The Microbiome Management Framework

A worked example

One root zone after heavy rain.

Rain fills the soil and the root zone runs short of oxygen. Days later the leaves are pale. Three different things may have happened, and each needs its own measurement to see.

A conceptual investigation: what one would measure, not an experiment the project has run.

Environmental change
Environmental conditions
Water fills the spaces between soil particles and oxygen falls. Oxygen moves through water far more slowly than through a drained soil.¹
Measure. Soil water content, soil oxygen or redox potential, soil temperature, and how long the soil stays saturated.
Microbial response
Microbial activity
Short of oxygen, some soil microbes use nitrate in its place and release the nitrogen as gas. Their own activity uses oxygen up faster in warm soil rich in organic matter.^{1, 2}
Measure. Nitrate and ammonium in the root zone, and nitrous oxide released from the soil, over time. Measures of microbial activity, kept apart from a list of which microbes are present.³
Plant response
Observable function
Roots need oxygen to grow and take up nutrients, so leaves can turn pale while nitrogen is still in the soil.¹
Measure. Leaf colour, leaf tissue nitrogen, root growth and root colour.
A path without microbes
Environmental conditions
Water can also carry nitrate down below the roots.^{1, 2}
Measure. Nitrate deeper in the soil, or in water draining from it.

A young plant in fine line above the soil line, its roots spreading through soil aggregates. Numbered markers show where each measurement is taken: 1 in the soil pores, 2 at the root surface, 3 on a leaf, 4 below the roots. — Where each measurement is taken. Illustration, not to scale.

What would tell them apart

The pattern each explanation predicts if it acted alone. In a real field they overlap.

Measurement	Roots short of oxygen	Microbes released nitrogen as gas	Water carried nitrate down
Nitrate in the root zone	Still present	Lower	Lower
Nitrous oxide from the soil	No rise expected	Higher	No rise expected
Nitrate below the roots	No rise expected	No rise expected	Higher
Root growth and colour	Reduced	May also be reduced	Can look normal
Leaf tissue nitrogen	Lower	Lower	Lower

Leaf nitrogen, lower in all three, cannot separate them on its own. A nearby patch that drained quickly, measured the same way at the same times, makes the pattern readable.

The central relationship

Conditions, communities and function belong in the same picture.

The framework considers three connected areas. Each provides information about the others, but a change in one does not automatically establish what caused a change elsewhere.

One field drawn in fine line: young plants, a cow grazing, a dog, and a woman walking past. — The framework in one picture: choose a living system. The horse and the trout are shown in their own drawings. Illustration; magnified views are conceptual and not to scale.

A grazing horse in outline with its digestive tract drawn inside. — The framework in one picture: choose a living system. The horse and the trout are shown in their own drawings. Illustration; magnified views are conceptual and not to scale.

A conceptual model for organising questions. The relationships, and the measurements that are useful, differ between systems.

All six living systems as text

The three framework areas in each living system, as the figure shows them. The magnified view named in the last column is drawn for that system alone.
Living system	Environmental conditions	Microbial activity	Observable function	Magnified view
Soil & plants	Moisture, oxygen, pH, temperature, plant residues and management.	Bacteria and fungi in the root zone, using the compounds the root releases.	Root mass and leaf tissue analysis.	The root zone
Horses	Forage and feeding, turnout and routine, travel, life stage and individual needs.	Bacteria in the large colon, fermenting forage fibre.	Manure consistency and body condition score.	The large colon
Companion animals	Food and extras, feeding routine, transitions and individual history.	In the dog shown, bacteria in the large intestine, working on fibre and food residue.	Faecal score and body condition score.	The large intestine
Livestock	Feed, forage quality, water, housing and transitions.	In the cow shown, bacteria and protozoa in the rumen, fermenting plant fibre.	Manure score and body condition score.	The rumen
Aquaculture	Water quality and temperature, feed, life stage and equipment.	Bacteria on feed particles in the trout intestine, a sparser community than in a mammal’s hindgut.	Weight gain, and for eggs, survival to hatch.	The trout intestine
Humans	Diet, fibre, routine and daily circumstances.	Bacteria in the large intestine, fermenting dietary fibre.	Stool form and gut transit time.	The large intestine

Guiding principles

Five principles of Microbiome Management.

They hold in every living system, whoever applies them, and connect biological understanding with practical investigation.

01
Begin with the conditions
Describe the environment before deciding what to change. Consider resources, physical conditions, management and recent transitions within the system.⁴
02
Ask about function as well as composition
Knowing which microbes are present answers a different question from knowing what they are doing. Keep community composition, microbial activity and host or system outcomes distinct.^{3, 5, 6}
03
Consider change over time
A single observation provides limited context. Establish a baseline, follow relevant measures and consider how the system responds as conditions change.⁷
04
Respect the wider management program
Nutrition, husbandry, growing practices, water management and professional care remain part of the picture. Interpret any proposed input within that wider context.
05
Match conclusions to evidence
Distinguish a plausible explanation, a reported observation and a result demonstrated under defined study conditions. Let the strength and relevance of the evidence determine the conclusion.

In digestive systems

Digestive Stability: function that holds through change.

In digestive systems, Digestive Stability means appropriate digestive function and the capacity to adapt through change.

The relevant observations depend on the species, life stage and circumstances. Digestive Stability is a working concept within the framework, not a diagnosis or a single validated score.

Stability does not mean an unchanging microbial community. The framework asks whether function remains appropriate as the living system changes.

01 Before the diet change
Function
Consider whether digestive function is appropriate for the individual and its circumstances.
02 Within two days of it
Adaptation
Consider how function changes through shifts in diet, routine, life stage or environment.
03 Settled, not as before
Recovery
Observe whether and how function returns toward its usual pattern after disruption, alongside any necessary professional care.

a Colon wall
b Food residue and fibre
c Bacteria
d Mucus layer

Illustration after Lin et al. 2022, twelve adult laboratory Beagles. One example. The community is drawn schematically, not from the data. Not to scale.

In twelve laboratory dogs, fermentation products settled within days of an abrupt diet change, while stools stayed looser than before. A settled community is not, by itself, function that held.⁸

For soil, plants and other environmental applications, use measures appropriate to those systems rather than the term Digestive Stability.

From idea to investigation

Start with five questions.

Use them to organise a discussion, a management review or a prospective evaluation. The questions stay the same in every living system; the biology that answers them does not.

The framework provides a way to connect existing practices and ask additional questions. It can be used when reviewing a nutrition program, considering a management change or evaluating an input.

Soil & plants

Horses

Companion animals

Livestock

Aquaculture

Humans

01
What system and question are we examining?
Practical output. A clear question and a defined scope.
Soil & plants. How do root-zone conditions relate to plant development?
Horses. How does digestive function vary through a change in routine or feeding?
Companion animals. How do dietary and routine changes relate to digestive observations?
Livestock. How do conditions and management relate to function during a defined production stage?
Aquaculture. How do the animal’s environment and application route affect the question being studied?
Humans. How do diet, routine and other circumstances relate to digestive experiences?
02
What conditions and recent changes matter?
Practical output. A description of the starting context.
Soil & plants. Soil or substrate, water, nutrients, physical conditions and management.
Horses. Forage and feeding, travel and routine, life stage and individual needs, and concurrent care.
Companion animals. Food and extras, feeding and access, routine and transitions, and individual history.
Livestock. Feed, water, housing and relevant management conditions.
Aquaculture. Water, feed, life stage, equipment and management.
Humans. Diet, fibre, routine and daily circumstances.
03
What evidence informs the options?
Practical output. A reasoned option with its supporting evidence and uncertainties.
Soil & plants. This library holds four studies of a humic or fulvic material (two in the living system, one in the lab, one across studies).
Horses. This library holds one background record and no study of a humic or fulvic material.
Companion animals. This library holds one study of a humic or fulvic material (in the lab) and two background records.
Livestock. This library holds five studies of a humic or fulvic material (five in the living system).
Aquaculture. This library holds two studies of a humic or fulvic material (two in the living system).
Humans. This library holds two studies of a humic or fulvic material (two in the living system) and one background record.
04
What will we observe, and over what period?
Practical output. An observation or evaluation plan.
Soil & plants. Growing conditions, root development and relevant plant measures. Measured on this system’s plate: root mass and leaf tissue analysis.
Horses. Feeding records, manure observations and professionally interpreted measures where appropriate. Measured on this system’s plate: manure consistency and body condition score.
Companion animals. Diet history, appetite, stool observations and the individual animal’s circumstances. Measured on this system’s plate: faecal score and body condition score.
Livestock. Intake, growth or production records, interpreted alongside management and health information. Measured on this system’s plate: cattle, manure score and body condition score; pigs, faecal score and average daily gain; poultry, litter condition and feed conversion ratio.
Aquaculture. Water conditions and appropriate animal or production measures. Measured on this system’s plate: survival to hatch and weight gain.
Humans. Relevant history and symptom patterns, interpreted with clinical assessment when needed. Measured on this system’s plate: stool form and gut transit time.
05
What can we conclude, and what needs another look?
Practical output. A documented interpretation and next decision.
Soil & plants. Whether the carbon in a fulvic material feeds the microbes living inside the plant: no study in this library has measured it.
Horses. Whether a preparation is used by particular hindgut microbes, or acts on their environment another way, needs its own evidence.
Companion animals. What humic or fulvic material does in a living dog or cat is still an open question.
Livestock. None of the trials in this library tested whether the microbial changes caused the production results.
Aquaculture. Each trout result belongs to its setting: an incubation result does not show what feeding does, and feed conversion was not measured.
Humans. Topical research does not establish an oral digestive effect, and this library holds no oral efficacy trial.

The questions travel. The biology remains specific.

What the framework adds to an existing program

Existing practice	Question the framework adds
Nutrition and resource supply	How might the available resources and their delivery influence the environment being examined?
Daily management	Which routines, conditions or recent changes deserve attention?
Professional assessment	What explanations and measurements should be considered before attributing an outcome to microbial activity?
Input selection	What evidence supports this preparation, application and intended role in this system?
Monitoring	What baseline and follow-up observations would make a change easier to interpret?

These examples illustrate questions and observations. They are not diagnostic criteria or evidence of product effects. A decision may involve changing management, investigating further, considering a suitable input or maintaining the current program. The framework does not presume that every situation requires an additional product.

See the questions on one worksheet

The questions, written down

One worksheet, filled in.

The observation worksheet puts the five questions on paper, with room for what usually goes unrecorded: the baseline, the unplanned changes and the other explanations.

Example. Hypothetical: no real horse, owner or record.

Print a blank worksheet

No scoring and no dosing. The worksheet organises observations; it does not diagnose, and it is not a substitute for veterinary, agronomic or medical advice.

Observation worksheet · Example

Hay to spring pasture, one horse

System and questionQuestion 1: Horses. One adult gelding moving from hay to spring pasture over two weeks. How do manure consistency and appetite change through the transition?
BaselineQuestion 2: Two weeks of notes before the change: hay type and amount, turnout hours, water, manure consistency each morning, appetite and body condition score. Dental and deworming dates checked.
Management changesQuestion 2: Planned: time on pasture lengthened step by step over 14 days, hay reduced as turnout grew. Unplanned: a cold, wet spell in week one, and a new horse in the next paddock on day 9.
Evidence consultedQuestion 3: Last spring’s notes for the same horse, and the veterinarian’s standing advice to change forage gradually.
MeasuresQuestion 4: Manure consistency, described in the same words by the same person each morning. Appetite at each feed. Body condition score and a weight-tape reading.
TimingQuestion 4: Daily through the 14 days of the change and the 14 days after. Body condition and weight tape on days 0, 14 and 28.
ObservationsQuestion 5: Looser manure on days 4 to 7, back to its usual form by day 12. Appetite and body condition unchanged.
Alternative explanationsQuestion 5: The wet spell, a different water source in the field, the new neighbour, and ordinary day-to-day variation. One horse with no comparison cannot separate the pasture from the weather.
Next stepsQuestion 5: Keep the step-by-step schedule for the next transition and record the weather beside it. Raise the looser days at the next routine veterinary visit. Contact the veterinarian promptly about any sign of colic, pain or lameness.

How to read the framework

Keep biological knowledge, interpretation and results distinct.

Biological knowledge

Scientific research describes relationships among environmental conditions, microbial communities and biological function. Specific explanations should be traceable to appropriate sources.

The project’s interpretation

Carbon Biome Project brings selected relationships together within the Microbiome Management Framework. Its definitions and organising principles can be refined as the work develops.

Evidence of an effect

Whether a particular action or preparation changes a particular outcome is a separate question. Answering it requires evidence relevant to the system, material, application and outcome.

One example: fulvic material at a rice root

Biological knowledge

Roots change the chemistry of the soil around them; the rhizosphere is the zone they influence.⁹

The project’s interpretation

The project reads this as one way these materials can matter at a root, through the root’s own chemistry. It does not carry the result into any animal or person.

Evidence of an effect

In rice seedlings grown short of phosphate, a fulvic preparation raised phosphorus uptake by about 20 percent. When the solution’s pH was held steady, the gain disappeared.¹⁰

Professional review can improve the accuracy and usefulness of the framework. It does not, by itself, establish the efficacy of an associated product.

How we interpret evidence

Sources and further reading

Ransom J. Impacts of flooding/waterlogging on crop development. NDSU Extension, North Dakota State University. 2020. ndsu.eduSaturated soil runs short of oxygen, faster when warm and biologically active; roots need oxygen to take up nutrients; nitrate can leach or be lost through denitrification.
Brune D, Killpack SC, Buchholz D. Nitrogen in the environment: denitrification. MU Extension WQ255, University of Missouri. 2017, reviewed 2022. extension.missouri.eduIn very wet soil, microbes short of oxygen convert nitrate to nitrogen gas; nitrate also moves with water below the root zone.
Carini P, Marsden PJ, Leff JW, et al. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nature Microbiology 2:16242. 2016. doi.org/10.1038/nmicrobiol.2016.242DNA-based surveys detect material from dead cells, so presence is not activity.
Lundberg DS, Lebeis SL, Paredes SH, et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488:86 to 90. 2012. doi.org/10.1038/nature11237Soil type and host plant both shape the root-associated bacterial community.
Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome datasets are compositional: and this is not optional. Frontiers in Microbiology 8:2224. 2017. doi.org/10.3389/fmicb.2017.02224Sequencing reports relative proportions, which limits what a change in composition can show.
Zhang Z, Qu Y, Li S, et al. Soil bacterial quantification approaches coupling with relative abundances reflecting the changes of taxa. Scientific Reports 7:4837. 2017. doi.org/10.1038/s41598-017-05260-wRelative and absolute abundance can move in different directions.
Morton V, Torgerson DJ. Regression to the mean: treatment effect without the intervention. Journal of Evaluation in Clinical Practice 11(1):59 to 65. 2005. doi.org/10.1111/j.1365-2753.2004.00505.xChange after a single high or low observation can occur without any intervention, which is why a baseline matters.
Lin CY, Jha AR, Oba PM, et al. Longitudinal fecal microbiome and metabolite data demonstrate rapid shifts and subsequent stabilization after an abrupt dietary change in healthy adult dogs. Animal Microbiome 4:46. 2022. doi.org/10.1186/s42523-022-00194-9Twelve laboratory dogs after an abrupt diet change: metabolites settled within about two days, stools stayed looser than before.
USDA Natural Resources Conservation Service. Soil Health Management. nrcs.usda.govRoots change the soil around them; the rhizosphere is the zone they influence.
Lv X, Li Q, Deng X, et al. Fulvic acid application increases rice seedlings performance under low phosphorus stress. BMC Plant Biology 24:703. 2024. doi.org/10.1186/s12870-024-05435-4Rice seedlings short of phosphate: phosphorus uptake, and the pH buffer that removed the gain.

Version and review

Version: 1.1, prepared 22 October 2026
First published: 19 October 2026
Prepared by: Carbon Biome Project
Review status: Prepared by the project team and checked against the sources it cites. External scientific review has not been completed.
In this version: A worked root-zone example; all six living systems in the central picture, each with its own magnified view; a completed example worksheet and a printable blank one; routes to each system’s evidence.
Cite as: Carbon Biome Project. The Microbiome Management Framework, version 1.1. 22 October 2026. carbonbiomeproject.com/framework/

Apply the framework in your field.

Each living system has its own page, its own evidence and its own open questions about organic matter and its humic and fulvic fractions.

Soil & plants
This library holds four studies of a humic or fulvic material (two in the living system, one in the lab, one across studies).
Explore soil & plants Its four records in the library
Horses
This library holds one background record and no study of a humic or fulvic material.
Explore horses Its record in the library
Companion animals
This library holds one study of a humic or fulvic material (in the lab) and two background records.
Explore companion animals Its three records in the library
Livestock
This library holds five studies of a humic or fulvic material (five in the living system).
Explore livestock Its five records in the library
Aquaculture
This library holds two studies of a humic or fulvic material (two in the living system).
Explore aquaculture Its two records in the library
Humans
This library holds two studies of a humic or fulvic material (two in the living system) and one background record.
Explore humans Its three records in the library

Interested in reviewing or developing this work? Contribute expertise.

Microbiome Management begins with the environment.

One root zone after heavy rain.

Environmental change

Microbial response

Plant response

A path without microbes

What would tell them apart

Conditions, communities and function belong in the same picture.

Environmental conditions

Microbial activity

Observable function

Feedback

All six living systems as text

Five principles of Microbiome Management.

Begin with the conditions

Ask about function as well as composition

Consider change over time

Respect the wider management program

Match conclusions to evidence

Digestive Stability: function that holds through change.

Function

Adaptation

Recovery

Start with five questions.

What system and question are we examining?

What conditions and recent changes matter?

What evidence informs the options?

What will we observe, and over what period?

What can we conclude, and what needs another look?

What the framework adds to an existing program

One worksheet, filled in.

Keep biological knowledge, interpretation and results distinct.

Biological knowledge

The project’s interpretation

Evidence of an effect

Sources and further reading

Version and review

Apply the framework in your field.

Soil & plants

Horses

Companion animals

Livestock

Aquaculture

Humans