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This page lists experimental SOPs from external sources. More community-shared protocols can be found on NFDI4Microbiota’s protocols.io workspace
The protocols from the International Human Microbiome Consortium IHMS and the Earth Microbiome Project EMP are well-established and experimentally validated for their given fields, human and earth microbiome research respectively.
Protocols from other sources, especially if provided by NFDI4Microbiota community members, have been successfully implemented and shared by individuals working in their given fields.
| Category | Title | Provider | Primary Source Link |
|---|---|---|---|
| DNA Extraction | Standard operating procedure for fecal samples DNA Extraction, protocol Q | International Human Microbiome Standards (IHMS) | SOP 06 |
| DNA Extraction | Standard operating procedure for fecal samples DNA Extraction, protocol H | International Human Microbiome Standards (IHMS) | SOP 07 |
| DNA Extraction | DNA Extraction Protocol | Earth Microbiome | DNA Extraction Protocol |
| DNA Extraction | DNA extraction: Shortened Godon protocol with optional enzymatic lysis | NFDI4Microbiota community member | CRC1832 Gut-liver-axis SOP |
| DNA Sequencing | 16S Illumina Amplicon Protocol | Earth Microbiome | 16S Illumina Amplicon Protocol |
| DNA Sequencing | 18S Illumina Amplicon Protocol | Earth Microbiome | 16S Illumina Amplicon Protocol |
| DNA Sequencing | ITS Illumina Amplicon Protocol | Earth Microbiome | ITS Illumina Amplicon Protocol |
| Lipid Extraction | Lipid and fatty acid extraction protocol from biological samples | NFDI4Microbiota community member | Bird et al (2011).Analytical Chemistry, 83(17), 6648–6657. |
| Medium Preparation | Media for freezing homogenised faecal samples for re-cultivation | NFDI4Microbiota community member | CRC1832 Gut-liver-axis SOP |
| Metabolite Extraction | Metabolite extraction from adherent mammalian cells | NFDI4Microbiota community member | Yuan et al. (2021). Nat Protoc 7, 872–881 (2012) |
| Metabolite Extraction | Metabolite extraction from plant tissue | NFDI4Microbiota community member | Novák et al. (2016). Current Protocols in Plant Biology, 1(2), 419–430. |
| Protein Purification | Proteomics TMT labelled SP3 method | NFDI4Microbiota community member | Protein purification. (2022). In EMBL. |
| Sample Collection | Standard operating procedure for fecal samples identification | International Human Microbiome Standards (IHMS) | SOP 01 |
| Sample Collection | Standard operating procedure for fecal samples self-Collection, laboratory analysis handled within 4 hours | International Human Microbiome Standards (IHMS) | SOP 02 |
| Sample Collection | Standard operating procedure for fecal samples self-Collection, laboratory analysis handled within 4 to 24 hours | International Human Microbiome Standards (IHMS) | SOP 03 |
| Sample Collection | Standard operating procedure for fecal samples frozen preserved self-Collection, laboratory analysis handled within 24 hours to 7 days | International Human Microbiome Standards (IHMS) | SOP 04 |
| Sample Collection | Standard operating procedure for fecal samples preserved in stabilizing solution self-Collection, laboratory analysis handled within 24 hours to 7 days | International Human Microbiome Standards (IHMS) | SOP 05 |
| Sample Processing | Biobank of human stool samples – sample processing | NFDI4Microbiota community member | CRC1832 Gut-liver-axis SOP |
| Sample Purification | Viral purification from bacterial culture | NFDI4Microbiota community member | protocols.io |