Web of ecological interactions in an experimental gut microbiota

The dynamics of all ecosystems are dictated by intrinsic, density‐dependent mechanisms and by density‐independent environmental forcing. In spite of the importance of the gastrointestinal microbiota in health and disease, the ecology of this system remains largely unknown. Here, we take an ecological approach to gut microbial community analysis, with statistical modelling of time series data from chemostats. This approach removes effects of host forcing, allowing us to describe a network of intrinsic interactions determining the dynamic structure of an experimental gut microbiota. Surprisingly, the main colonization pattern in this simplified model system resembled that of the human infant gut, suggesting a potentially important role of density‐dependent interactions in the early gut microbiota. Knowledge of ecological structures in microbial systems may provide us with a means of controlling such systems by modifying the strength and nature of interactions among microbes and between the microbes and their environment.     

Phylogenetic and ecological correlates of pollen morphological diversity in a Neotropical rainforest

Morphology varies enormously across clades, and the morphology of a trait may reflect ecological function or the retention of ancestral features. We examine the tension between ecological and phylogenetic correlates of morphological diversity through a case study of pollen grains produced by angiosperms in Barro Colorado Island, Panama (BCI). Using a molecular phylogeny of 730 taxa, we demonstrate a statistically significant association between morphological and genetic distance for these plants. However, the relationship is non‐linear, and while close relatives share more morphological features than distant relatives, above a genetic distance of ~ 0.7 increasingly distant relatives are not more divergent in phenotype. The pollen grains of biotically pollinated and abiotically pollinated plants overlap in morphological space, but certain pollen morphotypes and individual morphological traits are unique to these pollination ecologies. Our data show that the pollen grains of biotically pollinated plants are significantly more morphologically diverse than those of abiotically pollinated plants. Abstract in Spanish is available with online material.     

Impact of the factors shaping gut microbiota on obesity

Obesity is considered as a risk factor for chronic health diseases such as heart diseases, cancer and diabetes 2. Reduced physical activities, lifestyle, poor nutritional diet and genetics are among the risk factors associated with the development of obesity. In recent years, several studies have explored the link between the gut microbiome and the progression of diseases including obesity, with the shift in microbiome abundance and composition being the main focus. The alteration of gut microbiome composition affects both nutrients metabolism and specific gene expressions, thereby disturbing body physiology. Specifically, the abundance of fibre-metabolizing microbes is associated with weight loss and that of protein and fat-metabolizing bacteria with weight gain. Various internal and external factors such as genetics, maternal obesity, mode of delivery, breastfeeding, nutrition, antibiotic use and the chemical compounds present in the environment are known to interfere with the richness of the gut microbiota (GM), thus influencing weight gain/loss and ultimately the development of obesity. However, the effectiveness of each factor in potentiating the shift in microbes’ abundance to result in significant changes that can lead to obesity is not yet clear. In this review, we will highlight the factors involved in shaping GM, their influence on obesity and possible interventions. Understanding the influence of these factors on the diversity of the GM and how to improve their effectiveness on disease conditions could be keys in the treatment of metabolic diseases.     

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

Propionate is produced in the human large intestine by microbial fermentation and may help maintain human health. We have examined the distribution of three different pathways used by bacteria for propionate formation using genomic and metagenomic analysis of the human gut microbiota and by designing degenerate primer sets for the detection of diagnostic genes for these pathways. Degenerate primers for the acrylate pathway (detecting the lcdA gene, encoding lactoyl-CoA dehydratase) together with metagenomic mining revealed that this pathway is restricted to only a few human colonic species within the Lachnospiraceae and Negativicutes. The operation of this pathway for lactate utilisation in Coprococcus catus (Lachnospiraceae) was confirmed using stable isotope labelling. The propanediol pathway that processes deoxy sugars such as fucose and rhamnose was more abundant within the Lachnospiraceae (based on the pduP gene, which encodes propionaldehyde dehydrogenase), occurring in relatives of Ruminococcus obeum and in Roseburia inulinivorans. The dominant source of propionate from hexose sugars, however, was concluded to be the succinate pathway, as indicated by the widespread distribution of the mmdA gene that encodes methylmalonyl-CoA decarboxylase in the Bacteroidetes and in many Negativicutes. In general, the capacity to produce propionate or butyrate from hexose sugars resided in different species, although two species of Lachnospiraceae (C. catus and R. inulinivorans) are now known to be able to switch from butyrate to propionate production on different substrates. A better understanding of the microbial ecology of short-chain fatty acid formation may allow modulation of propionate formation by the human gut microbiota.     

宿主遗传因素对肠道菌群的影响

随着高通量测序技术的发展,人们逐渐认识到肠道菌群与人类的健康和疾病密切相关,并发现肠道菌群受很多因素的影响。除了研究传统饮食和药物对肠道菌群的改变外,近年来,科学家也开始注重遗传因素在塑造肠道菌群中的作用。遗传因素可决定宿主的饮食偏好、肠道的生理结构、肠道屏障功能和免疫功能等,而这些都直接与肠道菌群相互作用,参与肠道微生态平衡的构建和稳定。因此,在研究肠道菌群与疾病发生相关性的过程中也需要考虑遗传因素的重要性。随着基因敲除、无菌小鼠和菌群移植等实验技术的革新,以及主成分分析、数量性状基因座和全基因组关联性分析等大数据分析手段的提高,科学家能够深入研究宿主遗传基因与肠道菌群之间的关联性,从而证明宿主遗传基因在塑造肠道微生态的过程中具有重要作用。本文将首先简述肠道菌群与疾病发生之间可能存在的联系,然后从多方面综述遗传因素对肠道菌群的影响及主要的研究进展,从而为今后该领域的深入研究提供重要的指导,也为今后预防和治疗疾病提供新思路和新方法。     

母乳糖复合物对新生儿肠道菌群的影响

母乳是新生儿最理想的营养来源。母乳喂养不仅维持婴儿的发育,也促进有益的肠道微生物增殖。母乳中的糖复合物,包括游离的低聚糖、糖蛋白和糖脂,因在肠道健康和菌群调节方面起着重要作用而被越来越多的人所重视。这些糖类物质不仅能预防传染病,也可作为益生元调节肠道微生态。新生儿出生时肠道是不成熟的,复杂的母乳成分确保了肠道微环境成熟。婴儿的肠道微生物群的构成在出生后会发生连续变化。出生后的细菌定植是肠道发育和免疫系统成熟的必要条件。本文将母乳中糖物质及对婴儿肠道菌群的影响作一综述。     

Maternal effects on early-life gut microbiota maturation in a wild nonhuman primate

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The impact of bacteriophages on probiotic bacteria and gut microbiota diversity

The human body is colonized by a vast array of bacteria whose diversity is largely affected by predation of bacteriophages. Here, we discussed the impact of bacteriophages on the composition of human intestinal microbiota as well as on the survival and thus efficacy of probiotic bacteria in the human gut.     

Balancing reactive oxygen species generation by rebooting gut microbiota

Reactive oxygen species (ROS; free radical form O₂^•−, superoxide radical; OH^•, hydroxyl radical; ROO^•, peroxyl; RO^•, alkoxyl and non-radical form ¹O₂, singlet oxygen; H₂O₂, hydrogen peroxide) are inevitable companions of aerobic life with crucial role in gut health. But, overwhelming production of ROS can cause serious damage to biomolecules. In this review, we have discussed several sources of ROS production that can be beneficial or dangerous to the human gut. Micro-organisms, organelles and enzymes play crucial role in ROS generation, where NOX1 is the main intestinal enzyme, which produce ROS in the intestine epithelial cells. Previous studies have reported that probiotics play significant role in gut homeostasis by checking the ROS generation, maintaining the antioxidant level, immune system and barrier protection. With current knowledge, we have critically analysed the available literature and presented the outcome in the form of bubble maps to suggest that the probiotics help in controlling the ROS-specific intestinal diseases, such as inflammatory bowel disease (IBD) and colon cancer. Finally, it has been concluded that rebooting of the gut microbiota with probiotics, postbiotics or faecal microbiota transplantation (FMT) can have crucial implications in the structuring of gut communities for the personalized management of the gastrointestinal (GI) diseases.     

Community structure of the gut microbiota in sympatric species of wild Drosophila

Many aspects of animal ecology and physiology are influenced by the microbial communities within them. The underlying forces contributing to the assembly and diversity of gut microbiotas include chance events, host‐based selection and interactions among microorganisms within these communities. We surveyed 215 wild individuals from four sympatric species of Drosophila that share a common diet of decaying mushrooms. Their microbiotas consistently contained abundant bacteria that were undetectable or at low abundance in their diet. Despite their deep phylogenetic divergence, all species had similar microbiotas, thus failing to support predictions of the phylosymbiosis hypothesis. Communities within flies were not random assemblages drawn from a common pool; instead, many bacterial operational taxonomic units (OTUs) were overrepresented or underrepresented relative to the neutral expectations, and OTUs exhibited checkerboard distributions among flies. These results suggest that selective factors play an important role in shaping the gut community structure of these flies.     

Habitat-associated morphological divergence in two Neotropical fish species

We examined intraspecific morphological diversification between river channel and lagoon habitats for two Neotropical fish ( Bryconops caudomaculatus , Characidae; Biotodoma wavrini , Cichlidae). We hypothesized that differences between habitats (e.g. flow regime, foraging opportunities) might create selective pressures resulting in morphological divergence between conspecific populations. We collected fish from four channel-lagoon habitat pairs in the Río Cinaruco, Venezuela, and compared body morphology using geometric morphometrics. There were two aspects of divergence in both species: (1) placement of maximum body depth and (2) orientation of the mouth. For both species, maximum body depth was positioned more anteriorly (i.e. fusiform) in the river channel than in lagoons. Both species exhibited a relatively terminal mouth in lagoons compared to the channel. The mouth of B. caudomaculatus was relatively upturned, whereas the mouth of B. wavrini was relatively subterminal, in channel habitats. Observed morphological patterns are consistent with functional morphological principles suggesting adaptive divergence. We also show that spatial distance between habitats, presumably reflecting rates of population mixing, appears to have constrained diversification. For both species, morphological divergence increased with distance between habitats. Thus morphological divergence between channel and lagoon habitats apparently reflects a balance between diversification driven by natural selection, and homogenization driven by population mixing.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 689–698.     

三种跳虫肠道菌群的多样性分析及功能预测

【目的】跳虫在土壤生态系统中发挥着重要的作用。本研究旨在调查Sinella(Coecobrya)oligoseta,Proisotoma minuta和Tomocerus missus 3种跳虫肠道菌群的结构和多样性以及潜在功能。【方法】采用16S rDNA扩增子测序法对以上3种跳虫成虫肠道内容物中的菌群进行分析和比较;应用Tax4Fun法对其肠道菌群基因进行功能预测。【结果】3种跳虫中成虫肠道菌群多样性最高的是T.missus,最低的是S.(C.)oligoseta。在门水平上3种跳虫成虫肠道中最主要的菌群均为变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidetes),放线菌门(Actinobacteria)也具有较高的丰度;在属水平上S.(C.)oligoseta肠道中假单胞菌属Pseudomonas的丰度(16.21%)明显高于P.minuta和T.missus肠道中的丰度(分别为0.87%和1.37%);P.minuta肠道中弧菌属Vibrio的丰度(25.81%)明显高于S.(C.)oligoseta和T.missus肠...     

Long-term stability of the human gut microbiota in two different rat strains

Human microbiota associated rats are frequently used as a model to study host microbe interactions. This study investigated the long-term stability of the bacterial community in such rats. Following the association of two strains of germ-free rats (12 male animals each) with fecal bacteria from a human donor the development of the microbiota was monitored for 12 months by PCR-denaturing gradient gel electrophoresis. During this time the Dice similarity coefficient (Cs) for the fecal microbial community of the rats associated with a human microbiota in comparison to the donor sample ranged between 73% +/- 8 and 74% +/- 3 for the Wistar and the Fischer 344 rats, respectively. After 12 months the similarity coefficients were 78% +/- 9 and 76% +/- 7, respectively, while the similarity coefficients for rat sample replicates ranged from 77% +/- 7 to 88% +/- 5; the similarity coefficient of the donor sample replicates was 78% +/- 9. DNA sequences of bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria previously found in samples of human, mouse or pig intestinal origin. The results of this study suggest that the dominant human fecal microbiota can be maintained in the human microbiota associated rat model for at least one year.     

Evaluation of QIAamp DNA Stool Mini Kit for ecological studies of gut microbiota

Cell lysis efficiency and the quality of DNA extracts from complex bacterial ecosystems are two major concerns in molecular ecological studies of gut microbiota. In this study, we use PCR-denaturing gradient gel electrophoresis (DGGE) DNA profiling, random cloning and sequence analysis of 16S rRNA genes to compare the QIAamp DNA Stool Mini Kit with the bead beating technique in the preparation of DNA extracts from gut microbiota of pigs. We also developed a washing procedure that can release more than 93% of bacterial cells attached to the gut mucosa. Both the QIAamp kit and bead beating method lysed approximately 95% of bacterial cells. PCR-DGGE DNA profiles of ileal and cecal microbiota from both digesta and mucosa that were generated from the DNA extracts using the two methods were nearly identical. Random cloning and sequence analysis also demonstrated the high quality of DNA extracts using the two methods. Two random clone sets of 16S rRNA genes generated from the DNA extracts had a similar degree of bacterial diversity. Different preparations of DNA extract from a single sample using the QIAamp kit consistently produced similar PCR-DGGE DNA profiles with similarity indexes higher than 99%. Our data suggest the appropriateness of the QIAamp DNA Stool Mini Kit for the studies of gut microbial ecology and the effectiveness of the QIAamp kit in processing multiple samples for cell lysis and DNA extraction.     

The impact of the gut microbiota on human health: an integrative view

The human gut harbors diverse microbes that play a fundamental role in the well-being of their host. The constituents of the microbiota--bacteria, viruses, and eukaryotes--have been shown to interact with one another and with the host immune system in ways that influence the development of disease. We review these interactions and suggest that a holistic approach to studying the microbiota that goes beyond characterization of community composition and encompasses dynamic interactions between all components of the microbiota and host tissue over time will be crucial for building predictive models for diagnosis and treatment of diseases linked to imbalances in our microbiota.