宏基因组及培养组学技术在粪菌移植中的应用

粪菌移植技术（fecal microbiota transplantation,FMT）是利用健康人群的粪便或经过处理的粪便中的微生物来治疗消化、代谢等系统诸多疾病的一项古老而又新兴的技术。宏基因组、培养组等肠道微生物组前沿研究技术的飞速发展,为粪菌移植治疗疾病提供了强有力的研究和临床实践武器。宏基因组技术可全面揭示健康及疾病状态下肠道微生态的组成及功能变化,而培养组学技术则可以用来分离和鉴定人类肠道中的诸多在常规培养条件下未可培养菌,两项技术联用不仅可以使我们更为深入地理解粪菌移植在临床实践中的因果规律,还将有力推动粪菌移植技术在未来的应用与发展。基于此,本文综述了宏基因组及培养组学技术在粪菌移植中的应用及未来发展趋势。     

粪菌移植治疗儿童难治性功能性便秘4例

目的观察粪菌移植对儿童难治性功能性便秘的临床疗效并探讨其机制。方法对4例临床确诊为难治性功能性便秘患儿给予粪菌移植治疗,观察和记录患儿临床症状改善情况并收集供体和粪菌移植治疗前后患儿粪便标本,利用Illumina MiSeq测序平台进行16SrRNA测序,并对测序结果进行生物信息学分析。结果 4例患儿接受粪菌移植治疗后排便状况明显改善,大便次数增加、粪便硬度变软、腹部胀痛明显缓解。粪菌移植后,患儿肠道菌群多样性下降,患儿与供体的肠道菌群差异先增大后逐渐缩小。菌群分析显示患儿肠道有害菌受到抑制、有益菌增加。结论粪菌移植可有效改善儿童难治性功能性便秘的临床症状,具有疗程短、治疗方便、无明显不良反应等优点。     

粪菌移植通过微生物-肠-脑轴改善抑郁症的研究进展

人类粪菌移植(fecal microbiota transplantation,FMT)早在19世纪50年代的西方医学中便有临床应用.FMT已被证明可以很好地缓解艰难梭菌感染(Clostridium difficile infection,CDI)的胃肠道疾病,在调节微生物-肠-脑轴(microbiota-gut-br...     

Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice

Fecal microbiota transplantation (FMT) of human fecal samples into germ-free (GF) mice is useful for establishing causal relationships between the gut microbiota and human phenotypes. However, due to the intrinsic differences between human and mouse intestines and the different diets of the two organisms, it may not be possible to replicate human phenotypes in mice through FMT; similarly, treatments that are effective in mouse models may not be effective in humans. In this study, we aimed to identify human gut microbes that undergo significant and consistent changes (i.e., in relative abundances) after transplantation into GF mice in multiple experimental settings. We collected 16S rDNA-seq data from four published studies and analyzed the gut microbiota profiles from 1713 human–mouse pairs. Strikingly, on average, we found that only 47% of the human gut microbes could be re-established in mice at the species level, among which more than 1/3 underwent significant changes (referred to as “variable taxa”). Most of the human gut microbes that underwent significant changes were consistent across multiple human–mouse pairs and experimental settings. Consequently, about 1/3 of human samples changed their enterotypes, i.e., significant changes in their leading species after FMT. Mice fed with a controlled diet showed a lower enterotype change rate (23.5%) than those fed with a noncontrolled diet (49.0%), suggesting a possible solution for rescue. Most of the variable taxa have been reported to be implicated in human diseases, with some recognized as the causative species. Our results highlight the challenges of using a mouse model to replicate human gut microbiota-associated phenotypes, provide useful information for researchers using mice in gut microbiota studies, and call for additional validations after FMT. An online database named FMT-DB is publicly available at http://fmt2mice.humangut.info/#/.     

早期灌喂母源粪菌对新生仔猪肠道菌群发育的影响

【目的】粪菌移植(fecal microbiota transplantation,FMT)作为一种治疗手段,已在人类肠道疾病治疗中有较多应用,但在干预新生仔猪肠道菌群上的研究未见报道。本文旨在研究早期母源粪菌移植对新生仔猪肠道菌群发育的影响。【方法】选取一窝12头杜长大新生仔猪,随机分为粪菌处理组(feces treatment,FT)和对照组(control,CO)。FT组仔猪出生后1–5 d每日灌注母源粪菌接种液,CO组灌注等量生理盐水。于1、3、5、7、10、14、18和22日龄采集仔猪粪样,Miseq高通量测序分析仔猪粪便菌群。【结果】灌喂母源粪菌有增加仔猪肠道菌群丰富度的趋势;主坐标分析显示,两组仔猪粪样菌群结构簇并未分开,并在18和22日龄时靠近母猪粪样菌群结构簇;随日龄增加,两组仔猪肠道中的变形菌门丰度均显著降低,而厚壁菌门的丰度显著增加,且从10日龄起拟杆菌门和厚壁菌门之和约为90%;与对照组相比,灌喂母源粪菌增加了10日龄时Escherichia-Shigella的丰度,而降低了18日龄时该菌属的丰富度,18日龄时肠球菌属和普氏菌属的丰度则显著增加。【结论】1–3日龄口服灌喂母源粪菌液并不能影响仔猪肠道菌群的定殖,这一阶段主要受母体微生物结构的影响;灌喂粪菌液对仔猪肠道菌群定殖的影响最多持续10–14 d;而且仔猪在22 d左右,肠道菌群结构逐渐趋同于母猪肠道菌群。     

肠道微生态与非消化系统疾病的研究进展

人体肠道微生态系统是人体微生态系统中最大最复杂的一部分,参与机体代谢、免疫等各方面的生理作用。由于内外源性的病理因素导致肠道微生态的破坏可能会引起人体疾病。随着肠道微生态与消化道疾病研究的不断深入,越来越多的学者开始关注肠道微生态与非消化道疾病的相关性。近年来大量研究表明,肠道微生态与肥胖、神经精神病、皮肤病、心脑血管疾病、消化道外肿瘤、感染性疾病和自身免疫病等非消化系统疾病具有相关性。微生态制剂和粪菌移植可以通过调节肠道微生态平衡参与这类疾病的预防和治疗。肠道微生态系统与消化系统疾病的相关性已被广泛研究和阐述,本文侧重对肠道微生态与非消化系统疾病的研究进展进行综述。     

粪菌移植治疗艰难梭菌感染的研究进展

艰难梭菌感染(Clostridium difficile infection,CDI)是院内抗生素相关性腹泻的最重要因素之一,其主要临床表现包括血便、腹泻、中毒性巨结肠、伪膜性肠炎等。近年来,CDI发病率、复发率、死亡率和治疗费用均明显增加,但其各种治疗方法均有局限性,尤其是抗生素治疗复发性艰难梭菌感染已面临许多棘手问题。目前证实肠道菌群失调和CDI感染关系密切,肠道菌群紊乱后导致艰难梭菌过度繁殖并释放毒素,可导致艰难梭菌感染。粪菌移植作为重建肠道菌群的重要方式,已成为复发性、难治性艰难梭菌感染最有效的治疗方式之一,不良反应极少。本文就国内外粪菌移植治疗艰难梭菌感染的研究进展作一综述。     

Fecal microbiota transplants: emerging social representations in the English-language print media

This study investigates how English-language news sources have represented fecal microbiota transplants (FMT). FMT involves transferring stool from a healthy donor to a recipient with a dysfunctional intestinal flora in order to repopulate their gut microbiome. FMT applications are increasingly moving into mainstream clinical care. We investigate press coverage of stool transplants, as well as broader themes associated with health and the gut microbiome, in order to uncover emerging social representations. Our findings show that print media focused in particular on creating novel, mainly hopeful, social representations of feces through wordplay and punning, side-lining issues of risk and fear. We also identify changing metaphorical framings of microbes and bacteria from “enemies” to “friends”, and ways in which readers are familiarized with FMT through the depiction of the process as both mundane and highly medicalized.     

粪菌移植在临床治疗中的研究进展

粪菌移植的历史可以追溯到中国东晋时期。大量研究证实粪菌移植有可能成为许多疾病的有效治疗方法,现已逐渐应用于临床上并取得较好的疗效。粪菌移植可以通过增加短链脂肪酸,特别是丁酸盐的产量来减少肠道通透性,从而降低疾病的严重程度,这有助于维持上皮屏障的完整性。粪菌移植还可以通过抑制Th1分化、T细胞活性、白细胞粘附和炎症因子的产生来恢复免疫生态失调。目前对粪菌移植的研究主要集中在治疗艰难梭菌感染,但其他领域对粪菌移植研究的热情也日益高涨,如用于治疗炎症性肠病、代谢综合征和肠易激综合征等。本文对最新的粪菌移植在临床治疗中的研究进展作一综述。     

阴道菌群移植治疗细菌性阴道炎的发展现状及展望

细菌性阴道炎 (Bacterial vaginosis,BV) 是由患者阴道内菌群失调导致的一类疾病。当前常规的抗生素疗法可进一步加剧阴道菌群失衡、破坏阴道酸性环境、导致耐药,因此其对BV治愈率低,复发率高。作为一种新兴的活菌疗法,阴道菌群移植 (Vaginal microbiota transplantation,VMT) 直接将健康妇女完整的阴道菌群“嫁接”给患者,可迅速恢复患者阴道菌群的平衡,改善患者的整体健康。文中对VMT的发展历程进行了回顾,讨论了VMT发展过程中面临的难题及发展方向,以期寻求新的治疗BV的策略,加速VMT的临床应用。     

粪便微生物系移植通过影响炎症因子和肠道菌群结构缓解大鼠实验性结肠炎

炎症性肠病（inflammatory bowel disease,IBD）病因虽未明确,但目前认为,肠道细菌和肠黏膜免疫功能紊乱与IBD的发病密切相关。将40只SD大鼠分为健康对照组、模型组、粪便微生物系移植组（fecal microbiota transplantation,FMT）和柳氮磺胺吡啶组,后3组用2,4,6-三硝基苯磺酸（2,4,6-trinitrobenzene sulfonic acid, TNBS）灌肠造模,造模2 d后分别用粪便悬液和柳氮磺胺吡啶治疗1 w。末次给药后禁食1 d,对大鼠粪便进行菌群成分分析,股动脉取血,对K⁺ 、Na⁺ 、血清白蛋白（ALB）、白细胞计数（WBC）、中性粒细胞百分率（N%）、C-反应蛋白（CRP）、IL-1β、IL-10、IL-12和IL-17 水平进行检测,取结肠行病理学检查。结果发现,通过TNBS灌肠成功建立大鼠实验性结肠炎模型。与模型组比较,FMT组的K⁺和ALB明显升高(P<0.05),WBC、N%和CRP明显降低(P<0.05),IL-1β和IL-17明显降低(P<0.05),IL-10和IL-10/IL-12含量升高(P<0.05)。FMT能显著改善TNBS引起的肠道菌群变化,促进双歧杆菌的增殖而抑制脆弱拟杆菌和大肠杆菌的生长。上述结果证明,FMT可有效治疗炎症性肠病,其机制与其影响血清炎症因子水平和改善肠道菌群有关。     

Balancing reactive oxygen species generation by rebooting gut microbiota

Reactive oxygen species (ROS; free radical form O₂^•−, superoxide radical; OH^•, hydroxyl radical; ROO^•, peroxyl; RO^•, alkoxyl and non-radical form ¹O₂, singlet oxygen; H₂O₂, hydrogen peroxide) are inevitable companions of aerobic life with crucial role in gut health. But, overwhelming production of ROS can cause serious damage to biomolecules. In this review, we have discussed several sources of ROS production that can be beneficial or dangerous to the human gut. Micro-organisms, organelles and enzymes play crucial role in ROS generation, where NOX1 is the main intestinal enzyme, which produce ROS in the intestine epithelial cells. Previous studies have reported that probiotics play significant role in gut homeostasis by checking the ROS generation, maintaining the antioxidant level, immune system and barrier protection. With current knowledge, we have critically analysed the available literature and presented the outcome in the form of bubble maps to suggest that the probiotics help in controlling the ROS-specific intestinal diseases, such as inflammatory bowel disease (IBD) and colon cancer. Finally, it has been concluded that rebooting of the gut microbiota with probiotics, postbiotics or faecal microbiota transplantation (FMT) can have crucial implications in the structuring of gut communities for the personalized management of the gastrointestinal (GI) diseases.     

Early intervention with faecal microbiota transplantation: an effective means to improve growth performance and the intestinal development of suckling piglets

Recent studies indicate that early postnatal period is a critical window for gut microbiota manipulation to optimise the immunity and body growth. This study investigated the effects of maternal faecal microbiota orally administered to neonatal piglets after birth on growth performance, selected microbial populations, intestinal permeability and the development of intestinal mucosal immune system. In total, 12 litters of crossbred newborn piglets were selected in this study. Litter size was standardised to 10 piglets. On day 1, 10 piglets in each litter were randomly allotted to the faecal microbiota transplantation (FMT) and control groups. Piglets in the FMT group were orally administrated with 2ml faecal suspension of their nursing sow per day from the age of 1 to 3 days; piglets in the control group were treated with the same dose of a placebo (0.1M potassium phosphate buffer containing 10% glycerol (vol/vol)) inoculant. The experiment lasted 21 days. On days 7, 14 and 21, plasma and faecal samples were collected for the analysis of growth-related hormones and cytokines in plasma and lipocalin-2, secretory immunoglobulin A (sIgA), selected microbiota and short-chain fatty acids (SCFAs) in faeces. Faecal microbiota transplantation increased the average daily gain of piglets during week 3 and the whole experiment period. Compared with the control group, the FMT group had increased concentrations of plasma growth hormone and IGF-1 on days 14 and 21. Faecal microbiota transplantation also reduced the incidence of diarrhoea during weeks 1 and 3 and plasma concentrations of zonulin, endotoxin and diamine oxidase activities in piglets on days 7 and 14. The populations of Lactobacillus spp. and Faecalibacterium prausnitzii and the concentrations of faecal and plasma acetate, butyrate and total SCFAs in FMT group were higher than those in the control group on day 21. Moreover, the FMT piglets have higher concentrations of plasma transforming growth factor-β and immunoglobulin G, and faecal sIgA than the control piglets on day 21. These findings indicate that early intervention with maternal faecal microbiota improves growth performance, decreases intestinal permeability, stimulates sIgA secretion, and modulates gut microbiota composition and metabolism in suckling piglets.     

Microbial treatment in chronic constipation

Chronic functional constipation is a kind of common intestinal disease that occurs in children, adults and elderly people. This disease not only causes great influence to physiological function, but also results in varying degrees of psychological barriers. At present, constipation treatments continue to rely on traditional methods such as purgative therapy and surgery. However, these approaches can disrupt intestinal function. Recent research between intestinal diseases and gut microbiota has gradually revealed a connection between constipation and intestinal flora disturbance, providing a theoretical basis for microbial treatment in chronic constipation. Microbial treatment mainly includes probiotic preparations such as probiotics, prebiotics, synbiotics and fecal microbiota transplantation (FMT). Due to its safety, convenience and curative effect, probiotic preparations have been widely accepted, especially gradually developed FMT with higher curative effects. Microbial treatment improves clinical symptoms, promotes the recovery of intestinal flora, and has no complications during the treatment process. Compared with traditional treatments, microbial treatment in chronic constipation has advantages, and is worthy of further promotion from clinical research to clinical application.     

Fecal microbiota transplantation from young donor mice improves ovarian function in aged mice

Advanced maternal age is characterized by declines in the quantity and quality of oocytes in the ovaries, and the aging process is accompanied by changes in gut microbiota composition. However, little is known about the relationship between gut microbiota and ovarian aging. By using fecal microbiota transplantation (FMT) to transplant material from young (5-week-old) into aged (42-week-old) mice, we find that the composition of gut microbiota in FMT-treated mice presents a “younger-like phenotype” and an increase of commensal bacteria, such as Bifidobacterium and Ruminococcaceae. Moreover, the FMT-treated mice show increased anti-inflammatory cytokine IL-4 and decreased pro-inflammatory cytokine IFN-γ. Fertility tests for assessing ovarian function reveal that the first litter size of female FMT-treated mice is significantly higher than that of the non-FMT group. Morphology analysis demonstrates a dramatic decrease in follicle atresia and apoptosis as well as an increase in cellular proliferation in the ovaries of the FMT-treated mice. Our results also show that FMT improves the immune microenvironment in aged ovaries, with decreased macrophages and macrophage-derived multinucleated giant cells (MNGCs). These results suggest that FMT from young donors could be a good choice for delaying ovarian aging.     

粪菌移植研究的文献计量学和可视化分析

【背景】粪菌移植是近年医学领域研究的热点,不但能够治疗消化系统疾病,而且在神经及精神系统、心血管系统相关疾病的治疗中均有不错的疗效,有着广阔的应用前景。【目的】掌握国内外粪菌移植的研究现状、热点及发展趋势,为相关领域科研工作者的研究提供参考。【方法】基于Web of Science核心数据库,通过CiteSpace对2011-2021年的年度发文量、作者、国家、期刊、被引情况和关键词等进行可视化分析。【结果】筛选后共纳入4 905篇文献,目前全球粪菌移植研究的文献数量呈快速增长趋势;美国和中国是发文量最多的国家。中国学者的总发文量虽然位居世界第二,但中心度和篇均被引频次较低,说明受关注程度及学术影响力不足,在发文质量上还有待提高;Gastroenterology是国内外学者发文量最多的期刊,Frontiers in Microbiology是中国学者发文量最多的期刊;粪菌移植呈现出多学科交叉的发展特点;粪菌移植目前的研究热点主要与肠内疾病(炎症性肠病、艰难梭菌感染)和肠外疾病(如抑郁、冠状动脉粥样硬化等)有关;粪菌移植在未成年人中的应用、对胰岛素敏感度的影响、测序技术在肠道菌群的应用及...     

Feasibility of fecal microbiota transplantation via oral gavage to safely alter gut microbiome composition in marmosets

Disruption of microbial communities within human hosts has been associated with infection, obesity, cognitive decline, cancer risk and frailty, suggesting that microbiome-targeted therapies may be an option for improving healthspan and lifespan. The objectives of this study were to determine the feasibility of delivering fecal microbiota transplants (FMTs) to marmosets via oral gavage and to evaluate if alteration of the gut microbiome post-FMT could be achieved. This was a prospective study of marmosets housed at the Barshop Institute for Longevity and Aging Studies in San Antonio, Texas. Eligible animals included healthy young adult males (age 2–5 years) with no recent medication use. Stool from two donors was combined and administered in 0.5 ml doses to five young recipients once weekly for 3 weeks. Safety outcomes and alterations in the gut microbiome composition via 16S ribosomal RNA sequencing were compared at baseline and monthly up to 6 months post-FMT. Overall, significant differences in the percent relative abundance was seen in FMT recipients at the phylum and family levels from baseline to 1 month and baseline to 6 months post-FMT. In permutational multivariate analysis of variance analyses, treatment status (donor vs. recipient) (p = .056) and time course (p = .019) predicted β diversity (p = .056). The FMT recipients did not experience any negative health outcomes over the course of the treatment. FMT via oral gavage was safe to administer to young adult marmosets. The marmoset microbiome may be altered by FMT; however, progressive changes in the microbiome are strongly driven by the host and its baseline microbiome composition.     

Washed preparation of faecal microbiota changes the transplantation related safety,quantitative method and delivery

The safety, quantitative method and delivery of faecal microbiota transplantation (FMT) vary a lot from different countries in practice. Recently, the improved methodology of FMT based on the automatic filtration, washing process and the related delivery was named as washed microbiota transplantation (WMT). First, this study aimed to describe the methodology development of FMT from manual to washing preparation from 2012 to 2021 in China Microbiota Transplantation System (CMTS), a centralized stool bank for providing a national non-profit service. The secondary aim is to describe donor screenings, the correlation between faecal weight and treatment doses, incidence of adverse events and delivery decision. The retrospective analysis on the prospectively recorded data was performed. Results showed that the success rate of donor screening was 3.1% (32/1036). The incidence rate of fever decreased significantly from 19.4% (6/31) in manual FMT to 2.7% (24/902) in WMT in patients with ulcerative colitis (UC), which made UC a considerable disease model to reflect the quality control of faecal microbiota preparation. We defined one treatment unit as 10 cm³ microbiota precipitation (1.0 × 10¹³ bacteria) based on enriched microbiota instead of rough faecal weight. For delivering microbiota, colonic transendoscopic enteral tube is a promising way especially for multiple WMTs or frequent colonic administration of drugs combined with WMT. This study should help improve the better practice of FMT for helping more patients in the future.     

Treatment and mechanism of fecal microbiota transplantation in mice with experimentally induced ulcerative colitis

Restoring intestinal microbiota dysbiosis with fecal microbiota transplantation is considered as a promising treatment for ulcerative colitis. However, the mechanisms underlying its relieving effects remain unclear. Ulcerative colitis pathogenesis is associated with the involvement of immune cells and inflammatory cytokines. Here, we aimed to investigate the effect of fecal microbiota transplantation on T cell cytokines in a dextran sulfate sodium-induced ulcerative colitis mouse model. Five-aminosalicylic acid (5-ASA) was used as the positive control. Male C57BL/6 mice were randomly assigned to control, model (UC), UC + FMT, and UC + 5-ASA groups. Each group consisted of five mice. The establishment of the mouse model was verified by fecal occult-blood screening and hematoxylin–eosin staining. Results showed that fecal microbiota transplantation reduced colonic inflammation, significantly decreased T helper (Th)1 and Th17 cells, interferon-gamma, interleukin-2 and interleukin-17, as well as significantly increased Th2 and regulatory T (Treg) cells, interleukin-4, interleukin-10, and transforming growth factor-beta, and improved routine blood count. Furthermore, 16S rRNA gene-sequencing analysis showed a significant increase in the relative abundance of genus Akkermansia and a significant decrease in the relative abundance of genus Helicobacter in the ulcerative colitis group. Fecal microbiota transplantation restored the profile of the intestinal microbiota to that of the control group. These findings demonstrated the capability of fecal microbiota transplantation in controlling experimentally induced ulcerative colitis by improving Th1/Th2 and Th17/Treg imbalance through the regulation of intestinal microbiota.     

Focus: Microbiome: Treating Obesity and Metabolic Syndrome with Fecal Microbiota Transplantation

The worldwide prevalence of metabolic syndrome, which includes obesity and its associated diseases, is rising rapidly. The human gut microbiome is recognized as an independent environmental modulator of host metabolic health and disease. Research in animal models has demonstrated that the gut microbiome has the functional capacity to induce or relieve metabolic syndrome. One way to modify the human gut microbiome is by transplanting fecal matter, which contains an abundance of live microorganisms, from a healthy individual to a diseased one in the hopes of alleviating illness. Here we review recent evidence suggesting efficacy of fecal microbiota transplant (FMT) in animal models and humans for the treatment of obesity and its associated metabolic disorders.