Comparative analysis of human gut microbiota by barcoded pyrosequencing

Humans host complex microbial communities believed to contribute to health maintenance and, when in imbalance, to the development of diseases. Determining the microbial composition in patients and healthy controls may thus provide novel therapeutic targets. For this purpose, high-throughput, cost-effective methods for microbiota characterization are needed. We have employed 454-pyrosequencing of a hyper-variable region of the 16S rRNA gene in combination with sample-specific barcode sequences which enables parallel in-depth analysis of hundreds of samples with limited sample processing. In silico modeling demonstrated that the method correctly describes microbial communities down to phylotypes below the genus level. Here we applied the technique to analyze microbial communities in throat, stomach and fecal samples. Our results demonstrate the applicability of barcoded pyrosequencing as a high-throughput method for comparative microbial ecology.     

Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing

Human gut microbiota plays important roles in harvesting energy from the diet, stimulating the proliferation of the intestinal epithelium, developing the immune system, and regulating fat storage in the host. Characterization of gut microbiota, however, has been limited to western people and is not sufficiently extensive to fully describe microbial communities. In this study, we investigated the overall composition of the gut microbiota and its host specificity and temporal stability in 20 Koreans using 454-pyrosequencing with barcoded primers targeting the V1 to V3 region of the bacterial 16S rRNA gene. A total of 303,402 high quality reads covered each sample and 8,427 reads were analyzed on average. The results were compared with those of individuals from the USA, China and Japan. In general, microbial communities were dominated by five previously identified phyla: Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Proteobacteria. UPGMA cluster analysis showed that the species composition of gut microbiota was host-specific and stable over the duration of the test period, but the relative abundance of each member fluctuated. 43 core Korean gut microbiota were identified by comparison of sequences from each individual, of which 15 species level phylotypes were related to previously-reported butyrate-producing bacteria. UniFrac analysis revealed that human gut microbiota differed between countries: Korea, USA, Japan and China, but tended to vary less between individual Koreans, suggesting that gut microbial composition is related to internal and external characteristics of each country member such as host genetics and diet styles.     

Comparative metagenomics analysis reveals how the diet shapes the gut microbiota in several small mammals

The gut microbiomes of the host are large and complex communities, which helps to maintain homeostasis, improves digestive efficiency, and promotes the development of the immune system. The small mammals distributed in Sichuan Province are the most popular species for biodiversity research in Southwest China. However, the effects of different diets on the structure and function of the gut microbial community of these small mammals are poorly understood. In this study, whole‐metagenome shotgun sequencing has been used to analyze the composition and functional structures of the gut microbiota of seven small mammals in Laojunshan National Nature Reserve, Sichuan Province, China. Taxonomic classification revealed that the most abundant phyla in the gut of seven small mammals were Bacteroides, Proteobacteria, and Firmicutes. Moreover, Hafnia, Lactobacillus, and Yersinia were the most abundant genus in the gut microbiomes of these seven species. At the functional level, we annotated a series of KEGG functional pathways, six Cazy categories, and 46,163 AROs in the gut microbiomes of the seven species. Comparative analysis found that the difference in the gut microbiomes between the Soricidea and Muridae concentrated on the increase in the F/B (Firmicutes/Bacteroides) ratio in the Soricidea group, probably driven by the high‐fat and ‐calorie digestive requirements due to their insectivorous diet. The comparative functional profiling revealed that functions related to metabolism and carbohydrates were significantly more abundant in Muridae group, which may be attributed to their high carbohydrate digestion requirements caused by their herbivorous diet. These data suggested that different diets in the host may play an important role in shaping the gut microbiota, and lay the foundation for teasing apart the influences of heritable and environmental factors on the evolution of gut microbial communities.     

高原红细胞增多症患者肠道菌群变化研究

目的探究高原红细胞增多症患者肠道菌群变化及相关意义。方法招募西藏那曲地区血红蛋白(hemoglobin, HB)含量高于210 g/L的高原红细胞增多症患者12人,对照组(170 g/LHB210 g/L)42人,采集粪便、血液等样本。从中选取高原红细胞增多症患者9人,对照组16人粪便样本提取DNA,进行16S rRNA测序分析。结果高原红细胞增多症患者的血红蛋白水平以及红细胞比容显著高于对照组。红细胞增多症患者的肠道菌群整体结构改变不明显,多样性没有显著差异。红细胞增多症患者的粪便菌群出现厚壁菌门中梭状芽胞杆菌BB60属、纺锤链杆菌属、厌氧棒杆菌属、霍氏真杆菌,变形菌门中假单胞菌属,拟杆菌门中副拟杆菌属丰度的显著增高。这些菌属改变经KEGG预测分析显示与代谢紊乱相关。斯皮尔曼分析显示多种菌群改变与血红蛋白水平以及红细胞比容正相关。结论高原红细胞增多症患者肠道菌群出现紊乱,菌群变化与代谢紊乱和红细胞增多相关。     

Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis

A role for the intestinal microbiota is routinely cited as a potential aetiological factor in colorectal cancer initiation and progression. As the majority of bacteria in the gut are refractory to culture we investigated this ecosystem in subjects with colorectal cancer and with adenomatous polyposis who are at high risk of developing colorectal cancer, using culture-independent methods. Twenty colorectal cancer and 20 polypectomized volunteers were chosen for this analysis. An exploration of the diversity and temporal stability of the dominant bacteria and several bacterial subgroups was undertaken using 16S rRNA gene denaturing gradient gel electrophoresis and ribosomal intergenic spacer analysis (RISA). Metabonomic analysis of the distal gut microbiota's environment was also undertaken. A significantly reduced temporal stability and increased diversity for the microbiota of subjects with colorectal cancer and polyposis was evident. A significantly increased diversity of the Clostridium leptum and C. coccoides subgroups was also noted for both disease groups. A clear division in the metabonome was observed for the colorectal cancer and polypectomized subjects compared with control volunteers. The intestinal microbiota and their metabolites are significantly altered in both colorectal cancer and polypectomized subjects compared with controls.     

肠道菌群参与宿主免疫应答的作用及机制研究进展

肠道菌群作为动物体内重要的组成部分,能够直接参与机体的免疫调控作用,促进机体免疫系统发育,维持正常免疫功能。同时,免疫系统对肠道菌群又有调控和制约作用。本文主要综述了肠道菌群的组成以及影响肠道菌群变化的因素,系统阐述了肠道菌群与疾病相互作用的机制,总结了肠道菌群在宿主感染与免疫应答中的作用,为开展肠道菌群参与机体免疫应答的机制方面的研究提供新的思路。     

Molecular analysis of gut microbiota in obesity among Indian individuals

Obesity is a consequence of a complex interplay between the host genome and the prevalent obesogenic factors among the modern communities. The role of gut microbiota in the pathogenesis of the disorder was recently discovered; however, 16S-rRNA-based surveys revealed compelling but community-specific data. Considering this, despite unique diets, dietary habits and an uprising trend in obesity, the Indian counterparts are poorly studied. Here, we report a comparative analysis and quantification of dominant gut microbiota of lean, normal, obese and surgically treated obese individuals of Indian origin. Representative gut microbial diversity was assessed by sequencing fecal 16S rRNA libraries for each group (n=5) with a total of over 3000 sequences. We detected no evident trend in the distribution of the predominant bacterial phyla, Bacteroidetes and Firmicutes. At the genus level, the bacteria of genus Bacteroides were prominent among the obese individuals, which was further confirmed by qPCR (P less than 0.05). In addition, a remarkably high archaeal density with elevated fecal SCFA levels was also noted in the obese group. On the contrary, the treated-obese individuals exhibited comparatively reduced Bacteroides and archaeal counts along with reduced fecal SCFAs. In conclusion, the study successfully identified a representative microbial diversity in the Indian subjects and demonstrated the prominence of certain bacterial groups in obese individuals; nevertheless, further studies are essential to understand their role in obesity.     

Comparative study of gut microbiota from captive and confiscated-rescued wild pangolins

Pangolins are among the most critically endangered animals due to widespread poaching and worldwide trafficking. Captive breeding is considered to be one way to protect them and increase the sizes of their populations. However, comparative studies of captive and wild pangolins in the context of gut microbiota are rare. Here, the gut microbiome of captive and confiscated-rescued wild pangolins is compared, and the effects of different periods of captivity and captivity with and without antibiotic treatment are considered. We show that different diets and periods of captivity, as well as the application of antibiotic therapy, can alter gut community composition and abundance in pangolins. Compared to wild pangolins, captive pangolins have an increased capacity for chitin and cellulose/hemicellulose degradation, fatty acid metabolism, and short-chain fatty acid synthesis, but a reduced ability to metabolize exogenous substances. In addition to increasing the ability of the gut microbiota to metabolize nutrients in captivity, captive breeding imposes some risks for survival by resulting in a greater abundance of antibiotic resistance genes and virulence factors in captive pangolins than in wild pangolins. Our study is important for the development of guidelines for pangolin conservation, including health assessment, disease prevention, and rehabilitation of wild pangolin populations.     

慢性萎缩性胃炎患者肠道菌群特征

探讨不同炎症程度慢性萎缩性胃炎（CAG）患者肠道菌群特征,为该类患者的治疗提供参考。

对36例健康人（健康对照组）和8例轻度炎症（轻度炎症组）、26例中度炎症（中度炎症组）、8例重度炎症（重度炎症组）的CAG患者的粪便样本进行16S rRNA基因高通量测序（V4—V5区）,采用Sobs、Shannon、Simpson、Ace、Chao指数评估4组对象肠道菌群的物种丰富度与多样性;采用PLS-DA分析评估4组对象肠道微生物群落结构;采用LDA与LEfSe分析确定4组对象相对丰度存在显著差异的肠道菌群;采用PICRUSt预测CAG患者显著富集肠道菌属的代谢通路信息。

与健康对照组相比,轻、中、重度炎症组患者肠道菌群Sobs、Ace、Chao、Simpson指数有降低趋势,但差异均无统计学意义（均P＞0.05）。Ruminococcus_gnavus_group、norank_f_Ruminococcaceae、Erysipelatoclostridium、Actinomyces在轻度炎症组中显著富集,Flavonifractor、Sellimonas在中度炎症组中显著富集,Eubacterium_rectale_group、Erysipelotrichaceae_UCG-003、Tyzzerella_3、Coprococcus_1、Candidatus_Soleaferrea在重度炎症组中显著富集。此外,Lachnospiraceae_UCG-004、Eubacterium_nodatum_group的丰度在健康对照组、轻度炎症组、中度炎症组、重度炎症组中呈递增趋势;Anaerostipes、Ruminiclostridium_9、Halomonas、Pelagibacterium的丰度在健康对照组、轻度炎症组、中度炎症组、重度炎症组中呈递减趋势,但差异均无统计学意义（均P＞0.05）。PICRUSt分析结果显示4组对象肠道菌群代谢通路相似,但是代谢通路的丰度不同,其中重度炎症组患者肠道菌群代谢功能潜力高于健康对照组、轻度炎症组和中度炎症组。

CAG患者肠道菌群变化的总体特征为产丁酸盐的菌属丰度减少,促炎菌属的丰度增加。促炎菌属可能通过附着于肠道上皮导致黏膜屏障受损和肠道通透性增加,影响宿主免疫反应,引起炎症。

     

Metagenomic analysis of taxonomic and functional changes in gut microbiota of patients with the alcohol dependence syndrome

The first metagenomic study of gut microbiota in patients with the alcohol dependence syndrome (ADS) has been performed in the whole-genome sequencing (“shotgun”) format. Taxonomic analysis revealed changes in the relative abundance of the predominant bacteria associated with inflammatioln (including increased levels of Ruminococcus gnavus and R. torques, and decreased levels of Faecalibacterium and Akkermansia genera). The microbiota of ADS patients was characterized by the presence of opportunistic pathogens rarely detected in metagenomes of healthy individuals from different countries. Comparative analysis of total metabolic potential revealed increased relative abundance of KEGG pathways associated with the response to oxidative stress. ADS patients also had increased levels of two specific groups of genes encoding enzymes involved in the metabolism of alcohol, as well as virulence factors. It is possible that gut microbiota of ADS patients demonstrating changes in both taxonomic and functional composition plays a role in modulating the effects of alcohol on the host body     

Alterations in the gut microbiota of patients with acquired immune deficiency syndrome

Acquired immune deficiency syndrome (AIDS), caused by infection with human immunodeficiency virus (HIV), is associated with gastrointestinal disease, systemic immune activation and changes in the gut microbiota. Here, we aim to investigate the gut microbiota patterns of HIV‐infected individuals and HIV‐uninfected individuals in populations from South China. We enrolled 33 patients with HIV (14 participants treated with highly active antiretroviral therapy [HAART] for more than 3 months; the remaining 19 individuals had not received treatment) and 35 healthy controls (HC) for a cross‐sectional comparison of gut microbiota using stool samples. Gut microbial communities were profiled by sequencing the bacterial 16S rRNA genes. Dysbiosis was more common among patients with AIDS compared with healthy individuals. Dysbiosis was characterized by decreased α‐diversity, low mean counts of Bacteroidetes, Faecalibacterium, Prevotella, Bacteroides vulgatus, Dialister and Roseburia inulnivorans, and high mean counts of Proteobacteria, Enterococcus, Streptococcus, Lactobacillus, Lachnociostridium, Ruminococcus gnavus and Streptococcus vestibularis. Increased abundance of Bacilli was observed in homosexual patients. Proteobacteria were higher among heterosexual patients with HIV infections. Tenericutes were higher among patients with history of intravenous drug abuse. Restoration of gut microbiota diversity and a significant increase in abundance of Faecalibacterium, Blautia and Bacteroides were found in patients receiving HAART compared to those who did not receive. HIV infection‐associated dysbiosis is characterized by decreased levels of α‐diversity and Bacteroidetes, increased levels of Proteobacteria and the alterations of gut microbiota correlate with the route of HIV transmission. The imbalanced faecal microbiota of HIV infection is partially restored after therapy.     

血液恶性肿瘤患者肠道菌群分析

目的 将血液恶性肿瘤患者肠道菌群与健康个体进行比较,观察血液肿瘤患者肠道菌群结构的变化,探讨肠道菌群与血液恶性肿瘤发生发展的联系。方法 收集血液恶性肿瘤患者与健康志愿者粪便样品,提取样品中菌群总DNA,然后通过变性凝胶梯度电泳（DGGE）技术分析肠道菌群多样性和差异性。结果 血液恶性肿瘤组与健康组肠道菌群的DGGE指纹图谱有明显差异。与正常组相比,患者组肠道大肠埃希菌呈现过度增长趋势,有益菌柔嫩梭菌减少或缺失,某些患者肠道内一些细菌呈现特异性增长,如粪肠球菌、硫磺肠球菌、约氏不动杆菌等。结论 与健康对照组相比,血液恶性肿瘤患者肠道菌群结构与多样性发生改变,这可能为血液恶性肿瘤早期抗感染提供实验依据。     

Comparative analysis of the gut microbiota composition between two sea snakes,Hydrophis curtus,and Hydrophis cyanocinctus

Coral Reefs - Gut microbiota plays an important role in host nutrition, metabolism, immune, and homeostasis. Although there has been extensive research on gut microbiota over the past decade, few...     

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.     

Alterations in the gut microbiota and metabolite profiles of patients with Kashin-Beck disease,an endemic osteoarthritis in China

Kashin-Beck disease (KBD) is a severe osteochondral disorder that may be driven by the interaction between genetic and environmental factors. We aimed to improve our understanding of the gut microbiota structure in KBD patients of different grades and the relationship between the gut microbiota and serum metabolites. Fecal and serum samples collected from KBD patients and normal controls (NCs) were used to characterize the gut microbiota using 16S rDNA gene and metabolomic sequencing via liquid chromatography-mass spectrometry (LC/MS). To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria in the KBD patients, metagenomic sequencing of fecal samples from grade I KBD, grade II KBD and NC subjects was performed. The KBD group was characterized by elevated levels of Fusobacteria and Bacteroidetes. A total of 56 genera were identified to be significantly differentially abundant between the two groups. The genera Alloprevotella, Robinsoniella, Megamonas, and Escherichia_Shigella were more abundant in the KBD group. Consistent with the 16S rDNA analysis at the genus level, most of the differentially abundant species in KBD subjects belonged to the genus Prevotella according to metagenomic sequencing. Serum metabolomic analysis identified some differentially abundant metabolites among the grade I and II KBD and NC groups that were involved in lipid metabolism metabolic networks, such as that for unsaturated fatty acids and glycerophospholipids. Furthermore, we found that these differences in metabolite levels were associated with altered abundances of specific species. Our study provides a comprehensive landscape of the gut microbiota and metabolites in KBD patients and provides substantial evidence of a novel interplay between the gut microbiome and metabolome in KBD pathogenesis.Subject terms: Metagenomics, Metabolomics     

Characterization of gut microbiota composition in HIV-infected patients with metabolic syndrome

Journal of Physiology and Biochemistry - The presence of metabolic syndrome (MS) per se or its separated components in HIV-infected patients contributes to an accelerated aging and increased...     

Comparative study on gut microbiota in three Anura frogs from a mountain stream

Composition and diversity in gut microbiota are impacted by a wide variety of factors. The similarity of gut microbiota in related or sympatric species has been gaining recent traction. Here, 16S rRNA gene sequencing technology was employed to study the gut microbiota of three sympatric frog species, namely Odorrana tormota, O. graminea, and Amolops wuyiensis. In these three frog species, the most abundant phylum was Proteobacteria, followed by Bacteroidetes, Verrucomicrobia, and Firmicutes. The most abundant family was Burkholderiaceae in three species. The most dominant genera were Burkholderia, Caballeronia, and Paraburkholderia with the highest relative abundance in O. tormota, O. graminea, and A. wuyiensis, respectively. No differences were observed in alpha diversity indexes among the three frog species. However, bacterial similarity of gut microbiota was significantly different between O. tormota and A. wuyiensis and between O. graminea and A. wuyiensis. Metabolism‐related gene function was predominantly enriched in the gut microbiota of the three evaluated frog species. From these findings, that the relative abundance of the gut microbiota and predicted gene functions differed in three species, we conclude that there were significant differences in the gut microbiota of the three species. Similar alpha diversity and interspecific bacterial similarity in the gut might be related to bacterial transmission among the three Anura frogs evaluated in this study.