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Microbial community pattern detection in human body habitats via ensemble clustering framework

Peng Yang, Xiaoquan Su, Le Ou-Yang, Hon-Nian Chua, Xiao-Li Li, Kang Ning
2014 BMC Systems Biology  
In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial  ...  To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data.  ...  Ensemble clustering framework In this subsection, we proposed a novel ensemble clustering framework, namely Meta-EC, to perform microbial community pattern detection.  ... 
doi:10.1186/1752-0509-8-s4-s7 pmid:25521415 pmcid:PMC4290728 fatcat:kn6lyjvmyzgmpd57nusczlyph4

Application of Deep Learning in Microbiome

Qiang Zhu, Ban Huo, Han Sun, Bojing Li, Xingpeng Jiang
2020 Journal of Artificial Intelligence for Medical Sciences  
In particular, we discuss the current application and challenges of deep learning in microbial studies.  ...  In this survey, we introduce the application of machine learning in microbial data analysis and focus on microbial classification and feature selection tasks.  ...  However, it is estimated the number of microbial genes in the human body is much larger than the human genome.  ... 
doi:10.2991/jaims.d.201028.001 fatcat:hnopfambffdlrcgbi4x4ud6phi

Microbial Interrelationships across Sites of Breastfeeding Mothers and Infants at 6 Weeks Postpartum

Erin C. Davis, Mei Wang, Sharon M. Donovan
2022 Microorganisms  
Lastly, we identified twenty-one significant co-occurrence relationships between bacteria in human milk and on other maternal and infant body sites.  ...  These results demonstrate several unique microbial interrelationships between breastfeeding dyads, providing insight into potential mechanisms of microbial assembly in early life.  ...  Bacterial Co-Occurrence Patterns between Human Milk and Maternal and Infant Body Sites To further explore microbial interactions between mothers and infants, we utilized an ensemble approach in CoNet to  ... 
doi:10.3390/microorganisms10061155 pmid:35744673 fatcat:gzrqftd5iza63pcdcdosrylzn4

Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

Laura Judith Marcos-Zambrano, Kanita Karaduzovic-Hadziabdic, Tatjana Loncar Turukalo, Piotr Przymus, Vladimir Trajkovik, Oliver Aasmets, Magali Berland, Aleksandra Gruca, Jasminka Hasic, Karel Hron, Thomas Klammsteiner, Mikhail Kolev (+17 others)
2021 Frontiers in Microbiology  
to predict diseases and use microbial communities to stratify patients by their characterization of state-specific microbial signatures.  ...  Although the data presented here is more related to the bacterial community, many algorithms could be applied in general, regardless of the feature type.  ...  ACKNOWLEDGMENTS The authors are grateful to all COST Action CA18131 "Statistical and machine learning techniques in human microbiome studies" members for their contribution in discussion about evaluation  ... 
doi:10.3389/fmicb.2021.634511 pmid:33737920 pmcid:PMC7962872 fatcat:wbun4lkwwjen5ccdy4zb7mnz3q

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

S. Greenblum, P. J. Turnbaugh, E. Borenstein
2011 Proceedings of the National Academy of Sciences of the United States of America  
W e humans are mostly microbes. Microbial communities populate numerous sites in the human anatomy and harbor over 100 trillion microbial cells (1).  ...  Among the various body habitats, the most densely colonized is the distal gut.  ...  S.G. is supported by "Interdisciplinary Training in Genomic Sciences" National Human Genome Research Institute Grant T32 HG00035.  ... 
doi:10.1073/pnas.1116053109 pmid:22184244 pmcid:PMC3258644 fatcat:nvhch3yd3fet3bfhbdgtjvvrpm

Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome

Jens Christian Claussen, Jurgita Skiecevičienė, Jun Wang, Philipp Rausch, Tom H. Karlsen, Wolfgang Lieb, John F. Baines, Andre Franke, Marc-Thorsten Hütt, Reka Albert
2017 PLoS Computational Biology  
Here we present a novel analysis method based on Boolean operations applied to microbial co-occurrence patterns.  ...  , but also due to the high relevance of the microbiome in human health and disease.  ...  Author summary Over the last years the composition of microbial communities in the human gut, the gut microbiome, has gained prominence in clinical research.  ... 
doi:10.1371/journal.pcbi.1005361 pmid:28640804 pmcid:PMC5480827 fatcat:exbydysnjnbvlf7y7nnjgxaddy

Emerging Priorities for Microbiome Research

Chad M. Cullen, Kawalpreet K. Aneja, Sinem Beyhan, Clara E. Cho, Stephen Woloszynek, Matteo Convertino, Sophie J. McCoy, Yanyan Zhang, Matthew Z. Anderson, David Alvarez-Ponce, Ekaterina Smirnova, Lisa Karstens (+7 others)
2020 Frontiers in Microbiology  
Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external  ...  The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe  ...  ACKNOWLEDGMENTS We thank the NIH and NSF for the 2017 Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome, which sparked great conversations  ... 
doi:10.3389/fmicb.2020.00136 pmid:32140140 pmcid:PMC7042322 fatcat:hpo2ms7yxfbsthpvt4wswqtxiq

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data

C. De Filippo, M. Ramazzotti, P. Fontana, D. Cavalieri
2012 Briefings in Bioinformatics  
This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions.  ...  Metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems.  ...  Importantly, increasing interest in microbial community metabolic simulations is evident, as shown by the recent development of OptCom, a microbial community-addressed FBA framework [86] .  ... 
doi:10.1093/bib/bbs070 pmid:23175748 pmcid:PMC3505041 fatcat:rm3rv7rp3nht7jyqxkurirfcl4

Phylogenetic approaches to microbial community classification

Jie Ning, Robert G. Beiko
2015 Microbiome  
Results: We focused our attention on the classification of nine oral sites and dental plaque in particular, using data collected from the Human Microbiome Project.  ...  The microbiota from different body sites are dominated by different major groups of microbes, but the variations within a body site such as the mouth can be more subtle.  ...  Background Marker-gene profiles of human microbiota can provide a detailed view of microbial diversity across many body sites [1] .  ... 
doi:10.1186/s40168-015-0114-5 pmid:26437943 pmcid:PMC4593236 fatcat:tfobmpquonci5jupycy2fke44a

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome

Ohad Manor, Elhanan Borenstein
2017 Cell Host and Microbe  
Results Challenges and opportunities in linking microbiome taxonomic and functional data Consider a standard metagenomic comparative analysis, where samples from different habitats or from a disease cohort  ...  Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases.  ...  This work was supported in part by New Innovator Award DP2 AT007802-01 to EB.  ... 
doi:10.1016/j.chom.2016.12.014 pmid:28111203 pmcid:PMC5316541 fatcat:ca4tsrkqznh3bpbxa6r5xfuj6m

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

Samiran Banerjee, Florian Walder, Lucie Büchi, Marcel Meyer, Alain Y. Held, Andreas Gattinger, Thomas Keller, Raphael Charles, Marcel G. A. van der Heijden
2019 The ISME Journal  
communities.  ...  We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland.  ...  Once recruited inside the plant body, microbial adaptation and survival will depend on the host physiological patterns [26, 58, 110] .  ... 
doi:10.1038/s41396-019-0383-2 pmid:30850707 pmcid:PMC6591126 fatcat:ftswuo6y3jftbn3gg2l4zpmkf4

Application of Taxonomic Modeling to Microbiota Data Mining for Detection of Helminth Infection in Global Populations

Mahbaneh Eshaghzadeh Torbati, Makedonka Mitreva, Vanathi Gopalakrishnan
2016 Data  
In this paper, we test our hypothesis using classification models that detect helminth infection in microbiota of human fecal samples obtained from Indonesia and Liberia countries.  ...  Predictive modeling of such microbiota count data for classification of human infection from parasitic worms such as helminths can help in detection and management across global populations.  ...  The mixMC framework uses Principal Component Analysis (PCA) to visualize diversity patterns and sPLS-DA to find indicator species or determinant microbiota members discriminating habitats or body sites  ... 
doi:10.3390/data1030019 pmid:28239609 pmcid:PMC5325162 fatcat:ofqjftuxwrhp7h4nthngb364zy

CoNet app: inference of biological association networks using Cytoscape

Karoline Faust, Jeroen Raes
2016 F1000Research  
Though CoNet was developed with microbial community data from sequencing experiments in mind, it is designed to be generic and can detect associations in any data set where biological entities (such as  ...  Here we briefly describe its main features and illustrate its use on microbial count data obtained by 16S rDNA sequencing of arctic soil samples. The CoNet app is available at: .  ...  In this way, we could group body sites into microbial habitats, identify hub classes in the oral cavity and highlight the importance of competitive and parasitic interactions in plankton communities.  ... 
doi:10.12688/f1000research.9050.2 pmid:27853510 pmcid:PMC5089131 fatcat:7ssccmqldfhl5flgvqh5mmxoie

Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities

Ryan B. Ghannam, Laura G. Schaerer, Timothy M. Butler, Stephen M. Techtmann, Katherine McMahon
2020 mSphere  
Machine learning approaches have been used mostly to examine the human microbiome and, to some extent, microbial communities from the environment.  ...  Further, this study displays how global biogeographic patterning of aquatic microbial communities (and other systems) can be assessed through populations of the highly abundant and ubiquitous taxa that  ...  We thank the captain and crews of all of research vessels used in sampling. In particular, we thank Jamey Anderson and Christopher Pinnow for help in sample collection from ports in the Great Lakes.  ... 
doi:10.1128/msphere.00481-19 pmid:31996419 pmcid:PMC6992368 fatcat:nxtiupleivbjpnpl6ldecyu2fu

Microbial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants

Yvonne Vallès, Alejandro Artacho, Alberto Pascual-García, Maria Loreto Ferrús, María José Gosalbes, Juan José Abellán, M. Pilar Francino, David S. Guttman
2014 PLoS Genetics  
In spite of its major impact on life-long health, the process of microbial succession in the gut of infants remains poorly understood.  ...  Here, we analyze the patterns of taxonomic and functional change in the gut microbiota during the first year of life for a birth cohort of 13 infants.  ...  We also thank the midwives who collaborated in the recruitment of study volunteers as well as all the mothers and babies who generously participated in the study. Author Contributions  ... 
doi:10.1371/journal.pgen.1004406 pmid:24901968 pmcid:PMC4046925 fatcat:pq544tzhcrg2jmykjw5ct67f2a
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