Ecotoxicological effects of erythromycin on a multispecies biofilm model, revealed by metagenomic and metabolomic approaches

Integrated omics analysis reveals the alteration of gut microbiota and fecal metabolites in Cervus elaphus kansuensis

The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host's dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer (Cervus elaphus kansuensis), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis. The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. KEY POINTS: • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer.

Short-term exposure to triclocarban alters microbial community composition and metabolite profiles in freshwater biofilms

Triclocarban (TCC), an emerging contaminant in water environments, its effects on freshwater biofilms remain insufficiently understood. This study investigates the effects of TCC exposure (at concentrations of 10 μg L-1 and 10 mg L-1) on mature freshwater biofilms. TCC was found to inhibit biofilm activity as evidenced by changes in surface morphology and the ratio of live/dead cells. Moreover, both concentrations of TCC were observed to modify the structure of the biofilm community. Metabolomics analysis revealed an overlap in the toxicity mechanisms and detoxification strategies triggered by various concentrations of TCC in biofilms. However, the higher toxicity induced by 10 mg L-1 TCC resulted from the downregulation of proline betaine, disrupting the homeostasis of cellular osmotic pressure regulation in biofilms. Notably, lipid and lipid-like molecules showed high sensitivity to different concentrations of TCC, indicating their potential as biomarkers for TCC exposure. Annotation of the differential metabolites by KEGG revealed that alterations in amino acid and carbon metabolism constituted the primary response mechanisms of biofilms to TCC. Moreover, the biofilm demonstrated enhanced nucleic acid metabolism, which bolstered resistance against TCC stress and heightened tolerance. Furthermore, elevated TCC concentrations prompted more robust detoxification processes for self-defense. Overall, short-term exposure to TCC induced acute toxicity in biofilms, yet they managed to regulate their community structure and metabolic levels to uphold oxidative homeostasis and activity. This research contributes to a deeper comprehension of TCC risk assessment and policy control in aquatic environments.

New sensitive tools to characterize meta-metabolome response to short- and long-term cobalt exposure in dynamic river biofilm communities

Untargeted metabolomics is a non-a priori analysis of biomolecules that characterizes the metabolome variations induced by short- and long-term exposures to stressors. Even if the metabolite annotation remains lacunar due to database gaps, the global metabolomic fingerprint allows for trend analyses of dose-response curves for hundreds of cellular metabolites. Analysis of dose/time-response curve trends (biphasic or monotonic) of untargeted metabolomic features would thus allow the use of all the chemical signals obtained in order to determine stress levels (defense or damage) in organisms. To develop this approach in a context of time-dependent microbial community changes, mature river biofilms were exposed for 1 month to four cobalt (Co) concentrations (from background concentration to 1 × 10-6 M) in an open system of artificial streams. The meta-metabolomic response of biofilms was compared against a multitude of biological parameters (including bioaccumulation, biomass, chlorophyll a content, composition and structure of prokaryotic and eukaryotic communities) monitored at set exposure times (from 1 h to 28 d). Cobalt exposure induced extremely rapid responses of the meta-metabolome, with time range inducing defense responses (TRIDeR) of around 10 s, and time range inducing damage responses (TRIDaR) of several hours. Even in biofilms whose structure had been altered by Co bioaccumulation (reduced biomass, chlorophyll a contents and changes in the composition and diversity of prokaryotic and eukaryotic communities), concentration range inducing defense responses (CRIDeR) with similar initiation thresholds (1.41 ± 0.77 × 10-10 M Co2+ added in the exposure medium) were set up at the meta-metabolome level at every time point. In contrast, the concentration range inducing damage responses (CRIDaR) initiation thresholds increased by 10 times in long-term Co exposed biofilms. The present study demonstrates that defense and damage responses of biofilm meta-metabolome exposed to Co are rapidly and sustainably impacted, even within tolerant and resistant microbial communities.

Meta-metabolomic responses of river biofilms to cobalt exposure and use of dose-response model trends as an indicator of effects

The response of the meta-metabolome is rarely used to characterize the effects of contaminants on a whole community. Here, the meta-metabolomic fingerprints of biofilms were examined after 1, 3 and 7 days of exposure to five concentrations of cobalt (from background concentration to 1 × 10-5 M) in aquatic microcosms. The untargeted metabolomic data were processed using the DRomics tool to build dose-response models and to calculate benchmark-doses. This approach made it possible to use 100% of the chemical signal instead of being limited to the very few annotated metabolites (7%). These benchmark-doses were further aggregated into an empirical cumulative density function. A trend analysis of the untargeted meta-metabolomic feature dose-response curves after 7 days of exposure suggested the presence of a concentration range inducing defense responses between 1.7 × 10-9 and 2.7 × 10-6 M, and of a concentration range inducing damage responses from 2.7 × 10-6 M and above. This distinction was in good agreement with changes in the other biological parameters studied (biomass and chlorophyll content). This study demonstrated that the molecular defense and damage responses can be related to contaminant concentrations and represents a promising approach for environmental risk assessment of metals.

A systematic analysis of residue and risk of cyantraniliprole in the water-sediment system: Does metabolism reduce its environmental risk?

As a representative variety of diamide insecticides, cyantraniliprole has broad application prospects. In this study, the fate and risk of cyantraniliprole and its main metabolite J9Z38 in a water-sediment system were investigated. The present result showed that more J9Z38 was adsorbed in the sediment at the end of exposure. However, the bioaccumulation capacity of cyantraniliprole in zebrafish was higher than that of J9Z38. Cyantraniliprole had stronger influence on the antioxidant system and detoxification system of zebrafish than J9Z38. Moreover, cyantraniliprole induced more significant oxidative stress effect and more differentially expressed genes (DEGs) in zebrafish. Cyantraniliprole had significantly influence on the expression of RyR-receptor-related genes, which was confirmed by resolving their binding modes with key receptor proteins using AlphaFold2 and molecular docking techniques. In the sediment, both cyantraniliprole and J9Z38 had inhibitory effects on microbial community structure diversity and metabolic function, especially cyantraniliprole. The methane metabolism pathway, mediated by methanogens such as Methanolinea, Methanoregula, and Methanosaeta, may be the main pathway of degradation of cyantraniliprole and J9Z38 in sediments. The present results demonstrated that metabolism can reduce the environmental risk of cyantraniliprole in water-sediment system to a certain extent.

Synergistic Effects of Baicalin and Levofloxacin Against Hypervirulent Klebsiella pneumoniae Biofilm In Vitro

Hypervirulent Klebsiella pneumoniae (hvKp) strains that form biofilms have recently emerged worldwide; however, the mechanisms underlying biofilm formation and disruption remain elusive. In this study, we established a hvKp biofilm model, investigated its in vitro formation pattern, and determined the mechanism of biofilm destruction by baicalin (BA) and levofloxacin (LEV). Our results revealed that hvKp exhibited a strong biofilm-forming ability, forming early and mature biofilms after 3 and 5 d, respectively. Early biofilm and bacterial burden were significantly reduced by BA + LEV and EM + LEV treatments, which destroyed the 3D structure of early biofilms. Conversely, these treatments were less effective against mature biofilm. The expression of both AcrA and wbbM was significantly downregulated in the BA + LEV group. These findings indicated that BA + LEV might inhibit the formation of hvKp biofilm by altering the expression of genes regulating efflux pumps and lipopolysaccharide biosynthesis.

Effect of erythromycin on epiphytic bacterial communities and water quality in wetlands

The occurrence of antibiotics such as erythromycin (ERY) under macrolide group, has long been acknowledged for negatively affecting ecosystems in freshwater environments. However, the effects of ERY on water quality and microbial communities in epiphytic biofilms are poorly understood. Here, Scanning Electron Microscopy (SEM), High-throughput sequencing, and physicochemical analytical methods were employed to unravel the impact of ERY on the water quality and bacterial morphology, biodiversity, composition, interaction, and ecological function in epiphytic biofilms attached to Vallisneria natans and artificial plants in mesocosmic wetlands. The study showed that ERY exposure significantly impaired the nutrient removal capacity (TN, TP, and COD) and altered the epiphytic bacterial morphology of V. natans and artificial plants. ERY did not affect the bacterial α-diversity. Notwithstanding ERY decreased the bacterial composition, but the relative abundance of Proteobacteria and Patescibacteria spiked by 62.2 % and 54 %, respectively, in V. natans, while Desulfobacteria and Chloroflexi increased by 8.9 % and 11.2 %, respectively, in artificial plants. Notably, ERY disturbed the food web structure and metabolic pathways such as carbohydrate metabolism, amino acid metabolism, energy metabolism, cofactor and vitamin metabolism, membrane transport, and signal transduction. This study revealed that ERY exposure disrupted the bacterial morphology, composition, interaction or food web structure, and metabolic functions in epiphytic biofilm. These data underlined that ERY negatively impacts epiphytic bacterial communities and nutrient removal in wetlands.

Metabonomic profiling of clubroot-susceptible and clubroot-resistant radish and the assessment of disease-resistant metabolites

Plasmodiophora brassicae causes a serious threat to cruciferous plants including radish (Raphanus sativus L.). Knowledge on the pathogenic regularity and molecular mechanism of P. brassicae and radish is limited, especially on the metabolism level. In the present study, clubroot-susceptible and clubroot-resistant cultivars were inoculated with P. brassicae Race 4, root hairs initial infection of resting spores (10⁷ CFU/mL) at 24 h post-inoculation and root galls symptom arising at cortex splitting stage were identified on both cultivars. Root samples of cortex splitting stage of two cultivars were collected and used for untargeted metabonomic analysis. We demonstrated changes in metabolite regulation and pathways during the cortex splitting stage of diseased roots between clubroot-susceptible and clubroot-resistant cultivars using untargeted metabonomic analysis. We identified a larger number of differentially regulated metabolites and heavier metabolite profile changes in the susceptible cultivar than in the resistant counterpart. The metabolites that were differentially regulated in both cultivars were mostly lipids and lipid-like molecules. Significantly regulated metabolites and pathways according to the P value and variable important in projection score were identified. Moreover, four compounds, including ethyl α-D-thioglucopyranoside, imipenem, ginsenoside Rg1, and 6-gingerol, were selected, and their anti-P. brassicae ability and effects on seedling growth were verified on the susceptible cultivar. Except for ethyl α-D-thioglucopyranoside, the remaining could inhibit clubroot development of varing degree. The use of 5 mg/L ginsenoside Rg1 + 5 mg/L 6-gingerol resulted in the lowest disease incidence and disease index among all treatments and enhanced seedling growth. The regulation of pathways or metabolites of carbapenem and ginsenoside was further explored. The results provide a preliminary understanding of the interaction between radish and P. brassicae at the metabolism level, as well as the development of measures for preventing clubroot.

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.

Integrated omics analysis reveals differences in gut microbiota and gut-host metabolite profiles between obese and lean chickens

Abdominal fat is the major adipose tissue in chickens. In chicken, the deposition of abdominal fat affects meat yield and quality. Previous reports suggest that gut microbiota composition and function are associated with lipid metabolism. In this study, we used comparative metagenomics and metabolomics analysis to determine the gut microbiota and gut-host metabolite profiles in Shouguang (SG; a Chinese chicken breed with low-fat deposition) and Luqin (LQ; a fatty-type chicken breed with a fast growth rate) chickens. The results showed that LQ chickens had higher body weight, eviscerated yield, abdominal fat yield, abdominal fat ratio, and triglyceride (TG) content in the breast muscle than SG chickens. Untargeted metabolomics analyses showed a total of 11 liver metabolites, 19 plasma metabolites, and 30 cecal metabolites differentially enriched in LQ and SG chickens based on variable importance in the projection (VIP) ≥ 1 and P ≤ 0.05. These metabolites are involved in lipid and amino acid metabolism. The relative abundance of bacteria in the microbiota differed significantly between the 2 chicken breeds. The functional prediction of microbiota abundant in LQ chickens was starch and lactose degradation. Erysipelatoclostridium was abundant in LQ chickens and significantly positively correlated to palmitoyl ethanolamide (PEA), a key regulator of lipid metabolism. Our findings revealed differences in liver and plasma metabolites between chicken breeds with different adipose deposition capacities. Long-chain acylcarnitines might be important markers of adipose deposition differences in chickens. The cecum's microbial communities and metabolome profiles significantly differed between LQ and SG chickens. However, the relationship between cecal microbiota and their metabolites and liver and plasma metabolites is not thoroughly understood. Future research will focus on relating tissue metabolite changes to intestinal microbiota and their effects on body fat deposition.