Mulches assist degraded soil recovery via stimulating biogeochemical cycling: metagenomic analysis

Soil degradation of urban greening has caused soil fertility loss and soil organic carbon depletion. Organic mulches are made from natural origin materials, and represent a cost-effective and environment-friendly remediation method for urban greening. To reveal the effects of organic mulch on soil physicochemical characteristics and fertility, we selected a site that was covered with organic mulch for 6 years and a nearby lawn-covered site. The results showed that soil organic matter, total nitrogen, and available phosphorus levels were improved, especially at a depth of 0-20 cm. The activities of cellulase, invertase, and dehydrogenase in soil covered with organic mulch were 17.46%, 78.98%, and 283.19% higher than those under lawn, respectively. The marker genes of fermentation, aerobic respiration, methanogenesis, and methane oxidation were also enriched in the soil under organic mulch. Nitrogen cycling was generally repressed by the organic mulch, but the assimilatory nitrate and nitrite reduction processes were enhanced. The activity of alkaline phosphatase was 12.63% higher in the mulch-covered soil, and functional genes involved in phosphorus cycling were also enriched. This study presents a comprehensive investigation of the influence of organic mulch on soil microbes and provides a deeper insight into the recovery strategy for soil degradation following urban greening. KEY POINTS: • Long-term cover with organic mulches assists soil recovery from degradation • Soil physical and chemical properties were changed by organic mulches • Organic mulches enhanced genes involved in microbially mediated C and P cycling • Soil organic matter was derived from decomposition of organic mulch and carbon fixation • N cycling was repressed by mulches, except for assimilatory NO2- and NO3- reductions.

Microbial mechanisms in nitrogen fertilization: Modulating the re-mobilization of clay mineral-bound cadmium in agricultural soils

Soil cadmium (Cd) can affect crop growth and food safety, and through the enrichment in the food chain, it ultimately poses a risk to human health. Reducing the re-mobilization of Cd caused by the release of protons and acids by crops and microorganisms after stabilization is one of the significant technical challenges in agricultural activities. This study aimed to investigate the re-mobilization of stabilized Cd within the clay mineral-bound fraction of soil and its subsequent accumulation in crops utilizing nitrogen ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3--N), at 60 and 120 mg kg-1. Furthermore, the study harvested root exudates at various growth stages to assess their direct influence on the re-mobilization of stabilized Cd and to evaluate the indirect effects mediated by soil microorganisms. The results revealed that, in contrast to the NO3--N treatment, the NH4+-N treatment significantly enhanced the conversion of clay mineral-bound Cd in the soil to NH4NO3-extractable Cd. It also amplified the accumulation of Cd in edible amaranth, with concentrations in roots and shoots rising from 1.7-6.0 mg kg-1 to 4.3-9.8 mg kg-1. The introduction of NH4+-N caused a decrease in the pH value of the rhizosphere soil and stimulated the production and secretion organic and amino acids, such as oxalic acid, lactic acid, stearic acid, succinic acid, and l-serine, from the crop roots. Furthermore, compared to NO3--N, the combined interaction of root exudates with NH4+-N has a more pronounced impact on the abundance of microbial genes associated with glycolysis pathway and tricarboxylic acid cycle, such as pkfA, pfkB, sucB, sucC, and sucD. The effects of NH4+-N on crops and microorganisms ultimately result in a significant increase in the re-mobilization of stabilized Cd. However, the simulated experiments showed that microorganisms only contribute to 3.8-6.6 % of the re-mobilization of clay mineral-bound Cd in soil. Therefore, the fundamental strategy to inhibit the re-mobilization of stabilized Cd in vegetable cultivation involves the regulation of proton and organic acid secretion by crops.

Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification

Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database. In Centrifuger, the Burrows-Wheeler transformed genome sequences are losslessly compressed using a novel scheme called run-block compression. Run-block compression achieves sublinear space complexity and is effective at compressing diverse microbial databases like RefSeq while supporting fast rank queries. Combining this compression method with other strategies for compacting the Ferragina-Manzini (FM) index, Centrifuger reduces the memory footprint by half compared to other FM-index-based approaches. Furthermore, the lossless compression and the unconstrained match length help Centrifuger achieve greater accuracy than competing methods at lower taxonomic levels.

A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic

Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.

Insight into environmental adaptability of antibiotic resistome from surface water to deep sediments in anthropogenic lakes by metagenomics

The escalating antibiotic resistance threatens the long-term global health. Lake sediment is a vital hotpot in transmitting antibiotic resistance genes (ARGs); however, their vertical distribution pattern and driving mechanisms in sediment cores remain unclear. This study first utilized metagenomics to reveal how resistome is distributed from surface water to 45 cm sediments in four representative lakes, central China. Significant vertical variations in ARG profiles were observed (R2 = 0.421, p < 0.001), with significant reductions in numbers, abundance, and Shannon index from the surface water to deep sediment (all p-values < 0.05). ARGs also has interconnections within the vertical profile of the lakes: twelve ARGs persistently exist all sites and depths, and shared ARGs (e.g., vanS and mexF) were assembled by diverse hosts at varying depths. The 0-18 cm sediment had the highest mobility and health risk of ARGs, followed by the 18-45 cm sediment and water. The drivers of ARGs transformed along the profile of lakes: microbial communities and mobile genetic elements (MGEs) dominated in water, whereas environmental variables gradually become the primary through regulating microbial communities and MGEs with increasing sediment depth. Interestingly, the stochastic process governed ARG assembly, while the stochasticity diminished under the mediation of Chloroflexi, Candidatus Bathyarcaeota and oxidation-reduction potential with increasing depth. Overall, we formulated a conceptual framework to elucidate the vertical environmental adaptability of resistome in anthropogenic lakes. This study shed on the resistance risks and their environmental adaptability from sediment cores, which could reinforce the governance of public health issues.

Removal of sulfur and nitrogen pollutants in a sediment microbial fuel cell coupled with Vallisneria natans: Efficiency, microbial community structure, and functional genes

The rapid development of the economy has led to an increase in the sulfur and nitrogen load in surface water, which has the potential to cause river eutrophication and the emission of malodorous gases. A lab-scale sediment microbial fuel cell coupled with Vallisneria natans (P-SMFC) was designed for surface water remediation. The enhancement of pollutant removal performance of P-SMFC was evaluated in contrast to the SMFC system without plants (SMFC), the open-circuit control system with plants (C-P), and the open-circuit control system without plants (C-S), while illustrating the mechanisms of the sulfur and nitrogen transformation process. The results demonstrated that the effluent and sediment of P-SMFC had lower concentrations of sulfide compared to other systems. Furthermore, P-SMFC exhibited higher removal efficiency for COD (73.1 ± 8.7%), NH4+-N (80.5 ± 19.8%), and NO3--N (88.5 ± 11.8%) compared to other systems. The closed-circuit conditions and growth of Vallisneria natans create a favorable ecological niche for functional microorganisms involved in power generation, sulfur oxidation, and nitrogen transformation. Additionally, metagenomic analysis revealed that multifunctional bacteria possessing both denitrification and sulfur oxidation genes, such as Thiobacillus, Dechloromonas, and Bacillus, may play simultaneous roles in metabolizing sulfur and nitrogen, thus serving as integral factors in maintaining the performance of P-SMFC. In summary, these findings provide a theoretical reference for the concurrent enhancement of sulfur and nitrogen pollutants removal in P-SMFC and will facilitate its practical application in the remediation of contaminated surface water.

A study into the diversity of coral-associated bacteria using culture-dependent and culture-independent approaches in coral Dipsastraea favus from the Gulf of Kutch

Corals harbour ~25 % of the marine diversity referring to biodiversity hotspots in marine ecosystems. Global efforts to find ways to restore the coral reef ecosystem from various threats can be complemented by studying coral-associated bacteria. Coral-associated bacteria are vital components of overall coral wellbeing. We explored the bacterial diversity associated with coral Dipsastraea favus (D. favus) collected from the Gulf of Kutch, India, using both culture-dependent and metagenomic approaches. In both approaches, phylum Proteobacteria, Firmicutes, and Actinobacteria predominated, comprising the genera Vibrio, Bacillus, Shewanella, Pseudoalteromonas, Exiguobacterium and Streptomyces. Moreover, the majority of culturable isolates showed multiple antibiotic resistance index ≥0.2. In this study, specific bacterial diversity associated with coral sp. D. favus and its possible role in managing coral health was established. Almost 43 strains from the samples were successfully cultured, creating a base for exploring these microbes for their potential use in coral conservation methods.

Mechanisms of biochar assisted di-2-ethylhexyl phthalate (DEHP) biodegradation in tomato rhizosphere by metabolic and metagenomic analysis

The intensive accumulation of di-2-ethylhexyl phthalate (DEHP) in agricultural soils has resulted in severe environmental pollution that endangers ecosystem and human health. Biochar is an eco-friendly material that can help in accelerating organic pollutant degradation; nevertheless, its roles in enhancing DEHP removal in rhizosphere remain unclear. This work investigated the impacts of biochar dosage (0%-2.0%) on DEHP degradation performance in tomato rhizosphere by comprehensively exploring the change in DEHP metabolites, bacterial communities and DEHP-degrading genes. Our results showed a significant increase of rhizosphere pH, organic matter and humus by biochar amendment, which achieved a satisfactorily higher DEHP removal efficiency, maximally 77.53% in treatments with 1.0% of biochar. Biochar addition also remarkably changed rhizosphere bacterial communities by enriching some potential DEHP degraders of Nocardioides, Sphingomonas, Bradyrhizobium and Rhodanobacter. The abundance of genes encoding key enzymes (hydrolase, esterase and cytochrome P450) and DEHP-degrading genes (pht3, pht4, pht5, benC-xylZ and benD-xylL) were increased after biochar amendment, leading to the change in DEHP degradation metabolism, primarily from benzoic acid pathway to protocatechuic acid pathway. Our findings evidenced that biochar amendment could accelerate DEHP degradation by altering rhizosphere soil physicochemical variables, bacterial community composition and metabolic genes, providing clues for the mechanisms of biochar-assisted DEHP degradation in organic contaminated farmland soils.

Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season

Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65-17.1 mg/L), NH4+ (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.

Thermokarst lakes are hotspots of antibiotic resistance genes in permafrost regions on the Qinghai-Tibet Plateau

Antibiotic resistance genes (ARGs) are natural products and emerging pollutants in remote environments, including permafrost regions that are rapidly thawing due to climate warming. We investigated the role of thermokarst lakes (including sediment and water) in reserving ARGs compared to permafrost soils across the permafrost regions on the Qinghai-Tibet Plateau. As intrinsically connected distinct environments, permafrost soil, lake sediment, and lake water harbored 1239 ARGs in total, while a considerable number of same ARGs (683 out of 1239) concurrently presented in all these environments. Soil and sediment had a higher number of ARGs than water. Multidrug resistance genes were the most diverse and abundant in all three environments, where cls, ropB, mdfA, fabI, and macB were the top five most abundant ARGs while with different orders. Soil and sediment had similar ARG profiles, and the alpha and beta diversity of ARGs in sediment were positively correlated with that in soil. The beta diversity of ARG profiles between sediment and soil was highly contributed by turnover component (89%). However, turnover and nestedness components were almost equality contributed (46%-54%) to the beta diversity of ARG profiles between soil and water as well as between sediment and water. The results suggested that thermokarst lake sediments might inherit the ARGs in permafrost soils. Water ARGs are the subset of soil ARGs and sediment ARGs to a certain degree with species turnover playing a significant role. When accounting the ARGs in sediment and water together, thermokarst lakes had a significantly higher number of ARGs than permafrost soils, suggesting that thermokarst lakes act as the hotspots of ARGs in permafrost regions. These findings are disturbing especially due to the fact that tremendous number of thermokarst lakes are forming under accelerating climate change.

Enhanced denitrification performance in iron-carbon wetlands through biomass addition: Impact on nitrate and ammonia transformation

This study investigated the influence of biomass addition on the denitrification performance of iron-carbon wetlands. During long-time operation, the effluent NO3--N concentration of CW-BFe was observed to be the lowest, registering at 0.418 ± 0.167 mg/L, outperforming that of CW-Fe, which recorded 1.467 ± 0.467 mg/L. However, the effluent NH4+-N for CW-BFe increased to 1.465 ± 0.121 mg/L, surpassing CW-Fe's 0.889 ± 0.224 mg/L. Within a typical cycle, when establishing first-order reaction kinetics based on NO3--N concentrations, the introduction of biomass was found to amplify the kinetic constants across various stages in the iron-carbon wetland, ranging between 2.4 and 5.4 times that of CW-Fe. A metagenomic analysis indicated that biomass augments the reduction of NO3--N and NO2--N nitrogen and significantly bolsters the dissimilation nitrate reduction to ammonia pathway. Conversely, it impedes the reduction of N2O, leading to a heightened proportion of 2.715 % in CW-BFe's nitrogen mass balance, a stark contrast to CW-Fe's 0.379 %.

Metagenomic survey of viral diversity obtained from feces of piglets with diarrhea

Pigs are natural host to various zoonotic pathogens including viruses. In this study, we analyzed the viral communities in the feces of 89 piglets with diarrhea under one month old which were collected from six farms in Jiangsu Province of the Eastern China, using the unbiased virus metagenomic method. A total of 89 libraries were constructed, and 46937894 unique sequence reads were generated by Illumina sequencing. Overall, the family Picornaviridae accounted for the majority of the total reads of putative mammalian viruses. Ten novel virus genomes from different family members were discovered, including Parvoviridae (n = 2), Picobirnaviridae (n = 4) and CRESS DNA viruses (n = 4). A large number of phages were identified, which mainly belonged to the order Caudovirales and the family Microviridae. Moreover, some identified viruses were closely related to viruses found in non-porcine hosts, highlighting the potential for cross-species virus dissemination. This study increased our understanding of the fecal virus communities of diarrhea piglets and provided valuable information for virus monitoring and preventing.

A training program for improving the capacity of infection high-throughput sequencing and diagnosis in China

BACKGROUND

Infectious diseases are a serious threat to human especially since the COVID-19 outbreak has proved the importance and urgency of their diagnosis and treatment again. Metagenomic next-generation sequencing (mNGS) has been widely used and recognized in clinical and carried out localized testing in hospitals. Increasing the training of mNGS detection technicians can enhance their professional quality and more effectively realize the application value of the hospital platform.

METHODS

Based on the initial theoretical understanding and practice of the mNGS platform for localization construction, we have designed a training program to enhance the ability of technicians to detect pathogens by utilizing mNGS, and hence to conduct training practices nationwide.

RESULTS

Until August 30, 2022, the page views of online classes have reached 51,500 times and 6 of offline small-scale training courses have been conducted. A total of 67 trainees from 67 hospitals have participated in the training with a qualified rate of 100%. After the training course, the localization platform of 1 participating hospital has been put into use, 2 have added the mNGS localization platform for admission, among which 3 have expressed strong intention of localization.

CONCLUSIONS

This study focuses on the training procedures and practical experience of the project which is the first systematic standardized program of mNGS in the world. It solves the training difficulties in the current industry, and effectively promotes the localization construction and application of mNGS in hospitals. It has great development potential in the future and is worth further promotion.

Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing

The monkeypox virus (MPXV) has triggered a current outbreak globally. Genome sequencing of MPXV and rapid tracing of genetic variants will benefit disease diagnosis and control. It is a significant challenge but necessary to optimize the strategy and application of rapid full-length genome identification and to track variations of MPXV in clinical specimens with low viral loads, as it is one of the DNA viruses with the largest genome and the most AT-biased, and has a significant number of tandem repeats. Here we evaluated the performance of metagenomic and amplicon sequencing techniques, and three sequencing platforms in MPXV genome sequencing based on multiple clinical specimens of five mpox cases in Chinese mainland. We rapidly identified the full-length genome of MPXV with the assembly of accurate tandem repeats in multiple clinical specimens. Amplicon sequencing enables cost-effective and rapid sequencing of clinical specimens to obtain high-quality MPXV genomes. Third-generation sequencing facilitates the assembly of the terminal tandem repeat regions in the monkeypox virus genome and corrects a common misassembly in published sequences. Besides, several intra-host single nucleotide variations were identified in the first imported mpox case. This study offers an evaluation of various strategies aimed at identifying the complete genome of MPXV in clinical specimens. The findings of this study will significantly enhance the surveillance of MPXV.

Core and variable antimicrobial resistance genes in the gut microbiomes of Chinese and European pigs

Monitoring the prevalence of antimicrobial resistance genes (ARGs) is vital for addressing the global crisis of antibiotic-resistant bacterial infections. Despite its importance, the characterization of ARGs and microbiome structures, as well as the identification of indicators for routine ARG monitoring in pig farms, are still lacking, particularly concerning variations in antimicrobial exposure in different countries or regions. Here, metagenomics and random forest machine learning were used to elucidate the ARG profiles, microbiome structures, and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe. Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs ( P<0.05). ANT(6)-Ib, APH(3')-IIIa, and tet(40) were identified as shared core ARGs between the two pig populations. Furthermore, the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions. Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs, respectively. Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100% and 98.7%, respectively. Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy ( r=0.72-0.88). Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs. The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.

Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA

Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify debris occurring in peat, including their morphological description. However, this is strongly constrained by the researcher's ability to distinguish residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.

Riboflavin-loaded carbon cloth aids the anaerobic digestion of cow dung by promoting direct interspecies electron transfer

Cow dung generates globally due to increased beef and milk consumption, but its treatment efficiency remains low. Previous studies have shown that riboflavin-loaded conductive materials can improve anaerobic digestion through enhance direct interspecies electron transfer (DIET). However, its effect on the practical anaerobic digestion of cow dung remained unclear. In this study, carbon cloth loaded with riboflavin (carbon cloth-riboflavin) was added into an anaerobic digester treating cow dung. The carbon cloth-riboflavin reactor showed a better performance than other two reactors. The metagenomic analysis revealed that Methanothrix on the surface of the carbon cloth predominantly utilized the CO2 reduction for methane production, further enhanced after riboflavin addition, while Methanothrix in bulk sludge were using the acetate decarboxylation pathway. Furthermore, the carbon cloth-riboflavin enriched various major methanogenic pathways and activated a large number of enzymes associated with DIET. Riboflavin's presence altered the microbial communities and the abundance of functional genes relate to DIET, ultimately leading to a better performance of anaerobic digestion for cow dung.

Virome analysis of Desmodus rotundus tissue samples from the Amazon region

BACKGROUND

Bats are renowned for harboring a high viral diversity, their characteristics contribute to emerging infectious diseases. However, environmental and anthropic factors also play a significant role in the emergence of zoonotic viruses. Metagenomic is an important tool for investigating the virome of bats and discovering new viruses.

RESULTS

Twenty-four families of virus were detected in lung samples by sequencing and bioinfomatic analysis, the largest amount of reads was focused on the Retroviridae and contigs assembled to Desmodus rotundus endogenous retrovirus, which was feasible to acquire complete sequences. The reads were also abundant for phages.

CONCLUSION

This lung virome of D. rotundus contributes valuable information regarding the viral diversity found in bats, which is useful for understanding the drivers of viral cycles and their ecology in this species. The identification and taxonomic categorization of viruses hosted by bats carry epidemiological significance due to the potential for viral adaptation to other animals and humans, which can have severe repercussions for public health. Furthermore, the characterization of endogenized viruses helps to understanding the host genome and the evolution of the species.

Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems?

Antimicrobial resistance poses a serious threat to human health and is responsible for the death of millions of people annually. Hospital wastewater is an important hotspot for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). However, little is known about the relationship between phages and ARGs in hospital wastewater systems (HWS). In the present study, the viral diversity of 12 HWSs using data from public metagenomic databases was investigated. Viruses were widely found in both the influent and effluent of each HWS. A total of 45 unique ARGs were carried by 85 viral contigs, which accounted for only 0.14% of the total viral populations, implying that ARGs were not commonly present in phages. Three efflux pump genes were identified as shared between phages and bacterial genomes. However, the predominant types of ARGs in HWS such as aminoglycoside- and beta-lactam-resistance genes were rarely found in phages. Based on CRISPR spacer and tRNA matches, interactions between 171 viral contigs and 60 antibiotic-resistant genomes were predicted, including interactions involving phages and vancomycin-resistant Enterococcus_B faecium or beta-lactam-resistant Klebsiella pneumoniae. More than half (56.1%) of these viral contigs indicated lytic and none of them carried ARGs. As the vOTUs in this study had few ARGs and were primarily lytic, HWS may be a valuable source for phage discovery. Future studies will be able to experimentally validate these sequence-based results to confirm the suitability of HWS phages for pathogen control measures in wastewater.

Circulation of adenovirus and other viruses in urban drainage channels: an environmental surveillance in Belém, Amazon region, Brazil

Urban channels in amazon cities are very polluted, with garbage and sewage disposal in these aquatic environments, favoring the high dissemination of waterborne viruses such as human adenovirus (HAdV). The aim of this study was to perform the detection and molecular characterization of adenovirus in urban channels and in a wastewater treatment plant located in a metropolitan city in the Amazon. Additionally, metagenomic analyses were performed to assess viral diversity. Samples were concentrated by organic flocculation, analyzed by quantitative real time PCR (qPCR) and sequenced (Sanger e next generation sequencing). Cell culture was performed to verify the viability of HAdV particles. A total of 104 samples were collected, being the HAdV positivity of 76% (79/104). Among the positive samples, 29.1% (23/79) were characterized as HAdV-F40 (87%, 20/23), HAdV-F41 (8.7%, 2/23), and HAdV-B (4.3%, 1/23). Average precipitation rates ranged from 163 to 614 mm, while the pH ranged from 6.9 to 7.6. Eight positive samples were inoculated into A549 cells and in 4 of these, was observed changes in the structure of the cell monolayer, alteration in the structure of the cell monolayer was observed, but without amplification when analyzed by PCR. The metagenomic data demonstrated the presence of 14 viral families, being the most abundant: Myoviridae (41% of available reads), Siphoviridae (24.5%), Podoviridae (14.1%), and Autographiviridae (6.9%) with more than 85% of the total number of identified reads. This study reinforcing that continuous surveillance may contribute to monitoring viral diversity in aquatic environments and provide early warning of potential outbreaks.

Compositional and functional aberrance of the gut microbiota in treatment-naïve patients with primary Sjögren's syndrome

OBJECTIVES

To investigate the compositional and functional characteristics of the gut microbiota in primary Sjögren's syndrome (pSS) and compare them with those in systemic lupus erythematosus (SLE).

METHODS

Stool samples from 78 treatment-naïve pSS patients and 78 matched healthy controls were detected by shotgun metagenomic sequencing and compared with those from 49 treatment-naïve SLE patients. The virulence loads and mimotopes of the gut microbiota were also assessed by sequence alignment.

RESULTS

The gut microbiota of treatment-naïve pSS patients had lower richness and evenness and showed a different community distribution than that of healthy controls. The microbial species enriched in the pSS-associated gut microbiota included Lactobacillus salivarius, Bacteroides fragilis, Ruminococcus gnavus, Clostridium bartlettii, Clostridium bolteae, Veillonella parvula, and Streptococcus parasanguinis. Lactobacillus salivarius was the most discriminating species in the pSS patients, especially in those with interstitial lung disease (ILD). Among the differentiating microbial pathways, the superpathway of l-phenylalanine biosynthesis was also further enriched in pSS complicated with ILD. There were more virulence genes carried by the gut microbiota in pSS patients, most of which encoded peritrichous flagella, fimbriae, or curli fimbriae, three types of bacterial surface organelles involved in bacterial colonization and invasion. Five microbial peptides with the potential to mimic pSS-related autoepitopes were also enriched in the pSS gut. SLE and pSS shared significant gut microbial traits, including community distribution, altered microbial taxonomy and pathways, and enriched virulence genes. However, Ruminococcus torques was depleted in pSS patients but enriched in SLE patients compared to healthy controls.

CONCLUSIONS

The gut microbiota in treatment-naïve pSS patients was disturbed and shared significant similarity with that in SLE patients.

Alterations of fecal microbiome and metabolome in pemphigus patients

The role of gut microbiome and metabolic substances in the development of autoimmune diseases has gradually been revealed. However, the relevant gut features in pemphigus have not been well clarified. We collected stool samples from pemphigus patients and healthy controls (HCs). Metagenomic sequencing and liquid chromatography-mass spectrometry (LC/MS) metabolome sequencing were performed to analyze the compositional and metabolic alternations of the gut microbiome in pemphigus patients and HCs. We observed the reduced richness and diversity and greater heterogeneity in pemphigus patients, which was characterized by a significant decrease in Firmicutes and an increase in Proteobacteria. At the species level, Intestinal pathogenic bacteria such as Escherichia coli and Bacteroides fragilis were significantly enriched, while anti-inflammatory bacteria and butyric acid-producing bacteria were significantly reduced, which were related to clinical indicators (Dsg1/3 and PDAI). 4 species were selected by the machine learning algorithm to better distinguish pemphigus patients from healthy people. Metabolomic analysis showed that the composition of pemphigus patients was different from that of HCs. PE (18:3 (6Z,9Z, 12Z)/14:1 (9Z)) was the main metabolic substance in pemphigus and involved in a variety of metabolic pathways. While Retinol, flavonoid compounds and various amino acids decreased significantly compared with HCs. Furthermore, we found that differences in the levels of these metabolites correlated with changes in the abundance of specific species. Our study provides a comprehensive picture of gut microbiota and metabolites in pemphigus patients and suggests a potential mechanism of the aberrant gut microbiota and metabolites in the pathogenesis of pemphigus.

Unraveling impacts of inoculating novel microbial agents on nitrogen conversion during cattle manure composting: Core microorganisms and functional genes

The impacts of microbial agents on nitrogen conversion during composting is still not entirely clear. In this research, a novel microbial agent containing two thermotolerant nitrifying bacteria was identified and its impacts on nitrogen conversion, bacterial structure and functional genes during cattle manure composting were investigated. The results revealed that the inoculation enhancing the maturation of compost, increased the total nitrogen by 13.6-26.8%, reduced NH3 emission and the N2O emission by 24.8-36.1% and 22.7-32.1%, respectively. Particularly, the microbial agents mixed Acinetobacter radioresistens and Bacillus nitratireducens (1:1, treatment group 1) had the best nitrogen preservation effect. Furthermore, the inoculation not only produced diverse diazotroph community but could strength the co-occurrence between core microorganisms to promote nitrogen metabolism. The metagenomic analysis demonstrated that the inoculation decreased the abundance of nitrate reduction gene (nirS, norC, nap and nif), and increased the abundance of hao, thus facilitating nitrification and suppressing NH3 and N2O emission.

Simulated-sunlight enhances membrane aerated biofilm reactor performance in sulfamethoxazole removal and antibiotic resistance genes reduction

Membrane aerated biofilm reactors (MABRs) can be used to treat domestic wastewater containing sulfamethoxazole (SMX) because of their favorable performance in the treatment of refractory pollutants. However, biologics are generally subjected to antibiotics stress, which induces the production of antibiotic resistance genes (ARGs). In this study, a simulated-sunlight assisted MABR (L-MABR) was used to promote SMX removal and reduce ARGs production. The SMX removal efficiency of the l-MABR system was 9.62 % superior to that of the MABR system (83.13 %). In contrast from MABR, in the l-MABR, only 28.75 % of SMX was removed through microbial activity because functional bacteria were inactivated through radiation by simulated sunlight. In addition, photolysis (64.61 %) dominated SMX removal, and the best performing indirect photolysis process was the excited state of effluent organic matters (3EfOMs*). Through photolysis, ultraviolet (UV) and reactive oxygen species (ROS) enriched the SMX removal route, resulting in the SMX removal pathway in the l-MABR no longer being limited by enzyme catalysis. More importantly, because of the inactivation of functional bacteria, whether in the effluent or biofilm, the copy number of ARGs in the l-MABR was 1-3 orders of magnitude lower than that in the MABR. Our study demonstrates the feasibility of utilizing simulated-sunlight to enhance the antibiotic removal efficiency while reducing ARG production, thus providing a novel idea for the removal of antibiotics from wastewater.

Metagenomics insight into the long-term effect of ferrous ions on the mainstream anammox system

Anaerobic ammonium oxidation (anammox) bacteria have a high requirement for iron for their growth and metabolism. However, it remains unclear whether iron supplementation can sustain the stability of mainstream anammox systems at varying temperatures. Here, we investigated the long-term effects of Fe2+ on the mainstream anammox systems. Our findings revealed that the nitrogen removal efficiency (NRE) of the anammox system supplemented with 5 mg/L Fe2+ decreased from 76.5 ± 0.76% at 35 °C to 39.0 ± 9.9% at 25 °C. Notably, higher dosages of Fe2+ (15 mg/L and 30 mg/L) inhibited the anammox system, resulting in NREs of 15.9 ± 8.1% and 2.5 ± 1.1% at 25 °C, respectively. The results of microbial communities and function profiles suggested that the high Fe2+ dosage seriously affected the iron assimilation and utilization in the mainstream anammox system. This was evident from the decreased abundance of genes associated with Fe(II) transport and uptake, which in turn hindered the biosynthesis of intracellular iron-cofactors, resulting in decrease in the absolute abundance of Candidatus Brocadia, a key anammox bacterium, as well as a decline in NRE. Furthermore, our results showed that the anammox process was more susceptible to iron supplementation at 25 °C compared to 35 °C, which may be due to the oxidative stress reactions induced by combined lowered temperature and a high Fe2+ dosage. Overall, these findings offer a deeper understanding of the effect of iron in mainstream anammox systems, which can contribute to improved stability maintenance and effectiveness of anammox processes.

Bacteriophage-based biosensors for detection of pathogenic microbes in wastewater

Wastewater is discarded from several sources, including industry, livestock, fertilizer application, and municipal waste. If the disposed of wastewater has not been treated and processed before discharge to the environment, pathogenic microorganisms and toxic chemicals are accumulated in the disposal area and transported into the surface waters. The presence of harmful microbes is responsible for thousands of human deaths related to water-born contamination every year. To be able to take the necessary step and quick action against the possible presence of harmful microorganisms and substances, there is a need to improve the effective speed of identification and treatment of these problems. Biosensors are such devices that can give quantitative information within a short period of time. There have been several biosensors developed to measure certain parameters and microorganisms. The discovered biosensors can be utilized for the detection of axenic and mixed microbial strains from the wastewaters. Biosensors can further be developed for specific conditions and environments with an in-depth understanding of microbial organization and interaction within that community. In this regard, bacteriophage-based biosensors have become a possibility to identify specific live bacteria in an infected environment. This paper has investigated the current scenario of microbial community analysis and biosensor development in identifying the presence of pathogenic microorganisms.

Cross-alteration of murine skin and tick microbiome concomitant with pathogen transmission after Ixodes ricinus bite

BACKGROUND

Ticks are major vectors of diseases affecting humans such as Lyme disease or domestic animals such as anaplasmosis. Cross-alteration of the vertebrate host skin microbiome and the tick microbiome may be essential during the process of tick feeding and for the mechanism of pathogen transmission. However, it has been poorly investigated.

METHODS

We used mice bitten by field-collected ticks (nymphs and adult ticks) in different experimental conditions to investigate, by 16S rRNA gene metabarcoding, the impact of blood feeding on both the mouse skin microbiome and the tick microbiome. We also investigated by PCR and 16S rRNA gene metabarcoding, the diversity of microorganisms transmitted to the host during the process of tick bite at the skin interface and the dissemination of the pathogen in host tissues (blood, heart, and spleen).

RESULTS

Most of the commensal bacteria present in the skin of control mice were replaced during the blood-feeding process by bacteria originating from the ticks. The microbiome of the ticks was also impacted by the blood feeding. Several pathogens including tick-borne pathogens (Borrelia/Borreliella, Anaplasma, Neoehrlichia, Rickettsia) and opportunistic bacteria (Williamsia) were transmitted to the skin microbiome and some of them disseminated to the blood or spleen of the mice. In the different experiments of this study, skin microbiome alteration and Borrelia/Borreliella transmission were different depending on the tick stages (nymphs or adult female ticks).

CONCLUSIONS

Host skin microbiome at the bite site was deeply impacted by the tick bite, to an extent which suggests a role in the tick feeding, in the pathogen transmission, and a potentially important impact on the skin physiopathology. The diversified taxonomic profiles of the tick microbiome were also modified by the blood feeding. Video Abstract.

Metagenomics insights into high-rate nitrogen removal from municipal wastewater by integrated nitrification, partial denitrification and Anammox at an extremely short hydraulic retention time

To achieve high-rate nitrogen removal in municipal wastewater treatment through anaerobic ammonia oxidation (Anammox), the nitrification, partial denitrification, and Anammox processes were integrated by a step-feed strategy. An exceptional nitrogen removal load of 0.224 kg N/(m3·d) was achieved by gradient-reducing the hydraulic retention time (HRT) to 5 h. Metagenomic analysis demonstrated that Nitrosospira could express all genes encoding ammonia oxidation under low nitrogen and dissolved oxygen conditions (less than 0.5 mg/L), enabling complete nitrification. With the short of HRT, the relative abundance of Thauera increased from 2.8 % to 6.4 %. Frequent substrate exchanges at such extremely short HRT facilitated enhanced synergistic interactions among Nitrosospira, Thauera, and Candidatus Brocadia. These findings provide a comprehensive understanding of the utilization of Anammox combined processes for high-speed nitrogen removal in municipal wastewater treatment and the microbial interactions involved.

Radiation impacts gene redundancy and biofilm regulation of cryoconite microbiomes in Northern Hemisphere glaciers

BACKGROUND

Glaciers harbor diverse microorganisms adapted to extreme conditions with high radiation, fluctuating temperature, and low nutrient availability. In glacial ecosystems, cryoconite granules are hotspots of microbial metabolic activity and could influences the biogeochemical cycle on glacier surface. Climate change could influence glacier dynamics by changing regional meteorological factors (e.g., radiation, precipitation, temperature, wind, and evaporation). Moreover, meteorological factors not only influence glacier dynamics but also directly or indirectly influence cryoconite microbiomes. However, the relationship of the meteorological factors and cryoconite microbiome are poorly understood.

RESULTS

Here, we collected 88 metagenomes from 26 glaciers distributed in the Northern Hemisphere with corresponding public meteorological data to reveal the relationship between meteorological factors and variation of cryoconite microbiome. Our results showed significant differences in taxonomic and genomic characteristics between cryoconite generalists and specialists. Additionally, we found that the biogeography of both generalists and specialists was influenced by solar radiation. Specialists with smaller genome size and lower gene redundancy were more abundant under high radiation stress, implying that streamlined genomes are more adapted to high radiation conditions. Network analysis revealed that biofilm regulation is a ubiquitous function in response to radiation stress, and hub genes were associated with the formation and dispersion of biofilms.

CONCLUSION

These findings enhance our understanding of glacier cryoconite microbiome variation on a hemispheric scale and indicate the response mechanisms to radiation stress, which will support forecasts of the ecological consequences of future climate change. Video Abstract.

Cont-ID: detection of sample cross-contamination in viral metagenomic data

BACKGROUND

High-throughput sequencing (HTS) technologies completed by the bioinformatic analysis of the generated data are becoming an important detection technique for virus diagnostics. They have the potential to replace or complement the current PCR-based methods thanks to their improved inclusivity and analytical sensitivity, as well as their overall good repeatability and reproducibility. Cross-contamination is a well-known phenomenon in molecular diagnostics and corresponds to the exchange of genetic material between samples. Cross-contamination management was a key drawback during the development of PCR-based detection and is now adequately monitored in routine diagnostics. HTS technologies are facing similar difficulties due to their very high analytical sensitivity. As a single viral read could be detected in millions of sequencing reads, it is mandatory to fix a detection threshold that will be informed by estimated cross-contamination. Cross-contamination monitoring should therefore be a priority when detecting viruses by HTS technologies.

RESULTS

We present Cont-ID, a bioinformatic tool designed to check for cross-contamination by analysing the relative abundance of virus sequencing reads identified in sequence metagenomic datasets and their duplication between samples. It can be applied when the samples in a sequencing batch have been processed in parallel in the laboratory and with at least one specific external control called Alien control. Using 273 real datasets, including 68 virus species from different hosts (fruit tree, plant, human) and several library preparation protocols (Ribodepleted total RNA, small RNA and double-stranded RNA), we demonstrated that Cont-ID classifies with high accuracy (91%) viral species detection into (true) infection or (cross) contamination. This classification raises confidence in the detection and facilitates the downstream interpretation and confirmation of the results by prioritising the virus detections that should be confirmed.

CONCLUSIONS

Cross-contamination between samples when detecting viruses using HTS (Illumina technology) can be monitored and highlighted by Cont-ID (provided an alien control is present). Cont-ID is based on a flexible methodology relying on the output of bioinformatics analyses of the sequencing reads and considering the contamination pattern specific to each batch of samples. The Cont-ID method is adaptable so that each laboratory can optimise it before its validation and routine use.

A multicenter prospective study of comprehensive metagenomic and transcriptomic signatures for predicting outcomes of patients with severe community-acquired pneumonia

BACKGROUND

Severe community-acquired pneumonia (SCAP) results in high mortality as well as massive economic burden worldwide, yet limited knowledge of the bio-signatures related to prognosis has hindered the improvement of clinical outcomes. Pathogen, microbes and host are three vital elements in inflammations and infections. This study aims to discover the specific and sensitive biomarkers to predict outcomes of SCAP patients.

METHODS

In this study, we applied a combined metagenomic and transcriptomic screening approach to clinical specimens gathered from 275 SCAP patients of a multicentre, prospective study.

FINDINGS

We found that 30-day mortality might be independent of pathogen category or microbial diversity, while significant difference in host gene expression pattern presented between 30-day mortality group and the survival group. Twelve outcome-related clinical characteristics were identified in our study. The underlying host response was evaluated and enrichment of genes related to cell activation, immune modulation, inflammatory and metabolism were identified. Notably, omics data, clinical features and parameters were integrated to develop a model with six signatures for predicting 30-day mortality, showing an AUC of 0.953 (95% CI: 0.92-0.98).

INTERPRETATION

In summary, our study linked clinical characteristics and underlying multi-omics bio-signatures to the differential outcomes of patients with SCAP. The establishment of a comprehensive predictive model will be helpful for future improvement of treatment strategies and prognosis with SCAP.

FUNDING

National Natural Science Foundation of China (No. 82161138018), Shanghai Municipal Key Clinical Specialty (shslczdzk02202), Shanghai Top-Priority Clinical Key Disciplines Construction Project (2017ZZ02014), Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases (20dz2261100).

Metagenomics and proteomics profiling of extracellular polymeric substances from municipal waste sludge and their application for soil and water bioremediation

This study assessed the components of anaerobically digested sludge, activated sludge, and microbial and extracellular polymeric substance (EPS) enzymes to identify the mechanisms underlying nitrogen removal and soil regeneration. 16S rRNA gene amplicon-based sequencing was used to determine the microbial community composition and the related National Center for Biotechnology Information (NCBI) protein database was used to construct a conventional library from the observed community. EPS components were identified using gel-free proteomic (Liquid Chromatography with tandem mass spectrometry-LC/MS/MS) methods. Alginate-like EPS from aerobically activated sludge have strong potential for soil aggregation and water-holding capacity, whereas total EPS from anaerobic sludge have significant potential for ammonia removal under salt stress. Fourier transform infrared spectroscopy (FTIR) revealed that both EPS may contain proteins, carbohydrates, humic compounds, uronic acid, and DNA and determined the presence of O-H, N-H, C-N, CO, and C-H functional groups. These results demonstrate that the overall enzyme activity may be inactivated at 30 g L-1 of salinity. An annotation found in Kyoto Encyclopedia of Genes and Genomes (KEGG)- KEGG Automatic Annotation Server (KAAS) revealed that the top two metabolic activities in the EPS generated from the anaerobic sludge were methane and nitrogen metabolism. Therefore, we focused on the nitrogen metabolism reference map 00910. EPS from the anaerobically digested sludge exhibited nitrate reductase, nitrite reductase, and dehydrogenase activities. Assimilatory nitrate reduction, denitrification, nitrification, and anammox removed ammonia biochemically. The influence of microbial extracellular metabolites on water-holding capacity and soil aggregation was also investigated. The KAAS-KEGG annotation server was used to identify the main enzymes in the activated sludge-derived alginate-like extracellular EPS (ALE-EPS) samples. These include hydrolases, oxidoreductases, lyases, ligases, and transporters, which contribute to soil fertility and stability. This study improves our understanding of the overall microbial community structure and the associated biochemical processes, which are related to distinct functional genes or enzymes involved in nitrogen removal and soil aggregation. In contrast to conventional methods, microbial association with proteomics can be used to investigate ecological relationships, establishments, key player species, and microbial responses to environmental changes. Linking the metagenome to off-gel proteomics and bioinformatics solves the problem of analyzing metabolic pathways in complex environmental samples in a cost-effective manner.

Intestinal Microbiomics and Metabolomics Insights into the Hepatoprotective Effects of Lactobacillus paracasei CCFM1222 Against the Acute Liver Injury in Mice

In recent years, acute liver injury (ALI) has received wide-range attention in the world due to its relatively high morbidity and mortality. This study aimed to explore the hepatoprotective effect of Lactobacillus paracasei CCFM1222 against lipopolysaccharide (LPS)-induced ALI mice and further elaborate its mechanism of action from the perspective of intestinal microbiomics and metabolomics. The results displayed that L. paracasei CCFM1222 pretreatment significantly decreased the serum ALT, and AST levels, inhibited the releases of hepatic TNF-α, IL-1β, and IL-6 levels, and activated the SOD, CAT, and GSH-Px activities in LPS-treated mice. The cecal short-chain fatty acid (SCFAs) levels were increased in LPS-treated mice with L. paracasei CCFM1222 pretreatment. In addition, L. paracasei CCFM1222 pretreatment remarkably shifted the intestinal microbiota composition, including the higher abundance of Faecalibaculum, Bifidobacterium, and lower abundance of the Prevotellaceae NK3B31 group, which is positively associated with the cecal propionic, butyric, valeric, isobutyric, and isovaleric acids. The metabolomics based on UPLC-QTOF/MS revealed that L. paracasei CCFM1222 pretreatment significantly regulated the composition of feces metabolites in LPS-treated mice, especially the potential biomarker-related butanoate metabolism, vitamin B6 metabolism, D-glutamine and D-glutamate metabolism, tryptophan metabolism, caffeine metabolism, arginine biosynthesis, arginine, and proline metabolism. Moreover, L. paracasei CCFM1222 pretreatment remarkably regulated the expression of gene-associated ALI (including Tlr4, Myd88, Nf-kβ, iNOS, Cox2, Iκ-Bα, Nrf2, and Sirt-1). In conclusion, these results suggest the possibility that L. paracasei CCFM1222 supplementation has beneficial effects on preventing the occurrence and development of ALI by inhibiting the inflammatory responses and altering intestinal microbiota composition and their metabolites.

Revealing bacterial and fungal communities of the untapped forest and alpine grassland zones of the Western-Himalayan region

The Western Himalayas offer diverse environments for investigating the diversity and distribution of microbial communities and their response to both the abiotic and biotic factors across the entire altitudinal gradient. Such investigations contribute significantly to our understanding of the complex ecological processes that shape microbial diversity. The proposed study focuses on the investigation of the bacterial and fungal communities in the forest and alpine grasslands of the Western Himalayan region, as well as their relationship with the physicochemical parameters of soil. A total of 185 isolates were obtained using the culture-based technique belonging to Bacillus (37%), Micrococcus (16%), and Staphylococcus (7%). Targeted metagenomics revealed the abundance of bacterial phyla Pseudomonadota (23%) followed by Acidobacteriota (20.2%), Chloroflexota (15%), and Bacillota (11.3%). At the genera level, CandidatusUdaeobacter (6%), Subgroup_2 (5.5%) of phylum Acidobacteriota, and uncultured Ktedonobacterales HSB_OF53-F07 (5.2%) of Choloroflexota phylum were found to be preponderant. Mycobiome predominantly comprised of phyla Ascomycota (54.1%), Basidiomycota (24%), and Mortierellomycota (19.1%) with Archaeorhizomyces (19.1%), Mortierella (19.1%), and Russula (5.4%) being the most abundant genera. Spearman's correlation revealed that the bacterial community was most influenced by total nitrogen in the soil followed by soil organic carbon as compared to other soil physicochemical factors. The study establishes a fundamental relationship between microbial communities and the physicochemical properties of soil. Furthermore, the study provides valuable insights into the complex interplay between biotic and abiotic factors that influence the microbial community composition of this unique region across various elevations.

Multi-omics analysis of fecal samples in colorectal cancer Egyptians patients: a pilot study

BACKGROUND

Colorectal cancer (CRC) is a public health concern and the second most common disease worldwide. This is due to genetic coding and is influenced by environmental aspects, in which the gut microbiota plays a significant role. The purpose of this study was to compare the microbiota makeup of CRC patients with that of healthy control and to identify upregulated and downregulated proteins and metabolites in CRC patients. Using a next-generation sequencing approach, fecal samples of five females (4 CRC patients and one healthy control) were analyzed by BGI DNBSEQ-T7, Hong Kong, China. Furthermore, proteomics and metabolomics analysis were performed using LC-MS/MS technique.

RESULTS

Dysbiosis of gut microbiota has been observed in patients with CRC, with an increase in microbiota diversity at all taxonomic levels relative to healthy control. Where, at the functional level the bacterial species participate in many different pathways among them de novo nucleotide synthesis and amino acids pathways were aberrantly upregulated in CRC patients. Proteomics and metabolomics profiles of CRC patients showed different proteins and metabolites, a total of 360 and 158 proteins and metabolites, respectively were highly expressed compared to healthy control with fold change ≥ 1.2. Among the highly expressed proteins were transketolase, sushi domain-containing protein, sulfide quinone oxidoreductase protein, AAA family ATPase protein, carbonic anhydrase, IgG Fc-binding protein, nucleoside diphosphate kinase protein, arylsulfatase, alkaline phosphatase protein, phosphoglycerate kinase, protein kinase domain-containing protein, non-specific serine/threonine protein kinase, Acyl-CoA synthetase and EF-hand domain-containing protein. Some of the differential metabolites, Taurine, Taurocholic acid, 7-ketodeoxycholic acid, Glycochenodeoxycholic acid, Glycocholic acid, and Taurochenodeoxycholic acid that belong to bile acids metabolites.

CONCLUSIONS

Some bacterial species, proteins, and metabolites could be used as diagnostic biomarkers for CRC. Our study paves an insight into using multi-omics technology to address the relationship between gut microbiota and CRC.

Metagenomic analysis reveals the relationship between intestinal protozoan parasites and the intestinal microecological balance in calves

BACKGROUND

A close connection between a protozoan parasite and the balance of the other gut microbes of the host has been demonstrated. The calves may be naturally co-infected with many parasites, and the co-effects of parasites on other intestinal microbes of calves remain unclear. This study aims to preliminarily reveal the relationship between intestinal parasites and other intestinal microbes in calves.

METHODS

Fecal samples were collected from four calves with bloody diarrhea, four calves with watery diarrhea, and seven normal calves, and the microbial flora of the samples were analyzed by whole-genome sequencing. Protozoal parasites were detected in the metagenome sequences and identified using polymerase chain reaction (PCR).

RESULTS

Cryptosporidium, Eimeria, Giardia, Blastocystis, and Entamoeba were detected by metagenomic analysis, and the identified species were Giardia duodenalis assemblage E, Cryptosporidium bovis, Cryptosporidium ryanae, Eimeria bovis, Eimeria subspherica, Entamoeba bovis, and Blastocystis ST2 and ST10. Metagenomic analysis showed that the intestinal microbes of calves with diarrhea were disordered, especially in calves with bloody diarrhea. Furthermore, different parasites show distinct relationships with the intestinal microecology. Cryptosporidium, Eimeria, and Giardia were negatively correlated with various intestinal bacteria but positively correlated with some fungi. However, Blastocystis and Entamoeba were positively associated with other gut microbes. Twenty-seven biomarkers not only were significantly enriched in bloody diarrhea, watery diarrhea, and normal calves but were also associated with Eimeria, Cryptosporidium, and Giardia. Only Eimeria showed a distinct relationship with seven genera of bacteria, which were significantly enriched in the healthy calves. All 18 genera of fungi were positively correlated with Cryptosporidium, Eimeria, and Giardia, which were also significantly enriched in calves with bloody diarrhea. Functional genes related to parasites and diseases were found mainly in fungi.

CONCLUSIONS

This study revealed the relationship between intestinal protozoan parasites and the other calf gut microbiome. Different intestinal protozoan parasites have diametrically opposite effects on other gut microecology, which not only affects bacteria in the gut, but also is significantly related to fungi and archaea.

Potential of direct granulation and organic loading rate tolerance of aerobic granular sludge in ultra-hypersaline environment

Salt-tolerant aerobic granular sludge (SAGS) technology has shown potentials in the treatment of ultra-hypersaline high-strength organic wastewater. However, the long granulation period and salt-tolerance acclimation period are still bottlenecks that hinder SAGS applications. In this study, "one-step" development strategy was used to try to directly cultivate SAGS under 9% salinity, and the fastest cultivation process was obtained under such high salinity compared to the previous papers with the inoculum of municipal activated sludge without bioaugmentation. Briefly, the inoculated municipal activated sludge was almost discharged on Day 1-10, then fungal pellets appeared and it gradually transitioned to mature SAGS (particle size of ∼4156 μm and SVI₃₀ of 57.8 mL/g) from Day 11 to Day 47 without fragmentation. Metagenomic revealed that fungus Fusarium played key roles in the transition process probably because it functioned as structural backbone. RRNPP and AHL-mediated systems might be the main QS regulation systems of bacteria. TOC and NH₄⁺-N removal efficiencies maintained at ∼93.9% (after Day 11) and ∼68.5% (after Day 33), respectively. Subsequently, the influent organic loading rate (OLR) was stepwise increased from 1.8 to 11.7 kg COD/m³·d. It was found that SAGS could maintain intact structure and low SVI₃₀ (< 55 mL/g) under 9% salinity and the OLR of 1.8-9.9 kg COD/m³·d with adjustment of air velocity. TOC and NH₄⁺-N (TN) removal efficiencies could maintain at ∼95.4% (below OLR of 8.1 kg COD/m³·d) and ∼84.1% (below nitrogen loading rate of 0.40 kg N/m³·d) in ultra-hypersaline environment. Halomonas dominated the SAGS under 9% salinity and varied OLR. This study confirmed the feasibility of direct aerobic granulation in ultra-hypersaline environment and verified the upper OLR boundary of SAGS in ultra-hypersaline high-strength organic wastewater treatment.

Metagenomic analysis of antimicrobial resistance in ducks, workers, and the environment in duck farms, southern China

Duck farms are one of the important reservoirs of antimicrobial resistance genes (ARGs) that spread to humans and the environment. However, few studies have focused on the characteristics of antimicrobial profiles in duck farms. Here we explored the distribution characteristics and potential transmission mechanisms of ARGs in ducks, farm workers, and the environment in duck farms by a metagenomic approach. The results showed that the highest abundance and diversity of ARGs were found in duck manure. The abundance and diversity of ARGs in workers and environmental samples were higher than those in the control group. tet(X) and its variants were prevalent in duck farms, with tet(X10) being the most abundant. The genetic structure "tet(X)-like + α/β hydrolase" was found in ducks, workers, and the environment, implying that tet(X) and its variants have been widely spread in duck farms. Network analysis indicated that ISVsa3 and IS5075 might play an important role in the coexistence of ARGs and metal resistance genes (MRGs). The Mantel tests showed that mobile genetic elements (MGEs) were significantly correlated with ARG profiles. The results suggest that duck manure may be a potential hotspot source of ARGs, including tet(X) variants that spread to the surrounding environment and workers via MGEs. These results help us optimize the antimicrobials strategy and deepen our understanding of ARG spread in duck farms.

Metagenomics and network analysis decipher profiles and co-occurrence patterns of bacterial taxa in soils amended with biogas slurry

Microbial community and interaction play crucial roles in ecological functions of soil including nutrient cycling carbon storage, and water maintenance etc. Numerous studies have shown that the application of fertilizers alters bacterial diversity; However, it remains unknown whether and how the continuous application of biogas slurry from anaerobic digestion affects the spatiotemporal heterogeneity of soil layers, complexity and stability of microbial networks, and functions related to C and N cycling. Here, we investigated the bacterial taxa of purple soils treated with swine biogas slurry for four different periods (0, 1, 3 and 8 years) and five different soil depths (20, 40, 60, 80 and 100 cm). The results showed that the application period of biogas slurry and soil depth were two powerful drivers of bacterial diversity and communities. Biogas slurry input resulted in marked changes in the bacterial diversity and composition at the soil depths of 0-60 cm. The relative abundances of Acidobacteriota, Myxococcot, and Nitrospirota decreased, while Actinobacteria, Chloroflexi, and Gemmatimonadota increased with repeated biogas slurry input. The decreasing complexity and stability of the bacterial network with decreasing nodes, links, robustness, and cohesions were found with increasing years of biogas slurry application, suggesting that the bacterial network of soils treated by the biogas slurry became more vulnerability compared with the control. Also, the linkages between the keystone taxa and soil properties were weakened after biogas slurry input, leading to the cooccurrence patterns being less affected by the keystones in the high level of nutrients. Metagenomic analysis confirmed that biogas slurry input increased the relative abundance of liable-C degradation and denitrification genes, which could highly impact the network properties. Overall, our study could give comprehensive understandings on the impacts of biogas slurry amendment on soils, which could be useful for maintaining sustainable agriculture and soil health with liquid fertilization.

The key role of denitrification and dissimilatory nitrate reduction in nitrogen pollution along vertical landfill profiles from metagenomic perspective

Landfill are persistent sources of nitrogen (N) pollution even in the decades after closure. However, the biological pathways of N-pollution, particularly N₂O and NH₄⁺, at different landfill depths have received little attention. In this study, metagenomic analysis was conducted on landfill refuse from vertical reservoir profiles in two closed landfills named XT and MT. NH₄⁺ concentrations were found to be higher in deeper layers of MT, while greater potential for N₂O emissions occurred in XT and the shallow layers of MT. Furthermore, the community structure and function of N-metabolizing microbes were more strongly defined by landfill depth than landfill type. Denitrification, involving abundant nirK and norB genes, was identified as the major pathway for N₂O production in both XT and MT-shallow, while dissimilatory nitrate reduction with abundant nirBD genes was identified as the major pathway for NH₄⁺ accumulation. Microbes of norB-type and nirBD-type were positively affected by NO₃^- in XT, whereas negatively affected by contents of organic material and moisture in MT-shallow. The mechanism by which nitrogen fixation, with abundant nifH genes, contributes to NH₄⁺ accumulation in MT-deep should be further elucidated. These findings can provide a theoretical basis for governing scientific N-pollution control strategies throughout the entire landfill process.

Exploring community dynamics: Cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistically designed conditions

Oil-based paint seriously threatens biodiversity due to its complex composition and biocide toxicity. Therefore, it alters the microbial diversity abundance and in modern approaches like metagenomic, a powerful tool to get insight into pollutants effect on soil microbial community abundance. Thus, present study aimed at "exploring community dynamics: cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistical designed conditions". The total DNA from oil-based paints polluted soil was extracted by PowerSoil DNA Isolation Kit. The 16S rDNA genes were amplified using universal primers and PCR amplicons were sequenced for analysis of metagenomes to determine the bacterial microbiome abundance. A total 133,140 sequence reads, 2857 Operational Taxonomic Units (OTUs) of 16S rRNA genes, and 30 bacterial phyla were retrieved from all the oil-based paints polluted samples (C, R498, B698 and G492) with the significant increase in Firmicutes (18.90 %, 52.39 %, 49.75 %, 44.36 %) and Actinobacteria (26.66 %, 28.93 %, 28.17 %, 14.68 %) whereas a decrease in Proteobacteria (19.53 %, 6.32 %, 9.37 %, 16.21 %), Chloroflexi (16.93 %, 8.71 %, 9.78 %, 18.17 %), and Bacteroidetes (8.96 %, 0.36 %, 0.41 %, 0.11 %) was recorded respectively. Additionally, the 100 % removal of oil-based paints (R498, B698 and G492) was achieved by the cultivable microbial consortia in laboratory settings. On the other hand for the R498 single cultivable pure isolates exhibited biodegradation potential as "PDB20, 91 %", "PDB14, 81 %", and "PDB16, 87 %" while for the blue B698, "PDB4, 86 %", "PDB20, 89 %", "PDB5, and PDB2, 80%". Moreover, in case of G492, maximum % removal was achieved with "PDB20, 93 %", "PDB5, 90 %", "PDB6, 90 %", "PDB16, 88 %", "PDB2, and PDB4, 89%". Conclusively, in comparison to R498 and B698, maximum percent removal was displayed by G492 and this might be attributed due to difference in pigment. Cultivable consortia and individual pure isolates demonstrated >80 % contribution in the % removal of oil-based paints.

Deciphering of sulfonamide biodegradation mechanism in wetland sediments: from microbial community and individual populations to pathway and functional genes

Figuring out the comprehensive metabolic mechanism of sulfonamide antibiotics (SA) is critical to improve and optimize SA removal in the bioremediation process, but relevant studies are still lacking. Here, an approach integrating metagenomic analysis, degraders' isolation, reverse transcriptional quantification and targeted metabolite determination was used to decipher microbial interactions and functional genes' characteristics in SA-degrading microbial consortia enriched from wetland sediments. The SA-degrading consortia could rapidly catalyze ipso-hydroxylation and subsequent reactions of SA to achieve the complete mineralization of sulfadiazine and partial mineralization of the other two typical SA (sulfamethoxazole and sulfamethazine). Paenarthrobacter, Achromobacter, Pseudomonas and Methylobacterium were identified as the primary participants for the initial transformation of SA. Among them, Methylobacterium could metabolize the heterocyclic intermediate of sulfadiazine (2-aminopyrimidine), and the owning of sadABC genes (SA degradation genes) made Paenarthrobacter have relatively higher SA-degrading activity. Besides, the coexistence of sadABC genes and sul1 gene (SA resistance gene) gave Paenarthrobacter a dual resistance mechanism to SA. The results of reverse transcription quantification further demonstrated that the activity of sadA gene was related to the biodegradation of SA. Additionally, sadABC genes were relatively conserved in a few Microbacteriaceae and Micrococcaceae SA-degraders, but the multiple recombination events caused by densely nested transposase encoding genes resulted in the differential sequence of sadAB genes in Paenarthrobacter genome. These new findings provide valuable information for the selection and construction of engineered microbiomes.

Temporal hormetic response of soil microbes to cadmium: A metagenomic perspective

The hormetic response of microbes to cadmium (Cd) is often observed in soil, but the mechanisms are unclear. In this study, we proposed a novel perspective of hormesis that successfully explained the temporal hermetic response of soil enzymes and microbes, and the variation of soil physicochemical properties. Several soil enzymatic and microbial activities were stimulated by 0.5 mg·kg^-1 exogenous Cd, but inhibited at higher Cd dosages. The phenomena suggested the hormetic response to 0.5 mg·kg^-1 Cd was highly generalizable concerning soil enzymes and microbial activity. However, the response disappeared after incubation for >10 days. Soil respiration was also initially enhanced by exogenous Cd and decreased after consumption of labile soil organic matter. The metagenomic results revealed Cd stimulation of genes involved in labile soil organic matter decomposition. Additionally, Cd enriched the antioxidant enzymatic activity and abundances of the corresponding marker genes, rather than genes involved in the efflux-mediated heavy metal resistance. The microbes enhanced their primary metabolism to make up the energy gaps, with hormesis evident. The hormetic response disappeared after the labile compounds in soil were exhausted. Overall, this study illustrates the dose-dependence and temporal variation of stimulants and provides a novel and feasible strategy for the study of Cd in soil microorganisms.

Configuration of gut bacterial community profile and their potential functionality in the digestive tract of the wild and cultivated Indonesian shortfin elver-phase eels (Anguilla bicolor bicolor McClelland, 1844)

This study aimed to explore the bacteria present in the digestive tracts of wild and cultivated Indonesian shortfin eel during the elver phase. The eel has high export potential due to its vitamin and micronutrient content, but slow growth and vulnerability to collapse in farm conditions hinder its cultivation. The microbiota in the eel's digestive tract is crucial for its health, particularly during the elver phase. This study used Next Generation Sequencing to analyze the community structure and diversity of bacteria in the eels' digestive tracts, focusing on the V3-V4 regions of the 16S rRNA gene. Mothur software was used for data analysis and PAST v.3.26 was used to calculate alpha diversity. The results showed that Proteobacteria (64.18%) and Firmicutes (33.55%) were the predominant phyla in the digestive tract of cultivated eels, while Bacteroidetes (54.16%), Firmicutes (14.71%), and Fusobacteria (10.56%) were predominant in wild eels. The most prevalent genera in cultivated and wild elver were Plesiomonas and Cetobacterium, respectively. The microbiota in the digestive tract of cultivated eels was diverse despite uneven distribution. The KEGG database analysis revealed that the primary function of the microbiome was to facilitate the eel's absorption of nutrients by contributing significantly to the metabolism of carbohydrates and amino acids. This study's findings can aid in assessing eel health and improving eel farming conditions.

Revisiting the biological pathway for methanogenesis in landfill from metagenomic perspective-A case study of county-level sanitary landfill of domestic waste in North China plain

Landfill is the third highest contributor to anthropogenic methane (CH₄) emissions, produced primarily by the anaerobic decomposition of organic matter by microbes. However, how various microbial metabolic processes contribute to CH₄ production in domestic waste landfill remains elusive. We addressed this problem by investigating the methanogenic communities, methanogenic functional genes, KEGG modules and KEGG pathways in a county-level MSW sanitary landfill in North China Plain, China. Results showed that Methanomicrobiales, Methanobacteriales, Methanosarcinales, Micrococcales, Corynebacteriales and Bacillales were the dominant methanogens. M00357, M00346, M00567 and M00563 were the four major methane metabolic modules. The most abundant genes were ACSS, ackA and fwd with the relative abundance of 19.26-54.54%, 6.14-25.78% and 6.76-16.51%, respectively. The two essential genes of methanogenesis were detected with the relative abundance of 2.66-9.58% (mtr) and 1.63-9.14% (mcr). These findings indicated that acetotrophic and hydrogenotrophic methanogenesis were the major pathways. Methanomicrobiales, Methanosarcinales and Clostridiales were the key microbes to these pathways identified by co-occurrence network. Analysis of relative contribution of species to function further showed that Micrococcales, Corynebacteriales and Bacillales were special contributors to acetotrophic methanogenesis pathway. Redundancy analysis revealed that above functional genes and microbes were mainly controlled by NH₄⁺ and pH. Our results can help to provide develop the fine management strategies for methane utilization and emission reduction in landfill.

Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms

In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the environment, and humans, thereby threatening human health. Therefore, based on metagenomic analysis methods, ARGs and mobile genetic elements (MGEs) were annotated in pig manure samples from 6 pig farms in 3 regions of Shanxi Province, and the potential hosts of ARGs were analyzed. The results showed that a total of 14 ARG types were detected, including 182 ARG subtypes, among which tetracycline, phenol, aminoglycoside, and macrolide resistance genes were the main ones. ARG profiles, MGE composition, and microbial communities were significantly different in different regions as well as between different pig farms. In addition, Anaerobutyricum, Butyrivibrio, and Turicibacter were significantly associated with multiple ARGs, and bacteria such as Prevotella, Bacteroides, and the family Oscillospiraceae carried multiple ARGs, suggesting that these bacteria are potential ARG hosts in pig manure. Procrustes analysis showed that bacterial communities and MGEs were significantly correlated with ARG profiles. Variation partitioning analysis results indicated that the combined effect of MGEs and bacterial communities accounted for 64.08% of resistance variation and played an important role in ARG profiles. These findings contribute to our understanding of the dissemination and persistence of ARGs in actual production settings, and offer some guidance for the prevention and control of ARGs contamination.

Effects of OsomeFood Clean Label plant-based meals on the gut microbiome

BACKGROUND

Plant-based diets offer more beneficial microbes and can modulate gut microbiomes to improve human health. We evaluated the effects of the plant-based OsomeFood Clean Label meal range ('AWE' diet), on the human gut microbiome.

METHODS

Over 21 days, ten healthy participants consumed OsomeFood meals for five consecutive weekday lunches and dinners and resumed their regular diets for other days/meals. On follow-up days, participants completed questionnaires to record satiety, energy and health, and provided stool samples. To document microbiome variations and identify associations, species and functional pathway annotations were analyzed by shotgun sequencing. Shannon diversity and regular diet calorie intake subsets were also assessed.

RESULTS

Overweight participants gained more species and functional pathway diversity than normal BMI participants. Nineteen disease-associated species were suppressed in moderate-responders without gaining diversity, and in strong-responders with diversity gains along with health-associated species. All participants reported improved short-chain fatty acids production, insulin and γ-aminobutyric acid signaling. Moreover, fullness correlated positively with Bacteroides eggerthii; energetic status with B. uniformis, B. longum, Phascolarctobacterium succinatutens, and Eubacterium eligens; healthy status with Faecalibacterium prausnitzii, Prevotella CAG 5226, Roseburia hominis, and Roseburia sp. CAG 182; and overall response with E. eligens and Corprococcus eutactus. Fiber consumption was negatively associated with pathogenic species.

CONCLUSION

Although the AWE diet was consumed for only five days a week, all participants, especially overweight ones, experienced improved fullness, health status, energy and overall responses. The AWE diet benefits all individuals, especially those of higher BMI or low-fiber consumption.

Insight into universality and characteristics of nitrate reduction coupled with arsenic oxidation in different paddy soils

Nitrate reduction coupled with arsenic (As) oxidation strongly influences the bioavailability and toxicity of As in anaerobic environments. In the present study, five representative paddy soils developed from different parent materials were used to investigate the universality and characteristics of nitrate reduction coupled with As oxidation in paddy soils. Experimental results indicated that 99.8 % of highly toxic aqueous As(III) was transformed to dissolved As(V) and Fe-bound As(V) in the presence of nitrate within 2-8 d, suggesting that As was apt to be reserved in its low-toxic and nonlabile form after nitrate treatment. Furthermore, nitrate additions also significantly induced the higher abundance of 16S rRNA and As(III) oxidase (aioA) genes in the five paddy soils, especially in the soils developed from purple sand-earth rock and quaternary red clay, which increased by 10 and 3-5 times, respectively, after nitrate was added. Moreover, a variety of putative novel nitrate-dependent As(III)-oxidizing bacteria were identified based on metagenomic analysis, mainly including Aromatoleum, Paenibacillus, Microvirga, Herbaspirillum, Bradyrhizobium, Azospirillum. Overall, all these findings indicate that nitrate reduction coupled with As(III) oxidation is an important nitrogen-As coupling process prevalent in paddy environments and emphasize the significance of developing and popularizing nitrate-based biotechnology to control As pollution in paddy soils and reduce the risk of As compromising food security.

[Metagenomic next-generation sequencing of plasma for the identification of bloodstream infectious pathogens in severe aplastic anemia]

Objective: To analyze the diagnostic value of cell-free plasma metagenomic next-generation sequencing (mNGS) pathogen identification for severe aplastic anemia (SAA) bloodstream infection. Methods: From February 2021 to February 2022, mNGS and conventional detection methods (blood culture, etc.) were used to detect 33 samples from 29 consecutive AA patients admitted to the Anemia Diagnosis and Treatment Center of the Hematology Hospital of the Chinese Academy of Medical Sciences to assess the diagnostic consistency of mNGS and conventional detection, as well as the impact on clinical treatment benefits and clinical accuracy. Results: ①Among the 33 samples evaluated by mNGS and conventional detection methods, 25 cases (75.76%) carried potential pathogenic microorganisms. A total of 72 pathogenic microorganisms were identified from all cases, of which 65 (90.28%) were detected only by mNGS. ②All 33 cases were evaluated for diagnostic consistency, of which 2 cases (6.06%) were Composite, 18 cases (54.55%) were mNGS only, 2 cases (6.06%) were Conventional method only, 1 case (3.03%) was both common compliances (mNGS/Conventional testing) , and 10 cases (30.3%) were completely non-conforming (None) . ③All 33 cases were evaluated for clinical treatment benefit. Among them, 8 cases (24.24%) received Initiation of targeted treatment, 1 case (3.03%) received Treatment de-escalation, 13 cases (39.39%) received Confirmation, and the remaining 11 cases (33.33%) received No clinical benefit. ④ The sensitivity of 80.77%, specificity of 70.00%, positive predictive value of 63.64%, negative predictive value of 84.85%, positive likelihood ratio of 2.692, and negative likelihood ratio of 0.275 distinguished mNGS from conventional detection methods (21/12 vs 5/28, P<0.001) . Conclusion: mNGS can not only contribute to accurately diagnosing bloodstream infection in patients with aplastic anemia, but can also help to guide accurate anti-infection treatment, and the clinical accuracy is high.

Metagenomic insights into responses of microbial population and key functional genes to fulvic acid during partial nitritation

The long-term impact of fulvic acid (FA) on partial nitritation (PN) system was initially examined in this study. The obtained results revealed that the FA lower than 50 mg/L had negligible effect on the nitrite accumulation rate (NAR nearly 100%) and ammonium removal rate (ARR 56.85%), while FA over 50 mg/L decreased ARR from 56.85% to 0.7%. Sludge characteristics analysis found that appropriate FA (<50 mg/L) exposure promoted the settling performance and granulation of PN sludge by removing Bacteroidetes and accumulating Chloroflexi. The analysis of metagenomics suggested that the presence of limited FA (0-50 mg/L) stimulated the generation of NADH, which favors the denitrification and nitrite reduction. The negative impact of FA on the PN system could be divided into two stages. Initially, limited FA (50-120 mg/L) was decomposed by Anaerolineae to stimulate the growth and propagation of heterotrophic bacteria (Thauera). Increasing heterotrophs competed with AOB (Nitrosomonas) for dissolved oxygen, causing AOB to be eliminated and ARR to declined. Subsequently, when FA dosage was over 120 mg/L, Anaerolineae were inhibited and heterotrophic bacteria reduced, resulting in the abundance of AOB recovered. Nevertheless, the ammonium transformation pathway was suppressed because genes amoABC and hao were obviously reduced, leading to the deterioration of reactor performance. Overall, these results provide theoretical guidance for the practical application of PN for the treatment of FA-containing sewage.