High-fat diet alters gut microbiota physiology in mice

The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by high-calorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by Fourier-transform infrared- (FT-IR) and Raman micro-spectroscopy and (iii) metaproteome and metabolome via high-resolution mass spectrometry. High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the impact of the diet on cecal chemical fingerprints is greater than the impact of microbiota composition. Diet-driven changes in biochemical fingerprints of members of the Bacteroidales and Lachnospiraceae were also observed at the level of single cells, indicating that there were distinct differences in cellular composition of dominant phylotypes under different diets. Metaproteome and metabolome analyses based on the occurrence of 1760 bacterial proteins and 86 annotated metabolites revealed distinct HF diet-specific profiles. Alteration of hormonal and anti-microbial networks, bile acid and bilirubin metabolism and shifts towards amino acid and simple sugars metabolism were observed. We conclude that a HF diet markedly affects the gut bacterial ecosystem at the functional level.     

心肌缺血再灌注手术改变炎症相关肠道菌群

目的 探讨心肌缺血再灌注损伤对大鼠肠道菌群结构特征的影响。 方法 18只雄性Sprague Dawley大鼠随机分为假手术组(n=7)和模型组(n=11),分别对大鼠冠状动脉左前降支进行结扎和再灌注。再灌注60 min后,通过TTC染色检测总梗死面积,H&E染色和免疫组织化学观察炎症细胞浸润情况、16S rRNA高通量测序分析心肌缺血前和再灌注后粪便中微生物的结构组成变化。 结果 与假手术组相比,模型组心肌梗死面积增加,心肌中炎症细胞浸润以及CD68阳性巨噬细胞明显增多,变形菌门(Proteobacteria)的相对丰度增加,厚壁菌门(Firmicutes)的相对丰度降低。 结论 心肌缺血再灌注损伤改变了肠道菌群的分布,这可能与促进了受损心脏的炎症细胞浸润有关。     

Host genetic determinants of the gut microbiota of wild mice

Identifying a common set of genes that mediate host–microbial interactions across populations and species of mammals has broad relevance for human health and animal biology. However, the genetic basis of the gut microbial composition in natural populations remains largely unknown outside of humans. Here, we used wild house mouse populations as a model system to ask three major questions: (a) Does host genetic relatedness explain interindividual variation in gut microbial composition? (b) Do population differences in the microbiota persist in a common environment? (c) What are the host genes associated with microbial richness and the relative abundance of bacterial genera? We found that host genetic distance is a strong predictor of the gut microbial composition as characterized by 16S amplicon sequencing. Using a common garden approach, we then identified differences in microbial composition between populations that persisted in a shared laboratory environment. Finally, we used exome sequencing to associate host genetic variants with microbial diversity and relative abundance of microbial taxa in wild mice. We identified 20 genes that were associated with microbial diversity or abundance including a macrophage‐derived cytokine (IL12a) that contained three nonsynonymous mutations. Surprisingly, we found a significant overrepresentation of candidate genes that were previously associated with microbial measurements in humans. The homologous genes that overlapped between wild mice and humans included genes that have been associated with traits related to host immunity and obesity in humans. Gene–bacteria associations identified in both humans and wild mice suggest some commonality to the host genetic determinants of gut microbial composition across mammals.     

Ambient temperature alters body size and gut microbiota of Xenopus tropicalis

Temperature is important to determine physiological status of ectotherms. However, it is still not fully understood how amphibians and their symbiotic microbiota acclimate to ambient temperature. In this study, we investigated the changes of gut microbiota of Xenopus tropicalis at different temperatures under controlled laboratory conditions. The results showed that microbial communities were distinct and shared only a small overlap among froglet guts, culture water and food samples.Furthermore, the dominant taxa harbored in the gut exhibited low relative abundance in water and food. It indicates that bacterial taxa selected by amphibian gut were generally of low abundance in the external environment. Temperature could affect betadiversity of gut microbiota in terms of phylogenetic distance, but it did not affect alpha diversity. The composition of gut microbiota was similar in warm and cool treatments. However, signature taxa in different temperature environments were identified. The relationships between temperature, gut microbiota and morphology traits of X. tropicalis revealed in this study help us to predict the consequences of environmental changes on ectothermic animals.     

Gut-liver axis: gut microbiota in shaping hepatic innate immunity

Gut microbiota play an essential role in shaping immune cell responses. The liver was continuously exposed to metabolic products of intestinal commensal bacterial through portal vein and alteration of gut commensal bateria was always associated with increased risk of liver inflammation and autoimmune disease. Considered as a unique immunological organ, the liver is enriched with a large number of innate immune cells. Herein, we summarize the available literature of gut microbiota in shaping the response of hepatic innate immune cells including NKT cells, NK cells, γδ T cells and Kupffer cells during health and disease. Such knowledge might help to develop novel and innovative strategies for the prevention and therapy of innate immune cell-related liver disease.     

Polydatin alleviates bleomycin-induced pulmonary fibrosis and alters the gut microbiota in a mouse model

To investigate the effect and mechanism of polydatin on bleomycin (BLM)-induced pulmonary fibrosis in a mouse model. The lung fibrosis model was induced by BLM. The contents of TNF-α, LPS, IL-6 and IL-1β in lung tissue, intestine and serum were detected by ELISA. Gut microbiota diversity was detected by 16S rDNA sequencing; R language was used to analyse species composition, α-diversity, β-diversity, species differences and marker species. Mice were fed drinking water mixed with four antibiotics (ampicillin, neomycin, metronidazole, vancomycin; antibiotics, ABx) to build a mouse model of ABx-induced bacterial depletion; and faecal microbiota from different groups were transplanted into BLM-treated or untreated ABx mice. The histopathological changes and collagen I and α-SMA expression were determined. Polydatin effectively reduced the degree of fibrosis in a BLM-induced pulmonary fibrosis mouse model; BLM and/or polydatin affected the abundance of the dominant gut microbiota in mice. Moreover, faecal microbiota transplantation (FMT) from polydatin-treated BLM mice effectively alleviated lung fibrosis in BLM-treated ABx mice compared with FMT from BLM mice. Polydatin can reduce fibrosis and inflammation in a BLM-induced mouse pulmonary fibrosis model. The alteration of gut microbiota by polydatin may be involved in the therapeutic effect.     

Current understanding on the roles of gut microbiota in fish disease and immunity

正Intensive aquaculture has increased the severity and frequency of fish diseases. Given the functional importance of gut microbiota in various facets of host physiology, modulation of this microbiota is a feasible strategy to mitigate emerging diseases in aquaculture. To achieve this, a fundamental understanding of the interplay among fish health, microbiota,and invading pathogens is required. This commentary focuses on current knowledge regarding the associations between fish diseases, dysbiosis of gut microbiota, and immune responses.Furthermore, updated research on fish disease from an ecological perspective is discussed, including colonization     

A review on the interactions between gut microbiota and innate immunity of fish

Although fish immunology has progressed in the last few years, the contribution of the normal endogenous microbiota to the overall health status has been so far underestimated. In this context, the establishment of a normal or protective microbiota constitutes a key component to maintain good health, through competitive exclusion mechanisms, and has implications for the development and maturation of the immune system. The normal microbiota influences the innate immune system, which is of vital importance for the disease resistance of fish and is divided into physical barriers, humoral and cellular components. Innate humoral parameters include antimicrobial peptides, lysozyme, complement components, transferrin, pentraxins, lectins, antiproteases and natural antibodies, whereas nonspecific cytotoxic cells and phagocytes (monocytes/macrophages and neutrophils) constitute innate cellular immune effectors. Cytokines are an integral component of the adaptive and innate immune response, particularly IL-1 beta, interferon, tumor necrosis factor-alpha, transforming growth factor-beta and several chemokines regulate innate immunity. This review covers the innate immune mechanisms of protection against pathogens, in relation with the installation and composition of the normal endogenous microbiota in fish and its role on health. Knowledge of such interaction may offer novel and useful means designing adequate therapeutic strategies for disease prevention and treatment.     

Host immunity and pathogen strain contribute to intestinal disaccharidase impairment following gut infection

Infection or other inflammatory insults in the small intestine often result in reduced disaccharidase enzyme levels. Using a mouse model of giardiasis, we examined the role of host immunity and pathogen virulence in mediating disaccharidase deficiency postinfection (p.i.). C57BL/6J mice were infected with two strains, WB and GS, of the human parasite Giardia duodenalis. The levels of sucrase, maltase, and lactase decreased in wild-type mice p.i. with the GS strain but not with the WB strain. Both CD4-deficient and SCID mice failed to eliminate the infection and did not exhibit disaccharidase deficiency. β(2)-Microglobulin knockout animals controlled infections similar to wild-type mice but exhibited no decrease in disaccharidase activity. Analysis of cytokine production by spleen and mesenteric lymph node cells showed production of IL-4, IL-10, IL-13, IL-17, IL-22, TNF-α, and IFN-γ p.i. with both WB and GS, with IFN-γ being the dominant cytokine for both parasite strains. Mesenteric lymph node cells produced lower levels of cytokines compared with splenocytes in response to parasite extract, although the overall pattern was similar. These data suggest that T cell responses mediate parasite clearance whereas also contributing to pathogenesis. They also demonstrate that differences in pathogen strain can also determine the outcome of infection and further our understanding of the clinical variation seen in human giardiasis.     

Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts

Humans are colonized by a diverse collection of microbes, the largest numbers of which reside in the distal gut. The vast majority of humans coexist in a beneficial equilibrium with these microbes. However, disruption of this mutualistic relationship can manifest itself in human diseases such as inflammatory bowel disease. Thus the study of inflammatory bowel disease and its genetics can provide insight into host pathways that mediate host-microbiota symbiosis. Bacteria of the human intestinal ecosystem face numerous challenges imposed by human dietary intake, the mucosal immune system, competition from fellow members of the gut microbiota, transient ingested microbes and invading pathogens. Considering features of human resident gut bacteria provides the opportunity to understand how microbes have achieved their symbiont status. While model symbionts have provided perspective into host-microbial homeostasis, high-throughput approaches are becoming increasingly practical for functionally characterizing the gut microbiota as a community.     

New insights into the interactions between Blastocystis,the gut microbiota,and host immunity

The human gut microbiota is a diverse and complex ecosystem that is involved in beneficial physiological functions as well as disease pathogenesis. Blastocystis is a common protistan parasite and is increasingly recognized as an important component of the gut microbiota. The correlations between Blastocystis and other communities of intestinal microbiota have been investigated, and, to a lesser extent, the role of this parasite in maintaining the host immunological homeostasis. Despite recent studies suggesting that Blastocystis decreases the abundance of beneficial bacteria, most reports indicate that Blastocystis is a common component of the healthy gut microbiome. This review covers recent finding on the potential interactions between Blastocystis and the gut microbiota communities and its roles in regulating host immune responses.     

老年结直肠癌患者肠道菌群变化与机体免疫炎症营养相关性

目的探讨老年结直肠癌患者肠道菌群变化与机体免疫、炎症、营养指标的相关性,为结直肠癌的防治提供参考。方法纳入2016年1月至2018年6月在我院接受治疗的老年结直肠癌患者30例和同期健康查体的老年人群30例,收集粪便标本,采用FloraCheck~(TM)高通量测序技术对粪便样本中所有细菌的16S rRNA V3-V4区进行DNA测序,序列通过MiSeq 16S宏基因组APP及QIIME软件,分析两组人群间属水平上显著差异性菌群。比较两组人群炎性指标(TNF-α、IL-6、IL-1、IL-12)、营养指标(总蛋白、白蛋白、前白蛋白、转铁蛋白)和免疫指标(CD3~+、CD4~+、CD8~+、NK)的差异。分析老年结直肠癌患者肠道菌群变化与营养、炎症、免疫的内在联系。结果老年结直肠癌组和老年健康组人群免疫指标CD3~+、CD4~+、CD8~+、NK和CD4~+/CD8~+比较差异无统计学意义;炎性指标老年结直肠癌组TNF-α含量较对照组明显增高(t=3.769,P=0.001),两组人群IL-1、IL-6、IL-12比较差异无统计学意义;营养指标老年结直肠癌组白蛋白、前白蛋白较对照组明显下降(t=-4.107,P=0.001;t=-4.366,P=0.001),两组人群总蛋白、转铁蛋白比较差异无统计学意义。老年结直肠癌组肠道差异性菌属变化,包括Eubacterium、Ruminococcaceae_UCG-002、Peptostreptococcus、Porphyromonas和部分炎症指标、营养指标、免疫指标有明显相关性。结论老年结直肠癌患者肠道菌群结构和功能异常,可能是导致患者机体免疫损伤、炎症反应、营养不佳的主要原因之一。有针对性地对肠道菌群结构进行优化,改善肠道菌群对宿主的影响,是一种帮助老年结直肠癌患者促进健康的策略。     

Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity

The gut microbiota is a complex ecological community that plays multiple critical roles within a host. Known intrinsic and extrinsic factors affect gut microbiota structure, but the influence of host genetics is understudied. To investigate the role of host genetics upon the gut microbiota structure, we performed a longitudinal study in which we evaluated the hindgut microbiota and its association with animal growth and immunity across life. We evaluated three different growth stages in an Angus-Brahman multibreed population with a graduated spectrum of genetic variation, raised under variable environmental conditions and diets. We found the gut microbiota structure was changed significantly during growth when preweaning, and fattening calves experienced large variations in diet and environmental changes. However, regardless of the growth stage, we found gut microbiota is significantly influenced by breed composition throughout life. Host genetics explained the relative abundances of 52.2%, 40.0%, and 37.3% of core bacterial taxa at the genus level in preweaning, postweaning, and fattening calves, respectively. Sutterella, Oscillospira, and Roseburia were consistently associated with breed composition at these three growth stages. Especially, butyrate-producing bacteria, Roseburia and Oscillospira, were associated with nine single-nucleotide polymorphisms (SNPs) located in genes involved in the regulation of host immunity and metabolism in the hindgut. Furthermore, minor allele frequency analysis found breed-associated SNPs in the short-chain fatty acids (SCFAs) receptor genes that promote anti-inflammation and enhance intestinal epithelial barrier functions. Our findings provide evidence of dynamic and lifelong host genetic effects upon gut microbiota, regardless of growth stages. We propose that diet, environmental changes, and genetic components may explain observed variation in critical hindgut microbiota throughout life.Subject terms: Microbiome, Agricultural genetics     

肠道微生物与昆虫的共生关系

昆虫肠道栖息着大量的微生物。随着近年来研究肠道微生物的方法不断进步,尤其是基于16S rDNA的分子生物学方法的应用,人们对肠道微生物的了解逐渐加深。昆虫肠道对于微生物的拓殖存在一定的选择作用。肠道微生物对昆虫寄主的作用包括提供营养、利用拓殖抗性抵抗外来微生物侵袭、参与多重营养关系、引起昆虫免疫反应。长期进化过程中肠道微生物与昆虫发展出紧密的共生关系,微生物发展出一系列手段适应昆虫肠道环境。文章从以上几个方面对近年来的研究进展进行总结,并对昆虫肠道微生态学的实践意义和将来可能的研究热点进行展望。     

The gut microbiota: challenging immunology

For several decades the intestinal microbiota was mainly studied by those investigating infections and diseases associated with gut health, usually from a microbiology point of view. In the past few years, however, it has become apparent that the intestinal microbiota has widespread implications in the field of immunology, and researchers are being compelled to explain how the microbiota contributes to and/or affects their studies.     

The active human gut microbiota differs from the total microbiota

The human gut microbiota is considered one of the most fascinating reservoirs of microbial diversity hosting between 400 to 1000 bacterial species distributed among nine phyla with Firmicutes, Bacteroidetes and Actinobacteria representing around 75% of the diversity. One of the most intriguing issues relates to understanding which microbial groups are active players in the maintenance of the microbiota homeostasis.Here, we describe the diversity of active microbial fractions compared with the whole community from raw human fecal samples. We studied four healthy volunteers by 16S rDNA gene pyrosequencing. The fractions were obtained by cell sorting based on bacterial RNA concentration. Bacterial families were observed to appear or disappear on applying a cell sorting method in which flow cytometry was used to evaluate the active cells by pyronin-Y staining of RNA. This method was able to detect active bacteria, indicating that the active players differed from that observed in raw fecal material. Generally, observations showed that in the active fractions, the number of reads related to Bacteroidetes decreased whereas several families from Clostridiales (Firmicutes) were more highly represented. Moreover, a huge number of families appeared as part of the active fraction when cell sorting was applied, indicating reads that are simply statistically hidden by the total reads.     

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.