土壤环境基因组技术及其在新药发现中的应用

土壤是微生物最重要的生境，土壤微生物具有极大的多样性。然而传统培养技术只能得到约1％的微生物纯培养，其余都是未被纯培养微生物。利用土壤环境基因组技术，可以把未被纯培养微生物的基因克隆到载体中并在宿主中进行表达，获得比已培养微生物丰富的代谢产物多样性，这为我们发现新颖结构先导化合物以及新药开辟了新的道路。本文介绍应用环境基因组技术构建土壤DNA文库的思路和方法。     

The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal

Infectious diseases with epizootic consequences have not been fully studied in marine mammals. Presently, the unprecedented depth of sequencing, made available by high-throughput approaches, allows detailed comparisons of the microbiome in health and disease. This is the first report of the striped dolphin microbiome in different body sites. Samples from one striped female edematous dolphin were acquired from a variety of body niches, including the blowhole, oral cavity, oral mucosa, tongue, stomach, intestines and genital mucosa. Detailed 16S rRNA analysis of over half a million sequences identified 235 OTUs. Beta diversity analyses indicated that microbial communities vary in structure and cluster by sample origin. Pathogenic, Gram-negative, facultative and obligate anaerobic taxa were significantly detected, including Cetobacterium, Fusobacterium and Ureaplasma. Phocoenobacter and Arcobacter dominated the oral-type samples, while Cardiobacteriaceae and Vibrio were associated with the blowhole and Photobacterium were abundant in the gut. We report for the first time the association of Epulopiscium with a marine mammal gut.The striped dolphin microbiota shows variation in structure and diversity according to the organ type. The high dominance of Gram-negative anaerobic pathogens evidences a cetacean microbiome affected by human-related bacteria.     

Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3)

ObjectivesShotgun sequencing is increasingly applied in clinical microbiology for unbiased culture-independent diagnosis. While software solutions for metagenomics proliferate, integration of metagenomics in clinical care requires method standardization and validation. Virtual metagenomics samples could underpin validation by substituting real samples and thus we sought to develop a novel solution for simulation of metagenomics samples based on user-defined clinical scenarios.MethodsWe designed the Microbial Metagenomics Mock Scenario-based Sample Simulation (M₃S₃) workflow, which allows users to generate virtual samples from raw reads or assemblies. The M₃S₃ output is a mock sample in FASTQ or FASTA format. M₃S₃ was tested by generating virtual samples for 10 challenging infectious disease scenarios, involving a background matrix ‘spiked’ in silico with pathogens including mixtures. Replicate samples (seven per scenario) were used to represent different compositional ratios. Virtual samples were analysed using Taxonomer and Kraken db.ResultsThe 10 challenge scenarios were successfully applied, generating 80 samples. For all tested scenarios, the virtual samples showed sequence compositions as predicted from the user input. Spiked pathogen sequences were identified with the majority of the replicates and most exhibited acceptable abundance (deviation between expected and observed abundance of spiked pathogens), with slight differences observed between software tools.ConclusionsDespite demonstrated proof-of-concept, integration of clinical metagenomics in routine microbiology remains a substantial challenge. M₃S₃ is capable of producing virtual samples on-demand, simulating a spectrum of clinical diagnostic scenarios of varying complexity. The M₃S₃ tool can therefore support the development and validation of standardized metagenomics applications.     

脑脊液二代测序对病毒性脑炎的诊断价值：附三例报告

病毒性脑炎是一种累及脑膜和脑实质的中枢神经系统感染性疾病，其临床表现为发热、抽搐、头痛等。因病毒性脑炎早期缺乏特异性临床症状，且病死率和致残率均较高，所以早期诊断尤为重要。本文介绍了3例采用宏基因组测序（mNGS）技术早期诊断出儿童疱疹病毒性脑炎的病例资料，相较于病毒性脑炎的传统检测方法，脑脊液二代测序能及早地做出病原学诊断，在早期诊断和指导临床治疗方面有重要的参考价值。     

Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing

ObjectivesIt is important to determine the cause of increasing oral cancer occurrence and mortality rates in Japan, because the mortality rate has recently decreased in other developed countries. The impact of microbiota in carcinogenesis, especially in the digestive tract has been reported. This study aimed to clarify the relationship between oral cancer and oral microbiota in Japanese patients.MethodsDNA was extracted from salivary samples of 60 oral cancer patients and 80 non-cancer individuals as controls. We performed metagenomic analysis using 16S rRNA amplicon sequencing. Statistical analysis in this study was performed using R (version 3.5.0).ResultsOral cancer patients showed higher α-diversity compared to the control group, and the β-diversity between the two groups differed significantly. Further, there was a significant difference in the abundance ratio of bacterial genera between the two groups. Peptostreptococcus, Fusobacterium, Alloprevotella, and Capnocytophaga were more abundant in the cancer group compared to the control, whereas Rothia and Haemophilus were less abundant (p < 0.01). A negative correlation in the microbiota composition was confirmed between the operational taxonomic units (OTU) of genus Rothia and T-stage progression using the TNM classification method. We performed logistic regression analysis to investigate the impact factor for the oral cancer group, and the result showed that Chao 1 index and sex are statistically significant variables.ConclusionsIn this study, we observed an increased bacterial diversity in oral cancer patients and found distribution changes for some bacteria.     

Impact of laparoscopic Roux-en-Y gastric bypass and sleeve gastrectomy on gut microbiota: a metagenomic comparative analysis

BackgroundBariatric surgery is an effective therapeutic procedure for morbidly obese patients. The 2 most common interventions are sleeve gastrectomy (SG) and laparoscopic Roux-en-Y gastric bypass (LRYGB).ObjectivesThe aim of this study was to compare microbiome long-term microbiome after SG and LRYGB surgery in obese patients.SettingUniversity Hospital, France; University Hospital, United States; and University Hospital, Switzerland.MethodsEighty-nine and 108 patients who underwent SG and LRYGB, respectively, were recruited. Stools were collected before and 6 months after surgery. Microbial DNA was analyzed with shotgun metagenomic sequencing (SOLiD 5500 xl Wildfire). MSPminer, a novel innovative tool to characterize new in silico biological entities, was used to identify 715 Metagenomic Species Pan-genome. One hundred forty-eight functional modules were analyzed using GOmixer and KEGG database.ResultsBoth interventions resulted in a similar increase of Shannon’s diversity index and gene richness of gut microbiota, in parallel with weight loss, but the changes of microbial composition were different. LRYGB led to higher relative abundance of aero-tolerant bacteria, such as Escherichia coli and buccal species, such as Streptococcus and Veillonella spp. In contrast, anaerobes, such as Clostridium, were more abundant after SG, suggesting better conservation of anaerobic conditions in the gut. Enrichment of Akkermansia muciniphila was also observed after both surgeries. Function-level changes included higher potential for bacterial use of supplements, such as vitamin B12, B1, and iron upon LRYGB.ConclusionMicrobiota changes after bariatric surgery depend on the nature of the intervention. LRYGB induces greater taxonomic and functional changes in gut microbiota than SG. Possible long-term health consequences of these alterations remain to be established.     

通过宏基因组学研究肠道微生物对结直肠癌患者影响的最新进展

人类肠道微生物已越来越受到医学界的广泛关注,人类肠道微生物不仅在人类健康方面,而且在人类疾病的发生和发展方面都有很大的作用。人们不断发现微生物与癌症之间的联系,特别是肠道微生物群和肠道肿瘤之间的联系。宏基因组学作为微生物研究的一种重要研究方法,在微生物与结直肠癌研究中发挥越来越重要的作用。近年来,通过宏基因组学研究肠道微生物菌群的变化为结直肠癌的发生和发展提供了新的见解,并且强调了癌症微生物群中宿主-微生物和微生物间相互作用的重要性。本综述回顾了通过宏基因组学研究肠道微生物与结直肠癌之间的关系,希望为癌症预防、诊断和治疗提供新的机会。     

元基因组学研究可视化分析

利用可视化分析软件CiteSpace对Web of Science数据库中7 747篇元基因组学领域的研究文献,从数量、地区与机构、作者、研究基础和关键词等方面进行分析并绘制相关的可视化知识图谱,总结研究热点,梳理研究力量、重要文献及学术代表人物,以期更直观地展现元基因组学领域的科研状况。     

宏基因组学测序诊断曼氏裂头蚴病1例

患者于2000年无明显诱因发现下腹部游走性包块,20年来多次就诊,未明确病因。2020年8月11日发现包块游走于左侧腋前,微创手术取出不完整白色虫体3段,用宏基因组学测序鉴定虫体,明确诊断为曼氏裂头蚴病。2021年10月21日经手术取出完整虫体,患者康复出院;随访患者身体状况良好,全身未发现新包块。