Eukaryotic and Prokaryotic Microbiota Interactions.

Aly Kodio,Stéphane Ranque,Estelle Menu

doi:10.3390/microorganisms8122018

Abstract

The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies were analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.

Highlights

Several microorganisms have been isolated from different body parts of living beings
While studies on the eukaryotic microbiota remain relatively scarce, this review aimed at assessing the current knowledge on interactions between the prokaryotic and eukaryotic communities, derived from studies based on microbial genomics, metagenomics and/or culturomics approaches
We will briefly describe the methods that were used to characterise the microbial communities in the articles analysed including: culturomics and culture-based methods; polymerase chain reaction; denaturing gradient gel electrophoresis (DGGE); high throughput sequencing of 16S rRNA amplicons and whole genome shotgun (WGS)

Summary

Introduction

Several microorganisms have been isolated from different body parts of living beings. The community of microorganism living within a body, referred to as “microbiota”, is made up of bacteria, archaea, fungi, protozoa, metazoans (mainly helminths) and viruses. Other factors potentially influencing the bacterial intestinal microbiome include diet (animal proteins, fatty acids, carbohydrates, processed foods, dietary fibres) [6,7,8], age [5], stool consistency [9,10], physiological and metabolic status [11,12], medical practices (e.g., antibiotic treatments) [13], seasons [14] climate change [15], seasonal cycles [14] and the host’s genetic background [12,16,17,18]. The microbiological application of DNA-based assays, nucleotide sequencing and matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) considerably enhanced capacities to identify microorganisms [22,23]

Objectives

Methods

Results

Conclusion