Volatolomics in Bacterial Ecotoxicology, A Novel Method for Detecting Signatures of Pesticide Exposure?

How to sample Listeria monocytogenes culture for volatolomics by headspace extraction-gas chromatography-Q Exactive-Orbitrap mass spectrometry?

Volatolomics - branch of metabolomics focused on volatile organic compounds (VOCs) - provides a wealth of information for characterizing foodborne pathogens and their behavior. But there is no knowledge relating on how to sample microbial VOCs. The aim of the present study was to determine the most informative sampling mode for further volatolomics. Taking Listeria monocytogenes (L.monocytogenes) as a model pathogen and using case-control experiments based on 0-24 h cultures on liquid synthetic growth medium, bacteria volatolomics was performed by headspace solid phase microextraction - gas chromatography - Q Exactive - Orbitrap ™ mass spectrometry on three types of samples: (i) the whole culture, which contains global information diluted by the growth medium, (ii) the pellet collected after centrifugation of the whole culture, which concentrates bacterial cells; and (iii) the related supernatant which includes what the bacteria released into the growth medium. Compound Discoverer ™ software was used for automatic peak deconvolution of VOCs. The three sampling modes resulted in different and complementary L.monocytogenes candidate VOC markers: whole culture and pellet together cover 83 % of the candidate markers, while supernatant and supernatant-pellet combination reveal only 59 % and 74 %, respectively. The robustness of the candidate VOC markers identified together with the relevance of combining the different sampling modes are discussed.

Microbial Ecotoxicology-40 Years on

Although ecotoxicology was emerging as a field through the 1970s, the incorporation of microbial indicators into the framework has been slower to evolve. The exploration of microbes as sensitive toxicity tests began in the late 70s and early 80s (with the emergence of Microtox® and other simple tests). However, the applications have been limited, beyond water and wastewater screening. This opinion piece reflects my own perspective on the field-from my early excitement in the 1990s for its possibilities, to a sense of frustration at the slow pace of new development and applications in the field-despite the surge of "omics" options. While microbiology still fails to lead the field of ecotoxicology, the potential remains.

Extreme smells-microbial production of volatile organic compounds at the limits of life

Microbial volatile organic compounds (MVOCs) are diverse molecules produced by microorganisms, ranging from mere waste byproducts to important signalling molecules. While the interest in MVOCs has been increasing steadily, there is a significant gap in our knowledge of MVOCs in extreme environments with e.g. extreme temperatures or acidity. Microorganisms in these conditions are subjected to additional stress compared to their counterparts in moderate environments and in many cases have evolved unique adaptations, including the production of specialized MVOCs. This review highlights the diversity of MVOCs identified in extreme environments or produced by isolated extremophiles. Furthermore, we explore potential applications already investigated and discuss broader implications for biotechnology, environmental biology, and astrobiology.

Gut Microbiota, Metabolome, and Body Composition Signatures of Response to Therapy in Patients with Advanced Melanoma

Despite the recent breakthroughs in targeted and immunotherapy for melanoma, the overall survival rate remains low. In recent years, considerable attention has been paid to the gut microbiota and other modifiable patient factors (e.g., diet and body composition), though their role in influencing therapeutic responses has yet to be defined. Here, we characterized a cohort of 31 patients with unresectable IIIC-IV-stage cutaneous melanoma prior to initiation of targeted or first-line immunotherapy via the following methods: (i) fecal microbiome and metabolome via 16S rRNA amplicon sequencing and gas chromatography/mass spectrometry, respectively, and (ii) anthropometry, body composition, nutritional status, physical activity, biochemical parameters, and immunoprofiling. According to our data, patients subsequently classified as responders were obese (i.e., with high body mass index and high levels of total, visceral, subcutaneous, and intramuscular adipose tissue), non-sarcopenic, and enriched in certain fecal taxa (e.g., Phascolarctobacterium) and metabolites (e.g., anethole), which were potentially endowed with immunostimulatory and oncoprotective activities. On the other hand, non-response was associated with increased proportions of Streptococcus, Actinomyces, Veillonella, Dorea, Fusobacterium, higher neutrophil levels (and a higher neutrophil-to-lymphocyte ratio), and higher fecal levels of butyric acid and its esters, which also correlated with decreased survival. This exploratory study provides an integrated list of potential early prognostic biomarkers that could improve the clinical management of patients with advanced melanoma, in particular by guiding the design of adjuvant therapeutic strategies to improve treatment response and support long-term health improvement.

A GABA Receptor Modulator and Semiochemical Compounds Evidenced Using Volatolomics as Candidate Markers of Chronic Exposure to Fipronil in Apis mellifera

Among the various "omics" approaches that can be used in toxicology, volatolomics is in full development. A volatolomic study was carried out on soil bacteria to validate the proof of concept, and this approach was implemented in a new model organism: the honeybee Apis mellifera. Emerging bees raised in the laboratory in pain-type cages were used. Volatolomics analysis was performed on cuticles, fat bodies, and adhering tissues (abdomens without the digestive tract), after 14 and 21 days of chronic exposure to 0.5 and 1 µg/L of fipronil, corresponding to sublethal doses. The VOCs analysis was processed using an HS-SPME/GC-MS method. A total of 281 features were extracted and tentatively identified. No significant effect of fipronil on the volatolome could be observed after 14 days of chronic exposure. Mainly after 21 days of exposure, a volatolome deviation appeared. The study of this deviation highlighted 11 VOCs whose signal abundances evolved during the experiment. Interestingly, the volatolomics approach revealed a VOC (2,6-dimethylcyclohexanol) that could act on GABA receptor activity (the fipronil target) and VOCs associated with semiochemical activities (pheromones, repellent agents, and compounds related to the Nasonov gland) leading to a potential impact on bee behavior.

Federating young researchers in microbial ecotoxicology: EcotoxicoMicYR 2021, the first international webinar organized for and by young microbial ecotoxicology researchers

The EcotoxicoMicYR group was initially composed of 4 Ph.D. students and 4 post-doctoral researchers. In brief, the EcotoxicoMicYR webinar took place three Monday afternoons in a row from November 22 to December 6, 2021. These three half-day webinars reached a success beyond our expectations with 25 countries and 41 presentations. Keynote lectures were delivered by Dr Fabio Roldan (Pontificia Universidad Javeriana, Colombia), Dr Belinda Ferrari (The University of New South Wales, Australia), and Dr Ahmed Tlili (Eawag, Switzerland). Their presentations provided an insight on latest research developments in the microbial ecotoxicology field and highlighted their specific contribution to this discipline. Twenty-two oral presentations and 16 pre-recorded presentations were diffused.

Significance of the presence of antibiotics on the microbial consortium in wastewater - The case of nitrofurantoin and furazolidone

Antibiotics in wastewater leads to migration of pollutants and disrupts natural processes of mineralization of organic matter. In order to understand the mechanism of this, research was undertaken on the influence of nitrofurantoin (NFT) and furazolidone (FZD), on the behaviour of a consortium of microorganisms present in a model wastewater in a bioreactor. Our study confirmed biodegradation of the antibiotics by the microbial consortium, with the degradation efficiency within 10 days of 65% for FZD, but only 20% for NFT. The kinetic study proved that the presence of analysed antibiotics had no adverse effect on the microbes, but the consortium behaviour differ significantly with the NFT reducing the consumption of organic carbon in wastewater and increasing the production of extracellular biopolymeric and volatile organic compounds, and the FZD reducing assimilation of other carbon sources to a less extent, at the expense of cellular focus on biodegradation of this antibiotic.

In vitro antidiabetic, antioxidant activities and GC-MS analysis of Rhynchostylis Retusa and Euphorbia Neriifolia leaf extracts

This study aimed to assess the antidiabetic, and antioxidant potential of Rhynchostylis retusa and Euphorbia neriifolia, well known for traditional ethnomedicinal uses in North-east India. Leaf extracts prepared in water, methanol and petroleum ether were evaluated for in vitro antidiabetic and antioxidant assay using α-amylase inhibition, glucose diffusion method and DPPH radical scavenging activity. The α-amylase inhibition with E. neriifolia methanolic extract at 400 μg/ml (66.67%) and R. retusa aqueous extract at 300 μg/ml (58.15%) were stronger than in equivalent concentrations of acarbose, i.e., 62.17, and 51.52%, respectively. Aqueous extract R. retusa showed a maximum 67.65% inhibition of glucose diffusion at 180 min in comparison to control without leaf extract. The DPPH radical scavenging activity of E. neriifolia extract in methanol was significantly better than equivalent aqueous or ether extract. However, the solvent choice had little impact on antioxidant activity in R. retusa. GC-MS analysis revealed the presence of a large number of phytochemicals in methanol fraction of E. neriifolia aqueous extracts in comparison to R. retusa. Though the in vitro α-amylase inhibition or glucose diffusion retardation implied potential medicinal use of endangered orchid R. retusa and E. neriifolia, further investigation may be warranted for identification of relevant bio-active compounds and in vivo validation of their pharmacological properties.

Multidisciplinary approach to determine the effect of polybrominated diphenyl ethers on gut microbiota

Environmental health is increasingly compromised by persistent toxic substances, which may have serious implications in food safety and, thus, in human health. Polybrominated diphenyl ethers (PBDEs) are anthropogenic contaminants with endocrine disruption abilities and are commonly found in seafood, the main route of human exposure. Growing evidence points out that the human gut microbiota interacts with xenobiotics, which may lead to impairment of host homeostasis if functions of microbiota become compromised. The aim of this study was to ascertain if the physiological balance of human gut microbiome is affected by the presence and degree of exposure to PBDEs. Fermentation was performed in a batch closed-system using an inoculum made from fresh human stool. The volatolomic profile was analysed by solid-phase microextraction coupled to gas chromatography-mass spectrometry. Mesophilic, Gram-negative bacteria and coliforms were quantified by classic plating methods. Changes in the gut microbiome were evaluated after DNA extraction followed by deep sequencing of the 16S rDNA region. The exposure to PBDEs resulted in an imbalance in sulfur, short-chain fatty acids and aromatic organic compounds, changing the microbial volatolome in a dose- and time-dependent manner. Slight deviations in the microbial structure of human gut occurred in the presence of PBDEs, especially for high doses of exposure. For the first time, the impact of PBDEs on the microbial homeostasis of human gut microbiota was taken into consideration, revealing noteworthy modifications with serious health implications even at oral exposure doses considered as safe by worldwide regulatory entities.