强化玉米饮食对小鼠肠道菌群结构和功能的影响

【目的】采用高通量测序方法研究强化玉米饮食对小鼠肠道菌群结构的影响以及可提高宿主糖代谢相关菌群功能基因的分析。【方法】分别给予两组小鼠(各10只)常规饮食和强化玉米饮食(1/4的玉米粉加3/4的常规饮食成分),喂养10周,之后采集小鼠粪便样本,提取DNA,使用高通量测序仪进行宏基因组测序分析,比较两组小鼠肠道菌群和功能基因的差异。【结果】两组小鼠的终末体重没有明显差异。各样本DNA的测序有效率足够,肠道菌群的多样性存在一定差异。属放线菌门(Actinobacteria)的双歧杆菌(Bifidobacteriales)-B.pseudolongum分支和Coriobacteriia-Collinsella/Enterorhabdus分支的丰度在强化玉米饮食组的小鼠中显著升高,相应的宏基因组中涉及糖酵解和胆汁酸合成的一些酶和功能单元的含量也在强化玉米饮食组显著升高。【结论】强化玉米饮食可以提高肠道菌群中双歧杆菌等益生菌的丰度,增加宏基因组糖脂代谢相关基因和通路的含量,从而可能促进宿主的糖代谢功能。     

Seed dispersal of alien and native plants by vertebrate herbivores

Seed dispersal is crucial for the success and spread of alien plants. Herbivores often establish a dual relationship with plants: antagonist, through herbivory, and mutualist, through seed dispersal. By consuming plants, herbivores may disperse large amounts of seeds, and can facilitate the spread of alien plants. However, seed dispersal of alien plants by herbivores has been largely uninvestigated. I studied factors associated with dispersal of alien and native seeds by the three most important vertebrate herbivores in SW Australia: emus (Dromaius novaehollandia), western grey kangaroos (Macropus fuliginosus) and European rabbits (Oryctolagus cuniculus). Overall frequencies of alien and native seeds dispersed by these herbivores were determined by differences among them in (1) the plant groups they predominantly disperse, that differed in frequencies of aliens versus natives, and (2) the predominant dispersal of aliens or natives within those plant groups. Emus and kangaroos (natives) tended to disperse predominantly alien seeds within plant groups (defined by life forms, dispersal syndromes, and diaspore size), whereas rabbits (alien) tended to disperse predominantly natives. This agrees with the hypothesis that herbivores will use predominantly plants that have evolved in different areas, because of less effective defences against new enemies. Overall frequencies were consistent with this pattern in kangaroos and rabbits, but not in emus. Kangaroos dispersed mostly plant groups that were mainly aliens (herbaceous species and small and medium sized dispersal units and seeds), which together with their predominant use of aliens over natives within groups resulted in the highest overall frequency of alien seeds (73%). Rabbits were similar to kangaroos in the type of plants dispersed, but their predominant use of natives over aliens within groups contributed to an overall predominance of native seeds in their pellets (88%). Emus dispersed mostly plant groups that were mainly natives (e.g. woody species with big diaspores), resulting in low overall frequency of alien seeds (11%), despite their predominant use of aliens over natives within plant groups. Thus, the within-groups trend pointed to a facilitative role of native herbivores of plant invasions through seed dispersal, but was obscured by the different use by herbivores of plant groups with different frequency of aliens.     

Diet selection by vertebrate herbivores in the high arctic of Greenland

Microhistological analysis of fecal droppings indicates that graminoids (sedges, grasses, and rushes) and the only willow present, Salix arctica , are primary food items of the muskox Ovibos moschatus , arctic hare Lepus arcticus , and collared lemming Dicrostonyx groenlandicus in northern Greenland (79°-83°N). Plant biomass available during the peak growing season varied with vegetation types from < 2 g m⁻² in polar barrens to 34 g m⁻² in sedge fens. The clustered distribution of vegetation minimizes competition among vertebrate herbivores.     

Optimal diet choice for large herbivores: an extended contingency model

1. A more general contingency model of optimal diet choice is developed, allowing for simultaneous searching and handling, which extends the theory to include grazing and browsing by large herbivores.
2. Foraging resolves into three modes: purely encounter-limited, purely handling-limited and mixed-process, in which either a handling-limited prey type is added to an encounter-limited diet, or the diet becomes handling-limited as it expands.
3. The purely encounter-limited diet is, in general, broader than that predicted by the conventional contingency model.
4. As the degree of simultaneity of searching and handling increases, the optimal diet expands to the point where it is handling-limited, at which point all inferior prey types are rejected.
5. Inclusion of a less profitable prey species is not necessarily independent of its encounter rate and the zero-one rule does not necessarily hold: some of the less profitable prey may be included in the optimal diet. This gives an optimal foraging explanation for herbivores' mixed diets.
6. Rules are shown for calculating the boundary between encounter-limited and handling-limited diets and for predicting the proportion of inferior prey to be included in a two-species diet.
7. The digestive rate model is modified to include simultaneous searching and handling, showing that the more they overlap, the more the predicted diet-breadth is likely to be reduced.     

放牧家畜食性选择机制研究进展

动物的食性选择是一个十分复杂的主题.本文从不同角度,结合多学科的研究成果对放牧家畜食性选择机制问题进行了阐述：1）食性选择行为发生的机制,包括基于遗传和学习两方面的解释,其中动物具有的学习机制主要有来自动物个体的学习（采食后反馈、试错学习）、向其他社会群体的学习,以及在进行斑块、景观水平选择时,所采用的空间记忆、视觉线索和皮肤防御系统机制等;2）放牧家畜食性选择策略的4个综合性假说：经验法则、边际值法则、优化采食理论、最小总不适感概念;3）食性选择机制研究存在的问题与展望,诸如空间尺度问题、动物消化生理因素以及多因素互作研究的不足等.     

Stability of plant defense proteins in the gut of insect herbivores

Plant defense against insect herbivores is mediated in part by enzymes that impair digestive processes in the insect gut. Little is known about the evolutionary origins of these enzymes, their distribution in the plant kingdom, or the mechanisms by which they act in the protease-rich environment of the animal digestive tract. One example of such an enzyme is threonine (Thr) deaminase (TD), which in tomato (Solanum lycopersicum) serves a dual role in isoleucine (Ile) biosynthesis in planta and Thr degradation in the insect midgut. Here, we report that tomato uses different TD isozymes to perform these functions. Whereas the constitutively expressed TD1 has a housekeeping role in Ile biosynthesis, expression of TD2 in leaves is activated by the jasmonate signaling pathway in response to herbivore attack. Ingestion of tomato foliage by specialist (Manduca sexta) and generalist (Trichoplusia ni) insect herbivores triggered proteolytic removal of TD2's C-terminal regulatory domain, resulting in an enzyme that degrades Thr without being inhibited through feedback by Ile. This processed form (pTD2) of TD2 accumulated to high levels in the insect midgut and feces (frass). Purified pTD2 exhibited biochemical properties that are consistent with a postingestive role in defense. Shotgun proteomic analysis of frass from tomato-reared M. sexta identified pTD2 as one of the most abundant proteins in the excrement. Among the other tomato proteins identified were several jasmonate-inducible proteins that have a known or proposed role in anti-insect defense. Subtilisin-like proteases and other pathogenesis-related proteins, as well as proteins of unknown function, were also cataloged. We conclude that proteomic analysis of frass from insect herbivores provides a robust experimental approach to identify hyperstable plant proteins that serve important roles in defense.     

Experience influences diet mixing by herbivores: implications for plant biochemical diversity

We often assume the intrinsic value of a food or habitat is similar for individuals of a species and above a certain threshold density more profitable foods should always be preferred over less profitable foods. Nevertheless, individual herbivores differ in their preferences for foods due in part to experience, and experience in variable environments is variable. In this report, we show that how sheep learned about their foraging environment was crucial to the development of their dietary habits, and that experience with foods that contained plant secondary metabolites (PSM) markedly enhanced their use of PSM-containing foods, even when familiar, nutritious alternatives were available ad libitum. Lambs who learned to eat foods that contained either tannins, terpenes, or oxalates ate more when they could select two of the foods offered simultaneously (tannins-terpenes, tannins-oxalates, or terpenes-oxalates) than when they were offered only one food. Lambs offered foods containing all three toxins ate more than lambs offered two of the toxins, and their intake was comparable to lambs offered the food that contained no toxins. Experience and the availability of nutritious alternatives both influenced food choice when the preferences of lambs with 3 months’ experience mixing tannin, terpenes, and oxalates were compared with lambs naive to the toxin-containing foods. During these studies, all lambs were offered five foods, two of them familiar to all of the lambs (ground alfalfa and a 50:50 mix of ground alfalfa:ground barley) and three of them familiar only to experienced lambs (a ground ration containing either tannins, terpenes, or oxalates). Half of the lambs were offered the familiar foods ad libitum, while half of the lambs were offered only 200 g of each familiar food daily. Throughout the study, naive lambs ate much less of the foods with toxins if they had ad libitum as opposed to restricted access to the nutritious alternatives (66 vs 549 g d⁻¹). Experienced lambs also ate less of the foods with toxins if they had ad libitum, as opposed to restricted, access to the nutritious alternatives (809 vs 1497 g d⁻¹). In both cases, however, lambs with experience ate remarkably more than naive lambs of the foods containing the toxins, whether access to the alfalfa-barley alternatives was ad libitum (811 vs 71 g d⁻¹) or restricted (1509 vs 607 g d⁻¹). These differences in food preferences and intake persisted during trials 8 months later. Plant communities offer a diverse matrix of biochemicals to herbivores, which may produce an array of interactions not accounted for by the traditional approach of studying nutrients and plant secondary metabolites (PSM) in isolation. How herbivores experience nutrient-PSM interactions may influence defoliation patterns and the potential for plant survival within plant communities. Thus, learning to mix foods that differ in kinds and concentrations of nutrients and PSM can enhance diet breadth and promote more uniform use of all plants in a community, which can influence the structure and function of ecosystems. Conversely, lack of experience learning to eat a variety of foods can diminish diet breadth and result in less uniform use of plants in a community.     

Chemocommunication between bacteria and the higher vertebrate animals

Between bacteria and the higher vertebrate animals there are close chemocommunicational connections that are realized via signal molecules secreted by bacteria, on the hand, and vertebrate hormones and hormone-like substances, on the other hand. The review presents data on regulatory effects of biogenic amines (catecholamines and serotonin), peptide hormones, and immunoregulator of the higher vertebrates on the vitally important functions of bacterial cells, their virulence and survivability. It has been shown that some bacterial signal molecules, such as N-acylated derivatives of homoserine lactones, also are able to regulate fundamental cellular processes in the higher vertebrates. Deciphering of molecular mechanisms of information exchange between bacteria and the higher vertebrates is both of theoretical significance for studies on pathways of evolution of chemosignal systems in proand eukaryote organism and of practical significance for development of new approaches for treatment of bacterial infections.     

Problems with measuring diet selection of terrestrial,mammalian herbivores

Abstract The validity of methods used to measure diet selection has often been overlooked. This paper examines problems associated with the scale of food availability, perception of food by animals, measures of dietary composition, measures of food availability and diet selection indices. Most problems can be reduced by the choice of techniques consistent with the objective and degree of accuracy required, both of which should be clearly stated. In particular, the measured sample of food utilized by the animal should be spatially and temporally matched to the scale of food availability under consideration. In the past, researchers have tended to overstate the accuracy of their results. We support the view that the most appropriate analysis of diet selection is ranking food items in order of selection according to the value of the selection index.     

Comparative structure analysis of vertebrate ribonuclease P RNA.

Ribonuclease P cleaves 5'-precursor sequences from pre-tRNAs. All cellular RNase P holoenzymes contain homologous RNA elements; the eucaryal RNase P RNA, in contrast to the bacterial RNA, is catalytically inactive in the absence of the protein component(s). To understand the function of eucaryal RNase P RNA, knowledge of its structure is needed. Considerable effort has been devoted to comparative studies of the structure of this RNA from diverse organisms, including eucaryotes, primarily fungi, but also a limited set of vertebrates. The substantial differences in the sequences and structures of the vertebrate RNAs from those of other organisms have made it difficult to align the vertebrate sequences, thus limiting comparative studies. To expand our understanding of the structure of diverse RNase P RNAs, we have isolated by PCR and sequenced 13 partial RNase P RNA genes from 11 additional vertebrate taxa representing most extant major vertebrate lineages. Based on a recently proposed structure of the core elements of RNase P RNA, we aligned the sequences and propose a minimum consensus secondary structure for the vertebrate RNase P RNA.     

Worlds within worlds: evolution of the vertebrate gut microbiota

In this Analysis we use published 16S ribosomal RNA gene sequences to compare the bacterial assemblages that are associated with humans and other mammals, metazoa and free-living microbial communities that span a range of environments. The composition of the vertebrate gut microbiota is influenced by diet, host morphology and phylogeny, and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut microbiota is different from free-living communities that are not associated with animal body habitats. We propose that the recently initiated international Human Microbiome Project should strive to include a broad representation of humans, as well as other mammalian and environmental samples, as comparative analyses of microbiotas and their microbiomes are a powerful way to explore the evolutionary history of the biosphere.     

Differences in tolerance of pondweeds and charophytes to vertebrate herbivores in a shallow Baltic estuary

It has been suggested that herbivorous waterfowl may be important in shaping aquatic plant communities in shallow wetlands. As such, a shift from canopy forming pondweeds to bottom-dwelling charophytes in a formerly turbid pondweed dominated lake has been partly attributed to waterfowl herbivory. Here we study the separate and combined effects of both belowground herbivory in spring by whooper swans and Bewick ‘s swans, and grazing in summer by waterfowl and fish on the community composition in a shallow Baltic estuary during one year. The macrophyte community was dominated by charophytes (mainly Chara aspera) with Potamogeton pectinatus and Najas marina present as subdominants. Other species were rare. Both spring and summer herbivory had no effect on total plant biomass. However, P. pectinatus was more abundant in plots that were closed to spring and summer herbivores. N. marina was more abundant in grazed plots, whereas Chara spp. biomass remained unaffected. Probably belowground propagules of both C. aspera and P. pectinatus were consumed by swans but since C. aspera bulbils were numerous it may have compensated for the losses. P. pectinatus may not have fully recovered from foraging on tubers and aboveground biomass. Our results are in line with other studies in Chara dominated lakes, which found no effect of grazing on summer aboveground Chara biomass, whereas several studies report strong effects of herbivory in lakes dominated by P. pectinatus.     

Influence of dietary aconitine and nicotine on the gut microbiota of two lepidopteran herbivores

The gut microbiota plays an important role in pheromone production, pesticide degradation, vitamin synthesis, and pathogen prevention in the host animal. Therefore, similar to gut morphology and digestive enzyme activity, the gut microbiota may also get altered under plant defensive compound-induced stress. To test this hypothesis, Dendrolimus superans larvae were fed either aconitine- or nicotine-treated fresh leaves of Larix gmelinii, and Lymantria dispar larvae were fed either aconitine- or nicotine-treated fresh leaves of Salix matsudana. Subsequently, the larvae were sampled 72hr after diet administration and DNA extracted from larval enteric canals were employed for gut microbial 16S ribosomal RNA gene sequencing (338 F and 806 R primers). The sequence analysis revealed that dietary nicotine and aconitine influenced the dominant bacteria in the larval gut and determined their abundance. Moreover, the effect of either aconitine or nicotine on D. superans and L. dispar larvae had a greater dependence on insect species than on secondary plant metabolites. These findings further our understanding of the interaction between herbivores and host plants and the coevolution of plants and insects.     

Genome sequence of the vertebrate gut symbiont Lactobacillus reuteri ATCC 53608

Lactobacillus reuteri, inhabiting the gastrointestinal tracts of a range of vertebrates, is a true symbiont with effects established as beneficial to the host. Here we describe the draft genome of L. reuteri ATCC 53608, isolated from a pig. The genome sequence provides important insights into the evolutionary changes underlying host specialization.     

Diversity and resilience of the wood‐feeding higher termite Mironasutitermes shangchengensis gut microbiota in response to temporal and diet variations

Termites are considered among the most efficient bioreactors, with high capacities for lignocellulose degradation and utilization. Recently, several studies have characterized the gut microbiota of diverse termites. However, the temporal dynamics of the gut microbiota within a given termite with dietary diversity are poorly understood. Here, we employed 16S rDNA barcoded pyrosequencing analysis to investigate temporal changes in bacterial diversity and richness of the gut microbiota of wood‐feeding higher termite Mironasutitermes shangchengensis under three lignocellulose content‐based diets that feature wood, corn stalks, and filter paper. Compositions of the predominant termite gut residents were largely constant among the gut microbiomes under different diets, but each diet caused specific changes in the bacterial composition over time. Notably, microbial communities exhibited an unexpectedly strong resilience during continuous feeding on both corn stalks and filter paper. Members of five bacterial phyla, that is, Spirochaetes, Firmicutes, Actinobacteria, Tenericutes, and Acidobacteria, were strongly associated with the resilience. These findings provide insights into the stability of the gut microbiota in higher termites and have important implications for the future design of robust bioreactors for lignocellulose degradation and utilization.     

The influence of diet on the gut microbiota and its consequences for health

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Secondary structure of vertebrate telomerase RNA

Telomerase is a ribonucleoprotein enzyme that maintains telomere length by adding telomeric sequence repeats onto chromosome ends. The essential RNA component of telomerase provides the template for telomeric repeat synthesis. To determine the secondary structure of vertebrate telomerase RNA, 32 new telomerase RNA genes were cloned and sequenced from a variety of vertebrate species including 18 mammals, 2 birds, 1 reptile, 7 amphibians, and 4 fishes. Using phylogenetic comparative analysis, we propose a secondary structure that contains four structural domains conserved in all vertebrates. Ten helical regions of the RNA are universally conserved while other regions vary significantly in length and sequence between different classes of vertebrates. The proposed vertebrate telomerase RNA structure displays a strikingly similar topology to the previously determined ciliate telomerase RNA structure, implying an evolutionary conservation of the global architecture of telomerase RNA.     

Defence against vertebrate herbivores trades off into architectural and low nutrient strategies amongst savanna Fabaceae species

Herbivory contributes substantially to plant functional diversity and in ways that move far beyond direct defence trait patterns, as effective growth strategies under herbivory require modification of multiple functional traits that are indirectly related to defence. In order to understand how herbivory has shaped plant functional diversity, we need to consider the physiology and architecture of the herbivores and how this constrains effective defence strategies. Here we consider herbivory by mammals in savanna communities that range from semi‐arid to humid conditions. We posited that the saplings of savanna trees can be grouped into two contrasting defence strategies against mammals, namely architectural defence versus low nutrient defence. We provide a mechanistic explanation for these different strategies based on the fact that plants are under competing selection pressures to limit herbivore damage and outcompete neighbouring plants. Plant competitiveness depends on growth rate, itself a function of leaf mass fraction (LMF) and leaf nitrogen per unit mass (N_m). Architectural defence against vertebrates (which includes spinescence) limits herbivore access to plant leaf materials, and partly depends on leaf‐size reduction, thereby compromising LMF. Low nutrient defence requires that leaf material is of insufficient nutrient value to support vertebrate metabolic requirements, which depends on low N_m. Thus there is an enforced tradeoff between LMF and N_m, leading to distinct trait suites for each defence strategy. We demonstrate this tradeoff by showing that numerous traits can be distinguished between 28 spinescent (architectural defenders) and non‐spinescent (low nutrient defenders) Fabaceae tree species from savannas, where mammalian herbivory is an important constraint on plant growth. Distributions of the strategies along an LMF‐N_m tradeoff further provides a predictive and parsimonious explanation for the uneven distribution of spinescent and non‐spinescent species across water and nutrient gradients.