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Title: Combining compositional data sets introduces error in covariance network reconstruction

Journal Article · · ISME Communications
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
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Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
89233218CNA000001
OSTI ID:
2426739
Report Number(s):
LA-UR--23-32660
Journal Information:
ISME Communications, Journal Name: ISME Communications Journal Issue: 1 Vol. 4; ISSN 2730-6151
Publisher:
Springer NatureCopyright Statement
Country of Publication:
United States
Language:
English

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59 BASIC BIOLOGICAL SCIENCES
Bacterial Fungal Interactions
Biological Science
Microbiome
Transkingdom Network Inference