Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Preparation
2.2. RNA Extraction and Sequencing
2.3. Sequence Data Analysis
3. Results and Discussion
3.1. Reads and de novo Transcriptome Assembly
3.2. Evaluation of the Different de novo Transcriptome Assemblies
3.3. Transcript Annotation
3.4. Differential Expression
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Assembly | Gene | Uniprot Entry/ Blast Accession # | Percent Identity | E-Value | Ontology | Name | Genus | log FC | log CPM | FDR | Regulation |
---|---|---|---|---|---|---|---|---|---|---|---|
Trinity | TRINITY_DN12211_c0_g1 | WP_082183191.1 | 100.00 | 2.0 × 10−08 | Energy production and conversion | FAD-binding oxidoreductase | Rhizobium | −9.871 | 5.431 | 0.003 | down |
TRINITY_DN12794_c0_g1 | WP_126090172.1 | 73.08 | 2.5 × 10−02 | Transcription | LysR family transcriptional regulator | none available | −9.988 | 5.545 | 0.003 | down | |
TRINITY_DN16017_c0_g1 | KIV68812.1 | 100.00 | 2.0 × 10−36 | Carbohydrate transport and metabolism | Sucrose−6-phosphate hydrolase | Rhizobium | −9.852 | 5.412 | 0.003 | down | |
TRINITY_DN16123_c0_g1 | IHFA_CHRVO | 41.54 | 1.3 × 10−10 | Transcription | Integration host factor subunit alpha | none available | −9.635 | 5.202 | 0.008 | down | |
TRINITY_DN19317_c0_g1 | GLO22_ECOLI | 51.90 | 4.3 × 10−15 | Inorganic ion transport and metabolism | Hydroxyacylglutathione hydrolase GloC | Rhizobium | −9.756 | 5.319 | 0.010 | down | |
TRINITY_DN6555_c0_g1 | WP_164056586.1 | 100.00 | 2.0 × 10−17 | Replication, recombination and repair | AAA family ATPase | Rhizobium | −9.705 | 5.270 | 0.005 | down | |
TRINITY_DN8425_c0_g1 | WP_142779495.1 | 100.00 | 1.0 × 10−18 | Cell cycle control, cell division, chromosome partitioning | ParA family protein | Rhizobium | −9.602 | 5.170 | 0.008 | down | |
TRINITY_DN12673_c0_g1 | WP_042878669.1 | 97.53 | 2.0 × 10−25 | Amino acid transport and metabolism, Carbohydrate transport and metabolism | DMT family transporter | Aeromonas | 9.611 | 5.184 | 0.008 | up | |
TRINITY_DN14275_c0_g1 | WP_174060752.1 | 100.00 | 5.0 × 10−23 | Amino acid transport and metabolism, Inorganic ion transport and metabolism | ABC transporter permease | Rhizobium | 9.590 | 5.163 | 0.010 | up | |
TRINITY_DN14310_c0_g1 | WP_124801776.1 | 100.00 | 6.0 × 10−11 | Inorganic ion transport and metabolism | cation:proton antiporter | Epilithonimonas | 9.577 | 5.150 | 0.008 | up | |
TRINITY_DN16876_c0_g1 | YDDG_ECOLI | 66.67 | 6.9 × 10−08 | Amino acid transport and metabolism, Carbohydrate transport and metabolism | Aromatic amino acid exporter YddG | Acinetobacter | 9.751 | 5.318 | 0.003 | up | |
TRINITY_DN16965_c0_g1 | STY97430.1 | 95.16 | 1.0 × 10−33 | Coenzyme transport and metabolism | Dihydroneopterin aldolase | Moraxella | 9.920 | 5.481 | 0.003 | up | |
TRINITY_DN19448_c0_g1 | WP_204155761.1 | 82.05 | 4.0 × 10−15 | Cell motility, Intracellular trafficking, secretion, and vesicular transport | prepilin-type N-terminal cleavage/methylation domain-containing protein | Moraxella | 9.832 | 5.396 | 0.003 | up | |
TRINITY_DN19763_c0_g1 | Y2604_PSEAE | 69.09 | 6.5 × 10−21 | Cell wall/membrane/envelope biogenesis | Uncharacterized protein PA2604 | Pseudomonas | 9.985 | 5.544 | 0.004 | up | |
TRINITY_DN24104_c0_g1 | PTSBC_SALTM | 79.22 | 7.3 × 10−33 | Carbohydrate transport and metabolism | PTS system sucrose-specific EIIBC component | Aeromonas | 10.140 | 5.695 | 0.005 | up | |
TRINITY_DN9443_c0_g1 | WP_074855682.1 | 100.00 | 4.0 × 10−18 | Inorganic ion transport and metabolism | ArsC family reductase | Pseudomonas | 9.803 | 5.368 | 0.003 | up | |
Spades | NODE_11013_length_508_cov_2.086614_g10506 | YOXD_BACSU | 46.39 | 1.7 × 10−35 | Function unknown | Uncharacterized oxidoreductase YoxD | Epilithonimonas | 9.511 | 5.043 | 0.000 | up |
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Jacksch, S.; König, C.; Kaiser, D.; Weide, M.; Ratering, S.; Schnell, S.; Egert, M. Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study. Microorganisms 2021, 9, 1591. https://doi.org/10.3390/microorganisms9081591
Jacksch S, König C, Kaiser D, Weide M, Ratering S, Schnell S, Egert M. Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study. Microorganisms. 2021; 9(8):1591. https://doi.org/10.3390/microorganisms9081591
Chicago/Turabian StyleJacksch, Susanne, Christoph König, Dominik Kaiser, Mirko Weide, Stefan Ratering, Sylvia Schnell, and Markus Egert. 2021. "Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study" Microorganisms 9, no. 8: 1591. https://doi.org/10.3390/microorganisms9081591