Anaerobes dominate the microbiota of the gastrointestinal (GI) tract, where a significant portion of small molecules can be degraded or modified. However, the enormous metabolic capacity of gut anaerobes remains largely elusive in contrast to aerobic bacteria, mainly due to the requirement of sophisticated laboratory settings. In this study, we employed an in silico machine learning platform, MoleculeX, to predict the metabolic capacity of a gut anaerobe, Clostridium sporogenes, against small molecules. Experiments revealed that among the top seven candidates predicted as unstable, six indeed exhibited instability in C. sporogenes culture. We further identified several metabolites resulting from the supplementation of everolimus in the bacterial culture for the first time. By utilizing bioinformatics and in vitro biochemical assays, we successfully identified an enzyme encoded in the genome of C. sporogenes responsible for everolimus transformation. Our framework thus can potentially facilitate future understanding of small molecules metabolism in the gut, further improve patient care through personalized medicine, and guide the development of new small molecule drugs and therapeutic approaches.

Nonstarter lactic acid bacteria (NSLAB) are major contributors to the unique characteristics (e.g., aroma, flavor, texture) of dairy and nondairy fermented products. Lc. paracasei SRX10 is an NSLAB strain originally isolated from a traditional Greek cheese and previously shown to exhibit favorable biotechnological characteristics. More specifically, the strain showed tolerance to simulated gastrointestinal conditions, exopolysaccharide (EPS) biosynthetic capacity, and lack of hemolytic activity and was used in the production of yoghurt and feta cheese with distinct organoleptic characteristics. The aim of the present study was to investigate these traits at the genome level through whole-genome sequencing (WGS), annotation, and comparative genomics. Functional annotation of the genome revealed that Lc. paracasei SRX10 can utilize different carbon sources, leading to the generation of flavor compounds, including lactic acid, acetate, ethanol, and acetoin. Similarly, full clusters for fatty acid biosynthesis, protein and peptide degradation, as well as genes related to survival under extreme temperatures, osmotic shock, and oxidative stress were annotated. Importantly, no transferable antibiotic resistance genes or virulence factors were identified. Finally, strain-specific primers based on genome-wide polymorphisms were designed for the efficient and rapid identification of Lc. paracasei SRX10 via multiplex PCR in fermented products.

In arable soils, anthropogenic activities such as fertilizer applications have intensified soil acidification in recent years. This has resulted in frequent environmental problems such as aluminum (Al) and H+ stress, which negatively impact crop yields and quality in acidic soils. Biochar, as a promising soil conditioner, has attracted much attention globally. The present study was conducted in a greenhouse by setting up 2% biochar rate to investigate how biochar relieves Al3+ hazards in acidic soil by affecting soil quality, soil environment, and soil microbiomes. The addition of biochar significantly improved soil fertility and enzyme activities, which were attributed to its ability to enhance the utilization of soil carbon sources by influencing the activity of soil microorganisms. Moreover, the Al3+ contents were significantly decreased by 66.61-88.83% compared to the C0 level (without biochar treatment). In particular, the results of the 27Al NMR suggested that forms of AlVI (Al(OH)2+, Al(OH)+ 2, and Al3+) were increased by 88.69-100.44% on the surface of biochar, reducing the Al3+ stress on soil health. The combination of biochar and nitrogen (N) fertilizer contributed to the augmentation of bacterial diversity. The application of biochar and N fertilizer increased the relative abundance of the majority of bacterial species. Additionally, the application of biochar and N fertilizer had a significant impact on soil microbial metabolism, specifically in the biosynthesis of secondary metabolites (lipids and organic acids) and carbon metabolic ability. In conclusion, biochar can enhance soil microbial activity and improve the overall health of acidic soil by driving microbial metabolism. This study offers both theoretical and technical guidance for enhancing biochar in acidified soil and promoting sustainable development in farmland production.

Lithium (Li) is now widely used in green energies/clean technologies; however, due to its inefficient recycling and treatment, it is an emerging contaminant in aquatic systems. Bivalves, such as clams, are considered good bioindicators of pollution, hence we evaluated the biochemical effects of Li in the clam Venerupis corrugata. Clams were exposed (14 days) to an increasing Li gradient (0, 200, 400, 800 µg/L). Bioconcentration capacity tended to decrease with increasing Li exposure possibly due to efforts to eliminate Li from the cells, to avert damage. No influences on the clams\' metabolic capacity and protein content were observed. Antioxidant and detoxification defences were activated, especially at 400 and 800 µg/L of Li, avoiding lipid damage, while protein injuries were observed at higher concentrations. Furthermore, a loss of redox balance was observed. This study highlights the importance of preventing and regulating Li discharges into the environment, avoiding adverse consequences to aquatic ecosystems.

The family Halieaceae (OM60/NOR5 clade) is a gammaproteobacterial group abundant and cosmopolitan in coastal seawaters and plays an important role in response to phytoplankton blooms. However, the ecophysiology of this family remains understudied because of the vast gap between phylogenetic diversity and cultured representatives. Here, using six pure cultured strains isolated from coastal seawaters, we performed in-depth genomic analyses to provide an overview of the phylogeny and metabolic capabilities of this family. The combined analyses of 16S rRNA genes, genome sequences, and functional genes relevant to taxonomy demonstrated that each strain represents a novel species. Notably, two strains belonged to the hitherto-uncultured NOR5-4 and NOR5-12 subclades. Metabolic reconstructions revealed that the six strains likely have aerobic chemo- or photoheterotrophic lifestyles; five of them possess genes for proteorhodopsin or aerobic anoxygenic phototrophy. The presence of blue- or green-tuned proteorhodopsin in Halieaceae suggested their ability to adapt to light conditions varying with depth or coastal-to-open ocean transition. In addition to the genes of anaplerotic CO2 fixation, genes encoding a complete reductive glycine pathway for CO2 fixation were found in three strains. Putative polysaccharide utilization loci were detected in three strains, suggesting the association with phytoplankton blooms. Read mapping of various metagenomes and metatranscriptomes showed that the six strains are widely distributed and transcriptionally active in marine environments. Overall, the six strains genomically characterized in this study expand the phylogenetic and metabolic diversity of Halieaceae and likely serve as a culture resource for investigating the ecophysiological features of this environmentally relevant bacterial group. IMPORTANCE Although the family Halieaceae (OM60/NOR5 clade) is an abundant and cosmopolitan clade widely found in coastal seas and involved in interactions with phytoplankton, a limited number of cultured isolates are available. In this study, we isolated six pure cultured Halieaceae strains from coastal seawaters and performed a comparative physiological and genomic analysis to give insights into the phylogeny and metabolic potential of this family. The cultured strains exhibited diverse metabolic potential by harboring genes for anaplerotic CO2 fixation, proteorhodopsin, and aerobic anoxygenic phototrophy. Polysaccharide utilization loci detected in some of these strains also indicated an association with phytoplankton blooms. The cultivation of novel strains of Halieaceae and their genomic characteristics largely expanded the phylogenetic and metabolic diversity, which is important for future ecophysiological studies.

Due to the public health concern of arsenic, environmental management measures in mining areas had been implemented. To assess the effect of environmental management measures in the mining area comprehensively, arsenic accumulation in the urine, hair, nails, and urinary metabolites of residents in a realgar mining area in Hunan province, China were investigated in 2019, and the changes in arsenic levels in the biomarkers during 2012-2019 were tracked. The importance of confounding factors (age, sex, occupation, residence, clinical history, vegetable source, cooking fuel, smoking, alcohol consumption, BMI) was analyzed using the Boruta algorithm. After the implementation of environmental management measures (including ceasing mining and smelting activities, building landfills, adjusting the planting structure, and soil restoration), urine, hair, and nail arsenic concentration decreased drastically but were still excessive. Arsenic accumulation was highest in older male miners who were long settled in the mining area and consumed homegrown vegetables. The only factor for changes in urinary arsenic levels was the cooking fuel type; residents using wood as cooking fuel experienced sustained arsenic exposure. Occupation and sex were important for determining arsenic changes in the hair and nails. Short-term arsenic accumulation in urine was affected by arsenic exposure, while long-term accumulation in hair and nails by arsenic metabolic capacity. The percentage of urinary arsenic metabolism and arsenic methylation indices of the participants in the mining area were within the normal range (%iAs: 10-30 %, %MMA: 10-20 %, % DMA: 60-80 %); samples indicated worse metabolic capacity than the reference population. The arsenic metabolic capacity of male miners was relatively weak, probably aggravated by alcohol drinking and smoking. Without soil remediation, arsenic exposure will continue. Homegrown vegetables and biomass fuels should be abandoned; reduced cigarette and alcohol consumption is recommended. Urinary arsenic would be more proper for assessing environmental remediation in mining areas.

Notothenioidei fishes have evolved under stable cold temperatures; however, ocean conditions are changing globally, with polar regions poised to experience the greatest changes in environmental factors, such as warming. These stressors have the potential to dramatically affect energetic demands, and the persistence of the notothenioids will be dependent on metabolic capacity, or the ability to match energy supply with energy demand, to restore homeostasis in the face of changing climate conditions. In this study we examined aerobic metabolic capacity in three species, Trematomus bernacchii, T. pennellii and T. newnesi, and between two life stages, juvenile and adult, by assessing mitochondrial function of permeabilized cardiac fibers. Respiratory capacity differed among the adult notothenioids in this study, with greater oxidative phosphorylation (OXPHOS) respiration in the pelagic T. newnesi than the benthic T. bernacchii and T. pennellii. The variation in mitochondrial respiratory capacity was likely driven by differences in the mitochondrial content, as measured by citrate synthase activity, which was the highest in T. newnesi. In addition to high OXPHOS, T. newnesi exhibited lower LEAK respiration, resulting in greater mitochondrial efficiency than either T. bernacchii or T. pennellii. Life stage largely had an effect on mitochondrial efficiency and excess complex IV capacity, but there were little differences in OXPHOS respiration and electron transfer capacity, pointing to a lack of significant differences in the metabolic capacity between juveniles and adults. Overall, these results demonstrate species-specific differences in cardiac metabolic capacity, which may influence the acclimation potential of notothenioid fishes to changing environmental conditions.

Larval zebrafish is emerging as a new model organism for studying drug-induced liver injury (DILI) with superiorities in visual assessment, genetic engineering as well as high throughput. Metabolic bioactivation to form reactive intermediates is a common event that triggers DILI. This study first addressed the correlation between acetaminophen metabolism and hepatotoxicity in zebrafish larvae (3-day postfertilization) and demonstrated the occurrence of cytochrome P450 enzymes-mediated acetaminophen (APAP) bioactivation at early developmental stage through characterizing the dose-effect (0-1.6 mg/ml) and the time course (0-72 h) of liver injury and metabolism in the AB strain and LiPan transgenic line Tg(lfabp10a: DsRed; elaA:egfp) expressing the liver-specific fluorescent protein. APAP caused multiorgan developmental retardation and elicited dose- and time-dependent hepatotoxicity. Liver imaging revealed significant changes earlier than histological and biochemical measurements. APAP bioactivation in larval zebrafish was first confirmed by the detection of the glutathione conjugate of the reactive intermediate NAPQI (NAPQI-GSH) and subsequent mercapturate derivatives NAPQI-cysteine and NAPQI-N-acetylcysteine after even short (0.5-h postexposure) or low (0.2 mg/ml) APAP exposure. APAP overdose impaired metabolic function, in particular sulfation, whereas facilitated GSH depletion and APAP sulfate excretion. Meanwhile, APAP displayed triphasic accumulation in the larvae, agreeing with fluctuating metabolic capabilities with sulfation dominating the early larval developmental stage. Most importantly, the dose-response effects and time course of APAP accumulation and metabolism agree well with those of the liver injury development. Overall, larval zebrafish has developed mammalian-like metabolic function, enabling it an ideal model organism for high-throughput screening hepatotoxicity and mechanistic study of bioactivation-based DILI.

Most of the electric and electronic waste is not recycled and the release of its components into the environment is expected, including the rare-earth element Lanthanum (La), which has already been reported in the aquatic systems. Furthermore, considering climate change factors such as the predicted increase in temperature, the susceptibility of aquatic organisms to these rare elements may be modified. In light of this, the present study aimed to evaluate the relevance of temperature on La-derived effects in the mussel Mytilus galloprovincialis. Several biomarkers and La bioaccumulation were assessed in organisms exposed to 0 (control) and 10 μg/L of La at two distinct temperatures (17 and 22 °C) for 28 days. Results showed that temperature did not influence La bioaccumulation in mussels. However, exposure to La resulted in a decreased metabolic capacity and an enhancement of biotransformation enzymes activity, as a possible defense behavior of mussels to avoid La accumulation and toxicity. Nevertheless, antioxidant defenses were also inhibited leading to increased lipid peroxidation (LPO) levels. Warming alone seemed to cause a metabolic shutdown seen as reduced enzyme activities and protein carbonylation (PC) levels. Simultaneous La exposure and temperature rise caused combined effects on mussels, as they accused metabolic depression, biotransformation defenses activation, antioxidant capacity reduction, and higher cellular damage. Overall, this study highlights the need to perform environmental risk assessment studies, by considering emerging contaminants exposures at relevant concentrations, both at present and forecasted climate change scenarios.

Hadal zones are marine environments deeper than 6,000 m, most of which comprise oceanic trenches. Microbes thriving at such depth experience high hydrostatic pressure and low temperature. The genomic potentials of these microbes to such extreme environments are largely unknown. Here, we compare five complete genomes of bacterial strains belonging to Labrenzia aggregata (Alphaproteobacteria), including four from the Mariana Trench at depths up to 9,600 m and one reference from surface seawater of the East China Sea, to uncover the genomic potentials of this species. Genomic investigation suggests all the five strains of L. aggregata as participants in nitrogen and sulfur cycles, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), thiosulfate oxidation, and dimethylsulfoniopropionate (DMSP) biosynthesis and degradation. Further comparisons show that, among the five strains, 85% gene functions are similar with 96.7% of them encoded on the chromosomes, whereas the numbers of functional specific genes related to osmoregulation, antibiotic resistance, viral infection, and secondary metabolite biosynthesis are majorly contributed by the differential plasmids. A following analysis suggests the plasmidic gene numbers increase along with isolation depth and most plasmids are dissimilar among the five strains. These findings provide a better understanding of genomic potentials in the same species throughout a deep-sea water column and address the importance of externally originated plasmidic genes putatively shaped by deep-sea environment.