Comparison of ocular microbiomes between patients with and without dry eye / 中华实验眼科杂志

Objective:To explore the difference in ocular surface microbiota between patients with and without dry eye.Methods:Forty-two patients (42 eyes) diagnosed with dry eye were enrolled as dry eye group in the First Affiliated Hospital of Xi'an Jiaotong University from June to November 2020, and 37 controls without dry eye (37 eyes) were enrolled as control group in the same period.One eye was selected as the study eye, and the right eye was included when both eyes met the inclusion criteria.Swab samples from the conjunctival sac were obtained and sequenced.Sequencing of the V3-V4 region of the bacterial 16S rRNA gene was performed with Miseq PE301+ 8+ 301 platform.Operational taxonomic species (OTUs) clustering of microflora, comparison of alpha and beta diversity analysis of microflora between the two groups, annotation analysis of species and analysis of microbial markers were performed.The study protocol was approved by the Ethics Committee of The First Affiliated Hospital of Xi'an Jiaotong University (No.XJTU1AFCRC2018SJ-014). Written informed consent was obtained from each subject before any medical examination.Results:A total of 18 586 OTUs were obtained, and 3 674 OTUs were shared between the two groups.Alpha diversity analysis showed that there was no significant difference in observed species index, Chao index, Ace index, Shannon index and Simpson index between the two groups (all at P>0.05), suggesting there was no difference in microbiota richness between them.The PCoA analysis showed that the microbial compositions of the two groups were significantly different ( R2=0.039, F=3.100, P=0.022). The dominant flora of the two groups was similar, with Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria as the top 5 abundant bacterial phyla, with Pelomonas, Corynebacterium, Propionibacterium, Pseudomonas and Herbaspirillum as the top 5 bacterial genera.LEfSe analysis identified Tissierellaceae, Enhydrobater and Finegoldia as dominant bacterial genera in dry eye group, and Caulobacter and Curvibacter in control group. Conclusions:The composition of ocular surface microbiomes is different between dry eye patients and controls.

Study on tanshinones regulating root-associated microbiomes of Salvia miltiorrhiza / 中国中药杂志

The plant root-associated microbiomes include root microbiome and rhizosphere microbiome, which are closely related to plant life activities. Nearly 30% of photosynthesis products of plants are used to synthesize root compounds, there is evidence that root compounds regulate and significantly affect the root microbiome Tanshinones are the main hydrophobic components in Salvia miltiorrhiza. In order to study whether these compounds can regulate the root-associated microbiomes of S. miltiorrhiza, our study first identified a white root S. miltiorrhiza(BG) which contains little tanshinones. Retain of the fifth intron of tanshinones synthesis key enzyme gene SmCPS1 leading to the early termination of the SmCPS1 gene, and a stable white root phenotype. Further, wild type(WT) and BG were planted in greenhouse with nutrient soil(Pindstrup, Denmark) and Shandong soil(collected from the S. miltiorrhiza base in Weifang, Shandong), then high-throughput sequencing was used to analyze the root-associated microbiomes. The results showed that the tanshinones significantly affected the root-associated microbiomes of S. miltiorrhiza, and the impact on root microbiomes was more significant. There are significant differences between WT and BG root microbiomes in species richness, dominant strains and co-occurrence network. Tanshinones have a certain repelling effect on Bacilli which belongs to Gram-positive, while specifically attract some Gram-negative bacteria such as Betaproteobacteria and some specific genus of Alphaproteobacteria. This study determined the important role of tanshinones in regulating the structure of root-associated microbiomes from multiple angles, and shed a light for further improving the quality and yield of S. miltiorrhiza through microenvironment regulation.

Genetic diversity of 16S rRNA and mcrA genes from methanogenic archaeas

Methanogenic archaeas are found in aquatic and terrestrial environments and are fundamental in the conversion of organic matter into methane, a gas that has a potential use as renewable source of energy, which is also considered as one of the main agents of the greenhouse effect. The vast majority of microbial genomes can be identified by a conservative molecular marker, the 16S ribosomal gene. However, the mcrA gene have been using in studies of methanogenic archaea diversity as an alternative marker, highly conserved and present only in methanogens. This gene allows the expression of the enzyme Methyl-coenzyme M reductase, the main agent in converting by-products of anaerobic digestion into methane. In this context, we aimed to study the genetic diversity of mcrA and 16S rRNA genes sequences available in databases. The nucleotide sequences were selected from the NCBI. The heterozygosity and molecular diversity indexes were calculated using the Arlequin 3.5 software, with plots generated by package R v3.0. The diversity and heterozygosity indices for both genes may have been influenced by the number and size of the sequences. Descriptive analysis of genetic diversity generated by sequences deposited in databases allowed a detailed study of these molecules. It is known that the organisms in a population are genetically distinct, and that, despite having similarities in their gene composition, the differences are essential for their adaptation to different environments.

Microbial communities from arid environments on a global scale: a systematic review

Abstract Arid environments are defined by the lack of water availability, which is directly related to the mean annual precipitation (MAP), and high values of solar irradiation, which impacts the community composition of animals, plants, and the microbial structure of the soil. Recent advances in NGS technologies have expanded our ability to characterize micro- biomes, allowing environmental microbiologists to explore the complete microbial structure. Intending to identify and describe the state-of-the-art of bacterial communities in arid soils at a global scale, and to address the effect that some environmental features may have on them, we performed a systematic review based on the PRISMA guideline. Using a combination of keywords, we identified a collection of 66 studies, including 327 sampled sites, reporting the arid soil bacterial community composition by 16S rDNA gene high-throughput sequencing. To identify factors that can modulate bacterial communities, we extracted the geographical, environmental, and physicochemical data. The results indicate that even though each sampled site was catalogued as arid, they show wide variability in altitude, mean annual temperature (MAT), soil pH and electric conductivity, within and between arid environments. We show that arid soils display a higher abundance of Actinobacteria and lower abundance of Proteobacteria, Cyanobacteria, and Planctomycetes, compared with non-arid soil microbiomes, revealing that microbial structure seems to be strongly modulated by MAP and MAT and not by pH in arid soils. We observed that environmental and physicochemical features were scarcely described among studies, hence, we propose a reporting guideline for further analysis, which will allow deepening the knowledge of the relationship between the microbiome and abiotic factors in arid soil. Finally, to understand the academic collaborations landscape, we developed an analysis of the author's network, corroborating a low degree of connectivity and collaborations in this research topic. Considering that it is crucial to understand how microbial processes develop and change in arid soils, our analysis emphasizes the need to increase collaborations between research groups worldwide.

Oral microbiomes: more and more importance in oral cavity and whole body

Microbes appear in every corner of human life, and microbes affect every aspect of human life. The human oral cavity contains a number of different habitats. Synergy and interaction of variable oral microorganisms help human body against invasion of undesirable stimulation outside. However, imbalance of microbial flora contributes to oral diseases and systemic diseases. Oral microbiomes play an important role in the human microbial community and human health. The use of recently developed molecular methods has greatly expanded our knowledge of the composition and function of the oral microbiome in health and disease. Studies in oral microbiomes and their interactions with microbiomes in variable body sites and variable health condition are critical in our cognition of our body and how to make effect on human health improvement.