Keystone taxa as drivers of microbiome structure and functioning

S Banerjee, K Schlaeppi… - Nature Reviews …, 2018 - nature.com
Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have
shown that microbial communities harbour keystone taxa, which drive community …

From hairballs to hypotheses–biological insights from microbial networks

L Röttjers, K Faust - FEMS microbiology reviews, 2018 - academic.oup.com
Microbial networks are an increasingly popular tool to investigate microbial community
structure, as they integrate multiple types of information and may represent systems-level …

[HTML][HTML] Network analysis methods for studying microbial communities: A mini review

MS Matchado, M Lauber, S Reitmeier… - Computational and …, 2021 - Elsevier
Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities
in complex and contiguous environments. They engage in numerous inter-and intra …

Correlation and association analyses in microbiome study integrating multiomics in health and disease

Y **a - Progress in molecular biology and translational …, 2020 - Elsevier
Correlation and association analyses are one of the most widely used statistical methods in
research fields, including microbiome and integrative multiomics studies. Correlation and …

Disentangling interactions in the microbiome: a network perspective

M Layeghifard, DM Hwang, DS Guttman - Trends in microbiology, 2017 - cell.com
Microbiota are now widely recognized as being central players in the health of all organisms
and ecosystems, and subsequently have been the subject of intense study. However …

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

B Ma, H Wang, M Dsouza, J Lou, Y He, Z Dai… - The ISME …, 2016 - academic.oup.com
Soil microbiota play a critical role in soil biogeochemical processes and have a profound
effect on soil functions. Recent studies have revealed microbial co-occurrence patterns in …

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

S Weiss, W Van Treuren, C Lozupone, K Faust… - The ISME …, 2016 - academic.oup.com
Disruption of healthy microbial communities has been linked to numerous diseases, yet
microbial interactions are little understood. This is due in part to the large number of …

Hyperthermophilic composting accelerates the removal of antibiotic resistance genes and mobile genetic elements in sewage sludge

H Liao, X Lu, C Rensing, VP Friman… - … science & technology, 2018 - ACS Publications
Composting is an efficient way to convert organic waste into fertilizers. However, waste
materials often contain large amounts of antibiotic resistance genes (ARGs) and mobile …

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

D Berry, S Widder - Frontiers in microbiology, 2014 - frontiersin.org
Co-occurrence networks produced from microbial survey sequencing data are frequently
used to identify interactions between community members. While this approach has …

Life in the “plastisphere”: microbial communities on plastic marine debris

ER Zettler, TJ Mincer… - Environmental science & …, 2013 - ACS Publications
Plastics are the most abundant form of marine debris, with global production rising and
documented impacts in some marine environments, but the influence of plastic on open …