Antibiotics and microplastics are two major aquatic pollutants that have been associated to antibiotic resistance selection in the environment and are considered a risk to human health. However, ...little is known about the interaction of these pollutants at environmental concentrations and the response of the microbial communities in the plastisphere to sub-lethal antibiotic pollution. Here, we describe the bacterial dynamics underlying this response in surface water bacteria at the community, resistome and mobilome level using a combination of methods (next-generation sequencing and qPCR), sequencing targets (16S rRNA gene, pre-clinical and clinical class 1 integron cassettes and metagenomes), technologies (short and long read sequencing), and assembly approaches (non-assembled reads, genome assembly, bacteriophage and plasmid assembly).
Our results show a shift in the microbial community response to antibiotics in the plastisphere microbiome compared to surface water communities and describe the bacterial subpopulations that respond differently to antibiotic and microplastic pollution. The plastisphere showed an increased tolerance to antibiotics and selected different antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs). Several metagenome assembled genomes (MAGs) derived from the antibiotic-exposed plastisphere contained ARGs, virulence factors, and genes involved in plasmid conjugation. These include Comamonas, Chryseobacterium, the opportunistic pathogen Stenotrophomonas maltophilia, and other MAGs belonging to genera that have been associated to human infections, such as Achromobacter. The abundance of the integron-associated ciprofloxacin resistance gene aac(6')-Ib-cr increased under ciprofloxacin exposure in both freshwater microbial communities and in the plastisphere. Regarding the antibiotic mobilome, although no significant changes in ARG load in class 1 integrons and plasmids were observed in polluted samples, we identified three ARG-containing viral contigs that were integrated into MAGs as prophages.
This study illustrates how the selective nature of the plastisphere influences bacterial response to antibiotics at sub-lethal selective pressure. The microbial changes identified here help define the selective role of the plastisphere and its impact on the maintenance of environmental antibiotic resistance in combination with other anthropogenic pollutants. This research highlights the need to evaluate the impact of aquatic pollutants in environmental microbial communities using complex scenarios with combined stresses. Video Abstract.
•In vial addition of salt, limiting the presence of salts in the LC-MS/MS system.•A sample preparation reduced to a simple addition of salt in the vial.•Low matrix effect allowing external ...calibration with solvent standards.
Aminoglycosides are mostly used as veterinary antibiotics. In France, their consumption accounts for about 10% of all prescribed animal medicine. Due to their high polarity nature (log Kow < -3), they require chromatographic separation by hydrophilic interaction liquid chromatography or ion-pairing chromatography. This study presents the development of an ion pairing liquid chromatography with alkanesulfonates coupled to tandem mass spectrometry for the analysis of 10 aminoglycosides (spectinomycin, streptomycin, dihydrostreptomycin, kanamycin, apramycin, gentamicin, neomycin and sisomicin) in wastewater samples. The novelty of this method lies in the addition of the ion paring salt directly and only into the sample vial and not in the mobile phase, lowering the amount of salt added and consequently reducing signal inhibition. The optimized method was validated and showed satisfactory resolution, performances suitable with the analysis of aminoglycosides in wastewater samples, with limits of quantifications less than 10 ng/mL for most of the compounds, low matrix effects, high accuracy (85%-115% recoveries) and reproducibility (2%-12%RSD). It was then applied successfully to raw and treated wastewater samples.
The aim of this work was to study the extraction behavior of the main coffee antioxidants (caffeoylquinic acids, melanoidins and caffeine) and the antioxidant capacity, during brewing time in the ...most widely consumed coffee brew methods (filter and espresso) in coffee. Antioxidant capacity by colorimetric assays (Folin–Ciocalteau, ABTS and DPPH) and electron spin resonance spectroscopy techniques (Fremy's salt and TEMPO) were analyzed. In espresso coffee, more than 70% of the antioxidants (except dicaffeoylquinic acids, diCQA) of a coffee brew were extracted during the first 8s. In filter coffee, a U-shape antioxidants extraction profile was observed, starting later (after 75s) in Vietnam coffee than in Guatemala one, probably due to different wettability. Other technological parameters, such as turbulences and a longer contact time between water and ground coffee in filter coffeemaker, increased extraction efficiency, mainly in less polar antioxidant compounds as diCQA. In conclusion, these technological factors should be considered to optimize coffee antioxidants extraction that can be used as ingredients for functional foods.
► High water pressure increases antioxidants extraction speed in espresso coffee. ► Dicaffeoylquinic acids were released more slowly than the other antioxidants. ► U-shape antioxidants extraction profile was shown in filter coffee delayed in Robusta. ► Turbulences and longer contact time in filter coffeemaker favor extraction efficiency.
Antibiotics at sub-inhibitory concentrations are often found in the environment. Here they could impose selective pressure on bacteria, leading to the selection and dissemination of antibiotic ...resistance, despite being under the inhibitory threshold. The goal of this study was to evaluate the effects of sub-inhibitory concentrations of gentamicin on environmental class 1 integron cassettes in natural river microbial communities. Gentamicin at sub-inhibitory concentrations promoted the integration and selection of gentamicin resistance genes (GmRG) in class 1 integrons after only a one-day exposure. Therefore, sub-inhibitory concentrations of gentamicin induced integron rearrangements, increasing the mobilization potential of gentamicin resistance genes and potentially increasing their dissemination in the environment. This study demonstrates the effects of antibiotics at sub-inhibitory concentrations in the environment and supports concerns about antibiotics as emerging pollutants.
Heterocyclic volatile compounds present in coffee have been proposed as potent antioxidants, but their contribution to the antioxidant capacity of coffee is still unclear and controversial. The aim ...of this study was to assess the actual contribution of the main volatile compounds to the overall antioxidant capacity of coffee. A total of sixty-two and sixty-four volatile compounds were identified and quantified in Arabica and Robusta coffee, respectively, by static headspace-gas chromatography-mass spectrometry (SH-GC-MS). ABTS (2,2′-Azino-bi(3-ethylbenzo-thiazonile-6-sulfonic acid) diammonium salt) and DPPH (2,2-Diphenyl-1-picrylhydrazyl) antioxidant activity of the most abundant volatile heterocyclic compounds (7 furans (Fu), 3 pyrroles (Py) and 2 thiophenes (Th)), aldehydes (5) and diketones (2) was evaluated in model systems at different concentrations including those found in coffee. The model system with all the heterocyclic volatiles (Fu–Py–Th) was the most active followed by pyrroles and furans. Thiophenes were ineffective as radical scavengers at all concentrations including 100-fold, and aldehydes and ketones showed negligible activities in comparison to heterocyclic volatiles. In addition, only furans exhibited linear concentration dependent ABTS antioxidant activity and individual volatile model systems showed that only 2-methyl-tetrahydrofuran-3-one and pyrrole for ABTS, and also 1-methylpyrrole for DPPH, were the main volatile compounds responsible for the coffee antioxidant activity. However, the contribution of the heterocyclic volatile compounds to the overall antioxidant capacity of a filter coffee brew was almost insignificant, even at 100-fold concentrated Fu–Py–Th model system, accounting only for up to 3.3%.
•62 volatile compounds in Arabica coffee and 64 in Robusta are quantified (SH-GC-MS)•Furans, pyrroles and thiophenes model system is the most active in ABTS and DPPH•Thiophenes are ineffective radical scavengers up to 100-fold coffee concentration•Aldehydes and ketones show negligible antioxidant activity•Less than 3.3% antioxidant capacity of a filter coffee brew is due to volatiles
Winter tourism can generate environmental pollution and affect microbial ecology in mountain ecosystems. This could stimulate the development of antibiotic resistance in snow and its dissemination ...through the atmosphere and through snow melting. Despite these potential impacts, the effect of winter tourism on the snow antibiotic resistome remains to be elucidated. In this study, snow samples subjected to different levels of anthropogenic activities and surrounding forest were obtained from the Sudety Mountains in Poland to evaluate the impact of winter tourism on snow bacteria using a metagenomic approach. Bacterial community composition was determined by the sequencing of the V3-V4 hypervariable region of the 16S rRNA gene and the composition of the antibiotic resistome was explored by metagenomic sequencing. Whereas environmental factors were the main drivers of bacterial community and antibiotic resistome composition in snow, winter tourism affected resistome composition in sites with similar environmental conditions. Several antibiotic resistance genes (ARGs) showed a higher abundance in sites subjected to human activities. This is the first study to show that anthropogenic activities may influence the antibiotic resistome in alpine snow. Our results highlight the need to survey antibiotic resistance development in anthropogenically polluted sites.
Although Next-Generation Sequencing techniques have increased our access to the soil microbiome, each step of soil metagenomics presents inherent biases that prevent the accurate definition of the ...soil microbiome and its ecosystem function. In this study, we compared the effects of DNA extraction and sequencing depth on bacterial richness discovery from two soil samples. Four DNA extraction methods were used, and sequencing duplicates were generated for each DNA sample. The V3-V4 region of the 16S rRNA gene was sequenced to determine the taxonomical richness measured by each method at the amplicon sequence variant (ASV) level. Both the overall functional richness and antibiotic resistance gene (ARG) richness were evaluated by metagenomics sequencing. Despite variable DNA extraction methods, sequencing depth had a greater influence on bacterial richness discovery at both the taxonomical and functional levels. Sequencing duplicates from the same sample provided access to different portions of bacterial richness, and this was related to differences in the sequencing depth. Thus, the sequencing depth introduced biases in the comparison of DNA extraction methods. An optimisation of the soil metagenomics workflow is needed in order to sequence at a sufficient and equal depth. This would improve the accuracy of metagenomic comparisons and soil microbiome profiles.
: Dietary flavonoid intake is associated with a reduced risk of some cardiometabolic disorders, attributed in part to their claimed anti-inflammatory activity. Our aim was to investigate the ...potential association between specific urine flavonoid metabolites, liver enzymes, and inflammatory status in individuals with metabolic syndrome (MetS).
: In this cross-sectional study, clinical and dietary data from 267 participants, aged 55 to 75 years, participating in the PREDIMED Plus study (PREvención con DIeta MEDiterránea) were analyzed. At the baseline, spot urine samples were collected and seven urinary flavonoid metabolites were quantified using ultra-performance liquid chromatography coupled to triple quadrupole mass spectrometry (UPLC-Q-q-Q MS). Liver enzymes, inflammatory scores, and urinary flavonoid concentrations were inverse normally transformed.
: Adjusted linear regression models showed an inverse association between urinary citrus flavanone concentrations and gamma-glutamyl transferase (GGT) (all
-values <0.05). Naringenin 7'-GlcUA was significantly associated with a lower aggregate index of systemic inflammation (AISI) (
= -0.14; 95% CI: -0.27 to -0.02;
-value = 0.025) and systemic inflammation index (SII) (
= -0.14; 95% CI: -0.27 to -0.02;
-value = 0.028). To investigate the relationship between flavanone subclasses and GGT levels, we fitted a score of citrus-flavanones, and subjects were stratified into quartiles. The highest values of the citrus-flavanone score (per 1-SD increase) were associated with lower GGT levels (
= -0.41; 95% CI: -0.74 to -0.07), exhibiting a linear trend across quartiles (
-trend = 0.015).
: This cross-sectional study showed that higher urinary excretion of citrus-flavanone metabolites was associated with lower GGT levels in subjects diagnosed with MetS and obesity.
Antibiotics used in agriculture may reach the environment and stimulate the development and dissemination of antibiotic resistance in the soil microbiome. However, the scope of this phenomenon and ...the link to soil properties needs to be elucidated. This study compared the short-term effects of a range of gentamicin concentrations on the microbiome and resistome of bacterial enrichments and microcosms of an agricultural soil using a metagenomic approach. Gentamicin impact on bacterial biomass was roughly estimated by the number of 16SrRNA gene copies. In addition, the soil microbiome and resistome response to gentamicin pollution was evaluated by 16SrRNA gene and metagenomic sequencing, respectively. Finally, gentamicin bioavailability in soil was determined. While gentamicin pollution at the scale of µg/g strongly influenced the bacterial communities in soil enrichments, concentrations up to 1 mg/g were strongly adsorbed onto soil particles and did not cause significant changes in the microbiome and resistome of soil microcosms. This study demonstrates the differences between the response of bacterial communities to antibiotic pollution in enriched media and in their environmental matrix, and exposes the limitations of culture-based studies in antibiotic-resistance surveillance. Furthermore, establishing links between the effects of antibiotic pollution and soil properties is needed.
Abstract
Polar regions are increasingly exposed to ultraviolet light due to ozone depletion. Snowpacks contain photochemically active particles that, when irradiated, can lead to the production and ...accumulation of reactive species that can induce oxidative stress on snow microorganisms. This could generate a selective pressure on snowpack bacteria. In this study, snow microcosms were buried in a snowpack at Ny-Ålesund (Svalbard), either exposed to solar irradiation or incubated in the dark for 10 days, and the bacterial response to solar irradiation was evaluated in situ using a metagenomics approach. Solar irradiation induced a significant decrease in bacterial abundance and richness. Genes involved in glutathione synthesis, sulphur metabolism, and multidrug efflux were significantly enriched in the light, whereas genes related to cell wall assembly and nutrient uptake were more abundant in the dark. This is the first study demonstrating the response of snow bacterial communities to solar irradiation in situ and providing insights into the mechanisms involved. Our research shows that polar sun irradiation is sufficiently intense to impose a selective pressure on snow bacteria and supports the concern that increased ultraviolet exposure due to anthropogenic activities and climatic change could drive critical changes in the structure and functioning of snow bacterial communities.
Genes involved in the response to oxidative stress were significantly enriched in snow exposed to solar irradiation, whereas genes related to cell wall assembly and nutrient uptake were more abundant in the dark.
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