New tree growth acceleration technology using beneficial fungi could help forests grow 30% faster and combat climate change. The Arbor Day F
A breakthrough in tree growth acceleration could transform how we fight climate change through reforestation.
17 Apr 2025------
The tree growth acceleration technology - potentially boosting forest growth by 30 percent - has been developed by Funga PBC, and works by returning native fungal communities to tree roots before planting. These essential fungi were naturally present in forest soils but have vanished due to modern land management practices.
Scientists know that trees and fungi form a vital partnership in healthy forests because fungi create vast underground networks of microscopic threads called mycelium around tree roots. These fungal networks help trees absorb water and crucial nutrients like phosphorus and nitrogen from the soil.
In return, trees share up to 30 percent of the sugars they make through photosynthesis with their fungal partners. This exchange has evolved over millions of years, creating what scientists call a âmycorrhizal networkâ. These networks connect trees of different species, allowing them to share resources. Older, larger trees often support younger saplings through these fungal connections.
The accelerated tree growth has significant implications for fighting climate change. According to Fungaâs field trials, forests with restored fungal communities can capture up to 40 percent more carbon dioxide annually compared to conventional plantings.
âFungaâs method could create planet-shaping impact,â says Dan Lambe, chief executive of the Arbor Day Foundation.
Update 31 May 2023: an earlier edition of this article identified the price of Rebyota as $20,000; this was the rumored price prior to Rebyotaâs release in December  2022, when Stephen Skolnick wrote the article I referenced. When Rebyota was actually released in 2023, the average wholesale price (AWP) was $10,800. Thanks to Benjamin Jolley for catching this error, and to Stephen Skolnick for getting to the bottom of it.
Itâs been ten yearsâââto the day!âââsince I first started writing about the bizarre, amazing world of turd transplants, in which a sick person receives a microbiotic infusion in the form of some processed poop from a healthy person:
Gut biomes are one of those understudied, poorly understood medical areas that are both very promising and also full of sketchy medical claims from âsupplementâ companies, influencers, quacks and grifters. But in the decade since I first started tracking turd transplants (formally called âFecal Microbiota Transplantsâ or FMTs), a growing body of sound science has emerged on the subject.
One thing thatâs increasingly undeniable is that the composition of your microbial nation is related in significant ways to both your physical and mental health. Whatâs more, as antibiotic resistant âsuper bugsâ proliferate, FMTs are becoming increasingly central to treating dangerous gut infections that otherwise stand a high chance of killing you.
âEat Shit and Prosperâ is Stephen Skolnickâs delightfully named newsletter about poop and health science. Skolnick is a physicist by training, but has a long history of collaboration with Openbiome, a nonprofit that coordinates between doctors, patients and donors to provide safe FMTs:
https://stephenskolnick.substack.com/
In an edition of Eat Shit from last December, Skolnick recounts the amazing history and dismaying future of FMTs. In 2013, the FDA announced it would regulate FMTs as âInvestigational New Drugs,â which could only be administered as part of a registered clinical trial:
At that point, FMTs were already in widespread use by docs to treat otherwise untreatable cases of Clostridioides difficile (C. diff), an antibiotic resistant bacterial infection that literally makes you shit yourself to death. These doctors were in no position to run registered clinical trials, which meant that they would have to stop using the most effective therapy they had for a potentially lethal infection.
Doctors and patients kicked up a fuss, and the FDA walked back its guidance, announcing that it would exercise âdiscretionâ in enforcing its Investigational New Drug rule, giving a pass to docs who were treating C. diff with FMTs:
Thatâs where things have stood for the past decade or so. The âdiscretionâ rule means that patients could still get FMTs, but their insurance wouldnât cover it. But even if you had cash to pay for an FMT, your doc probably wouldnât administer it for anything except a C. diff infection, despite the promising signs that FMT can help treat other conditions, and despite the generally safe nature of FMTs.
If your doc did give you an FMT, chances are good that they sourced their poop from Openbiome. Openbiome recruits very healthy people, gets them to poop in a bag, then processes the poopâââremoving nonbacterial solids, testing it for pathogens, freezing it, portioning it, and sending it to docs. All this is done at cost, and itâs not cheap: $1â2k/treatment, mostly due to cold-chain logistics (the poop is shipped at -80C).
Despite the cost, and despite the limitations on treatment, the Openbiome method has proved very reliable. Indeed, FMTs as a whole are pretty darned safe, with the most common side-effects being transient gas and bloating. In the past decade, thereâve been a total of six âadverse effectsâ associated with Openbiomeâs 5,000+ procedures, all in severely immunocompromised people, and none conclusively linked to the treatment:
A decade into this system, the FDA has taken the next step forwardâââonly itâs actually a step backwards.
During this intervening decade, a pharma company called Ferring has conducted clinical trials on FMTs and received approval for an FMT product called Rebyota. The process for making Rebyota is effectively identical to the process used by Openbiome: collect poop, remove solids, test for pathogens, add glycerol, freeze and ship.
The main difference between Rebyota and Openbiomeâs poop is price. While Openbiome charges $1â2k per treatment, Rebyota charges $10,800
Thatâs some expensive shit!
Fine. Getting Rebyota through clinical trials means that insurers might start covering it, and perhaps some patients will prefer brand-name poop to open-source poop. But as part of the FDAâs approval of Rebyota, the agency also rescinded its âdiscretionary enforcementâ guidance, making it illegal for docs to source their poop from Openbiome:
For Ferring, this is a monopoly on shit, one that lets them charge patients $10.8k for poop that costs $1â2k to process. The FDA does not claim that this is being done in the name of safety. Instead, an FDA official told Skonick that the goal was to âincentivize innovation without creating an access crisis.â
That is, the FDA changed its guidance and put nonprofit stool banks out of business because it wants to incentivize pharma companies to perform expensive clinical trials, and it believes that these companies wonât pay for trials if they have to compete with the likes of Openbiome, which would make it impossible to charge 900% markups on poop.
Trials are important! Evidence-based medicine is important! But Ferringâs clinical trials didnât tell us anything we didnât already know. FMTs were already the best therapy we had for C. diff. Testing Rebyota against a placebo didnât tell us anything newâââunlike testing Rebyota against the existing therapies, e.g. product from open stool banks.
Such a trial might have given rise to a very different regulatory outcome, because the cure rate reported by Rebyota is much lower than the cure rate from Openbiomeâs own interventions:
That is, using the $1k poop from Openbiome seems to be much more effective than using the $10.8k poop from Ferring. But Openbiome, a nonprofit, hasnât been able to perform the kind of rigorousâââand expensiveâââclinical trial that Ferring funded.
This points to a significant problem with the FDAâs model. The agency wants good clinical data for the medicines it regulates, as it should, It presumes that the only way to get that data is through granting commercial exclusivity to a for-profit, which ends up costing patients vast sums, and locking many patients out altogether.
This creates all kinds of new dangers. 150,000 people/year in the US contract Recurrent Clostridium difficile Infection (RCdI). FMT increases the cure rate by 20% relative to antibiotics alone. That means that if everyone with RCdI gets a poop transplant, 30,000 extra people will get better. Thatâs a big number!
For well insured people, Rebyota probably represents a cash-savingsâââif your insurance covers the $10,800 procedure, you might pay $500 out of pocket, which is far less than the $1â2K youâd pay to get an Openbiome poop transplant. But if youâre uninsured or underinsured, the FDAâs new enforcement rules mean that youâre now on the hook for $10,800.
The FDA did carve out a loophole: if your doc or their hospital are willing to prepare the poop transplant themselves, they can administer that. On the one hand, preparing a poop transplant isnât that hardâââsome people do them at home, on their own:
But on the other hand, thereâs been exactly one death conclusively linked to FMT, and it was from one of these hospital-prepared transplants (the patient had just had a marrow transplant for cancer that wiped out their immune system, and the donor had a novel pathogen that the hospital failed to test for).
So the FDA has created a situation where, if you canât afford a $10,800 proprietary formulation, your only option is to convince your doc or hospital to prepare their own poop transplant, which will cost less than the $10.8k for Rebyota, but more than the $1â2k from Openbiome, which has all kinds of economies of scale. And if you do manage it, youâll be getting a procedure that has a much worse safety track-record than the Openbiome process that the FDA just killed.
The FDA has an important role to play here, but as with so many policy questions, how the FDA plays that role depends on things that are far upstream from the agency and its decisions. The choice to fund medical trials through the promise of exclusivityâââand with it, extremely high marginsâââputs the FDA in the position of choosing winners in the marketplace: Ferring wins, Openbiome loses.
Ironically, this is the thing that exclusivity is supposed to prevent. By using profit to incentivize medical research, the FDA is supposed to be recruiting the Invisible Hand as its partner in regulation. But exclusivity is incompatible with the idea of medicine as a public good. The tens (hundreds) of millions that Americans will pay for $10.8k poop transplants from Ferring will add up to far more than it would cost to underwrite clinical trials for an open process like Openbiomeâs.
The result: both Americansâ wallets and Americansâ guts suffer.
Catch me on tour with Red Team Blues in Hay-on-Wye, Oxford, Manchester, Nottingham, London, and Berlin!
If youâd like an essay-formatted version of this post to read or share, hereâs a link to it on pluralistic.net, my surveillance-free, ad-free, tracker-free blog:
Citrus greening disease, or Huanglongbing (HLB), is deadly, incurable, and the most significant threat to the citrus industry. Most HLB research focuses on the tree canopy, but scientists in California studied the impact of HLB on root systems. They recently published the first study to report on the response of two different varieties of citrus to the causal bacterium, 'Candidatus Liberibacter asiaticus' using metabolomics and microbiome technologies.
Citrus greening disease, or Huanglongbing (HLB), is deadly, incurable, and the most significant threat to the citrus industry. Most HLB research focuses on the tree canopy, but scientists in California studied the impact of HLB on root systems. They recently published the first study to report on the response of two different varieties of citrus to the causal bacterium, 'Candidatus Liberibacter asiaticus' using metabolomics and microbiome technologies.
"Metabolomics is a cutting-edge field of study that provides snapshot information about the metabolism of living things," explains author Emily M. T. Padhi, "while microbiome studies provide valuable information about the microbial communities living in a particular ecological nicheâsome microbes are beneficial to the host, while others can be harmful."
Padhi and colleagues wanted to see how the root system of two varieties of citrus responded to HLB. They collected roots from healthy and infected Lisbon lemon and Washington Navel orange trees grown in greenhouses at the same time and under the same conditions.
They found that both varieties experienced a reduction in root sugars and amino acids when exposed to HLB. However, they also found differences. While the concentration of malic acid and quinic acid (two metabolites involved in plant defense) increased in the navel roots, they decreased in the lemon roots. They also found that the beneficial bacteria Burkholderia increased substantially in navel plants but not in lemons, which contradicts previous studies...
Flies can be more than pesky picnic crashers, they may be potent pathogen carriers, too, according to an international team of researchers.
In a study of the microbiomes of 116 houseflies and blowflies from three different continents, researchers found, in some cases, these flies carried hundreds of different species of bacteria, many of which are harmful to humans. Because flies often live close to humans, scientists have long suspected they played a role in carrying and spreading diseases, but this study, which was originally initiated at Penn State's Eberly College of Science, adds further proof, as well as insights into the extent of that threat.
"We believe that this may show a mechanism for pathogen transmission that has been overlooked by public health officials, and flies may contribute to the rapid transmission of pathogens in outbreak situations," said Donald Bryant, Ernest C. Pollard Professor of Biotechnology and professor of biochemistry and molecular biology, Penn State.
According to Stephan Schuster, former professor of biochemistry and molecular biology, Penn State, and now research director at Nanyang Technological University, Singapore, the researchers were able to investigate the microbial content of individual fly body parts, including legs and wings. The legs appear to transfer most of the microbial organisms from one surface to another, he added.
"The legs and wings show the highest microbial diversity in the fly body, suggesting that bacteria use the flies as airborne shuttles," said Schuster. "It may be that bacteria survive their journey, growing and spreading on a new surface. In fact, the study shows that each step of hundreds that a fly has taken leaves behind a microbial colony track, if the new surface supports bacterial growth."
Blowflies and housefliesâboth carrion fly speciesâare often exposed to unhygienic matter because they use feces and decaying organic matter to nurture their young, where they could pick up bacteria that could act as pathogens to humans, plants and animals. The study also indicates that blowflies and houseflies share over 50 percent of their microbiome, a mixture of host-related microorganisms and those acquired from the environments they inhabit. Surprisingly, flies collected from stables carried fewer pathogens than those collected from urban environments.
Ana Carolina M. Junqueira et al. The microbiomes of blowflies and houseflies as bacterial transmission reservoirs, Scientific Reports (2017). DOI: 10.1038/s41598-017-16353-x
Researchers used a scan electron microscope to find where bacterial cells and particles attach to the fly body. The electron microscope captures an up close look at the head of a blowfly in this picture. Credit: Ana Junqueira and Stephan Schuster
Once weeds take root in a field and spread, they become difficult to eradicate. But how are they so successful at overrunning the desired crops?
Weeds and other invasive plants associate with microorganisms found in the soil which support their growth and health. However, it has been found that weeds often interact differently with soil microorganisms than crops do. As a result, the solution to preventing weed growth may lie in altering the soilâs structure through methods such as tillage and herbicide treatments, thus making the soil habitable for the crops alone.
Image: Dandelion, field, grass and meadow by Jason Long. Public domain via Unsplash.
Not under the skin, but on it: Living together brings couples' microbiomes together
Couples who live together share many things: Bedrooms, bathrooms, food, and even bacteria. After analyzing skin microbiomes from cohabitating couples, microbial ecologists at the University of Waterloo, in Canada, found that people who live together significantly influence the microbial communities on each other's skin.
The commonalities were strong enough that computer algorithms could identify cohabitating couples with 86 percent accuracy based on skin microbiomes alone, the researchers report this week in mSystems, an open-access journal of the American Society for Microbiology.
However, the researchers also reported that cohabitation is likely less influential on a person's microbial profile than other factors like biological sex and what part of the body is being studied. In addition, the microbial profile from a person's body usually looks more like their own microbiome than like that of their significant other.
"You look like yourself more than you look like your partner," says Ashley Ross, who led the study while a graduate student in the lab of Josh Neufeld.
Bacteria from 300-year-old Ovid poetry volume inspires 'bio-artist'
There was more than poetry trapped between the leather covers of a 300-year-old volume of Ovidâs Metamorphoses: blood, sweat and snot feature in an art installation that displays the bacteria within its pages.
The sweat and the droplets from an ancient sneeze that spattered one page were contributed by centuries of previous owners and readers of the book â but the blood was the artistâs own, donated by Sarah Craske as part of the medium for cultivating the organisms.
Craske found the rare early English translation of Ovidâs epic Latin poem, published in London in 1735, in a junk shop in Margate. Photograph: PartPR
