Absolute Abundance Research Articles

Absolute Membrane Protein Abundance of P-gp, BCRP and MRPs in Term Human Placenta Tissue and Commonly Used Cell Systems: Application in PBPK Modeling of Placental Drug Disposition.

The placenta acts as a barrier, excluding noxious substances whilst actively transferring nutrients to the fetus, mediated by various transporters. This study quantified the expression of key placental transporters in term human placenta (n=5) and BeWo, BeWo b30, and JEG-3 placenta cell lines. Combining these results with pregnancy physiologically-based pharmacokinetic (PBPK) modeling, we demonstrate the utility of proteomic analysis for predicting placental drug disposition and fetal exposure. Using targeted proteomics with QconCAT standards, we found significant expression of P-gp, BCRP, MRP2, MRP4, and MRP6 in the human placenta (0.05 - 0.25 pmol/mg membrane protein) with only regional differences observed for P-gp. Unexpectedly, both P-gp and BCRP were below the limit of quantification in the regularly used BeWo cells, indicating that this cell line may not be suitable for the study of placental P-gp and BCRP-mediated transport. In cellular and vesicular overexpression systems, P-gp and BCRP were detectable as expected. Vesicle batches showed consistent P-gp expression correlating with functional activity (N-methyl-quinidine (NMQ) transport). However, BCRP activity (Estrone 3-sulfate (E1S) transport) did not consistently align with expression levels. Incorporating in vitro transporter kinetic data, along with placental transporter abundance, into a PBPK model enabled the evaluation of fetal exposure. Simulation with a hypothetical drug indicated that estimating fetal exposure relies on the intrinsic clearances of relevant transporters. To minimize interlaboratory discrepancies, expression data was generated using consistent proteomic methodologies in the same lab. Integration of this data in pregnancy-PBPK modeling offers a promising tool to investigate maternal, placental and fetal drug exposure. Significance Statement This study quantified the expression of key transporters in human placenta and various placental cell lines, revealing significant expression variations. By integrating these data with PBPK modeling, the study highlights the importance of transporter abundance data in understanding and predicting placental drug disposition.

Multi-omics reveals the molecular mechanisms of rapid growth in distant hybrid fish

Distant hybridization usually results in heterosis. In previous studies, we obtained an improved fish (WR-II, 2n = 100) with rapid growth through distant hybridization. To investigate the molecular mechanisms underlying the rapid growth of WR-II, the intestinal structure, microbiome and metabolome of the gut and the transcriptome of muscle were compared between WR-II and its parents (WCC and RCC, 2n = 100). The results revealed that WR-II had more intestinal folds, and the height, width and goblet cell density of the intestinal folds were greater than those of its parents. The absolute abundances of the probiotics Ralstonia and Salinivibrio were significantly greater in WR-II than in the parents (p < 0.05), and the probiotic Cupriavidus was found in only WR-II. A total of 481 and 718 differentially abundant metabolites (DMs) were identified in WR-II vs. WCC and WR-II vs. RCC, respectively. These DMs were enriched mainly in pathways related to metabolism, protein synthesis and development, such as fumaric acid, sphingosine, betaine and 5′-adenylic acid (AMP). A total of 5680 and 11,795 differentially expressed genes (DEGs) were identified in WR-II vs. WCC and WR-II vs. RCC, respectively. These DEGs were enriched mainly in pathways related to protein synthesis and substance metabolism. Growth-related genes such as irs1, irs2, foxo1, igf1r, and akt were upregulated in WR-II. Multi-omics analysis revealed that Salinivibrio can promote the level of AMP, which then regulates the expression of irs1 and foxo1, thus promoting the growth of WR-II. This study revealed the mechanism of rapid growth of WR-II from the probiotics, metabolites and genes, which provides evidence for the molecular mechanism of heterosis.

Mitochondrial Abundance and Function Differ Across Muscle Within Species.

Background: Mitochondria are considered the powerhouse of cells, and skeletal muscle cells are no exception. However, information regarding muscle mitochondria from different species is limited. Methods: Different muscles from cattle, pigs and chickens were analyzed for mitochondrial DNA (mtDNA), protein and oxygen consumption. Results: Bovine oxidative muscle mitochondria contain greater mtDNA (p < 0.05), protein (succinate dehydrogenase, SDHA, p < 0.01; citrate synthase, CS, p < 0.01; complex I, CI, p < 0.05), and oxygen consumption (p < 0.01) than their glycolytic counterpart. Likewise, porcine oxidative muscle contains greater mtDNA (p < 0.01), mitochondrial proteins (SDHA, p < 0.05; CS, p < 0.001; CI, p < 0.01) and oxidative phosphorylation capacity (OXPHOS, p < 0.05) in comparison to glycolytic muscle. However, avian oxidative skeletal muscle showed no differences in absolute mtDNA, SDHA, CI, complex II, lactate dehydrogenase, or glyceraldehyde 3 phosphate dehydrogenase compared to their glycolytic counterpart. Even so, avian mitochondria isolated from oxidative muscles had greater OXPHOS capacity (p < 0.05) than glycolytic muscle. Conclusions: These data show avian mitochondria function is independent of absolute mtDNA content and protein abundance, and argue that multiple levels of inquiry are warranted to determine the wholistic role of mitochondria in skeletal muscle.

Deciphering the Cape Gooseberry Fruits Mycobiome for Further Safety Improvement Postharvest.

Cape gooseberries are exquisitely flavored fruits; their rapid deterioration reduces their shelf life. Understanding the unique mycobiome of fruit peels is an essential step in identifying the taxa causing postharvest loss. The current study proposes to analyze the fungal communities of cape gooseberry peels collected from an organic orchard at unripe and ripe stages and purchased from open-air market sites, using the ITS2 region metabarcoding. According to the Kruskal-Wallis test, there were no statistically significant differences found in either the phylogenetic or non-phylogenetic alpha diversity indices. Significant differences in fungal communities were observed between the market and orchard groups based on beta diversity results. Ascomycota (85.72-96.76%), Basidiomycota (3.21-13.91%), and Chytridiomycota (0.07-9.35%) were the most common fungal phyla, their abundance varying with the ripening stage and origin. Dothideomycetes in the orchard group and Saccharomycetes in the market group were the two most prevalent classes. Furthermore, we investigate which taxa showed a significant difference in abundance between the two conditions (market vs. orchard) using the analysis of compositions of microbiomes with bias correction (ANCOM-BC) test. Regardless of the phase, the orchard samples exhibited a notable increase in the mean absolute abundance of various beneficial fungal taxa, including Tilletiopsis washingtonensis and Articulospora proliferata, whereas the market samples demonstrated a high abundance of harmful yeasts and molds such as Meyerozyma guilliermondii, Candida railenensis, and Botrytis caroliniana. Although it is unclear how these microorganisms augment at the market sites and might impact the fruit quality after harvest, from a fruit safety perspective, it is essential to comprehend the diversity and variation of the mycobiome composition at different ripening stages to further develop strategies to improve food safety postharvest.

Assessing the feasibility of adjusting the dry matter content utilizing corn grits and cottonseed meal and inoculating with Lactiplantibacillus plantarum in the production of fermented feed from kitchen waste

The feasibility of converting kitchen waste into fermented feed was investigated by adjusting the dry matter (DM) content through addition of corn grits or cottonseed meal, in conjunction with inoculation of lactic acid bacteria (LAB). The LAB-inoculated (LP) group exhibited acidic aroma and excellent sensory quality, producing significantly lower ammoniacal nitrogen throughout the fermentation process (p < 0.05). On day 3, pH value of the LP group dropped below 4.2 and the lactic acid concentration reached 50 g/kg DM. On day 9, Lactobacillus was the dominant genus in the fermented feed of the LP group, reducing the risk of undesirable fermentation. On day 60, the absolute abundance of bacteria in the LP group was low, and the feed hygiene indices met the national standard. LAB inoculation to produce fermented feed achieved stability on day 3, and remained stable for at least 60 days without spoilage.

Measurement of absolute abundance of crystallins in human and αA N101D transgenic mouse lenses using 15N-labeled crystallin standards

Stable isotope labeled standards of all major human lens crystallins were created to measure the abundance of lens endogenous crystallins from birth to adulthood. All major human crystallins (αA, αB, βA2, βA3/A1, βA4, βB1, βB2, βB3, γA, γB, γC, γD, γS) were cloned with N-terminal 6 x His tagged SUMO for ease of purification and the ability to generate natural N-termini by SUMO protease cleavage when producing crystallins for structure/function studies. They were then expressed in 15N-enriched media, quantified by mass spectrometry, and mixed in proportions found in young human lens to act as an artificial lens standard. The absolute quantification method was tested using soluble protein from 5-day, 23-day, 18-month, and 18-year-old human lenses spiked with the 15N artificial lens standard. Proteins were trypsinized, relative ratios of light and heavy labeled peptides determined using high-resolution precursor and data independent MS2 scans, and data analysis performed using Skyline software. Crystallin abundances were measured in both human donor lenses and in transgenic mouse αA N101D cataract lenses. Technical replicates of human crystallin abundance measurements were performed with average coefficients of variation of approximately 2% across all 13 crystallins. αA crystallin comprised 27% of the soluble protein of 5-day-old lens and decreased to 16% by 18-years of age. Over this time period αB increased from 6% to 9% and the αA/αB ratio decreased from 4.5/1 to 2/1. γS-crystallin also increased nearly 2-fold from 7% to 12%, becoming the 3rd most abundant protein in adult lens, while βB1 increased from 14% to 20%, becoming the most abundant crystallin of adult lens. Minor crystallins βA2, βB3, and γA comprised only about 1% each of the newborn lens soluble protein, and their abundance dropped precipitously by adulthood. While 9 of the SUMO tagged crystallins were useful for purification of crystallins for structural studies, γA, γB, γC, and γD were resistant to cleavage by SUMO protease. The abundance of WT and N101D human αA in transgenic mouse lenses was approximately 40-fold lower than endogenous mouse αA, but the deamidation mimic human αA N101D was less soluble than human WT αA. The high content of αA and the transient abundance of βA2, βB3, and γA in young lens suggest these crystallins play a role in early lens development and growth. βB1 becoming the most abundant crystallin may result from its role in promoting higher order β-crystallin oligomerization in mature lens. The full set of human crystallin expression vectors in the Addgene repository should be a useful resource for future crystallin studies. 15N labeling of these crystallins will be useful to accurately quantify crystallins in lens anatomic regions, as well as measure the composition of insoluble light scattering crystallin aggregates. The standards will also be useful to measure the abundance of crystallins expressed in transgenic animal models.

Bacterial Community Structure Modulates Soil Phosphorus Turnover at Early Stages of Primary Succession

AbstractMicrobes are the drivers of soil phosphorus (P) cycling in terrestrial ecosystems; however, the role of soil microbes in mediating P cycling in P‐rich soils during primary succession remains uncertain. This study examined the impacts of bacterial community structure (diversity and composition) and its functional potential (absolute abundances of P‐cycling functional genes) on soil P cycling along a 130‐year glacial chronosequence on the eastern Tibetan Plateau. Bacterial community structure was a better predictor of soil P fractions than P‐cycling genes along the chronosequence. After glacier retreat, the solubilization of inorganic P and the mineralization of organic P were significantly enhanced by increased bacterial diversity, changed interspecific interactions, and abundant species involved in soil P mineralization, thereby increasing P availability. Although 84% of P‐cycling genes were associated with organic P mineralization, these genes were more closely associated with soil organic carbon than with organic P. Bacterial carbon demand probably determined soil P turnover, indicating the dominant role of organic matter decomposition processes in P‐rich alpine soils. Moreover, the significant decrease in the complexity of the bacterial co‐occurrence network and the taxa‐gene‐P network at the later stage indicates a declining dominance of the bacterial community in driving soil P cycling with succession. Our results reveal that bacteria with a complex community structure have a prominent potential for biogeochemical P cycling in P‐rich soils during the early stages of primary succession.

Metagenomics-based insights into the microbial community dynamics and flavor development potentiality of artificial and natural pit mud

Strong-flavor Baijiu (SFB) production has relied on pit mud (PM) as a starter culture. The maturation time of natural PM (NPM) is about 30 years, so artificial PM (APM) with a shorter maturation time has attracted widespread attention. This study reveals the microbial and functional dissimilarities of APM and NPM, and helps to elucidate the different metabolic roles of microbes during substrate degradation and flavor formation. Significant differences in the microbial community were observed between APM and NPM, manifesting as variations in the abundance of core microorganisms. Total of 187 high-quality metagenome-assembled genomes (MAGs) were obtained based on the metagenomic binning technology, mainly including Firmicutes (n = 106), Bacteroidota (n = 15) and Chloroflexota (n = 14). Furthermore, the relative concentration of flavor compounds in 4-year APM was similar to those in 30-year NPM, but different from those in 100-year NPMs. Methanosarcina, Methanobacterium, Methanoculleus, Anaerolineae bacterium and Aminobacterium were the key bacteria responsible for the flavor differences. From a functional perspective, amino acid and carbohydrate metabolism were key functions of PM microbial, and showed differences between APM and NPM. Finally, substrate degradation and flavor generation pathways were found to exist in multiple microorganisms. Combine the relative abundance of microorganisms with the absolute abundance of enzymes, Clostridium, Lactobacillus, Petrimonas, Methanoculleus, Prevotella, Methanobacterium, Methanosarcina, Methanothrix, Proteiniphilum, Bellilinea, Anaerolinea, Anaeromassilibacillus, Syntrophomonas and Brevefilum were identified as the key microorganisms in APM and NPM.

MecE, MecB, and MecC proteins orchestrate methyl group transfer during dichloromethane fermentation.

Dichloromethane (DCM), a common hazardous industrial chemical, is anaerobically metabolized by four bacterial genera: Dehalobacter, Dehalobacterium, Ca. Dichloromethanomonas, and Ca. Formimonas. However, the pivotal methyltransferases responsible for DCM transformation have remained elusive. In this study, we investigated the DCM catabolism of Dehalobacterium formicoaceticum strain EZ94, contained in an enriched culture, using a combination of biochemical approaches. Initially, enzymatic assays were conducted with cell-free protein extracts, after protein separation by blue native polyacrylamide gel electrophoresis. In the slices with the highest DCM transformation activity, a high absolute abundance of the methyltransferase MecC was revealed by mass spectrometry. Enzymatic activity assays with heterologously expressed MecB, MecC, and MecE from strain EZ94 showed complete DCM transformation only when all three enzymes were present. Our experimental results, coupled with the computational analysis of MecB, MecC, and MecE sequences, enabled us to assign specific roles in DCM transformation to each of the proteins. Our findings reveal that both MecE and MecC are zinc-dependent methyltransferases responsible for DCM demethylation and re-methylation of a product, respectively. MecB functions as a cobalamin-dependent shuttle protein transferring the methyl group between MecE and MecC. This study provides the first biochemical evidence of the enzymes involved in the anaerobic metabolism of DCM.IMPORTANCEDichloromethane (DCM) is a priority regulated pollutant frequently detected in groundwater. In this work, we identify the proteins responsible for the transformation of DCM fermentation in Dehalobacterium formicoaceticum strain EZ94 using a combination of biochemical approaches, heterologous expression of proteins, and computational analysis. These findings provide the basis to apply these proteins as biological markers to monitor bioremediation processes in the field.

Differential insights into the distribution characteristics of archaeal communities and their response to typical pollutants in the sediments and soils of deep-water reservoir

This study focused on the Fengshuba deep-water reservoir in South China, and systematically explored the distribution characteristics of archaeal communities in the sediment and soil in water level fluctuation zones and their response mechanisms to typical pollutants. The results show that Euryarchaeota and Bathyarchaeota are the dominant phyla in sediment archaeal communities, while Thaumarchaeota dominates in soil. The absolute abundance of archaea in the sediments was lower than that in the soils, but the diversity and richness of archaeal communities were higher than those in the soils. Seasonal changes affected the composition of sediment archaeal communities, and the archaeal compositions in the two habitats also showed significant differences. The neutral community model indicates that the assembly of archaeal communities in sediments is mainly governed by stochastic processes, while deterministic processes dominate in soils. The responses of archaeal communities to pollutants in the two habitats were significantly different. Among them, the carbon-nitrogen ratio and tetracycline concentration are the key factors driving seasonal changes in the archaeal communities in the sediment. Structural equation modeling further showed that the archaeal community in the sediment was positively correlated with organochlorine pesticides and antibiotics, while the archaeal community in the soil showed an opposite trend. This study provides new insights into the complexity of interactions between archaeal communities and typical contaminants in reservoir systems.

Alpha–Proton Differential Flow of a Coronal Mass Ejection at 15 Solar Radii

Alpha–proton differential flow (V α p ) of coronal mass ejections (CMEs) and solar wind from the Sun to 1 au and beyond could influence the instantaneous correspondence of absolute abundances of alpha particles (He2+/H+) between the solar corona and interplanetary space as the abundance of a coronal source can vary with time. Previous studies based on Ulysses and Helios showed that V α p is negligible within CMEs from 5 to 0.3 au, similar to slow solar wind (<400 km s−1). However, recent new observations using Parker Solar Probe (PSP) revealed that the V α p of slow wind increases to ∼60 km s−1 inside 0.1 au. It is important to answer whether the V α p of CMEs exhibits similar behavior near the Sun. In this Letter, we report the V α p of a CME measured by PSP at ∼15 R ⊙ for the first time, which demonstrates that the V α p of CMEs is obvious and complex inside 0.1 au while keeping lower than the local Alfvén speed. A very interesting point is that the same one CME duration can be divided into A and B intervals clearly with Coulomb number below and beyond 0.5, respectively. The means of V α p and alpha-to-proton temperature ratios of interval A (B) is 96.52 (21.96) km s−1 and 7.65 (2.23), respectively. This directly illustrates that Coulomb collisions play an important role in reducing the nonequilibrium features of CMEs. Our study indicates that the absolute elemental abundances of CMEs also might vary during their propagation.

Temperature, sediment resuspension, and salinity drive the prevalence of Vibrio vulnificus in the coastal Baltic Sea

ABSTRACT The number of Vibrio -related infections in humans, e.g., by Vibrio vulnificus , has increased along the coasts of the Baltic Sea. Due to climate change, vibriosis risk is expected to increase. It is, therefore, pertinent to design a strategy for mitigation of the vibriosis threat in the Baltic Sea area, but a prerequisite is to identify the environmental conditions promoting the occurrence of pathogenic Vibrio spp., like V. vulnificus . To address this, we sampled three coastal Baltic sites in Finland, Germany, and Denmark with salinities between 6 and 21 from May to October 2022. The absolute and relative abundances of Vibrio spp. and V. vulnificus in water were compared to environmental conditions, including the presence of the eelgrass Zostera marina , which has been suggested to reduce pathogenic Vibrio species abundance. In the water column, V. vulnificus only occurred at the German station between July and August at salinity 8.1–11.2. Temperature and phosphate (PO 4 3– ) were identified as the most influencing factors for Vibrio spp. and V. vulnificus . The accumulation of Vibrio spp. in the sediment and the co-occurrence with sediment bacteria in the water column indicate that sediment resuspension contributed to V. vulnificus abundance. Interestingly, V. vulnificus co-occurred with specific cyanobacteria taxa, as well as specific bacteria associated with cyanobacteria. Although we found no reduction in Vibrio spp. or V. vulnificus associated with eelgrass beds, our study underscores the importance of extended heatwaves and sediment resuspension, which may elevate the availability of PO 4 3– , for Vibrio species levels at intermediate salinities in the Baltic Sea. IMPORTANCE Elevated sea surface temperatures are increasing the prevalence of pathogenic Vibrio at higher latitudes. The recent increase in Vibrio -related wound infections and deaths along the Baltic coasts is, therefore, of serious health concern. We used culture-independent data generated from three Baltic coastal sites in Denmark, Germany, and Finland from May to October (2022), with a special focus on Vibrio vulnificus , and combined it with environmental data. Our temporal model shows that temperature, combined with sediment resuspension, drives the prevalence of V. vulnificus at intermediate salinities in the coastal Baltic Sea.

Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels.

Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.

Anaerobic bacteria dominate the cholesteatoma tissue of chronic suppurative otitis media patients

The aim of this study was to investigate both the microbial composition and absolute abundance of clinically relevant bacteria in tissue specimens from patients with chronic suppurative otitis media with cholesteatoma (CSOM with cholesteatoma). Mastoid mucosa and cholesteatoma tissue from eleven subjects with CSOM with cholesteatoma, and mastoid mucosa from ten controls were examined using standard hospital culture swabs, Gram staining, bacterial 16S rRNA gene sequencing, Droplet Digital PCR (ddPCR), and multiplex PCR. Positive results from culture swabs were reported in half the CSOM with cholesteatoma samples and 1 control sample. In contrast, ddPCR detected bacterial genes copies in all 11 mucosa and cholesteatoma of CSOM subjects and 3 control samples. The average bacterial gene copies in tissue samples with CSOM with cholesteaotoma (1.6 ± 0.7 log10) was significantly higher compared to healthy controls (0.3 ± 1.6). These results were corroborated with Gram-staining that identified the large presence of Gram-positive cocci cells in the cholesteatoma tissue of CSOM subjects which were not seen in the mucosa of controls. The most abundant genus detected by sequencing in the mucosa and cholesteatoma of CSOM samples was Anaerococcus (93.5% of all reads), and genus Meiothermus (0.9%) in the control sample. The 3 samples with the highest sequencing reads (>300) were further analysed using multiplex PCR to identify the dominant Anaerococcus species. Anaerococcus hydrogenalis was the dominant species identified in these samples. In contract, commonly named ear pathogens, genera Staphylococcus and Pseudomonas, were detected in low numbers (<0.001% of all sequencing reads) and low prevalence (2/16 samples) in the tissue samples of this study.The results show that culture severely underestimated the bacterial diversity in CSOM samples and investigating tissue rather than standard culture swabs might be advantageous to understanding the disease process. The high abundance of bacteria and the large presence of Gram-positive cells detected in the cholesteatoma tissue of CSOM compared to mucosa of CSOM or controls could be members from the genus Anaerococcus. Anaerococcus may well be a pathogen in CSOM with cholesteatoma, but their role in this condition requires further investigation.

Relationships between benthic macroinvertebrates and environmental variables of Nyamuhinga River, Lake Kivu southwest basin, Sud-Kivu, Democratic Republic of the Congo.

Benthic macroinvertebrate abundance and taxa richness associated with environmental variables were monitored monthly from September 2015 to August 2016 in the Nyamuhinga River. The benthic macroinvertebrate samples were collected using a D-frame aquatic net employing the man-time method. Environmental variables including pH, temperature, conductivity, and total dissolved solids (TDS) were measured using a Combo HI 98129 and GREISIN-GER 020 multimeters, and water flow was assessed using the Float Method procedure. The Shannon-Wiener and equitability indices were then calculated to assess diversity and richness, facilitating the comparison of diversity within sites or stations. A total of 35,142 macroinvertebrate individuals were collected from the 12 sampling sites belonging to 29 genera, 27 families, and 9 orders. Diptera were the most abundant (71.83%) followed by Odonata (9.13%) and Ephemeroptera (7.11%). The findings showed that taxa richness decreased from upstream to downstream. At the same time, absolute abundance increased from downstream to upstream due to riparian vegetation, substrate type, plant debris, and organic matter which are habitats for benthic macroinvertebrates in the river. Environmental variables such as flow, pH, temperature, conductivity, and TDS varied between sites and stations because of habitat disturbances, contaminant discharges into the catchment, and inflow of tributary waters into the river. The canonical correspondence analysis (CCA) results displayed that Eristalis and Chironomus were strongly associated with the flow, conductivity, TDS, temperature, and pH at the downstream sites related to anthropogenic activities from the catchment. From our results, the Nyamuhinga River needs conservation master plan/guidelines and increased awareness to reduce environmental impacts in Bukavu River catchments in the Lake Kivu basin.

Metagenomic Profiling of Internationally Sourced Sewage Influents and Effluents Yields Insight into Selecting Targets for Antibiotic Resistance Monitoring.

It has been debated whether wastewater treatment plants (WWTPs) primarily act to attenuate or amplify antibiotic resistance genes (ARGs). However, ARGs are highly diverse with respect to their resistance mechanisms, mobilities, and taxonomic hosts and therefore their behavior in WWTPs should not be expected to be universally conserved. We applied metagenomic sequencing to wastewater influent and effluent samples from 12 international WWTPs to classify the behavior of specific ARGs entering and exiting WWTPs. In total, 1079 different ARGs originating from a variety of bacteria were detected. This included ARGs that could be mapped to assembled scaffolds corresponding to nine human pathogens. While the relative abundance (per 16S rRNA gene) of ARGs decreased during treatment at 11 of the 12 WWTPs sampled and absolute abundance (per mL) decreased at all 12 WWTPs, increases in relative abundance were observed for 40% of the ARGs detected at the 12th WWTP. Also, the relative abundance of mobile genetic elements (MGE) increased during treatment, but the fraction of ARGs known to be transmissible between species decreased, thus demonstrating that increased MGE prevalence may not be generally indicative of an increase in ARGs. A distinct conserved resistome was documented in both influent and effluent across samples, suggesting that well-functioning WWTPs generally attenuate influent antibiotic resistance loads. This work helps inform strategies for wastewater surveillance of antibiotic resistance, highlighting the utility of tracking ARGs as indicators of treatment performance and relative risk reduction.

Study on the relationship between adolescent myopia and gut microbiota via 16S rRNA sequencing

Myopia has become a global public health problem, with a high incidence among adolescents. In recent years, the correlation between gut microbiota and various diseases has become a research hotspot. This paper analyzes the relationship between myopia and gut microbiota in adolescents based on 16S rRNA sequencing, opening up a new avenue for the prevention and control of myopia. 80 adolescents aged 6–15 years were included; fecal samples were collected to compare their diversity and species differences. There was no significant difference in α diversity when considering richness and evenness at the same time (P > 0.05). While the group difference in β diversity reached a significant level (R2 = 0.022, P < 0.05). The absolute quantification and relative abundance of phylum level Firmicutes and Actinobacteriota are different; among the top 30 genera, myopic group only one genus decreased in absolute quantification, while 13 genera decreased in relative quantification; so LEfSe analysis was performed, and the result showed that microbial community composition changed under Linear discriminant analysis (LDA) score, the top ten changes are shown in the figure; the Wilcoxon Rank sum test also found some significant changes in the absolute abundance of differential microbiota among different groups, at the phylum level, one bacterial phylum decreased and three bacterial phyla increased; at the genus level, 2 bacteria genera decreased and 29 bacteria genera increased. Functional pathways prediction found many myopic-related pathways were functionally enhanced in myopic patients (P < 0.05). Multivariate logistic regression analysis results showed that the area under the curve (AUC) of myopic patients predicted was close to or equal to 1. In conclusion, adolescent myopia is closely related to the gut microbiota, and the characteristic gut microbiota can distinguish myopia from healthy controls to a large extent. Therefore, it can be considered to regulate these characteristic gut microbiota to prevent and control myopia.

Rapid removal of multidrug-resistant bacteria and multidrug-resistant genes in drinking water and hospital wastewater using permanganate/bisulfite oxidation

Bacterial pathogens with multidrug resistance (MDR) characteristics pose a significant public health concern, impeding the effective utilization of antibiotics. In this study, a bisulfite/permanganate (PM/BS) process was used for the rapid inactivation of antibiotic-resistant bacteria (ARBs) and the elimination of antibiotic-resistance genes (ARGs). Targeting multidrug-resistant Escherichia coli (MDR E. coli), the PM/BS process rapidly reduced 3.09-log and 1.05-log within 10 s in real hospital effluent and tap water, respectively. Control experiments revealed enhancements in the inactivation of MDR E. coli with the presence of dissolved oxygen, Fe3+, Mg2+, and Cl−, whereas CO32− and HA inhibited water disinfection. Additionally, the PM/BS process significantly reduced the absolute abundance of two mobile genetic elements (MGEs) and a total of 52 ARGs across nine classes. These genes are responsible for MDR E. coli resistance to clinically important cephalosporins and carbapenems. The removal efficiencies of nine classes of ARGs varied from 91.49 to 98.17 % in ultrapure water and from 28.58 to 87.18 % in hospital effluent, respectively. The average removal efficiency of MGEs in hospital effluent also reached 71.94 %. In-situ generated Mn (III)aq and SO4∙- were further found as key contributors to the rapid inactivation of MDR E. coli and the reduction of ARGs and MGEs. This resulted in severe damage to cell membranes, significant K+ leakage, and protein degradation in MDR E. coli. These findings highlight the potential of the PM/BS process for rapid and efficient inactivation of ARBs and ARGs in both wastewater and drinking water, offering an alternative to traditional oxidants and opening avenues for the application of reactive Mn (III) species in disinfection.

The effect of extracellular polymeric substances on the distribution and transmission of antibiotic resistance genes treating antibiotic wastewater via microbial electrolysis cells

Microbial electrolysis cells (MEC) have emerged as a prominent technology for the treatment of antibiotics-containing wastewater in recent years. However, there remains a dearth of comprehensive exploration regarding the influence of extracellular polymers substances (EPS) on the distribution and transmission of antibiotic resistance genes (ARGs) in MEC. In this study, we quantified the distribution of ARGs in MEC by Fluorescence quantitative polymerase chain reaction and explored with emphasis on impact of EPS component on ARGs transmission at under different concentrations of roxithromycin. Results showed that the absolute abundance of ARGs in the electrode biofilm was 1–2 orders of magnitude higher than that in the anolyte. Specifically, EPS-associated ARGs accounted for 2.31%–11.18% of ARGs in electrode biofilm. The presence of elevated roxithromycin concentration led to electroactive microorganisms (Geobacter and Geothrix) as potential hosts of ARGs. In addition, both protein and polysaccharide content in the electrode biofilm increased with increasing roxithromycin concentration and showed positive correlations with EPS-associated ARGs. Fluorescence quenching experiments further elucidated that tryptophan and tyrosine residues in EPS could bind to ARGs effectively, contributing the hindering the ARGs transmission between hosts. Therefore, increased EPS content within electrode biofilm could reduce the concentration of ARGs present in anolyte while also influencing ARGs distribution throughout MEC. This study provides valuable insights into the distribution of ARGs in MEC systems and the role of EPS in regulating ARGs migration.

Soil carbon mineralization decreased in desert steppe by light grazing but not fencing management

Fencing off grassland soils emits massive amounts of carbon into the atmosphere. Whether grazing management in desert steppes with fragile ecosystems can mitigate this trend remains highly uncertain. Here, we examined how soil carbon mineralization, as well as its underlying mechanisms, varied with grazing intensity by sheep in a long-term (17 − year) experiment in the desert steppe. Carbon mineralization decreased by 15 % − 55 % under different grazing intensities compared to fencing controls. Soil organic carbon (SOC) maintained high levels under light grazing, whereas it decreased with increasing grazing intensity. Reductions in plant carbon and absolute microbial abundance due to grazing, coupled with changes in soil carbon quality and the environment, drove the reduction in carbon mineralization. We suggest that mechanisms of carbon mineralization can be integrated into predictive modelling efforts to better understand the impact of grazing on carbon fluxes in ecologically fragile, but globally important, arid and semi-arid grasslands.