Rapid detection for infected ascites in cirrhosis using metagenome next-generation sequencing: A case series

Empirical antibiotic therapy in patients with spontaneous bacterial peritonitis (SBP) is common as pathogen(s) are identified in only 5%-20% patients using conventional culture-based techniques. Metagenome next-generation sequencing (mNGS) test is a promising approach for the diagnosis of infectious disease. The clinical application of mNGS for infected ascites in cirrhotic patients is rarely reported. Here, we describe three cases to preliminarily explore the potential role of mNGS for microbiological diagnosis of ascites infection in an exploratory manner. The clinical performance of ascites mNGS in cirrhotic patients remains to be further evaluated.     

Rural and urban microbiota: To be or not to be?

A multitude of metagenomic studies has brought to light an enormous richness of human gut microbiota compositions. In this space of possible configurations, clinical specialists are trying to mine the markers of healthy microbiota via case-control and longitudinal studies. We have discovered potentially beneficial communities while examining the microbial diversity in rural Russians in comparison with the urban dwellers. In this addendum, we further examine the data by elaborating on some of the less common types and suggesting the possible co-metabolism of their drivers. In the light of the first validated clinically effective bacterial transplantation, we discuss the concept of a reference healthy microbiota, outline the problems encountered on the way to its restoration in the developed world, and speculate if rural communities can serve as a source for its prototype.     

Host Genome,Epigenome, and Oral Microbiome Interactions: Toward Personalized Periodontal Therapy

Periodontal diseases are multidimensional and complex. Bacterial content is the initiator, but disease progression depends on genetic and environmental parameters related to the host. Although bone loss magnitude is the common resulting outcome, the biologic process likely represents a unique inflammatory response characteristic to every individual. Therefore, it is obvious that practitioners must take into account the influence of these parameters and tailor a treatment accordingly. New, emerging deoxyribonucleotide‐based technologies allow integration of the biologic impact of the environment, and periodontists should be prepared to incorporate these technologies into their practice to advance personalized medicine. This commentary provides updated insights on the distinctiveness of inflammation per individual in terms of microbiome and genome specificity and cites some educational resources helpful for implementing individualized therapy.     

Probiotics maintain the intestinal microbiome homeostasis of the sailors during a long sea voyage

ABSTRACT

The challenging conditions encountered during long sea voyages increase the risk of health-threatening physiological and psychological stress for sailors compared with land-based workers. However, how the intestinal microbiota responds to a long sea voyage and whether there is a feasible approach for protecting gut health during sea voyage are still unexplored. Here, we designed a 30-d longitudinal study including a placebo group (n = 42) and a probiotic group (n = 40) and used shotgun metagenomic sequencing to explore the impacts of sea voyage on the intestinal microbiome of sailors. By comparing the intestinal microbiome of subjects in the placebo group at baseline (d 0) and at the end of the sea voyage (d 30), we observed an alteration in the intestinal microbiome during the long sea voyage based on the microbial structure; the results revealed an increase in the species Streptococcus gordonii and Klebsiella pneumoniae as well as a decrease in some functional features. However, the change in the microbial structure of sailors in the probiotic group between d 0 and d 30 was limited, which indicated a maintenance effect of probiotics on intestinal microbiome homeostasis. At the metagenomic strain level, a generally positive correlation was observed between probiotics and the strains belonging to Bifidobacterium longum and Bifidobacterium animalis, whereas a common negative correlation was observed between probiotics and Clostridium leptum; this result revealed the potential mechanism of maintaining intestinal microbiome homeostasis by probiotics. The present study provided a feasible approach for protecting gut health during a long sea voyage.     

口腔微生物宏基因组学总DNA制备的方法学初探

目的：比较不同时间段人类口腔唾液微生物总DNA制备方法。方法：采用酚氯仿抽提法、QIAamp DNA Micro Kit法制备健康人群不同时间段口腔唾液微生物总DNA。使用紫外分光光度计,PCR等鉴定提取的总DNA。结果：两种方法均成功制备了口腔微生物总DNA。不同方法提取的总DNA在片段大小,纯度,得率等方面存在差异。短期内不同时间段口腔唾液微生物总DNA无显著差异。结论：两种总DNA提取方法均可用于宏基因组学研究,可根据不同的实验目的,选择更适合的方法。同一供体短期内不同时间段的唾液可混合用于宏基因组学研究。     

Significance of the gut microbiome in multistep colorectal carcinogenesis

Colorectal cancer (CRC) is highly prevalent worldwide. In 2018, there were over 1.8 million new cases. Most sporadic CRC develop from polypoid adenomas and are preceded by intramucosal carcinoma (stage 0), which can progress into more malignant forms. This developmental process is known as the adenoma‐carcinoma sequence. Early detection and endoscopic removal are crucial for CRC management. Accumulating evidence suggests that the gut microbiota is associated with CRC development in humans. Comprehensive characterization of this microbiota is of great importance to assess its potential as a diagnostic marker in the very early stages of CRC. In this review, we summarized recent studies on CRC‐associated bacteria and their carcinogenic mechanisms in animal models, human cell lines and human cohorts. High‐throughput technologies have facilitated the identification of CRC‐associated bacteria in human samples. We have presented our metagenome and metabolome studies on fecal samples collected from a large Japanese cohort that revealed stage‐specific phenotypes of the microbiota in CRC. Furthermore, we have discussed the potential carcinogenic mechanisms of the gut microbiota, from which we can infer whether changes in the gut microbiota are a cause or effect in the multi‐step process of CRC carcinogenesis.     

World Workshop on Oral Medicine VII: Targeting the microbiome for oral medicine specialists—Part 1. A methodological guide

Advances in high‐throughput sequencing technologies have allowed for a rapid increase in knowledge about the human microbiome in both healthy and diseased states, which is expected to increase our understanding of multifactorial diseases. The World Workshop on Oral Medicine VII chose the microbiome as one of its topics of focus. Part 1 of this review provides updated knowledge in the field of microbiome research, describes the advantages and disadvantages of currently available sequencing technologies, and proposes a seven‐step “recipe” for designing and performing studies that is supported by contemporary evidence. Part 2 of this review in a companion paper discusses the results of high‐throughput sequencing studies published to date on the microbiota associated with oral mucosal diseases. The goal of this collective enterprise is to encourage more oral medicine specialists to become engaged in multidisciplinary collaborations to investigate the role of the microbiome in relation to oral diseases, which could potentially lead to enhanced diagnosis, risk assessment and treatment of these patients.     

汉坦病毒核酸检测试剂参考品的研制

[摘要]　目的　研制汉坦病毒核酸检测试剂参考品并制定其质量评价标准。方法　收集汉坦病毒阳性和阴性临床分离株样本，制备汉坦病毒RNA噬菌体模拟样本，使用宏基因组测序方法和实时荧光定量聚合酶链式反应检测方法进行核酸序列鉴定。选择合适样本组成参考品并使用不同试剂对参考品进行协作标定。根据标定结果确定汉坦病毒核酸检测试剂参考品的质量标准，并评估其稳定性。结果　汉坦病毒核酸检测试剂参考品由20份样本组成，包括阳性参考品5份（PC01～PC05）、阴性参考品11份（NC01～NC11）、精密性参考品2份（R01、R02）以及检出限参考品2份（S01、S05）。其中，检出限参考品1:10梯度稀释后，要求S02、S03为汉坦病毒汉滩型阳性，S06、S07为汉坦病毒汉城型阳性，其余样本不做要求。稳定性评价结果表明，汉坦病毒核酸检测试剂参考品经25 ℃室温放置24 h或反复冻融3次均不影响参考品性能。结论　本研究研制了汉坦病毒核酸检测试剂参考品，并制定了其质量标准，可应用于相关定性检测试剂的质量评价。     

深龋微生物宏基因组测序结果比对不同数据库的研究

目的:探讨深龋微生物宏基因组测序结果物种注释时比对不同数据库的差异。方法:收集青少年第一恒磨牙深龋样本共16份,提取DNA后基因组高通量测序。测序结果分别比对NCBI nr数据库及HOMD数据库,分析应用不同数据库时深龋微生物组成的差异性。结果:深龋微生物在纲分类水平上,两种数据库中相对丰度位于前10微生物均为放线菌纲、芽孢杆菌纲、拟杆菌纲、红蝽菌纲、Negativicutes纲、梭杆菌纲、梭菌纲、β-变形菌纲、黄杆菌纲和互养菌纲。在属分类水平上,两种数据库中相对丰度位于前10微生物均为乳杆菌属、放线菌属、欧氏菌属、普氏菌属、丙酸杆菌属、链球菌属、月形单胞菌属、棒杆菌属、纤毛菌属和类斯氏菌属。物种比例水平在两数据库中得到的数值有微小差异,但无明显统计学意义(P>0.05)。结论:深龋样本宏基因组数据分别于NCBI nr和HOMD数据库注释后,微生物数量及结构无明显差异。