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AMYBO is a diverse community of people interested in unlocking the secrets of protein fermentation. Our aim is that anyone will be able to produce tasty, nutritious protein at a lower financial cost and much lower environmental cost than by raising animals to eat.
Initially, we have quite a list of questions to answer:
You are invited to join us in creating pages on this site addressing these issues (and any other’s we haven’t yet thought of)
Join UsStep one in protein development is deciding which protein to develop first. Choice of bioreactor, feedstocks and downstream processing are all dependent on the organisms we use and the proteins they produce. This page is very much a work in progress and your input would be hugely welcome.
We mention a number of commercial “closed source” companies in these sections. We fully support their efforts to bring the benefits of alternative proteins. Commercial competition has brought many excellent innovations to market. Many companies seek to do good, even before seeking profit, however there is a risk that good companies and/or their IP gets acquired by less benevolent enterprises. Shareholder primacy means that some of the world’s poorest, in the most challenging environments may not benefit as much as they could from the innovations that they need most. Open source projects like this serve to benefit all corporations (as they can access our data) while also ensuring our innovations have the potential to benefit all.
Biotechnology is providing amazing advances in many areas of food production including:
These are currently ranked in order that Martin envisages attempting them, but if you are working on open science projects around any of these, please do get in touch.
Plants are definitely a more sustainable source of protein than highly inefficient traditional meat. Only a fraction of the protein that livestock eats makes its way into the meat that we eat.
Plant-based protein production still requires significantly more land, and in many cases more water, carbon emissions, fertilisers, pesticides, herbicides, etc. than any of the biotech proteins listed above. Given the inefficiencies of current agribusiness cultivation, this results in significant discharge of nutrients and other environmentally detrimental chemicals into water courses.
There are many improvements that can be made to crop cultivation. For example The Land Institute are doing wonderful work on perennial crops. Many small (and not-so-small) scale farmers and horticulturalists are doing wonderful things around both increasing yields and decreasing environmental impact.
Climate change poses an existential threat, it is essential that we reduce GHG emissions from food production and all other activities. Even if we manage this we still need to adapt to climate change. There are already populated places on earth where natural crop cultivation is impossible. Microbial protein production could be sustainable in all such regions. Our challenge is to ensure that it is economically viable and available to all who need it.
Tofu and Tempeh are examples of ancient meat alternatives. Beanburgers and veggie burgers took the next step in vegetarian fast food. More recently companies like Beyond Meat and Impossible Foods have taken great strides in meat alternatives.
We are inclined to leave plant based meat to well-funded enterprises, as they generally offer no nutritional benefits over the plants they are made from, and naturally requires plants, which have their own downsides.
Single-cell proteins (SCP), sometimes called microbial proteins, are edible unicelular microorganisms containing high amounts of protein. These can be farmed using biomass fermentation:
Biomass fermentation is where the whole microbe (or a dried version) is the product of fermentation.
Given the relative ease of downstream processing when the whole microbe is used, and their gastronomic potential, biomass fermentation may be the preferred route for open source fermentation.
Most types of living microbe could potentially be used for biomass fermentation. We’ll break these down into fungi (yeasts and moulds), bacteria and algae:
While we, and many others previously reported that Solar Foods use Cupriavidus necator to produce their proprietary Solein largely from air, their EU Novel Food application indicates that they are using a Xanthobacter species.
Solar Foods take carbon dioxide and water vapour from air. They use solar powered hydrolysis to split the water, providing hydrogen which the bacterium can use as its energy source. Ammonia is used as the nitrogen source.
Novo-Nutrients and Kiverdi are thought to use Cupriavidus necator. The full genomes of the H16 strain and JMP134 strain have been sequenced.
Through photosynthesis, algae use sunlight to produce sugar and oxygen from carbon dioxide and water. Nitrogen can be metabolised from urea, meaning all major feedstocks are freely available.
As such (and since a number of algae, containing all essential amino acids, are already sold as ‘superfoods’ for human consumption) algal protein may be the quickest win. That said, it may not be as gastronomically appealing as other proteins on our shortlist.
Spirulina is commonly used as a food supplement, but Spirulina Gnocchi has been proposed by the European Space Agency for Mars Missions. It has a slightly sweet nutty taste. Spirulina is technically a cyanobateria rather than algae, which means the risk of cyanotoxins (e.g. microcystin, alkaloids and BMAA) need to be mitigated.
Chlorella arguably tastes worse than Spirulina. They also have a lower protein concentration and cellulose walls. In their favour: they are single celled, so may be easier to process, and should not produce cyanotoxins.
Quorn mycoprotein is a well known proprietary product of biomass fermentation. It uses Fusarium venenatum, a filamentous fungi. Quorn’s original patents expired in 2010 but their £30M fermentation towers may prove challenging for open source development.
Sustainable Bioproducts, Inc and 3F Bio Ltd have also submitted Fusarium venenatum GRAS (Generally Recognised As Safe) notices to the US-FDA.
Harrison Lab have published bioinformatic analysis of Fusarium venenatum genomes on GitHub.
Precision fermentation is where microbes are used to produce particular chemicals. Insulin and rennet are common cited products of precision fermentation.
Precision fermentation can be used to produce pretty much any chemical. Ingredients that are currently being produced using precision fermentation include:
Real Vegan Cheese are a non-profit research project using precision fermentation to produce casein - the main protein in milk, cheese, yoghurt and similar dairy products.
The separation processes required to extract the end products of precision fermentation will likely make it a more complex process than biomass fermentation. As such we anticipate that the proteins will be more expensive to make and somewhat harder to democratise.
Precision fermentation also generally involves genetic engineering. We anticipate that corporations who invest in the development of custom strains for precision fermentation may be less inclined to open source them, so we very much welcome the Open Science work of Real Vegan Cheese.
Rennet was traditionally obtained from the stomach linings of calves and lambs. A very high proportion of rennet used in cheese making is now produced via commercial precision fermentation.
The Good Food Institute and New Harvest have useful primers on cultivated meat and cellular argiculture. This may play an important role in mimicking and replacing traditional meat. However, the complexity and cost of doing so, without any significant nutritional benefits over single-cell proteins, mean that it may be best left to well-funded enterprises..?
Commercial competition is an established means of driving innovation. However, as with the microbes and processes, development of either open source or generic equipment may be necessary to ensure that those who most need them can afford them.
Using an open source equipment also enables you to both customise it’s capabilities, and contribute to it’s development.
General purpose lab ware should be relatively easy to procure, and toxicity and chemical analysis can initially be outsourced to commercial labs. There are some more expensive pieces of equipment to focus on:
Once you have determined which protein you wish to cultivate, the next question is what you are going to cultivate it in. There is a need for development of better and more efficient bioreactors across the board - but, given the nature of this project, it makes sense to, at least initially, restrict our scope to open source bioreactors.
“The Pioreactor is an open-source, affordable, and extensible bioreactor platform.”
It currently comes in a cute and cost-effective 20 ml version that can be used in batch, fed batch, continuous, chemostat, turbidostat & PID morbidostat modes. While the software is already open source, we understand from the founder that the hardware and 3D designs are due to be made open source in 2023.
Exciting features for AMYBO (as of June 2023):
Wish list (as of June 2023):
Watch also Open source bioreactor
Concerns (as of June 2023):
Also see resources on Ottawa Bio Science Website)
Concerns (as of October 2023):
Watch Photobioreactor (Phenobottle)
Concerns (as of June 2023):
See also biorxiv article
Concerns (as of June 2023):
See also IRNAS
Concerns (as of June 2023):
See also Biomakespace and Hackster
Concerns (as of June 2023):
This is a short list, there are a number of open source autoclave control projects:
But the only open source project that claims to deliver a full autoclave, is in our opinion just a thermal steriliser, as it doesn’t appear to pressurise the sterilisation volume.
It may well be that open source autoclaves are too risky. The probability of an explosion with an incorrectly constructed unit is high and the consequences could be lethal.
Given the high risk and low volumes of sales a commercial autoclave would likely be the most expensive item on our equipment list. So we should consider pressure cookers:
#### Metallic Black GPC201SS-20 5.5L 1000W Pressure Cooker
Exciting features for AMYBO (as of June 2023):
* Low price
* Can be used outside the kitchen (no hob required)
Concerns (as of June 2023):
* Can it accurately monitor and control temperature and pressure?
* Will condensation be an issue? (Autoclaves use dry steam)
See also Open Autoclave: Build an open-source off-grid medical instrument sterilizer, Open Source Medical Autoclave for Developing World, Open Autoclave: a Humanitarian Maker Project
Concerns (as of June 2023):
Microscopes are third on the list of major open source equipment, because it is very possible to conduct fermentation without a microscope. It would however be much more difficult and less rewarding if you could never see your microbes. Microscopy also plays a valuable role in detecting contamination by unwanted microbes.
Fortunately there are a good number of open source microscopy projects:
See also:
See also A versatile and customizable low-cost 3D-printed open standard for microscopic imaging
See also A Research Grade Open Source Microscope — Made with FreeCAD
The basic concept of Pioflo is that we turn the tried-and-tested Pioreactor into a flow through cell. This means that any size of Ideal CSTR can be converted to a bioreactor by adding a Pioflo to control the CSTR using real-time measurement of optical density.
Lets discuss next steps at forum.amybo.org - and check out the write up to date below:
We do all our experiments in the open, and we try to make them as easy to reproduce as possible. We not only share our experimental protocols (like recipes for running your experiments) but also the results.
Here are some experiments we’ve done:
Describes how to get started with CO2 sparging on the Pioreactor.
Connect the CO2 regulator to the Sodastream cylinder using the adapter and a wrench.
Connect one end of ~20cm PU tubing to the regulator and the other end to a check valve.
Connect another short piece of PU tubing to the other end of the check valve and attach a 3/16" barb female Luer lock connector. Attach two 1/16" barb male Luer lock connectors to each end of ~10cm of 1/16" silicone tubing and connect to the 3/16" connector and the Pioreactor port.
Connect the barrel power cord to PWM channel 4 on the one end. You can either solder Dupont female square head wires to the power cord, or crimp a TE Connectivity AMP connector as in the image.
Plug the other end of the power cord into the solenoid of the regulator.
Make sure that your Pioreactor supports 12V on the PWM channels and that a 12V power supply is connected to the barrel jack of the Pioreactor HAT.
pioreactor-relay-plugin plugin.relay:[PWM]
# map the PWM channels to externals.
# hardware PWM are available on channels 2 & 4.
1=stirring
2=media
3=waste
4=relay
5=heating
Test that it works by manually turning on the relay in the Activities tab of the Manage screen of the Pioreactor UI. You should hear the solenoid turn on and CO2 rushing into the Pioreactor vial. You can adjust the amount of CO2 sparged using the dial on the regulator.
Create a new experiment profile and copy and paste the following into the profile:
experiment_profile_name: CO2 sparging every hour
metadata:
author: Gerrit Niezen
description: Turns on the relay for 10 seconds every hour
common:
jobs:
relay:
actions:
- type: repeat
hours_elapsed: 1.0
repeat_every_hours: 1.0
actions:
- type: log
hours_elapsed: 0.0 # relative to the repeat loop, 1h
options:
message: "Sparging CO2 for 10 seconds"
level: info
- type: start
hours_elapsed: 0.0
options:
start_on: True
- type: stop
hours_elapsed: 0.00278
When the experiment profile is running it should sparge CO2 for 10 seconds every hour.
To ensure that the Pioreactors we’re using are working as expected, we ran an experiment where we used the exact same experimental conditions with two Pioreactors, with the hope to produce the same results.
The original experiment is described on the Pioreactor website.
The raw results from the experiment are available as CSV files on GitHub.
We’re still optimising the kit list for Hydrogen Oxidising Bacteria (HOB) enrichment, please see this discussion on the Bill of Materials for the latest.
We’re reasonably happy with our mesonutrients (other than the vitamin pill & perhaps the Calcium Chloride) but more work is required for us to be able to recommend an optimal food grade micronutrient solution. In the meantime there are many options if you’re happy to go non-food grade - see Trace element solution for our latest thoughts.
AMYBO and its contributors accept no liability for anyone
If we are proposing potentially new methods of producing food for human consumption, and making those methods available to all, there is a significant risk to human health.
This website discusses untested and unregulated methods of producing food for human consumption - do not copy them or take any action without at least taking advice from your doctor and a team of experts who are able to review your plans, risk assessments and physical/biological/chemical setup and toxicity/pathogenicity/etc. testing protocols. Please also see our disclaimer.
Last updated July 06, 2023
The information provided by AMYBO, a trading name of andeye Ltd (‘we’, ‘us’, or ‘our") on AMYBO.org (the ‘Site’) is for general informational purposes only. All information on the Site is provided in good faith, however we make no representation or warranty of any kind, express or implied, regarding the accuracy, adequacy, validity, reliability, availability, or completeness of any information on the Site. UNDER NO CIRCUMSTANCE SHALL WE HAVE ANY LIABILITY TO YOU FOR ANY LOSS OR DAMAGE OF ANY KIND INCURRED AS A RESULT OF THE USE OF THE SITE OR RELIANCE ON ANY INFORMATION PROVIDED ON THE SITE. YOUR USE OF THE SITE AND YOUR RELIANCE ON ANY INFORMATION ON THE SITE IS SOLELY AT YOUR OWN RISK.
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The Site cannot and does not contain biotechnological/engineering/environmental/food/medical/health/legal advice. The biotechnological/engineering/environmental/food/medical/health/legal information is provided for general informational and educational purposes only and is not a substitute for professional advice. Accordingly, before taking any actions based upon such information, we encourage you to consult with the appropriate professionals. We do not provide any kind of biotechnological/engineering/environmental/food/medical/health/legal advice. THE USE OR RELIANCE OF ANY INFORMATION CONTAINED ON THE SITE IS SOLELY AT YOUR OWN RISK.
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For considering AMYBO for Kickstarting for Good. I’ve just recorded this bang up to date <9 minute introduction for you. If the science bores you (starting 2m 55s in), feel free to skip to the finance section 7m 10s in:
Forgive me for not fully customising the video for Kickstarting for Good. I imagine you’d appreciate my making a fully recyclable video as I thought we could do with a general-use pitch video… If you’d like a fully customised version, lets arrange a time for a video call.
Otherwise, here are some other things that you should probably know about this website:
Please add a comment to one of our YouTube videos or drop us a line at [email protected] with any suggestions or questions you may have - or just to say hello, it’s good to know people are reading this.
If you’re comfortable with GitHub (or would like to learn) we’d absolutely love it if you were happy to dive in and edit our pages directly:
We welcome contributions and improvements to the AMYBO.org website. We want this to be as easy as possible so considered a wiki. However, given the controversial nature and risks associated with protein production for human consumption, we decided that an approvals process was required.
Since we’ll be using GitHub for software development, and potentially also for hardware and procedure development, it made sense to use this for community development of the website. If you struggle at all with GitHub development, please get in touch via [email protected]
We use Hugo to format and generate our website, the Docsy theme for styling and site structure, and Netlify to manage the deployment of the site. Hugo is an open-source static site generator that provides us with templates, content organisation in a standard directory structure, and a website generation engine. You write the pages in Markdown (or HTML if you want), and Hugo wraps them up into a website.
All submissions, including submissions by project members, require review. We use GitHub pull requests for this purpose. Consult GitHub Help for more information on using pull requests.
Here’s a quick guide to updating the docs. It assumes you’re familiar with the GitHub workflow and you’re happy to use the automated preview of your doc updates:
If you’ve just spotted something you’d like to change while using the docs, Docsy has a shortcut for you:
If you want to run your own local Hugo server to preview your changes as you work:
Follow the instructions in Getting started to install Hugo and any other tools you need. You’ll need at least Hugo version 0.45 (we recommend using the most recent available version), and it must be the extended version, which supports SCSS.
Fork the AMYBO pages repo repo into your own project, then create a local copy using git clone. Don’t forget to use --recurse-submodules or you won’t pull down some of the code you need to generate a working site.
git clone --recurse-submodules --depth 1 https://github.com/AMYBO-org/pages
Run hugo server in the site root directory. By default your site will be available at localhost:1313/. Now that you’re serving your site locally, Hugo will watch for changes to the content and automatically refresh your site.
Continue with the usual GitHub workflow to edit files, commit them, push the changes up to your fork, and create a pull request.
If you’ve found a problem in the docs, but you’re not sure how to fix it yourself, please create an issue in the AMYBO pages repo. You can also create an issue about a specific page by clicking the Create Issue button in the top right hand corner of the page.
AMYBO is a community and we want it to be community led. As such both the name and the logo are placeholders for the community to fill in.
We consider AMYBO to be a placeholder backronym. That is it’s an acronym that stands for something the community still needs to decide on. We’re in no great rush to fill it, as we want to leave space for literary creatives to join us & contribute alongside biotechnologists and developers.
Please reach out to [email protected] with any backronym suggestions.
Likewise with the “AMYBO NEEDS A LOGO” logo, we welcome visual creatives to the community & would love to see their take on the logo. Some might say there’s a bit more urgency to the logo than the backronym. Say for example if we wanted to join the APA or any similar logo collection. Without the community explanation, we may look like we’re not taking ourselves seriously.
So what do we want in a logo?
Please let us know your thoughts at [email protected]