Metatranscriptome of human faecal microbial communities in a cohort of adult men

Abstract

The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological interaction network reconstruction, which remained stable over the six-month timespan, as did strain tracking within and between participants. These results provide an initial characterization of human faecal microbial ecology into core, subject-specific, microorganism-specific and temporally variable transcription, and they differentiate metagenomically versus metatranscriptomically informative aspects of the human faecal microbiome.

Functional profiles of coronal and dentin caries in children

“…Genes mapped to several viral taxa as previously described [27]. In the current report the principal viruses detected from gene expression sequences were the murine osteosarcoma virus and the dasheen mosaic virus which is a plant virus.…”

“…The ability to examine functional profiling of the oral biofilm community focuses on addressing the question ‘What are the microbes in my community-of-interest doing (or capable of doing)?’ in addition to providing a new approach to examine the oral microbiota in health and disease [27]. Compared with 16S profiling, metatranscriptomic analysis can provide a better picture of the species that are metabolically active in different caries types[11] and thus revealing the community function which is more relevant to disease states.…”

Stability of the human faecal microbiome in a cohort of adult men

“…Prospective cohort studies characterizing the microbiome in relation to lifestyle data, such as dietary and medication information, have already begun to explore inter-individual variation and will be essential in mechanistically understanding the interactions between the faecal microbiome and the host in the context of health and disease 17,43–45 . Continuing to improve our understanding of the stability of the faecal microbiome function is critical not only in determining the ecological dynamics of the human microbiome 25 , but also for the promotion of human health.…”

“…Specifically, we hypothesized that inter-individual differences in faecal microbiome communities and metagenomes would persist over short- (24–72 h) and intermediate-term (6 months) intervals, but that metatranscriptomes would demonstrate greater variability over time. The work described here characterizing faecal microbial stability is accompanied by further research on molecular function in the faecal metagenome and metatranscriptome population 25 . These studies will provide a foundation for leveraging the faecal microbiome as a biomarker for population-based cohort studies and provide insight into how metagenomics and metatranscriptomics relate to each other over time.…”

Emerging Role of the Gut Microbiome in Nonalcoholic Fatty Liver Disease: From Composition to Function

“…It is increasingly recognized that the metagenome encodes substantial redundancy among microorganisms and that there is incongruence between species abundance and transcriptional activity. 37 This was exemplified in a study of lean and obese individuals who were better differentiated based on their gut metagenome, as opposed to their taxonomic profile. 38 …”