Characterization of microbial consortia adapted to degrade space organic waste
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1123629 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29780100_1.fastq.gz | Fastqsanger.gz | |||
| SRR29780100_2.fastq.gz | Fastqsanger.gz | |||
| SRR29780101_1.fastq.gz | Fastqsanger.gz | |||
| SRR29780101_2.fastq.gz | Fastqsanger.gz | |||
| SRR29780102_1.fastq.gz | Fastqsanger.gz |
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Project description:Synthetic microbial consortia represent a new frontier for synthetic biology given that they can solve more complex problems than monocultures. However, most attempts to co-cultivate these artificial communities fail because of the ‘‘winner-takes-all’’ in nutrients competition. In soil, multiple species can coexist with a spatial organization. Inspired by nature, here we show that an engineered spatial segregation method can assemble stable consortia with both flexibility and precision. We create microbial swarmbot consortia (MSBC) by encapsulating subpopulations with polymeric microcapsules. The crosslinked structure of microcapsules fences microbes, but allows the transport of small molecules and proteins. MSBC method enables the assembly of various synthetic communities and the precise control over the subpopulations. These capabilities can readily modulate the division of labor and communication. Our work integrates the synthetic biology and material science to offer new insights into consortia assembly and server as foundation to diverse applications from biomanufacturing to engineered photosynthesis.
2022-07-04 | PXD034417 | Pride
Project description:The consortia enriched from Chinese cabbage waste Raw sequence reads
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Project description:Two consortia (Consortium A and Consortium B) that can use 1,4-dioxane (a groundwater contaminant of emerging concern) as the sole carbon source were enriched from Rice University (Houston, TX, USA) campus soil. Phylogenetic analysis by 16S rRNA sequencing revealed the dominant genus in both of the consortia is Mycobacterium (56% in Consortium A and 49% in Consortium B). The predominance of Mycobacterium spp, in these consortia support the notion that this is an important and commonly encountered genus of dioxane degraders. Among other genera present that make at least 2% of these consortia, only Afipia encompasses a strain (i.e., Afipia sp. D1) that was reported to degrade dioxane as sole carbon and energy source. A nested PCR analysis using two degenerate primers to target the hydroxylase alpha subunit of groups 3 to 6 SDIMOs was performed to gain insights into which enzymes were responsible for dioxane degradation by these consortia. The purified products obtained from the second PCR run were sequenced and compared to genes databases (NCBI) encompassing all of the currently reported SDIMOs. The dominant SDIMO genes in Consortium A corresponded to a group-6 putative propane monooxygenase-like SDIMO (98.8%); while in Consortium B, SDIMO genes from both groups 5 (47.3%) and 6 (51.9%) were observed. In both consortia, the relative abundance of thmA/dxmA gene was negligible (0.03%), which is consistent with the negative amplification of these genes as verified in qPCR. Overall, the high relative abundance of group-6 putative propane monooxygenases in our two consortia suggests the novel finding that group 6-SDIMOs could also play an important role in dioxane degradation. This underscores the need for further research on genes and enzymes involved in dioxane biodegradation to develop novel biomarkers that can be useful for forensic analysis and performance assessment of bioremediation and natural attenuation at dioxane-impacted sites. DNA was extracted from bacteria biomass harvested in exponential growth phase, when half or more of the added dioxane (100 mg/L) was consumed. Total DNA extractions were performed using the UltraClean® Microbial DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) according to the manufacturer’s protocol. The V4 region of the 16S rRNA gene was amplified by PCR using the forward 515F and reverse 806R primers. Sequencing was performed at MR DNA (www.mrdnalab.com, Shallowater, TX, USA) by Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). Final OTUs were taxonomically classified using BLASTn against the RDPII (http://rdp.cme.msu.edu) and NCBI (www.ncbi.nlm.nih.gov) databases.Previously designed degenerate primers NVC57, NVC58, NVC65 and NVC66 to target conserved regions in the soluble di-iron monooxygenases (SDIMO) alpha subunit gene (groups 3 to 6) were used to examine the presence and diversity of SDIMO genes in these two consortia. A nested PCR strategy was used to increase the PCR product yield. In the first run, the PCR mixture contained 1 µL of NVC65 and NVC58 primer mixture (10 µM), 20 ng of the extracted genomic DNA, 12.5 µL of KAPA HiFi HotStart ReadyMix (2X) (KAPA Biosystems, Wilmington, MA, USA), and nuclease-free water to yield a total volume of 25 µL. PCR was performed in a Bio-Rad Thermal Cycler (Bio-Rad, Hercules, CA, USA) with the following temperature profile: initial denaturation (94°C, 5 min), then 29 amplification cycles (94°C for 30 s, 55°C for 30 s, 72°C for 1 min per kb) and a final extension (72°C for 5 min). The length of the PCR products in the first run was checked by 1% agarose gel and DNA bands of the correct size (1100 bp) were excised and purified. 20 ng of the purified PCR product was used as the DNA template in the second run, with the second set of primers (NVC57 and NVC66). The purified product (420 bp) from the second PCR was sent to MR DNA (www.mrdnalab.com, Shallowater, TX, USA) for Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). A database including all of the currently reported SDIMO genes on NCBI was created and used to taxonomically classify the final OTUs.
2018-05-01 | GSE97757 | GEO
Project description:Two consortia (Consortium A and Consortium B) that can use 1,4-dioxane (a groundwater contaminant of emerging concern) as the sole carbon source were enriched from Rice University (Houston, TX, USA) campus soil. Phylogenetic analysis by 16S rRNA sequencing revealed the dominant genus in both of the consortia is Mycobacterium (56% in Consortium A and 49% in Consortium B). The predominance of Mycobacterium spp, in these consortia support the notion that this is an important and commonly encountered genus of dioxane degraders. Among other genera present that make at least 2% of these consortia, only Afipia encompasses a strain (i.e., Afipia sp. D1) that was reported to degrade dioxane as sole carbon and energy source. A nested PCR analysis using two degenerate primers to target the hydroxylase alpha subunit of groups 3 to 6 SDIMOs was performed to gain insights into which enzymes were responsible for dioxane degradation by these consortia. The purified products obtained from the second PCR run were sequenced and compared to genes databases (NCBI) encompassing all of the currently reported SDIMOs. The dominant SDIMO genes in Consortium A corresponded to a group-6 putative propane monooxygenase-like SDIMO (98.8%); while in Consortium B, SDIMO genes from both groups 5 (47.3%) and 6 (51.9%) were observed. In both consortia, the relative abundance of thmA/dxmA gene was negligible (0.03%), which is consistent with the negative amplification of these genes as verified in qPCR. Overall, the high relative abundance of group-6 putative propane monooxygenases in our two consortia suggests the novel finding that group 6-SDIMOs could also play an important role in dioxane degradation. This underscores the need for further research on genes and enzymes involved in dioxane biodegradation to develop novel biomarkers that can be useful for forensic analysis and performance assessment of bioremediation and natural attenuation at dioxane-impacted sites. DNA was extracted from bacteria biomass harvested in exponential growth phase, when half or more of the added dioxane (100 mg/L) was consumed. Total DNA extractions were performed using the UltraClean® Microbial DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) according to the manufacturer’s protocol. The V4 region of the 16S rRNA gene was amplified by PCR using the forward 515F and reverse 806R primers. Sequencing was performed at MR DNA (www.mrdnalab.com, Shallowater, TX, USA) by Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). Final OTUs were taxonomically classified using BLASTn against the RDPII (http://rdp.cme.msu.edu) and NCBI (www.ncbi.nlm.nih.gov) databases.Previously designed degenerate primers NVC57, NVC58, NVC65 and NVC66 to target conserved regions in the soluble di-iron monooxygenases (SDIMO) alpha subunit gene (groups 3 to 6) were used to examine the presence and diversity of SDIMO genes in these two consortia. A nested PCR strategy was used to increase the PCR product yield. In the first run, the PCR mixture contained 1 µL of NVC65 and NVC58 primer mixture (10 µM), 20 ng of the extracted genomic DNA, 12.5 µL of KAPA HiFi HotStart ReadyMix (2X) (KAPA Biosystems, Wilmington, MA, USA), and nuclease-free water to yield a total volume of 25 µL. PCR was performed in a Bio-Rad Thermal Cycler (Bio-Rad, Hercules, CA, USA) with the following temperature profile: initial denaturation (94°C, 5 min), then 29 amplification cycles (94°C for 30 s, 55°C for 30 s, 72°C for 1 min per kb) and a final extension (72°C for 5 min). The length of the PCR products in the first run was checked by 1% agarose gel and DNA bands of the correct size (1100 bp) were excised and purified. 20 ng of the purified PCR product was used as the DNA template in the second run, with the second set of primers (NVC57 and NVC66). The purified product (420 bp) from the second PCR was sent to MR DNA (www.mrdnalab.com, Shallowater, TX, USA) for Illumina MiSeq paired-end sequencing (approximately 2×300 bp as the read length). Sequence data were processed using MR DNA analysis pipeline. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). A database including all of the currently reported SDIMO genes on NCBI was created and used to taxonomically classify the final OTUs.
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Project description:Probiotics have been suggested as one solution to counter detrimental health effects by SARS-CoV-2, however, data so far is scarce. We tested the effect of two probiotic consortia, OL-1 and OL-2, against SARS-CoV2 in ferrets and assessed their effect on cytokine production and transcriptome in a human monocyte- derived macrophage (Mf) and dendritic cell (DC) model. The results showed that the consortia significantly reduced the viral load, modulated immune response, and regulated viral receptor expression in ferrets compared to placebo. In human Mf and DC model, OL-1 and OL-2 induced cytokine production and genes and related to SARS-CoV-2 anti-viral immunity. The study results indicate that probiotic stimulation of the ferret immune system leads to improved anti-viral immunity against SARS-COV-2 and that critical genes and cytokines for anti-SARS-CoV-2 immunity are stimulated in human immune cells in vitro. The effect of the consortia against SARS-CoV-2 warrants further investigations in human clinical trials.
2022-04-01 | GSE180390 | GEO
Project description:Probiotics have been suggested as one solution to counter detrimental health effects by SARS-CoV-2, however, data so far is scarce. We tested the effect of two probiotic consortia, OL-1 and OL-2, against SARS-CoV2 in ferrets and assessed their effect on cytokine production and transcriptome in a human monocyte- derived macrophage (Mf) and dendritic cell (DC) model. The results showed that the consortia significantly reduced the viral load, modulated immune response, and regulated viral receptor expression in ferrets compared to placebo. In human Mf and DC model, OL-1 and OL-2 induced cytokine production and genes and related to SARS-CoV-2 anti-viral immunity. The study results indicate that probiotic stimulation of the ferret immune system leads to improved anti-viral immunity against SARS-COV-2 and that critical genes and cytokines for anti-SARS-CoV-2 immunity are stimulated in human immune cells in vitro. The effect of the consortia against SARS-CoV-2 warrants further investigations in human clinical trials.
2022-04-01 | GSE180389 | GEO
Project description:Organic UV filters are important ingredients in many personal care products, including sunscreens. Evaluating the biodegradability of organic UV filters is key to estimate their recalcitrance and environmental fate and thus central to their overall environmental risk assessment. In order to further understand the degradation process, the aim was to investigate whether specific consortia could degrade certain UV filters. Several bacterial strains were isolated from enrichment cultures actively degrading octocrylene (OC), butyl methoxydibenzoylmethane (BM), homosalate (HS), and 2-ethylhexyl salicylate (ES) and were utilized to construct an in-house consortium. This synthetic consortium contained 27 bacterial strains and degraded OC, BM, HS, and ES 60-80% after 12 days, but not benzophenone-3 (BP3), methoxyphenyl triazine (BEMT), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT), diethylhexyl butamido triazone (DBT), ethylhexyl triazone (EHT), or diethylamino hydroxybenzoyl hexyl benzoate (DHHB). Furthermore, several commercial microbial mixtures from Greencell were tested to assess their degradation activity toward the same organic UV filters. ES and HS were degraded by some of the commercial consortia, but to a lesser extent. The rest of the tested UV filters were not degraded by any of the commercial bacterial mixes. These results confirm that some organic UV filters are recalcitrant to biodegradation, while others are degraded by a specific set of microorganisms.
| S-EPMC10754744 | biostudies-literature
Project description:Anaerobic methane-oxidizing consortia metagenomes and metatranscriptomes
| PRJNA418316 | ENA