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Mulberry has high crude protein and biologically active compounds but is difficult to be ensiled due to the lack of adequate epiphytic LAB. This study aimed to investigate the effects of inoculation with Lactiplantibacillus plantarum and Pediococcus pentosaceus isolated from mulberry with higher antioxidant capacity alone or in combination with Streptococcus bovis on chemical characteristics, antioxidant capacity, bacterial community, and metabolite composition of mulberry silage. The results showed that all inoculation groups had higher dry matter and lower pH than the control group, particularly in LP (dry matter, DM, 32.03% and pH = 4.44) and LP_PP_SB (DM, 31.68% and pH = 4.26) after 60 days of ensiling. Ammonia nitrogen (AN) content was the lowest in both LP_SB and LP_PP_SB groups, which were 1.86 g/kg FM and 1.05 g/kg FM, respectively, (P < 0.05). Only the LP_PP_SB group showed increased polyunsaturated fatty acids (PUFA, 1.2851 g/kg DM, P < 0.05) than the control group. Ferric-reducing antioxidant power (FRAP) values were increased in all inoculation-treated groups compared with the control group (P < 0.05). 2,2-Diphenyl-1-picrylhydrazyl (DDPH), 3-ethylbenzothiazoline-6-sulfonic acid (ABTS), and FRAP exhibited the highest levels in the LP_PP- and LP_PP_SB-treated groups. Enterobacter was dominant in both the control and SB-treated groups, and the relative abundance was 41.18% and 32.35%, respectively (P < 0.05). The relative abundance of Lactiplantibacillus was higher in the LP-, LP_PP-, and LP_SB-treated groups (81.84%−82.69%). Relative abundance of Pediococcus was higher in the PP-, PP_SB-, and LP_PP_SB-treated groups (74.27%−85.27%). Untargeted metabolomics analysis results showed that five flavonoids (apigenin, eriodictyol, quercetin-3-glucoside, rutin, and kaempferol-3-O-rutinoside)were upregulated in all inoculation groups (except for the SB-treated groups). Among them, eriodictyol was both positively correlated with ABTS and FRAP and also showed the highest relative abundance in the LP_PP- and LP_PP_SB-treated groups. To the best of our knowledge, this study was the first to investigate the relationship between inoculants of epiphytic lactic acid bacteria and antioxidant capacity by 16s rRNA Illumina sequencing technology and untargeted metabolomics analysis, respectively. Consequently, inoculated L. plantarum, P. pentosaceus alone, respectively, or in combination with S. bovis increased the relative abundance of Lactiplantibacillus and Pediococcus and decreased the relative abundance of Enterobacter, particularly in the LP_PP_SB-treated group. In addition, inoculants could increase the relative abundance of five flavonoids (apigenin, eriodictyol, quercetin-3-glucoside, rutin, and kaempferol-3-O-rutinoside), especially eriodictyol to improve the antioxidant capacity of mulberry silage.

IntroductionPanax notoginseng is a precious Chinese medicinal material. Soil fumigation can control soil-borne disease and overcome the continuous cropping obstacles of P. notoginseng. However, chloropicrin (CP) fumigation can kill non-target soil microorganisms and reduce microbial diversity, but the long-time impacts of CP fumigation on soil microbial are less reported.MethodsWe studied the long-term effects of CP fumigation on soil microbes with high-throughput gene sequencing, and correlated the changes in the composition of microbial communities with environmental factors like soil physicochemical properties and soil enzyme activities. This study mainly focuses on the recovery characteristics of soil microbe after soil fumigation by evaluating the ecological restoration of P. notoginseng soil, its sustained control effect on plant diseases, and its promotion effect on crop growth by focusing on the CP fumigation treatment.ResultsThe results showed that CP fumigation significantly increased soil available phosphorus (P) to 34.6 ~ 101.6 mg/kg and electrical conductivity (EC) by 18.7% ~ 34.1%, respectively. High-throughput gene sequencing showed that soil fumigation with CP altered the relative abundance of Trichoderma, Chaetomium, Proteobacteria, and Chloroflexi in the soil while inhibiting a lot of Fusarium and Phytophthora. The inhibition rate of Phytophthora spp. was still 75.0% in the third year after fumigation. Fumigation with CP enhanced P. notoginseng’s survival rate and stimulated plant growth, ensuring P. notoginseng’s healthy in the growth period. The impact of fumigation on microbial community assembly and changes in microbial ecological niches were characterized using normalized stochasticity ratio (NST) and Levins’ niche breadth index. Stochasticity dominated bacterial community assembly, while the fungal community was initially dominated by stochasticity and later by determinism. Fumigation with CP reduced the ecological niches of both fungi and bacteria.ConclusionIn summary, the decrease in microbial diversity and niche caused by CP fumigation could be recovered over time, and the control of soil pathogens by CP fumigation remained sustainable. Moreover, CP fumigation could overcome continuous cropping obstacles of P. notoginseng and promote the healthy growth of P. notoginseng.

Dark septate endophytes (DSE) are typical root endophytes with the ability to enhance plant growth and tolerance to heavy metals, but the underlying mechanisms are unclear. Here, the physiological and molecular mechanisms of a DSE strain, Exophiala pisciphila, in mitigating cadmium (Cd, 20 mg/kg) toxicity in maize were investigated. Our results showed, under Cd stress, E. pisciphila inoculation enhanced the biomass of maize and reduced both inorganic and soluble forms of Cd (high toxicity) by 52.6% in maize leaves, which may be potentially contributing to Cd toxicity mitigation. Besides, E. pisciphila inoculation significantly affected the expression of genes involved in the signal transduction and polar transport of phytohormone, and then affected abscisic acid (ABA) and indole-3-acetic acid (IAA) contents in maize roots, which was the main reason for promoting maize growth. In addition, E. pisciphila also made a 27% increase in lignin content by regulating the expression of genes involved in the synthesis of it, which was beneficial to hinder the transport of Cd. In addition, E. pisciphila inoculation also activated glutathione metabolism by the up-regulation of genes related to glutathione S-transferase. This study helps to elucidate the functions of E. pisciphila under Cd stress, sheds light on the mechanism of detoxifying Cd and provides new insights into the protection of crops from heavy metals.

ObjectiveIn this work, polyvinyl alcohol (PVA) and sodium alginate (SA) were used as entrapped carriers and Artemisia argyi stem biochar (ABC) was used as an absorption carrier to immobilize aerobic denitrifying bacteria screened from landfill leachate, thus a new carbon-based functional microbial material (PVA/SA/ABC@BS) was successfully prepared.MethodsThe structure and characteristics of the new material were revealed by using a scanning electron microscope and Fourier transform infrared spectroscopy, and the performance of the material for treating landfill leachate under different working conditions was studied.ResultsABC had abundant pore structures and that the surface contained many oxygen-containing functional groups, carboxyl groups, and amide groups, etc. and it had good absorbing performance and strong acid and alkali buffering capacity, which was beneficial to the adhesion and proliferation of microorganisms. After adding ABC as a composite carrier, the damage rate of immobilized particles was decreased by 1.2%, and the acid stability, alkaline stability, and mass transfer performance were increased by 9.00, 7.00, and 56%, respectively. When the dosage of PVA/SA/ABC@BS was 0.017g/ml, the removal rates of nitrate nitrogen (NO3−-N) and ammonia nitrogen (NH4+-N) were the highest, which were 98.7 and 59.4%, respectively. When the pH values were 11, 7, 1, and 9, the removal rates of chemical oxygen demand (COD), NO3−-N, nitrite nitrogen (NO2−-N) and NH4+-N reached the maximum values, which were 14.39, 98.38, 75.87, and 79.31%, respectively. After PVA/SA/ABC@BS was reused in 5 batches, the removal rates of NO3−-N all reached 95.50%.ConclusionPVA, SA and ABC have excellent reusability for immobilization of microorganisms and degradation of nitrate nitrogen. This study can provide some guidance for the great application potential of immobilized gel spheres in the treatment of high concentration organic wastewater.

BackgroundThe pathogens of suspected spinal tuberculosis (TB) include TB and non-TB bacteria. A rapid and effective diagnostic method that can detect TB and non-TB pathogens simultaneously remains lacking. Here, we used metagenomic next-generation sequencing (mNGS) to detect the pathogens in patients with suspected spinal TB.MethodsThe enrolled patients with suspected spinal TB were regrouped three times into patients with spinal infection and controls, patients with spinal TB and controls, and patients with non-TB spinal infection and controls. We tested the three groups separately by using mNGS and conventional detection methods.ResultsUltimately, 100 patients were included in this study. Pathogens were detected in 82 patients. Among the 82 patients, 37 had TB and 45 were infected with other bacteria. In patients with spinal infection, the sensitivity of the mNGS assay was higher than that of culture and pathological examination (p

Spiroplasma mirum, small motile wall-less bacteria, was originally isolated from a rabbit tick and had the ability to infect newborn mice and caused cataracts. In this study, the whole genome and antigen proteins of S. mirum were comparative analyzed and investigated. Glycolysis, pentose phosphate pathway, arginine metabolism, nucleotide biosynthesis, and citrate fermentation were found in S. mirum, while trichloroacetic acid, fatty acids metabolism, phospholipid biosynthesis, terpenoid biosynthesis, lactose-specific PTS, and cofactors synthesis were completely absent. The Sec systems of S. mirum consist of SecA, SecE, SecDF, SecG, SecY, and YidC. Signal peptidase II was identified in S. mirum, but no signal peptidase I. The relative gene order in S. mirum is largely conserved. Genome analysis of available species in Mollicutes revealed that they shared only 84 proteins. S. mirum genome has 381 pseudogenes, accounting for 31.6% of total protein-coding genes. This is the evidence that spiroplasma genome is under an ongoing genome reduction. Immunoproteomics, a new scientific technique combining proteomics and immunological analytical methods, provided the direction of our research on S. mirum. We identified 49 proteins and 11 proteins (9 proteins in common) in S. mirum by anti-S. mirum serum and negative serum, respectively. Forty proteins in S. mirum were identified in relation to the virulence. All these proteins may play key roles in the pathogeny and can be used in the future for diagnoses and prevention.

IncX3 plasmids are narrow host range plasmids mostly found in Enterobacteriaceae with great conjugation ability, high stability, no fitness cost, and the ability to improve biofilm formation in their bacterial hosts. IncX3 plasmids have spread swiftly, primarily in several nations and among different species over the last 10 years. blaNDM, blaKPC, and blaOXA-181 are the carbapenemase genes carried by IncX3 plasmids. Among them, blaNDM is often located on the IncX3 plasmid, which is deemed as the primary vehicle of blaNDM transmission. Isolates harboring IncX3 plasmids are found in nations all over the world from human, animal, and environmental sources. Cointegrate plasmids related to IncX3 have recently been discovered to increase the antibiotic resistance spectrum and potentially broaden the host range of plasmids, restricting the use of antibiotics in the clinic. There are, however, few reviews based on the physiological and epidemiological properties of IncX3 plasmid, as well as studies on the plasmid itself. Hence, we conducted a retrospective literature review to summarize the characteristics of IncX3 plasmids aiming to provide a theoretical basis for controlling the global prevalence of IncX3 plasmids and directions for further research on the functions of the related genes on the IncX3 plasmid.

This study illustrated the texture changes of Shewanella baltica-inoculated Litopenaeus vannamei during refrigerated storage with the exogenous addition of Lactobacillus plantarum SS-128. The group inoculated with SS-128 had an improved texture compared with that inoculated with the luxS-mutant group (ΔluxS). Proteomics were conducted to analyze the protein alterations in L. vannamei and supernatant, respectively. During storage, many texture-related proteins, including myosin heavy chain and beta-actin, were maintained due to luxS. Some endogenous enzymes related to the energy metabolism and hydrolysis of L. vannamei were downregulated. The luxS-induced interaction with S. baltica showed significant changes in the expression of some critical enzymes and pathways. The ATP-dependent zinc metalloprotease FtsH and protease subunit HslV were downregulated, and the oxidative phosphorylation and glycosaminoglycan degradation pathways in S. baltica were inhibited, resulting in the slow deterioration of L. vannamei. By exploring the mechanism underlying SS-128-led manipulation of the metabolism of spoilage bacteria, we clarified the texture maintenance mechanism of luxS in SS-128, providing theoretical evidence for SS-128 application in food preservation.

Helicobacter pylori exhibit specific geographic distributions that are related to clinical outcomes. Despite the high infection rate of H. pylori throughout the world, the genetic epidemiology surveillance of H. pylori still needs to be improved. This study used the single nucleotide polymorphisms (SNPs) profiling approach based on whole genome sequencing (WGS) to facilitate genomic population analyses of H. pylori and encourage the dissemination of microbial genotyping strategies worldwide. A total number of 1,211 public H. pylori genomes were downloaded and used to construct the typing tool, named HpTT (H. pylori Typing Tool). Combined with the metadata, we developed two levels of genomic typing, including a continent-scale and a country scale that nested in the continent scale. Results showed that Asia was the largest isolate source in our dataset, while isolates from Europe and Oceania were comparatively more widespread. More specifically, Switzerland and Australia are the main sources of widespread isolates in their corresponding continents. To integrate all the typing information and enable researchers to compare their dataset against the existing global database easily and rapidly, a user-friendly website (https://db.cngb.org/HPTT/) was developed with both genomic typing tools and visualization tools. To further confirm the validity of the website, ten newly assembled genomes were downloaded and tested precisely located on the branch as we expected. In summary, the H. pylori typing tool (HpTT) is a novel genomic epidemiological tool that can achieve high-resolution analysis of genomic typing and visualizing simultaneously, providing insights into the genetic population structure, evolution analysis, and epidemiological surveillance of H. pylori.

The overall gut microbial profile of patients with small intestinal bacterial overgrowth (SIBO) has not been thoroughly investigated. We investigated the microbial communities of mucosal specimens from the duodenum, ileum, sigmoid colon, and feces of patients with and without SIBO, as diagnosed by lactulose breath testing. The bacteria present in the mucosal and fecal samples were identified using 16S rRNA gene sequencing. Further analysis was performed using the linear discriminant analysis (LDA) effect size method, random forest analysis, and receiver operating characteristic analysis. The microbial diversities of the fecal samples were significantly lower than those of the mucosal samples from the duodenum, ileum, and sigmoid colon (P < 0.001, P < 0.001, and P < 0.001, respectively), while the bacterial compositions of the ileac mucosal samples and sigmoid mucosal samples were similar. The bacterial composition of either the fecal or duodenal mucosal samples were significantly different from those of the other three groups (ANOSIM R = 0.305, P = 0.001). The bacterial compositions of the mucosal samples of the duodenum, ileum, and sigmoid colon in the SIBO + subjects were significantly different from those of the SIBO− subjects (ANOSIM P = 0.039, 0.002, and 0.007, respectively). The relative abundances of 7, 18, and 8 genera were significantly different (LDA score > 3) in the mucosal samples of the duodenum, ileum, and sigmoid colon between the SIBO + and SIBO− groups. Four genera (Lactobacillus, Prevotella_1, Dialister, and norank_f__Ruminococcaceae) showed similar changes among the mucosal samples of the duodenum, ileum, and sigmoid colon in the SIBO + subjects. A signature consisting of four genera in the duodenal mucosa, three genera in the ileac mucosa, or six genera in the mucosa of the sigmoid colon exhibited predictive power for SIBO (area under the curve = 0.9, 0.93, and 0.87, respectively). This study provides a comprehensive profile of the gut microbiota in patients with SIBO. Dysbiosis was observed in the mucosa-associated gut microbiome but not in the fecal microbiome of patients with SIBO. Furthermore, we identified mucosa-associated taxa that may be potential biomarkers or therapeutic targets of SIBO. Further investigation is needed on their mechanisms and roles in SIBO.

Catabolic acetolactate synthase (cALS) plays a crucial role in the quality of liquor because of its ability to catalyze the synthesis of the endogenous precursor product α-acetolactate of the aromatic compound tetramethylpyrazine (TTMP) and acetoin. However, the vulnerability of cALS to acidic conditions limits its application in the Chinese liquor brewing industry. Here we report the biochemical characterization of cALS from B. licheniformis T2 (BlALS) that was screened from Chinese liquor brewing microorganisms. BlALS showed optimal activity levels at pH 7.0, and the values of Km and Vmax were 27.26 mM and 6.9 mM⋅min–1, respectively. Through site-directed mutagenesis, we improved the stability of BlALS under acidic conditions. Replacing the two basic residues of BlALS with acidic mutations (N210D and H399D) significantly improved the acid tolerance of the enzyme with a prolonged half-life of 2.2 h (compared with wild-type BlALS of 0.8 h) at pH 4.0. Based on the analysis of homologous modeling, the positive charge area of the electrostatic potential on the protein surface and the number of hydrogen bonds near the active site increased, which helped BlALSN210D–H399D to withstand the acidic environment; this could extend its application in the food fermentation industry.

Cilia are highly conserved organelles present in almost all types of eukaryotic cells, and defects in cilia structure and/or function are related to many human genetic disorders. Single-celled ciliated protists, which possess diverse types of cilia, are remarkable model organisms for studying cilia structures and functions. Euplotes vannus is a representative ciliate with many intriguing features; for example, it possesses extensively fragmented somatic genomes and a high frequency of + 1 programmed ribosomal frameshifting. However, the molecular mechanisms underlying these remarkable traits remain largely unknown, mainly due to the lack of efficient genetic manipulation tools. Here, we describe the first application of a morpholino-based strategy to knockdown gene expression in E. vannus. Through interfering with the function of two ciliary genes, ZMYND10 and C21ORF59, we showed that these two genes are essential for the ciliary motility and proliferation of E. vannus cells. Strikingly, both ZMYND10- and C21ORF59-knockdown cells developed shorter cilia in the ventral cirri, a special type of ciliary tuft, suggesting a novel role for these genes in the regulation of cilia length. Our data provide a new method to explore gene function in E. vannus, which may help us to understand the functions of evolutionarily conserved cilia-related genes as well as other biological processes in this intriguing model.

BackgroundStreptococcus pyogenes is a major cause of severe, invasive infections in humans. The bacterial pathogen harbors a wide array of virulence factors and exhibits high genomic diversity. Rapid changes of circulating strains in a community are common. Understanding the current prevalence and dynamics of S. pyogenes lineages could inform vaccine development and disease control strategies.MethodsWe used whole-genome sequencing (WGS) to characterize all invasive S. pyogenes isolates obtained through the United States Center for Disease Control and Prevention’s Active Bacterial Core surveillance (ABCs) in 2016 and 2017. We determined the distribution of strain features, including emm type, antibiotic resistance determinants, and selected virulence factors. Changes in strain feature distribution between years 2016 and 2017 were evaluated. Phylogenetic analysis was used to identify expanding lineages within emm type.ResultsSeventy-one emm types were identified from 3873 isolates characterized. The emm types targeted by a 30-valent M protein-based vaccine accounted for 3230 (89%) isolates. The relative frequencies of emm types collected during the 2 years were similar. While all isolates were penicillin-susceptible, erythromycin-resistant isolates increased from 273 (16% of 2016 isolates) to 432 (23% of 2017 isolates), mainly driven by increase of the erm-positive emm types 92 and 83. The prevalence of 24 virulence factors, including 11 streptococcal pyrogenic toxins, ranged from 6 to 90%. In each of three emm types (emm 49, 82, and 92), a subgroup of isolates significantly expanded between 2016 and 2017 compared to isolates outside of the subgroup (P-values < 0.0001). Specific genomic sequence changes were associated with these expanded lineages.ConclusionsWhile the overall population structure of invasive S. pyogenes isolates in the United States remained stable, some lineages, including several that were antibiotic-resistant, increased between 2016 and 2017. Continued genomic surveillance can help monitor and characterize bacterial features associated with emerging strains from invasive infections.

Radiation therapy is a cornerstone of modern management methods for malignancies but is accompanied by diverse side effects. In the present study, we showed that food additives such as polysorbate 80 (P80) exacerbate irradiation-induced gastrointestinal (GI) tract toxicity. A 16S ribosomal RNA high-throughput sequencing analysis indicated that P80 consumption altered the abundance and composition of the gut microbiota, leading to severe radiation-induced GI tract injury. Mice harboring fecal microbes from P80-treated mice were highly susceptible to irradiation, and antibiotics-challenged mice also represented more sensitive to radiation following P80 treatment. Importantly, butyrate, a major metabolite of enteric microbial fermentation of dietary fibers, exhibited beneficial effects against P80 consumption-aggravated intestinal toxicity via the activation of G-protein-coupled receptors (GPCRs) and maintenance of the intestinal bacterial composition in irradiated animals. Moreover, butyrate had broad therapeutic effects on common radiation-induced injury. Collectively, our findings demonstrate that P80 are potential risk factors for cancer patients during radiotherapy and indicate that butyrate might be employed as a therapeutic option to mitigate the complications associated with radiotherapy.

The association of Zika virus (ZIKV) infection and severe complications including neurological sequelae especially fetal microcephaly has aroused global attentions since its outbreak in 2015. Currently, there are no vaccines or therapeutic drugs clinically approved for treatments of ZIKV infection, however. And the drugs used for treating ZIKV in pregnant women require a higher safety profile. Here, we identified an anti-asthmatic drug, montelukast, which is of safety profile for pregnant women and exhibited antiviral efficacy against ZIKV infection in vitro and in vivo. And we showed that montelukast could disrupt the integrity of the virions to release the viral genomic RNA, hence irreversibly inhibiting viral infectivity. In consideration of the neuro-protective activity that montelukast possessed, which was previously reported, it is promising that montelukast could be used for patients with ZIKV infection, particularly for pregnant women.

Invasive pneumococcal disease (IPD) has greatly decreased since implementation in the U.S. of the 7 valent conjugate vaccine (PCV7) in 2000 and 13 valent conjugate vaccine (PCV13) in 2010. We used whole genome sequencing (WGS) to predict phenotypic traits (serotypes, antimicrobial phenotypes, and pilus determinants) and determine multilocus genotypes from 5334 isolates (~90% of cases) recovered during 2015–2016 through Active Bacterial Core surveillance. We identified 44 serotypes; 26 accounted for 98% of the isolates. PCV13 serotypes (inclusive of serotype 6C) accounted for 1503 (28.2%) isolates, with serotype 3 most common (657/5334, 12.3%), while serotypes 1 and 5 were undetected. Of 305 isolates from children 0.12 μg/ml) was found among 22.4% (1193/5334) isolates, with higher penicillin MICs (2–8 μg/ml) found in 8.0% (425/5334) of isolates that were primarily (372/425, 87.5%) serotypes 35B and 19A. Most (792/1193, 66.4%) penicillin-nonsusceptible isolates were macrolide-resistant, 410 (34.4%) of which were erm gene positive and clindamycin-resistant. The proportion of macrolide-resistant isolates increased with increasing penicillin MICs; even isolates with reduced penicillin susceptibility (MIC = 0.06 μg/ml) were much more likely to be macrolide-resistant than basally penicillin-susceptible isolates (MIC < 0.03 μg/ml). The contribution of recombination to strain diversification was assessed through quantitating 35B/CC558-specific bioinformatic pipeline features among non-CC558 CCs and determining the sizes of gene replacements. Although IPD has decreased greatly and stabilized in the post-PCV13 era, the species continually generates recombinants that adapt to selective pressures exerted by vaccines and antimicrobials. These data serve as a baseline for monitoring future changes within each invasive serotype.

Background: Huang-Lian-Jie-Du-Decoction (HLJDD), a prescription of traditional Chinese medicine, has been clinically used to treat diabetes for thousands of years and its mechanism was reported to be related to gut microbiota. However, no study has explored the effect of HLJDD on the gut microbiota in type 2 diabetes mellitus (T2DM) yet. Therefore, in this study, we investigated the modulation of gut microbiota induced by HLJDD treatment in T2DM in order to unveil the underlying mechanism.Methods: A combination of high-fat diet (HFD) and streptozotocin (STZ) was used to induce T2DM in rats. Bacterial communities in the fecal samples from the control group, the T2DM model group, and the HLJDD-treated T2DM group were analyzed by 16S gene sequencing, followed with a subset sample analyzed by shotgun sequencing.Results: The HLJDD treatment significantly ameliorated hyperglycemia and inflammation in T2DM rats. Additionally, our results indicated that HLJDD treatment could not only restore the gut dysbiosis in T2DM rats, which was proved by an increasing amount of short chain fatty acids (SCFAs)-producing and anti-inflammatory bacteria such as Parabacteroides, Blautia, and Akkermansia as well as a decreasing amount of conditioned pathogenic bacteria (e.g., Aerococcus, Staphylococcus, and Corynebacterium), but also modulate the dysregulated function of gut microbiome in T2DM rats, including an up-regulation in bile acid biosynthesis as well as a reduction in glycolysis/gluconeogenesis and nucleotide metabolism.Conclusion: HLJDD treatment could ameliorate hyperglycemia and restore the dysregulated microbiota structure and function to a normal condition mainly by increasing SCFAs-producing bacteria and reducing conditioned pathogenic bacteria in T2DM rats, which provides insights into the mechanism of HLJDD treatment for T2DM from the view of gut microbiota.

The influence of soil fumigation on microorganisms involved in transforming nitrogen remains little understood, despite the use of fumigants for many decades to control soil-borne pathogens and plant-parasitic nematodes. We used real-time PCR (quantitative polymerase chain reaction) and 16S rRNA gene amplicon sequencing techniques to monitor changes in the diversity and community structure of microorganisms associated with nitrogen transfer after the soil was fumigated with dazomet (DZ). We also examined nitrous oxide (N2O) emissions from these microorganisms present in fumigated fluvo-aquic soil and lateritic red soil. Fumigation with DZ significantly reduced the abundance of 16S rRNA and nitrogen cycling functional genes (nifH, AOA amoA, AOB amoA, nxrB, narG, napA, nirK, nirS, cnorB, qnorB, and nosZ). At the same time, N2O production rates increased between 9.9 and 30 times after fumigation. N2O emissions were significantly correlated with NH4+, dissolved amino acids and microbial biomass nitrogen, but uncorrelated with functional gene abundance. Diversity indices showed that DZ temporarily stimulated bacterial diversity as well as caused a significant change in bacterial community composition. For example, DZ significantly decreased populations of N2-fixing bacteria Mesorhizobium and Paenibacillus, nitrifiers Nitrosomonas, and the denitrifiers Bacillus, Pseudomonas, and Paracoccus. The soil microbial community had the ability to recover to similar population levels recorded in unfumigated soils when the inhibitory effects of DZ fumigation were no longer evident. The microbial recovery rate, however, depended on the physicochemical properties of the soil. These results provided useful information for environmental safety assessments of DZ in China, for improving our understanding of the N-cycling pathways in fumigated soils, and for determining the potential responses of different N-cycling groups after fumigation.

This study investigated the effects of dietary essential oils (EOs) on intestinal microbial composition and metabolic profiles in weaned piglets. The piglets were fed the same basal diet supplemented with EOs (EO) or without EOs (Con) in the current study. The results showed that the body weight gain was significantly increased, while the diarrhea incidence was significantly reduced in the EO group. In addition, EOs could modify the intestinal microbial composition of weaned piglets. The relative abundances of some beneficial bacterial species such as Bacilli, Lactobacillales, Streptococcaceae, and Veillonellaceae were significantly increased in the EO group. Metabolomics analysis indicated that protein biosynthesis, amino acid metabolism, and lipid metabolism were enriched in the EO group. And correlation analysis demonstrated that some gut bacterial genera were highly correlated with altered gut microbiota-related metabolites. Taken together, this study indicated that dietary EOs not only altered microbial composition and function but modulated the microbial metabolic profiles in the colon, which might help us understand EOs’ beneficial effects on intestinal health of weaned piglets.

Background:Clostridioides difficile infection (CDI) is an important cause of morbidity and mortality among hospitalized patients. In China, however, hospital staff do not routinely test for CDI, leading to under-diagnosis and poor patient outcomes. Locally generated CDI data can help assess the magnitude of the problem and strengthen approaches for CDI prevention and control.Methods: We prospectively monitored hospital-onset hospital-associated (HOHA) CDI in four intensive care units (ICUs) from June 2013 to September 2014 in a large teaching hospital in China. We collected clinical information from all ICU patients with ≥ 3 episodes of diarrhea occurring within a 24-h period at least 48 h following admission (suspect case definition). Stool specimens were collected from all suspect cases of CDI and cultured for C. difficile. Polymerase chain reaction (PCR) was used to detect toxin genes from positive isolates; multi-locus sequence typing (MLST) was used for typing and identifying novel strains. We estimated the incidence rate as the number of HOHA CDI cases per 10,000 patient days; 95% confidence intervals were generated to assess rate differences between the four ICUs.Results: A total of 593 hospital-onset diarrhea patients met the suspect case definition during the study period. Of these, 47 patients (8%) were positive for C. difficile and toxin genes. The HOHA-CDI incidence rate was 14.1 cases per 10,000 patient days (95% CI: 10.5–18.6). Six patients with HOHA CDI died. ST54 (n = 14, 20%) was the most common type of HOHA-CDI strain circulating in the hospital during the study period and was linked to a temporal cluster (outbreak) involving two (NICU and GICU) of the four ICUs.Conclusion: HOHA-CDI occurs among ICU patients at this teaching hospital, supporting the importance of routine testing for CDI. Information on strain distribution can help detect CDI outbreaks. Detection of ST54 strain in a temporal cluster suggests possible gaps in infection control practices that should be investigated and addressed as needed.

This study was conducted to investigate the effect of exogenous fecal microbiota transplantation on gut bacterial community structure, gut barrier and growth performance in recipient piglets. Twelve litters of Duroc × Landrace × Yorkshire piglets of the same birth and parity were weighed and divided into two groups. One group (recipient piglets) was inoculated orally with fecal microbiota suspension of healthy adult Jinhua pigs daily from day 1 to day 11. The other (control) was given orally the same volume of sterile physiological saline at the same time. The experiment lasted 27 days. The results showed that the relative abundance of Firmicutes, Prevotellaceae, Lachnospiraceae, Ruminococcus, Prevotella, and Oscillospira in the colon of recipient piglets was increased. Proteobacteria, Fusobacteriaceae, Clostridiaceae, Pasteuriaceae, Alcaligenaceae, Bacteroidaceae, Veillonellaceae, Sutterella, Escherichia, and Bacteroides in the colon of recipient piglets were decreased. An average daily weight gain of recipient piglets was increased, and diarrhea incidence of the recipient was decreased during the trial. Intestinal morphology and tight junction barrier of recipient piglets were improved. The optical density of sIgA+ cells, the number of goblet cells and relative expressions of MUC2 in the intestinal mucosa of recipient piglets were enhanced. Protein expressions of β-defensin 2 and mRNA expressions of TLR2 and TLR4 in the intestinal mucosa of recipient piglets were also increased. These findings supported that the exogenous fecal microbiota had significant effects on animal’s growth performance, intestinal barrier function, and innate immune via modulating the composition of the gut microbiota.

Inflammatory bowel disease (IBD) results from alterations in intestinal flora and the immune system. Sulfasalazine (SASP) is a sulfa antimicrobial used to treat IBD in clinic for years. However, how SASP affects gut microbes and its potential functions remains unclear. To investigate the relationships of SASP, IBD, and gut microbiome, we used 2,4,6-trinitrobenzenesulfonic acid (TNBS) to induce experimental colitis in rats, and analyzed the microbiota in the fecal samples, which come from the control group (treated with ethanol + saline), the model group (treated with TNBS-ethanol + saline) and the SASP group (treated with TNBS-ethanol + SASP), with 16S gene sequencing and followed up a subset sample using shotgun sequencing. The study found that SASP treatment could not only restore the TNBS-induced gut dysbiosis, which was proved by the increasing amount of SCFAs-producing bacteria and lactic acid-producing bacteria as well as the decreasing amount of Proteobacteria, but also modulate the dysregulated function of the TNBS-induced colitis to resemble that of the control group, including an increased capacity for basic metabolism (carbohydrate metabolism, citrate cycle) and a decrease in the oxidative stress (riboflavin, sulfur, cysteine) as well as bacterial pathogenesis (cell motility and secretion, bacterial motility proteins, flagellar assembly). Moreover, a higher proportion of Mycoplasma was observed in the SASP group, which may associate with infertility. In all, the study provides insight into specific microbial clades and pathways linked with SASP treatment to elaborate the mechanism for treatment of IBD.

Non-structural protein 7 (NSP7), which can be further cleaved into NSP7α and NSP7β, is one of the most conserved proteins of porcine reproductive and respiratory syndrome virus (PRRSV). NSP7 plays a role in provoking the humoral immune system in PRRSV-infected swine, but its structure and function are still not fully understood. Here, we analyzed the expression of NSP7, NSP7α, and NSP7β in PRRSV-infected MARC-145 cells. The solution structure of NSP7α was determined by using nuclear magnetic resonance (NMR). Although the structure provided little clue to its function, based on the structure of NSP7α, we predicted and further identified some key amino acids on NSP7α for the interaction of NSP7α with NSP9, the RNA dependent RNA polymerase of PRRSV. This study provided some new insights into the structure and function of PRRSV NSP7.

Background: The pathogens of suspected spinal tuberculosis (TB) include TB and non-TB bacteria. A rapid and effective diagnostic method that can detect TB and non-TB pathogens simultaneously remains lacking. Here, we used metagenomic next-generation sequencing (mNGS) to detect the pathogens in patients with suspected spinal TB. Methods: The enrolled patients with suspected spinal TB were regrouped three times into patients with spinal infection and controls, patients with spinal TB and controls, and patients with non-TB spinal infection and controls. We tested the three groups separately by using mNGS and conventional detection methods. Results: Ultimately, 100 patients were included in this study. Pathogens were detected in 82 patients. Among the 82 patients, 37 had TB and 45 were infected with other bacteria. In patients with spinal infection, the sensitivity of the mNGS assay was higher than that of culture and pathological examination (p < 0.001, p < 0.001). The specificity of the mNGS assay was not statistically different from that of culture and pathological examination (p = 1.000, p = 1.000). In patients with spinal TB, no statistical difference was found between the sensitivity of the mNGS assay and that of Xpert and T-SPOT.TB (p = 1.000, p = 0.430). The sensitivity of the mNGS assay was higher than that of MGIT 960 culture and pathological examination (p < 0.001, p = 0.006). The specificities of the mNGS assay, Xpert, MGIT 960 culture, and pathological examination were all 100%. The specificity of T-SPOT.TB (78.3%) was lower than that of the mNGS assay (100%; p < 0.001). In patients with non-TB spinal infection, the sensitivity of the mNGS assay was higher than that of bacterial culture and pathological examination (p < 0.001, p < 0.001). The specificity of the mNGS assay was not statistically different from that of bacterial culture and pathological examination (p = 1.000, p = 1.000). Conclusion: Data presented here demonstrated that mNGS can detect TB and non-TB bacteria simultaneously, with high sensitivity, specificity and short detection time. Compared with conventional detection methods, mNGS is a more rapid and effective diagnostic tool for suspected spinal TB. [ABSTRACT FROM AUTHOR]

IntroductionPanax notoginseng, a medicinal herb in China, is attacked by several pathogens during its cultivation. Dazomet (DZ) is a soil fumigant that is effective in controlling soil-borne pathogens, but its long-term effects on P. notoginseng growth and soil properties are unknown.MethodsWe conducted field experiments over two consecutive years to assess the impact of three concentrations of DZ fumigation (35 kg/666.7 m2, 40 kg/666.7 m2, and 45 kg/666.7 m2) on soil physicochemical properties, microbial diversity, and P. notoginseng growth. Correlation analyses were performed between microbial community changes and soil properties, and functional predictions for soil microorganisms were conducted.ResultsDZ fumigation increased total nitrogen, total phosphorus, total potassium, available phosphorus, available potassium, and ammonia nitrogen levels in the soil. DZ fumigation promoted the nutrient accumulation and improvement of agronomic traits of P. notoginseng, resulted in a 2.83–3.81X yield increase, with the highest total saponin content increasing by 24.06%. And the 40 kg/666.7 m2 treatment had the most favorable impact on P. notoginseng growth and saponin accumulation. After DZ fumigation, there was a decrease in the relative abundance of pathogenic fungi such as Fusarium, Plectosphaerella, and Ilyonectria, while beneficial bacteria such as Ramlibacter, Burkholderia, and Rhodanobacteria increased. The effects of fumigation on soil microorganisms and soil physicochemical properties persisted for 18 months post-fumigation. DZ fumigation enhanced the relative abundance of bacteria involved in the biosynthesis of secondary metabolites and arbuscular mycorrhizal fungi, reduced the relative abundance of plant–animal pathogenic fungi, reduced the occurrence of soil-borne diseases.ConclusionIn conclusion, DZ fumigation enhanced soil physicochemical properties, increased the proportion of beneficial bacteria in the soil, and rebalanced soil microorganism populations, consequently improving the growth environment of P. notoginseng and enhancing its growth, yield, and quality. This study offers a theoretical foundation for DZ fumigation as a potential solution to the continuous cropping issue in perennial medicinal plants such as P. notoginseng.

IntroductionA variety of studies have shown a link between the gut microbiota and autoimmune diseases, but the causal relationship with Henoch-Schönlein purpura (HSP) and immune thrombocytopenic purpura (ITP) is unknown.MethodsThis study investigated the bidirectional causality between gut microbiota and HSP and ITP using Mendelian randomization (MR). Large-scale genetic data of gut microbiota at phylum to species level from the MiBioGen consortium and the Dutch Microbiome Project were utilized. Genome-wide association studies (GWAS) summary statistics for HSP and ITP came from FinnGen R10. Various MR methods were applied to infer causal relationships, including inverse variance weighted (IVW), maximum likelihood (ML), cML-MA, MR-Egger, weighted median, weighted model, and MR-PRESSO. Multiple sensitivity analyses and Bonferroni correction were conducted to enhance robustness and reliability.ResultsBased on the IVW estimates, 23 bacterial taxa were identified to have suggestive associations with HSP and ITP. Remarkably, after Bonferroni correction, family Alcaligenaceae (OR = 2.86, 95% CI = 1.52–5.37; IVW, p = 1.10 × 10−3, ML, p = 1.40 × 10−3) was significantly associated with ITP as a risk factor, while family Bacteroidales S24 7group (OR = 0.46, 95% CI = 0.29–0.74; IVW, p = 1.40 × 10−3) was significantly associated with ITP as a protective factor. No significant associations between HSP and ITP and gut microbiota were found in reverse analyses.ConclusionOur study provides evidence of causal effects of gut microbiota on HSP and ITP, highlighting the importance of further research to clarify the underlying mechanisms and develop targeted therapeutic interventions for these autoimmune diseases.

IntroductionHigher alcohols are volatile compounds produced during alcoholic fermentation that affect the quality and safety of the final product. This study used a correlation analysis of transcriptomics and metabolomics to study the impact of the initial addition of SO2 (30, 60, and 90 mg/L) on the synthesis of higher alcohols in Saccharomyces cerevisiae EC1118a and to identify key genes and metabolic pathways involved in their metabolism.MethodsTranscriptomics and metabolomics correlation analyses were performed and differentially expressed genes (DEGs) and differential metabolites were identified. Single-gene knockouts for targeting genes of important pathways were generated to study the roles of key genes involved in the regulation of higher alcohol production.ResultsWe found that, as the SO2 concentration increased, the production of total higher alcohols showed an overall trend of first increasing and then decreasing. Multi-omics correlation analysis revealed that the addition of SO2 affected carbon metabolism (ko01200), pyruvate metabolism (ko00620), glycolysis/gluconeogenesis (ko00010), the pentose phosphate pathway (ko00030), and other metabolic pathways, thereby changing the precursor substances. The availability of SO2 indirectly affects the formation of higher alcohols. In addition, excessive SO2 affected the growth of the strain, leading to the emergence of a lag phase. We screened the ten most likely genes and constructed recombinant strains to evaluate the impact of each gene on the formation of higher alcohols. The results showed that ADH4, SER33, and GDH2 are important genes of alcohol metabolism in S. cerevisiae. The isoamyl alcohol content of the EC1118a-ADH4 strain decreased by 21.003%; The isobutanol content of the EC1118a-SER33 strain was reduced by 71.346%; and the 2-phenylethanol content of EC1118a-GDH2 strain was reduced by 25.198%.ConclusionThis study lays a theoretical foundation for investigating the mechanism of initial addition of SO2 in the synthesis of higher alcohols in S. cerevisiae, uncovering DEGs and key metabolic pathways related to the synthesis of higher alcohols, and provides guidance for regulating these mechanisms.

The complexity of crude oil composition, combined with the fluctuating oxygen level in contaminated environments, poses challenges for the bioremediation of oil pollutants, because of compound-specific microbial degradation of petroleum hydrocarbons under certain conditions. As a result, facultative bacteria capable of breaking down petroleum hydrocarbons under both aerobic and anaerobic conditions are presumably effective, however, this hypothesis has not been directly tested. In the current investigation, Shewanella putrefaciens CN32, a facultative anaerobic bacterium, was used to degrade petroleum hydrocarbons aerobically (using O2 as an electron acceptor) and anaerobically (using Fe(III) as an electron acceptor). Under aerobic conditions, CN32 degraded more saturates (65.65 ± 0.01%) than aromatics (43.86 ± 0.03%), with the following order of degradation: dibenzofurans > n-alkanes > biphenyls > fluorenes > naphthalenes > alkylcyclohexanes > dibenzothiophenes > phenanthrenes. In contrast, under anaerobic conditions, CN32 exhibited a higher degradation of aromatics (53.94 ± 0.02%) than saturates (23.36 ± 0.01%), with the following order of degradation: dibenzofurans > fluorenes > biphenyls > naphthalenes > dibenzothiophenes > phenanthrenes > n-alkanes > alkylcyclohexanes. The upregulation of 4-hydroxy-3-polyprenylbenzoate decarboxylase (ubiD), which plays a crucial role in breaking down resistant aromatic compounds, was correlated with the anaerobic degradation of aromatics. At the molecular level, CN32 exhibited a higher efficiency in degrading n-alkanes with low and high carbon numbers relative to those with medium carbon chain lengths. In addition, the degradation of polycyclic aromatic hydrocarbons (PAHs) under both aerobic and anaerobic conditions became increasingly difficult with increased numbers of benzene rings and methyl groups. This study offers a potential solution for the development of targeted remediation of pollutants under oscillating redox conditions.

To characterize the formation mechanism and characteristics of two cointegrate plasmids in Salmonella enterica serotype Enteritidis strain S13, plasmids from strain S13 and three corresponding transconjugants were subjected to whole genome sequencing and analyzed using bioinformatics tools. The traits of two fusion plasmids in transconjugants were characterized by stability and conjugation experiments. Sequence analysis indicated that strain S13 contained four plasmids, including mcr-1 -bearing pS13-1, bla CTX–M–55-carrying pS13-2, tet (M)-bearing pS13-3, and floR -carrying pS13-4. IncN1-F33:A–:B– plasmid pS13-2, respectively, fused with IncFI:A–:B– plasmid pS13-3 and IncX1 plasmid pS13-4, which generated two cointegrate plasmids, designated pS13D and pS13F, which involved in two intermolecular replicative mechanisms mediated by IS 26 and the novel transposon Tn 6952 (Δ Tn AS3 -IS 26 - Δ IS Ecp1 - ramA - Δ IS 26 - Δ Tn AS1), respectively. This is the first report of the fusion of the IncN1-F33:A–:B– plasmid and IncFI:A–:B– plasmid mediated by IS 26 , and with IncX1 plasmid mediated by Tn 6952. The formation and evolution of cointegrate plasmids could expand the resistance and host spectrum of fusion plasmids. [ABSTRACT FROM AUTHOR]