Host genetic and environmental effects on mouse intestinal microbiota

The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.     

涠洲岛造礁石珊瑚群落变化特征及其环境影响因子

以涠洲岛造礁石珊瑚群落为研究对象,分析其群落物种组成、多样性、Raunkiaer频度和种间Spearman轶相关,探讨群落组成与水环境因子的相关性,并结合近10年来涠洲岛造礁石珊瑚变化情况,找出涠洲岛造礁石珊瑚群落的主导影响因素。结果表明：（1）近10年来涠洲岛造礁石珊瑚覆盖率显著降低,珊瑚形态组成趋于块状化,尽管珊瑚群落多样性较高,但群落分布较松散,群落结构较不稳定,部分优势种种间竞争较激烈。（2）悬浮物含量是影响石珊瑚群落最显著的环境因子。石珊瑚优势种群在不同水深中分布差异显著,泥沙覆盖率、营养盐对不同石珊瑚种群影响差异较大,大型海藻覆盖率在局部区域对优势珊瑚形成较强的竞争关系。（3）营养盐和泥沙沉积物的增加与涠洲岛近海养殖业及生活排污、海岸工程及海岸侵蚀密切相关。     

Spatial organization of intestinal microbiota in the mouse ascending colon

Complex microbial populations are organized in relation to their environment. In the intestine, the inner lining (mucosa) is a potential focal point for such organization. The proximal murine colon contains mucosal folds that are known to be associated with morphologically distinct microbes. To identify these microbes, we used the technique of laser capture microdissection (LCM) to sample microbes associated with these folds (interfold region) and within the central lumen (digesta region). Using 16S rRNA gene tag pyrosequencing, we found that microbes in the interfold region were highly enriched for the phylum Firmicutes and, more specifically, for the families Lachnospiraceae and Ruminococcaceae. Other families such as Bacteroidaceae, Enterococcaceae and Lactobacillaceae were all enriched in the digesta region. This high-resolution system to capture and examine spatial organization of intestinal microbes should facilitate microbial analysis in other mouse models, furthering our understanding of host–microbial interactions.     

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     

Host and microbiota factors that control Klebsiella pneumoniae mucosal colonization in mice

Klebsiella pneumoniae is both an opportunistic pathogen and a commensal organism. We have previously reported that K. pneumoniae strain IA565 (KpIA565) is non-pathogenic in a murine model of acute pneumonia. In this study, KpIA565 was inoculated into wild-type mice and found to stably colonize and persist in the nasal cavity and gastrointestinal tract of mice for up to 3weeks post-inoculation. Intranasal inoculation of wild-type or germ-free mice with KpIA565 resulted in similar bacterial levels in the nasal cavity, suggesting KpIA565 nasal colonization is independent of normal nasal microbiota. In contrast, KpIA565 gastrointestinal tract colonization was significantly higher in germ-free mice than in wild-type mice, indicating that members of the endogenous microbiota regulate KpIA565 colonization. In the presence of non-specific dextran sodium sulfate-induced inflammation, KpIA565 gastrointestinal tract colonization was significantly higher when compared to non-DSS treated mice. Interestingly, KpIA565 colonization was unaffected by Citrobacter rodentium-induced gastrointestinal tract inflammation. However, gastrointestinal tract colonization with K. pneumoniae strain IA565 had no impact on the inflammatory histopathology in either colitis model. This study is the first to identify and describe mechanisms influencing the growth and behavior of a murine commensal strain of K. pneumoniae.     

Changing importance of environmental factors driving secondary succession on molehills

Question: Species composition during secondary succession is influenced by a number of factors, such as soil moisture, disturbance timing and surrounding vegetation. How does the importance of these factors change over the course of succession? Methods: We set up a full‐factorial block design using molehills differing in (a) disturbance timing, (b) soil moisture and (c) composition of surrounding vegetation, and recorded the cover of all species present on the molehills over 3 years. M1ultiple regression analyses on the dissimilarity matrices of community composition and of environmental factors were applied for each of five age classes of molehills to estimate the effect of the single factors at different stages of succession. Results: The timing of disturbance did not significantly affect community composition at any stage of succession. In contrast, the effects of soil moisture and surrounding vegetation changed significantly over time, with moisture being more important at earlier stages of succession and surrounding vegetation at later stages. Conclusion: The importance of environmental factors for species composition change significantly over the course of secondary succession. Instead of aggregating the effects of environmental factors over time, future studies should consider underlying dynamics of recolonization more comprehensively.     

How environmental factors regulate mutagenesis and gene transfer in microorganisms

This review is focused on the physiological and evolutionary strategies of the processes occurring during the entry of microbial cells into stationary phase and the subsequent period of stasis. The molecular mechanisms adapting microorganisms from exponential growth to a static state involve activation and complex regulation of the stationary factor Sigma-S, which directs RNA polymerase to the specific promoters. As a result the static cells acquire general resistance (simultaneous tolerances) to different environmental stresses. In parallel with the physiological adaptation to stasis, diverse genetical processes are aimed towards resuming the growth of the static cells. Different types of mutagenesis occur: (i) in cells entering stasis and (ii) in static cells (adaptive mutagenesis). Cessation of growth induces the transient hypermutator state resulting in the accumulation of random mutations in the subpopulation of the static cells. If by chance, one or a few of such mutations lead to resumption of division, the growing cell will return to a normal mechanism of spontaneous mutagenesis. Another mechanism for generating genetical variability in stressed cells involves transposons and conjugative plasmids. Stresses can stimulate the excision of some transposons, which, in turn, can generate chromosomal mutations and activate intracellular mechanisms of mutagenesis. Under stress some conjugative plasmids activate genes encoding antirestriction proteins that repress restriction-modification systems of the recipient cells. Moreover, under stress special cellular mechanisms decrease (alleviate) the activity of restriction-modification systems which, in turn, enhance the probability of gene transfer into the stressed cells. Under stress, the efficiency of inter-species genetical barriers also decreases. This, stimulates inter-species gene transfer and may lead to a burst of incipient speciation in the population of non-growing cells. After resumption of growth the genetical barriers leading to isolation will be restored. In general, the cessation of growth “switches on”, and resumption of growth “switches off”, a set of special processes that are responsible for generating bursts of genetical variability in populations of microorganisms. This article is dedicated to the memory of Nikolai V Timofeev-Ressovsky (1900–1981).     

中国白酒发酵过程中的核心微生物群及其与环境因子的关系

【目的】揭示白酒酿造过程复杂微生物群落中的核心微生物群(core microbiota),定量分析核心微生物群的环境调控因素。【方法】通过高通量测序揭示发酵过程中的微生物群落结构,使用气相色谱-质谱联仪(GC-MS)测定发酵过程中的挥发性化合物。采用微生物群落与挥发性化合物轮廓关联分析获得风味代谢的功能微生物群(functional microbiota);通过微生物共现性网络分析,获得群落组成中的共现微生物群(co-occurring microbiota),两类微生物群的集合即为白酒酿造的核心微生物群。利用冗余分析(redundancy analysis)和蒙特卡洛置换检验(Monte Carlo permutation test)研究每个环境因素对该核心微生物群的影响。【结果】白酒发酵过程中的核心微生物群主要包含10个属,分别是Lactobacillus、Saccharomyces、Candida、Rhizopus、Saccharomycopsis、Pichia、Dipodascus、Bacillus、Thermoascus和Lactococcus。冗余分析和蒙特卡洛置换检验表明,化学因素(还原糖和乙醇)对核心微生物群的变化比物理因素(水分、温度和酸度)具有更加重要的影响作用,此外物理-化学因素的相互作用对核心微生物群的驱动也有很大的影响。【结论】本研究揭示了白酒发酵过程中的微生物群落组成和代谢物轮廓的变化规律及其二者之间的相关关系,确立了发酵过程中的核心微生物群并量化了影响核心微生物群变化的环境因素,为实现合成微生物组生产白酒及其定向调控奠定理论基础。     

Beyond genetics. Influence of dietary factors and gut microbiota on type 1 diabetes

Type 1 diabetes (T1D) is an autoimmune disease ultimately leading to destruction of insulin secreting β-cells in the pancreas. Genetic susceptibility plays an important role in T1D etiology, but even mono-zygotic twins only have a concordance rate of around 50%, underlining that other factors than purely genetic are involved in disease development. Here we review the influence of dietary and environmental factors on T1D development in humans as well as animal models. Even though data are still inconclusive, there are strong indications that gut microbiota dysbiosis plays an important role in T1D development and evidence from animal models suggests that gut microbiota manipulation might prove valuable in future prevention of T1D in genetically susceptible individuals.     

Host and viral genetics of chronic infection: a mouse model of gamma-herpesvirus pathogenesis.

A general association of human and primate lymphotropic herpesviruses (gamma-herpesviruses) with the development of lymphomas, as well as other tumors, especially in immunocompromised hosts, has been well documented. The lack of relevant small animal models for human gamma-herpesviruses has impeded progress in understanding the role of these viruses in the development of chronic disease. Recent research characterizing infection of inbred strains of mice with a murine gamma-herpesvirus, gamma-herpesvirus 68 (gammaHV68), is providing insights into viral and host factors involved in the establishment and control of chronic gamma-herpesvirus infection.     

An experimental study of old-field succession in relation to different environmental factors

From 1984 to 1986, old-field succession on sterilized sand and loam was studied under different water- and nutrient regimes. Within one month, moss and phanerogam species appeared on all experimental plots but further succession was rather varied. Salix species established quickly on loam and formed within 3 years a shrub layer up to 3 m in height. On sand, woody plant species were observed only at a high ground-water level. On loam, the well-known old-field succession from short-living therophytes to long-living phanerophytes of clearings and woodlands proceeded very quickly. In contrast, on sand, therophytes, hemicryptophytes and herbaceous chamaephytes of ruderal- and grassland communities were still dominant after three years. A high ground-water level as well as mineral fertilization had sometimes positive, sometimes negative effects on this succession. Periodic estimates of cover, made during the succession were supplemented at the end of the experiment by the measurements of phytomass and bioelement storage. The highest amount of biomass was measured on the three loamy soils where shrub layers were well developed. In comparison with data published elsewhere, the above-ground biomass of 2.2–2.8 kg dry matter m^-2 and the below-ground biomass up to 7.2 kg dry matter m^-2 were both extraordinarily high. Over the three years, the vegetation on sandy soils accumulated between 1.2 and 5.1 g N m^-2 yr^-1 and on loamy soils between 17.1 and 24.7 g N m^-2 yr^-1.     

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.     

Neighbourhood interactions and environmental factors influencing old‐pasture succession in the Central Pyrenees

Abstract. The shrub Buxus sempervirens and the trees Abies alba and Fagus sylvatica have recently recolonized old‐pastures in the Central Pyrenees. We mapped all live and dead individuals (> 1.3 m tall) in a large forest plot in Ordesa Valley to examine the importance of density‐dependent processes during recolonization. Biotic interactions were inferred from changes in horizontal structure and the influences of neighbours on tree survival. Buxus differentially influenced establishment and survival of tree species, thereby controlling future canopy composition and spatial structure. The rapidly invading Abies formed denser patches on elevated sites less occupied by Buxus, whereas Fagus preferentially established within shrubs. Abies reached densities which led to intense intraspecific competition and high mortality rates among saplings. Self‐thinning in Abies led to smaller numbers of regularly spaced survivors, and greater relative dominance of Fagus. Disregarding intraspecific effects and abiotic environment, Abies survival was significantly lower under Buxus shrubs, which suggests that the spatial location and abundance of Abies was constrained by the location of Buxus. Fagus survival was not related to Buxus density, but remained significantly lower in denser Abies patches. The higher mortality of Fagus in denser Abies patches, and the resulting spatial segregation of the species, reflects asymmetric interspecific competition. Inhibition from Buxus shrubs and intraspecific competition prevent invading Abies from dominating and may therefore help in maintaining a mixed Abies‐Fagus stand.     

仔猪结肠中产甲烷菌群多样性及其与环境因子的相关性

【目的】为评价仔猪结肠中产甲烷菌群多样性及其与环境因子(日粮类型、断奶应激及日龄)的相关性。【方法】分别采集了7、14、21、24和35日龄仔猪结肠内容物,进行基因组总DNA的提取,运用变性梯度凝胶电泳(Denaturing gradient gel electrophoresis,DGGE)技术分析各结肠样总DNA的产甲烷菌的PCR产物,同时研究了与甲烷生成相关的结肠内挥发性脂肪酸(Volatile fatty acid,VFA)的变化情况。【结果】结果表明,仔猪结肠内容物中乙酸、丙酸和总挥发性脂肪酸(Total volatile fatty acid,TVFA)浓度随日龄增加而显著升高(P<0.05),但丁酸浓度未有显著性变化(P>0.05);基于Dice模式的UPGMA聚类分析的DGGE指纹图谱结果显示,7-24日龄结肠样的产甲烷菌群落结构相似性较高,聚集到一个分支上;而35日龄的结肠样聚集到另一分支上;冗余分析(Redundancy analysis,RDA)结果表明,日龄和日粮类型与产甲烷菌群落结构的关联度较高;序列分析表明,仔猪结肠食糜中甲烷菌群主要以甲烷短杆菌为主,同时存在另一类未知甲烷菌。【结论】本研究表明,甲烷短杆菌是仔猪结肠中的优势产甲烷菌,日龄和日粮类型与仔猪结肠中产甲烷菌群落结构的相关性最强。