Microbial metatranscriptomic investigations across contaminant gradients of the Detroit River

Falk, Nicholas; Reid, Thomas; Skoyles, Adam; Grgicak‐Mannion, Alice; Drouillard, Ken G.; Weisener, Christopher G.

doi:10.1016/j.scitotenv.2019.06.451

Cited by 29 publications

(11 citation statements)

References 40 publications

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“…The metatranscriptomics represents valuable devices for all-inclusive cataloging microbial quality and transcript profiles and reflecting generally metabolic capacities [71]. Falk et al [72] uncovered that microbial genomic potential can be remade by metagenomic investigation of environmentally extracted DNA, metatranscriptomics can shed light on the deciphered items of DNA, giving riches of data on add up to flag-bearer RNA (mRNA) yield; an intermediary for quality expression. As microorganisms are coupled to numerous biogeochemical cycles within the environment, metatranscriptomic considers of anthropogenically affected dregs are profitable in numerous aspects; 1) understanding critical reactions of the biosphere to irritations, 2) evaluating in case and how microbial communities are working to direct the impacts of bequest defilement in oceanic frameworks, and 3) investigating microbial differing qualities as a work of humaninduced scene changes.…”

Section: Metatranscriptomicsmentioning

confidence: 99%

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

et al. 2020

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The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.

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Section: Metatranscriptomicsmentioning

confidence: 99%

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

et al. 2020

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“…In the analysis of base composition and quality, GC accounts for a higher proportion than AT, with GC accounting for more than 50%, and the proportion of base mass at each position Q20 increased after denoising. In addition, through the ribosome comparison, the percentages of the rRNA in the DB pig and the Landrace pig samples were 99.42 and 99.29%, respectively [43]. Compared with the reference genome, the percentages of mapped reads from DB pig and Landrace pig longissimus dorsi muscle samples were 90.83 and 93.06%, respectively.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing

Song

Zeng

et al. 2019

Bioscience Reports

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RNA-seq analysis was used to identify differentially expressed genes (DEGs) at the genetic level in the longissimus dorsi muscle from two pigs to investigate the genetic mechanisms underlying the difference in meat quality between Debao pigs and Landrace pigs. Then, these DEGs underwent functional annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein–protein interaction (PPI) analyses. Finally, the expression levels of specific DEGs were assessed using qRT-PCR. The reference genome showed gene dosage detection of all samples which showed that the total reference genome comprised 22342 coding genes, including 14743 known and 190 unknown genes. For detection of the Debao pig genome, we obtained 14168 genes, including 13994 known and 174 unknown genes. For detection of the Landrace pig genome, we obtained 14404 genes, including 14223 known and 181 unknown genes. GO analysis and KEGG signaling pathway analysis show that DEGs are significantly related to metabolic regulation, amino acid metabolism, muscular tissue, muscle structure development etc. We identified key genes in these processes, such as FOS, EGR2, and IL6, by PPI network analysis. qRT-PCR confirmed the differential expression of six selected DEGs in both pig breeds. In conclusion, the present study revealed key genes and related signaling pathways that influence the difference in pork quality between these breeds and could provide a theoretical basis for improving pork quality in future genetic thremmatology.

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“…Functional profiles derived from metagenomic and metatranscriptomic data were also shown to be useful in the context of aquatic ecosystem monitoring, both in freshwater (Thompson et al, ; Cheaib et al, ; Falk et al, ) and in marine environments (Kisand et al, ; Galand et al, ; Birrer et al, ). Predicted functional profiles from bacterial 16S dataset were also explored in the vicinity of offshore oil and gas platforms, showing consistent functional turnovers along the gradient of impact (Laroche et al, ).…”

Section: Discussionmentioning

confidence: 99%

Bacterial communities’ taxonomic and functional turnovers both accurately predict marine benthic ecological quality status

Cordier

2019

Environmental DNA

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The acquisition of biodiversity data is of prime importance to perform an efficient ecosystem management and ensure the sustainable provisioning of marine ecosystem services. Recent efforts are enforcing environmental genomic methodologies, especially environmental DNA (eDNA) metabarcoding, as a way forward to document biodiversity in a faster and cost‐effective way. Currently implemented biomonitoring regulations, such as the Marine Strategy Framework Directive (MSFD), rely on benthic macroinvertebrate indicator taxa to compute biotic indices (BIs) values and derive an ecological quality assessment. Recent work demonstrated that targeting those macroinvertebrates remains challenging, because of various technical and biological biases. Instead, bacterial communities’ profiles depicted by eDNA metabarcoding data have been shown to mirror macroinvertebrate communities’ variation and can be used to accurately predict the BI values using supervised machine learning (SML). Other studies showed that functional profiles, as obtained by metagenomic or metatranscriptomic approaches, vary along pollution gradient in aquatic ecosystems, demonstrating their potential as powerful indicators. Here, a 16S bacterial dataset collected in the vicinity of aquaculture sites, impacted by organic enrichment of the sea bottom, was used to generate two set of features consisting in either OTU profiles (taxonomic turnover) or predicted gene content using the tax4fun tool (functional turnover) that uses taxonomic annotations to infer functional capabilities based on evolutionary models. Both datasets were leading to accurate predictive models, with comparative performance. These results indicate that both taxonomic and functional turnovers of bacterial communities encompass powerful indicators that could be leveraged by marine biomonitoring programs.

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Microbial metatranscriptomic investigations across contaminant gradients of the Detroit River

Cited by 29 publications

References 40 publications

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing

Bacterial communities’ taxonomic and functional turnovers both accurately predict marine benthic ecological quality status

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