This is where the AMYBO documentation lives - lets keep all the learning available and usefully organised here. If you’re new you may want to start of with the:
Other content such as discussions, trial results, case studies, and community updates should live in the Forum.
1 - Overview
How we hope to democratise food.
What is AMYBO?
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.
What are we doing now?
Initially, we have quite a list of questions to answer:
Which single cell protein should we ferment first? Are we all agreed that Hydrogen Oxidising Bacteria should be our main initial focus?
What equipment will we need to ferment it? Is everyone happy that we’re focusing in on our HOB-modified Pioreactor as our main community research tool?
How should we share our results to best accelerate open source development?
Determine next steps required to produce safe nutritious delicious protein
2 - Proteins
What proteins should we produce?
Step 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.
A note on “closed source” enterprises
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.
Biotech Proteins
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.
Meat & Plant Protein
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.
Plant Based Meat
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.
2.1 - Single-Cell Protein
Which single-cell proteins should we produce?
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
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:
Bacteria
Xanthobacter spp.
While we, and manyothers 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.
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.
Arthrospira platensis
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
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.
Fungi
Fusarium venenatum
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.
Harrison Lab have published bioinformatic analysis of Fusarium venenatum genomes on GitHub.
2.2 - Precision Fermentation
What is Precision Fermentation and could we implement it?
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:
Casein
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
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.
2.3 - Cultivated Meat
How is cultivated meat made?
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..?
3 - Equipment
Which equipment should we use?
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:
3.1 - Bioreactors
Which bioreactors should we use?
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):
it appears to be more affordable than most automated bioreactors
it will soon be fully open source, hence customisable
it is clearly under active development
it is available for sale with excellent lead times
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:
How can this maintain pressure, and if it doesn’t, how can it be called an autoclave?
3.3 - Microscopes
Which microscopes should we use?
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:
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:
4.1 - Control Testing
A simple control test evaluating results between Pioreactors by Gerrit Niezen
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.
Pour 300mL tap water into the pressure cooker, place the three vials on the metal trivet in the pressure cooker and turn to a high setting.
Once the water in the cooker starts to boil, steam will come out of the open valve. Put the heaviest weight (15lb) weight on top of the valve.
The steam will lift the weight and start to escape. As soon as the steam starts to escape, start timing the sterilization and turn down the heat so that the steam is only just escaping and not rushing out. Aim to maintain a gentle hissing.
After 20 minutes turn off the heat and leave to cool.
Wait until pressure is completely reduced then lift the weight off the valve allowing any remaining steam to escape. Never open the pressure cooker until the steam
valve has been opened to release the pressure.
Running the experiment
Dilute a small amount of baker’s yeast in 15mL of YPD broth media
Innoculate the three sterile vials with the same amount (just a drop) of culture from the stock solution.
Wipe the vials and place them in the Pioreactors.
Start a new experiment on your Pioreactor dashboard.
Select Manage all Pioreactors
Start Stirring activity
Start Temperature automation activity and set to 30°C
Start OD reading activity
Go back to the graphs and check that an Optical Density (OD) signal is being received.
Select Manage all Pioreators again and start Growth rate.
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.
Media
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.
Setup
5 - Risk management
How do we manage risk?
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.
6 - Legal
READ THIS BEFORE TAKING ANY ACTION
DO NOT TRY THIS AT HOME
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.
6.1 - Disclaimer
AMYBO is not liable for your actions or inactions
DISCLAIMER
Last updated July 06, 2023
WEBSITE DISCLAIMER
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.
EXTERNAL LINKS DISCLAIMER
The Site may contain (or you may be sent through the Site) links to other websites or content belonging to or originating from third parties or links to websites and features in banners or other advertising. Such external links are not investigated, monitored, or checked for accuracy, adequacy, validity, reliability, availability, or completeness by us. WE DO NOT WARRANT, ENDORSE, GUARANTEE, OR ASSUME RESPONSIBILITY FOR THE ACCURACY OR RELIABILITY OF ANY INFORMATION OFFERED BY THIRD-PARTY WEBSITES LINKED THROUGH THE SITE OR ANY WEBSITE OR FEATURE LINKED IN ANY BANNER OR OTHER ADVERTISING. WE WILL NOT BE A PARTY TO OR IN ANY WAY BE RESPONSIBLE FOR MONITORING ANY TRANSACTION BETWEEN YOU AND THIRD-PARTY PROVIDERS OF PRODUCTS OR SERVICES.
PROFESSIONAL DISCLAIMER
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.
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:
We launched it 26 June 2023.
It initially started as a research document repository.
But we then launched the YouTube channel where we started running weekly livestreams that took over from initial documentation.
The YouTube channel wasn’t getting as many subscribers as we hoped, probably because YouTube only promotes livestreams while they are streaming.
So we moved to regular edited YouTube videos, which definitely got more views.
Hours after posting the New Year New Culture video, I (Martin) got a payment failure notification from my bank. I had been so frantically working on the videos, buying anything we needed (and a few things we didn’t) that I took my eyes off the cashflow.
From that point focus has shifted to grant applications. We collaborate on these in a ClickUp account, hence there hasn’t been as much action in our other channels as we would have liked.
There is however a tonne of other stuff we’ve been working on, so please do get in touch, I/we would love to chat.
8 - Contribution Guidelines
How to contribute to the AMYBO community
Reach out to us
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:
Editing AMYBO.org
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]
Web stack
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.
Quick start
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’re not yet ready for a review, add “WIP” to the PR name to indicate
it’s a work in progress. (Don’t add the Hugo property
“draft = true” to the page front matter, because that prevents the
auto-deployment of the content preview described in the next point.)
Wait for the automated PR workflow to do some checks. When it’s ready,
you should see a comment like this: deploy/netlify — Deploy preview ready!
Click Details to the right of “Deploy preview ready” to see a preview
of your updates.
Continue updating your doc and pushing your changes until you’re happy with
the content.
When you’re ready for a review, add a comment to the PR, and remove any
“WIP” markers.
Updating a single page
If you’ve just spotted something you’d like to change while using the docs, Docsy has a shortcut for you:
Click Edit this page in the top right hand corner of the page.
If you don’t already have an up to date fork of the project repo, you are prompted to get one - click Fork this repository and propose changes or Update your Fork to get an up to date version of the project to edit. The appropriate page in your fork is displayed in edit mode.
Follow the rest of the Quick start process above to make, preview, and propose your changes.
Previewing your changes locally
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.
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.
Creating an issue
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.
Useful resources
Docsy user guide: All about Docsy, including how it manages navigation, look and feel, and multi-language support.
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.
Logo
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?
It’s common in logo competitions to seek a logo that encapsulates what the organisation does, or its main product(s). But if you look at any lists of the world’s most recognisable logos you’ll probably see <3% that even allude to what the organisation does.
Most top logos are just a name, many use an image that conveys an emotion rather than a product: car brands often go with powerful animals or geometric symbols, penguins have been used by OS & book publishers, a small business trying to use a pear logo was famously challenged by a company using a more recognisable fruit…
Do we just want a nice font for AMYBO? If so, what do we mean by a nice font?
Do we stick with black on white for accessibility, low cost printing & the ability to use different colours for different purposes without going off-brand? Or do we want to pick a specific colour?
If we just use AMYBO in a nice font, what do we use for square favicons and circular YouTube logos, etc?