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\nImage Credit: FOTOGRIN\/Shutterstock.com<\/p>\n
In this interview, Sheela Muley, Product Manager at Molecular\u202fDevices, and Dr\u202fSushmita\u202fSudarshan, Application Scientist in Assay Development at Molecular\u202fDevices, talk about innovative approaches to microbiome research, with a focus on automation in anaerobic workflows. They discuss how next\u2011generation tools are helping to unlock the uncultured majority of the microbiome and streamline microbial screening for novel therapeutics.<\/p>\n
Can you please introduce yourselves and your roles at Molecular\u202fDevices?<\/p>\n
Muley: <\/b>I\u2019m Sheela\u202fMuley, Product Manager at Biopharma at Molecular\u202fDevices. In my role, I oversee the development and commercialization of microbial and mammalian clone\u2011screening platforms.<\/p>\n
Dr<\/b>\u202fSudarshan:<\/b> I\u2019m Sushmita\u202fSudarshan, Application Scientist in Assay Development at Molecular\u202fDevices. I work on translating microbial workflows into automated solutions, especially focusing on high\u2011throughput and anaerobic applications.<\/p>\n
\nImage Credit: FOTOGRIN\/Shutterstock.com<\/p>\n
Why is the microbiome such an important research frontier right now?<\/p>\n
Muley:<\/b> The microbiome<\/a> is a key influencer of our immune system, metabolism, and even our mood and neurological health. We have trillions of microbes in our body, and they encode far more genes than our human genome. So, understanding that community and converting it into therapeutics has tremendous potential.<\/p>\n We also know that only about a third of gut microbial species are culturable today, meaning 60\u201170% remain uncultured. That gap drives the need for new technologies and workflows.<\/p>\n We only know about 30 to 40 percent of our microbiome\u2026 so how do we get to that 100\u202f% of this uncultured and unexplorable diversity?<\/p>\n Dr Muley, Product Manager at Biopharma at Molecular\u202fDevices<\/p>\n<\/blockquote>\n So, the microbiome is not just descriptive; it\u2019s actionable if we develop the right tools.<\/p>\n What are the major challenges in anaerobic microbiome workflows?<\/p>\n Muley:<\/b> A big challenge is culturing strict anaerobes. The gut and many environmental microbiomes are oxygen\u2011free or low\u2011oxygen habitats, and manual workflows inside anaerobic chambers are slow, error\u2011prone, and lack standardization and throughput. Preservation of sample integrity, sterility, and traceability is critical.<\/p>\n The functional gap here is going from genotype (NGS) to phenotype and interaction, which requires culturing, isolating, picking colonies, and so on.<\/p>\n How does the QPix\u202fFLEX\u2011system help address those challenges?<\/p>\n Muley:<\/b> We developed our QPix\u202fFLEX microbial screening platform to automate plating, streaking, colony picking, hit\u2011picking, and liquid handling in a compact form factor compatible with anaerobic (hypoxic) chambers.<\/p>\n It includes features like a high\u2011resolution colour imaging camera for morphology and pigment detection, barcode tracking to reduce human error, sterilization modes (UV, ultrasonic baths, optional HEPA), the ability to use disposable tips, and a deck layout designed for flexibility.<\/p>\n We were able to pick three times more colonies within a week \u2026 saving\u00a0one to three days of picking.<\/p>\n Dr Muley, Product Manager at Biopharma at Molecular\u202fDevices<\/p>\n<\/blockquote>\n By integrating multiple workflow steps in one instrument, we reduce instrument footprint, reduce sample exposure to oxygen, standardize protocols, and improve throughput.<\/p>\n Dr.\u202fSudarshan, could you walk us through some of the platform’s core automated processes and explain how they translate into time savings or consistency?<\/p>\n Dr<\/b>\u202fSudarshan:<\/b> Absolutely. The four core processes we emphasize are:<\/p>\n How does the system maintain anaerobic\u2011friendly workflows and preserve sample integrity?<\/p>\n Dr<\/b>\u202fSudarshan:<\/b> The system is purpose\u2011built for anaerobic integration:<\/p>\n These design choices ensure we\u2019re automating microbial workflows while preserving the viability of oxygen\u2011sensitive microbes and enhancing reproducibility.<\/p>\n The colour\u2011camera and colony morphology classification sounds powerful. Could you explain how that works and why it\u2019s important?<\/p>\n Dr<\/b>\u202fSudarshan:<\/b> The system uses a 20\u2011megapixel CMOS colour camera combined with intelligent software to generate RGB histograms for each colony image. Colonies can be classified based on colour intensity (red, green, blue channels) and morphology parameters (compactness, aspect ratio, diameter).<\/p>\n For example, a blue colony (LacZ positive) vs a white colony (LacZ negative) can be separated by their RGB profiles. The operator interface allows for the selection of a reference colony and the grouping of similar colonies automatically. The software includes thresholding algorithms (e.g., Fensalke local threshold) for high\u2011fidelity detection even under low contrast.<\/p>\n This means you\u2019re not just picking by size or location, you can pick based on phenotype (pigment, expression marker), which is critical for microbiome workflows or engineered strains.<\/p>\n What genomics methods do you recommend for the isolates obtained through these high\u2011throughput workflows?<\/p>\n Muley:<\/b> For microbial identification and genomic anal,ysis we typically use 16S rRNA sequencing for species\u2011level identification of anaerobic isolates. For functional or protein\u2011fingerprint data, MALDI\u2011TOF is useful (e.g., for strain ID post\u2011isolation). If you want both genotype and function, you could combine 16S (or full\u2011genome sequencing) with MALDI\u2011TOF or phenotypic assays. The key is linking genotype to phenotype in a systematic, reproducible way.<\/p>\n Looking ahead: How does automation in microbiome research reshape the future?<\/p>\n Dr<\/b>\u202fSudarshan:<\/b> Automation enables labs of all sizes, not just large pharma, to participate meaningfully in microbiome culturomics.<\/p>\n By replacing manual, error\u2011prone workflows with automated, traceable ones, we make it possible to tap into the uncultured majority, accelerate probiotic discovery, and translate the microbiome into next\u2011generation therapeutics.<\/p>\n Muley:<\/b> Indeed, the next breakthrough in a condition like Alzheimer\u2019s, depression, or cardiovascular disease may come from the microbiome. But it requires robust workflows and automation to scale discovery. We hope to see automation become infrastructure rather than a luxury, facilitating faster, reproducible science across industry and academia.<\/p>\n Finally, what advice would you offer researchers embarking on anaerobic microbiome screening?<\/p>\n Muley:<\/b> Start by thinking about the full workflow: sample collection (and maintaining anaerobic environment), plating, isolation, colony picking, tracking, and analysis. If your instrument or workflow only solves one step, you risk bottlenecks elsewhere.<\/p>\n Dr<\/b>\u202fSudarshan:<\/b> Prioritize sterility, traceability, and automation early. Use barcoding, imaging, and integrated tracking so you\u2019re not just picking colonies, you\u2019re building reproducible datasets. And don\u2019t wait to pick large colonies, automated imaging enables earlier picks, saving time and reducing contamination risk.<\/p>\n About the Interviewees Sheela\u202fMuley is Product Manager, Biopharma at Molecular\u202fDevices, where she leads the microbial and mammalian clone\u2011screening portfolio. With over 20 years of experience in life\u2011science She holds a doctorate in a relevant life\u2011science discipline (specific institution not public). Her expertise\u00a0encompasses automation, instrumentation validation, and translating evolving technologies into market\u2011ready scientific tools. She regularly presents on emerging trends such as microbiome culturomics and anaerobic automation workflows. Dr\u202fSushmita\u202fSudarshan<\/p>\n Dr\u202fSushmita\u202fSudarshan is Application Scientist in Assay Development at Molecular\u202fDevices, specialising in microbial research, assay automation, and lab instrumentation. She earned her PhD in Molecular Biology from the University\u202fof\u202fTexas at Dallas.\u00a0<\/p>\n With over a decade of experience spanning academic and industry labs, she has developed and validated automated microbial workflows, including integration of high\u2011content imaging, colony picking, and traceable analytics. Her work supports bacterial, anaerobic, and synthetic biology applications across research and therapeutic development.<\/p>\n About Molecular Devices UK Ltd Molecular Devices<\/a> is one of the world\u2019s leading providers of high-performance bioanalytical measurement systems, software, and consumables for life science research, pharmaceutical, and biotherapeutic development. Included within a broad product portfolio are platforms for high-throughput screening, genomic and cellular analysis, colony selection, and microplate detection. These leading-edge products enable scientists to improve productivity and effectiveness, ultimately accelerating research and the discovery of new therapeutics. Molecular Devices is committed to the continual development of innovative solutions for life science applications. The company is headquartered in Silicon Valley, California, with offices around the globe. For more information, please visit www.moleculardevices.com<\/a>.\u00a0<\/p>\n","protected":false},"excerpt":{"rendered":"In this interview, Sheela Muley, Product Manager at Molecular\u202fDevices, and Dr\u202fSushmita\u202fSudarshan, Application Scientist in Assay Development at Molecular\u202fDevices,…\n","protected":false},"author":2,"featured_media":164282,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[74],"tags":[38090,2235,70222,18,5506,3289,10419,18330,19,5963,1666,17,55843,49988,168,6106,76051,7184,11623,172,864,82,3471],"class_list":{"0":"post-164281","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-technology","8":"tag-assay","9":"tag-automation","10":"tag-contamination","11":"tag-eire","12":"tag-genes","13":"tag-genome","14":"tag-genomic","15":"tag-heat","16":"tag-ie","17":"tag-imaging","18":"tag-immune-system","19":"tag-ireland","20":"tag-life-science","21":"tag-liquid-handling","22":"tag-metabolism","23":"tag-microbiome","24":"tag-morphology","25":"tag-oxygen","26":"tag-phenotype","27":"tag-research","28":"tag-software","29":"tag-technology","30":"tag-therapeutics"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@ie\/115497346491590006","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/164281","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/comments?post=164281"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/164281\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media\/164282"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media?parent=164281"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/categories?post=164281"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/tags?post=164281"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}\n
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For example, our colour imaging enables grouping of colonies based on RGB intensity, helping differentiate pigmented or reporter strains (e.g., blue vs white on X\u2011gal media, or coliform differentiation on ECC agar)
These automated steps reduce manual steps, reduce errors, and ensure consistent volume dispensing (validated via absorbance). They also enable the selection of smaller colonies earlier, avoiding contaminants’ overgrowth. That translates into days of time saved and increased colony yield and reproducibility.<\/li>\n<\/ul>\n\n
\nSheela\u202fMuley<\/p>\n![](\"https:\/\/www.europesays.com\/ie\/wp-content\/uploads\/2025\/11\/ImageForNews_821274_17615602924649643.jpg\")
instrumentation, high\u2011throughput screening, and assay commercialization, Sheela Muley has overseen product initiatives spanning analytical platforms and cell\u2011based screening workflows.\u00a0<\/p>\n![](\"https:\/\/www.europesays.com\/ie\/wp-content\/uploads\/2025\/11\/ImageForNews_821274_17615602850016685.jpg\")
<\/p>\n![](\"https:\/\/www.europesays.com\/ie\/wp-content\/uploads\/2025\/11\/ImageForSupplier_2416_16772484635611892.jpg\")
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