消化道微生态标准化样本库共识

生物样本库主要是指标准化收集、处理、储存和应用健康和疾病生物体的器官、组织、细胞、血液、体液、分泌物、排泄物及生物大分子衍生物等各种生物样本,以及与这些样本相关的临床、检验、病理、影像、治疗、随访、患者知情同意等信息,包括质量控制、信息管理与应用系统。人类消化道生存着众多微生物,包括细菌、古生菌、真菌、病毒和原虫等[1]。肠道微生物与宿主长期共同进化,构成肠道微生态,影响着宿主的健康。随着测序等高通量技术和生物信息学发展,以消化道微生态（主要是细菌和真菌）样本为基础的研究使得我们对消化道微生态的认知和应用向前推进了一大步[2],成为国内外重要的研究热点。然而,消化道微生态样本的采集、制备、储存等是后续研究的第一步,对检测和分析结果有着重要的影响[3]。统一标准、高质量的生物样本是研究数据真实性、可重复性、一致性及整合数据和应用等的根本基础,也是进行基础和临床大数据研究的重要保障。消化道微生态样本可用于基因组、转录组、蛋白质组、代谢组、培养组、营养组、微生态移植、转化医学等多方面研究。目前尚缺乏消化道微生态样本库构建的标准及规范,制定共识意见非常迫切和必要。     

胆汁致消化道黏膜损伤机制的研究进展

胆汁是由肝细胞分泌的胆道内的消化液,为等渗溶液,主要成分包括胆盐、胆汁酸、胆红素、还原型谷胱甘肽及其结合物、氧化型谷胱甘肽等。在消化期,胆汁可由肝脏和胆囊大量排到十二指肠,将脂肪乳化成微滴以利于消化;还能促进脂肪酸及脂溶性维生素的吸收。生理状态下胆汁不会反流入胃及食管,也不会损伤肠道。病理状态下胆汁会反流入胃甚至反流到食管损伤胃及食管黏膜,在一些情况下胆汁甚至会损伤肠道的黏膜。目前认为胆汁是较明确的致癌因素,与消化道肿瘤的相关性较大,但仍缺乏针对性的防治方案。明确胆汁对消化道黏膜的损伤机制,有助探索消化道肿瘤防治的新靶点。本文回顾了近年来有关胆汁对食管黏膜、胃黏膜及肠黏膜损伤机制的研究进展,以期为进一步的研究提供思路。     

胆道微生态的研究进展

人体微生态是微生物与宿主在长期相互作用过程中形成的特殊生态系统,在人体的健康与疾病中起着重要作用。目前对消化系统微生态的研究主要集中在肠道,而胆道系统可能存在独特的微生态体系,它们与胆道系统的健康和疾病之间的关系尚不明确,研究人员探讨了胆道的微生物群与胆囊结石、胆总管结石、Oddi括约肌受损、胆总管结石复发、原发性硬化性胆管炎和胆道肿瘤等肝胆疾病的发生发展、诊断和治疗的关系。本文从健康人群、肝移植供肝者的胆道及以上疾病着手,对胆道微生态的相关研究和进展作一综述。

     

原发性肝癌H-ras12V小鼠肠道微生态的初步研究

目的 探索原发性肝癌小鼠（H-ras12V小鼠）肠道微生态的特异性。方法 设立7月龄的H-ras12V小鼠为实验组,C57BL/6J常态小鼠为对照组。小鼠在标准饮食下饲养2个月。于实验第8周无菌收集小鼠粪便,进行V3‒V4高可变区16S rDNA基因组测序,分析两组小鼠肠道菌群多样性和组成的差异。结果 肝癌小鼠成瘤率为100%。α多样性：稀释曲线趋于平缓,样品测序数据量较合理。β多样性：通过Anosim分析确定两组组间差异显著大于组内差异（R=0.2857,P=0.0037）。菌群结构：门水平优势菌群有拟杆菌门、厚壁菌门、变形菌门等,属水平优势菌群有Barnesiella、Alloprevotella、拟杆菌属等。显著性差异物种：通过Kruskal-Wallis test分析,发现拟杆菌属等7个属差异有统计学意义（P<0.05）。结论 原发性肝癌H-ras12V小鼠肠道微生态多样性和菌群结构有显著差异,其中拟杆菌属及其特殊结构鞘脂与肝硬化及肿瘤关系密切,可能与肝癌存在联系。     

肝硬化患者肠道菌群失衡的研究现状

肝硬化是我国的一种常见病,近年来越来越多的研究表明肝硬化及其并发症（如门静脉高压、自发性腹膜炎、肝性脑病及肝癌等）都与肠道菌群失衡有着密切的联系。肝脏和肠道通过“肠—肝轴”紧密联系在一起,肝硬化时因小肠细菌过度生长、肠黏膜屏障功能受损、机体免疫功能下降等因素,导致细菌移位、肠道微生态失衡。而肠道微生态失衡又会使肝功能障碍进一步发展,引起肝性脑病等并发症。本文就目前国内外对肝硬化及其并发症与肠道细菌及真菌菌群失衡的研究进行综述。     

肠道菌群与肝癌的研究进展

微生态是微生物与机体在长期进化和相互作用过程中形成的特殊生态系统,对机体健康与疾病起着重要作用。肠道菌群作为人体微生态的重要组成部分,通过营养代谢、免疫调节和基因调控参与人体内一系列重要的生理和病理过程。肠道菌群失调可导致胆汁酸代谢异常、内毒素释放、肠道稳态破坏、模式识别受体激活等,这些都可直接或间接促进肝癌的发展。本文从以上因素着手,通过文献检索对肠道菌群与肝癌发生发展关系的研究作一简要综述。     

黄褐斑病人皮损区皮肤菌群的研究

首次应用定位、定量和定性方法对５１例黄褐斑病人皮损区菌群进行微生态学的研究,并将结果与１０４例健康人面部菌群及经治后１０例病人菌群进行比较,结果表明黄褐斑病皮损区过路菌改变明显,象产色素的微球菌及革兰氏阴性杆菌数量增加（５×１０￣３／ｃｍ２）,分离率高（１７－３９％）,与健康人相比（５×１０￣２／ｃｍ￣２及１～３％）差异显著（Ｐ＜０．０５或Ｐ＜０．０１）。经治后黄褐斑病人常住厌氧菌增加（从６８,５２％到１００％,Ｐ＜０．０５）,使用皮肤微生态制剂调整菌群,有利于恢复微生态平衡     

肠道、肺部菌群直接或通过肠—肺轴对呼吸系统慢性疾病的影响

人体寄生的微生物与人体为共生关系,数量庞大,并形成不同的微生态系统,影响人体免疫、代谢、内分泌等生理过程。菌群失衡导致微生态紊乱,从而导致相关疾病的发生发展。呼吸系统慢性疾病患者常有肠道菌群和肺部菌群的改变,肠道菌群通过肠—肺轴影响呼吸系统免疫及呼吸系统慢性疾病,肺部菌群的改变导致肺部疾病的同时亦会通过血流引起肠道菌群的变化。近年来随着高通量测序及生物信息学技术的发展,相关研究也越发被重视,本文着重对肠道菌群、肺部菌群通过肠—肺轴或直接在肺部免疫及呼吸系统慢性疾病中所起的作用进行综述。     

菌群16S rRNA基因测序的聚类分析方法研究进展

16S核糖体RNA（16S rRNA）基因测序是微生物分析的重要手段。16S rRNA基因测序的原始数据复杂,存在许多误差,分析前一般需要先进行序列质量控制,即对数据进行去噪、去冗余和去嵌合,最终将质量控制后的数据分为可操作分类单元（OTU）或ASV,在OTU或ASV基础上再进行菌群的各种分析。经过多年改进,聚类方法逐渐以UPARSE、DADA2、Deblur和UNOISE3等为主流,OTU聚类已经不能满足研究的需求,而ASV聚类使得菌群分析更加准确。本文除了综述聚类方法的研究进展外,还介绍了USEARCH、MOTHUR和QIIME等多种16S基因测序分析工具软件的相关研究进展。

     

中国微生态调节剂临床应用专家共识(2020版)

正肠道是人体最庞大和最重要的微生态系统,是激活和维持肠道生理功能的关键因素,同时与感染、肝病、消化道疾病、肿瘤、糖尿病、肥胖、自闭症、阿尔茨海默病、高血压的发生发展等密切相关,肠道微生态为各类相关疾病,甚至是肿瘤免疫治疗提供诊断工具与治疗策略[1]。微生态干预在人H7N9高致病性禽流感及新型冠状病毒肺炎(COVID-19)的综合治疗中也受到了高度重视。高通量宏基因测序技术应用研究发现,肠道内可能栖息着种类更多的细菌,其总生物量接近于     

Meta-analyses of human gut microbes associated with obesity and IBD

Recent studies have linked human gut microbes to obesity and inflammatory bowel disease, but consistent signals have been difficult to identify. Here we test for indicator taxa and general features of the microbiota that are generally consistent across studies of obesity and of IBD, focusing on studies involving high-throughput sequencing of the 16S rRNA gene (which we could process using a common computational pipeline). We find that IBD has a consistent signature across studies and allows high classification accuracy of IBD from non-IBD subjects, but that although subjects can be classified as lean or obese within each individual study with statistically significant accuracy, consistent with the ability of the microbiota to experimentally transfer this phenotype, signatures of obesity are not consistent between studies even when the data are analyzed with consistent methods. The results suggest that correlations between microbes and clinical conditions with different effect sizes (e.g. the large effect size of IBD versus the small effect size of obesity) may require different cohort selection and analysis strategies.     

宿主遗传因素对肠道菌群的影响

随着高通量测序技术的发展,人们逐渐认识到肠道菌群与人类的健康和疾病密切相关,并发现肠道菌群受很多因素的影响。除了研究传统饮食和药物对肠道菌群的改变外,近年来,科学家也开始注重遗传因素在塑造肠道菌群中的作用。遗传因素可决定宿主的饮食偏好、肠道的生理结构、肠道屏障功能和免疫功能等,而这些都直接与肠道菌群相互作用,参与肠道微生态平衡的构建和稳定。因此,在研究肠道菌群与疾病发生相关性的过程中也需要考虑遗传因素的重要性。随着基因敲除、无菌小鼠和菌群移植等实验技术的革新,以及主成分分析、数量性状基因座和全基因组关联性分析等大数据分析手段的提高,科学家能够深入研究宿主遗传基因与肠道菌群之间的关联性,从而证明宿主遗传基因在塑造肠道微生态的过程中具有重要作用。本文将首先简述肠道菌群与疾病发生之间可能存在的联系,然后从多方面综述遗传因素对肠道菌群的影响及主要的研究进展,从而为今后该领域的深入研究提供重要的指导,也为今后预防和治疗疾病提供新思路和新方法。     

胰腺疾病的肠道微生物群研究进展

肠道微生物群是指存在于人体消化道内的微生物组成的复杂群落。随着16S rRNA基因测序和宏基因组测序等高通量测序技术的发展,肠道微生物群已被证明与多种疾病息息相关。三大胰腺疾病与肠道微生物群密切相关,急性胰腺炎（acute pancreatitis,AP）、慢性胰腺炎（chronic pancreatitis,CP）和胰腺癌患者肠道微生物群的构成和丰度均与健康人群不同。反之,肠道微生物群的改变会减慢或加速胰腺疾病的发生发展。益生菌和抗菌药物的使用及粪菌移植等可减轻胰腺炎症反应,缓解胃肠道症状,影响胰腺癌化疗和免疫治疗的效果,因此可为胰腺疾病的诊疗提供新策略。本文总结了AP、CP和胰腺癌的肠道微生物群研究,阐述了疾病发生时肠道微生物群的变化、与胰腺相互作用的机制以及目前的主要研究技术,探讨了肠道微生物群在胰腺疾病诊疗中的研究进展。

     

中国人群肠道微生物鸟枪法宏基因组测序研究进展

肠道微生物与人类健康的相关性研究仍然是当前生命科学研究领域的前沿热点之一。不依赖培养的16Sr RNA基因高通量测序是当前的主要研究手段。但随着测序成本的降低和数据分析方法的日渐成熟,宏基因组鸟枪法测序因具有信息量更大、更全等优势,将逐渐成为今后一段时间内研究肠道微生物组的重要手段。美国在人类微生物组计划的资助下,对30 805份样品进行了肠道微生物宏基因测序分析。通过NCBI Pub Med和SRA数据库检索,共发现72项研究收集了约10000份中国人的肠道样品用于宏基因组测序。但到目前为止,仅56项研究进行了公开发表,其中与代谢性疾病相关的文献16篇,与感染和免疫性疾病相关的文献16篇,与心脑血管疾病相关的文献12篇。由于采样地点以北京、广州、上海等大城市为主,测序平台和测序分析方法均存在较大差异,且大部分研究仍以相关性分析为主,相关研究成果在临床疾病诊疗中所发挥的作用仍非常有限。规范采样方法、标准化测序平台和数据分析流程,开展多中心平行研究将有助于数据整合和比较分析。同时,结合使用转录组、蛋白质组和培养组学等多组学方法开展功能验证和分子作用机制研究,将有利于更好地将肠道微生物研究...     

Effects of lactoferrin and lactoperoxidase‐containing food on the oral microbiota of older individuals

The oral microbiota influences health and disease states. Some gram‐negative anaerobic bacteria play important roles in tissue destruction associated with periodontal disease. Lactoferrin (LF) and lactoperoxidase (LPO) are antimicrobial proteins found in saliva; however, their influence on the whole oral microbiota currently remains unknown. In this randomized, double‐blinded, placebo‐controlled study, the effects of long‐term ingestion of LF and LPO‐containing tablets on the microbiota of supragingival plaque and tongue coating were assessed. Forty‐six older individuals ingested placebo or test tablets after every meal for 8 weeks. The relative abundance of bacterial species was assessed by 16S rRNA gene high‐throughput sequencing. Most of the bacterial species in supragingival plaque and tongue coating that exhibited significant decreases in the test group were gram‐negative bacteria, including periodontal pathogens. Decreases in the total relative abundance of gram‐negative organisms in supragingival plaque and tongue coating correlated with improvements in assessed variables related to oral health, such as oral malodor and plaque accumulation. Furthermore, there was significantly less microbiota diversity in supragingival plaque at 8 weeks in the test group than in the placebo group and low microbiota diversity correlated with improvements in assessed variables related to oral health. These results suggest that LF and LPO‐containing tablets promote a shift from a highly diverse and gram‐negative‐dominated to a gram‐positive‐dominated community in the microbiota of supragingival plaque and tongue coating. This microbial shift may contribute to improvements in oral health, including oral malodor and state of the gingiva.

     

肠道菌群与肥胖关系的研究进展

西方化的高脂饮食方式造成了越来越多的肥胖人群。高脂饮食在一定程度上可以改变肠道菌群的结构组成和功能,促进宿主对食物营养的吸收,从而增加体重形成肥胖。高脂饮食诱导的肥胖者肠道菌群的改变会导致宿主能量吸收增加,肠道通透性和炎症增加,而有减肥功能的短链脂肪酸合成能力下降。最近研究发现肠道菌群也可以通过影响中枢神经系统,尤其是下丘脑相关基因的表达来控制食欲,从而调控肥胖的形成。本文系统介绍了最近几年高脂饮食诱导肥胖的研究,总结了一些与肥胖形成有密切关系的肠道菌群以及其在肥胖形成中的作用机制,为进一步研究肠道菌群与肥胖之间的调控作用奠定了基础。最后总结了肠道菌群可以作为一个预防和治疗肥胖的有效靶点,可以通过在食物中添加有益菌或者通过菌群移植来治疗肥胖。     

Integrated analysis of miRNA and mRNA expression profiles in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis

Insect gut microbiota has been reported to participate in regulating host multiple biological processes including metabolism and reproduction. However, the corresponding molecular mechanisms remain largely unknown. Recent studies suggest that microRNAs (miRNAs) are involved in complex interactions between the gut microbiota and the host. Here, we used next-generation sequencing technology to characterize miRNA and mRNA expression profiles and construct the miRNA–gene regulatory network in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis. A total of 3016 differentially expressed genes (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Based on the integrated analysis of miRNA and mRNA sequencing data, 229 negatively correlated miRNA–gene pairs were identified from the miRNA–mRNA network. Gene ontology enrichment analysis indicated that DEMs could target several genes involved in the metabolic process, oxidation–reduction process, oogenesis, and insulin signaling pathway. Finally, real-time quantitative polymerase chain reaction further verified the accuracy of RNA sequencing results. In conclusion, our study provides the profiles of miRNA and mRNA expressions under antibiotics treatment and provides an insight into the roles of miRNAs and their target genes in the interaction between the gut microbiota and its host.     

Effects of Dietary Inclusion of β-Hydroxy-β-Methylbutyrate on Growth Performance,Fat Deposition,Bile Acid Metabolism,and Gut Microbiota Function in High-Fat and High-Cholesterol Diet-Challenged Layer Chickens

Excessive lipid deposition in layer chickens due to inappropriate feeding adversely affects egg production; however, nutritional manipulation methods to deal with this issue are still limited. β-hydroxy-β-methylbutyrate (HMB), a metabolite of L-leucine, was recently reported as a lipid-lowering nutrient in mice and pigs, although its role in layers had not been investigated. Here, we employed high-fat and high-cholesterol diet (HFHCD)−challenged growing layers as an obese model to explore HMB function in the regulation of lipid metabolism and the potential mechanisms involved. We found that dietary supplementation with (0.05% or 0.10%) HMB significantly reduced HFHCD−induced bodyweight growth in layers, mainly due to reduction in abdominal fat deposition. Mechanistically, HMB supplementation enhanced hepatic bile acid synthesis from cholesterol through elevating expression of Cyp7a1, a gene coding a key enzyme in bile acid synthesis. Furthermore, 16S rRNA gene sequencing revealed that HMB supplementation remodeled the diversity and composition of the layers’ cecal microbiota, and the abundance of Bacteroidetes at the phylum level were especially affected. Correlation analysis further indicated a strong negative association between Bacteroidetes abundance and lipid metabolism−related parameters. Taken together, these data suggest that dietary HMB supplementation could improve abdominal fat deposition in layers, probably through modulating hepatic bile acid synthesis and gut microbiota function.     

Sows affect their piglets’ faecal microbiota until fattening but not their Salmonella enterica shedding status

Recent studies have shown that Salmonella shedding status affects sows’ microbiota during gestation and that these modifications are reflected in the faecal microbiota of their piglets at weaning. The aims of this study were: (a) to evaluate the persistence, up to the fattening period, of the previously measured link between the microbiota of piglets and their mothers’ Salmonella shedding status; and (b) measure the impact of the measured microbiota variations on their Salmonella excretion at this stage. To achieve this, 76 piglets born from 19 sows for which the faecal microbiota was previously documented, were selected in a multisite production system. The faecal matter of these swine was sampled after 4 weeks, at the fattening stage. The Salmonella shedding status and faecal microbiota of these animals were described using bacteriological and 16S rRNA gene amplicon sequencing respectively. The piglet digestive microbiota association with the Salmonella shedding status of their sows did not persist after weaning and did not affect the risk of Salmonella excretion during fattening, while the birth mother still affected the microbiota of the swine at fattening. This supports the interest in sows as a target for potentially transferrable microbiota modifications.