The cutaneous microbiome in skin cancer - A systematic review.

The overall incidence of skin cancer has risen over the past half a decade worldwide and is associated with significant morbidity and mortality. Recent advances in molecular testing have allowed us to better characterize microbiome alterations in skin cancer. However, literature specific to skin microbiome and skin cancer remain heterogenous and scattered. A systematic review was performed to identify the existing literature and its usefulness in providing microbiome-based biomarkers. A search of the databases (PubMed, Medline, EMBASE, GoogleScholar) was conducted from June to July 2022 in accordance with the PRISMA guidelines. A total of 1,543 articles were identified, of which 16 were selected for inclusion in the review (11 articles on cancer of the keratinocytes and 5 articles on melanoma). Increased Staphylococcus (S.) aureus prevalence with decline in commensal organisms is seen in squamous cell carcinoma (SCC) and actinic keratosis (AK), compared to healthy skin. While the microbiome of melanoma appears to be distinct from healthy skin, limited data is available to draw meaningful conclusions. Our review summarizes the current evidence on the microbiome of keratinocyte skin cancers and melanoma. The study establishes that the microbiome of these cancers is altered from healthy skin and that this dysbiosis involves both pathogenic and commensal organisms.

Metagenomic analysis reveals indole signaling effect on microbial community in sequencing batch reactors: Quorum sensing inhibition and antibiotic resistance enrichment.

Indole is an essential signal molecule in microbial studies. However, its ecological role in biological wastewater treatments remains enigmatic. This study explores the links between indole and complex microbial communities using sequencing batch reactors exposed to 0, 15, and 150 mg/L indole concentrations. A concentration of 150 mg/L indole enriched indole degrader Burkholderiales, while pathogens, such as Giardia, Plasmodium, and Besnoitia were inhibited at 15 mg/L indole concentration. At the same time, indole reduced the abundance of predicted genes in the "signaling transduction mechanisms" pathway via the Non-supervised Orthologous Groups distributions analysis. Indole significantly decreased the concentration of homoserine lactones, especially C14-HSL. Furthermore, the quorum-sensing signaling acceptors containing LuxR, the dCACHE domain, and RpfC showed negative distributions with indole and indole oxygenase genes. Signaling acceptors' potential origins were mainly Burkholderiales, Actinobacteria, and Xanthomonadales. Meanwhile, concentrated indole (150 mg/L) increased the total abundance of antibiotic resistance genes by 3.52 folds, especially on aminoglycoside, multidrug, tetracycline, and sulfonamide. Based on Spearman's correlation analysis, the homoserine lactone degradation genes which were significantly impacted by indole negatively correlated with the antibiotic resistance gene abundance. This study brings new insights into the effect of indole signaling on in biological wastewater treatment plants.

Succession of diversity, functions, and interactions of the fungal community in activated sludge under aromatic hydrocarbon stress.

Although fungi are regarded as the important degraders of aromatic hydrocarbons (AHs) in various environments, the dynamic succession and interaction of their community under aromatic hydrocarbon stress has been rarely reported. In this study, we systematically investigated the responses of the fungal community and the associations among fungal species when facing the continuous stress of two typical AHs, benzene and naphthalene. Using high-throughput sequencing technology, we demonstrated that fungal diversity displayed a significant downward trend during six weeks of continuous aromatic hydrocarbon treatment. Community succession was observed during the operational period, and the relative abundance of some typical degraders, such as Exophiala sp. and Candida sp., increased during the later period of operation. Meanwhile, by predicting the functions of the fungal community through PICRUSt2, we found that some relevant enzymes, such as peroxidase, dioxygenase, and monooxygenase, may play an important role in the degradation process and maintaining overall community multifunctionality. Furthermore, the measurement of modified normalized stochasticity ratio (MST) indicated that continuous aromatic hydrocarbon stress resulted in a stronger deterministic process in community assembly over time, suggesting environmental selection dominated succession of the fungal community in activated sludge. Finally, molecular ecological network analysis (MENA) demonstrated that, the cooperative behaviors among members, the network keystone genera related to biodegradation, such as Exophiala sp. and Haglerozyma sp., and a well-organized topological structure, together, maintained the structural stability of the fungal community under AH stress. Our study provides new insights for understanding the stability of fungal communities during the degradation of contaminants in activated sludge.

Indole metabolism by phenol-stimulated activated sludges: Performance, microbial communities and network analysis.

Indole and phenol often coexist in the coking wastewater, while the effects of phenol on microbial communities of indole metabolism were less explored. In this study, the microbial interactions within activated sludge microbial communities stimulated by indole (group A) or by indole and phenol (group B) were systematically investigated in sequencing batch reactors (SBRs). The results showed that the removal of indole was increased by adding phenol. By using high-throughput sequencing technology, it was found that α-diversity was reduced in both groups. According to the relative abundance analysis, the indole-degrading genus Comamonas was the core genus in both groups (33.94% and 61.40%). But another indole-degrading genus Pseudomonas was only enriched in group A with 12.22% relative abundance. Meanwhile, common aromatic degrading genus Dyella and Thermomonas were enriched only in group B. It was found that the relative abundance of cytochrome P450 and styrene degradation enzymes were increased in group B by PICRUSt analysis. Based on the phylogenetic molecular ecological networks (pMENs), module hub OTU_1149 (Burkholderia) was only detected in group B, and the positive interactions between the key functional genus Burkholderia and other bacteria were increased. This study provides new insights into our understanding of indole metabolism communities stimulated by phenol, which would provide useful information for practical coking wastewater treatment.

Succession of function, assembly, and interaction of microbial community in sequencing biofilm batch reactors under selenite stress.

The mechanism of interaction between selenite, a toxic substance, and the microbial community in wastewater is still not well understood. Herein, nine sequencing biofilm batch reactors were used to systematically investigate the response of the microbial community to the continuous selenite stress. The results showed that selenite affected the reactor performance and reduced the biofilm mass. Also, it increased the proportion of the living cells, and changed the protein and polysaccharide composition of the biofilm as well as cellular secretions. Selenite facilitated the removal of NO3-N, according to water-quality and bioinformatics analyses. As such, the selenite was converted into selenium nanoparticles. α-diversity analysis further revealed that 20 µM selenite enhanced the microbial community resilience, while 200 µM selenite had the reverse effect. Community composition analysis showed that Variovorax, Rhizobium, and Simkania had positive correlations with selenite (P < 0.05). Functional prediction suggested that selenite changed the C, N, and S cycle functions. Furthermore, determinism dominated the community assembly process, and the deterministic proportion increased with the increase of selenite concentration. Network analysis showed that selenite improved the stability and positive correlation ratio of the overall microbial network, and accelerated the communication between microorganisms. However, when compared with the 20 µM selenite, the 200 µM selenite boosted the competition and parasitism/predation among microorganisms. Low-abundance genera played a key role in the network of selenite-reducing microbial community. In addition, under selenite stress, biofilm network exhibited better stability and faster information exchange than suspended network, and the positive association between biofilm and suspended microorganisms increased. All in all, this research sheds light on the interaction between selenite and microbial community, as well as provides crucial information on selenium-containing wastewater.

Interaction of graphene-family nanomaterials with microbial communities in sequential batch reactors revealed by high-throughput sequencing.

The accelerated development and application of graphene-family nanomaterials (GFNs) have increased their release to various environments and converged in wastewater treatment plants (WWTPs). However, little is known about the interactions between GFNs and microbes in WWTPs. In this study, the interaction of graphene oxide (GO) or graphene (G) at different concentrations with microbial communities in sequential batch reactors was investigated. Transmission electron microscopy and Raman spectroscopy analyses showed that the structures of GFNs were obviously changed, which suggested GFNs could be degraded by some microbes. Significantly higher DNA concentration and lower cell number in high-concentration GO group were detected by DNA leakage test and qPCR analysis, which confirmed the microbial toxicity of GO. The chemical oxygen demand and ammonia nitrogen removals were significantly affected by G and GO with high concentrations. Further, high-throughput sequencing confirmed the composition and dynamic changes of microbial communities under GFNs exposure. Saccharibacteria genera incertae sedis (12.55-28.05%) and Nakamurella (20.45-29.30%) were the predominant genera at two stages, respectively. FAPROTAX suggested 12 functional groups with obvious changes related to the biogeochemical cycle of C, N and S. Molecular ecological network analysis showed that the networks were more complex in the presence of GFNs, and the increased negative interactions reflected more competition relationships in microbial communities. This study is the first to report the effect of GFNs on network of microbial communities, which provides in-depth insights into the complex and highlights concerns regarding the risk of GFNs to WWTPs.

Rod-shaped gold nanoparticles biosynthesized using Pb2+-induced fungus Aspergillus sp. WL-Au.

Gold nanoparticles (AuNPs) attracted much attention owing to their distinguished characteristics and applications. In this study, rod-shaped AuNPs were biosynthesized using Pb2+-induced fungus Aspergillus sp. The synthesized AuNPs showed a UV-vis absorption peak at 534 nm. Scanning electron microscopy and transmission electron microscopy analyses showed that rod-shaped AuNPs were biosynthesized and attached on the mycelia surfaces. Energy-dispersive spectrometer analysis identified gold as the unique metallic composition of synthesized nanoparticles. X-ray powder diffraction analysis showed that the AuNPs were face-centered cubic crystalline structure. Furthermore, Fourier transform infrared spectroscopy analysis detected functional groups, including C = O, C-O-C, amine I and II which played active roles in AuNPs formation. In addition, the main shape of synthesized AuNPs changed from sphere to rod-shape with the increase of biomass and Pb2+ concentration. This study reports quite uniform rod-shaped AuNPs biosynthesized using Pb2+-induced fungus Aspergillus sp. WL-Au for the first time. This will provide a valid alternative for oriented biosynthesis of AuNPs.

QSP: An open sequence database for quorum sensing related gene analysis with an automatic annotation pipeline.

Quorum sensing (QS) has attracted great attention due to its important role in the bacterial interactions and its relevance to water management. With the development of high-throughput sequencing technology, a specific database for QS-related sequence annotation is urgently needed. Here, Hidden Markov Model (HMM) profiles for 38 types of QS-related proteins were built using a total of 4024 collected seed sequences. Based on both homolog search and keywords confirmation against the non-redundant database, we established a QS-related protein (QSP) database, that includes 809,721 protein sequences and 186,133 nucleotide sequences, downloaded available at: https://github.com/chunxiao-dcx/QSP. The entries were classified into 38 types and 315 subtypes among 91 bacterial phyla. Furthermore, an automatic annotation pipeline, named QSAP, was developed for rapid annotation, classification and abundance quantification of QSP-like sequences from sequencing data. This pipeline provided the two homolog alignment strategies offered by Diamond (Blastp) or HMMER (Hmmscan), as well as a data cleansing function for a subset or union set of the hits. The pipeline was tested using 14 metagenomic samples from various water environments, including activated sludge, deep-sea sediments, estuary water, and reservoir water. The QSAP pipeline is freely available for academic use in the code repository at: https://github.com/chunxiao-dcx/QSAP. The establishment of this database and pipeline, provides a useful tool for QS-related sequence annotation in a wide range of projects, and will increase our understanding of QS communication in aquatic environments.

Selenium nanoparticles with photocatalytic properties synthesized by residual activated sludge.

The treatment and disposal of residual activated sludge is a worldwide problem and the research on its reuse is still only in the earliest stages. Selenite is a toxic pollutant, while selenium nanoparticles (SeNPs) are environmentally friendly and have promising application prospects. At present, the reduction mechanism of selenite under the complex system is still poorly understood. In order to explore the mechanism of SeNPs synthesis by activated sludge resource utilization, SeNPs were synthesized by activated sludge extracts of domestic sewage (DSeNPs) and coking sewage (CSeNPs), respectively. The synthesis process, zeta potential and morphology size of SeNPs were changed by pH value, extract concentration and extract composition. Under the same synthesis conditions, the morphologies of DSeNPs and CSeNPs were mainly spherical and pseudo-spherical, while CSeNPs also contained pseudo-rod shape particles. The sizes and crystal grains of CSeNPs were smaller than those of DSeNPs. Compared with DSeNPs, a specific protein (~35 kDa) was found on the surface of CSeNPs using SDS-PAGE. By analyzing the fluorescence images of the two SeNPs, it was found that the relative contents of proteins, α-d-glucopyranose polysaccharides, and ß-d-glucopyranose polysaccharides on their surfaces were obviously different (P < 0.05). The present study demonstrated that proteins, polysaccharides, humic-like and fulvic acid-like substances cooperated in the formation and stabilization of SeNPs. Furthermore, CSeNPs (bandgap: 1.68 eV) had more desirable photocatalytic performance than DSeNPs (bandgap: 1.84 eV). Under the light condition, CSeNPs could degrade Rhodamine B faster without adding hydrogen peroxide. This experiment provided a new insight into the resource utilization of activated sludge and a reference for the synthesis of nanometer selenium with excellent performance.

DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation.

Biodegradation of aromatic compounds is ubiquitous in the environment and important for controlling organic pollutants. Aromatic ring-hydroxylating dioxygenases (ARHDs) are responsible for the first and rate-limiting step of aerobic biodegradation of aromatic compounds. The ARHD α subunit is a good biomarker for studying functional microorganisms in the environment, however their diversity and corresponding primer coverage are unclear, both of which require a comprehensive sequence database for the ARHD α subunit. Here amino acid sequences of the ARHD α subunit were collected, and a total of 103 sequences were selected as seed sequences that were distributed in 72 bacterial genera with 34 gene names. Based on both homolog search and keyword confirmation against the GenBank, a sequence database of ARHD (DARHD) has been established and 6367 highly credible sequences were retrieved. DARHD contained 407 bacterial genera capable of degrading 38 aromatic substrates, and intricate relationships among the gene name, aromatic substrate and microbial taxa were observed. Thereafter, a total of 136 pairs of primers were collected and assessed. Results showed coverages of most published primers were low. Our research provides new insights for understanding the diversity of ARHD α subunit, and gives guidance on the design and application of primers in the future.

A rare case of polyarteritis nodosa associated with nontuberculous mycobacterial infection.

Clinicians should be aware that cutaneous PAN can present with significant extracutaneous and constitutional symptoms which make it hard to differentiate from systemic PAN. The condition can also rarely be associated with NTM infections.

Performance and Microbial Community Analysis of Bioaugmented Activated Sludge System for Indigo Production from Indole.

Indole is a typical nitrogen-containing aromatic pollutant in coking wastewater, and it can be used for the microbial production of indigo, one of the oldest dyestuffs. In this study, the activated sludge system bioaugmented with two indigo-producing bacterial strains, wild strain Comamonas sp. MQ and recombinant Escherichia coli (ND_IND), was constructed to investigate indigo bioproduction from indole. During the operation, the bioaugmentation could promote the production of indigo, especially in early stages, and the indigo yields gradually increased from 17.5 ± 0.4 to 44.3 ± 0.5 mg/L with the increase of influent indole (80 to 282 mg/L). Illumina MiSeq sequencing revealed that the microbial community could have a noticeable shift driven by the bioaugmentation and high indole pressure. The indigenous bacteria could be more responsible for indigo production, and the dominant genera Comamonas, Diaphorobacter, Paracoccus, Aquamicrobium, Pseudomonas, and Truepera could be the key functional taxa. Based on FAPROTAX (Functional Annotation of Prokaryotic Taxa) analysis, the nitrogen metabolism-related functional groups could play important roles in indole biotransformation and indigo biosynthesis. This study should provide insights into microbial production of indigo by microbial communities.

Biosynthesis of gold nanoparticles using fungus Trichoderma sp. WL-Go and their catalysis in degradation of aromatic pollutants.

An efficient green method of gold nanoparticles (AuNPs) biosynthesis was achieved by cell-free extracts of fungus Trichoderma sp. WL-Go. Based on UV-Vis spectra, AuNPs biosynthesised by cell-free extracts with 90 mg/l protein exhibited a characteristic absorption band at 556 nm and was stable for 7 days. Transmission electron microscopy images revealed that the as-synthesised AuNPs were spherical and pseudo-spherical, and the average size was calculated to be 9.8 nm with a size range of 1-24 nm. The AuNPs illustrated their good catalytic activities for reduction of nitro-aromatics (2-nitrophenol, 3-nitrophenol, 4-nitrophenol, 2-nitroaniline, 3-nitroaniline) with catalytic rate constants of 7.4 × 10-3 s-1, 10.3 × 10-3 s-1, 4.9 × 10-3 s-1, 5.8 × 10-3 s-1, 15.0 × 10-3 s-1, respectively. Meanwhile, the AuNPs also showed excellent catalytic performance in decolourisation of azo dyes with decolourisation efficiency from 82.2 to 97.5%. This study provided a green gentle method for AuNPs synthesis as well as exhibiting efficient catalytic capability for degradation of aromatic pollutants.

[Characterization of Au-Ag nanoparticles biosynthesized by fungus Mariannaea sp. HJ].

Biosynthesis of gold-silver alloy nanoparticles (Au-AgNPs) is a simple operation and ecological friendly, but with limited reports on the availability of fungal resources. In this study, cell-free extracts of Mariannaea sp. HJ was used to synthesize Au-AgNPs, and the effects of the different ratios of Au and Ag ion concentrations on the synthesis of Au-AgNPs were also studied. The results clearly showed that the ratio of Au and Ag ion concentrations had an impact on the composition of Au-AgNPs. With the Ag ion increasing, the color of culture supernatant changed from light purple to brown and an obvious blue shift of characteristic absorption peak was observed in UV-vis spectra, indicating an increase of the percentage of Ag in the Au-AgNPs. Transmission electron microscope showed that the morphologies of the Au-AgNPs were mainly spherical and pseudo spherical, and the average particle sizes of the Au-AgNPs at three different ion concentrations, including 0.5:0.5, 0.5:1.5 and 0.5:3.0, were 19.24 nm, 15.99 nm and 19.33 nm, respectively. X-ray diffraction results showed that the Au-AgNPs had a surface-centered cubic structure. Fourier transform infrared spectroscopy was used to characterize and speculate the involvement of -OH, -NH3 and -COOH functional groups in the reduction and stability process of Au-AgNPs. Furthermore, 4-nitrophenol (4-NP) was used to explore catalytic activity of Au-AgNPs. Catalytic experiments demonstrated that the Au-AgNPs had a good catalytic activity on 4-NP reduction with a catalytic reaction rate constant of 7.85×10⁻³ s⁻¹. In brief, the present study suggested that Mariannaea sp. HJ could synthesize Au-AgNPs with good dispersity, and had a potential application in the catalytic reduction of nitro aromatic hydrocarbons.

Characterization of biogenic selenium nanoparticles derived from cell-free extracts of a novel yeast Magnusiomyces ingens.

A facile one-pot and effective green process for biogenic selenium nanoparticles (SeNPs) was obtained using the cell-free extracts of a novel yeast Magnusiomyces ingens LH-F1. The corresponding absorption peak of SeNPs was observed at ~ 560 nm by UV-vis spectrophotometer. In the present study, SeO2 2 mM, protein 500 mg L-1 and pH 7 were preferable to the biosynthesis of SeNPs. The effects of pH, SeO2 concentration and protein concentration on the synthesis process were different. Transmission electron microscopy image exhibited that all the SeNPs were spherical and quasi-spherical with the diameters mainly distributed in 70-90 nm (average particles size was 87.82 ± 2.71 nm). X-ray diffraction suggested that the nanoparticles were composed of standard hexagonal crystalline Se with high purity. Fourier transform infrared spectroscopy indicated that some biomolecules such as hydroxyl, carboxyl and amino groups in the yeast cell-free extracts might be involved in the formation of SeNPs. Analyses of sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that two proteins with low molecular weight approximately ~ 16 and ~ 21 kDa were detected on the surface of SeNPs and in the extracts, which could play the role of natural stabilizers and confer stability to synthesized SeNPs; whereas, unbound proteins on the SeNPs surface could act as reducing agents. Antibacterial analysis showed that the SeNPs could inhibit Arthrobacter sp. W1 (Gram positive) but not E. coli BL21 (Gram negative), which could provide reference for antimicrobial application of biogenic SeNPs.