代谢互养关系在维持微生物物种多样性中的作用

互养关系（cross-feeding）是微生物物种之间普遍存在的一种相互关系,其中物种利用环境中其他成员的代谢产物以促进自身生长的情形称为代谢互养关系,这种关系对物种间的竞争结果往往有很大影响,甚至会改变种群结构。为了研究代谢互养关系在维持微生物物种多样性中的作用,构建包含不同代谢互养关系的资源竞争模型,这些模型既体现了微生物物种竞争资源时种群密度及资源量的动态,也展示了物种利用其他竞争者的代谢资源对自身生存状况的影响。数值模拟结果显示：（1）考虑微生物中不同的代谢互养关系结构：两物种间单向互养、双向互养以及多物种间的互养,不同的互养关系都可以促进竞争物种稳定共存,竞争中处于劣势的物种通过利用其他竞争成员的代谢产物,打破外界资源量对其生长的限制,改变原本消亡的命运;而处于优势的物种则通过利用其他竞争成员的代谢产物,增大种群密度。（2）多物种竞争同一种有限资源时,不是所有物种都能共存,在四物种模拟中,原本处于最劣势的物种灭绝,其余三者共存。物种产生代谢资源对其本身是"不利"的,如果在模拟中物种利用代谢资源的能力相同,那么物种竞争外界资源的劣势就很可能无法被抵消。通过改变资源利用率发现只有互养关系中代谢资源的利用可以弥补劣势种在竞争外界资源时的不足,多物种才可以全部共存。（3）验证数值模拟结果的普遍性,分析参数变化对共存的影响,结果表明代谢互养关系促进的共存对代谢资源相关参数不敏感,参数的改变只影响平衡态时物种的种群密度。所以,代谢互养关系可以促进相互竞争的微生物物种共存,即微生物之间的互养关系很可能是维持物种多样性的一种机制。     

Context-Dependent Competition in a Model Gut Bacterial Community

Understanding the ecological processes that generate complex community structures may provide insight into the establishment and maintenance of a normal microbial community in the human gastrointestinal tract, yet very little is known about how biotic interactions influence community dynamics in this system. Here, we use natural strains of Escherichia coli and a simplified model microbiota to demonstrate that the colonization process on the strain level can be context dependent, in the sense that the outcome of intra-specific competition may be determined by the composition of the background community. These results are consistent with previous models for competition between organisms where one competitor has adapted to low resource environments whereas the other is optimized for rapid reproduction when resources are abundant. The genomic profiles of E. coli strains representing these differing ecological strategies provide clues for deciphering the genetic underpinnings of niche adaptation within a single species. Our findings extend the role of ecological theory in understanding microbial systems and the conceptual toolbox for describing microbial community dynamics. There are few, if any, concrete examples of context-dependent competition on a single trophic level. However, this phenomenon can have potentially dramatic effects on which bacteria will successfully establish and persist in the gastrointestinal system, and the principle should be equally applicable to other microbial ecosystems.     

Assembly of the human intestinal microbiota

Complex microbial ecosystems occupy the skin, mucosa and alimentary tract of all mammals, including humans. Recent advances have highlighted the tremendous diversity of these microbial communities and their importance to host physiology, but questions remain about the ecological processes that establish and maintain the microbiota throughout life. The prevailing view, that the gastrointestinal microbiota of adult humans is a climax community comprised of the superior competitors for a stable set of niches, does not account for all of the experimental data. We argue here that the unique history of each community and intrinsic temporal dynamics also influence the structure of human intestinal communities.     

Diversity of the human gastrointestinal tract microbiota revisited

Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.     

A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities

Background  

The human gastrointestinal (GI) tract contains a diverse collection of bacteria, most of which are unculturable by conventional microbiological methods. Increasingly molecular profiling techniques are being employed to examine this complex microbial community. The purpose of this study was to develop a microarray technique based on 16S ribosomal gene sequences for rapidly monitoring the microbial population of the GI tract.     

The role of viral and bacterial pathogens in gastrointestinal cancer

The association of Helicobacter pylori (H. pylori) with gastric cancer is thus far the best understood model to comprehend the causal relationship between a microbial pathogen and cancer in the human gastrointestinal tract. Besides H. pylori, a variety of other pathogens are now being recognized as potential carcinogens in different settings of human cancer. In this context, viral causes of human cancers are central to the issue since these account for 10-20% of cancers worldwide. In the case of H. pylori and gastric cancer, as well as the human papillomavirus and anal cancer, the causal relationship between the infectious agent and the related cancer in the gastrointestinal tract has been clearly confirmed by epidemiological and experimental studies. Similarly, Epstein-Barr virus and the oncogenic JC virus are being suggested as possible causative agents for cancers in the upper and lower gastrointestinal tract. This review discusses various viral and microbial pathogens and their oncogenic properties in the evolution of gastrointestinal carcinogenesis and summarizes the available experimental data make a convincing agreement favoring the associations between infectious agents and specific human cancers.     

Involvement of ghrelin-growth hormone secretagogue receptor system in pathoclinical profiles of digestive system cancer

Ghrelin receptor has been shown to be expressed along the human gastrointestinal tract. Recent studies showed that ghrelin and a synthetic ghrelin receptor agonist improved weight gain and lean body mass retention in a rat model of cancer cachexia by acting on ghrelin receptor, that is, growth hormone secretagogue receptor （GHS-R）. This study aims to explore the expression and the distribution of ghrelin receptor in human gastrointestinal tract cancers and to investigate the possible involvement of the ghrelin- GHS-R system in human digestive cancers. Surgical human digestive cancer specimens were obtained from various portions of the gastrointestinal tract from different patients. The expression of ghrelin receptor in these tissues was detected by tissue microarray technique. Our results showed that ghrelin receptor was expressed in cancers throughout the gastrointestinal tract, mainly in the cytoplasm of mucosal layer cells. Its expression level possibly correlated with organ type, histological grade, tumor-nodes-metastases stage, and nutrition status （weight loss） of the patients. For the first time, we identified the distribution of ghrelin receptor in digestive system cancers. Our results implied that the ghrelin-GHS-R system might be involved in the pathoclinical profiles of digestive cancers.     

EVOLUTIONARY DIVERGENCE AND CHARACTER DISPLACEMENT IN TWO PHENOTYPICALLY-VARIABLE,COMPETING SPECIES

Theoretical studies of character displacement lead to the view that evolutionary divergence depends primarily on incomplete utilization of available resources. Those models which incorporate constraints preventing complete utilization of resources, even in the absence of competitors, all predict character displacement. Those models which allow greater flexibility of resource use within a species predict correspondingly less divergence. Indeed, Matessi and Jayakar (1980, 1981) based their conditions for occurrence of character displacement on underutilization of resources. I extend a model used by Slatkin (1980, 1983) and Taper and Case (1985) which allows each species to fully utilize its resources in the absence of competitors. I concentrate on the biologically reasonable case in which the species, though similar, differ in their ecological characteristics. As a result of this greater biological realism, I arrive at a different conclusion regarding the conditions which lead to character displacement. The presence of a variety of biological differences between species—including as a subset those which result from resource underutilization—leads to divergence with respect to a quantitatively inherited character, due to interspecific competitive interactions. The resulting displacement can be large and depends little on the parameters chosen. The only exception, involving a character with very low heritability, occurs when the non-interactive phenotypic differences are much greater than those associated with studies of character displacement in natural populations. Thus, under conditions comparable to those encountered in the field, involving similar yet not identical species, evolutionary divergence is a consequence of interspecific competition.     

Competition of two microbial populations for a single resource in a chemostat when one of them exhibits wall attachment

It is known that two microbial populations competing for a single resource in a homogeneous environment with time-invariant inputs cannot coexist in a steady state. The case where two microbial populations compete for a single resource in a chemostat but one of them exhibits attachment to the chemostat walls is studied theoretically. Because of the cells' attachment to the walls, the environment is no longer homogeneous. The present article considers the case where the attached cells form no more than a monolayer. Other situations occur, often frequently, but we do not consider them here. Two models are used to represent the attachment to the walls: the Topiwala-Hamer model and a model which assumes that the attachment of microbial cells to the solid surfaces is a reversible process. The first model does not allow the population that exhibits wall attachment to wash out from the chemostat, in contrast to the second model (which nevertheless reduces to the first one in the limit). It has been found that in most of the possible cases for both models, the two competitors can coexist in a stable steady state for a wide range of the operating parameters space. The results of the stability analysis are discussed and analytical expressions for the conditions and the boundaries of the domains of stable coexistence are given for all the possible situations that may arise.     

Living in the city: resource availability, predation, and bird population dynamics in urban areas

This article explores factors that shape population structure in novel environments that have received scant theoretical attention: cities. Urban bird populations exhibit higher densities and lower diversity. Some work suggests this may result from lower predation pressure and more predictable and abundant resources. These factors may lead to populations with few winners and many losers regarding access to food, body condition, and reproductive success. We explore these hypotheses with an individual-energy-based competition model with two phenotypes of differing foraging ability. We show that low frequency resource fluctuations favor strong competitors and vice versa. We show that low predation skews equilibrium populations in favor of weak competitors and vice versa. Increasing the time between resource pulses can thus shift population structure from weak to strong competitor dominance. Given recent evidence for more constant resource input and lower predation in urban areas, the model helps understand observed urban bird population structure.     

Clutch-size behavior and coexistence in ephemeral-patch competition models

Systems of patchy, ephemeral resources often support surprisingly diverse assemblages of consumer insects. Aggregation of consumer individuals over the landscape of patches has been suggested as one mechanism that can stabilize competition among consumer species. One mechanism for larval aggregation is the laying of eggs in clutches by females traveling among patches to distribute their total fecundity. We use simulation models to explore the consequences, for coexistence of competitors, of larval aggregation that arises from clutch laying. Contrary to some previous treatments, we find that clutch laying can be strongly stabilizing and under certain conditions can be sufficient to allow competitors to coexist stably. We extend these models by considering clutch size as a variable that responds to the abundance of resource patches. Such a relationship might be expected because females should lay their eggs in fewer but larger clutches when the cost of travel among patches is high (because patches are rare). When females adjust clutch size in response to resource abundance, coexistence can be easiest when resource patches are scarce and most difficult when resources are abundant.     

Isolation of RNA from bacterial samples of the human gastrointestinal tract

The human gastrointestinal (GI) tract contains a complex microbial community that consists of numerous uncultured microbes. Therefore, nucleic-acid-based approaches have been introduced to study microbial diversity and activity, and these depend on the proper isolation of DNA, rRNA and mRNA. Here, we present an RNA isolation protocol that is suitable for a wide variety of GI tract samples. The procedure for isolating DNA from GI tract samples is described in another Nature Protocols article. One of the benefits of our RNA isolation protocol is that sampling can be performed outside the laboratory, which offers possibilities for implementation in large intervention studies. The RNA isolation is based on mechanical disruption, followed by isolation of nucleic acids using phenol:chloroform:isoamylalcohol extraction and removal of DNA. In our laboratory, this protocol has resulted in the isolation of rRNA and mRNA of sufficient quality and quantity for microbial diversity and activity studies. Depending on the number of samples, the sample type and the quenching procedure chosen, the whole procedure can be performed within 2.5-4 h.     

Metagenomic Analysis of the Pygmy Loris Fecal Microbiome Reveals Unique Functional Capacity Related to Metabolism of Aromatic Compounds

The animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host. An analysis of 78,619 pyrosequencing reads generated from pygmy loris fecal DNA extracts was performed to help better understand the microbial diversity and functional capacity of the pygmy loris gut microbiome. The taxonomic analysis of the metagenomic reads indicated that pygmy loris fecal microbiomes were dominated by Bacteroidetes and Proteobacteria phyla. The hierarchical clustering of several gastrointestinal metagenomes demonstrated the similarities of the microbial community structures of pygmy loris and mouse gut systems despite their differences in functional capacity. The comparative analysis of function classification revealed that the metagenome of the pygmy loris was characterized by an overrepresentation of those sequences involved in aromatic compound metabolism compared with humans and other animals. The key enzymes related to the benzoate degradation pathway were identified based on the Kyoto Encyclopedia of Genes and Genomes pathway assignment. These results would contribute to the limited body of primate metagenome studies and provide a framework for comparative metagenomic analysis between human and non-human primates, as well as a comparative understanding of the evolution of humans and their microbiome. However, future studies on the metagenome sequencing of pygmy loris and other prosimians regarding the effects of age, genetics, and environment on the composition and activity of the metagenomes are required.     

Priority versus brute force: when should males begin guarding resources?

When should males begin guarding a resource when both resources and guarders vary in quality? This general problem applies, for example, to migrant birds occupying territories in the spring and to precopula in crustaceans where males grab females before they molt and become receptive. Previous work has produced conflicting predictions. Theory on migrant birds predicts that the strongest competitors should often arrive first, whereas some models of mate guarding have predicted that the strongest competitors wait and then simply usurp a female from a weaker competitor. We build a general model of resource guarding that allows varying the ease with which takeovers occur. The model is phrased in terms of mate-guarding crustaceans, but the same logic can be applied to other forms of resource acquisition where priority plays a role but takeovers might be possible too. The race to secure breeding positions can lead to strong competitors (large males) taking females earliest, even though this means accepting a lower-quality female. Paradoxically, this means that small males, which have fewer breeding opportunities, are more choosy than larger ones. Such solutions are found when takeovers are impossible. The easier the takeovers and the higher the rate of finding guarded resources, the more likely are solutions where guarding durations are short, where strong competitors begin guarding only just before breeding, and where they do this by usurping the resource. The relationship between an individual's competitive ability and its timing of resource acquisition can also be nonlinear if takeovers are moderately common; if this is the case, then males of intermediate size guard the longest.     

Consumer effects on the vital rates of their resource can determine the outcome of competition between consumers

Current competition theory does not adequately address the fact that competitors may affect the survival, growth, and reproductive rates of their resources. Ecologically important interactions in which consumers affect resource vital rates range from parasitism and herbivory to mutualism. We present a general model of competition that explicitly includes consumer-dependent resource vital rates. We build on the classic MacArthur model of competition for multiple resources, allowing direct comparison with expectations from established concepts of resource-use overlap. Consumers share a stage-structured resource population but may use the different stages to different extents, as they do the different independent resources in the classic model. Here, however, the stages are dynamically linked via consumer-dependent vital rates. We show that consumers' effects on resource vital rates result in two important departures from classic results. First, consumers can coexist despite identical use of resource stages, provided each competitor shifts the resource stage distribution toward stages that benefit other species. Second, consumers specializing on different resource stages can compete strongly, possibly resulting in competitive exclusion despite a lack of resource stage-use overlap. Our model framework demonstrates the critical role that consumer-dependent resource vital rates can play in competitive dynamics in a wide range of biological systems.     

Fusing spatial resource heterogeneity with a competition–colonization trade-off in model communities

Two commonly cited mechanisms of multispecies coexistence in patchy environments are spatial heterogeneity in competitive abilities caused by variation in resources and a competition–colonization trade-off. In this paper, a model that fuses these mechanisms together is presented and analyzed. The model suggests that spatial variation in resource ratios can lead to multispecies coexistence, but this mechanism by itself is weak when the number of resources for which species compete is small. However, spatial resource heterogeneity is a powerful mechanism for multispecies coexistence when it acts synergistically with a competition–colonization trade-off. The model also shows how resource supply can control the competitive balance between species that are weak competitors but superior colonizers and strong competitors/inferior colonizers. This provides additional theoretical support for a possible explanation of empirically observed hump-shaped relationships between species diversity and ecological productivity.     

Using the angle frequency method to detect signals of competition and predation in experimental time series

Identifying interactions among organisms is central to the study of ecology. The Angle Frequency Method (AFM) allows the detection of interactions in time series data. The AFM takes pairwise data plotted in phase diagrams and identifies signals (vector directions in phase diagrams) associated with particular interactions. Using microbial experimental systems consisting of predators (bacteriophage T4) and prey/competitors (strains of Escherichia coli), we demonstrate that the AFM can identify predator–prey and competitive interactions. The level of control afforded by such microbial experimental systems allows direct tests of the utility and robustness of the AFM. Signals of predation were distinct from signals of competition, with the strongest signal of predation corresponding to the collapse of the predator population at low prey densities. Signals of competition reflected the difference in competitive strength between the superior and the inferior competitors. In addition, the effects of invasion and resource enrichment on interactions in the laboratory communities were detectable using the AFM. Our analyses support results from model simulations and analyses of lake time series by identifying similar sets of signals characteristic of predation and competition, and demonstrate that the AFM is an effective tool in rigorous studies of time series.     

Spatial and Temporal Resource Use by Feral and Abandoned Dogs

We compared spatial and temporal patterns of resource use by feral and abandoned domestic dogs (Canis familiaris) on the Navajo reservation in Arizona and New Mexico. Community dumps provide locally abundant food resources utilized both by feral dogs and dogs abandoned at the dump site. Although population parameters were much the same for feral and abandoned dogs, the use of space varied distinctly and reflected behavioral differences in the way each population responded to the absence of human control, the need to acquire food, and the developmental state of pups. Temporal use of resources by feral dogs varied seasonally with the age of pups in one pack, but not in a second pack. Priority of access to local resources may be influenced by aggressive interactions among dogs at a dump. Barking may serve to warn dogs already present at a dump that competitors have arrived.     

Isolation of DNA from bacterial samples of the human gastrointestinal tract

The human gastrointestinal (GI) tract contains a complex microbial community that develops in time and space. The most widely used approaches to study microbial diversity and activity are all based on the analysis of nucleic acids, DNA, rRNA and mRNA. Here, we present a DNA isolation protocol that is suitable for a wide variety of GI tract samples, including biopsies with minute amounts of material. The protocol is set up in such a way that sampling can be performed outside the laboratory, which offers possibilities for implementation in large intervention studies. The DNA isolation is based on mechanical disruption, followed by isolation of nucleic acids using phenol:chloroform:isoamylalcohol extraction. In addition, it includes an alternative DNA isolation protocol that is based on a commercial kit. These protocols have all been successfully used in our laboratory, resulting in isolation of DNA of sufficient quality for microbial diversity studies. Depending on the number of samples and sample type, the whole procedure will take approximately 2.5-4 hours.     

Phytoplankton competition in deep biomass maximum

Resource competition in heterogeneous environments is still an unresolved problem of theoretical ecology. In this article, I analyze competition between two phytoplankton species in a deep water column, where the distributions of main resources (light and a limiting nutrient) have opposing gradients and co-limitation by both resources causes a deep biomass maximum. Assuming that the species have a trade-off in resource requirements and the water column is weakly mixed, I apply the invasion threshold analysis (Ryabov and Blasius, Ecol Lett 14:220–228, 2011) to determine relations between environmental conditions and phytoplankton composition. Although species deplete resources in the interior of the water column, the resource levels at the bottom and surface remain high. As a result, the slope of resources gradients becomes a new crucial factor which, rather than the local resource values, determines the outcome of competition. The value of resource gradients nonlinearly depend on the density of consumers. This leads to complex relationships between environmental parameters and species composition. In particular, it is shown that an increase of both the incident light intensity or bottom nutrient concentrations favors the best light competitors, while an increase of the turbulent mixing or background turbidity favors the best nutrient competitors. These results might be important for prediction of species composition in deep ocean.