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.

Screening Novel Drugresistant Mutations in Mycobacterium tuberculosis Strains by Using the Amplicon Sequencing Method / 中国生物化学与分子生物学报

Tuberculosis is one of the seriously public problems. The increasing drug-resistant tuberculosis is the key problem for controlling tuberculosis. Rapid and accurate diagnosis is important for further treatment. In this study‚ a next-generation sequencing method based on amplicon sequencing was constructed to screen the mutations in 17 drug-resistant genes of five first-line anti-tuberculosis drugs. A total of 65 mutations were identified in 26 clinic drug-resistant tuberculosis strains‚ including 33 hotspot mutations‚ 9 rare mutations‚ and 23 novel mutations. The pathogenesis‚ conservation‚ and partial structures caused by 18 novel missense mutations were predicted. The results showed that 14 novel mutations showed high conservation in nine species. All these 14 mutations could change the partial structure of protein. According to the detection and analysis results of this study‚ it is speculated that these newly discovered mutations may be potential drug-resistant mutations. It is a rapid‚ accurate and comprehensive method for the detection of drug-resistant mutations in first-line drug-resistant Mycobacterium tuberculosis‚ which could identify hotspot and rare mutations together with novel mutations. The detection method may be used for clinical diagnosis and basic research.

Application of nanopore sequencing in environmental microbiology research / 生物工程学报

The development of high-throughput sequencing techniques enabled a deeper and more comprehensive understanding of environmental microbiology. Specifically, the third-generation sequencing techniques represented by nanopore sequencing have greatly promoted the development of environmental microbiology research due to its advantages such as long sequencing reads, fast sequencing speed, real-time monitoring of sequencing data, and convenient machine carrying, as well as no GC bias and no PCR amplification requirement. This review briefly summarized the technical principle and characteristics of nanopore sequencing, followed by discussing the application of nanopore sequencing techniques in the amplicon sequencing, metagenome sequencing and whole genome sequencing of environmental microorganisms. The advantages and challenges of nanopore sequencing in the application of environmental microbiology research were also analyzed.

Investigation and research on fungal diversity of Platycladi Semen on Chinese market / 中国中药杂志

In the process of harvesting, production and processing, storage, and transportation, the traditional Chinese medicine Platycladi Semen is prone to mildew due to its own and environmental factors, which can nourish the production of toxic or pathogenic fungi, and even produce mycotoxins, which affects the safety of clinical medication. The 2020 edition of Chinese Pharmacopoeia limits the highest standard of aflatoxin content in Platycladi Semen. However, there are few studies on the fungal contamination of Platycladi Semen, and it is difficult to prevent and control it in a targeted manner. Therefore, based on the Illumina NovaSeq6000 platform, this article uses ITS sequence amplicon technology to analyze the distribution and diversity of fungi in 27 batches of commercially available Platycladi Semen in the Chinese market. A total of 10 phyla, 35 classes, 93 orders, 193 families, 336 genera, and 372 species of fungi were identified in China. Among them, Aspergillus, Alternaria spp. were dominant, 20 batches of samples were detected for A. flavus, 10 batches of samples were detected for A. nidulans, and all samples were detected for potential pathogenic fungi such as A. fumigatus and A. niger. According to diversity analysis, the diversity of the fungal communities in the samples from Gansu province was high, the samples in Shandong province contain the largest number of fungal species, and the samples in Guangxi province had the lo-west diversity and the least number of species. In most samples, pathogenic fungi such as A. fumigatus, A. niger, A. flavus, A. parasiticus were detected in varying degrees. This study systematically investigated the fungal contamination of Platycladi Semen from the markets in the last link of the its industrial chain, and clarified the distribution of Platycladi Semen fungi, especially toxin-producing fungi, and provided theoretical basis for the targeted prevention and control of fungal contamination in Platycladi Semen.

Preface for microbiome sequencing and analysis / 生物工程学报

Microbes are the most important commensal organisms in humans, animals and plants, and are the major habitants in soil, sediment, water, air and other habitats. The analysis of microbiome in these habitats has become a basic research technique. As a fast developing technology in recent years, microbiome sequencing and analysis have been widely used in human health, environmental pollution control, food industry, agriculture and animal husbandry and other fields. In order to sort out and summarize the current status, development and application prospects of microbiome sequencing and analysis technologies, this special issue has prepared a collection of 16 papers in this field, that comprise sample preservation and processing, single microbe genome sequencing and analysis, and microbiome feature analysis in special habitats, microbiome related databases and algorithms, and microbiome sequencing and analysis expert consensus. It also introduced in detail the development trend of the microbiome sequencing and analysis, in order to promote the rapid development of the microbiome sequencing and analysis industry and scientific research in China, and provide necessary reference for the healthy development of related industries.