substrates. Product validation by chromatography and mass spectrometry confirms every lead, while anaerobic and long-term droplet cultivation extends discovery to environmental and gut microbiomes that resist standard culture.

Our screening platform is designed as a modular, phenotype-first system: the assay format is chosen to match your target, readout, and throughput needs, ensuring that genetic diversity translates directly into measurable performance gains.

Services

A Six-Step Path From Inquiry To Hits

Each project follows a six-step workflow from assay design to documented delivery, with the screening modality selected to match your phenotype and throughput target.

1

Project Consultation

Goal & assay design

2

Assay & Biosensor Build

Reporter, substrate, readout

3

Library Formatting

Plate / droplet / FACS prep

4

Screening & Sorting

Execute at chosen scale

5

Hit Verification

HPLC / GC / LC-MS/MS

6

Report & Handoff

Hit list + data package

Service Details

Each modality trades scale for resolution — many programs combine broad droplet discovery with plate or FACS refinement. Pick the one that matches your starting point and goal.

Illustration of conventional microplate-based screening with automated colony pickers and liquid handlers processing 1536-well plates.

Conventional Screening

We run 96/384/1536-well microplate assays with automated colony screening, plate readers, and robotic liquid handling for reproducible, high-density characterization of thousands of clones. Best for: medium-throughput quantification where bulk reads are sufficient.

Illustration of cell-based screening with a flow cytometer and FACS nozzle sorting fluorescent microbial cells.

Cell-Based Screening

We apply flow cytometry and FACS, fluorescence and luminescence reporter systems, and advanced droplet sorting to isolate rare high-performers from large cell populations. Best for: cell-surface or intracellular phenotypes with a fluorescent proxy.

Illustration of ultra-high-throughput droplet microfluidics with picoliter droplets flowing through a sorting junction.

Ultra-High-Throughput Screening

We encapsulate single cells in picoliter or microliter droplets for single-cell compartmentalization, on-chip or off-chip incubation, and fluorescence-activated droplet sorting at ultra-high throughput. Best for: million-scale discovery in one run.

Illustration of functional biosensor screening where an intracellular biosensor converts metabolite concentration into a fluorescent signal inside a cell.

Functional Biosensor Screening

We deploy genetically encoded intracellular biosensors, metabolite-to-optical-signal conversion, dual-cell biosensor systems, and aptamer/riboswitch-coupled droplet screening to enrich producers without modified substrates. Best for: non-fluorescent small-molecule targets.

Illustration of product validation and quantification with a chromatography instrument and mass spectrometer analyzing a sample.

Product Validation & Quantification

We confirm screened leads by HPLC/UPLC, GC, and LC-MS/MS to convert relative reporter signals into absolute titers, purities, and identities. Best for: de-risking hits before scale-up.

Illustration of an automated integrated screening line linking droplet generation, cultivation, optical detection, and plate collection.

Automated Integrated Screening

We operate end-to-end automation integrating droplet generation, multi-mode cultivation, multi-parameter optical detection (visible, fluorescence, luminescence, chemiluminescence), intelligent sorting, and multi-well plate collection. Best for: unattended, reproducible campaigns.

Illustration of environmental microbial screening with anaerobic droplet cultivation recovering cells from soil and gut microbiome samples.

Environmental Microbial Screening

We apply anaerobic droplet cultivation, soil and gut microbiome single-cell isolation, and long-term droplet incubation to recover uncultured microorganisms and functional taxa missed by standard plating. Best for: bioprospecting and microbiome discovery.

Technique Coverage Matrix

Modality Technique Target / Representative Hosts Deliverable
Conventional Microplate-based screening (96/384/1536-well), automated colony screening, automated liquid handling Bacteria, yeast, fungi, actinomycetes Ranked hit list
Cell-based Flow cytometry & FACS, fluorescence/luminescence reporters, droplet sorting Bacteria, yeast, mammalian / hybridoma Isolated clones
Ultra-high-throughput Droplet microfluidics (pL / µL encapsulation, single-cell compartmentalization, FADS), biosensor-coupled screening Bacteria, yeast, enzymes Top variants
Functional biosensor Genetically encoded intracellular biosensors, metabolite-to-optical conversion, dual-cell systems, aptamer/riboswitch-coupled droplet screening Bacteria, yeast High-producer isolates
Validation HPLC / UPLC, GC, LC-MS/MS Culture supernatants, cell lysates Quantified titer
Integrated End-to-end automation: droplet generation, multi-mode cultivation, multi-parameter optical detection, intelligent sorting, multi-well collection Bacteria, yeast, fungi Validated hits
Environmental Anaerobic droplet cultivation, soil / gut microbiome single-cell isolation, long-term droplet incubation Environmental & gut microbiomes, uncultured taxa Recovered isolates

Service Specifications & QC Standards

01 · Instrumentation & Capability

  • Microplate screening across 96, 384, and 1536-well formats with automated readers.
  • Flow cytometry, FACS, and fluorescence/luminescence reporter platforms.
  • Droplet microfluidics for picoliter/microliter encapsulation and fluorescence-activated droplet sorting.
  • Genetically encoded biosensor design and dual-cell / aptamer / riboswitch coupling.
  • HPLC/UPLC, GC, and LC-MS/MS for orthogonal hit confirmation.
  • Anaerobic and long-term droplet cultivation for environmental and gut microbiomes.
  • Compatibility with bacteria, yeast, fungi, actinomycetes, and environmental samples.

02 · Typical Data Range

Droplet generation rate Up to 106 droplets / sec
FACS sorting throughput Up to 105 events / sec
Plate formats 96 / 384 / 1536-well
Detection modes Visible, fluorescence, luminescence, chemiluminescence, MS
Species coverage 5+ categories
Process conditions Phenotype- and host-matched

03 · Deliverables

Hit list Ranked candidates with readout values
Raw & processed data Plots, gating, sort logs
Confirmation HPLC/UPLC, GC, LC-MS/MS
Documentation Assay protocol, QC metrics, sort parameters
Sample Requirements

What To Send Us

To initiate a high-throughput screening project, please provide the following information about your starting material and target phenotype.

Required Optional Not Accepted
  • Pure, axenic starting culture or mutant library (plates / glycerol stocks)
  • Strain name and taxonomic identification (or construct list for targeted work)
  • Biosafety classification (e.g., BSL-1) and known sensitivities
  • Screening target and desired phenotype or product
  • Prior screening or evolution history
  • Desired throughput and scale
  • Preferred readout (fluorescence, absorbance, MS)
  • Biosensor construct or reporter plasmid
  • Contaminated or mixed cultures
  • Uncharacterized pathogens (BSL-2 or above without clearance)
  • Environmental isolates lacking collection permits
  • Non-viable or heavily lysed samples

Recommended Starting Material By Scale

Plate-based (103–104 clones) 1–2 glycerol vials or a fresh slant
Droplet / FACS (106–108 cells) Plates plus glycerol stocks
Biosensor screening Plasmid / biosensor construct plus host strain

Storage & Shipping: Ship cultures on dry ice for glycerol stocks or as stabilized agar slants at ambient temperature with cushioning. Avoid temperature excursions and do not ship under conditions that cause complete lysis. For biosensor and targeted projects, ship dry DNA or plasmids with a documented sequence file. Contact our team via the contact form before dispatch for biosafety clearance.

Advantages

Why Teams Screen With Us

Seven-Modal Coverage

Plate, cell, droplet, biosensor, validation, integrated, and environmental screening are delivered from one platform, so you can move from broad discovery to precise confirmation without changing vendors.

Single-Cell Resolution

Compartmentalize individual cells in picoliter droplets or sort them by FACS for true single-cell phenotypes, free of population averaging.

Phenotype-Matched Readouts

Fluorescence, luminescence, absorbance, and mass spectrometry are matched to the target molecule for an accurate signal-to-phenotype link.

Million-Scale Throughput

Droplet microfluidics operates at ultra-high throughput, compressing weeks of plate work into a single day of sorting.

Biosensor Integration

Genetically encoded biosensors convert intracellular metabolites into optical signals, enabling enrichment of non-fluorescent products without modified substrates.

Seamless Library Handoff

Libraries built by our mutant library construction service drop straight into screening with no reformatting or rework.

Documented, Heritable Hits

Every hit ships with sort logs, QC metrics, and confirmation by HPLC/UPLC, GC, or LC-MS/MS for confident downstream evolution.

Customer Reviews

Trusted by Screening Teams Worldwide

Applications

Where High-Throughput Screening Creates Value

Illustration representing industrial enzyme screening.

Industrial Enzymes

Activity, thermostability, pH scope

Illustration representing organic acid and metabolite screening.

Organic Acids & Metabolites

Titer, yield, pathway flux

Illustration representing biofuel producer screening.

Biofuels

Substrate tolerance, yield

Illustration representing pharmaceutical protein and antibody screening.

Pharma Proteins & Antibodies

Secretion, display-based hits

Illustration representing probiotic and gut microbiome screening.

Probiotics & Gut Microbiome

Function, colonization traits

Illustration representing environmental bioremediation screening.

Environmental Bioremediation

Degradation, uncultured taxa

Case Study

Proven Across Droplet And Biosensor Platforms

Ultra-High-Throughput Screening: Droplet Microfluidics Enriches α-Amylase Producers In Bacillus licheniformis

A fluorescence-activated droplet sorting platform was developed for single-cell screening of Bacillus licheniformis α-amylase producers. Single cells were encapsulated in monodisperse water-in-oil droplets with a fluorogenic starch substrate, incubated off-chip for protein expression, and sorted by fluorescence intensity. A model binary-strain mixture achieved 45.6-fold enrichment at a sorting rate of 300 droplets per second. Applied to an ARTP-mutagenized library comprising 2.1 million droplets, the platform isolated clones displaying over 50% improvement in α-amylase productivity. Hereditary stability was confirmed by subculturing the top ten performers on fresh agar plates and re-analyzing their enzyme activities, with nine of ten strains maintaining 40–60% improvement over wild type. This validates droplet microfluidics as a practical ultra-high-throughput route from mutant library to validated lead strain.

Evaluation of alpha-amylase production by the sorted mutants.
Figure 1. Evaluation of α-amylase production by the sorted mutants. (Yuan, et al. 2022)

Functional Biosensor Screening: FACS Isolates Corynebacterium glutamicum L-Histidine Producers

A metabolite-responsive biosensor (pSenHis) was coupled to FACS to screen Corynebacterium glutamicum CgHis2 l-histidine producers. Across more than 600 independent chemical mutagenesis experiments and over 200 biosensor-based FACS screenings, more than 50,000 fluorescence-elevated variants were isolated and over 4,500 characterized in depth. One hundred independently evolved variants accumulated 10–80% more l-histidine in microtiter plate cultivations, with the best isolate producing 82% more than the starting strain. Comparative genome analysis of these 100 variants identified novel mutational hotspots beyond known biosynthetic targets, and combining selected beneficial modifications yielded a reverse-engineered strain with a doubled l-histidine titer and product yield in lab-scale bioreactor cultivations — demonstrating biosensor-guided single-cell screening as a systematic path to maximum performance.

l-histidine accumulation and biomass formation of 100 FACS-isolated Corynebacterium glutamicum variants compared with the reference strain.
Figure 2. l-histidine accumulation and biomass formation of 100 FACS-isolated Corynebacterium glutamicum CgHis2 variants. (Baumann, et al. 2023)

Pair With Directed Evolution

Screened hits pass directly into our evolution service for iterative refinement, or back to library construction for another diversity round.

Explore Evolution →

FAQs

Common Questions

Q: Which screening modality should I choose for my project?

Use plate-based screening for thousands of clones with bulk readouts, FACS or flow cytometry for millions of cells with a fluorescent proxy, and droplet microfluidics for million-scale single-cell discovery. Biosensor screening fits non-fluorescent small molecules; environmental screening fits anaerobic or uncultured samples.

Q: Can you screen libraries we constructed elsewhere?

Yes. Libraries arrive as plates, glycerol stocks, or plasmid pools and are formatted for screening without rework. Provide the strain identity, biosafety class, and the target phenotype so we can select the readout.

Q: How do you couple non-fluorescent products to a fluorescent readout?

We use genetically encoded intracellular biosensors that convert metabolite concentration into an optical signal, dual-cell systems, and aptamer/riboswitch-coupled droplet screening — avoiding fluorophore-modified substrates that may leak or interfere.

Q: What throughput can your droplet and FACS platforms reach?

Droplet microfluidics operates at kHz–MHz frequencies for generation and sorting, and FACS analyzes up to 105 events per second, compressing campaigns that would take weeks on plates into days.

Q: Do you validate hits with mass spectrometry?

Yes. Every lead is confirmed by HPLC/UPLC, GC, or LC-MS/MS to report absolute titer, purity, and identity rather than only a relative reporter signal, de-risking downstream evolution and fermentation.

Q: Can biosensor screening be applied to environmental or uncultured samples?

Long-term anaerobic droplet cultivation and soil/gut microbiome single-cell isolation recover functional taxa missed by standard plating, while biosensor and aptamer readouts enable activity-based selection within droplets.

Q: How are screened hits delivered and preserved?

Hits ship as glycerol stocks or plates with a ranked hit list, raw and processed data, sort logs, and a QC report including orthogonal confirmation, ready for evolution or scale-up.

Q: Can screening be paired with directed evolution?

Yes. Screened hits transfer directly into our Strain Directed Evolution Service for iterative refinement, or back to Mutant Library Construction for another diversity round.

Ready To Screen Your Library?

Tell us your target phenotype and throughput — our team will design the assay and select the screening modality that fits.

Inquiry

Explore The Strain Engineering Platform

Mutant Library Construction

Diversity generation

High-Throughput Screening

Million-scale discovery

Strain Directed Evolution

Iterative enhancement

Adaptive Laboratory Evolution

Industrial robustness

View the full platform →

References:

  1. Yuan, H., et al. (2022). Ultrahigh-throughput screening of industrial enzyme-producing strains by droplet-based microfluidics system. Journal of Industrial Microbiology and Biotechnology, 49(3), kuac007.
  2. Baumann, P. T., et al. (2023). Beyond rational—biosensor-guided isolation of 100 independently evolved bacterial strain variants and comparative analysis of their genomes. BMC Biology, 21(1), 183.
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  • Our products/services are NOT intended for therapeutic use in private practice.
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