Documentation
Input file format
The input files for MLP are species-level taxonomic profiles obtained using mOTUs v2.5, mOTUs v3.0.1, metaphlan3 (mpa_v30_CHOCOPhlAn_201901), or metaphlan4 (mpa_vJan21_CHOCOPhlAnSGB_202103) (with default options).
Example input files from the study Franzosa EA et al., 2018 are available here.
- mOTUs v2.5 (Milanese A et al., 2019)
- mOTUs v3.0 (Ruscheweyh HJ et al., 2022)
- MetaPhlAn3 (Beghini F et al., 2021)
- MetaPhlAn4 (Blanco-Míguez A et al., 2023)
Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese, Daniel R Mende, Lucas Paoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Alves, Paul I Costea, Luis Pedro Coelho, Thomas S B Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller, Shinichi Sunagawa
Nat Commun. 2019 Mar 4;10(1):1014. doi: 10.1038/s41467-019-08844-4.
| SAMN08049618 | SAMN08049619 | SAMN08049620 | SAMN08049621 | SAMN08049622 | |
|---|---|---|---|---|---|
| 'Candidatus Kapabacteria' thiocyanatum [ref_mOTU_v25_10354] | 0 | 0 | 0 | 0 | 0 |
| -1 | 0.03769520732364 | 0.06446335078534 | 0.036877637130802 | 0.016954022988506 | 0.044651782739087 |
| Abiotrophia defectiva [ref_mOTU_v25_04788] | 0 | 0 | 0 | 0 | 0 |
| Absiella dolichum [ref_mOTU_v25_03694] | 0 | 5.45E-05 | 0 | 0.002298850574713 | 0.000166611129623 |
| Acaricomes phytoseiuli [ref_mOTU_v25_06702] | 0 | 0 | 0 | 0 | 0 |
| Acaryochloris marina [ref_mOTU_v25_10941] | 0 | 0 | 0 | 0 | 0 |
| Acetanaerobacterium elongatum [ref_mOTU_v25_10763] | 0 | 0 | 0 | 0 | 0 |
| Acetitomaculum ruminis [ref_mOTU_v25_06703] | 0 | 0 | 0 | 0 | 0 |
| Acetivibrio ethanolgignens [ref_mOTU_v25_10828] | 0 | 0 | 0 | 0 | 0 |
| Acetoanaerobium sticklandii/noterae [ref_mOTU_v25_04651] | 0 | 0 | 0 | 0 | 0 |
Hans-Joachim Ruscheweyh, Alessio Milanese, Lucas Paoli, Nicolai Karcher, Quentin Clayssen, Marisa Isabell Keller, Jakob Wirbel, Peer Bork, Daniel R Mende, Georg Zeller, Shinichi Sunagawa
Microbiome. 2022 Dec 5;10(1):212. doi: 10.1186/s40168-022-01410-z.
| SAMN08049618 | SAMN08049619 | SAMN08049620 | SAMN08049621 | SAMN08049622 | |
|---|---|---|---|---|---|
| 'Candidatus Kapabacteria' thiocyanatum [ref_mOTU_v3_10354] | 0 | 0 | 0 | 0 | 0 |
| unassigned | 0.063561502830674 | 0.071905274488698 | 0.071508201942985 | 0.038923869490555 | 0.032241555783009 |
| Abiotrophia defectiva [ref_mOTU_v3_04788] | 0 | 0 | 0 | 0 | 0 |
| Absiella dolichum [ref_mOTU_v3_03694] | 0 | 5.38E-05 | 0 | 0.002289639381797 | 0.000170590242238 |
| Acaricomes phytoseiuli [ref_mOTU_v3_06702] | 0 | 0 | 0 | 0 | 0 |
| Acaryochloris marina [ref_mOTU_v3_10941] | 0 | 0 | 0 | 0 | 0 |
| Acetanaerobacterium elongatum [ref_mOTU_v3_10763] | 0 | 0 | 0 | 0 | 0 |
| Acetitomaculum ruminis [ref_mOTU_v3_06703] | 0 | 0 | 0 | 0 | 0 |
| Acetivibrio ethanolgignens [ref_mOTU_v3_10828] | 0 | 0 | 0 | 0 | 0 |
| Acetoanaerobium sticklandii/noterae [ref_mOTU_v3_04651] | 0 | 0 | 0 | 0 | 0 |
Francesco Beghini, Lauren J McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Valles-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A Franzosa, Nicola Segata
Elife. 2021 May 4:10:e65088. doi: 10.7554/eLife.65088.
| SAMN08049618 | SAMN08049619 | SAMN08049620 | SAMN08049621 | SAMN08049622 | |
|---|---|---|---|---|---|
| k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_arboriphilus | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera_stadtmanae | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Euryarchaeota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus|s__Candidatus_Methanomassiliicoccus_intestinalis | 0 | 0 | 0 | 0 | 0 |
| k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum_massiliense | 0 | 0 | 0 | 0 | 0 |
| k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum_sp_oral_taxon_183 | 0 | 0 | 9.25E-05 | 0 | 0 |
| k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_georgiae | 0 | 0 | 0 | 0 | 0 |
| k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_graevenitzii | 0 | 0 | 0 | 0 | 0 |
| k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_hongkongensis | 0 | 0 | 0 | 0 | 0 |
| k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_johnsonii | 0 | 1.50E-06 | 0.0002093 | 0 | 0 |
Aitor Blanco-Míguez, Francesco Beghini, Fabio Cumbo, Lauren J McIver, Kelsey N Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D Huang, Andrew Maltez Thomas, William A Nickols, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E Berry, Tim D Spector, Eric A Franzosa, Edoardo Pasolli, Francesco Asnicar, Curtis Huttenhower, Nicola Segata
Nat Biotechnol. 2023 Nov;41(11):1633-1644. doi: 10.1038/s41587-023-01688-w. Epub 2023 Feb 23.
| SAMN08049618 | SAMN08049619 | SAMN08049620 | SAMN08049621 | SAMN08049622 | |
|---|---|---|---|---|---|
| k__Archaea|p__Candidatus_Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__GGB260|s__GGB260_SGB362 | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Candidatus_Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccaceae_unclassified|s__Methanomassiliicoccaceae_archaeon_DOK | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Candidatus_Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccaceae_unclassified|s__Methanomassiliicoccaceae_unclassified_SGB380 | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Candidatus_Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccaceae|g__Methanomassiliicoccus|s__Candidatus_Methanomassiliicoccus_intestinalis | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Candidatus_Thermoplasmatota|c__Thermoplasmata|o__Methanomassiliicoccales|f__Methanomassiliicoccales_unclassified|g__Methanomassiliicoccales_unclassified|s__Methanomassiliicoccales_archaeon | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Crenarchaeota|c__Thermoprotei|o__Thermoproteales|f__Thermofilaceae|g__GGB1567|s__GGB1567_SGB2154 | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_arboriphilus | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii | 0 | 0 | 0 | 0 | 0 |
| k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanosphaera|s__Methanosphaera_stadtmanae | 0 | 0 | 0 | 0 | 0 |
| k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinobacteria_unclassified|f__Actinobacteria_unclassified|g__GGB39918|s__GGB39918_SGB47522 | 0 | 0 | 0 | 0 | 0 |
Output file
There are two file formats for the output.
- Microbial load: The first column represents the sample ID and the second column shows the predicted microbial load.
- Quantitative microbiome profile: The microbiome profile in which each value represents the absolute abundance of the species. The absolute abundance is calculated by multiplying the original relative abundance with the predicted microbial load of the sample.
| sample ID | predicted load |
|---|---|
| SAMN08049618 | 43,095,870,120 |
| SAMN08049619 | 136,144,114,276 |
| SAMN08049620 | 90,907,568,999 |
| SAMN08049621 | 62,170,429,824 |
| SAMN08049622 | 103,133,802,784 |
| SAMN08049623 | 39,008,294,213 |
| SAMN08049624 | 36,931,027,904 |
| SAMN08049625 | 77,549,297,071 |
| SAMN08049626 | 71,232,831,244 |
| SAMN08049627 | 33,308,813,736 |
| sample ID | -1 | Acetobacter sp. [ref_mOTU_v25_03587] | Acidaminococcus intestini [ref_mOTU_v25_01949] | Acinetobacter sp. [ref_mOTU_v25_02372] | Acinetobacter sp. [ref_mOTU_v25_03673] |
|---|---|---|---|---|---|
| SAMN08049618 | 1624507758.96551 | 0 | 0 | 0 | 0 |
| SAMN08049619 | 8776305795.94757 | 0 | 0 | 0 | 0 |
| SAMN08049620 | 3352456341.97509 | 0 | 0 | 0 | 0 |
| SAMN08049621 | 1054038896.4405 | 0 | 0 | 0 | 0 |
| SAMN08049622 | 4605108154.94715 | 0 | 17183239.3841312 | 17183239.3841312 | 0 |
| SAMN08049623 | 136615552.92761 | 0 | 0 | 0 | 0 |
| SAMN08049624 | 191038625.291764 | 0 | 2329739.33282639 | 0 | 0 |
| SAMN08049625 | 3042666677.1734 | 0 | 0 | 0 | 0 |
| SAMN08049626 | 1726065346.76828 | 0 | 0 | 0 | 0 |
| SAMN08049627 | 595525316.697626 | 0 | 6767333.1442912 | 0 | 548153984.687586 |