RNA-Seq comparative analysis reveals the response of Enterococcus faecalis TV4 under fluoride exposure

Whole genome analyses of toxicants tolerance genes of Apis mellifera gut-derived Enterococcus faecium strains

BACKGROUND

Because of its social nature, the honeybee is regularly exposed to environmental toxicants such as heavy metals and xenobiotics. These toxicants are known to exert strong selective pressure on the gut microbiome's structure and diversity. For example, resistant microbial members are more likely to dominate in maintaining a stable microbiome, which is critical for bee health. Therefore, the aim of this study was to examine the Enterococcus faecium strains isolated from bee guts for their in vitro growth and tolerability to diverse heavy metals and xenobiotics. An additional aim was to analyze the genomes of E. faecium isolates to assess the molecular bases of resistance and compare them with E. faecium species isolated from other environmental sources.

RESULTS

The E. faecium bee isolates were able to tolerate high levels (up to 200 mg/L) of toxicants, including cadmium, zinc, benzoate, phenol and hexane. Moreover, the isolates could tolerate toluene and copper at up to 100 mg/L. The genome of E. faecium Am5, isolated from the larval stage of Apis mellifera gut, was about 2.7 Mb in size, had a GC content of 37.9% and 2,827 predicted coding sequences. Overall, the Am5 genome features were comparable with previously sequenced bee-gut isolates, E. faecium Am1, Bee9, SM21, and H7. The genomes of the bee isolates provided insight into the observed heavy metal tolerance. For example, heavy metal tolerance and/or regulation genes were present, including czcD (cobalt/zinc/cadmium resistance), cadA (exporting ATPase), cutC (cytoplasmic copper homeostasis) and zur (zinc uptake regulation). Additionally, genes associated with nine KEGG xenobiotic biodegradation pathways were detected, including γ-hexachlorocyclohexane, benzoate, biphenyl, bisphenol A, tetrachloroethene, 1,4-dichlorobenzene, ethylbenzene, trinitrotoluene and caprolactam. Interestingly, a comparative genomics study demonstrated the conservation of toxicant resistance genes across a variety of E. faecium counterparts isolated from other environmental sources such as non-human mammals, humans, avians, and marine animals.

CONCLUSIONS

Honeybee gut-derived E. faecium strains can tolerate a variety of heavy metals. Moreover, their genomes encode many xenobiotic biodegradation pathways. Further research is required to examine E. faecium strains potential to boost host resistance to environmental toxins.

Microbially induced calcium precipitation coupled with medical stone-coated sponges: A targeted strategy for enhanced nitrate and fluoride removal from groundwater

The coexistence of nitrate and fluoride in groundwater is of high concern due to its potential environmental impacts and health risks. Medical stone-coated sponges, as a microbial activity promoter and slow-release calcium source, were introduced into an immobilized bioreactor for enhanced removal of nitrate and fluoride. Under the hydraulic retention time of 3 h, nitrate, fluoride, and calcium contents of 16.5, 3.0, and 100 mg L^-1, the average removal efficiencies of nitrate, fluoride, and calcium reached 99.49%, 74.26%, and 70.43%, respectively. Co-precipitation and chemisorption were the mechanisms for fluoride and calcium removal. Medical stone load improved the competitiveness of dominant bacteria and electron transport activity, accelerated the denitrification process, and stimulated biofilm formation. High fluoride level (5.0 mg L^-1) inhibited the nitrate removal and aromatic protein production. The fluoride content changes altered the carbon source preference of the microbial community, which preferred to use amino acids and carbohydrates under a higher fluoride content. The introduction of medical stones significantly accelerated the fluoride and nitrate removal, providing a new insight for the application of microbially induced calcium precipitation technique in the remediation of low-calcium groundwater.

In-depth insights into the disruption of the microbiota-gut-blood barrier of model organism (Bombyx mori) by fluoride

Fluoride is a serious health risk to animals and humans. The microbiota-gut-blood barrier (MGBB) plays an indispensable role in maintaining the systematic homeostasis of host organisms. However, the toxic effects of fluoride on MGBB of organisms have not been extensively investigated. Here, we used the silkworm interspecies model to explore the adverse effects of fluoride on the gut microbiota and intestinal tissue and circulating metabolites of organisms. Results showed that fluoride exposure significantly declined the body weight gain and survival rate of organisms and evidently damaged intestinal epithelial cells. In addition, fluoride altered the composition and abundance of intestinal microbiota, which was accompanied by changing gene expression levels of antimicrobial peptides in intestinal tissue. Shifts in the relative abundance of Enterococcus, Aquabacterium, Aureimonas and Methylobacterium in the gut had significant correlations with the concentrations of certain differential metabolites (e.g., amino acids, nucleotides, and nucleotide derivatives) in the bloodstream. Moreover, most circulating metabolites in related nucleotide metabolism pathways were upregulated, whereas those in the pathways of amino acid metabolism were downregulated. This study deepens our understanding of the disruptive effect of fluoride on the MGBB of host organisms and may provide a new insight into the preventive therapy of fluoride-induced diseases.

Bacillus symbiont drives alterations in intestinal microbiota and circulating metabolites of lepidopteran host

The symbiotic association between bacterial symbionts and insect hosts is a complicated process that is not completely understood. Herein, we used a silkworm model to study the association between symbiotic Bacillus and lepidopteran insect by investigating the changes in intestinal microbiota and hemolymph circulating metabolites of silkworm after symbiotic Bacillus subtilis treatment. Results showed that B. subtilis can generate a variety of primary and secondary metabolites, such as B vitamins and antimicrobial compounds, to provide micronutrients and enhance the pathogen resistance of their insect host. Shifts in the relative abundance of Enterococcus, Brevibacterium, Buttiauxella, Pseudomonas, Brevundimonas, and Limnobacter had significant correlations with the concentrations of differential metabolites (e.g., phospholipids and certain amino acids) in insect hemolymph. The antimicrobial compounds secreted by B. subtilis were the primary driving force for the reconstruction of intestinal microbiota. Meanwhile, the altered levels of circulating metabolites in multiple metabolic pathways were potential an adaptive mechanism of insect hosts in response to the shifts of intestinal microbiota. Our findings provided concrete evidence that bacterial intestinal symbiont can alter the physiological state of insects and highlighted the importance of the compositional alterations of intestinal microbiota as a source of variation in circulating metabolites of insect hosts. This article is protected by copyright. All rights reserved.

Gut Microbiota Dysbiosis Influences Metabolic Homeostasis in Spodoptera frugiperda

Insect gut microbiota plays important roles in acquiring nutrition, preventing pathogens infection, modulating immune responses, and communicating with environment. Gut microbiota can be affected by external factors such as foods and antibiotics. Spodoptera frugiperda (Lepidoptera: Noctuidae) is an important destructive pest of grain crops worldwide. The function of gut microbiota in S. frugiperda remains to be investigated. In this study, we fed S. frugiperda larvae with artificial diet with antibiotic mixture (penicillin, gentamicin, rifampicin, and streptomycin) to perturb gut microbiota, and then examined the effect of gut microbiota dysbiosis on S. frugiperda gene expression by RNA sequencing. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the most dominant phyla in S. frugiperda. We found that the composition and diversity of gut bacterial community were changed in S. frugiperda after antibiotics treatment. Firmicutes was decreased, and abundance of Enterococcus and Weissella genera was dramatically reduced. Transcriptome analysis showed that 1,394 differentially expressed transcripts (DETs) were found between the control and antibiotics-treated group. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that antibiotics-induced dysbiosis affected many biological processes, such as energy production, metabolism, and the autophagy–lysosome signal pathway. Our results indicated that dysbiosis of gut microbiota by antibiotics exposure affects energy and metabolic homeostasis in S. frugiperda, which help better understand the role of gut microbiota in insects.

Effects of fluoride on PIWI-interacting RNA expression profiling in testis of mice

Excessive fluoride intake can damage testis by breaking the integrity of sperm DNA and changing the expression profiles of testicular mRNAs and microRNAs. However, the effects of fluoride on the expression of PIWI-interacting RNAs (piRNAs) in mouse testes have not been reported. In this study, we determined the effect of fluoride on PIWI-interacting RNA expression profiling in testis of mice, using deep-sequencing technology. Compared to the control, 50 mg/L sodium fluoride (NaF) exposure led to a reduced testicular organ coefficient, semen quality, and testosterone level, and altered the testicular microstructure. Furthermore, NaF exposure also changed the expression of 28 piRNAs that regulate 182 target genes in mouse testes. In mice given water containing 50 mg/L NaF, the following four pathways were enriched and overexpressed: lysosomal, Jak-STAT, chemokine, and ubiquitin-mediated proteolysis. Among the piRNAs affecting the lysosomal pathway, piR-mmu-1277316, piR-mmu-8060747, and piR-mmu-1566415 levels were increased. We also observed increased levels of the following target gene mRNAs in lysosomal pathwa in the 50 mg/L NaF-treated group: Gga2, Ap4e1, Gla, and Ap1s3. These findings are in line with the results of piRNA-sequencing and suggest that piRNAs in the testis could be potential biomarkers for fluoride reproductive toxicity.

Transcriptome analysis of Cyclocarya paliurus flavonoids regulation of differently expressed genes in Enterococcus faecalis under low pH stress

Enterococcus faecalis (E. faecalis) is an indigenous intestinal bacterium and has potential to be applied as probiotic supplement. Low pH is one of the main stresses that E. faecalis has to deal with to colonize in the gastrointestinal tract. Previous study indicated low concentration of flavonoids may enhance the tolerance of probiotic to environmental stress. In the present research, transcriptome analysis was employed to investigate the influence of Cyclocarya paliurus flavonoids (CPF) on E. faecalis exposed to low pH environment. The results revealed that under the stress of low pH, genes related to cell wall and membrane, transmembrane transport, metabolism process, energy production, and conversion stress proteins were significantly differentially expressed. And certain undesired changes of which (such as genes for MFS transporter were downregulated) could be partially mitigated by CPF intervention, indicating their capacity to improve the low pH tolerance of E. faecalis. Results from this study deepened our understanding of the beneficial role of CPF on the probiotic in the gastrointestinal environment.

Membrane Exporters of Fluoride Ion

Microorganisms contend with numerous and unusual chemical threats and have evolved a catalog of resistance mechanisms in response. One particularly ancient, pernicious threat is posed by fluoride ion (F^-), a common xenobiotic in natural environments that causes broad-spectrum harm to metabolic pathways. This review focuses on advances in the last ten years toward understanding the microbial response to cytoplasmic accumulation of F^-, with a special emphasis on the structure and mechanisms of the proteins that microbes use to export fluoride: the CLC^F family of F^-/H⁺ antiporters and the Fluc/FEX family of F^- channels.

Gas Chromatography-Mass Spectrometry Based Midgut Metabolomics Reveals the Metabolic Perturbations under NaF Stress in Bombyx mori

Fluoride tolerance is an important economic trait in sericulture, especially in some industrial development regions. Analyses of physiological changes involving structural damage to the insect body and molecular analyses of some related genes have focused on this area; however, the changes that occur at the metabolic level of silkworms after eating fluoride-contaminated mulberry leaves remain unclear. Here, metabonomic analysis was conducted using gas chromatography-mass spectrometry (GC-MS) to analyze the changes in midgut tissue after NaF stress using silkworm strains 733xin (susceptible stain) and T6 (strain resistant to fluoride), which were previously reported by our laboratory. Differential metabolomics analysis showed that both T6 and 733xin strains displayed complex responses after exposure to 200 mg/kg NaF. The purine metabolism and arginine and proline metabolic pathways of fluoride-tolerant strains reached significant levels, among which 3′-adenylic acid and hypoxanthine were significantly upregulated, whereas guanine, allantoic acid, xanthine, N-acetyl-L-glutamic acid, and pyruvate were significantly downregulated. These metabolic pathways may be related to the fluoride tolerance mechanism of NaF poisoning and tolerant strains.