Crossing Kingdoms: How the Mycobiota and Fungal-Bacterial Interactions Impact Host Health and Disease

Abstract

The term “microbiota” invokes images of mucosal surfaces densely populated with bacteria. These surfaces and the luminal compartments they form indeed predominantly harbor bacteria. However, research from this past decade has started to complete the picture by focusing on important but largely neglected constituents of the microbiota: fungi, viruses, and archaea. The community of commensal fungi, also called the mycobiota, interacts with commensal bacteria and the host. It is thus not surprising that changes in the mycobiota have significant impact on host health and are associated with pathological conditions like Inflammatory Bowel Disease (IBD). In this review we will give an overview of why the mycobiota is an important research area and different mycobiota research tools. We will specifically focus on distinguishing transient and actively colonizing fungi of the oral and gut mycobiota and their role in health and disease. In addition to correlative and observational studies, we will discuss mechanistic studies on specific cross-kingdom interactions of fungi, bacteria, and the host.

Mycobiome and Cancer: What Is the Evidence?

“…There is a plethora of laboratory methods to detect live fungi or a genome of fungal communities including, among others culture, fluorescent microscopy, amplicon sequencing and whole-genome shotgun (WGS) metagenomics, or high-throughput sequencing (HTS) metabarcoding studies [1,59,79]. Overall, sequencing methodologies reveal fungal DNA in a specimen independent of fungal viability.…”

“…In analogy to 16S sequencing for bacteria, amplicon sequencing employs distinct primers for fungi to amplify the internal transcribed spacer (ITS) region or the 18S region of the nuclear ribosomal RNA (rRNA) gene locus, permitting the discrimination of fungal species [59]. Sequencing the ITS region of the nuclear rRNA operon is the gold standard in Sanger sequencing-based species detection and HTS-based methods [80,81].…”

“…The advantages of using the full ITS region instead of ITS1 or ITS2 with third-generation HTS platforms such as Oxford Nanopore or Pacific Biosciences include the higher taxonomic discrimination and the decreased amplification of non-living microorganisms; however, a shortcoming is the low performance with poor-quality samples due to the DNA deterioration, where full ITS sequencing may be impossible [1]. Overall, the disadvantages of the amplicon sequencing comprise the paucity of a complete annotated reference database, taking into account the complex taxonomic composition of the fungal community as well as the amplification errors inherent to PCR [59].…”

“…Intestinal fungi and bacteria interact through a variety of ways, including the secretion of metabolites and toxins, the development of biofilms, and physical attachment, thus influencing host immune responses. Based on in vitro and in vivo research data on bacterial and fungal interplay, it was shown that synergistic associations generally enhance pathogenicity whilst antagonistic relations limit bacterial or fungal virulence [59].…”

“…Some examples of antagonistic actions between bacteria and fungi with beneficial or neutral actions in gut health include: (1) the antifungal activity of Serratia marcescens, Salmonella typhimurium and Acinetobacter baumannii on eliminating the hyphal and yeast forms of Candida albicans or limiting the formation of biofilm and infection [59]; (2) the restriction of hyphal growth of Candida albicans by Clostridium difficile via the production of p-cresol [63].…”