Digester microbiome report
1. Results
| Item | Genomes, share of reads | Status |
|---|---|---|
| Methanogens (all routes) | 5 genomes, 1.5 % | ok |
| Acetate route (acetate-consuming methanogens) | Methanosarcina flavescens, 0.49 % | note |
| H₂/CO₂ route (hydrogen-consuming methanogens) | 5 genomes, 1.5 % | ok |
| Methyl route (methyl-consuming methanogens) | 1 genome, 0.49 % | ok |
| Cellulose breakdown (genomes carrying the enzymes) | 27 genomes, 15.6 % | ok |
| Cellulose breakdown (genomes with enzymes anchored outside the cell) | 6 genomes, 1.9 % | ok |
| Protein breakdown (genomes carrying the enzymes) | 89 genomes, 56.0 % | ok |
| Propionate pathway (genomes carrying it) | 25 genomes, 20.4 % | ok |
| Ammonia release from ethanolamine (genomes carrying the pathway) | 1 genome, 0.45 % | note |
| Butyrate oxidation | — | not assessed |
| Ethanol fermentation | — | not assessed |
| Lactate fermentation | — | not assessed |
| Direct interspecies electron transfer | — | not assessed |
| Energy conservation | — | not assessed |
Share of reads = share of reads mapped to the 1,635-genome catalogue. Genomes below 0.1 % of reads are not in this report. ok = nothing unusual. note = thin or present, not a fault by itself. The Findings name the measurement to check. If that measurement is normal, the row is a baseline for the next sample. If it is not, see the Suggestions. attention = a route is missing or very weak. See the Suggestions before a change of feed or load. not assessed = no reliable marker, not zero. An expert set the status thresholds. Plant data has not calibrated them yet.
2. Findings
- 5 genomes carry mcrA, the marker gene for methane formation. Together they are 1.5 % of the mapped reads.
- One genome, Methanosarcina flavescens, carries the acetate route (0.49 %). The whole acetate route depends on this one genome. It tolerates ammonia and acid peaks. It needs more acetate than Methanothrix (literature [1, 2], see Method).
- 5 genomes carry the H₂/CO₂ route (1.5 %). The most abundant H₂/CO₂ specialist is Methanoculleus sp. (0.49 %).
- 27 genomes carry most of the cellulose and hemicellulose genes (15.6 %). In 6 of them (1.9 %) the enzymes carry a domain that holds the enzyme on the cell surface or on the fibre. These enzymes are built to work outside the cell. This test does not detect an enzyme that leaves the cell without such a domain. The count is therefore a minimum.
- 25 genomes carry the propionate pathway (20.4 %). The same genes can work in both directions, towards propionate and away from it. DNA does not show the direction.
- 1 genome (0.45 %) can release ammonia from ethanolamine. Ethanolamine occurs in manure and in slaughter waste. This is capacity, not a measurement. Read it together with your NH₄⁺-N data.
3. Suggestions
These suggestions come from the genes that the community carries. They are not operating instructions. The process data (FOS/TAC, VFA, gas, pH) are the measure of each step, not this report. The plant operator makes the decisions on feed, load and additives. Magrittr OÜ is not responsible for those decisions or their results. The suggestions below assume a wet stirred-tank reactor (CSTR).
- Compare these results with your FOS/TAC (VOA/TAC), NH₄⁺-N, propionate, pH and temperature from the same weeks, and with this reactor's own history. [3]
Why: Genes show capacity. The process data show what the reactor does now. FOS/TAC values differ between plants. - Take the next sample in 3 months, or sooner after a change of feed or an upset, at the same point and before feeding.
Why: One sample is a baseline. The second sample shows what moved. The interval and the time before feeding are our protocol, kept the same so that two samples compare. - The genes do not support a higher loading rate before the next sample. [4]
Why: The acetate route is thin: Methanosarcina flavescens, 0.49 % of mapped reads. 2 genomes carry the Wood–Ljungdahl pathway, so bacteria may also oxidise the acetate. That route is slower and may need a long retention time.
4. Analyst's comment
The analyst wrote this section and checked it. Every number in it comes from the tables in this report.
The acetate route rests on one genome, Methanosarcina flavescens, at 0.49 %. No other genome in this sample carries it.
5. Methanogens
| Genome | Routes | Share of reads | Completeness | Contamination |
|---|---|---|---|---|
| Methanoculleus sp. | H₂/CO₂ | 0.49 % | 85 % | 1.6 % |
| Methanosarcina flavescens | acetate, H₂/CO₂, methyl | 0.49 % | 100 % | 0.4 % |
| Methanoculleus thermohydrogenotrophicum | H₂/CO₂ | 0.21 % | 96 % | 0.5 % |
| Methanoculleus bourgensis | H₂/CO₂ | 0.19 % | 85 % | 2.1 % |
| Methanobacterium sp. | H₂/CO₂ | 0.13 % | 100 % | 0.0 % |
CheckM2 measured the completeness and the contamination. A route is only as complete as the genome that carries it. A methanogen without a route is more often an incomplete genome than a missing pathway.
6. Most abundant genomes
| Genome | Share of reads |
|---|---|
| Acholeplasmataceae bacterium | 5.8 % |
| Cloacimonadaceae bacterium | 5.5 % |
| Darwinibacteriaceae bacterium | 4.3 % |
| Saccharofermentanales bacterium | 3.9 % |
| Bacteroidales bacterium | 3.8 % |
| Darwinibacteriaceae bacterium | 3.6 % |
| Bacilli bacterium | 2.9 % |
| Bacilli bacterium | 2.5 % |
| Caldicoprobacterales bacterium | 2.4 % |
| Darwinibacteriaceae bacterium | 2.3 % |
7. Not assessed
This method reads genes. It shows what the organisms can do. It does not measure what they do now. FOS/TAC shows acidification in days. Genes change in weeks. 5 panel modules have no reliable marker. This report shows them as not assessed, not as zero: butyrate oxidation, ethanol fermentation, lactate fermentation, direct interspecies electron transfer, energy conservation. Assumed present in every genome and not scored: glycolysis.
8. Method
Genomes and abundances: Campanaro et al. 2020, Biotechnol Biofuels 13:25 (CC BY), NCBI PRJNA602310. The report includes genomes at ≥ 0.1 % of reads in this sample. The scorer compared each genome with the marker panel digestome v0, 126 HMMs. The panel has 20 modules. The models come from NCBIfam, Pfam and Rhea. The panel does not use KEGG. A route appears only when a genome has the mcrA gene and the genes of that route. The H₂/CO₂ route also includes methanogens that reduce CO₂ with formate. Taxonomy: GTDB-Tk 2.7.1, GTDB release 232. The result tables (genomes, modules, routes, risks) give every number in this report, and we deliver those tables with it.
Provenance. The same inputs always give the same report. These values identify the inputs:
| digestome commit | 8a90aa0 (plant tables scored 2026-09-22 with GTDB-Tk lineages, jobs 1473613-1473616) |
| panel | digestome v0, 126 HMMs |
| HMMER | 3.3.2 |
| GTDB-Tk | 2.7.1 |
| GTDB release | r232 |
| result tables (sha256) | feab16db4d06 |
| lineage policy acetate_lineages.tsv (sha256) | fd2b05701089 |
| suggestion rules (sha256) | 4546b50350f3 |
| status thresholds (sha256) | d3944969b61c |
| renderer commit | 129346f |
| GTDB-Tk summaries (sha256) | 396bfcedb3a1 |
| analyst's comment (sha256) | 9be27b92b072 |
Statements about the properties of a genus or a pathway are from the literature, not measured in this sample:
- Jetten MSM, Stams AJM, Zehnder AJB (1992) Methanogenesis from acetate: a comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp. FEMS Microbiol Rev 8:181–198.
- De Vrieze J, Hennebel T, Boon N, Verstraete W (2012) Methanosarcina: the rediscovered methanogen for heavy duty biomethanation. Bioresour Technol 112:1–9.
- Handbook: Drosg B (2013) Process monitoring in biogas plants. IEA Bioenergy Task 37.
- Handbook: Schnürer A, Jarvis Å (2018) Microbiology of the biogas process. Swedish University of Agricultural Sciences.
A handbook supports the lever and its direction. No handbook bases a decision on the microbial community.