Shotgun metagenome sequencing of Chinese gut microbiota: a review / 生物工程学报

The research on the relationship between gut microbiota and human health continues to be a hot topic in the field of life science. Culture independent 16S rRNA gene high-throughput sequencing is the current main research method. However, with the reduction of sequencing cost and the maturity of data analysis methods, shotgun metagenome sequencing is gradually becoming an important method for the study of gut microbiome due to its advantages of obtaining more information. With the support from the human microbiome project, 30 805 metagenome samples were sequenced in the United States. By searching NCBI PubMed and SRA databases, it was found that 72 studies collecting about 10 000 Chinese intestinal samples were used for metagenome sequencing. To date, only 56 studies were published, including 16 related to metabolic diseases, 16 related to infectious and immune diseases, and 12 related to cardiovascular and cerebrovascular diseases. The samples were mainly collected in Beijing, Guangzhou, Shanghai and other cosmopolitan cities, where great differences exist in sequencing platforms and methods. The outcome of most studies are based on correlation analysis, which has little practical value in guiding the diagnosis and treatment of clinical diseases. Standardizing sampling methods, sequencing platform and data analysis process, and carrying out multi center parallel research will contribute to data integration and comparative analysis. Moreover, insights into the functional verification and molecular mechanism by using the combination of transcriptomics, proteomics and culturomics will enable the gut microbiota research to better serve the clinical diagnosis and treatment.

The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markers

Background: Microsatellite loci often used as a genetic tool for estimating genetic diversity population variation in a wide variety of different species. The application of microsatellite markers in genetics and breeding includes investigating the genetic differentiation of wild and cultured populations, assessing and determining the genetic relationship of different populations. The aim of this work is to develop several microsatellite markers via highthroughput sequencing and characterize these markers in commercially important bivalve Ruditapes philippinarum. Results: Among the two populations of R. philippinarum studied, 110 alleles were detected. The number of alleles at the cultured population ranged from 3 to 17 (mean NA = 6.897) and wild population ranged from 2 to 15 (mean NA = 6.793). The observed and expected heterozygosities of cultured population ranged from 0.182 to 0.964, and from 0.286 to 0.900, with an average of 0.647 and 0.692, respectively. The observed and expected heterozygosities of wild population ranged from 0.138 to 1.000, and from 0.439 to 0.906, with an average of 0.674 and 0.693, respectively. The polymorphism information content ranged from 0.341 to 0.910 with an average of 0.687. Sixteen and thirteen microsatellite loci deviated significantly from Hardy­Weinberg equilibrium after correction for multiple tests in cultured and wild population, respectively. Conclusions: Twenty-nine novel microsatellite loci were developed using Illumina paired-end shotgun sequencing and characterized in two population of R. philippinarum.

Genome of Leptospira borgpetersenii strain 4E, a highly virulent isolate obtained from Mus musculus in southern Brazil

A previous study by our group reported the isolation and characterisation of Leptospira borgpetersenii serogroup Ballum strain 4E. This strain is of particular interest because it is highly virulent in the hamster model. In this study, we performed whole-genome shotgun genome sequencing of the strain using the SOLiD sequencing platform. By assembling and analysing the new genome, we were able to identify novel features that have been previously overlooked in genome annotations of other strains belonging to the same species.

Study of ocular surface macro genome in dry eye patients / 眼科新进展

Objective To investigate the difference in ocular surface microbiota between dry eye patients and healthy subjects,and discuss the role of microbiota in dry eye.Methods Twenty cases of dry eye patients and 90 cases of healthy subjects were collected in the PLA General Hospital and Zhongshan Ophthalmic Center.The samples of conjunctiva impression cytology were collected from all subjects,and then metagenomic shotgun sequencing was performed following the DNA extraction.The differences in alpha diversity and metabolic pathways of the ocular surface microbiota between dry eye patients and healthy subjects were evaluated.Results There was no significant difference in alpha diversity of the microbial community between dry eye patients and healthy subjects (P =0.13).However,an increase of 15 species and a decrease of 10 species were detected on the ocular surface of dry eye patients.The enriched antibiotic resistance genes in dry eye patients were more than healthy subjects.Conclusion Although the alpha diversity of the microbial community on ocular surface between dry eye patients and healthy subjects are not distinguishable,a significant difference could be found in relative abundance and metabolic pathways,suggest that these specific microbiome may be related to the pathogenesis and disease progression of dry eye.