Unravelling rich microbial diversity


Bioinformatics

There is a growing appetite to acquire metagenomic sequencing data from environmental samples and biotechnologically utilised complex microbial communities as seen in anaerobic digestion (AD) and water treatment. The bioinformatics-based analyses of these metagenomes show them harbouring 100s of microbial species, many of which have never been cultivated under laboratory conditions and some forming completely new ‘candidate phylum’. For example, a recent sequencing project of anaerobic digester reactor samples has identified over 900 new bacterial and 40 new archaeal species.



Whilst bioinformatics analysis of samples can shed some light on the potential functions of new bacteria and Archaea, we can only fully understand their true function through direct biochemical and physiological studies. Only then will it be possible to harvest this new microbial diversity and exploit them for new biotechnological applications.



Fascinating Microbial Physiologies

The two groups of microbes that present particularly interesting physiologies and potential candidates as biochemical factory are anaerobes and thermophiles.


Some microbes are slow growers making growth measurement challenging under different conditions and researching their physiology much more difficult. Others grow at such extreme temperatures that laboratory equipment cannot support their measurement and bespoke systems are not easily reproducible.


Anaerobes possess amazingly diverse and versatile metabolic activity that makes them fascinating candidates as microbial biochemical factories. Studying anaerobic physiology means developing a greater understanding of their specific growth dynamics, yields, biomass production, nutrient absorption and optimisation and productivity.


Thermophilic anaerobes are amazing microbes because higher environmental temperatures and enzymes that function only at these extremes, provide higher reaction rates than mesophilic microorganisms.

Thermophiles are fascinating microorganisms that include fungi, algae, cyanobacteria, and protozoa.

Thermophiles grow best at temperatures higher than 45°C and hyperthermophiles at over 90°C. The molecular mechanisms that enable them to metabolise, grow and tolerate such extreme conditions can help unlock advanced industrial, biochemical and chemical treatments and even applications in mining and processing of metals.


Their enzymes have been described as potential engineering platforms for the production of fuels and industrial chemicals because of their ability to catalyse industrially significant reactions at high temperatures. Harnessing and unlocking thermophilic molecular mechanisms can help create recombinant mesophilic hosts for producing thermophilic enzymes. Their physiology is a fascinating candidate for hot and extreme industrial processes. Since some thermophiles survive on minerals, metals and gases their metabolic processes and their enzymes hold promise for industrial, biochemical, biotechnological and other applications.


We only need to remember taq polymerase used in PCR !



Unlocking the Promise of Bioinformatics

The key to unlocking the benefits of bioinformatics and genome sequence data to biotechnology is identifying microbes, characterising them and understanding their genomics, biochemistry and physiology.


Having the right tools to allow us to go from bioinformatics data to actual isolated microbial species and communities is key to the understanding and beneficial exploitation of microbes.

On this journey, a key challenge is to use appropriate devices that can grow different types of microbes from anaerobes to aerobes, chemotrophs and thermophiles to identify, characterise and understand their physiology. By combining a range of available tools microbes can be identified & characterised, such as with staining, morphology, flow cytometry, and genome sequencing for example.


However, few tools are available for identifying and characterising microbial physiology, measuring their microbial growth and responses to environmental changes and stimuli. Some microbes are very challenging to culture because of their preferred extreme growing conditions, yet their physiologies that are adapted to more challenging conditions, may hold great promise.


Obtaining data on growth dynamics allows the characterisation of microbial physiology and the optimisation of biotechnological applications.


Studying anaerobic physiology, especially of thermophilic anaerobes, is very challenging experimentally.

There are not many devices capable of measuring anaerobic and thermophilic growth rates over extended periods with high-resolution data and non-disruptive sampling techniques reproducibly and repeatably.


Measuring Microbial Physiology & Growth

Growth measurement devices need to provide comparable measurements, reproducibly, obtain high-resolution data and permit standardised methods across devices. Data must be obtained with a high enough resolution to allow for mathematical modelling and statistical analysis. Data must also be obtained over long periods of time for slow growing cultures. Devices need to support different conditions over the growth period and record physiologically significant events. Overall, these are very demanding criteria and few devices have these capabilities.


Existing laboratory equipment can be used to measure microbial growth, such as spectrophotometers and plate readers, but they have important limitations that make long-term measurement difficult if not impossible under certain conditions.




For example, thermophiles grow at such temperature extremes that laboratory equipment cannot support their measurement and laboratories that develop bespoke systems mean that their physiological data is not easily reproducible.



Automated High-Resolution Data with MicrobeMeter

There are however, dedicated and innovative devices from Humane Technologies that measure microbial growth for many days at a time even under extreme conditions. For example we believe our MicrobeMeter HighTemperature device that measures continuous thermophilic growth at up to 85˚C and transmits data via Bluetooth is probably a world first automated, continuous microbial growth device with wireless data.



MicrobeMeter offers significant advantages compared with other laboratory devices such as spectrophotometers and plate readers. We have found many researchers have to delay or wait to use their spectrophotometers and plate readers to take readings. In some cases, laboratory staff make out-of-hours visit to the laboratory to record measurements. Taking samples out of a culture can risk contamination as well as being experimentally disruptive.


MicrobeMeter is an affordable, dedicated microbial growth meter for automated continuous recording of publication-ready data, transmitted directly to a computer (even when you are out of the laboratory !). MicrobeMeter supports high-resolution un-interrupted microbial growth experiments with data transmitted directly to a computer for analysis and publication.


MicrobeMeter’s automation and continuous data capture capability offers high experimental productivity without interruption.

Capturing high-resolution data and recording physiological dynamics by identifying when and under what conditions they occur, is vital to studying microbial dynamics and characterising microbes.


MicrobeMeter offers a wide dynamic range of environmental conditions. The MicrobeMeter range of products is capable of culturing microbes from 25˚C through to 85˚C. MicrobeMeter Dynamic is capable of culturing mesophiles from 25˚C through to thermophiles at up to 85˚C. It serves many purposes in one single device with the versatility and flexibility, all within a single small footprint device.


Microbemeter 2.0 measures the growth dynamics of strict anaerobes over long periods of time with high-resolution data, automatically. The plot to the right shows data obtained for strict anaerobes Desulfovibrio vulgaris and Methanosarcinabarkeri.

The data was collected every 5 minutes over ~3 days and ~20 days respectively.



MicrobeMeter HighTemperature is a device specific to thermophiles operating between 75˚C and 85˚C for automated continuous recording of publication-ready data, transmitted directly to a computer directly from the incubator !


Interestingly, there has recently been success in using microbial growth measurement to help unravel bioinformatics. An example is a publication in 2020 that identified a Sulfoglycolytic Entner-Doudoroff Pathway in Rhizobium leguminosarum using bioinformatics (Appl Environ Microbiol 2020 Jul 20;86(15):e00750-20. doi: 10.1128/AEM.00750-20.) using a MicrobeMeter device.


Conclusion

Evolution has provided rich microbial diversity over millennia. The journey to realise the promise of bioinformatics is a long road of discovery. Understanding microbial growth and their dynamics is key to studying the genomics, biochemistry and physiology of microorganisms and the benefits they offer. To unravel these benefits life science laboratories need equipment and devices that offer high productivity, high-resolution data, comparable and repeatable experiments and the capability of culturing microbes under variable conditions. Only then will it be possible to harvest this microbial diversity and exploit them for new biotechnological, medical, agricultural and other applications.


For more information about our devices for measuring microbial growth dynamics, from anaerobes to thermophiles (up to 85 deg C) go to: https://humanetechnologies.co.uk/products


Contact us for more information or a brochure at: contact@humanetechnologies.co.uk


Humane Technologies Limited is a company spun-out of a University Life Science department. A company registered in England, UK, company number: 11143927.

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