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Metagenomic sequencing has emerged as a transformative tool in infectious disease diagnosis, offering a comprehensive and unbiased approach to pathogen detection. Leveraging international standards and guidelines is essential for ensuring the quality and reliability of metagenomic sequencing in clinical practice. This review explores the implications of international standards and guidelines for the application of metagenomic sequencing in infectious disease diagnosis. By adhering to established standards, such as those outlined by regulatory bodies and expert consensus, healthcare providers can enhance the accuracy and clinical utility of metagenomic sequencing. The integration of international standards and guidelines into metagenomic sequencing workflows can streamline diagnostic processes, improve pathogen identification, and optimize patient care. Strategies in implementing these standards for infectious disease diagnosis using metagenomic sequencing are discussed, highlighting the importance of standardized approaches in advancing precision infectious disease diagnosis initiatives. [ABSTRACT FROM AUTHOR]

Aichi virus C , a species in the genus Kobuvirus , causes diarrhea diseases in pigs and goats and pose health threat and economic loss for stock farming. A nearly complete genome sequence of caprine kobuvirus GCCDC14 was obtained from an anal swab of a black goat died from diarrhea collected in Hubei, China in 2019. Phylogenetic analyses suggested that GCCDC14 is a novel genotype of Aichi virus C, forming a sister branch to other caprine kobuviruses, with P1 and VP0 genes more closely related to porcine kobuviruses and VP3 in an independent branch. Compared to previous caprine kobuviruses, unique amino acid changes in the poly- l -proline type II helix structure of VP0 and VP1 were found, which may affect the cellular machinery of host and pathogenicity. This study indicates the presence of the kobuvirus with continuously evolving features and emphasizes the surveillance and genetic evolution investigation of kobuviruses for safety of husbandry. [Display omitted] • First detection of caprine kobuvirus in black goats in central China. • This caprine kobuvirus had varying degrees of amino acid mutations in the poly- l -proline type Ⅱ helix structural region of VP0 and VP1. • Homology comparsion and phylogenetic trees showed that the caprine kobuvirus was probably a novel genotype of Aichi virus C , forming a separate cluster within it. [ABSTRACT FROM AUTHOR]

The microbiome is of great interest due to its potential influence on the occurrence and treatment of some human illnesses. It may be regarded as disruptions to the delicate equilibrium that humans ordinarily maintain with their microorganisms or the microbiota in their environment. The focus of this review is on the methodologies and current understanding of the functional microbiome in pregnancy outcomes. We present how novel techniques bring new insights to the contemporary field of maternal–fetal medicine with a critical analysis. The maternal microbiome in late pregnancy has been extensively studied, although data on maternal microbial changes during the first trimester are rare. Research has demonstrated that, in healthy pregnancies, the origin of the placental microbiota is oral (gut) rather than vaginal. Implantation, placental development, and maternal adaptation to pregnancy are complex processes in which fetal and maternal cells interact. Microbiome dysbiosis or microbial metabolites are rising as potential moderators of antenatal illnesses related to the placenta, such as fetal growth restriction, preeclampsia, and others, including gestational diabetes and preterm deliveries. However, because of the presence of antimicrobial components, it is likely that the bacteria identified in placental tissue are (fragments of) bacteria that have been destroyed by the placenta's immune cells. Using genomic techniques (metagenomics, metatranscriptomics, and metaproteomics), it may be possible to predict some properties of a microorganism's genome and the biochemical (epigenetic DNA modification) and physical components of the placenta as its environment. Despite the results described in this review, this subject needs further research on some major and crucial aspects. The phases of an in utero translocation of the maternal gut microbiota to the fetus should be explored. With a predictive knowledge of the impacts of the disturbance on microbial communities that influence human health and the environment, genomics may hold the answer to the development of novel therapies for the health of pregnant women. [ABSTRACT FROM AUTHOR]

Most zoonotic pathogens originate from mammals and avians, but viral diversity and related biosafety risk assessment in lower vertebrates also need to be explored. Amphibians are an important group of lower vertebrates that played a momentous role in animal evolution. To elucidate the diversity of RNA viruses in one important species of amphibians, the Asiatic toad (Bufo gargarizans), we obtained 44 samples including lung, gut, liver, and kidney tissues from Asiatic toads in Sichuan and Jilin provinces, China, for viral metagenomics sequencing. More than 20 novel RNA viruses derived from the order Bunyavirales and 7 families of Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, and Virgaviridae were discovered, which were distinct from previously described viruses and formed new clusters, as revealed by phylogenetic analyses. Notably, a novel bastrovirus, AtBastV/GCCDC11/2022, of the family Astroviridae was identified from the gut library, the genome of which contains three open reading frames, with the RNA-dependent RNA polymerase (RdRp) coded by ORF1 closely related to that of hepeviruses, and ORF2 encoding an astrovirus-related capsid protein. Notably, phenuiviruses were discovered for the first time in amphibians. AtPhenV1/GCCDC12/2022 and AtPhenV2/GCCDC13/2022 clustered together and formed a clade with the group of phenuiviruses identified from rodents. Picornaviruses and several invertebrate RNA viruses were also detected. These findings improve our understanding of the high RNA viral diversity in the Asiatic toad and provide new insights in the evolution of RNA viruses in amphibians. [ABSTRACT FROM AUTHOR]

Many studies have reported microbial signatures in thrombi at major vascular sites, such as the coronary artery and the middle cerebral artery, which are critical for maintaining proper blood flow and oxygenation. Chronic thromboembolic pulmonary hypertension (CTEPH) is a condition involving non-resolving thrombosis that has not been fully studied. This study explored the microbial taxonomy and functional profiles of both fresh and organized thrombi associated with CTEPH to investigate the role of microbiota in thrombus non-resolving. In this study, 12 CTEPH fresh thrombi and 12 organized thrombi were collected from 14 patients with CTEPH. Metagenomic sequencing was employed to explore the genomic information of all microorganisms in the thrombus samples. Our data demonstrated a diverse range of microorganisms in CTEPH thrombi, whether fresh or organized. Notably, a considerable proportion (54.7 %) of sequencing data could not be classified into the relative microbial taxa, highlighting the complexity and novelty of the thrombus ecosystem. Although there were no significant differences in microbial community structure between the two groups, the abundance of dominant microbial species varied. Leuconostoc sp. DORA 2 , Staphylococcus aureus, and Aliidongia dinghuensis were common dominant species in CTEPH thrombus. Organized thrombus significantly increased the relative abundance of Staphylococcus aureus, which was confirmed to effectively distinguish between organized and fresh thrombi by LeFSe analysis and random forest analysis. Functional annotation using both the KEGG and eggNOG databases revealed that organized thrombi exhibit stronger metabolic functions, particularly in amino acid metabolism. Our findings suggest that microbial composition and function may play an important role in thrombus organization. Targeting inflammation to prevent thrombosis presents promising opportunities for further research in this area. • Metagenomics sequencing is performed first to characterize the microbiota of CTEPH fresh and organized thrombi. • Microbial taxonomy classification results reveal the complexity and novelty of the thrombus ecosystem. • The abundance of dominant microbial species differs between organized and fresh thrombi. • Organized thrombus significantly increased the relative abundance of Staphylococcus aureus compared to fresh thrombi. • Organized thrombi exhibit stronger metabolic functions, particularly in amino acid metabolism. [ABSTRACT FROM AUTHOR]

The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches. In this study, we aimed to evaluate and compare the performance of these methods to screen antibiotic resistance genes in animal faecal, wastewater, and water samples. Water and wastewater samples were from hospital effluent, different treatment stages of two treatment plants, and of the receiving river at the discharge point. The animal samples were from pig and chicken faeces. Antibiotic resistance gene coverage, sensitivity, and usefulness of the quantitative information were analyzed and discussed. While both methods were able to distinguish the resistome profiles and detect gradient stepwise mixtures of pig and chicken faeces, qPCR presented higher sensitivity for the detection of a few antibiotic resistance genes in water/wastewater. In addition, the comparison of predicted and observed antibiotic resistance gene quantifications unveiled the higher accuracy of qPCR. Metagenomics analyses, while less sensitive, provided a markedly higher coverage of antibiotic resistance genes compared to qPCR. The complementarity of both methods and the importance of selecting the bestmethod according to the study purpose are discussed. [ABSTRACT FROM AUTHOR]

Nitrate-dependent anaerobic methane oxidation (Nitrate-DAMO) is a novel and sustainable process that removes both nitrogen and methane. Previously, the metabolic pathway of Nitrate-DAMO has been intensively studied with some results. However, the production and consumption of nitrous oxide (N 2 O) in the Nitrate-DAMO system were widely disregarded. In this study, a Nitrate-DAMO system was used to investigate the effect of operational parameters (C/N ratio, pH, and temperature) on N 2 O accumulation, and the optimal operating conditions were determined (C/N = 3, pH = 6.5, and temperature = 20 °C). In this study, an enzyme kinetic model was used to fit the nitrate nitrogen degradation and the nitrous oxide production and elimination under different operating conditions. The thermodynamic model of N 2 O production and elimination in the system also has been constructed. Multiple linear regression analysis found that pH was the most important factor influencing N 2 O accumulation. The Metagenomics sequencing results showed that alkaline pH promoted the abundance of Nor genes and denitrifying bacteria, which were significantly and positively correlated with N 2 O emissions. And alkaline pH also promoted the production of Mdo genes related to the N 2 O-driven AOM reaction, indicating that part of the N 2 O was consumed by denitrifying bacteria and the other part was consumed by the N 2 O-driven AOM reaction. These findings reveal the mechanism of N 2 O production and consumption in DAMO systems and provide a theoretical basis for reducing N 2 O production and greenhouse gas emissions in actual operation. [Display omitted] • The optimum operation conditions of the N-DAMO system were explored. • The enzyme kinetic model well fitted to the measured N 2 O production. • Alkaline increased the abundance of Nor genes, leading to N 2 O accumulation. • N 2 O reductase activity decreased with increasing pH. • The production and consumption pathways of N 2 O in the N-DAMO system were proposed. [ABSTRACT FROM AUTHOR]

Wepreviously demonstrated in non-human primates (NHP) thatMediterranean diet consumption shifted the proportional abundance of Lactobacillus in the breast and gut. This data highlights a potential link about gutbreast microbiome interconnectivity. To address this question, we compared bacterial populations identified in matched breast and faecal samples fromourNHP study. Dietary pattern concurrently shifted two species in both regions; Streptococcus lutetiensis and Ruminococcus torques. While we observe similar trends in Lactobacillus abundances in the breast and gut, the species identified in each region vary; Mediterranean diet increased Lactobacillus_ unspecified species in breast but regulated L. animalis and L. reuteri in the gut. We also investigated the impact of gut permeability on the breast microbiome. Regardless of dietary pattern, subjects that displayed increased physiological measures of gut permeability (elevated plasma lipopolysaccharide, decreased villi length, and decreased goblet cells) displayed a significantly different breast microbiome. Gut barrier dysfunction was associated with increased a-diversity and significant different β-diversity in the breast tissue. Taken together our data supports the presence of a breast microbiome influenced by diet that largely varies from the gut microbiome population but is, however, sensitive to gut permeability. [ABSTRACT FROM AUTHOR]

Metagenomics data provide rich information for the detection of foodborne pathogens from food and environmental samples that are mixed with complex background bacteria strains. While pathogen detection from metagenomic sequencing data has become an activity of increasing interest, shotgun sequencing of uncultured food samples typically produces data that contain reads from many different organisms, making accurate strain typing a challenging task. Particularly, as many pathogens may contain a common set of genes that are highly similar to those from normal bacteria in food samples, traditional strain-level abundance profiling approaches do not perform well at detecting pathogens of very low abundance levels. To overcome this limitation, we propose an abundance correction method based on species-specific genomic regions to achieve high sensitivity and high specificity in target pathogen detection at low abundance. [ABSTRACT FROM AUTHOR]

Background: Colorectal cancer (CRC) screening reduces CRC incidence and mortality. However, current screening methods are either hampered by invasiveness or suboptimal performance, limiting their effectiveness as primary screening methods. To aid in the development of a non-invasive screening test with improved sensitivity and specificity, we have initiated a prospective biomarker study (CRCbiome), nested within a large randomized CRC screening trial in Norway. We aim to develop a microbiome-based classification algorithm to identify advanced colorectal lesions in screening participants testing positive for an immunochemical fecal occult blood test (FIT). We will also examine interactions with host factors, diet, lifestyle and prescription drugs. The prospective nature of the study also enables the analysis of changes in the gut microbiome following the removal of precancerous lesions.Methods: The CRCbiome study recruits participants enrolled in the Bowel Cancer Screening in Norway (BCSN) study, a randomized trial initiated in 2012 comparing once-only sigmoidoscopy to repeated biennial FIT, where women and men aged 50-74 years at study entry are invited to participate. Since 2017, participants randomized to FIT screening with a positive test result have been invited to join the CRCbiome study. Self-reported diet, lifestyle and demographic data are collected prior to colonoscopy after the positive FIT-test (baseline). Screening data, including colonoscopy findings are obtained from the BCSN database. Fecal samples for gut microbiome analyses are collected both before and 2 and 12 months after colonoscopy. Samples are analyzed using metagenome sequencing, with taxonomy profiles, and gene and pathway content as primary measures. CRCbiome data will also be linked to national registries to obtain information on prescription histories and cancer relevant outcomes occurring during the 10 year follow-up period.Discussion: The CRCbiome study will increase our understanding of how the gut microbiome, in combination with lifestyle and environmental factors, influences the early stages of colorectal carcinogenesis. This knowledge will be crucial to develop microbiome-based screening tools for CRC. By evaluating biomarker performance in a screening setting, using samples from the target population, the generalizability of the findings to future screening cohorts is likely to be high.Trial Registration: ClinicalTrials.gov Identifier: NCT01538550 . [ABSTRACT FROM AUTHOR]

Although immunomodulatory activities of Dendrobium officinale polysaccharide has been investigated for many years, yet the potential contribution of its metabolite derived from intestinal microbes on immunoregulation effect has not been reported. In this study, polysaccharide DOW-5B with average molecular weight of 39.4 kDa was isolated from the stem of Dendrobium officinale Kimura et Migo. The carbohydrate content was 91.97% and no protein was detected. The monosaccharide analysis showed this polysaccharide was composed of glucuronic acid and glucose at a molar ratio (M/G) of 1.2:19.4. Animal test indicated DOW-5B increased the diversity of gut microbiota on mice. Beneficial microbes such as Ruminococcus , Eubacterium , Clostridium , Bifidobacterium , Parabacteroides and Akkermansia muciniphila increased while harmful bacteria in Proteobacteria decreased. Surprisingly, DOW-5B promoted gut microbes to generate more butyrate and mainly produced by Parabacteroides HGS0025. Further, we found the health of large intestine as well as immunity response of mice was improved. In addition, Parabacteroides HGS0025 positively correlated with butyrate, IgM, IL-10, and TNF-α products in intestine and mice blood, respectively. The data suggested that Dendrobium officinale polysaccharide has function on immunity may be mediated by butyrate. It adds new evidence to support the basis of how herbal polysaccharides affect immunity. Unlabelled Image [ABSTRACT FROM AUTHOR]

Omics data usually have ultra-high dimension (p) and small sample size (n). Standard support vector machines (SVMs), which minimize the L2 norm for the primal variables, only lead to sparse solutions for the dual variables. L1 based SVMs, directly minimizing the L1 norm, have been used for feature selection with omics data. However, most current methods directly solve the primal formulations of the problem, which are not computationally scalable. The computational complexity increases with the number of features. In addition, L1 norm is known to be asymptotically biased and not consistent for feature selection. In this paper, we develop an efficient method for sparse support vector machines with L0 norm approximation. The proposed method approximates the L0 minimization through solving a series of L2 optimization problems, which can be formulated with dual variables. It finds the optimal solution for p primal variables through estimating n dual variables, which is more efficient as long as the sample size is small. L0 approximation leads to sparsity in both dual and primal variables, and can be used for both feature and sample selections. The proposed method identifies much less number of features and achieves similar performances in simulations. We apply the proposed method to feature selections with metagenomic sequencing and gene expression data. It can identify biologically important genes and taxa efficiently. [ABSTRACT FROM AUTHOR]

Corydalis saxicola Bunting (CS), a traditional Chinese folk medicine, has been effectively used for treating liver disease in Zhuang nationality in South China. However, the main anti-liver fibrosis ingredients in CS are incompletely understood. To elucidate the main anti-liver fibrosis ingredients in CS and its underlying mechanism. Firstly, spectrum-effect relationship (SER) strategy was applied to identify the major ingredients against liver fibrosis in CS. Subsequently, 1H NMR metabonomics and metagenomics sequencing techniques were used to clarify the intervention of palmatine (PAL) on liver fibrosis. Furthermore, the expression of tight junction proteins and the levels of liver inflammation factors were examined, the effect of PAL on microbiota was verified by FMT. The SER model revealed that PAL was the most important active ingredient in CS. 1H NMR fecal metabonomics showed that PAL could reserve the abnormal levels of gut microbial-mediated metabolites of liver fibrosis, such as isoleucine, taurine, butyrate, propionate, lactate, glucose, which mainly involved in amino acid metabolism, intestinal flora metabolism and energy metabolism. Metagenomics sequencing found that PAL could callback the abundance of s__Lactobacillus_murinus, s__Lactobacillus_reuteri, s__Lactobacillus_johnsonii, s__Lactobacillus_acidophilus and s__Faecalibaculum_rodentium to varying degree. Furthermore, the intestinal barrier function and the levels of hepatic inflammation factors were significantly ameliorated by PAL. FMT demonstrated that the therapeutic efficiency of PAL was closely associated with gut microbiota. The effects of CS on liver fibrosis were attributed in part to PAL by alleviating metabolic disorders and rebalancing gut microbiota. The SER strategy may be a useful method for the discovery of active constituents in natural plants. • SER strategy was used to identify the main active ingredients in CS. • PAL was revealed as the main component of CS against liver fibrosis. • PAL could improve CCl 4 -induced liver fibrosis by ameliorating metabolic disorder and rebalancing gut microbiota. [ABSTRACT FROM AUTHOR]

[Display omitted] • Environmental persistent free radicals enhanced hydrolases activity. • Environmental persistent free radicals improved the ratio of coenzyme factor pair. • The abundance of the propionic acid-related ([EC:7.1.1.2]) gene was increased. • The methanogenesis ([EC:2.1.1.86]) was inhibited. The conversion of organic matter in waste activated sludge (WAS) into high value-added chemicals of volatile fatty acids (VFAs) has become a focus of attention worldwide. However, the conversion of WAS to a certain acid among VFAs is difficult. Herein, for the first time, biochar was used to promote sludge solubilization, hydrolysis and acidogenic fermentation for the production of propionic acid. The results illustrated that biochar (prepared at 450 °C, containing environmental persistent free radicals (EPFRs) of 15.91 × 1015 spins/g) stimulated sludge solubilization, hydrolysis and VFAs production, enhancing sludge cell lysis rate, VFAs production, propionic acid ratio, protease, α-glucosidase and nicotinamide adenine dinucleotide hydrogen (NADH)/nicotinamide adenine dinucleotide (NAD+) ratio by 10.53 %, 107.42 %, 17.52 %, 68 %, 32 % and 76.10 % respectively, compared with those observed in the control group without biochar addition. And once the EPFRs were shielded, they decreased. The signal of EPFRs decreased from 15.91 × 1015 spins/g to 15.20 × 1015 spins/g on day 2 and 8.50 × 1015 spins/g on day 4. The EPFRs contained in the biochar played an important role in the intermediary function and interfered with the bacterial metabolic pathways. Metagenomics sequencing also revealed that biochar EPFRs promoted the sludge acidogenic fermentation to produce propionic acid ([EC:7.1.1.2]) and partly inhibited acetic acid production ([EC:1.2.1.3]). This study reveals that biochar could promote sludge solubilization, hydrolysis and promote propionic acid production, which could be used as a new strategy for acid production in the future. [ABSTRACT FROM AUTHOR]

• Diosgenin reduces bone loss in ovariectomized rats. • Diosgenin restores the composition of GM in ovariectomized rats. • Diosgenin prevents the up-regulation of metabolism pathways. Diosgenin (DIO) is an aglycone of steroid saponins acquired from plants, including Dioscorea alata , Smilax China , and Trigonella foenum graecum , acting as an anti-osteoporosis, anti-diabetic, anti-hyperlipidemic, anti-inflammatory. Recent studies have demonstrated that DIO reduces bone loss. This study aimed to investigate the effects of DIO on the gut microbiota (GM) of ovariectomized (OVX) osteoporotic rats. Female Sprague-Dawley rats were randomly divided into sham operation (sham + vehicle group) or ovariectomy. For 12 weeks, OVX rats were treated using a vehicle (OVX + vehicle group) and DIO (OVX + DIO group). Subsequently, ELISA was conducted to determine serum estradiol levels, micro-CT scanning was performed to evaluate bone quality, and feces were collected for metagenomics sequencing to examine the structure and function of GM. Raw reads were filtered to remove chimera sequences. Operational taxonomic units (OTUs) were clustered in the filtered reads. A Venn diagram analysis was conducted to study the common and unique OTUs in the sham + vehicle, OVX + vehicle, and OVX + DIO groups. LEfSe analysis was conducted to evaluate the specific GM of the three groups. The GM functions were analyzed using the KEGG and CAZy databases. After a 12-week treatment, DIO administration prevented OVX-induced weight gain and increased the estradiol levels. DIO treatment improved the bone microstructure and structural parameters of rat tibias. Metagenomics sequencing results identified 1139, 1207, and 1235 operational taxonomic units (OTUs) in the sham + vehicle, OVX + vehicle, and OVX + DIO groups, respectively. The percentage of common OTUs was 41.2%. Treatment with DIO restored the composition of GM in OVX rats by increasing the abundance of Coriobacteriia Adlercreutzia, Romboutsia, and Romboutsia_idealis and reducing the abundance of Betaproteobacteria, Gammaproteobacteria, Methanobacteria, Bacteroides, Phocaeicola, Alistipes, Bacteroids_uniformis, Bacteroids_xylanisolvens. The anti-osteoporosis effect of DIO can be regulated through environmental information processing, organismal Systems, Cellular Processes, human diseases, metabolism, and genetic information processing. Meanwhile, treatment with DIO improved GM homeostasis by increasing the metabolism of carbohydrates, other amino acids, and glycans and reducing translation, energy metabolism, and nucleotide metabolism. DIO can reduce bone loss by regulating the structural composition and function of GM, a novel strategy for preventing osteoporosis. [ABSTRACT FROM AUTHOR]

• Nitrogen and COD removal performance were well obtained with COD/N ratio of 0.63. • The anammox coupled with DNRA pathway was main reason for SAA increase. • The acetate was mainly used by AnAOB with functional genes ADP-acs and AMP-acs. • The propionate stimulated the enrichment of DB. In current study, the underlying mechanism of coupling dissimilatory nitrate reduction to ammonium (DNRA) pathway with anaerobic ammonium oxidation (anammox) process was explored through metagenomics sequencing analysis in an anammox granular system treating pharmaceutical wastewater under varying COD/N ratios. It was found that average NH 4 +-N and NO 2 --N concentration in effluent was stabled around 2.89 ± 2.53 and 14.23 ± 9.23 mg L-1 with nitrogen removal efficiency (NRE) increase to 85.3% when influent COD/N ratio was around 0.63. Besides, metagenomics sequencing analysis revealed that different COD/N ratios significantly influenced the abundances of functional nitrogen and carbon metabolic genes and microbial community succession. The low COD/N ratio strengthened DNRA pathway in Ca. Kuenenia_stuttgartiensis , as well as the abundance of functional gene nrf. The abundance of the genes encoding acetate degradation, for example, AMP-acs , ADP-acs and AckA increased, suggesting the acetate could stimulate the multiple carbon metabolic potentials of AnAOB. On the contrary, the genes encoding for propionate metabolism were enriched in denitrification bacteria. Our findings revealed the new insight into the mixotrophic characteristic of AnAOB which might help widen engineering application of anammox proocess in various industrial wastewater. [ABSTRACT FROM AUTHOR]

Recent studies have demonstrated that dysbiosis of the gut microbiota is associated with psoriasis, but these studies showed some conflicting results. Our study examined differences in microbiome composition associated in people with psoriasis and those without. Comparing individuals with their healthy partners was a second strategy. We explored the fecal microbiota among 32 nontreated plaque psoriasis patients, 15 healthy controls and 17 healthy couples by metagenomic gene sequencing. The relative levels of intestinal microbiota of the psoriasis cohort differed from those in healthy controls and these patients' partners. However, there was no microbial diversity among these three cohorts. On the level of the phylum, Firmicutes and Bacteroidetes ' relative abundances were reversed. Escherichia coli was significantly enriched in the psoriasis group compared with the healthy people and the healthy spouses. Gene functional analysis indicated that Ribosome (ko03010) was upregulated, Flagellar assembly (ko02040) and Bacterial chemotaxis (ko02030) were downregulated in the psoriasis cohort compared with the healthy individuals and the healthy spouses. The microbiota in severe psoriasis patients differed from those with milder conditions. These findings strongly support the association between intestinal flora and psoriasis. It is necessary to perform more meaningful experiments to identify whether the differences of gut microbiota are the cause or consequences of psoriasis in future. • None of the participants had taken any medication for 6 months before the study began. • We explored patients and their healthy spouses as subgroups. • Escherichia coli was significantly enriched in the psoriasis group compared with the healthy people and the healthy spouses. • These findings strongly support the association between intestinal flora and psoriasis. [ABSTRACT FROM AUTHOR]

Porcine epidemic diarrhea virus (PEDV) frequently causes diarrhea outbreaks. However, whether newly discovered enteric viruses such as porcine kobuvirus (PKV) and porcine astroviruses (PAstVs) are also correlated with diarrhea is still unclear. Diarrhea outbreaks were reported in a PEDV-vaccinated pig farm in Xinjiang Uygur Autonomous Region of China from 2019 to 2020. PEDV was a common pathogen detected in fecal samples by routine RT-PCR assays. The PEDV positive fecal sample was used for pathogenic analysis due to the failure isolation of PEDV. The challenged neonatal piglets appeared watery diarrhea within one day post infection (dpi) and all died within 6 dpi. Histopathological and immunohistochemical examinations supported that PEDV is a major pathogen causing intestinal lesions. To further explore enteric viruses associated with neonatal piglet diarrhea, metagenomics sequencing was performed for the diarrheic piglets. Remarkably, PKV was the most abundant virus (58.33%) followed by PEDV (34.45%) and PAstVs (7.22%), which were also confirmed by real-time RT-PCR assays. Significant in vivo replications of PEDV and PKV could only be observed in challenged piglets whilst PAstVs maintained similar virus loads in both challenged and mock infected piglets. Overall, this study provides first pathogenic and metagenomic evidence that significant proliferations of PEDV and PKV are closely associated with severe diarrhea in neonatal piglets, while PAstVs likely play limited roles in neonatal piglet diarrhea. • Pathogenic analysis suggested that PEDV is likely associated with 2019–2020 Xinjiang diarrhea outbreaks. • Metagenomics sequencing identified PEDV, PKV and PAstVs from severe diarrheic piglets. • Significant in vivo replications of PEDV and PKV were only detected in diarrheic neonatal piglets. • PAstVs maintained similar virus loads in both challenged and mock infected piglets during the animal study. • PEDV and PKV are closely associated with diarrheic diseases while PAstVs may play a limited role in neonatal piglet diarrhea. [ABSTRACT FROM AUTHOR]

• Biochar stimulated DNRA and enhanced the NRE of anammox system at low COD/N (0.1–0.5). • Ca. Jettenia caeni was the main bacteria responsible for DNRA metabolism. • The improved ETC by biochar was the reason for the improved anammox SAA and NRE. • Biochar increased the anammox-related (hzs) and complete DNRA-related genes abundance. Coupling dissimilatory nitrate reduction to ammonium (DNRA) pathway with anammox process has a prominent advantage in enhancement of nitrogen removal. However, the anammox bacteria driven-DNRA is difficult to proceed at normal autotrophic circumstance. Herein, for the first time, biochar (prepared by bamboo) was used as a mediator to stimulate the DNRA pathway of anammox bacteria under varying chemical oxygen demand (COD) to nitrogen (COD/N) ratios (0.1–0.7), and the underlying stimulation mechanism was elucidated by metagenomics sequencing analysis. Results showed that biochar addition (10 g/L) stimulated DNRA pathway of anammox bacteria at low COD/N ratios (0.1–0.5), thus enhancing the nitrogen removal efficiency (NRE) of the anammox system by 7.2%–16.4% and 0.9%–3.0%, respectively, compared to that of tests without sodium acetate and biochar (p <0.05). This enhancement was attributed to the improved extracellular electron accepting capacity of anammox biomass by biochar. The easily obtained electrons (from sodium acetate) further increased the relative abundances of anammox-related (hzs) and complete DNRA-related (nap AB and nrf AH) genes (p <0.05), which catalyze electron-consuming reactions. The stimulated anammox pathway and DNRA pathway further increased the specific anammox activity and the relative abundance of anammox bacteria (especially Ca. Jettenia) by 15.5%–23.0% and 11.3%–82.6% compared with that without biochar, respectively. Metagenomics sequencing also revealed that anammox bacteria, Ca. Jettenia caeni , was the main bacteria for DNRA metabolism in this system. Our findings reveal that biochar could selectively stimulate DNRA pathway of anammox bacteria affiliated by a low amount of carbon, which provides a novel strategy to improve the nitrogen removal of anammox-based processes. [Display omitted]. [ABSTRACT FROM AUTHOR]

The presence of Microcystis aeruginosa (M. aeruginosa) can affect the transference of antibiotic resistance genes (ARGs), and the presence of carbon-based copper nanocomposites (CCN) can affect the growth of M. aeruginosa. However, the effect of CCN on M. aeruginosa and ARGs is not fully understood. In this study, metagenomic sequencing was employed to analyze the movability of ARGs, their potential transfer, and possible hosts in photobioreactor treating urban water. The results uggested that 20 mg/L of CCN changed the composition and abundance of microorganisms in urban water, significantly promoted the flocculation of M aeruginosa , and decreased the composing proportion of Cyanophyta sp. and M aeruginosa. The results indicated that 20 mg/L of CCN significantly decreased the absolute abundance and ARGs proportions which mediated by plasmids (32.7 %). Furthermore, the lower co-occurrence probability of ARGs and mobile genetic elements (MGEs) suggested that 20 mg/L of CCN weakened the movability potential of ARGs mediated by MGEs such as plasmids. Among the 452 metagenome-assembled genomes (MAGs), 95 MAGs belonging to 41 bacterial categories were identified as possible ARG hosts. These results will provide insights into the control of harmful cyanobacteria and the management of ARGs in urban water. [Display omitted] • The 20 mg/L of CCN significantly promoted the flocculation of M aeruginosa. • The 20 mg/L of CCN significantly decreased the ARGs proportions which mediated by plasmids. • The 20 mg/L of CCN weakened the movability potential of ARGs mediated by MGEs. [ABSTRACT FROM AUTHOR]

Background: Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore™ sequencing of clinical respiratory specimens.Methods: We conducted a case-control study of mechanically-ventilated patients with pneumonia (nine culture-positive and five culture-negative) and without pneumonia (eight controls). We collected endotracheal aspirates and applied a microbial DNA enrichment method prior to metagenomic sequencing with the Oxford Nanopore MinION device. For reference, we compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing.Results: Human DNA depletion enabled in depth sequencing of microbial communities. In culture-positive cases, Nanopore revealed communities with high abundance of the bacterial or fungal species isolated by cultures. In four cases with resistant clinical isolates, Nanopore detected antibiotic resistance genes corresponding to the phenotypic resistance in antibiograms. In culture-negative pneumonia, Nanopore revealed probable bacterial pathogens in 1/5 cases and Candida colonization in 3/5 cases. In controls, Nanopore showed high abundance of oral bacteria in 5/8 subjects, and identified colonizing respiratory pathogens in other subjects. Nanopore and 16S sequencing showed excellent concordance for the most abundant bacterial taxa.Conclusions: We demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive microbiologic cultures, and clinically actionable information obtained from sequencing in culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes. [ABSTRACT FROM AUTHOR]