The influence of Amphotericin B (AmB) dose and the addition of fluconazole (Flu) on the AmB + 5-flucytosine (5FC) regimen for cryptococcal meningitis (CM) treatment remain debatable.

The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662-4000 m below water surface. Actinobacterial sequences represented 1.2-9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling.

Soil-borne pest diseases result in large annual agricultural losses globally. Fungal bio-control agents are an alternative means of controlling pest diseases; however, soil fungistasis limits the effect of fungal agents. Nutrients can relieve soil fungistasis, but the mechanisms behind this process remain poorly understood. In this study, we determined and quantified the transcriptomes of Arthrobotrys oligospora, a nematode-trapping fungus, derived from samples of fresh conidia, germinated conidia, soil fungistatic conidia, and glucose-relieved conidia. The transcriptomes of fungistatic and glucose-relieved conidia were significantly different from those of the other two conidia samples. KEGG pathway analyses showed that those genes upregulated in fungistatic and glucose-relieved conidia were mainly involved in translation and substance metabolism, and the downregulated genes were mainly involved in MAPK pathway, autophagy, mitophagy, and endocytosis. As being different from the transcriptome of fungistatic conidia, upregulated genes in the transcriptome of glucose-relieved conidia are also related to replication and repair, spliceosome, oxidative phosphorylation, autophagy, and degradation pathway (lysosome, proteasome, and RNA degradation). And the upregulated genes resulted from comparison of glucose-relieved conidia and fungistatic conidia were enriched in metabolic pathways, cycle, DNA replication, and repair. The differentially splicing events in the transcriptome of glucose-relieved conidia are far more than that of other two transcriptomes, and genes regulated by differentially splicing were analyzed through KEGG pathway analysis. Furthermore, autophagy genes were proved to play important role in resisting soil fungistasis and glucose-mediated soil fungistasis relief. These data indicate that, in addition to being a carbon and energy source for conidia germination, glucose may also help to relieve soil fungistasis by activating many cellular processes, including autophagy, DNA replication and repair, RNA alternative splicing, and degradation pathways.

Nutrient inputs to forest ecosystems significantly influence aboveground plant community structure and ecosystem functioning. However, our knowledge of the influence of nitrogen (N) and/or phosphorus (P) inputs on belowground microbial communities in subtropical forests is still unclear. In this study, we used quantitative polymerase chain reaction and Illumina Miseq sequencing of the bacterial 16S rRNA gene to investigate bacterial abundance, diversity, and community composition in a Chinese fir plantation. The fertilization regimes were as follows: untreated control (CK), P amendment (P), N amendment (N), and N with P amendment (NP). Additions of N decreased soil pH and bacterial 16S rRNA gene abundance by 3.95 (from 4.69 to 3.95) and 3.95 × 109 copies g-1 dry soil (from 9.27 × 109 to 3.95 × 109 g-1 dry soil), respectively. Bacterial richness and diversity decreased with N addition (N and NP) rather than only P input. Proteobacteria, Acidobacteria, and Actinobacteria were the major phylum across all treatments. Nitrogen addition increased the relative abundance of Proteobacteria and Actinobacteria by 42.0 and 10.5%, respectively, while it reduced that of Acidobacteria by 26.5%. Bacterial community structure in the CK and P treatments was different from that in the N and NP treatments upon principle coordinates analysis. Phosphorus addition did not significantly affect soil bacterial communities, and no interactions between N and P inputs on microbial traits were observed. Soil pH and mineral N availability appeared to have a cooperative effect on bacterial abundance and community structure, with soil pH being the key influencing factor by canonical correspondence analysis. These results indicate that inorganic N rather than P fertilization affected both bacterial abundance and community composition in subtropical forests.

Bacterial symbionts of insects affect a wide array of host traits including fitness and immunity. Octodonta nipae (Maulik), commonly known as hispid leaf beetle is a destructive palm pest around the world. Understanding the dynamics of microbiota is essential to unravel the complex interplay between O. nipae and its bacterial symbionts. In this study, bacterial 16S rRNA V3-V4 region was targeted to decipher the diversity and dynamics of bacterial symbionts across different life stages [eggs, larvae, pupae, and adult (male and female)] and reproductive organs (ovaries and testis) of O. nipae. Clustering analysis at ≥97% similarity threshold produced 3,959 operational taxonomic units (OTUs) that belonged to nine different phyla. Proteobacteria, Actinobacteria, and Firmicutes represented the bulk of taxa that underwent notable changes during metamorphosis. Enterobacteriaceae and Dermabacteraceae were the most abundant families in immature stages (eggs, larvae, and pupae), while Anaplasmataceae family was dominated in adults (male and female) and reproductive organs (ovaries and testis). The genus Serratia and Lactococcus were most abundant in eggs, whereas Pantoea and Brachybacterium represented the bulk of larvae and pupae microbiota. Interestingly the genus Wolbachia found positive to all tested samples and was recorded extremely high (>64%) in the adults and reproductive organs. The bacteria varied across the developmental stages and responsible for various metabolic activities. Selection choice exerted by the insect host as a result of its age or developmental stage could be the main reason to ascertain the shift in the bacteria populations. Maternally inherited Wolbachia was found to be an obligate endosymbiont infecting all tested life stages, body parts, and tissues. These outcomes foster our understanding of the intricate associations between bacteria and O. nipae and will incorporate in devising novel pest control strategies against this palm pest.

MraW is a 16S rRNA methyltransferase and plays a role in the fine-tuning of the ribosomal decoding center. It was recently found to contribute to the virulence of Staphylococcus aureus. In this study, we examined the function of MraW in Escherichia coli O157:H7 and found that the deletion of mraW led to decreased motility, flagellar production and DNA methylation. Whole-genome bisulfite sequencing showed a genome wide decrease of methylation of 336 genes and 219 promoters in the mraW mutant including flagellar genes. The methylation level of flagellar genes was confirmed by bisulfite PCR sequencing. Quantitative reverse transcription PCR results indicated that the transcription of these genes was also affected. MraW was furtherly observed to directly bind to the four flagellar gene sequences by electrophoretic mobility shift assay (EMSA). A common flexible motif in differentially methylated regions (DMRs) of promoters and coding regions of the four flagellar genes was identified. Reduced methylation was correlated with altered expression of 21 of the 24 genes tested. DNA methylation activity of MraW was confirmed by DNA methyltransferase activity assay in vitro and repressed by DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-aza). In addition, the mraW mutant colonized poorer than wild type in mice. We also found that the expression of mraZ in the mraW mutant was increased confirming the antagonistic effect of mraW on mraZ. In conclusion, mraW was found to be a DNA methylase and have a wide-ranging effect on E. coli O157:H7 including motility and virulence in vivo via genome wide methylation and mraZ antagonism.

Previous studies have identified oral administration of antibiotics and gut-impacting drugs as critical drivers for fecal antibiotic resistance (AR) and microbiome disruption in lab mice, but the practical implications of these findings have yet to be validated in hosts nurtured in conventional environment. Using ampicillin (Amp) as a way to extrapolate the general effect of antibiotics, this project examined the impact of drug administration routes on fecal microbiota and resistome using poultry raised in a teaching farm. AR genes were found to be abundant in the feces of young Leghorn chicks without previous antibiotic treatment. In chickens seeded with bla CMY-2 + Escherichia coli, 300 mg/kg body weight of Amp was orally administered for 5 days. This led to the fecal microbiota switching from Firmicutes occupied (95.60 ± 2.62%) and Lactobacillus rich, to being dominated by Proteobacteria (70.91 ± 28.93%), especially Escherichia/Shigella. However, when Amp was given via muscle injection, Firmicutes was mostly retained (i.e., from 83.6 ± 24.4% pre- to 90.4 ± 15.2% post-treatment). In control chickens without seeding with bla CMY-2 + E. coli, oral Amp also led to the increase of Proteobacteria, dominated by Klebsiella and Escherichia/Shigella, and a reduction of Firmicutes. Specifically within Firmicutes, Enterococcus, Clostridium, etc. were enriched but Lactobacillus was diminished. The fecal resistome including Ampr genes was more abundant in chickens receiving oral Amp than those treated with muscle injection, but the difference was primarily within 1 log. The data illustrated that both drug administration routes and pre-existing gut microbiota have profound impacts on gut microbiome disruption when antibiotic treatment is given. In hosts nurtured in a conventional environment, drug administration route has the most evident impact on gut microbiota rather than the size of the targeted bla CMY-2 + gene pool, likely due to the pre-existing bacteria that are (i) less susceptible to Amp, and/or (ii) with Ampr- or multidrug resistance-encoding genes other than bla CMY-2 +. These results demonstrated the critical interplay among drug administration routes, microbiota seeded through the gastrointestinal tract, AR, gut microbiota disruption, and the rise of common opportunistic pathogens in hosts. The potential implications in human and animal health are discussed.