Experiment Overview
| Repository ID: | FR-FCM-ZYL3 | Experiment name: | MCFA production from corn silage: Flow cytometric characterization of the chain elongating microbiome dynamics | MIFlowCyt score: | 81.12% |
| Primary researcher: | Johannes Lambrecht | PI/manager: | Johannes Lambrecht | Uploaded by: | Johannes Lambrecht |
| Experiment dates: | 2015-10-01 - 2016-06-30 | Dataset uploaded: | Jun 2018 | Last updated: | Oct 2019 |
| Keywords: | [flow cytometry] [process monitoring ] [microbial community] [single cell analytics] [microbial chain elongation] [16S rRNA gene sequencing] [caproic acid] [caprylic acid] [MCFA] [anaerobic fermentation] | Manuscripts: | |||
| Organizations: |
Helmholtz Centre for Environmental Research GmbH - UFZ, Environmental microbiology, Leipzig, (Germany)
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| Purpose: | Flow cytometric characterization of the chain elongating microbiome dynamics | ||||
| Conclusion: | The production of MCFAs from complex, lactate-containing substrate without the addition of external electron donors is possible with high titers and yields. Caproate production was optimal at pH 5.5 and linked to lactate-based chain elongation, while the highest caprylate concentration was reached at pH 6.25 and connected to ethanol-based chain elongation. Lactate-producing organisms played a major role in supporting the MCFA production. The process was realised in a well-established reactor design, which will greatly ease scaling and profitable implementation of the process. Flow cytometric single cell analysis enabled fast analysis and evaluation of structure, function and dynamics of the MCFA-producing microbial community. | ||||
| Comments: | None | ||||
| Funding: | This work was funded by the Fachagentur Nachwachsende Rohstoffe e.V. (FNR) (Project Biogas-Fingerprint Nr. 22008313) on behalf of the German Federal Ministry of Food and Agriculture (BMEL), the Central Innovation Programme for SMEs (ZIM) of the Federal Ministry for Economic Affairs and Energy (BMWi) (Project INAR-ABOS, 16KN043222) and the Program-Oriented Funding of the Helmholtz Association (Program Renewable Energies, Topic Bioenergy). The funding agencies had neither influence on the design of the study, the collection, analysis and interpretation of the data nor the writing of the manuscript. | ||||
| Quality control: | Calibration of the cytometric set-up in the linear range was performed using 1 µm blue fluorescent (F 8815) and 2 µm yellow-green fluorescent FluoSpheres (F8827, Molecular Probes, ThermoFisher Scientific, Waltham, USA). The instrument was calibrated in the log range using blue fluorescent beads (0.5 μm and 1 μm, Fluoresbrite BB Carboxylate microspheres, 360 nm excitation-maximum, 407 nm emission maximum, PolyScience, Niles, USA), which were also added to each sample to ensure the measurement stability. Escherichia coli BL21 (DE3) was used as biological standard for control of every staining procedure (dot plots of beads and E. coli in Additional file 1 S9). | ||||
Experiment variables
| Timepoints | |
|---|---|
| · 1 | 4.25 day 001 20151007.fcs |
| · 3 | 4.25 day 003 20151009.fcs |
| · 6 | 4.25 day 006 20151012.fcs |
| · 8 | 4.25 day 008 20151014.fcs |
| · 13 | 4.25 day 013 20151019.fcs |
| · 15 | 4.25 day 015 20151021.fcs |
| · 17 | 4.25 day 017 20151023.fcs |
| · 20 | 4.25 day 020 20151026.fcs |
| · 22 | 4.25 day 022 20151028.fcs |
| · 24 | 4.25 day 024 20151030.fcs |
| · 27 | 4.25 day 027 20151102.fcs |
| · 29 | 4.25 day 029 20151104.fcs |
| · 31 | 4.25 day 031 20151106.fcs |
| · 34 | 4.25 day 034 20151109.fcs |
| · 36 | 4.25 day 036 20151111.fcs |
| · 38 | 4.25 day 038 20151113.fcs |
| · 41 | 4.25 day 041 20151116.fcs |
| · 45 | 4.25 day 045 20151120.fcs |
| · 48 | 4.25 day 048 20151123.fcs |
| · 50 | 4.25 day 050 20151125.fcs |
| · 52 | 4.25 day 052 20151127.fcs |
| · 55 | 4.25 day 055 20151130.fcs |
| · 57 | 4.25 day 057 20151202.fcs |
| · 62 | 4.25 day 062 20151207.fcs |
| · 64 | 4.25 day 064 20151209.fcs |
| · 66 | 4.25 day 066 20151211.fcs |
| · 69 | 4.25 day 069 20151214.fcs |
| · 71 | 4.25 day 071 20151216.fcs |
| · 73 | 4.25 day 073 20151218.fcs |
| · 76 | 4.25 day 076 20151221.fcs |
| · 83 | 4.25 day 083 20151228.fcs |
| · 90 | 4.25 day 090 20160104.fcs |
| · 92 | 4.25 day 092 20160106.fcs |
| · 94 | 4.25 day 094 20160108.fcs |
| · 97 | 4.25 day 097 20160111.fcs |
| · 99 | 4.25 day 099 20160113.fcs |
| · 101 | 4.25 day 101 20160115.fcs |
| · 104 | 4.25 day 104 20160118.fcs |
| · 106 | 4.25 day 106 20160120.fcs |
| · 108 | 4.25 day 108 20160122.fcs |
| · 111 | 4.25 day 111 20160125.fcs |
| · 115 | 4.25 day 115 20160129.fcs |
| · 118 | 4.25 day 118 20160201.fcs |
| · 120 | 4.25 day 120 20160203.fcs |
| · 122 | 4.25 day 122 20160205.fcs |
| · 125 | 4.25 day 125 20160208.fcs |
| · 127 | 4.25 day 127 20160210.fcs |
| · 129 | 4.25 day 129 20160212.fcs |
| · 132 | 4.25 day 132 20160215.fcs |
| · 134 | 4.25 day 134 20160217.fcs |
| · 136 | 4.25 day 136 20160219.fcs |
| · 139 | 4.25 day 139 20160222.fcs |
| · 141 | 4.25 day 141 20160224.fcs |
| · 146 | 4.25 day 146 20160229.fcs |
| · 148 | 4.25 day 148 20160302.fcs |
| · 150 | 4.25 day 150 20160304.fcs |
| · 153 | 4.25 day 153 20160307.fcs |
| · 155 | 4.25 day 155 20160309.fcs |
| · 157 | 4.25 day 157 20160311.fcs |
| · 160 | 4.25 day 160 20160314.fcs |
| · 162 | 4.25 day 162 20160316.fcs |
| · 164 | 4.25 day 164 20160318.fcs |
| · 167 | 4.25 day 167 20160321.fcs |
| · 169 | 4.25 day 169 20160323.fcs |
| · 175 | 4.25 day 175 20160329.fcs |
| · 181 | 4.25 day 181 20160404.fcs |
| · 183 | 4.25 day 183 20160406.fcs |
| · 185 | 4.25 day 185 20160408.fcs |
| · 188 | 4.25 day 188 20160411.fcs |
| · 190 | 4.25 day 190 20160413.fcs |
| · 195 | 4.25 day 195 20160418.fcs |
| · 197 | 4.25 day 197 20160420.fcs |
| · 199 | 4.25 day 199 20160422.fcs |
| · 202 | 4.25 day 202 20160425.fcs |
| · 204 | 4.25 day 204 20160427.fcs |
| · 206 | 4.25 day 206 20160429.fcs |
| · 209 | 4.25 day 209 20160502.fcs |
| · 211 | 4.25 day 211 20160504.fcs |
| · 216 | 4.25 day 216 20160509.fcs |
| · 218 | 4.25 day 218 20160511.fcs |
| · 220 | 4.25 day 220 20160513.fcs |
| · 225 | 4.25 day 225 20160518.fcs |
| · 227 | 4.25 day 227 20160520.fcs |
| · 230 | 4.25 day 230 20160523.fcs |
| · 232 | 4.25 day 232 20160525.fcs |
| · 234 | 4.25 day 234 20160527.fcs |
| · 237 | 4.25 day 237 20160530.fcs |
| · 239 | 4.25 day 239 20160601.fcs |
| · 241 | 4.25 day 241 20160603.fcs |
| Sample Type | |
|---|---|
| · Main timeline | 4.25 day 001 20151007.fcs · 4.25 day 003 20151009.fcs · 4.25 day 006 20151012.fcs · 4.25 day 008 20151014.fcs · 4.25 day 013 20151019.fcs · 4.25 day 015 20151021.fcs · 4.25 day 017 20151023.fcs · 4.25 day 020 20151026.fcs · 4.25 day 022 20151028.fcs · 4.25 day 024 20151030.fcs · 4.25 day 027 20151102.fcs · 4.25 day 029 20151104.fcs · 4.25 day 031 20151106.fcs · 4.25 day 034 20151109.fcs · 4.25 day 036 20151111.fcs · 4.25 day 038 20151113.fcs · 4.25 day 041 20151116.fcs · 4.25 day 045 20151120.fcs · 4.25 day 048 20151123.fcs · 4.25 day 050 20151125.fcs · 4.25 day 052 20151127.fcs · 4.25 day 055 20151130.fcs · 4.25 day 057 20151202.fcs · 4.25 day 062 20151207.fcs · 4.25 day 064 20151209.fcs · 4.25 day 066 20151211.fcs · 4.25 day 069 20151214.fcs · 4.25 day 071 20151216.fcs · 4.25 day 073 20151218.fcs · 4.25 day 076 20151221.fcs · 4.25 day 083 20151228.fcs · 4.25 day 090 20160104.fcs · 4.25 day 092 20160106.fcs · 4.25 day 094 20160108.fcs · 4.25 day 097 20160111.fcs · 4.25 day 099 20160113.fcs · 4.25 day 101 20160115.fcs · 4.25 day 104 20160118.fcs · 4.25 day 106 20160120.fcs · 4.25 day 108 20160122.fcs · 4.25 day 111 20160125.fcs · 4.25 day 115 20160129.fcs · 4.25 day 118 20160201.fcs · 4.25 day 120 20160203.fcs · 4.25 day 122 20160205.fcs · 4.25 day 125 20160208.fcs · 4.25 day 127 20160210.fcs · 4.25 day 129 20160212.fcs · 4.25 day 132 20160215.fcs · 4.25 day 134 20160217.fcs · 4.25 day 136 20160219.fcs · 4.25 day 139 20160222.fcs · 4.25 day 141 20160224.fcs · 4.25 day 146 20160229.fcs · 4.25 day 148 20160302.fcs · 4.25 day 150 20160304.fcs · 4.25 day 153 20160307.fcs · 4.25 day 155 20160309.fcs · 4.25 day 157 20160311.fcs · 4.25 day 160 20160314.fcs · 4.25 day 162 20160316.fcs · 4.25 day 164 20160318.fcs · 4.25 day 167 20160321.fcs · 4.25 day 169 20160323.fcs · 4.25 day 175 20160329.fcs · 4.25 day 181 20160404.fcs · 4.25 day 183 20160406.fcs · 4.25 day 185 20160408.fcs · 4.25 day 188 20160411.fcs · 4.25 day 190 20160413.fcs · 4.25 day 195 20160418.fcs · 4.25 day 197 20160420.fcs · 4.25 day 199 20160422.fcs · 4.25 day 202 20160425.fcs · 4.25 day 204 20160427.fcs · 4.25 day 206 20160429.fcs · 4.25 day 209 20160502.fcs · 4.25 day 211 20160504.fcs · 4.25 day 216 20160509.fcs · 4.25 day 218 20160511.fcs · 4.25 day 220 20160513.fcs · 4.25 day 225 20160518.fcs · 4.25 day 227 20160520.fcs · 4.25 day 230 20160523.fcs · 4.25 day 232 20160525.fcs · 4.25 day 234 20160527.fcs · 4.25 day 237 20160530.fcs · 4.25 day 239 20160601.fcs · 4.25 day 241 20160603.fcs |
