Network analysis methods for studying microbial communities: A mini review.
Monica Steffi Matchado,Michael Lauber,Sandra Reitmeier,Tim Kacprowski,Tim Kacprowski,Jan Baumbach,Jan Baumbach,Dirk Haller,Markus List +8 more
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TLDR
A comprehensive overview of state-of-the-art methods to infer intra-kingdom interactions ranging from simple correlation-to complex conditional dependence-based methods can be found in this paper.Abstract:
Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities in complex and contiguous environments. They engage in numerous inter- and intra- kingdom interactions which can be inferred from microbiome profiling data. In particular, network-based approaches have proven helpful in deciphering complex microbial interaction patterns. Here we give an overview of state-of-the-art methods to infer intra-kingdom interactions ranging from simple correlation- to complex conditional dependence-based methods. We highlight common biases encountered in microbial profiles and discuss mitigation strategies employed by different tools and their trade-off with increased computational complexity. 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.read more
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iNAP: An integrated network analysis pipeline for microbiome studies
Kai Feng,Xi Peng,Zheng Zhang,Songsong Gu,Qing He,Wenli Shen,Zhujun Wang,Danrui Wang,Qiu-Long Hu,Yan Li,Shuang Wang,Ye Deng +11 more
TL;DR: Integrated network analysis pipeline (iNAP) as discussed by the authors is an online analysis pipeline for generating and analyzing comprehensive ecological networks in microbiome studies, which is implemented in two sections, that is, network construction and network analysis, and integrates many open access tools.
Journal ArticleDOI
Best practices in metabarcoding of fungi: From experimental design to results
Leho Tedersoo,Mohammad Bahram,Lucie Zinger,R. Henrik Nilsson,Peter G. E. Kennedy,Teng Yang,Sten Anslan,Vladimir S. Mikryukov +7 more
TL;DR: It is demonstrated that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity and specific methods for compositional data analyses provide more reliable estimates of shifts in community structure.
Journal ArticleDOI
Age-related diseases, therapies and gut microbiome: A new frontier for healthy aging
TL;DR: In this article , the development of integrated microbiome-based intervention strategies, aimed at favoring a eubiotic configuration and trajectory, could therefore represent an innovative approach for the promotion of healthy aging and the achievement of longevity.
Journal ArticleDOI
Prevalence of Actinobacteria in the production of 2-methylisoborneol and geosmin, over Cyanobacteria in a temperate eutrophic reservoir
TL;DR: The Eagle Creek Reservoir, a eutrophic temperate reservoir, is frequently impacted by seasonal odorous episodes, and during the spring 2013 outbreak of 2-methylisoborneol (MIB) and geosmin (GSM) (120.9 and 51.4 ng L−1, respectively), a shotgun metagenomics approach illustrated the dominance of Actinobacteria (genus Streptomyces) rather than Cyanobacteria, formerly assumed to be the main producers as discussed by the authors .
Journal ArticleDOI
Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions.
TL;DR: The available approaches for absolute quantification are highly diverse and challenging, especially for quantification in differing biological situations, such as distinguishing between live and dead cells, quantification of specific taxa, enumeration of low biomass samples, large sample size feasibility, and the detection of various other cellular features as discussed by the authors.
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