Antibiotic resistance genes in the Actinobacteria phylum

Gut microbiota disturbances in hospitalized older adults with malnutrition and clinical outcomes

OBJECTIVE

Malnutrition is one of the most threatening conditions in geriatric populations. The gut microbiota has an important role in the host's metabolic and muscular health: however, its interplay with disease-related malnutrition is not well understood. We aimed to identify the association of malnutrition with the gut microbiota and predict clinical outcomes in hospitalized acutely ill older adults.

METHODS

We performed a secondary longitudinal analysis in 108 geriatric patients from a prospective cohort evaluated at admission and 72 h of hospitalization. We collected clinical, demographic, nutritional, and 16S rRNA gene-sequenced gut microbiota data. Microbiota diversity, overall composition, and differential abundance were calculated and compared between patients with and without malnutrition. Microbiota features associated with malnutrition were used to predict clinical outcomes.

RESULTS

Patients with malnutrition (51%) had a different microbiota composition compared to those who were well-nourished during hospitalization (ANOSIM R = 0.079, P = 0.003). Patients with severe malnutrition showed poorer α-diversity at admission (Shannon P = 0.012, Simpson P = 0.018) and follow-up (Shannon P = 0.023, Chao1 P = 0.008). Differential abundance of Lachnospiraceae NK4A136 group, Subdoligranulum, and Faecalibacterium prausnitzii were significantly lower and inversely associated with malnutrition, while Corynebacterium, Ruminococcaceae Incertae Sedis, and Fusobacterium were significantly increased and positively associated with malnutrition. Corynebacterium, Ruminococcaceae Incertae Sedis, and the overall composition were important predictors of critical care in patients with malnutrition during hospitalization.

CONCLUSION

Older adults with malnutrition, especially in a severe stage, may be subject to substantial gut microbial disturbances during hospitalization. The gut microbiota profile of patients with malnutrition might help us to predict worse clinical outcomes.

Hybrid nutraceutical of 2-ketoglutaric acid in improving inflammatory bowel disease: Role of prebiotics and TAK1 inhibitor

The main cause of inflammatory bowel disease (IBD) is abnormal intestinal permeability due to the disruption of the tight junction of the intestinal barrier through a pathogen-mediated inflammatory mechanism and an imbalance of the gut microbiota. This study aimed to evaluate whether 2-ketoglutaric acid alleviated permeability dysfunction with tight junction localization, activated the transforming growth factor beta-activated kinase 1 (TAK1) inflammation pathway, and regulated the homeostasis of the intestinal microbiome in vitro and in vivo IBD model. Our findings revealed that 2-ketoglutaric acid significantly suppressed abnormal intestinal permeability, delocalization of tight junction proteins from the intestinal cell, expression of inflammatory cytokines, such as TNF-α, both in vitro and in vivo. 2-Ketoglutaric acid was found to directly bind to TAK1 and inhibit the TNF receptor-associated factor 6 (TRAF6)-TAK1 interaction, which is related to the activation of nuclear factor kappa B (NF-κB) pathways, thereby regulating the expression of mitogen-activated protein kinase. Dietary 2-ketoglutaric acid also alleviated gut microbiota dysbiosis and IBD symptoms, as demonstrated by improvements in the intestine length and the abundance of Ligilactobacillus, Coriobacteriaceae_UCG_002, and Ruminococcaceae_unclassified in mice with colitis. This study indicated that 2-ketoglutaric acid binds to TAK1 for activity inhibition which is related to the NF-κB pathway and alleviates abnormal permeability by regulating tight junction localization and gut microbiome homeostasis. Therefore, 2-ketoglutaric acid is an effective nutraceutical agent and prebiotic for the treatment of IBD.

Lactiplantibacillus plantarum ELF051 Alleviates Antibiotic-Associated Diarrhea by Regulating Intestinal Inflammation and Gut Microbiota

Probiotics are widely recognized for their ability to prevent and therapy antibiotic-associated diarrhea (AAD). This study was designed to evaluate Lactiplantibacillus plantarum ELF051 ability to prevent colon inflammation and its effect on gut microbial composition in a mouse model of AAD. The mice were intragastrically administered triple antibiotics for 7 days and then subjected to L. plantarum ELF051 for 14 days. The administration of L. plantarum ELF051 ameliorated the pathological changes in the colon tissue, downregulated interleukin (IL)-1β and tumor necrosis factor (TNF)-α, and upregulated IL-10, and increased the intestinal short-chain fatty acids (SCFAs) level. Lactiplantibacillus plantarum ELF051 also regulated the Toll-like receptor/myeloid differentiation primary response 88/nuclear factor kappa light chain enhancer of activated B cells (TLR4/MyD88/NF-κB) and the phosphatidylinositol 3-kinase/protein kinase B/ NF-κB (PI3K/AKT/ NF-κB) inflammatory signaling pathways. 16S rRNA analyses showed that L. plantarum ELF051 increased the abundance and diversity of gut bacteria, restoring gut microbiota imbalance. A Spearman's rank correlation analysis showed that lactobacilli are closely associated with inflammatory markers and SCFAs. This work demonstrated that L. plantarum ELF051 can attenuate antibiotic-induced intestinal inflammation in a mouse AAD model by suppressing the pro-inflammatory response and modulating the gut microbiota.

pH drives the spatial variation of antibiotic resistance gene profiles in riparian soils at a watershed scale

Owing to convenient water access, riparian areas are often sites for intensive livestock breeding industries and agriculture, which can increase the spread of antibiotic resistance genes (ARGs). However, studies on ARG profiles in riparian soils are limited and there is little information regarding the factors influencing ARGs at a watershed scale. Here, we analyzed ARG profiles, bacterial communities, and soil properties in riparian soils under different land-use types. A total of 124 ARGs and 25 mobile genetic elements (MGEs) were detected in the riparian soils, which covered almost all major classes of antibiotics. Non-metric multidimensional scaling analysis showed that both the distance to the water reservoir and land-use types played important roles in shaping ARG profiles in riparian soils at a watershed scale. Downstream soils harbored three times the abundance of ARGs compared with upstream and midstream soils. Distance-decay analysis indicated that the similarity of ARG profiles and bacterial community composition decreased significantly with the increase of geographical distance (p < 0.001). When taking the land-use type into consideration, the relative abundance and diversity of ARGs and MGEs in orchard and farmland soils were significantly higher than those in wasteland soils. This indicated that anthropogenic activities can also affect ARG patterns in riparian soils. MGE abundance was identified as major driving factors of ARG profiles. In addition, among all the examined soil properties, soil pH was found to be more important than nutrients and organic carbon in shaping ARG profiles. Our findings provide valuable data on ARG distribution in riparian soils in a reservoir catchment and highlight downstream soils is crucial for ensuring water source security.

Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing

BACKGROUND

We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in 18O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced.

RESULTS

An increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with 18O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.

CONCLUSIONS

The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.

The Application of Hydroxyapatite NPs for Adsorption Antibiotic from Aqueous Solutions: Kinetic, Thermodynamic, and Isotherm Studies

Antibiotic pollution has become a serious concern due to the extensive use of antibiotics, their resistance to removal, and their detrimental effects on aquatic habitats and humans. Hence, developing an efficient antibiotic removal process for aqueous solutions has become vital. Amoxicillin (Amox) is one of the antibiotics that has been efficiently removed from an aqueous solution using hydroxyapatite nanoparticles (HAP NPs). The current study synthesizes and utilizes hydroxyapatite nanoparticles as a cost-effective adsorbent. Adsorbent dose, pH solution, initial Amox concentration, equilibrium time, and temperature are among the factors that have an evident impact on Amox antibiotic adsorption. The (200) mg dose, pH (5), temperature (25) °C, and time (120) min are shown to be the best-optimized values. The nonlinear Langmuir’s isotherm and pseudo-second-order kinetic models with equilibrium capacities of 4.01 mg/g are highly compatible with the experimental adsorption data. The experimental parameters of the thermodynamic analysis show that the Amox antibiotic adsorption onto HAP NPs powder is spontaneous and exothermic.

Fecal microbiota transplantation attenuates Escherichia coli infected outgrowth by modulating the intestinal microbiome

BACKGROUND

Given the crucial role of gut microbiota in animal and human health, studies on modulating the intestinal microbiome for therapeutic purposes have grasped a significant attention, of which the role of fecal microbiota transplantation (FMT) has been emphasized.

METHODS

In the current study, we evaluated the effect of FMT on gut functions in Escherichia coli (E. coli) infection by using mice model. Moreover, we also investigated the subsequently dependent variables of infection, i.e., body weight, mortality, intestinal histopathology, and the expression changes in tight junction proteins (TJPs).

RESULTS

The FMT effectively decreased weight loss and mortality to a certain extent with the restoration of intestinal villi that resulted in high histological scores for jejunum tissue damage (p < 0.05). The effect of FMT on alleviating the reduction of intestinal TJPs was also proved by immunohistochemistry analysis and mRNA expression levels. Moreover, the abundance of health-threatening bacteria, belonging to phylum Proteobacteria, family Enterobacteriaceae and Tannerellaceae, genus Escherichia-Shigella, Sphingomonas, Collinsella, etc., were significantly increased, whereas beneficial bacteria, belonging to phylum Firmicutes, family Lactobacillaceae, genus Lactobacillus were decreased in the gut of infected mice. Furthermore, we sought to investigate the association of clinical symptoms with FMT treatment with modulation in gut microbiota. According to beta diversity, the microbial community of gut microbiota results reflected the similarities between non-infected and FMT groups. The improvement of the intestinal microbiota in FMT group was characterized by the significant high level of beneficial microorganisms with the synergistic decrease of Escherichia-Shigella, Acinetobacter, and other taxa.

CONCLUSION

The findings suggest a beneficial host-microbiome correlation following fecal microbiota transplanatation for controlling gut infections and pathogens-associated diseases.

Enterococcus faecium R-026 combined with Bacillus subtilis R-179 alleviate hypercholesterolemia and modulate the gut microbiota in C57BL/6 mice

Probiotics have been demonstrated to lower total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) in individuals with mild hypercholesterolemia. Our previous study found that intervention with Bacillus subtilis R-179 and Enterococcus faecium R-026, well-known probiotics, improved obesity-associated dyslipidemia through ameliorating the gut microbiota, but similar studies on hypercholesterolemia have not been reported to date. Here, we investigated the therapeutic effect of live combined B. subtilis R-179 and E. faecium R-026 (LCBE) in a C57BL/6 mouse model of hypercholesterolemia. A total of 40 mice were administered with a high-cholesterol diet (containing 1.2% cholesterol) to establish a state of hypercholesterolemia for 4 weeks. Then, mice were divided into one model group (group M) and three treatment groups (n = 10 per group), which were administered with LCBE at 0.023 g/mouse/day (group L) or 0.230 g/mouse/day (group H), or atorvastatin 0.010 g/kg/day (group A), for 5 weeks while on a high-cholesterol diet. LCBE at high doses significantly alleviated the symptoms of group M and reduced serum TC, LDL-C, and lipopolysaccharide (LPS). LCBE improved liver steatosis and adipocyte enlargement caused by a high-cholesterol diet. In addition, the administration of LCBE regulated the change in gut microbiota and diversity (Shannon index). Compared with group M, the relative abundance of Actinobacteriota, Colidextribacter, and Dubosiella dramatically decreased in the treatment groups, which were positively correlated with serum TC and LPS. These findings indicated that the mechanism of action of LCBE in treating hypercholesterolemia may be modulation of the gut microbiota. In conclusion, LCBE ameliorated lipid accumulation, reduced inflammation, and alleviated the gut microbiota imbalance in hypercholesterolemic mice. These findings support the probiotic role of LCBE as a clinical candidate for the treatment of hypercholesterolemia.

Exploring the microbiome, antibiotic resistance genes, mobile genetic element, and potential resistant pathogens in municipal wastewater treatment plants in Brazil

Wastewater treatment plants (WWTPs) have been widely investigated in Europe, Asia and North America regarding the occurrence and fate of antibiotic resistance (AR) elements, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and antibiotic resistant bacteria and pathogens. However, monitoring data about AR elements in municipal WWTPs in Brazil are scarce. This study investigated the abundance of intI1, five ARGs (sul1, tetA, blaTEM, ermB and qnrB) and 16S rRNA in raw and treated wastewater of three WWTPs, using different sewage treatments named CAS (Conventional activated sludge), UASB/BTF (UASB followed by biological trickling filter) and MAS/UV (modified activated sludge with UV disinfection stage). Bacterial diversity and the presence of potentially pathogenic groups were also evaluated, and associations between genetic markers and the bacterial populations were presented. All WWTPs decreased the loads of genetic markers finally discharged to receiving water bodies and showed no evidence of being hotspots for antimicrobial resistance amplification in wastewater, since the abundances of intI1 and ARGs within the bacterial population were not increased in the treated effluents. UASB/BTF showed a similar performance to that of the CAS and MAS/UV, reinforcing the sanitary and environmental advantages of this biological treatment, widely applied for wastewater treatment in warm climate regions. Bacterial diversity and richness increased after treatments, and bacterial communities in wastewater samples differed due to catchment areas and treatment typologies. Potential pathogenic population underwent considerable decrease after the treatments; however, strong significant correlations with intI1 and ARGs revealed potential multidrug-resistant pathogenic bacteria (Aeromonas, Arcobacter, Enterobacter, Escherichia-Shigella, Stenotrophomonas and Streptococcus) in the treated effluents, although in reduced relative abundances. These are contributive results for understanding the fate of ARGs, MGEs and potential pathogenic bacteria after wastewater treatments, which might support actions to mitigate their release into Brazilian aquatic environments in the near future.

Long-term chemically protected sodium butyrate supplementation in broilers as an antibiotic alternative to dynamically modulate gut microbiota

Chemically protected sodium butyrate (CSB) is a new kind of sodium butyrate. Our previous study found that 1,000 mg/kg of CSB had the potential capacity of improving growth performance and promoting early development of small intestine in broilers. This study aimed to investigate the effect of long-term antibiotics or CSB supplementation for intestinal microflora dynamical regulation in broilers. One hundred ninety-two 1-day-old Arbor Acres male broilers were randomly allocated into 3 dietary treatment (8 replicates per treatment) and fed with a basal diet (CON), a diet supplemented with the antibiotics (enramycin, 8 mg/kg and aureomycin, 100 mg/kg) (ANT), or a diet supplemented with 1,000 mg/kg of CSB, respectively. Results showed that dietary supplementation of CSB or ANT treatment elevated the weight gain and feed conversion ratio (FCR; P < 0.05), as compared with control (CON) group. Additionally, CON, CSB, or ANT administration dynamically altered the gut microbiota composition as time goes on. The increased presence of potential pathogens, such as Romboutsia and Shuttleworthia, and decreased beneficial bacteria such as Alistipes, Akkermansia, and Bacteroides were verified in new gut homeostasis reshaped by long-term antibiotics treatment, which has adverse effects on intestinal development and health of broilers. Conversely, CSB supplementation could dynamically enhance the relative abundance of Bacteroides, and decrease Romboutsia and Shuttleworthia in new microflora, which has positive effects on intestinal bacteria of broilers compared with CON group. Meanwhile, CSB supplementation was significantly increased the concentration of propionic acid and total short chain fatty acids (total SCFA; P < 0.05) in comparison with CON and ANT groups. Moreover, CSB treatment significantly increased anti-inflammatory and antioxidative capacities (P < 0.05) of broilers compared with ANT group. Taken together, we revealed characteristic structural changes of gut microbiota throughout long-term CSB or ANT supplementation in broilers, which provided a basic data for evaluating the mechanism of action affecting intestinal health by CSB or ANT administration and CSB as an alternative to antibiotics in the broilers industry.

Gegen Qinlian decoction restores the intestinal barrier in bacterial diarrhea piglets by promoting Lactobacillus growth and inhibiting the TLR2/MyD88/NF-κB pathway

Acute bacterial diarrhea is a severe global problem with a particularly high incidence rate in children. The microecology inhabiting the intestinal mucosa is the key factor leading to diarrhea. Gegen Qinlian decoction (GQD) is used to treat bacterial diarrhea, however, its underlying mechanism remains unclear. Thus, this study aimed to clarify the restorative effect of GQD on the intestinal barrier from the perspective of gut microbiota. A Tibetan piglet model with bacterial diarrhea was established through orally administered Escherichia coli, and diarrheal piglets were treated with GQD for three days. After treatment, GQD significantly ameliorated the diarrheal symptoms. GQD decreased the levels of IL-6, LPS, and DAO, and increased SIgA, ZO-1, and occludin levels in intestinal mucosa, indicating the restoration of intestinal barrier. GQD modulated the microbial compositions inhabited on the intestinal mucosa, especially an increase of the Lactobacillus. Spearman analysis showed that Lactobacillus was the key genus of intestinal barrier-related bacteria. Bacterial culture in vitro validated that GQD directly promoted Lactobacillus growth and inhibited E. coli proliferation. Moreover, the expressions of TLR2, MyD88, and NF-κB in the colon decreased after GQD treatment. In conclusion, GQD may treat diarrhea and restore the intestinal mucosal barrier by facilitating Lactobacillus growth and inhibiting the TLR2/MyD88/NF-κB signaling pathway.

Unveiling the risks and critical mechanisms of polyhexamethylene guanidine on the antibiotic resistance genes propagation during sludge fermentation process

This study mainly investigated the environmental risks of polyhexamethylene guanidine (PHMG) occurred in waste activated sludge (WAS) on the antibiotic resistance genes (ARGs) spread during anaerobic fermentation, and disclosed the critical mechanisms. The total ARGs abundance was increased by 32.2-46.4% at different stressing levels of PHMG. The main resistance mechanism categories of ARGs shifted to the target alternation and efflux pump. PHMG disintegrated WAS structure and increased the cell permeability, which benefitted the mobile genetic elements (MGEs) release and horizontal transfer of ARGs. Besides, PHMG induced the enrichment of potential ARGs hosts (i.e., Burkholderia, Bradyrhizobium and Aeromonas). Moreover, PHMG upregulated the metabolic pathways (i.e., two-component system, quorum sensing, and ATP-binding cassette transporters) and critical genes expression (i.e., metN, metQ, rpfF, rstA and rstB) related with ARGs generation and dissemination. Structural equation model analysis revealed that microbial community structure was the predominant contributor to the ARGs propagation.

Differential variations of intracellular and extracellular antibiotic resistance genes between treatment units in centralized sewage sludge treatment plants

Centralized sludge treatment plants (CSTPs) are implicated as strong hotspots of antibiotic resistance genes (ARGs). However, the knowledge gap on the fate of intracellular and extracellular ARGs (iARGs and eARGs), and the functionality of resistant hosts limit risk assessment and management of CSTP resistome. Here, the flow of iARGs and eARGs across treatment units and analyses of ARG hosts were systematically explored in three full-scale CSTPs using quantitative metagenomic approaches. We found that 29% of sludge ARGs could be removed, with iARGs being dominant in the produced biosolids. The treatment process significantly affected the variations of iARG and eARG abundance while no significant difference in composition between iARGs and eARGs was observed in CSTPs. 15% of 295 recovered genomes were identified as antibiotic-resistant hosts, among which Actinobacteriota tended to encode multiple resistance. The key functions of ARG hosts were relative to the biological organic removal (e.g., carbohydrates). There also existed relationships between certain resistance mechanisms and functional traits, indicating that ARGs might take part in the physiological process of microorganisms in the sludge treatment. These findings provide important insight into the differential resistome variations and host functionality, which would be crucial in the management of antibiotic resistance in CSTPs.

Systematic whole-genome sequencing reveals an unexpected diversity among actinomycetoma pathogens and provides insights into their antibacterial susceptibilities

Mycetoma is a neglected tropical chronic granulomatous inflammatory disease of the skin and subcutaneous tissues. More than 70 species with a broad taxonomic diversity have been implicated as agents of mycetoma. Understanding the full range of causative organisms and their antibiotic sensitivity profiles are essential for the appropriate treatment of infections. The present study focuses on the analysis of full genome sequences and antibiotic inhibitory concentration profiles of actinomycetoma strains from patients seen at the Mycetoma Research Centre in Sudan with a view to developing rapid diagnostic tests. Seventeen pathogenic isolates obtained by surgical biopsies were sequenced using MinION and Illumina methods, and their antibiotic inhibitory concentration profiles determined. The results highlight an unexpected diversity of actinomycetoma causing pathogens, including three Streptomyces isolates assigned to species not previously associated with human actinomycetoma and one new Streptomyces species. Thus, current approaches for clinical and histopathological classification of mycetoma may need to be updated. The standard treatment for actinomycetoma is a combination of sulfamethoxazole/trimethoprim and amoxicillin/clavulanic acid. Most tested isolates had a high IC (inhibitory concentration) to sulfamethoxazole/trimethoprim or to amoxicillin alone. However, the addition of the β-lactamase inhibitor clavulanic acid to amoxicillin increased susceptibility, particularly for Streptomyces somaliensis and Streptomyces sudanensis. Actinomadura madurae isolates appear to have a particularly high IC under laboratory conditions, suggesting that alternative agents, such as amikacin, could be considered for more effective treatment. The results obtained will inform future diagnostic methods for the identification of actinomycetoma and treatment.

Metagenomics analysis of probable transmission of determinants of antibiotic resistance from wastewater to the environment - A case study

During mechanical-biological treatment, wastewater droplets reach the air with bioaerosols and pose a health threat to wastewater treatment plant (WWTP) employees and nearby residents. Microbiological pollutants and antimicrobial resistance determinants are discharged to water bodies with treated wastewater (TWW), which poses a potential global epidemiological risk. In the present study, the taxonomic composition of microorganisms was analyzed, and the resistome profile and mobility of genes were determined by metagenomic next-generation sequencing in samples of untreated wastewater (UWW), wastewater collected from an activated sludge (AS) bioreactor, TWW, river water collected upstream and downstream from the wastewater discharge point, and in upper respiratory tract swabs collected from WWTP employees. Wastewater and the emitted bioaerosols near WWTP's facilities presumably contributed to the transmission of microorganisms, in particular bacteria of the phylum Actinobacteria and the associated antibiotic resistance genes (ARGs) (including ermB, ant(2″)-I, tetM, penA and cfxA2) to the upper respiratory tract of WWTP employees. The discharged wastewater increased the taxonomic diversity of microorganisms and the concentrations of various ARGs (including bacA, emrE, sul1, sul2 and tetQ) in river water. This study fills in the knowledge gap on the health risks faced by WWTP employees. The study has shown that microbiological pollutants and antimicrobial resistance determinants are also in huge quantities discharged to rivers with TWW, posing a potential global epidemiological threat.

Ralstonia solanacearum Infection Disturbed the Microbiome Structure Throughout the Whole Tobacco Crop Niche as Well as the Nitrogen Metabolism in Soil

Infections of Ralstonia solanacearum result in huge agricultural and economic losses. As known, the proposal of effective biological measures for the control of soil disease depends on the complex interactions between pathogens, soil microbiota and soil properties, which remains to be studied. Previous studies have shown that the phosphorus availability increased pathobiome abundance and infection of rhizosphere microbial networks by Ralstonia. Similarly, as a nutrient necessary for plant growth, nitrogen has also been suggested to be strongly associated with Ralstonia infection. To further reveal the relationship between soil nitrogen content, soil nitrogen metabolism and Ralstonia pathogens, we investigated the effects of R. solanacearum infection on the whole tobacco niche and its soil nitrogen metabolism. The results demonstrated that Ralstonia infection resulted in a reduction of the ammonium nitrogen in soil and the total nitrogen in plant. The microbes in rhizosphere and the plant’s endophytes were also significantly disturbed by the infection. Rhodanobacter which is involved in nitrogen metabolism significantly decreased. Moreover, the load of microbial nitrogen metabolism genes in the rhizosphere soil significantly varied after the infection, resulting in a stronger denitrification process in the diseased soil. These results suggest that the application management strategies of nitrogen fertilizing and a balanced regulation of the rhizosphere and the endophytic microbes could be promising strategies in the biological control of soil-borne secondary disasters.

Performance and mechanism of the in situ restoration effect on VHCs in the polluted river water based on the orthogonal experiment: photosynthetic fluorescence characteristics and microbial community analysis

Volatile halogenated hydrocarbons (VHCs) attracted many attentions due to its toxicity and persistence in the environment. In this research, a novel in situ ecological restoration reactor was applied to the degradation of VHCs in polluted river water. The optimized working condition adaptation of the in situ restoration technique was evaluated through orthogonal tests. The experiments showed that when the water depth was 0.4 m, the HRT was 5 days, and the current velocity was 1 m/s, the optimal removal efficiency of VHCs in the reactor was achieved. And the removal rates of CHCl₃, CCl₄, C₂HCl₃, and C₂Cl₄ reached 70.27%, 70.59%, 67.74%, and 81.82%, respectively. The results showed that both HRT and water depth were significantly related to the removal efficiency of reactor. The physiological state of the plants was analyzed by fitting rapid light curve (RLC) model, which showed that the accumulation of VHCs inhibited the photosynthetic performance of plants. Moreover, the microbial community structures of fillers were tested by high-throughput sequencing, and the findings supported that the microbial community made a great response to adapt to the changes in environment of the reactor. The relative abundance of Rhodocyclaceae increased slightly, which hinted that it had good adaptability to VHCs in polluted river water. The research results confirmed that in situ ecological restoration reactor was a potential approach for removal VHCs in polluted river water.

Microbial community and antimicrobial resistance in fecal samples from wild and domestic ruminants in Maiella National Park, Italy

This study aimed to provide new insights about antimicrobial resistance genes abundance and microbial communities of wild and domestic ruminants in wildlife-livestock interface. In total, 88 fecal samples were recovered from Apennine chamois, red deer, goat, cattle and sheep, and were collected in pools. The populations under study were selected based on ecological data useful to define sympatric and non-sympatric populations. Samples were screened for commonly used in farms under study or critically important antimicrobial resistance genes (aadA2, TetA, TetB, TetK, TetM, mcr-1). The microbial community composition was found to be different based on the species and land use of animals under study. Indeed, it was mostly characterized by phyla Firmicutes in bovine, Bacteroidota in chamois and Proteobacteria in red deer. Additionally, positive correlations between antibiotic resistance genes and microbial taxa (e.g., Tet genes correlated with Firmicutes and Patescibacteria) were described. Of the antimicrobials investigated, the abundance of mcr-1 gene suggests the importance of monitoring the wildlife in order to detect the emerging resistance genes contamination in environment. This study provides new data that highlight the importance of multidisciplinary and uncultured study in order to describe the spreading of antimicrobial resistance and related contamination in the environment.

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Multidisciplinary approach including ecological data, real time PCRs and 16S rRNA analysis

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Microbial communities composition of rare species as Apennine chamois

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Evaluation of antibiotic resistance genes abundance in feces of wild and domestic ruminants

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Detection of mcr-1 resistance gene relevant for Public Health

Enduring Effect of Antibiotic Timentin Treatment on Tobacco In Vitro Shoot Growth and Microbiome Diversity

Plant in vitro cultures initiated from surface-sterilized explants often harbor complex microbial communities. Antibiotics are commonly used to decontaminate plant tissue culture or during genetic transformation; however, the effect of antibiotic treatment on the diversity of indigenous microbial populations and the consequences on the performance of tissue culture is not completely understood. Therefore, the aim of this study was to assess the effect of antibiotic treatment on the growth and stress level of tobacco (Nicotiana tabacum L.) shoots in vitro as well as the composition of the plant-associated microbiome. The study revealed that shoot cultivation on a medium supplemented with 250 mg L^-1 timentin resulted in 29 ± 4% reduced biomass accumulation and a 1.2-1.6-fold higher level of oxidative stress injury compared to the control samples. Moreover, the growth properties of shoots were only partially restored after transfer to a medium without the antibiotic. Microbiome analysis of the shoot samples using multivariable region-based 16S rRNA gene sequencing revealed a diverse microbial community in the control tobacco shoots, including 59 bacterial families; however, it was largely dominated by Mycobacteriaceae. Antibiotic treatment resulted in a decline in microbial diversity (the number of families was reduced 4.5-fold) and increased domination by the Mycobacteriaceae family. These results imply that the diversity of the plant-associated microbiome might represent a significant factor contributing to the efficient propagation of in vitro tissue culture.

Characterization of Bifidobacterium asteroides Isolates

Bifidobacteria have long been recognized as bacteria with probiotic and therapeutic features. The aim of this work is to characterize the Bifidobacterium asteroides BA15 and BA17 strains, isolated from honeybee gut, to evaluate its safety for human use. An in-depth assessment was carried out on safety properties (antibiotic resistance profiling, β-hemolytic, DNase and gelatinase activities and virulence factor presence) and other properties (antimicrobial activity, auto-aggregation, co-aggregation and hydrophobicity). Based on phenotypic and genotypic characterization, both strains satisfied all the safety requirements. More specifically, genome analysis showed the absence of genes encoding for glycopeptide (vanA, vanB, vanC-1, vanC-2, vanD, vanE, vanG), resistance to tetracycline (tetM, tetL and tetO) and virulence genes (asa1, gelE, cylA, esp, hyl).

New Estimation of Antibiotic Resistance Genes in Sediment Along the Haihe River and Bohai Bay in China: A Comparison Between Single and Successive DNA Extraction Methods

Sediment is thought to be a vital reservoir for antibiotic resistance genes (ARGs). Often, studies describing and comparing ARGs and their potential hosts in sediment are based on single DNA extractions. To date, however, no study has been conducted to assess the influence of DNA extraction efficiency on ARGs in sediment. To determine whether the abundance of ARGs is underestimated, we performed five successive extraction cycles with a widely used commercial kit in 10 sediment samples collected from the Haihe River and Bohai Bay. Our results showed that accumulated DNA yields after five extractions were 1.8–3.1 times higher than that by single DNA extractions. High-throughput sequencing showed that insufficient DNA extraction could generate PCR bias and skew community structure characterization in sediment. The relative abundances of some pathogenic bacteria, such as Enterobacteriales, Lactobacillales, and Streptomycetales, were significantly different between single and successive DNA extraction samples. In addition, real-time fluorescent quantitative PCR (qPCR) showed that ARGs, intI1, and 16S rRNA gene abundance strongly increased with increasing extraction cycles. Among the measured ARGs, sulfonamide resistance genes and multidrug resistance genes were dominant subtypes in the study region. Nevertheless, different subtypes of ARGs did not respond equally to the additional extraction cycles; some continued to have linear growth trends, and some tended to level off. Additionally, more correlations between ARGs and bacterial communities were observed in the successive DNA extraction samples than in the single DNA extraction samples. It is suggested that 3–4 additional extraction cycles are required in future studies when extracting DNA from sediment samples. Taken together, our results highlight that performing successive DNA extractions on sediment samples optimizes the extractable DNA yield and can lead to a better picture of the abundance of ARGs and their potential hosts in sediments.

Investigating the Effect of an Oxytetracycline Treatment on the Gut Microbiome and Antimicrobial Resistance Gene Dynamics in Nile Tilapia (Oreochromis niloticus)

Antibiotics play a vital role in aquaculture where they are commonly used to treat bacterial diseases. However, the impact of antibiotic treatment on the gut microbiome and the development of antimicrobial resistance in Nile tilapia (Oreochromis niloticus) over time remains to be fully understood. In this study, fish were fed a single treatment of oxytetracycline (100 mg/kg/day) for eight days, followed by a 14-day withdrawal period. Changes in the distal gut microbiome were measured using 16S rRNA sequencing. In addition, the abundance of antimicrobial resistance genes was quantified using real-time qPCR methods. Overall, the gut microbiome community diversity and structure of Nile tilapia was resilient to oxytetracycline treatment. However, antibiotic treatment was associated with an enrichment in Plesiomonas, accompanied by a decline in other bacteria taxa. Oxytetracycline treatment increased the proportion of tetA in the distal gut of fish and tank biofilms of the treated group. Furthermore, the abundance of tetA along with other tetracycline resistance genes was strongly correlated with a number of microbiome members, including Plesiomonas. The findings from this study demonstrate that antibiotic treatment can exert selective pressures on the gut microbiome of fish in favour of resistant populations, which may have long-term impacts on fish health.

Insights into the roles of fungi and protist in the giant panda gut microbiome and antibiotic resistome

The mammal gut is a rich reservoir of antibiotic resistance genes (ARGs), and the relationship between bacterial communities and ARGs has been widely studied. Despite ecological significance of microeukaryotes (fungi and protists), our understanding of their roles in the mammal gut microbiome and antibiotic resistome is still limited. Here, we used amplicon sequencing, metagenomic sequencing and high-throughput quantitative PCR to examine microbiomes and antibiotic resistomes of 41 giant panda fecal samples from individuals with different genders, ages, sampling sites and diet. Our results show that diverse protists inhabit in the giant panda gut ecosystem, dominated by consumers. Higher abundance of protistan consumers was detected in the elder compared to sub-adult and adult giant pandas. Diet is the main driving factor of variation in ARGs in the giant panda gut microbiome. Weighted correlation network analysis identified two key microbial modules from multitrophic communities, which all contributed to the variation in ARGs in the giant panda gut. Protists occupied an important position in the two modules which were dominated by fungal taxa. Deterministic processes made a more important contribution to microbial community assembly of the two modules than to bacterial, fungal and protistan communities. This study sheds new light on how key microbial modules contribute to the variation in ARGs, which is crucial in understanding dynamics of antibiotic resistome in the mammal gut, particularly endangered species.

High-Throughput Single-Cell Technology Reveals the Contribution of Horizontal Gene Transfer to Typical Antibiotic Resistance Gene Dissemination in Wastewater Treatment Plants

The spread of antibiotic resistance genes (ARGs) has gained much attention worldwide, while the contribution of vertical gene transfer (VGT) and horizontal gene transfer (HGT) is still elusive. Here, we improved an emerging high-throughput single-cell-based technology, emulsion, paired isolation, and concatenation polymerase chain reaction (epicPCR), by lengthening the sequence of ARG in the fused ARG-16S rRNA fragments to cover the variance of both ARG and its hosts. The improved epicPCR was applied to track the hosts of a widely detected ARG, sul1 gene, in five urban wastewater treatment plants (UWTPs) during two seasons. The sul1 host bacteria were highly diverse and mostly classified as Proteobacteria and Bacteroidetes. Clear seasonal divergence of α-diversity and interaction networks were present in the host community. The consensus phylogenetic trees of the sul1 gene and their host demonstrated incorrespondence on the whole and regularity on abundant groups, suggesting the important role of both HGT and VGT, respectively. The relative importance of these two ways was further measured; HGT (54%) generally played an equal or even more important role as VGT (46%) in UWTPs. The application of the improved epicPCR technology provides a feasible approach to quantify the relative contributions of VGT and HGT in environmental dissemination of ARGs.

Marine Actinomycetes, New Sources of Biotechnological Products

The Actinomycetales order is one of great genetic and functional diversity, including diversity in the production of secondary metabolites which have uses in medical, environmental rehabilitation, and industrial applications. Secondary metabolites produced by actinomycete species are an abundant source of antibiotics, antitumor agents, anthelmintics, and antifungals. These actinomycete-derived medicines are in circulation as current treatments, but actinomycetes are also being explored as potential sources of new compounds to combat multidrug resistance in pathogenic bacteria. Actinomycetes as a potential to solve environmental concerns is another area of recent investigation, particularly their utility in the bioremediation of pesticides, toxic metals, radioactive wastes, and biofouling. Other applications include biofuels, detergents, and food preservatives/additives. Exploring other unique properties of actinomycetes will allow for a deeper understanding of this interesting taxonomic group. Combined with genetic engineering, microbial experimental evolution, and other enhancement techniques, it is reasonable to assume that the use of marine actinomycetes will continue to increase. Novel products will begin to be developed for diverse applied research purposes, including zymology and enology. This paper outlines the current knowledge of actinomycete usage in applied research, focusing on marine isolates and providing direction for future research.

Antimicrobial activity of Actinobacteria isolated from dry land soil in Yazd, Iran

Historically, many important secondary metabolites including antibiotics used in clinic are purified from the cultural broths of Actinobacteria, which were inhabited in soil. Yazd is located in the center of Iran, the south of the Dasht-e Kavir and the west of the Dasht-e Lut; accordingly it has a hot, dry climate with long summers. In the present study, 18 strains of Actinobacteria isolated from 60 soil samples from Yazd-Iran. Pure isolates were screened for antibacterial activity against the ATCC strains by using two methods: single line streak method and spot inoculation method. ATCC strains include four antibiotic resistant ATCC strains (Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae and, Acinetobacter baumannii) and three antibiotic sensitive strains (Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli) and, Bacillus subtilis. Seven isolates exhibited antimicrobial activity against the ATCC strains (38.8%). Identification of type I and type II polyketide synthases (pksI, pksII) and nonribosomal peptide synthetase (NRPS) genes were done for these 7 isolates and all of 7 strains, possessed at least one of these genes. The results of this study confirm that soil Actinobacteria bear a great ability to produce antibacterial compounds against resistant and sensitive test organisms.

Role of Williamsia and Segniliparus in human infections with the approach taxonomy, cultivation, and identification methods

The genera Williamsia and Segniliparus are of aerobic actinomycetes and at the time of writing, they have 12 and 2 species, respectively. These genera cause various infections in humans. In this review, we surveyed their taxonomy, isolation, identification, as well as their role to cause human infections.

Exploring antibiotic resistance in environmental integron-cassettes through intI-attC amplicons deep sequencing

INTRODUCTION

Freshwater ecosystems provide propitious conditions for the acquisition and spread of antibiotic resistance genes (ARGs), and integrons play an important role in this process.

MATERIAL AND METHODS

In the present study, the diversity of putative environmental integron-cassettes, as well as their potential bacterial hosts in the Velhas River (Brazil), was explored through intI-attC and 16S rRNA amplicons deep sequencing. RESULTS AND DISCUSSION: ORFs related to different biological processes were observed, from DNA integration to oxidation-reduction. ARGs-cassettes were mainly associated with class 1 mobile integrons carried by pathogenic Gammaproteobacteria, and possibly sedentary chromosomal integrons hosted by Proteobacteria and Actinobacteria. Two putative novel ARG-cassettes homologs to fosB3 and novA were detected. Regarding 16SrRNA gene analysis, taxonomic and functional profiles unveiled Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Betaproteobacteria, Alphaproteobacteria, and Actinobacteria classes were the main contributors for KEGG orthologs associated with resistance.

CONCLUSIONS

Overall, these results provide new information about environmental integrons as a source of resistance determinants outside clinical settings and the bacterial community in the Velhas River.

Removal of antibiotic resistant bacteria and antibiotic resistance genes in wastewater effluent by UV-activated persulfate

The emerging antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are increasingly appreciated to be as important as microbial contaminants. This paper focused on UV-activated persulfate (UV/PS), an advanced oxidation process, in removing ARB and ARGs from secondary wastewater effluent. Results showed that the inactivation efficiency of macrolides-resistant bacteria (MRB), sulfonamides-resistant bacteria (SRB), tetracyclines-resistant bacteria (TRB) and quinolones-resistant bacteria (QRB) by UV/PS reached 96.6 %, 94.7 %, 98.0 % and 99.9 % in 10 min, respectively. UV/PS also showed significant removal efficiency on ARGs. The reduction of total ARGs reached 3.84 orders of magnitude in UV/PS which is more than that in UV by 0.56 log. Particularly, the removal of mobile genetic elements (MGE) which might favor the horizontal gene transfer of ARGs among different microbial achieved 76.09 % by UV/PS. High-throughput sequencing revealed that UV/PS changed the microbial community. The proportions of Proteobacteria and Actinobacteria that pose human health risks were 4.25 % and 1.6 % less than UV, respectively. Co-occurrence analyzes indicated that ARGs were differentially contributed by bacterial taxa. In UV/PS system, hydroxyl radical and sulfate radical contributed to the removal of bacteria and ARGs. Our study provided a new method of UV/PS to remove ARGs and ARB for wastewater treatment.