Dataset Information

Chemotherapy Alters the Phylogenetic Molecular Ecological Networks of Intestinal Microbial Communities.

ABSTRACT: Intestinal microbiota is now widely known to play key roles in nutritional uptake, metabolism, and regulation of human immune responses. There are multiple studies assessing intestinal microbiota changes in response to chemotherapy. In this study, microbial phylogenetic molecular ecological networks (pMENs) were firstly used to study the effects of chemotherapy on the intestinal microbiota of colorectal cancer (CRC) patients. Based on the random network model, we demonstrated that overall network structures and properties were significantly changed by chemotherapy, especially in average path length, average clustering coefficient, average harmonic geodesic distance and modularity (P < 0.05). The taxa in the module tended to co-exclude rather than co-occur in CRC patient networks, indicating probably competition relationships. The co-exclude correlations were decreased by 37.3% from T0 to T5 in response to chemotherapy. Significantly negative correlations were observed in positive/negative OTU degree and tumor markers (P < 0.05). Furthermore, the topological roles of the OTUs (module hubs and connectors) were changed with the chemotherapy. For example, the OTU167, OTU8, and OTU9 from the genera Fusobacterium, Bacteroides, and Faecalibacterium, respectively, were identified as keystone taxa, which were defined as either "hubs" or OTUs with highest connectivity in the network. These OTUs were significantly correlated with tumor markers (P < 0.05), suggesting that they probably were influenced by chemotherapy. The pMENs constructed in this study predicted the potential effects of chemotherapy on intestinal microbial community co-occurrence interactions. The changes may have an effect on the therapeutic effects. However, larger clinical samples are required to identify the conclusion.

SUBMITTER: Cong J

PROVIDER: S-EPMC6524687 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Chemotherapy Alters the Phylogenetic Molecular Ecological Networks of Intestinal Microbial Communities.

Cong Jing J Zhu Jingjuan J Zhang Chuantao C Li Tianjun T Liu Kewei K Liu Dong D Zhou Na N Jiang Man M Hou Helei H Zhang Xiaochun X

Frontiers in microbiology 20190507

Intestinal microbiota is now widely known to play key roles in nutritional uptake, metabolism, and regulation of human immune responses. There are multiple studies assessing intestinal microbiota changes in response to chemotherapy. In this study, microbial phylogenetic molecular ecological networks (pMENs) were firstly used to study the effects of chemotherapy on the intestinal microbiota of colorectal cancer (CRC) patients. Based on the random network model, we demonstrated that overall networ ...[more]

PMID: 31134034

Similar Datasets

Project description:UNLABELLED: Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO(2), is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual framework to discern phylogenetic molecular ecological networks using metagenomic sequencing data of 16S rRNA genes from grassland soil microbial communities, which were sampled from a long-term free-air CO(2) enrichment experimental facility at the Cedar Creek Ecosystem Science Reserve in Minnesota. Our experimental results demonstrated that an RMT-based network approach is very useful in delineating phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data. The structure of the identified networks under ambient and elevated CO(2) levels was substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher-order organization, topological roles of individual nodes, and network hubs, suggesting that the network interactions among different phylogenetic groups/populations were markedly changed. Also, the changes in network structure were significantly correlated with soil carbon and nitrogen contents, indicating the potential importance of network interactions in ecosystem functioning. In addition, based on network topology, microbial populations potentially most important to community structure and ecosystem functioning can be discerned. The novel approach described in this study is important not only for research on biodiversity, microbial ecology, and systems microbiology but also for microbial community studies in human health, global change, and environmental management. IMPORTANCE: The interactions among different microbial populations in a community play critical roles in determining ecosystem functioning, but very little is known about the network interactions in a microbial community, owing to the lack of appropriate experimental data and computational analytic tools. High-throughput metagenomic technologies can rapidly produce a massive amount of data, but one of the greatest difficulties is deciding how to extract, analyze, synthesize, and transform such a vast amount of information into biological knowledge. This study provides a novel conceptual framework to identify microbial interactions and key populations based on high-throughput metagenomic sequencing data. This study is among the first to document that the network interactions among different phylogenetic populations in soil microbial communities were substantially changed by a global change such as an elevated CO(2) level. The framework developed will allow microbiologists to address research questions which could not be approached previously, and hence, it could represent a new direction in microbial ecology research.

Project description:Ecological networks of two interacting guilds of species, such as flowering plants and pollinators, are common in nature, and studying their structure can yield insights into their resilience to environmental disturbances. Here we develop analytical methods for exploring the strengths of interactions within bipartite networks consisting of two guilds of phylogenetically related species. We then apply these methods to investigate the resilience of a plant-pollinator community to anticipated climate change. The methods allow the statistical assessment of, for example, whether closely related pollinators are more likely to visit plants with similar relative frequencies, and whether closely related pollinators tend to visit closely related plants. The methods can also incorporate trait information, allowing us to identify which plant traits are likely responsible for attracting different pollinators. These questions are important for our study of 14 prairie plants and their 22 insect pollinators. Over the last 70 years, six of the plants have advanced their flowering, while eight have not. When we experimentally forced earlier flowering times, five of the six advanced-flowering species experienced higher pollinator visitation rates, whereas only one of the eight other species had more visits; this network thus appears resilient to climate change, because those species with advanced flowering have ample pollinators earlier in the season. Using the methods developed here, we show that advanced-flowering plants did not have a distinct pollinator community from the other eight species. Furthermore, pollinator phylogeny did not explain pollinator community composition; closely related pollinators were not more likely to visit the same plant species. However, differences among pollinator communities visiting different plants were explained by plant height, floral color, and symmetry. As a result, closely related plants attracted similar numbers of pollinators. By parsing out characteristics that explain why plants share pollinators, we can identify plant species that likely share a common fate in a changing climate.

Project description:BackgroundThe interaction of the gut microbiota with key metabolic and physiological processes may be associated with poor growth outcomes in animals born with intrauterine growth restriction (IUGR).ResultsGrowth performance, plasma hormone concentrations, and intestinal microbiota composition were analyzed in IUGR pigs and in normal birth weight (NBW) pigs when the NBW pigs reached 25, 50, and 100 kg of body weight (BW). Compared to NBW pigs, IUGR pigs had lower initial, weaned, and final BW, and lower average daily gain and average daily feed intake in all the considered time points. In the 25 kg BW group, IUGR pigs had higher concentrations of plasma ghrelin and pancreatic polypeptide (PP), but lower insulin concentration than NBW pigs, while the situation was reversed in the 50 kg BW group. As compared to NBW pigs, IUGR pigs had higher microbial alpha diversity in the jejunum and ileum; in the 50 and 100 kg BW groups, IUGR pigs had higher Firmicutes abundance but lower Proteobacteria abundance in the jejunum, and lower Lactobacillus abundance in the jejunum and ileum; in the 25 kg BW group, IUGR pigs showed higher unclassified Ruminococcaceae abundance in the ileum; and in 25 and 50 kg BW groups, IUGR pigs showed lower Ochrobactrum abundance in the jejunum. Spearman's correlation revealed that Lactobacillus was negatively correlated with growth performance, while unclassified Ruminococcaceae was positively correlated. Predictive metagenomic analysis detected significantly different expression of genes in the intestinal microbiota between IUGR and NBW pigs, suggesting different metabolic capabilities between the two groups.ConclusionsGrowing-finishing IUGR pigs showed lower growth performance, higher microbial alpha diversity, and differences in plasma hormone concentrations compared to NBW pigs. Alterations in the abundance of Firmicutes, Proteobacteria, Ruminococcaceae, Lactobacillus, and Ochrobactrum in the small intestine may be associated with IUGR, and may therefore serve as a future target for gut microbiota intervention in growing-finishing IUGR pigs.

Dataset Information

Chemotherapy Alters the Phylogenetic Molecular Ecological Networks of Intestinal Microbial Communities.

Publications

Chemotherapy Alters the Phylogenetic Molecular Ecological Networks of Intestinal Microbial Communities.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets