Unlocking Microbiome Function: How Biolog Tools Support Microbiome Research and the Development of Probiotics, Therapeutics, and More

Over the last decade, the microbiome has shifted from a scientific curiosity to one of the most promising frontiers in human health. Whether it’s a gut microbe that boosts immunity, an oral microbe that prevents cavities, or a probiotic designed to metabolize specific dietary components, each discovery brings growing excitement.

Researchers are increasingly motivated by a simple but profound truth: when we understand how microbes behave, we can begin to shape them into powerful tools for healing. High‑throughput sequencing and metagenomics have enabled huge leaps in knowing which species are present and what they may potentially be capable of, but the need for a clear picture of microbial function remains.

How do candidate strains use substrates?
How do they interact with one another?
How do they adapt to the environments we place them in?
Are they in an optimal environment to make critical metabolites?

As the field pushes toward live biotherapeutic products, evidence-backed probiotics, next-gen biomarkers, and other advancements, understanding these functional traits is essential.

Biolog’s Toolkit for Microbiome Research

Biolog technologies have been cited in more than 7,000 publications to-date, fueling discoveries across many disciplines.

Here’s an overview of how these tools are commonly used by microbiome researchers to advance their discoveries and assist with the development of probiotics and microbiome therapeutics:

Chambers and Media for Growing Fastidious Anaerobes

Many of the most biologically important microbes in gut, oral, respiratory, and vaginal microbiomes are strict anaerobes or highly oxygen-sensitive. These organisms often play outsized roles in host health, immune modulation, and metabolite production, yet they are routinely underrepresented or entirely missed in functional studies due to oxygen exposure during sampling, transport, or culture. For microbiome researchers developing probiotics or live biotherapeutic products, the ability to reliably culture and study these organisms is crucial.

Biolog offers a wide range of anaerobic solutions including:

TruPRAS™ Media: Biolog offers transport media, liquid culture media, enriched agar plates, as well as large volume bags containing pre-reduced media that are all produced and packaged under strict anaerobic conditions to preserve sample viability, eliminate oxygen damage, and simplify handling. Options include a wide range of selective media (such as Bacteroides Bile Esculin Agar for selective growth of Bacteroides and differentiation of B. fragilis), general growth media (such as Brucella Blood Agar), and custom media for specific needs.

Anaerobic MediaMatcher™: Identifying optimal growth conditions for anaerobic isolates can be a major bottleneck. The Anaerobic MediaMatcher microplate accelerates this process by testing 47 distinct media formulations in parallel, enabling rapid selection of conditions that support robust growth and reproducible downstream phenotyping.

Anaerobic Chambers: Biolog’s AS-500 chamber creates stable oxygen-free (anaerobic) or controlled low‑oxygen (hypoxic) conditions for culturing and handling fastidious microbes. This enables isolation, growth, and testing of anaerobes under conditions that better reflect their native environments, helping maximize growth and preserve physiological relevance and functional behavior, making data more consistent and reliable . With flexible configuration options for accommodating lab instrumentation (such as colony pickers) or additional workspace, the AS-500 chamber provides oxygen-free comfort no matter your throughput.

Together these tools help with isolation and growth of anaerobes that would otherwise be missed, helping researchers include the “difficult to culture” or “unculturable” portion of the microbiome in their studies. This capability is especially critical for probiotic discovery, strain optimization, and mechanistic studies where functional performance—not just presence—determines success.

Check out this video where Cynthia Sears, M.D., Professor at Johns Hopkins University School of Medicine, discusses the significant role that Biolog chambers and media have played in her gut microbiome research for more than 20 years.

GEN III and AN Microplates for Microbial Identification

Biolog’s GEN III and AN identification microplates are specialized 96-well microplates that leverage 94 unique biochemical assays and two control wells to phenotypically identify an organism. These include 70+ carbon utilization assays (employing common microbial nutrient sources like d-maltose and pectin) and 20+ chemical sensitivity assays. When inoculated with a bacterial isolate and then incubated, measured and analyzed, GEN III plates create a metabolic fingerprint of the microbe, based on which nutrients it eats and how it reacts to certain chemicals. This allows researchers to:

Rapidly identify and differentiate isolates by comparing their metabolic fingerprint against a database with thousands of species
Obtain preliminary functional profiling insights
Validate predictions from genomic data (e.g. “this strain has the gene for metabolizing carbohydrate X — does it actually use it?”)

publication Highlight

Mollova et al. (2023). “Illuminating the Genomic Landscape of Lactiplantibacillus plantarum PU3—A Novel Probiotic Strain Isolated from Human Breast Milk, Explored through Nanopore Sequencing”. Microorganisms. https://www.mdpi.com/2076-2607/11/10/2440

See how researchers used Biolog GEN III Microplates to metabolically characterize a novel probiotic strain isolated from human breast milk. Along with providing critical functional insights, the phenotypic data helped validate their genomic findings from sequencing studies.

Phenotype MicroArrays (PM Plates) for Comprehensive Microbial Characterization

PM plates – a series of more than 20 microplates spanning hundreds of different substrates – allow researchers to dive deeper into microbial function and evaluate hundreds to thousands of phenotypes in a single experiment. In a microbiome context, this means you can:

Map functional niches of strains isolated from microbiome samples
Compare strains based on nutrient utilization, ion tolerance, pH preference, antibiotic susceptibility, and more, which can aid in understanding strain interactions as well as identifying optimal strains for production use
Optimize culture conditions for production strains based on knowledge of their optimal growth conditions

Why do these types of insights matter for a microbiome researcher? Phenotype MicroArrays provide reproducible functional data to complement and validate genomics results. Rather than relying solely on taxonomy or gene predictions, you can select isolates or consortia based on measurable metabolic behavior. This moves you beyond correlation into causation, which means stronger publications, better grant proposals, and clearer probiotic and therapeutic pathways.

PreBioM Plates for Gut Microbiome Research

PreBioM plates offer a targeted phenotyping solution for gut microbiome and probiotics researchers based on the impact of prebiotics on microbial function. The three-plate series contains 90 unique prebiotic substrates – ranging from simple sugars to dietary fibers – tailored to investigate the intricate interplay between prebiotics and the microbiome.

Researchers are using these plates to:

Comprehensively explore the gut microbiome
Monitor functional changes in microbiome samples under perturbation or intervention
Mitigate the risk of phenotypic drift of production strains and ensure product consistency
Drive standardization of microbiome therapies, ensuring safety and efficacy
Optimize bioprocesses to produce synbiotics, probiotics, and postbiotics
Test interactions and competition between microbiome community members

publication Highlight

Mollova et al. (2025). “In Vitro Probiotic Modulation of Specific Dietary Complex Sugar Consumption in Fecal Cultures in Infants”. Microorganisms. https://www.mdpi.com/2076-2607/13/10/2352

See how researchers used Biolog PreBioM plates to profile how a probiotic strain (Bifidobacterium bifidum) modulates the uptake of complex dietary sugars and prebiotic fibers when co-cultured with infant fecal microbiome samples.

Odin System for Automation, Throughput, and a Streamlined End-to-End Workflow

High‑throughput functional workflows require robust instrumentation, and that’s where the Odin™ system comes in. Odin automates incubation (up to 8 plates per run for Odin VIII and up to 50 plates per run for Odin L), read‑out, and advanced analysis of microplate data, enabling microbiome researchers to:

Process large numbers of plates with less manual handling
Obtain high‑resolution kinetic data (growth curves, substrate use dynamics) rather than static end‑point readings
Run pairwise or multi-condition comparisons easily

Webinar

Microbial community analysis made easy with Odin Software

See how the Odin system helps researchers go from sample to insight quickly, featuring an example of microbial community analysis with PreBioM data.

Practical Workflow Example: Gut Microbiome Isolate

Here’s an example of how a gut microbiome research team might integrate Biolog tools into their workflow:

Isolate Anaerobes — Using Biolog’s anaerobic media and chamber, culture isolates from stool samples under no- or low‑oxygen conditions.
Confirm Identity & Function — Use Identification Microplates to obtain metabolic fingerprints and verify identity/function of isolates.
Deep Functional Characterization — Use PM plates and PreBioM plates to test substrate utilization, stress responses, and more for key isolates.
Community‑level Functional Assessment — Use PreBioM plates on stool community samples (such as before and after dietary intervention or probiotic treatment) to measure shifts in substrate utilization and other functions across the community.
High‑Throughput Experimentation — Run all plates on Odin, generating high quality, standardized data and integrate with sequencing or metabolomics results to map functional and taxonomic profiles.
Insights & Translation — Identify isolates or community behaviors that correlate with host outcomes (e.g. improved function, reduced inflammation, altered metabolite profile), enabling mechanistic insight or strain selection for translational strategy.
Scale Up Production – Move final candidate strains or consortia into manufacturing with TruPRAS anaerobic bagged media that supports production of live biotherapeutic products.

Biolog Lab Services (BLS) for POC Projects and Expanding Your Microbiome Research Without Expanding Your Lab

Not every microbiome research team has the time, infrastructure, or specialized equipment needed to perform large-scale phenotypic testing—especially when working with strict anaerobes or complex functional assays. Biolog Lab Services (BLS) bridges this gap by providing contract phenotyping and microbial testing services that leverage the same Biolog platforms used in leading research labs worldwide.

Some of these offerings include:

Anaerobic Testing Services: BLS offers newly expanded anaerobic testing services, enabling functional characterization of oxygen-sensitive microbes under controlled anaerobic or hypoxic conditions. This includes growth profiling, substrate utilization, and stress response testing for fastidious gut and mucosal microbes.

Phenotyping Services: Researchers can outsource testing using GEN III Microplates, Phenotype MicroArrays (PM), and PreBioM plates to evaluate nutrient utilization, chemical sensitivities, and prebiotic interactions for individual strains or microbial communities. BLS can help profile candidate probiotic strains, compare isolates, and identify functional traits that align with therapeutic or formulation goals—supporting strain selection decisions with reproducible phenotypic data.

Case Study

When Oxygen Gets in the Way: How Anaerobic Testing Services Enable Microbial Innovation

See how Biolog Lab Services helped a probiotics manufacturer go from struggling with inconsistent data to a rock-solid launch in just weeks.

By outsourcing complex or high-throughput phenotyping to Biolog Lab Services, microbiome researchers can focus on discovery and translation—while still gaining access to robust functional data generated using standardized, well-validated Biolog methodologies.

Wrapping Up

The future of microbiome research lies not only in learning which microbes are present, but in what they are doing and how that behavior impacts the host or environment. Biolog’s phenotyping tools bridge the gap between microbial presence and microbial function, empowering researchers in gut, skin, oral and respiratory microbiome fields to achieve deeper, actionable insights.

If you’d like to learn more about how Biolog products can fit into your lab’s workflow, we’d love to connect and share resources tailored to your niche. Also feel free to peruse the additional resources linked below.