Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

Abstract

Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ.

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

“…In this Article, we expand our recently developed methodologies for integrated multi-omic analyses of microbial consortia 36,37 to systematically explore the variability of the different omes and their relationships in the context of a case study of familial T1DM. Our study allowed us to link the expression of diseaseassociated microbial functions to distinct taxa, which demonstrates the necessity for integrated multi-omic analyses of microbiota in the context of human disease research.…”

The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials

“…Including information from other omics levels especially from the metabolomics, may confirm the actual functional activity [41]. At the same time, although increasing information is becoming available on the bacteria, the involvement and impact of mycobiome and the virome in GvHD is poorly understood.…”

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

“…However, only few have studied the relationship between DOC characteristics and microbial functional traits in streams (McArthur et al, 1985;Koetsier et al, 1997). Although with a traditional focus on plants and animals, the concept of functional traits (i.e., specialists versus generalists) now becomes increasingly established in microbial ecology with notable examples from soil (Lennon et al, 2012), wastewater (Muller et al, 2014) and marine ecosystems (Mou et al, 2008). Understanding the relationship between microbial community structure and specialisation in response to resources may shed new light on the ecological mechanisms underlying the carbon cycling in stream ecosystems (Battin et al, 2008).…”