scholarly journals Large-scale metabolic interaction network of the mouse and human gut microbiota

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Roktaek Lim ◽  
Josephine Jill T. Cabatbat ◽  
Thomas L. P. Martin ◽  
Haneul Kim ◽  
Seunghyeon Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Large Scale ◽  
Interaction Network ◽  
Cell Types ◽  
System Level ◽  
Data Resource ◽  
Molecule Transport ◽  
Health And Disease ◽  
Metabolic Activities ◽  
Small Molecule Transport

Abstract The role of our gut microbiota in health and disease is largely attributed to the collective metabolic activities of the inhabitant microbes. A system-level framework of the microbial community structure, mediated through metabolite transport, would provide important insights into the complex microbe-microbe and host-microbe chemical interactions. This framework, if adaptable to both mouse and human systems, would be useful for mechanistic interpretations of the vast amounts of experimental data from gut microbiomes in murine animal models, whether humanized or not. Here, we constructed a literature-curated, interspecies network of the mammalian gut microbiota for mouse and human hosts, called NJC19. This network is an extensive data resource, encompassing 838 microbial species (766 bacteria, 53 archaea, and 19 eukaryotes) and 6 host cell types, interacting through 8,224 small-molecule transport and macromolecule degradation events. Moreover, we compiled 912 negative associations between organisms and metabolic compounds that are not transportable or degradable by those organisms. Our network may facilitate experimental and computational endeavors for the mechanistic investigations of host-associated microbial communities.

scholarly journals Species-wide Metabolic Interaction Network for Understanding Natural Lignocellulose Digestion in Termite Gut Microbiota

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Pritam Kundu ◽  
Bharat Manna ◽  
Subham Majumder ◽  
Amit Ghosh
Keyword(s):  
Gut Microbiota ◽  
Structural Complexity ◽  
Interaction Network ◽  
Biofuel Production ◽  
System Level ◽  
Metagenomic Data ◽  
Metabolic Interaction ◽  
Nasutitermes Corniger ◽  
Termite Gut ◽  
Microbial Symbionts

Abstract The structural complexity of lignocellulosic biomass hinders the extraction of cellulose, and it has remained a challenge for decades in the biofuel production process. However, wood-feeding organisms like termite have developed an efficient natural lignocellulolytic system with the help of specialized gut microbial symbionts. Despite having an enormous amount of high-throughput metagenomic data, specific contributions of each individual microbe to achieve this lignocellulolytic functionality remains unclear. The metabolic cross-communication and interdependence that drives the community structure inside the gut microbiota are yet to be explored. We have contrived a species-wide metabolic interaction network of the termite gut-microbiome to have a system-level understanding of metabolic communication. Metagenomic data of Nasutitermes corniger have been analyzed to identify microbial communities in different gut segments. A comprehensive metabolic cross-feeding network of 205 microbes and 265 metabolites was developed using published experimental data. Reconstruction of inter-species influence network elucidated the role of 37 influential microbes to maintain a stable and functional microbiota. Furthermore, in order to understand the natural lignocellulose digestion inside N. corniger gut, the metabolic functionality of each influencer was assessed, which further elucidated 15 crucial hemicellulolytic microbes and their corresponding enzyme machinery.

scholarly journals Biomarkers of a Healthy Nordic Diet—From Dietary Exposure Biomarkers to Microbiota Signatures in the Metabolome

Nutrients ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 27 ◽  
Author(s):  
Rikard Landberg ◽  
Kati Hanhineva
Keyword(s):  
Gut Microbiota ◽  
Observational Studies ◽  
Large Scale ◽  
Dietary Assessment ◽  
Dietary Exposure ◽  
Current Status ◽  
Dietary Interventions ◽  
Nordic Diet ◽  
Health And Disease ◽  
The Impact

Whole diets and dietary patterns are increasingly highlighted in modern nutrition and health research instead of single food items or nutrients alone. The Healthy Nordic Diet is a dietary pattern typically associated with beneficial health outcomes in observational studies, but results from randomized controlled trials are mixed. Dietary assessment is one of the greatest challenges in observational studies and compliance is a major challenge in dietary interventions. During the last decade, research has shown the great importance of the gut microbiota in health and disease. Studies have have both shown that the Nordic diet affects the gut microbiota and that the gut microbiota predicts the effects of such a diet. Rapid technique developments in the area of high-throughput mass spectrometry have enabled the large-scale use of metabolomics both as an objective measurement of dietary intake as well as in providing the final readout of the endogenous metabolic processes and the impact of the gut microbiota. In this review, we give an update on the current status on biomarkers that reflect a Healthy Nordic Diet or individual components thereof (food intake biomarkers), biomarkers that show the effects of a Healthy Nordic Diet and biomarkers reflecting the role of a Healthy Nordic Diet on the gut microbiota as well as how the gut microbiota or derived molecules may be used to predict the effects of a Healthy Nordic Diet on different outcomes.

scholarly journals Publisher Correction: Large-scale metabolic interaction network of the mouse and human gut microbiota

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Roktaek Lim ◽  
Josephine Jill T. Cabatbat ◽  
Thomas L. P. Martin ◽  
Haneul Kim ◽  
Seunghyeon Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Large Scale ◽  
Interaction Network ◽  
Human Gut ◽  
Metabolic Interaction ◽  
Human Gut Microbiota

scholarly journals Multiregional profiling of the brain transmembrane proteome uncovers novel regulators of depression

2021 ◽  
Vol 7 (30) ◽  
pp. eabf0634
Author(s):  
Shanshan Li ◽  
Huoqing Luo ◽  
Ronghui Lou ◽  
Cuiping Tian ◽  
Chen Miao ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Large Scale ◽  
Transmembrane Protein ◽  
Interaction Network ◽  
Brain Regions ◽  
Protein Distribution ◽  
Data Resource ◽  
Proteomic Approach ◽  
Rich Data ◽  
The Brain

Transmembrane proteins play vital roles in mediating synaptic transmission, plasticity, and homeostasis in the brain. However, these proteins, especially the G protein–coupled receptors (GPCRs), are underrepresented in most large-scale proteomic surveys. Here, we present a new proteomic approach aided by deep learning models for comprehensive profiling of transmembrane protein families in multiple mouse brain regions. Our multiregional proteome profiling highlights the considerable discrepancy between messenger RNA and protein distribution, especially for region-enriched GPCRs, and predicts an endogenous GPCR interaction network in the brain. Furthermore, our new approach reveals the transmembrane proteome remodeling landscape in the brain of a mouse depression model, which led to the identification of two previously unknown GPCR regulators of depressive-like behaviors. Our study provides an enabling technology and rich data resource to expand the understanding of transmembrane proteome organization and dynamics in the brain and accelerate the discovery of potential therapeutic targets for depression treatment.

Building a Culture of Ethical, Comparable, Authentic Assessment

2019 ◽  
pp. 463-481
Author(s):  
Andrew Reid ◽  
Julie Ballantyne
Keyword(s):  
Teaching And Learning ◽  
Large Scale ◽  
Authentic Assessment ◽  
Subject Area ◽  
Music Educators ◽  
System Level ◽  
Diverse Range ◽  
Effective Learning ◽  
School Based ◽  
The Subject

In an ideal world, assessment should be synonymous with effective learning and reflect the intricacies of the subject area. It should also be aligned with the ideals of education: to provide equitable opportunities for all students to achieve and to allow both appropriate differentiation for varied contexts and students and comparability across various contexts and students. This challenge is made more difficult in circumstances in which the contexts are highly heterogeneous, for example in the state of Queensland, Australia. Assessment in music challenges schooling systems in unique ways because teaching and learning in music are often naturally differentiated and diverse, yet assessment often calls for standardization. While each student and teacher has individual, evolving musical pathways in life, the syllabus and the system require consistency and uniformity. The challenge, then, is to provide diverse, equitable, and quality opportunities for all children to learn and achieve to the best of their abilities. This chapter discusses the designing and implementation of large-scale curriculum as experienced in secondary schools in Queensland, Australia. The experiences detailed explore the possibilities offered through externally moderated school-based assessment. Also discussed is the centrality of system-level clarity of purpose, principles and processes, and the provision of supportive networks and mechanisms to foster autonomy for a diverse range of music educators and contexts. Implications for education systems that desire diversity, equity, and quality are discussed, and the conclusion provokes further conceptualization and action on behalf of students, teachers, and the subject area of music.

scholarly journals BOARD INVITED REVIEW: The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health1

2019 ◽  
Vol 97 (9) ◽  
pp. 3741-3757 ◽  
Author(s):  
Nirosh D Aluthge ◽  
Dana M Van Sambeek ◽  
Erin E Carney-Hinkle ◽  
Yanshuo S Li ◽  
Samodha C Fernando ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Therapeutic Potential ◽  
Animal Health ◽  
Microbial Colonization ◽  
Critical Importance ◽  
Specific Host ◽  
Microbiome Research ◽  
Health And Disease ◽  
The Impact

Abstract A variety of microorganisms inhabit the gastrointestinal tract of animals including bacteria, archaea, fungi, protozoa, and viruses. Pioneers in gut microbiology have stressed the critical importance of diet:microbe interactions and how these interactions may contribute to health status. As scientists have overcome the limitations of culture-based microbiology, the importance of these interactions has become more clear even to the extent that the gut microbiota has emerged as an important immunologic and metabolic organ. Recent advances in metagenomics and metabolomics have helped scientists to demonstrate that interactions among the diet, the gut microbiota, and the host to have profound effects on animal health and disease. However, although scientists have now accumulated a great deal of data with respect to what organisms comprise the gastrointestinal landscape, there is a need to look more closely at causative effects of the microbiome. The objective of this review is intended to provide: 1) a review of what is currently known with respect to the dynamics of microbial colonization of the porcine gastrointestinal tract; 2) a review of the impact of nutrient:microbe effects on growth and health; 3) examples of the therapeutic potential of prebiotics, probiotics, and synbiotics; and 4) a discussion about what the future holds with respect to microbiome research opportunities and challenges. Taken together, by considering what is currently known in the four aforementioned areas, our overarching goal is to set the stage for narrowing the path towards discovering how the porcine gut microbiota (individually and collectively) may affect specific host phenotypes.

scholarly journals Modulation of Gut Microbiota and Oxidative Status by β-Carotene in Late Pregnant Sows

2020 ◽  
Vol 7 ◽  
Author(s):  
Xupeng Yuan ◽  
Jiahao Yan ◽  
Ruizhi Hu ◽  
Yanli Li ◽  
Ying Wang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dietary Supplementation ◽  
Basal Diet ◽  
Fecal Microbiota ◽  
Control Group ◽  
Metabolic Activities ◽  
The Impact ◽  
Positive Effect ◽  
Β Carotene

Recent evidences suggest that gut microbiota plays an important role in regulating physiological and metabolic activities of pregnant sows, and β-carotene has a potentially positive effect on reproduction, but the impact of β-carotene on gut microbiota in pregnant sows remains unknown. This study aimed to explore the effect and mechanisms of β-carotene on the reproductive performance of sows from the aspect of gut microbiota. A total of 48 hybrid pregnant sows (Landrace × Yorkshire) with similar parity were randomly allocated into three groups (n = 16) and fed with a basal diet or a diet containing 30 or 90 mg/kg of β-carotene from day 90 of gestation until parturition. Dietary supplementation of 30 or 90 mg/kg β-carotene increased the number of live birth to 11.82 ± 1.54 and 12.29 ± 2.09, respectively, while the control group was 11.00 ± 1.41 (P = 0.201). Moreover, β-carotene increased significantly the serum nitric oxide (NO) level and glutathione peroxidase (GSH-Px) activity (P < 0.05). Characterization of fecal microbiota revealed that 90 mg/kg β-carotene increased the diversity of the gut flora (P < 0.05). In particular, β-carotene decreased the relative abundance of Firmicutes including Lachnospiraceae AC2044 group, Lachnospiraceae NK4B4 group and Ruminococcaceae UCG-008, but enriched Proteobacteria including Bilophila and Sutterella, and Actinobacteria including Corynebacterium and Corynebacterium 1 which are related to NO synthesis. These data demonstrated that dietary supplementation of β-carotene may increase antioxidant enzyme activity and NO, an important vasodilator to promote the neonatal blood circulation, through regulating gut microbiota in sows.

scholarly journals Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sun Sook Chung ◽  
Joseph C F Ng ◽  
Anna Laddach ◽  
N Shaun B Thomas ◽  
Franca Fraternali
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Interaction Network ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Short Loop ◽  
New Strategy ◽  
Loop Network ◽  
Protein Protein Interaction Network

Abstract Direct drug targeting of mutated proteins in cancer is not always possible and efficacy can be nullified by compensating protein–protein interactions (PPIs). Here, we establish an in silico pipeline to identify specific PPI sub-networks containing mutated proteins as potential targets, which we apply to mutation data of four different leukaemias. Our method is based on extracting cyclic interactions of a small number of proteins topologically and functionally linked in the Protein–Protein Interaction Network (PPIN), which we call short loop network motifs (SLM). We uncover a new property of PPINs named ‘short loop commonality’ to measure indirect PPIs occurring via common SLM interactions. This detects ‘modules’ of PPI networks enriched with annotated biological functions of proteins containing mutation hotspots, exemplified by FLT3 and other receptor tyrosine kinase proteins. We further identify functional dependency or mutual exclusivity of short loop commonality pairs in large-scale cellular CRISPR–Cas9 knockout screening data. Our pipeline provides a new strategy for identifying new therapeutic targets for drug discovery.

scholarly journals Contribution of Ionotropic Glutamatergic Receptors to Excitability and Attentional Signals in Macaque Frontal Eye Field

2021 ◽  
Author(s):  
Miguel Dasilva ◽  
Christian Brandt ◽  
Marc Alwin Gieselmann ◽  
Claudia Distler ◽  
Alexander Thiele
Keyword(s):  
Attentional Control ◽  
Large Scale ◽  
Neuronal Excitability ◽  
Cell Types ◽  
Receptor Activation ◽  
Frontal Eye Field ◽  
Control Signals ◽  
Cognitive Operations ◽  
Eye Field ◽  
Large Scale Networks

Abstract Top-down attention, controlled by frontal cortical areas, is a key component of cognitive operations. How different neurotransmitters and neuromodulators flexibly change the cellular and network interactions with attention demands remains poorly understood. While acetylcholine and dopamine are critically involved, glutamatergic receptors have been proposed to play important roles. To understand their contribution to attentional signals, we investigated how ionotropic glutamatergic receptors in the frontal eye field (FEF) of male macaques contribute to neuronal excitability and attentional control signals in different cell types. Broad-spiking and narrow-spiking cells both required N-methyl-D-aspartic acid and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor activation for normal excitability, thereby affecting ongoing or stimulus-driven activity. However, attentional control signals were not dependent on either glutamatergic receptor type in broad- or narrow-spiking cells. A further subdivision of cell types into different functional types using cluster-analysis based on spike waveforms and spiking characteristics did not change the conclusions. This can be explained by a model where local blockade of specific ionotropic receptors is compensated by cell embedding in large-scale networks. It sets the glutamatergic system apart from the cholinergic system in FEF and demonstrates that a reduction in excitability is not sufficient to induce a reduction in attentional control signals.

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