Viewing bacterial colonization through the lens of systems biology

MR Barron, VB Young - Msystems, 2022 - Am Soc Microbiol
The gastrointestinal ecosystem is formed from interactions between the host, indigenous gut
microbiota, and external world. When colonizing the gut, bacteria must overcome barriers …

The ecosystem services of animal microbiomes

EA McKenney, K Koelle, RR Dunn… - Molecular ecology, 2018 - Wiley Online Library
Microbiologists often evaluate microbial community dynamics by formulating functional
hypotheses based on ecological processes. Indeed, many of the methods and terms …

Molecular commensalism—how to investigate underappreciated health-associated polymicrobial communities

A Labossiere, M Ramsey, J Merritt, J Kreth - Mbio, 2023 - Am Soc Microbiol
The study of human commensal bacteria began with the first observation of prokaryotes>
340 years ago. Since then, the study of human-associated microbes has been justifiably …

Omics approaches to study host–microbiota interactions

P van Baarlen, M Kleerebezem, JM Wells - Current opinion in microbiology, 2013 - Elsevier
Highlights•Intestinal microbiota has profound effects on human physiology and the immune
system.•We need more time course studies on microbiota in prospective cohorts.•The small …

Contextual organismality: Beyond pattern to process in the emergence of organisms

SL Díaz-Muñoz, AM Boddy, G Dantas, CM Waters… - …, 2016 - academic.oup.com
Biologists have taken the concept of organism largely for granted. However, advances in the
study of chimerism, symbiosis, bacterial-eukaryote associations, and microbial behavior …

[HTML][HTML] Microbial systems ecology to understand cross-feeding in microbiomes

V Mataigne, N Vannier, P Vandenkoornhuyse… - Frontiers in …, 2021 - frontiersin.org
Understanding how microorganism-microorganism interactions shape microbial
assemblages is a key to deciphering the evolution of dependencies and co-existence in …

Building the microbiome in health and disease: niche construction and social conflict in bacteria

L McNally, SP Brown - … of the Royal Society B: Biological …, 2015 - royalsocietypublishing.org
Microbes collectively shape their environment in remarkable ways via the products of their
metabolism. The diverse environmental impacts of macro-organisms have been collated …

[HTML][HTML] Human microbiome: symbiosis to pathogenesis

LH Lee, SH Wong, SF Chin, V Singh… - Frontiers in …, 2021 - frontiersin.org
Researchers have come a long way in microorganism research since the first discovery of
microbes as seen through an ingenious hand-held microscope over 300 years ago. In late …

The microbiome explored: recent insights and future challenges

M Blaser, P Bork, C Fraser, R Knight… - Nature Reviews …, 2013 - nature.com
One of the most exciting scientific advances in recent years has been the realization that
commensal microorganisms are not simple'passengers' in our bodies, but instead have key …

The role of the microbiome in host evolution

O Kolodny, BJ Callahan… - … Transactions of the …, 2020 - royalsocietypublishing.org
In the last decade, we have witnessed a major paradigm shift in the life sciences: the
recognition that the microbiome, ie the set of microorganisms associated with healthy …