scholarly journals Controlling complex microbial communities: a network-based approach

2017 ◽  
Author(s):  
Marco Tulio Angulo ◽  
Claude H. Moog ◽  
Yang-Yu Liu
Keyword(s):  
Microbial Communities ◽  
Hydrothermal Vents ◽  
Well Being ◽  
Natural Ecosystems ◽  
Healthy Human ◽  
Form Complex ◽  
Control Framework ◽  
Gnotobiotic Mice ◽  
Ircinia Oros ◽  
Systematic Framework

Microbes comprise nearly half of all biomass on Earth. Almost every habitat on Earth is teeming with microbes, from hydrothermal vents to the human gastrointestinal tract. Those microbes form complex communities and play critical roles in maintaining the integrity of their environment or the well-being of their hosts. Controlling microbial communities can help us restore natural ecosystems and maintain healthy human microbiota. Yet, our ability to precisely manipulate microbial communities has been fundamentally impeded by the lack of a systematic framework to control them. Here we fill this gap by developing a control framework based on the new notion of structural accessibility. This framework allows identifying minimal sets of “driver species” through which we can achieve feasible control of the entire microbial community. We numerically validate our control framework on large microbial communities, and then we demonstrate its application for controlling the gut microbiota of gnotobiotic mice infected withClostridium difficileand the core microbiota of the sea spongeIrcinia oros.

scholarly journals Predicting microbiome compositions through deep learning.

2021 ◽  
Author(s):  
Sebastian Michel-Mata ◽  
Xu-Wen Wang ◽  
Yang-Yu Liu ◽  
Marco Tulio Angulo
Keyword(s):  
Deep Learning ◽  
Microbial Communities ◽  
Synthetic Data ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Training Data ◽  
Oral Microbiota ◽  
Form Complex

Microbes can form complex communities that perform critical functions in maintaining the integrity of their environment1,2 or the well-being of their hosts3-6. Successfully managing these microbial communities requires the ability to predict the community composition based on the species assemblage7. However, making such a prediction remains challenging because of our limited knowledge of the diverse physical8, biochemical9, and ecological10,11 processes governing the microbial dynamics. To overcome this challenge, here we present a deep learning framework that automatically learns the map between species assemblages and community compositions from training data. First, we systematically validate our framework using synthetic data generated by classical population dynamics models. Then, we apply it to experimental data of both in vitro and in vivo communities, including ocean and soil microbial communities12,13, Drosophila melanogaster gut microbiota14, and human gut and oral microbiota15. Our results demonstrate how deep learning can enable us to understand better and potentially manage complex microbial communities.

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

scholarly journals Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shenzheng Zeng ◽  
Sukontorn Khoruamkid ◽  
Warinphorn Kongpakdee ◽  
Dongdong Wei ◽  
Lingfei Yu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Well Being ◽  
Pacific White Shrimp ◽  
Shrimp Farming ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Shrimp Culture ◽  
Water And Sediment ◽  
Surrounding Environment ◽  
Shrimp Production

Abstract The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The “Aquamimicry system”, mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

scholarly journals Human gut microbial communities dictate efficacy of anti-PD-1 therapy in a humanized microbiome mouse model of glioma

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Kory J Dees ◽  
Hyunmin Koo ◽  
J Fraser Humphreys ◽  
Joseph A Hakim ◽  
David K Crossman ◽  
...  
Keyword(s):  
Mouse Model ◽  
Microbial Communities ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Microbial Composition ◽  
Healthy Human ◽  
Fecal Transplantation ◽  
Host Interaction ◽  
Shotgun Metagenomic Sequencing ◽  
Mouse Lines

Abstract Background Although immunotherapy works well in glioblastoma (GBM) preclinical mouse models, the therapy has not demonstrated efficacy in humans. To address this anomaly, we developed a novel humanized microbiome (HuM) model to study the response to immunotherapy in a preclinical mouse model of GBM. Methods We used 5 healthy human donors for fecal transplantation of gnotobiotic mice. After the transplanted microbiomes stabilized, the mice were bred to generate 5 independent humanized mouse lines (HuM1-HuM5). Results Analysis of shotgun metagenomic sequencing data from fecal samples revealed a unique microbiome with significant differences in diversity and microbial composition among HuM1-HuM5 lines. All HuM mouse lines were susceptible to GBM transplantation, and exhibited similar median survival ranging from 19 to 26 days. Interestingly, we found that HuM lines responded differently to the immune checkpoint inhibitor anti-PD-1. Specifically, we demonstrate that HuM1, HuM4, and HuM5 mice are nonresponders to anti-PD-1, while HuM2 and HuM3 mice are responsive to anti-PD-1 and displayed significantly increased survival compared to isotype controls. Bray-Curtis cluster analysis of the 5 HuM gut microbial communities revealed that responders HuM2 and HuM3 were closely related, and detailed taxonomic comparison analysis revealed that Bacteroides cellulosilyticus was commonly found in HuM2 and HuM3 with high abundances. Conclusions The results of our study establish the utility of humanized microbiome mice as avatars to delineate features of the host interaction with gut microbial communities needed for effective immunotherapy against GBM.

IMMU-09. HUMAN MICROBIOTA INFLUENCE THE EFFICACY OF IMMUNOTHERAPY IN A MOUSE MODEL OF GLIOBLASTOMA

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi93-vi94
Author(s):  
Kory Dees ◽  
Hyunmin Koo ◽  
James Humphreys ◽  
Joseph Hakim ◽  
David Crossman ◽  
...  
Keyword(s):  
Mouse Model ◽  
Microbial Communities ◽  
Mouse Models ◽  
Gut Microbiome ◽  
Positive Response ◽  
Checkpoint Inhibitors ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Microbial Composition ◽  
Healthy Human

Abstract Although immunotherapy works well in glioblastoma (GBM) pre-clinical mouse models, the therapy has unfortunately not demonstrated efficacy in humans. In melanoma and other cancers, the composition of the gut microbiome has been shown to determine responsiveness or resistance to immune checkpoint inhibitors (anti-PD-1). Most pre-clinical cancer studies have been done in mouse models using mouse gut microbiomes, but there are significant differences between mouse and human microbial gut compositions. To address this inconsistency, we developed a novel humanized microbiome (HuM) model to study the response to immunotherapy in a pre-clinical mouse model of GBM. We used five healthy human donors for fecal transplantation of gnotobiotic mice. After the transplanted microbiomes stabilized, the mice were bred to generate five independent humanized mouse lines (HuM1-HuM5). Analysis of shotgun metagenomic sequencing data from fecal samples revealed a unique microbiome with significant differences in diversity and microbial composition among HuM1-HuM5 lines. Interestingly, we found that the HuM lines responded differently to anti-PD-1. Specifically, we demonstrate that HuM2 and HuM3 mice are responsive to anti-PD-1 and displayed significantly increased survival compared to isotype controls, while HuM1, HuM4, and HuM5 mice are resistant to anti-PD-1. These mice are genetically identical, and only differ in the composition of the gut microbiome. In a correlative experiment, we found that disrupting the responder HuM2 microbiome with antibiotics abrogated the positive response to anti-PD-1, indicating that HuM2 microbiota must be present in the mice to elicit the positive response to anti-PD-1 in the GBM model. The question remains of whether the “responsive” microbial communities in HuM2 and HuM3 can be therapeutically exploited and applicable in other tumor models, or if the “resistant” microbial communities in HuM1, HuM4, and HuM5 can be depleted and/or replaced. Future studies will assess responder microbial transplants as a method of enhancing immunotherapy.

scholarly journals Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Haiyan Chu ◽  
Gui-Feng Gao ◽  
Yuying Ma ◽  
Kunkun Fan ◽  
Manuel Delgado-Baquerizo
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Ecosystem Functions ◽  
Soil Microbial ◽  
Microbial Biogeography ◽  
Recent Advances ◽  
Technological Advances ◽  
Global Change Scenarios ◽  
Changing World

ABSTRACT Soil microbial communities are fundamental to maintaining key soil processes associated with litter decomposition, nutrient cycling, and plant productivity and are thus integral to human well-being. Recent technological advances have exponentially increased our knowledge concerning the global ecological distributions of microbial communities across space and time and have provided evidence for their contribution to ecosystem functions. However, major knowledge gaps in soil biogeography remain to be addressed over the coming years as technology and research questions continue to evolve. In this minireview, we state recent advances and future directions in the study of soil microbial biogeography and discuss the need for a clearer concept of microbial species, projections of soil microbial distributions toward future global change scenarios, and the importance of embracing culture and isolation approaches to determine microbial functional profiles. This knowledge will be critical to better predict ecosystem functions in a changing world.

scholarly journals Assessment of the Spatial Dynamics and Interactions among Multiple Ecosystem Services to Promote Effective Policy Making across Mediterranean Island Landscapes

2018 ◽  
Vol 10 (9) ◽  
pp. 3285 ◽  
Author(s):  
Roxanne Lorilla ◽  
Konstantinos Poirazidis ◽  
Stamatis Kalogirou ◽  
Vassilis Detsis ◽  
Aristotelis Martinis
Keyword(s):  
Ecosystem Services ◽  
Spatial Dynamics ◽  
Well Being ◽  
Temporal Variations ◽  
Spatial And Temporal Variation ◽  
Natural Ecosystems ◽  
Economic Resilience ◽  
Central Mediterranean ◽  
Ionian Islands ◽  
Trade Offs

To manage multiple ecosystem services (ES) effectively, it is essential to understand how the dynamics of ES maintain healthy ecosystems to avoid potential negative impacts on human well-being in the context of sustainable development. In particular, the Ionian Islands in the central Mediterranean are characterized by high natural, ecological, and recreational value; however, the intensification of human activities over time has resulted in the loss of natural ecosystems, which might have negatively impacted ES. Here, we aimed to assess and understand the spatiotemporal dynamics of ES supply and how these components interact across the Ionian Islands to optimize future ES provision and mitigate current trade-offs. We quantified multiple ecosystem services and analyzed their interactions at a temporal scale across the four prefectures of the Ionian Islands. Seven ES were quantified covering all three ES sections (provisioning, regulating and maintenance, and cultural) of the Common International Classification of Ecosystem Services (CICES). ES interactions were investigated by analyzing ES relationships, identifying ES bundles (sets of ES that repeatedly occur together across space and time), and specifying ES occurrence within bundles. The three ES groups exhibited similar patterns on some islands, but differed on islands with areas of high recreation in parallel to low provisioning and regulating ES. Temporal variations showed both stability and changes to the supply of ES, as well as in the interactions among them. Different patterns among the islands were caused by the degree of mixing between natural vegetation and olive orchards. This study identified seven ES bundles that had distinct compositions and magnitudes, with both unique and common bundles being found among the islands. The olive grove bundle delivered the most ES, while the non-vegetated bundle delivered negligible amounts of ES. Spatial and temporal variation in ES appear to be determined by agriculture, land abandonment, and increasing tourism, as well as the occurrence of fires. Knowledge about the spatial dynamics and interactions among ES could provide information for stakeholders and decision-making processes to develop appropriate sustainable management of the ecosystems on the Ionian Islands to secure ecological, social, and economic resilience.

scholarly journals Environmental Role of National Parks

2015 ◽  
Vol 9 (1) ◽  
pp. 1 ◽  
Author(s):  
Molla Mekonnen Alemu
Keyword(s):  
National Parks ◽  
Raw Materials ◽  
Well Being ◽  
Food Sources ◽  
Extensive Literature ◽  
Spiritual Values ◽  
Natural Ecosystems ◽  
Weather Events ◽  
Access To Food

The natural ecosystems are endangered due to human behavior; the razing of forests is diminishing the world’s oxygen supply and potentially irreplaceable natural resources. Wetlands are being drained, eliminating breeding environments for millions of birds and reproducing grounds for fish; cherished fauna and flora species are being endangered from extinction. Clean water, clean air, access to food sources, buffers of weather events, cultural and spiritual values, and raw materials for consumers, are some of the ecosystem services that ensure the well-being of humanity. Well-managed protected areas are a proven mechanism in the protection and conservation of healthy ecosystems and the services they provide. National Parks are essentially planned to shelter the lasting "wilderness" of a given country and have principally dedicated on the maintenance of extraordinary areas or emblematic species. This paper is aimed at exploring the environmental role of national parks by having an extensive literature review and come up with recommendations which can help the conservation of national parks.

scholarly journals Applying indirect open-circuit calorimetry to study energy expenditure in gnotobiotic mice harboring different human gut microbial communities

Microbiome ◽  
2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Ilia G. Halatchev ◽  
David O’Donnell ◽  
Matthew C. Hibberd ◽  
Jeffrey I. Gordon
Keyword(s):  
Microbial Communities ◽  
Energy Homeostasis ◽  
Open Circuit ◽  
Microbial Consortia ◽  
Illustrative Case ◽  
Bacterial Strains ◽  
Human Gut ◽  
New Methods ◽  
Gnotobiotic Mice ◽  
Environmental Microbes

AbstractGiven the increasing use of gnotobiotic mouse models for deciphering the effects of human microbial communities on host biology, there is a need to develop new methods for characterizing these animals while maintaining their isolation from environmental microbes. We describe a method for performing open-circuit indirect calorimetry on gnotobiotic mice colonized with gut microbial consortia obtained from different human donors. In this illustrative case, cultured collections of gut bacterial strains were obtained from obese and lean co-twins. The approach allows microbial contributions to host energy homeostasis to be characterized.

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