Session Type: ePosters
Session Title: ePosters
Authors(s): D. Salamon (1), A. Krawczyk (1), B. Zapala (2), A. Sroka-Oleksiak (1), A. Potasiewicz (3), A. Nikiforuk (3), T. Gosiewski (1)
Authors Affiliations(s): (1) Jagiellonian University Medical College, Faculty of Medicine, Chair of Microbiology, Department of Molecular Medical Microbiology, Poland, (2) Jagiellonian University Medical College, Faculty of Medicine, Department of Clinical Biochemistry, Poland, (3) Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Behavioural Neuroscience and Drug Development, Poland
Background:
Amplicon-based next-generation sequencing of the 16S ribosomal RNA (rRNA) gene are a culture-free method used to identify and analyze bacteria present within a given sample.The prokaryotic 16S rRNA gene has conserved regions and also nine variable regions (V1-V9) which are frequently used for phylogenetic classification of genus or species in diverse microbial populations (metagenomics studies). Our aim was to compare the efiicacy of 16S rRNA sequencing performed on the two NGS platforms: MiSeq System and iSeq 100 System (Illumina).
Methods:The materials were 20 fecal samples taken from rats (schizophrenia model and control group), which are part of a project on gut microbiota in rat model of schizophrenia. From specimen bacterial DNA was isolated and 16S libraries were amplified by PCR. Metagenomic analysis was performed based on the protocol for preparing samples for sequencing the variable V3 and V4 regions of the 16S rRNA gene (the Illumina MiSeq System) on two platforms: MiSeq and iSeq.
Results:Sequencing of 20 fecal samples gave 1,601,646 and 2,245,756 reads at the phylum level (L2), 1,508,570 and 2,135,705 reads at the genus level (L6) and 1,129,624 and 1,107,853 on the species level (L7) for MiSeq and iSeq, respectively. At the L2 level, the abundance of taxa is comparable for both platforms. The difference in the number of taxa and the abundance of individual taxa at the L6 level is shown in Figure 1. The analysis of biodiversity shows statistically significant differences (p <0.05) between both platforms for beta diversity at L3-L7 levels and alpha diversity at levels: L2 expressed in ACE and Fisher, L6 Simpson and Fisher and L7 Chao1, ACE and Fisher indices. The Rarefaction Curve plot is showing that 16S rRNA sequencing performed on MiSeq have statistically higher (p=0.01) number of different species (operational taxonomic units - OTUs) with increasing number of sequences than observed on iSeq 100 System (Figure 2.).
Conclusions:
The iSeq 100 System may be used to evaluate the bacterial profile of the samples to create an overall picture. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition of the samples studied.
Keyword(s): next-generation sequencing, 16S rRNA gene, NGS platformsCOI Other: This study was supported by National Science Centre (Poland) within the framework of project grant no. 2019/03/X/NZ5/00953
Session Type: ePosters
Session Title: ePosters
Authors(s): D. Salamon (1), A. Krawczyk (1), B. Zapala (2), A. Sroka-Oleksiak (1), A. Potasiewicz (3), A. Nikiforuk (3), T. Gosiewski (1)
Authors Affiliations(s): (1) Jagiellonian University Medical College, Faculty of Medicine, Chair of Microbiology, Department of Molecular Medical Microbiology, Poland, (2) Jagiellonian University Medical College, Faculty of Medicine, Department of Clinical Biochemistry, Poland, (3) Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Behavioural Neuroscience and Drug Development, Poland
Background:
Amplicon-based next-generation sequencing of the 16S ribosomal RNA (rRNA) gene are a culture-free method used to identify and analyze bacteria present within a given sample.The prokaryotic 16S rRNA gene has conserved regions and also nine variable regions (V1-V9) which are frequently used for phylogenetic classification of genus or species in diverse microbial populations (metagenomics studies). Our aim was to compare the efiicacy of 16S rRNA sequencing performed on the two NGS platforms: MiSeq System and iSeq 100 System (Illumina).
Methods:The materials were 20 fecal samples taken from rats (schizophrenia model and control group), which are part of a project on gut microbiota in rat model of schizophrenia. From specimen bacterial DNA was isolated and 16S libraries were amplified by PCR. Metagenomic analysis was performed based on the protocol for preparing samples for sequencing the variable V3 and V4 regions of the 16S rRNA gene (the Illumina MiSeq System) on two platforms: MiSeq and iSeq.
Results:Sequencing of 20 fecal samples gave 1,601,646 and 2,245,756 reads at the phylum level (L2), 1,508,570 and 2,135,705 reads at the genus level (L6) and 1,129,624 and 1,107,853 on the species level (L7) for MiSeq and iSeq, respectively. At the L2 level, the abundance of taxa is comparable for both platforms. The difference in the number of taxa and the abundance of individual taxa at the L6 level is shown in Figure 1. The analysis of biodiversity shows statistically significant differences (p <0.05) between both platforms for beta diversity at L3-L7 levels and alpha diversity at levels: L2 expressed in ACE and Fisher, L6 Simpson and Fisher and L7 Chao1, ACE and Fisher indices. The Rarefaction Curve plot is showing that 16S rRNA sequencing performed on MiSeq have statistically higher (p=0.01) number of different species (operational taxonomic units - OTUs) with increasing number of sequences than observed on iSeq 100 System (Figure 2.).
Conclusions:
The iSeq 100 System may be used to evaluate the bacterial profile of the samples to create an overall picture. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition of the samples studied.
Keyword(s): next-generation sequencing, 16S rRNA gene, NGS platformsCOI Other: This study was supported by National Science Centre (Poland) within the framework of project grant no. 2019/03/X/NZ5/00953
Session Type: ePosters
Session Title: ePosters
Authors(s): D. Salamon (1), A. Krawczyk (1), B. Zapala (2), A. Sroka-Oleksiak (1), A. Potasiewicz (3), A. Nikiforuk (3), T. Gosiewski (1)
Authors Affiliations(s): (1) Jagiellonian University Medical College, Faculty of Medicine, Chair of Microbiology, Department of Molecular Medical Microbiology, Poland, (2) Jagiellonian University Medical College, Faculty of Medicine, Department of Clinical Biochemistry, Poland, (3) Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Behavioural Neuroscience and Drug Development, Poland
Background:
Amplicon-based next-generation sequencing of the 16S ribosomal RNA (rRNA) gene are a culture-free method used to identify and analyze bacteria present within a given sample.The prokaryotic 16S rRNA gene has conserved regions and also nine variable regions (V1-V9) which are frequently used for phylogenetic classification of genus or species in diverse microbial populations (metagenomics studies). Our aim was to compare the efiicacy of 16S rRNA sequencing performed on the two NGS platforms: MiSeq System and iSeq 100 System (Illumina).
Methods:The materials were 20 fecal samples taken from rats (schizophrenia model and control group), which are part of a project on gut microbiota in rat model of schizophrenia. From specimen bacterial DNA was isolated and 16S libraries were amplified by PCR. Metagenomic analysis was performed based on the protocol for preparing samples for sequencing the variable V3 and V4 regions of the 16S rRNA gene (the Illumina MiSeq System) on two platforms: MiSeq and iSeq.
Results:Sequencing of 20 fecal samples gave 1,601,646 and 2,245,756 reads at the phylum level (L2), 1,508,570 and 2,135,705 reads at the genus level (L6) and 1,129,624 and 1,107,853 on the species level (L7) for MiSeq and iSeq, respectively. At the L2 level, the abundance of taxa is comparable for both platforms. The difference in the number of taxa and the abundance of individual taxa at the L6 level is shown in Figure 1. The analysis of biodiversity shows statistically significant differences (p <0.05) between both platforms for beta diversity at L3-L7 levels and alpha diversity at levels: L2 expressed in ACE and Fisher, L6 Simpson and Fisher and L7 Chao1, ACE and Fisher indices. The Rarefaction Curve plot is showing that 16S rRNA sequencing performed on MiSeq have statistically higher (p=0.01) number of different species (operational taxonomic units - OTUs) with increasing number of sequences than observed on iSeq 100 System (Figure 2.).
Conclusions:
The iSeq 100 System may be used to evaluate the bacterial profile of the samples to create an overall picture. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition of the samples studied.
Keyword(s): next-generation sequencing, 16S rRNA gene, NGS platformsCOI Other: This study was supported by National Science Centre (Poland) within the framework of project grant no. 2019/03/X/NZ5/00953
Session Type: ePosters
Session Title: ePosters
Authors(s): D. Salamon (1), A. Krawczyk (1), B. Zapala (2), A. Sroka-Oleksiak (1), A. Potasiewicz (3), A. Nikiforuk (3), T. Gosiewski (1)
Authors Affiliations(s): (1) Jagiellonian University Medical College, Faculty of Medicine, Chair of Microbiology, Department of Molecular Medical Microbiology, Poland, (2) Jagiellonian University Medical College, Faculty of Medicine, Department of Clinical Biochemistry, Poland, (3) Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Behavioural Neuroscience and Drug Development, Poland
Background:
Amplicon-based next-generation sequencing of the 16S ribosomal RNA (rRNA) gene are a culture-free method used to identify and analyze bacteria present within a given sample.The prokaryotic 16S rRNA gene has conserved regions and also nine variable regions (V1-V9) which are frequently used for phylogenetic classification of genus or species in diverse microbial populations (metagenomics studies). Our aim was to compare the efiicacy of 16S rRNA sequencing performed on the two NGS platforms: MiSeq System and iSeq 100 System (Illumina).
Methods:The materials were 20 fecal samples taken from rats (schizophrenia model and control group), which are part of a project on gut microbiota in rat model of schizophrenia. From specimen bacterial DNA was isolated and 16S libraries were amplified by PCR. Metagenomic analysis was performed based on the protocol for preparing samples for sequencing the variable V3 and V4 regions of the 16S rRNA gene (the Illumina MiSeq System) on two platforms: MiSeq and iSeq.
Results:Sequencing of 20 fecal samples gave 1,601,646 and 2,245,756 reads at the phylum level (L2), 1,508,570 and 2,135,705 reads at the genus level (L6) and 1,129,624 and 1,107,853 on the species level (L7) for MiSeq and iSeq, respectively. At the L2 level, the abundance of taxa is comparable for both platforms. The difference in the number of taxa and the abundance of individual taxa at the L6 level is shown in Figure 1. The analysis of biodiversity shows statistically significant differences (p <0.05) between both platforms for beta diversity at L3-L7 levels and alpha diversity at levels: L2 expressed in ACE and Fisher, L6 Simpson and Fisher and L7 Chao1, ACE and Fisher indices. The Rarefaction Curve plot is showing that 16S rRNA sequencing performed on MiSeq have statistically higher (p=0.01) number of different species (operational taxonomic units - OTUs) with increasing number of sequences than observed on iSeq 100 System (Figure 2.).
Conclusions:
The iSeq 100 System may be used to evaluate the bacterial profile of the samples to create an overall picture. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition of the samples studied.
Keyword(s): next-generation sequencing, 16S rRNA gene, NGS platformsCOI Other: This study was supported by National Science Centre (Poland) within the framework of project grant no. 2019/03/X/NZ5/00953