Loam Bio wins USDA APHIS clearance via soil metagenomics
Loam Bio has received regulatory clearance from the USDA Animal and Plant Health Inspection Service (APHIS) to expand use of its fungal biological product across additional US states, after EarthOptics deployed a soil metagenomic database to document species indigeneity in place of conventional soil sampling.
The approach, which EarthOptics describes as a first for APHIS permitting, could meaningfully cut the time and capital biologicals developers spend on state-by-state regulatory evidence gathering.
How the verification worked
Under standard APHIS practice, companies seeking to deploy a soil microorganism in a given state must first demonstrate that the organism already occurs there naturally. Historically, that meant physical soil collection, isolation of the target strain, and sequencing repeated for every state in scope. EarthOptics instead compared genome assemblies supplied by Loam Bio for two fungal strains against its proprietary metagenomic database, which the company says covers more than 10,000 US field sites and is the largest of its kind.
The resulting reports documented natural occurrence at state-level resolution without requiring new soil collection. EarthOptics applies a three-layer verification: whole-genome identity confirmation rather than single-marker matching; testing against a reference library of closely related species to rule out look-alikes; and a minimum evidence threshold before a find is reported. The company states a species discrimination accuracy above 99.9%, with a false-positive rate below 0.04%.
Joshua Kling, senior bioinformatician at EarthOptics, said the team had spent months working through the evidence with Loam Bio to ensure the reporting answered USDA reviewers' questions directly. "That work is now behind us, and the path is considerably shorter for the companies that follow," he said.
Mark Schulte, senior manager of US product development at Loam Bio, said the service had moved the company's expansion timeline forward by removing what would otherwise have been seasons of soil collection before permitting could even begin.
Market context and regulatory read-across
The biologicals market for agriculture has expanded rapidly over the past decade, driven by grower demand for input alternatives, tightening scrutiny of synthetic agrochemicals, and the emergence of voluntary carbon markets that favour biological soil interventions. Loam Bio's CarbonBuilder technology centres on root-associated fungi that it says convert plant-captured carbon into more stable soil carbon pools, generating carbon credits through its SecondCrop programme.
Regulatory bottlenecks have been a persistent constraint on commercialisation in this space. APHIS permitting for soil microorganisms is distinct from EPA registration under FIFRA, and the two processes can run in parallel, but indigeneity evidence has long been one of the slower elements of the APHIS track. If EarthOptics' metagenomic approach wins broader acceptance from USDA reviewers, it could accelerate the commercialisation pipeline for a range of fungal and bacterial soil biologicals currently in development across the sector.
EarthOptics chief executive Lars Dyrud said the company is now accepting new TruOrigin engagements for the 2027 permitting cycle, signalling that it intends the Loam Bio project to serve as a template for future clients rather than a one-off demonstration. The near-term question for the industry is whether USDA will formalise guidance recognising metagenomic databases as standard evidence for indigeneity, which would further lower the barrier for new entrants and reduce the regulatory premium that currently advantages well-capitalised incumbents.