Raman-activated sorting of antibiotic-resistant bacteria in human gut microbiota

The antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in human gut microbiota have significant impact on human health. While high throughput metagenomic sequencing reveals genotypes of microbial communities, the functionality, phenotype and heterogeneity of human gut microbiota are still elusive. In this study, we applied Raman microscopy and deuterium isotope probing (Raman–DIP) to detect metabolic active ARB (MA-ARB) in situ at the single-cell level in human gut microbiota from two healthy adults. We analysed the relative abundances of MA-ARB under different concentrations of amoxicillin, cephalexin, tetracycline, florfenicol and vancomycin. To establish the link between phenotypes and genotypes of the MA-ARB, Raman-activated cell sorting (RACS) was used to sort MA-ARB from human gut microbiota, and mini-metagenomic DNA of the sorted bacteria was amplified, sequenced and analysed. The sorted MA-ARB and their associated ARGs were identified. Our results suggest a strong relation between ARB in human gut microbiota and personal medical history. This study demonstrates that the toolkit of Raman–DIP, RACS and DNA sequencing can be useful to unravel both phenotypes and genotypes of ARB in human gut microbiota at the single-cell level.     

肠道菌群与microRNA的交互在促结直肠癌中的作用

结直肠癌是西方国家最常见的癌症之一,多数患者伴有肠道菌群的改变。有研究表明,肠道菌群通过microRNA调节宿主基因的表达,而宿主的microRNA同样调节菌群的生长和基因表达。因此,本文概述了肠道菌群与宿主microRNA相互作用的具体机制,以及这种交互作用在结直肠癌的发生、发展、治疗阶段的研究进展。为进一步深入研究肠道菌群与结直肠癌的关系提供理论基础。     

Effects of ultra-strong static magnetic field on the gut microbiota of humans and mice

To explore the effect of ultra-strong static magnetic field on gut microbiota, 16 T static magnetic field was used to study the changes in the structure and composition of human and mouse gut microbiota in this environment. In the mouse gut microbiota, at the genus level, the magnetic field significantly decreased the relative abundances of Escherichia-Shigella, Lactobacillus, Enterococcus, Burkholderia-Caballeronia-Paraburkholderia, Parasutterella, and Ralstonia and significantly increased those of Parabacteroides, Alloprevotella, Alistipes, Odoribacter, Bacteroides, Mucispirillum, Sutterella, and Prevotellaceae_UCG-001. Similarly, at the genus level, the relative abundances of Bacteroides, Parabacteroides, Romboutsia, and Streptococcus significantly decreased in the human gut microbiota. Contrary to the changing trend of the abundance in the mouse gut, the abundances of Bacteroides and Parabacteroides in the human gut were significantly reduced under magnetic field. The BugBase phenotypic prediction analysis showed that the relative abundances of five phenotypes, including anaerobism, mobile elements, potential pathogenicity, stress-tolerant, and biofilm formation, changed significantly in the mouse gut microbiota, while the relative abundances of two phenotypes, including Gram-positive and Gram-negative phenotypes, changed significantly in the human gut microbiota. The 16 T magnetic field could differently affect the composition, structure, and phenotypes of gut microbiota in human and mice, suggesting the importance of model selection in studying the biological effects of magnetic field.     

The art of targeting gut microbiota for tackling human obesity

Recently, a great deal of interest has been expressed regarding strategies to tackle worldwide obesity because of its accelerated wide spread accompanied with numerous negative effects on health and high costs. Obesity has been traditionally associated with an imbalance in energy consumed when compared to energy expenditure. However, growing evidence suggests a less simplistic event in which gut microbiota plays a key role. Obesity, in terms of microbiota, is a complicated disequilibrium that presents many unclear complications. Despite this, there is special interest in characterizing compositionally and functionally the obese gut microbiota with the help of in vitro, animal and human studies. Considering the gut microbiota as a factor contributing to human obesity represents a tool of great therapeutic potential. This paper reviews the use of antimicrobials, probiotics, fecal microbial therapy, prebiotics and diet to manipulate obesity through the human gut microbiota and reveals inconsistencies and implications for future study.     

Comparison of the Distal Gut Microbiota from People and Animals in Africa

The gut microbiota plays a key role in the maintenance of healthy gut function as well as many other aspects of health. High-throughput sequence analyses have revealed the composition of the gut microbiota, showing that there is a core signature to the human gut microbiota, as well as variation in its composition between people. The gut microbiota of animals is also being investigated. We are interested in the relationship between bacterial taxa of the human gut microbiota and those in the gut microbiota of domestic and semi-wild animals. While it is clear that some human gut bacterial pathogens come from animals (showing that human – animal transmission occurs), the extent to which the usually non-pathogenic commensal taxa are shared between humans and animals has not been explored. To investigate this we compared the distal gut microbiota of humans, cattle and semi-captive chimpanzees in communities that are geographically sympatric in Uganda. The gut microbiotas of these three host species could be distinguished by the different proportions of bacterial taxa present. We defined multiple operational taxonomic units (OTUs) by sequence similarity and found evidence that some OTUs were common between human, cattle and chimpanzees, with the largest number of shared OTUs occurring between chimpanzees and humans, as might be expected with their close physiological similarity. These results show the potential for the sharing of usually commensal bacterial taxa between humans and other animals. This suggests that further investigation of this phenomenon is needed to fully understand how it drives the composition of human and animal gut microbiotas.     

Combined hormonal contraceptives are associated with minor changes in composition and diversity in gut microbiota of healthy women

Recent human and animal studies have found associations between gut microbiota composition and serum levels of sex hormones, indicating that they could be an important factor in shaping the microbiota. However, little is known about the effect of regular hormonal fluctuations over the menstrual cycle or CHC-related changes of hormone levels on gut microbiota structure, diversity and dynamics. The aim of this study was to investigate the effect of CHCs on human gut microbiota composition. The effect of CHC pill intake on gut microbiota composition was studied in a group of seven healthy pre-menopausal women using the CHC pill, compared to the control group of nine age-matched healthy women that have not used hormonal contraceptives in the 6 months prior to the start of the study. By analysing the gut microbiota composition in both groups during one menstrual cycle, we found that CHC usage is associated with a minor decrease in gut microbiota diversity and differences in the abundance of several bacterial taxa. These results call for further investigation of the mechanisms underlying hormonal and hormonal contraceptive-related changes of the gut microbiota and the potential implications of these changes for women's health.     

银杏双黄酮和银杏内酯B与人体肠道菌群体外互作研究

【目的】银杏提取物在防治心血管系统和神经系统疾病方面发挥重要功能。鉴于肠道菌群已被认定为一个新兴的药物作用靶标,研究银杏双黄酮和银杏内酯与人体肠道菌群之间的相互作用具有非常重要的意义,这将为进一步理解银杏提取物的功能和作用机制奠定基础。【方法】本研究使用人体肠道菌群体外批量发酵、细菌总量测定、细菌16S rDNA高通量测序、气相色谱和液相色谱检测等方法,对银杏双黄酮和银杏内酯B单独或复合在体外与人体肠道菌群的相互作用进行研究。【结果】银杏双黄酮和银杏内酯B单独添加对人体肠道菌群总量、肠道菌群结构组成和短链脂肪酸产量没有显著影响。但有意思的是,复合添加银杏双黄酮和银杏内酯B后,Coriobacteriaceae科和Cupriavidus属细菌的比例显著升高,Gemella菌细菌比例显著降低。功能基因预测分析发现,编码K00076、K12143、K07716和K00220的基因在复合添加银杏双黄酮和银杏内酯B后显著富集。K00076和K00220是氧化还原酶,催化CH-OH供体基团的电子转移,可能参与银杏双黄酮和银杏内酯B的代谢和修饰。HPLC检测发现,人体肠道菌群体外对银杏双黄酮和银杏内脂B的降解修饰率分别为70%和35%左右。【结论】体外复合添加银杏双黄酮和银杏内酯B可显著改变肠道某些细菌的丰度。同时,体外研究表明肠道菌群具有代谢修饰银杏双黄酮和银杏内酯B的功能。     

Beneficial modulation of the gut microbiota

The human gut microbiota comprises approximately 100 trillion microbial cells and has a significant effect on many aspects of human physiology including metabolism, nutrient absorption and immune function. Disruption of this population has been implicated in many conditions and diseases, including examples such as obesity, inflammatory bowel disease and colorectal cancer that are highlighted in this review. A logical extension of these observations suggests that the manipulation of the gut microbiota can be employed to prevent or treat these conditions. Thus, here we highlight a variety of options, including the use of changes in diet (including the use of prebiotics), antimicrobial-based intervention, probiotics and faecal microbiota transplantation, and discuss their relative merits with respect to modulating the intestinal community in a beneficial way.     

Human activity can influence the gut microbiota of Darwin's finches in the Galapagos Islands

The gut microbiota of animal hosts can be influenced by environmental factors, such as unnatural food items that are introduced by humans. Over the past 30 years, human presence has grown exponentially in the Galapagos Islands, which are home to endemic Darwin's finches. Consequently, humans have changed the environment and diet of Darwin's finches, which in turn, could affect their gut microbiota. In this study, we compared the gut microbiota of two species of Darwin's finches, small ground finches (Geospiza fuliginosa) and medium ground finches (Geospiza fortis), across sites with and without human presence, where finches prefer human‐processed and natural food, respectively. We predicted that: (a) finch microbiota would differ between sites with and without humans due to differences in diet, and (b) gut microbiota of each finch species would be most similar where finches have the highest niche overlap (areas with humans) compared to the lowest niche overlap (areas without humans). We found that gut bacterial community structure differed across sites and host species. Gut bacterial diversity was most distinct between the two species at the site with human presence compared to the site without human presence, which contradicted our predictions. Within host species, medium ground finches had lower bacterial diversity at the site with human presence compared to the site without human presence and bacterial diversity of small ground finches did not differ between sites. Our results show that the gut microbiota of Darwin's finches is affected differently across sites with varying human presence.     

(S)-雌马酚对肠道菌群的体外调控作用及其可代谢性研究

[目的]研究(S)-雌马酚对人体肠道菌群的体外调控作用和人体肠道菌群对(S)-雌马酚的代谢衍生作用。[方法]采用人体肠道菌群体外批量发酵、细菌16S rRNA基因高通量测序、气相色谱、液相色谱和质谱等检测(S)-雌马酚与人体肠道菌群体外相互作用。[结果]体外添加(S)-雌马酚对总体人肠道菌群结构和短链脂肪酸产量影响不明显。添加0.45 mmol/L (S)-雌马酚组与对照组相比,未检测到相对丰度发生显著变化的细菌;添加0.90 mmol/L (S)-雌马酚组与对照组相比,显著增加了肠杆菌科(Enterobacteriaceae)等条件致病菌的相对丰度,减少了潜在益生菌粪球菌属(Coprococcus)的比例。代谢分析发现,发酵培养液中(S)-雌马酚的浓度降低了约15%−30%,推测可能被微生物进一步降解或衍生修饰。[结论]从体外调控肠道菌群的角度判断,0.45 mmol/L (S)-雌马酚相对较安全,而0.90 mmol/L (S)-雌马酚可能会破坏肠道菌群平衡。(S)-雌马酚可以被人体肠道菌群进一步代谢,其特定代谢产物的结构与功能及其体内生物安全性有待进一步研究。     

Envisioning emerging frontiers on human gut microbiota and its applications

The human gut microbiota is involved in multiple health-influencing host interactions during the host’s entire life span. Microbes colonize the infant gut instantaneously after birth and subsequently the founding and interactive progress of this early gut microbiota is considered to be driven and modulated by different host- and microbe-associated forces. A rising number of studies propose that the composition of the human gut microbiota in the early stages of life impact on the human health conditions at later stages of life. This notion has powered research aimed at detailed investigations of the infant gut microbiota composition. Nevertheless, the molecular mechanisms supporting the gut microbiome functionality and the interaction of the early gut microbes with the human host remain largely unknown.     

肠道菌群在脊髓损伤后胃肠道炎症反应中的研究进展

脊髓损伤(spinal cord injury, SCI)目前尚无有效的治疗手段。脊髓损伤后,患者常伴有严重的胃肠功能障碍,严重影响患者的生活质量。研究发现,脊髓损伤后肠道菌群的紊乱和脊髓损伤后的胃肠道功能障碍密切相关。因此,本文围绕脊髓损伤后肠道菌群的变化,探讨肠道菌群在迷走神经、下丘脑-垂体-肾上腺和肠道菌群代谢物3个途径中发挥的作用,及与胃肠道炎症反应相关的研究进展。     

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/#/.     

饮食因素对肠道菌群影响的研究进展

人体肠道内定植了约1014个微生物,种类有1 000多种,它们作为"人体的第十三个生理系统",直接参与了机体的各种代谢活动,与人体健康密切相关。研究显示,肠道菌群的构成和稳定受到诸多宿主和环境因素的影响,其中饮食因素起着至关重要的作用。因此,本文用膳食金字塔将食物进行分类,介绍了膳食中谷类、果蔬类、豆类、奶类、鱼肉类、油脂类和糖类对肠道菌群的调节作用,以期为相关研究的开展、相应疾病的防治提供参考。     

Gut microbiota composition of Japanese macaques associates with extent of human encroachment

In recent decades, human–wildlife interaction and associated anthropogenic food provisioning has been increasing and becoming more severe due to fast population growth and urban development. Noting the role of the gut microbiome in host physiology like nutrition and health, it is thus essential to understand how human–wildlife interactions and availability of anthropogenic food in habitats can affect an animal's gut microbiome. This study, therefore, set out to examine the gut microbiota of Japanese macaques (Macaca fuscata) with varying accessibility to anthropogenic food and the possibility of using gut microbiota as indicator for macaques’ reliance on anthropogenic food. Using 16S ribosomal RNA gene sequencing, we described the microbial composition of Japanese macaques experiencing different types of human disturbance and anthropogenic food availability—captive, provisioned, crop‐raiding, and wild. In terms of alpha diversity, our results showed that observed richness of gut microbiota did not differ significantly between disturbance types but among collection sites, whereas Shannon diversity index differed by both disturbance types and sites. In terms of beta diversity, captive populations harbored the most distinctive gut microbial composition, and had the greatest difference compared with wild populations. Whereas for provisioned and crop‐raiding groups, the macaques exhibited intermediate microbiota between wild and captive. We identified several potential bacterial taxa at different taxonomic ranks whose abundance potentially could help in assessing macaques’ accessibility to anthropogenic food. This study revealed the flexibility of the gut microbiome of Japanese macaques and provided possible indices based on the gut microbiome profile in assessing macaques’ accessibility to/reliance on anthropogenic foods.     

A metagenomic study of the gut microbiome in PTB’S disease

BackgroundThere is an abundant link between the gut microbiota and human health and it plays a critical role in the clinic. It is recognized that microbial dysregulation contributes to the pathogenesis of tuberculosis (TB) but the underlying mechanisms remain unclear. In this study, we investigated the association of gut microbiome composition with TB as well as its possible roles in the development of this disease.MethodsFecal samples were collected from 10 TB patients and 20 healthy control samples. DNA extracted from fecal samples was subjected to 16S rDNA gene sequencing analysis on the Illumina MiSeq platform.ResultsCompared with healthy control samples, the gut microbiome of patients with TB was characterized by the decreased Alpha diversity. Perhaps, the decrease of microbial diversity which results in microbial dysregulation is the reason for clinical patients with more symptoms. The PTB group showed the most unique microbiota by higher abundance of Bifidobacteriaceae, Bifidobacteriales, Coriobacteriaceae, Coriobacteriales, Actinobacteria, Caulobacteraceae, Phyllobacteriaceae, Rhizobiales, Burkholderiaceae, Burkholderiaceae. Inflammatory status in PTB patients may be associated with the increased abundance of Clostridia and decreased abundance of Prevotella. We found that the abundance of Solobacterium and Actinobacteria was higher in the patients. There were 4 significant differences (p < 0.05) in the two groups which belonged to four metabolic categories, including endocytosis, phosphotransferase system (PTS), toluene degradation, and amoebiasis.ConclusionWe applied the approach of metagenomic sequencing to characterize the features of gut microbiota in PTB patients. The present study provided a detailed analysis of the characterization of the gut microbiota in patients based on the clinic. According to the metagenome analysis, our results indicated that the gut microbiota in PTB patients was significantly different from healthy control samples as characterized by the bacteria and metabolic pathway. The richness of the gut microbiota in patients was revealed. It was hypothesized that the above-mentioned changes of the gut microbiota could exert an impact on the development of PTB through the downstream regulation of the immune status of the host by way of the gut–lung axis.     

肥胖患者HFA小鼠模型的建立

目的研究肥胖患者的肠道菌群在无菌小鼠体内的定植规律。方法选取20只无菌KM小鼠,接种肥胖患者的粪便,构建菌群人源化(HFA)动物模型,利用变性梯度凝胶电泳技术(DGGE)评价患者肠道菌群在无菌小鼠体内的定植规律。结果 HFA小鼠菌群平均丰富度(richness,S)为12.04±3.68,肥胖患者的条带S为24,为HFA小鼠S的2倍;肥胖患者Shannon指数(H')为3.02,HFA小鼠平均H'为2.46±0.33;HFA小鼠与人肠道菌群的总相似度为26%;大部分雌性HFA小鼠与雄性HFA小鼠在聚类分析图上分离,且雄性HFA小鼠与患者更为相似。结论HFA小鼠体内能部分模拟肥胖患者的微生物区系,且与患者性别相同的小鼠模拟得更好。本实验建立的HFA模型为肥胖与肠道菌群关系的进一步研究提供新的选择。     

Gut Microbiota is Not Modified by Randomized, Double-Blind, Placebo-Controlled Trial of VSL#3 in Diarrhea-Predominant Irritable Bowel Syndrome

Irritable Bowel Syndrome (IBS) is a common condition that negatively impacts the quality of life for many individuals. The exact etiology of this disorder is largely unknown; however, emerging studies suggest that the gut microbiota is a contributing factor. Several clinical trials show that probiotics, such as VSL#3, can have a favorable effect on IBS. This double-blind, randomized placebo-controlled study has been conducted in diarrhea-predominant IBS subjects in order to investigate the effect of VSL#3 on the fecal microbiota. The bacterial composition of the fecal microbiota was investigated using high-throughput microarray technology to detect 16S RNA. Twenty four subjects were randomized to receive VSL#3 or placebo for 8 weeks. IBS symptoms were monitored using GSRS and quality of life questionnaires. A favorable change in Satiety subscale was noted in the VSL #3 groups. However, the consumption of the probiotic did not change the gut microbiota. There were no adverse events or any safety concerns encountered during this study. To summarize, the use of VSL#3 in this pilot study was safe and showed improvement in specific GSRS-IBS scores in diarrhea-predominant IBS subjects. The gut microbiota was not affected by VSL#3 consumption suggesting that the mechanism of action is not directly linked to the microbiota.     

肠道微生物对肥胖影响

肠道微生物是哺乳动物最密集的微生物群落,也是最多样化的微生物群落之一。随着宏基因组学的不断发展,肠道微生物成为热门的研究领域。肠道微生物具有保护和代谢等功能,在胰岛素抵抗和肥胖等疾病中发挥重要作用。本文介绍了肠道微生物及其代谢物通过调节食欲、神经递质合成分泌、炎性反应进而调节肥胖,探讨了肠道微生物的影响因素,展望了肠道微生物对治疗人类肥胖的应用前景。     

The gut microbiota links disease to human genome evolution

A large number of studies have established a causal relationship between the gut microbiota and human disease. In addition, the composition of the microbiota is substantially influenced by the human genome. Modern medical research has confirmed that the pathogenesis of various diseases is closely related to evolutionary events in the human genome. Specific regions of the human genome known as human accelerated regions (HARs) have evolved rapidly over several million years since humans diverged from a common ancestor with chimpanzees, and HARs have been found to be involved in some human-specific diseases. Furthermore, the HAR-regulated gut microbiota has undergone rapid changes during human evolution. We propose that the gut microbiota may serve as an important mediator linking diseases to human genome evolution.