The multi-omics promise in context: from sequence to microbial isolate

Gutleben, Johanna; Mares, Maryam Chaib De; Elsas, Jan Dirk van; Smidt, Hauke; Overmann, Joerg; Sipkema, Detmer

doi:10.1080/1040841x.2017.1332003

Cited by 171 publications

(107 citation statements)

References 143 publications

(170 reference statements)

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“…In order to study adaptation at a community level a combination of several techniques is needed, as most environmental species are as yet uncultivable (Koskella & Vos, 2015). As such, a mix of cultivation dependent approaches and multi-omics analyses may well be a good option to predict and follow the activity and succession of the used inoculum (Gutleben et al, 2018). Cultivation-independent methods to monitor the microbial community dynamics (e.g., taxonomic or functional diversity) coupled to modeling techniques can lead to the discovery of common patterns associated with the biodegradation of a molecule (Head et al, 2006).…”

Section: Adaptation At the Community Levelmentioning

confidence: 99%

Implications of microbial adaptation for the assessment of environmental persistence of chemicals

Poursat

Spanning

Voogt

et al. 2019

Critical Reviews in Environmental Science and Technology

100

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Persistency of organic chemicals is a key property in their environmental risk assessment. Information on persistency is often derived from the results of biodegradability screening tests such as the ready biodegradability tests (RBTs). RBTs are, however, not designed for this purpose and suffer from several problems that lead to a high variability of the results and, hence, to difficulties in their interpretation. The origin and exposure history of the inocula used for biodegradability testing can lead to highly variable outcomes. Microbial adaptation to chemicals and its impact on biodegradation needs further investigation in order to have a better understanding of their effects on persistency assessments of chemicals. It is well described that microbial adaptation stimulates biodegradation of organic chemicals. Several mechanisms responsible for these phenomena have been described, amongst which are i) shifts in community composition or abundances, ii) mutations within populations, iii) horizontal gene transfer or iv) recombination events. These adaptation processes may well be mimicked under laboratory conditions, but the outcome remains difficult to predict as we lack a fundamental understanding of the adaptive responses. This review aims to bring together our current knowledge regarding microbial adaptation and its implication for the testing of biodegradation of chemicals. Abbreviations BHRBroad host range plasmid HGT

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Section: Adaptation At the Community Levelmentioning

confidence: 99%

Implications of microbial adaptation for the assessment of environmental persistence of chemicals

Poursat

Spanning

Voogt

et al. 2019

Critical Reviews in Environmental Science and Technology

100

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“…Furthermore, information obtained by HTS methods can help make better cultivation conditions and improve the capacity to isolate rare microorganisms present in air samples. This complementarity will give a better look at the complexity of aerosol samples using both methods (Gutleben et al 2018). Figure 1.…”

Section: Core Microbiome Of Bioaerosolsmentioning

confidence: 99%

On the interpretation of bioaerosol exposure measurements and impacts on health

Mbareche

Morawska

Duchaine

2019

Journal of the Air & Waste Management Association

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Bioaerosols are recognized as one of the main transmission routes for infectious diseases and are responsible for other various types of health effects through inhalation and potential ingestion. Associating exposure with bioaerosol and health problems is challenging, and adequate exposure monitoring is a top priority for aerosol scientists. The multiple factors affecting bioaerosol content, the variability in the focus of each bioaerosol exposure study, and the variations in experimental design and the standardization of methods make bioaerosol exposure studies very difficult. Therefore, the health impacts of bioaerosol exposure are still poorly understood. This paper presents a brief description of a state-of-the-art development in bioaerosol exposure studies supported by studies on several related subjects. The main objective of this paper is to propose new considerations for bioaerosol exposure guidelines and the development of tools and study designs to better interpret bioaerosol data. The principal observations and findings are the discrepancy of the applicable methods in bioaerosol studies that makes result comparison impossible. Furthermore, the silo mentality helps in creating a bigger gap in the knowledge accumulated about bioaerosol exposure. Innovative and original ideas are presented for aerosol scientists and health scientists to consider and discuss. Although many examples cited herein are from occupational exposure, the discussion has relevance to any human environment. This work gives concrete suggestions for how to design a full bioaerosol study that includes all of the key elements necessary to help understand the real impacts of bioaerosol exposure in the short term. The creation of the proposed bioaerosol public database could give crucial information to control the public health.Implications: How can we move toward a bioaerosol exposure guidelines? The creation of the bioaerosol public database will help accumulate information for long-term association studies and help determine specific exposure biomarkers to bioaerosols. The implementation of such work will lead to a deeper understanding and more efficient utilization of bioaerosol studies to prevent public health hazards. PAPER HISTORY

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“…RNAseq approaches facilitate primer free metatranscriptomics to reveal global gene expression profiles. It is now a widely used method in environmental microbiology and has allowed scientists to gain formidable insight into the genome-scale mechanisms used by microbes to adapt to changing environmental conditions (Shakya et al, 2013;Gutleben et al, 2018). However, it generally comes at high cost and requires extensive data analysis.…”

Section: Introductionmentioning

confidence: 99%

Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts

Cholet

Ijaz

Smith

2020

Preprint

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SummaryRT-Q-PCR, and RT-PCR amplicon sequencing, provide a convenient, target-specific, high-sensitivity approach for gene expression studies and are widely used in environmental microbiology. Yet, the effectiveness and reproducibility of the reverse transcription step has not been evaluated. Therefore, we tested a combination of four commercial reverse transcriptases with two priming techniques to faithfully transcribe 16S rRNA and amoA transcripts from marine sediments. Both enzyme and priming strategy greatly affected quantification of the exact same target with differences of up to 600-fold. Furthermore, the choice of RT system significantly changed the communities recovered. For 16S rRNA, both enzyme and priming had a significant effect with enzyme having a stronger impact than priming. Inversely, for amoA only the change in priming strategy resulted in significant differences between the same sample. Specifically, more OTUs and better coverage of amoA transcripts diversity were obtained with GS priming indicating this approach was better at recovering the diversity of amoA transcripts. Moreover, sequencing of RNA mock communities revealed that, even though transcript α diversities (i.e. OTU counts within a sample) can be biased by the RT, the comparison of β diversities (i.e. differences in OTU counts between samples) is reliable as those biases are reproducible between environments.Originality-Significance StatementIs the complementary DNA (cDNA) produced after Reverse Transcription (RT) a faithful representation of the starting RNA? This is a fundamental and important question for transcriptomic-based studies in environmental microbiology that aim to quantify and/or examine the diversity of transcripts via RT approaches. Yet little is known about the reliability and reproducibility of this step. Here, we evaluated the effect of the two main components of the RT reaction – the retro transcriptase enzyme and priming strategy (gene specific vs random priming), on the quantification and diversity of cDNA. We found that both have a significant impact. We further provide evidence to enable informed choices as to the enzyme and priming combinations to improve the performance of RT-PCR approaches. Taken together, this work will improve the reliability and reproducibility of transcript-based studies in environmental microbiology.

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The multi-omics promise in context: from sequence to microbial isolate

Cited by 171 publications

References 143 publications

Implications of microbial adaptation for the assessment of environmental persistence of chemicals

Implications of microbial adaptation for the assessment of environmental persistence of chemicals

On the interpretation of bioaerosol exposure measurements and impacts on health

Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts

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