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Microbial Co-occurrence Relationships in the Human Microbiome

Karoline Faust, J. Fah Sathirapongsasuti, Jacques Izard, Nicola Segata, Dirk Gevers, Jeroen Raes, Curtis Huttenhower, Christos A. Ouzounis
2012 PLoS Computational Biology  
in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome.  ...  This approach thus serves to open new opportunities for future targeted mechanistic studies of the microbial ecology of the human microbiome.  ...  Acknowledgments We thank the other members of the Human Microbiome Project consortium for study design and data production.  ... 
doi:10.1371/journal.pcbi.1002606 pmid:22807668 pmcid:PMC3395616 fatcat:2yavbh5gunbkbbw7dhceblp3km

Emerging trends and focus of human gastrointestinal microbiome research from 2010–2021: a visualized study

Xingzhu Yuan, Chengting Chang, Xinrong Chen, Ka Li
2021 Journal of Translational Medicine  
CiteSpace was used to construct country and author co-occurrence map; conduct journal, citation cocitation analysis, and reference co-citation knowledge map; and form a keywords co-occurrence map, a clustering  ...  In addition, researchers (2018–2021) focused on the gastrointestinal microbial community and the diversity of certain types of microbes.  ...  All countries and regions in the world have studied the human The author co-occurrence knowledge map of the human gastrointestinal microbiome during 2010-2021.  ... 
doi:10.1186/s12967-021-03009-8 fatcat:i3gge3tzkrc3zhtuapwnqmyixy

Characterization of microbial associations in human oral microbiome

Min Su Lee, Sangyoon Oh, Haixu Tang
2014 Bio-medical materials and engineering  
In this paper, we built an association network among microorganisms from the human oral microbiome.  ...  Within the same community, some microorganisms tend to co-exist, whereas some others tend to avoid each other.  ...  In this study, we constructed an accurate microbial co-occurrence and mutual-exclusion network for the human oral microbiome.  ... 
doi:10.3233/bme-141202 pmid:25227089 fatcat:4sad2swvkfan5ozorc655mwtjy

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

Bin Ma, Yiling Wang, Shudi Ye, Shan Liu, Erinne Stirling, Jack A Gilbert, Karoline Faust, Rob Knight, Janet K Jansson, Cesar Cardona, Lisa Röttjers, Jianming Xu
2020 Microbiome  
The high number of specialist edges highlights that environmental specific co-occurrence relationships are essential features across microbiomes.  ...  Microbial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems,  ...  This research was financially supported by the National Natural Science  ... 
doi:10.1186/s40168-020-00857-2 pmid:32498714 pmcid:PMC7273686 fatcat:umqpdddhpreexlrckr5kynvr5i

Network analysis methods for studying microbial communities: A mini review

Monica Steffi Matchado, Michael Lauber, Sandra Reitmeier, Tim Kacprowski, Jan Baumbach, Dirk Haller, Markus List
2021 Computational and Structural Biotechnology Journal  
They engage in numerous inter- and intra- kingdom interactions which can be inferred from microbiome profiling data.  ...  Finally, we discuss current limitations that motivate further method development to infer inter-kingdom interactions and to robustly and comprehensively characterize microbial environments in the future  ...  Decoding complex microbial co-occurrence relationships is associated with three main challenges.  ... 
doi:10.1016/j.csbj.2021.05.001 pmid:34093985 pmcid:PMC8131268 fatcat:ba6wne7jprat3jgnngfbzkebq4

Networking in the Plant Microbiome

Marcel G. A. van der Heijden, Martin Hartmann
2016 PLoS Biology  
A new paper in this issue of PLOS Biology by Agler et al. highlights the presence of microbial hubs in these networks that may act as mediators between the plant and its microbiome.  ...  Emerging studies with plants reveal that these microbiomes are structured and form complex, interconnected microbial networks.  ...  Microbial taxa that frequently co-occur with other taxa in microbial co-occurrence networks potentially play a key role within the microbiome, as they might interact with many other microbial taxa.  ... 
doi:10.1371/journal.pbio.1002378 pmid:26871440 pmcid:PMC4752285 fatcat:be7yh5lyyvfrra5qw7vl3jjecm

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups

Deepak Yadav, Tarini Shankar Ghosh, Sharmila S. Mande
2016 Gut Pathogens  
Amongst European gut-microbiomes, the co-occurrence network obtained for the Danish population was observed to be most dense.  ...  To summarise, the present study identifies geography and age specific patterns in the composition as well as microbial interactions in gut microbiomes.  ...  However, the company provided support only in the form of salaries for authors, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation  ... 
doi:10.1186/s13099-016-0099-z pmid:27158266 pmcid:PMC4858888 fatcat:ck5tg5a23rchtk4ujkzghdfb2m

Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys [article]

Ravichandra Vemuri, Chrissy Sherrill, Matt Davis, Kylie Kavanagh
2020 bioRxiv   pre-print
Microbial community co-occurrence analysis revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys.  ...  While it is known that the gut microbiome and physiological systems interact, the relationship between the microbiome in an aged body system remains to be clearly defined, particularly in the context of  ...  RV performed data analysis and interpretation and participated in manuscript preparation. CS performed data analysis and interpretation and participated in manuscript preparation.  ... 
doi:10.1101/2020.05.17.100560 fatcat:47yks4depndihk6jnsgd2i4kpe

Microbial "social networks"

Mitch Fernandez, Juan D Riveros, Michael Campos, Kalai Mathee, Giri Narasimhan
2015 BMC Genomics  
Results: The tools developed provide a framework for analyzing relationships between bacterial taxa modeled as bacterial co-occurrence networks.  ...  Conclusions: Microbial relationships are similar to those found in social networks.  ...  Acknowledgements This work was partially supported by a grant from the Florida Department of Health grant 09KW- 10  ... 
doi:10.1186/1471-2164-16-s11-s6 pmid:26576770 pmcid:PMC4652466 fatcat:2gvw36wcdnafpj44vbfebzlx74

A framework for detecting and quantifying relationship alterations in microbial community [article]

Zhi Liu, Kai Mi, Zhenjiang Xu, Qiankun Zhang, Xingyin Liu
2020 bioRxiv   pre-print
Examining the relationship alteration (RA) in microbiome between different healthy status provides additional hints about the pathogenesis of human disease.  ...  The performance of PM2RA were evaluated in synthetic data, and found to show higher specificity and sensitivity than the co-occurrence-based methods.  ...  The relationships are usually modeled by the linear correlation between two types of microbes [12] [13] [14] , and co-occurrence networks are constructed to describe the whole microbial relationship.  ... 
doi:10.1101/2020.04.09.033688 fatcat:i6r6vqmmxna2zmmhqd6yxjbsqq

A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships

Suyeon Kim, Ishwor Thapa, Ling Zhang, Hesham Ali
2019 BMC Genomics  
The obtained results highlight the importance of the microbial communities and their inter-relationships and show how these microbial structures are correlated with Crohn's disease.  ...  Microbiomes play vital roles in shaping environments and stabilize them based on their compositions and inter-species relationships among its species.  ...  Acknowledgements We thank Bioinformatics group at UNO for useful discussions regarding the content of this work. About this supplement  ... 
doi:10.1186/s12864-019-6288-7 pmid:31856723 pmcid:PMC6923821 fatcat:jnherx7fvrhudikpiytd3pe57a

Revealing microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation [article]

Shion Hosoda, Suguru Nishijima, Tsukasa Fukunaga, Masahira Hattori, Michiaki Hamada
2019 bioRxiv   pre-print
In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method, which was first proposed for the classification of documents in natural language processing.  ...  We applied LDA to a large-scale human gut metagenome dataset and found that a four-assemblage LDA model can represent relationships between enterotypes and assemblages with high interpretability.  ...  Acknowledgements The computations in this research were performed using the supercomputing facilities at the National Institute of Genetics in Research Organization of Information and Systems.  ... 
doi:10.1101/664219 fatcat:xcwlrm222fafbigykguedfzslm

The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome

Paurush Praveen, Ferenc Jordan, Corrado Priami, Melissa J. Morine
2015 Microbiome  
An integrative study on the diet, the microbiota, and genomic activity at the transcriptomic level may give an insight into the role of diet in shaping the human/microbiome relationship.  ...  Conclusions: Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed.  ...  Acknowledgements The authors thank the other team members at the Microsoft Research-University of Trento Centre for Computational and Systems Biology for the many interesting discussions on the topic.  ... 
doi:10.1186/s40168-015-0104-7 pmid:26399409 pmcid:PMC4581423 fatcat:sfnbe2uedrglzi5egfgiunjeie

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

Zhigang Zhang, Jiawei Geng, Xiaodan Tang, Hong Fan, Jinchao Xu, Xiujun Wen, Zhanshan Ma, Peng Shi
2013 The ISME Journal  
Human gut microbiota shows high inter-subject variations, but the actual spatial distribution and co-occurrence patterns of gut mucosa microbiota that occur within a healthy human instestinal tract remain  ...  Furthermore, spatial co-occurring network analysis of mucosa microbial inhabitants together with occupancy (that is habitat generalists, specialists and opportunist) analyses implies that ecological relationships  ...  ZZ, JG, XT and HF generated the data. ZZ, JG, JX, XW, ZM and PS analysed the data. ZZ, ZM and PS wrote the manuscript with inputs from the other members of the team.  ... 
doi:10.1038/ismej.2013.185 pmid:24132077 pmcid:PMC3960530 fatcat:j5c6afstyzchpiukkvc7ur6esy

Co-existence of network architectures supporting the human gut microbiome

C.V. Hall, A. Lord, R. Betzel, M. Zakrewski, L.A. Simms, A. Zalesky, G. Radford-Smith, L. Cocchi
2019 iScience  
Microbial organisms of the human gut microbiome do not exist in isolation but form complex and diverse interactions to maintain health and reduce risk of disease development.  ...  Here, we leverage recent methodological advances in network modeling to assess whether communities in the human microbiome exhibit a single network structure or whether co-existing mesoscale network architectures  ...  Using the WSBM framework, we sought to (1) establish whether the human microbiome exhibits a unique or heterogeneous mesoscale network architecture; (2) understand the patterns of microbial co-occurrence  ... 
doi:10.1016/j.isci.2019.11.032 pmid:31812808 pmcid:PMC6911941 fatcat:yiacp4lsr5hxllgcwglv3r6l7i
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