Solving the challenges towards high throughput and simplifying traditional methods for microbiome research.
Before we start, let’s dive in the different microbiomes, and why research matters. The human microbiome is becoming increasingly recognized as a cornerstone of our health (Ghosh et al., 2022). Recent studies have identified links between the microbiome and many aspects of health, including mental health, skin health, and heart health (Chakraborty et al., 2024).
But it’s not just our own microbiome that matters — microbial communities in the environment are just as vital. The microbiome of soil, water, and air has important applications for biodiversity and the overall well-being of the biosphere. Microbial communities play essential roles in the recycling and sequestration of nutrients and in plant health by promoting soil quality for the growth of crops. Some beneficial microbes can help plants absorb more nutrients from their environment and thereby promote plant health and crop yield (Harman et al., 2021). Less than 1% of environmental microbes have been cultured to date, leaving room for even greater discoveries and innovations in the future (Yu et al., 2022).
Rare microbial species: unlocking discoveries, and current obstacles in microbiome research.
The isolation and cultivation of rare microbial species have resulted in some of the most significant discoveries in recent years. These breakthroughs underscore the vast potential for uncovering additional applications of microbial species that have yet to be characterized.
Although isolating and studying rare microbial species is crucial, several significant challenges make species difficult to isolate, which slows the progress of research and development initiatives.
- Time Consuming manual handling of large bacterial populations, increasing the risk of contamination and mislabelling (Franco-Duarte et al., 2019; Needs et al., 2021).
- Specific Growth Requirements These factors may include the presence of other species with which they share a symbiotic relationship, as well as a complex interplay of conditions such as pH, temperature, oxygen levels, and other variables (Gupta et al., 2017).
- Low Abundance Less abundant microbes can be difficult to isolate, particularly with manual methods, where they may be overgrown by more abundant or faster-growing microbes (Cena et al., 2021; Han & Vaishnava, 2023).
- Effective Cell Detection Traditional methods often lack the sensitivity needed to reliably identify and isolate individual microbes, particularly in complex samples. Additionally, isolating microbes under anaerobic conditions further complicates detection (Börner, 2016).
Emerging technologies transforming microbiome research workflows.
Several important technologies are emerging to address challenges in modern microbiology workflows, collectively allowing for higher throughput and better resolution for studying and culturing novel and rare species.
- Microfluidics Particularly powerful when isolating single cells from complex microbiome samples, microfluidics can provide individual culture environments for single cells, allowing massive throughput at small scales.
- Molecular Techniques and genomics These techniques include advanced genome sequencing, which offers both high throughput and high resolution for identifying different species.
- Automation and Culturomics Particularly powerful for driving faster and more accurate microbiological workflows, automation eliminates the need for manual manipulation of bacterial cultures, which is time-consuming, prone to contamination, and incompatible with the isolation of novel species.
Solutions to improve and optimize microbiology workflows.
The application of single-cell dispensing (SCD) allows high-throughput, label-free sorting of microscopic particles in microbiome research. Dispensing single cells directly onto agar to obtain single-cell colonies, or dispensing into liquid medium contained in a 384 wellplate format dramatically decreases valuable time compared to the traditional ‘inoculation -> colony picking -> 3x re-streaking’ workflow and eliminates the risk of contamination during hands-on activities as shown in the figure above.
Combining the latest technology in bacterial cell sorting- and single-cell dispensing with the benefits of automation can elevate any microbiome-related workflow into a high-throughput operation.
Imagine the efficiency in discovering novel, rare species from any mixed sample when utilizing the power of open-source liquid handling systems that perform cherry-picking under sterile conditions.
The integration of advanced single-cell dispensing, bacterial cell sorting, and automation marks a turning point in microbiome research. By dramatically increasing throughput, reducing hands-on time, and minimizing contamination risks, these technologies are reshaping how researchers isolate and study rare microbial species.
Imagine the efficiency in discovering novel, rare species from any mixed sample when utilizing the power of open-source liquid handling systems that perform cherry-picking under sterile conditions. Yes, the path toward unlocking the full diversity of the microbiome has never been more accessible.
And we’re here to help you make that leap!
