On this interview, Sheela Muley, Product Supervisor at Molecular Units, and Dr Sushmita Sudarshan, Software Scientist in Assay Improvement at Molecular Units, discuss modern approaches to microbiome analysis, with a concentrate on automation in anaerobic workflows. They focus on how subsequent‑era instruments are serving to to unlock the uncultured majority of the microbiome and streamline microbial screening for novel therapeutics.
Are you able to please introduce yourselves and your roles at Molecular Units?
Muley: I’m Sheela Muley, Product Supervisor at Biopharma at Molecular Units. In my position, I oversee the event and commercialization of microbial and mammalian clone‑screening platforms.
Dr Sudarshan: I’m Sushmita Sudarshan, Software Scientist in Assay Improvement at Molecular Units. I work on translating microbial workflows into automated options, particularly specializing in excessive‑throughput and anaerobic functions.
Why is the microbiome such an vital analysis frontier proper now?
Muley: The microbiome is a key influencer of our immune system, metabolism, and even our temper and neurological well being. We have now trillions of microbes in our physique, they usually encode much more genes than our human genome. So, understanding that group and changing it into therapeutics has large potential.
We additionally know that solely a few third of intestine microbial species are culturable right now, which means 60‑70% stay uncultured. That hole drives the necessity for brand spanking new applied sciences and workflows.
We solely learn about 30 to 40 p.c of our microbiome… so how will we get to that 100 % of this uncultured and unexplorable range?
Dr Muley, Product Supervisor at Biopharma at Molecular Units
So, the microbiome is not only descriptive; it’s actionable if we develop the suitable instruments.
What are the most important challenges in anaerobic microbiome workflows?
Muley: An enormous problem is culturing strict anaerobes. The intestine and lots of environmental microbiomes are oxygen‑free or low‑oxygen habitats, and guide workflows inside anaerobic chambers are gradual, error‑inclined, and lack standardization and throughput. Preservation of pattern integrity, sterility, and traceability is vital.
The purposeful hole right here goes from genotype (NGS) to phenotype and interplay, which requires culturing, isolating, selecting colonies, and so forth.
How does the QPix FLEX‑system assist handle these challenges?
Muley: We developed our QPix FLEX microbial screening platform to automate plating, streaking, colony selecting, hit‑selecting, and liquid dealing with in a compact type issue appropriate with anaerobic (hypoxic) chambers.
It contains options like a excessive‑decision color imaging digicam for morphology and pigment detection, barcode monitoring to cut back human error, sterilization modes (UV, ultrasonic baths, non-obligatory HEPA), the power to make use of disposable suggestions, and a deck format designed for flexibility.
We have been capable of decide thrice extra colonies inside per week … saving one to 3 days of selecting.
Dr Muley, Product Supervisor at Biopharma at Molecular Units
By integrating a number of workflow steps in a single instrument, we cut back instrument footprint, cut back pattern publicity to oxygen, standardize protocols, and enhance throughput.
Dr. Sudarshan, might you stroll us by a few of the platform’s core automated processes and clarify how they translate into time financial savings or consistency?
Dr Sudarshan: Completely. The 4 core processes we emphasize are:
- Colony selecting (color and morphology-based)
- Plating and streaking (onto agar trays, Omni‑Trays, Petri dishes)
- Liquid dealing with (by way of 4‑channel expandable pipetting head)
- Hit‑selecting / cherry‑selecting (mapping outlined colonies into grasp plates)
For instance, our color imaging permits grouping of colonies based mostly on RGB depth, serving to differentiate pigmented or reporter strains (e.g., blue vs white on X‑gal media, or coliform differentiation on ECC agar)
These automated steps cut back guide steps, cut back errors, and guarantee constant quantity dishing out (validated by way of absorbance). In addition they allow the collection of smaller colonies earlier, avoiding contaminants’ overgrowth. That interprets into days of time saved and elevated colony yield and reproducibility.
How does the system keep anaerobic‑pleasant workflows and protect pattern integrity?
Dr Sudarshan: The system is objective‑constructed for anaerobic integration:
- A compact footprint so it matches inside commonplace anaerobic or hypoxic chambers
- It avoids warmth or compressor‑based mostly sterilization, so selecting pins can stay air‑dried (or use disposable suggestions) with out introducing oxygen or warmth shock to strains
- The system was examined inside a hypoxic chamber with 5% hydrogen for 1.8 years for stability
- Automation reduces the variety of occasions plates are moved in/out of the chamber, lowering publicity to ambient air, contamination danger, and stress.
These design decisions guarantee we’re automating microbial workflows whereas preserving the viability of oxygen‑delicate microbes and enhancing reproducibility.
The color‑digicam and colony morphology classification sounds highly effective. Might you clarify how that works and why it’s vital?
Dr Sudarshan: The system makes use of a 20‑megapixel CMOS color digicam mixed with clever software program to generate RGB histograms for every colony picture. Colonies will be labeled based mostly on color depth (purple, inexperienced, blue channels) and morphology parameters (compactness, facet ratio, diameter).
For instance, a blue colony (LacZ optimistic) vs a white colony (LacZ adverse) will be separated by their RGB profiles. The operator interface permits for the collection of a reference colony and the grouping of comparable colonies mechanically. The software program contains thresholding algorithms (e.g., Fensalke native threshold) for top‑constancy detection even underneath low distinction.
This implies you’re not simply selecting by dimension or location, you possibly can decide based mostly on phenotype (pigment, expression marker), which is vital for microbiome workflows or engineered strains.
What genomics strategies do you suggest for the isolates obtained by these excessive‑throughput workflows?
Muley: For microbial identification and genomic anal,ysis we sometimes use 16S rRNA sequencing for species‑stage identification of anaerobic isolates. For purposeful or protein‑fingerprint information, MALDI‑TOF is helpful (e.g., for pressure ID submit‑isolation). In order for you each genotype and performance, you would mix 16S (or full‑genome sequencing) with MALDI‑TOF or phenotypic assays. The bottom line is linking genotype to phenotype in a scientific, reproducible approach.
Wanting forward: How does automation in microbiome analysis reshape the longer term?
Dr Sudarshan: Automation permits labs of all sizes, not simply giant pharma, to take part meaningfully in microbiome culturomics.
By changing guide, error‑inclined workflows with automated, traceable ones, we make it doable to faucet into the uncultured majority, speed up probiotic discovery, and translate the microbiome into subsequent‑era therapeutics.
Muley: Certainly, the following breakthrough in a situation like Alzheimer’s, despair, or heart problems might come from the microbiome. But it surely requires strong workflows and automation to scale discovery. We hope to see automation change into infrastructure fairly than a luxurious, facilitating sooner, reproducible science throughout trade and academia.
Lastly, what recommendation would you supply researchers embarking on anaerobic microbiome screening?
Muley: Begin by fascinated about the complete workflow: pattern assortment (and sustaining anaerobic surroundings), plating, isolation, colony selecting, monitoring, and evaluation. In case your instrument or workflow solely solves one step, you danger bottlenecks elsewhere.
Dr Sudarshan: Prioritize sterility, traceability, and automation early. Use barcoding, imaging, and built-in monitoring so that you’re not simply selecting colonies, you’re constructing reproducible datasets. And don’t wait to select giant colonies, automated imaging permits earlier picks, saving time and lowering contamination danger.
In regards to the Interviewees
Sheela Muley
Sheela Muley is Product Supervisor, Biopharma at Molecular Units, the place she leads the microbial and mammalian clone‑screening portfolio. With over 20 years of expertise in life‑science
instrumentation, excessive‑throughput screening, and assay commercialization, Sheela Muley has overseen product initiatives spanning analytical platforms and cell‑based mostly screening workflows.
She holds a doctorate in a related life‑science self-discipline (particular establishment not public). Her experience encompasses automation, instrumentation validation, and translating evolving applied sciences into market‑prepared scientific instruments. She often presents on rising developments akin to microbiome culturomics and anaerobic automation workflows.
Dr Sushmita Sudarshan
Dr Sushmita Sudarshan is Software Scientist in Assay Improvement at Molecular Units, specialising in microbial analysis, assay automation, and lab instrumentation. She earned her PhD in Molecular Biology from the College of Texas at Dallas.
With over a decade of expertise spanning educational and trade labs, she has developed and validated automated microbial workflows, together with integration of excessive‑content material imaging, colony selecting, and traceable analytics. Her work helps bacterial, anaerobic, and artificial biology functions throughout analysis and therapeutic improvement.
About Molecular Units UK Ltd
Molecular Units is likely one of the world’s main suppliers of high-performance bioanalytical measurement methods, software program, and consumables for all times science analysis, pharmaceutical, and biotherapeutic improvement. Included inside a broad product portfolio are platforms for high-throughput screening, genomic and mobile evaluation, colony choice, and microplate detection. These modern merchandise allow scientists to enhance productiveness and effectiveness, finally accelerating analysis and the invention of recent therapeutics. Molecular Units is dedicated to the continuous improvement of modern options for all times science functions. The corporate is headquartered in Silicon Valley, California, with workplaces across the globe. For extra info, please go to www.moleculardevices.com.