Infant fungal communities: current knowledge and research opportunities

Ward et al. BMC Medicine (2017) 15:30 DOI 10.1186/s12916-017-0802-z Clinical insights into the human microbiome REVIEW Open Access Infant fungal communities: current knowledge and research opportunities Tonya L. Ward1, Dan Knights1,2 and Cheryl A. Gale3* Abstract The microbes colonizing the infant gastrointestinal tract have been implicated in later-life disease states such as allergies and obesity. Recently, the medical research community has begun to realize that very early colonization events may be most impactful on future health, with the presence of key taxa required for proper immune and metabolic development. However, most studies to date have focused on bacterial colonization events and have left out fungi, a clinically important sub-population of the microbiota. A number of recent findings indicate the importance of host-associated fungi (the mycobiota) in adult and infant disease states, including acute infections, allergies, and metabolism, making characterization of early human mycobiota an important frontier of medical research. This review summarizes the current state of knowledge with a focus on factors influencing infant mycobiota development and associations between early fungal exposures and health outcomes. We also propose next steps for infant fungal mycobiome research, including longitudinal studies of mother–infant pairs while monitoring long-term health outcomes, further exploration of bacterium–fungus interactions, and improved methods and databases for mycobiome quantitation. Keywords: Mycobiome, Fungi, Microbiome, Bacteria, Infant, Microbiota, Mycobiota, Development Background The beneficial role of microbial colonization to human health is becoming increasingly clear. Recent efforts to define a healthy microbiota show that the microbial communities inhabiting our bodies are diverse and complex, and that colonization dynamics during early life may have lasting impacts on adult health [1]. The term “microbiome” describes the community of microbes living on and within an organism using genetic analysis, usually within a particular niche or body site. Most literature discussing the microbiome, however, pertains only to the bacterial microbiota. Although bacteria constitute the majority of the non-host biomass of humans, they are not the only microorganisms contributing to the microbial ecosystem of the host. For example, human-associated fungi have been largely overlooked. On a cellular basis, approximately 0.1% of the microbes in the adult intestine are fungi, and these fungi are estimated to represent approximately 60 unique species [2, 3]. Although fungi can be * Correspondence: 3 Department of Pediatrics, University of Minnesota, 2450 Riverside Ave, Minneapolis, MN 55454, USA Full list of author information is available at the end of the article human pathogens, especially in association with underlying immunodeficiencies, many fungi are benign commensal inhabitants of human body niches and some have been shown to confer health benefits. For example, previous culture-based and targeted PCR approaches for characterizing the mycobiota have shown humans to be colonized with commensal fungi across multiple body sites [4, 5]. Some species, such as Saccharomyces boulardii, have been shown to be effective at preventing and treating human gastrointestinal (GI) diseases (e.g., diarrhea, inflammatory bowel disease, irritable bowel syndrome) [6, 7]. Importantly, overgrowth of fungi leading to infections is more common in infants than adults and can result in significant morbidity and mortality in at-risk infants such as those born prematurely [8–10]. Thus, knowing what a healthy fungal microbiota (mycobiota) is composed of and what factors affect its establishment and maturation during infancy is important if we are to learn how early-life microbial communities affect pediatric and adult health. With the advent of next-generation sequencing and introduction of low-cost bacterial community profiling approaches, such as 16S rDNA amplicon sequencing, © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Ward et al. BMC Medicine (2017) 15:30 bacterial microbiomes can now be more easily and quickly characterized than ever before. In contrast, development of robust methods to characterize humanassociated mycobiota has lagged behind that for bacterial community characterization due to difficulties in sequencing low human-associated fungal biomass and fungal cultivation issues preventing reference sequence generation [11, 12]. Until recently, the majority of published fungal microbiota analyses have relied upon culturing fungi, a method that is less sensitive than sequencing-based approaches [11, 12]. Because fungi are much less abundant than bacteria in most, if not all, human niches, a shotgun metagenomic sequencing approach for the characterization of fungal communities has not been productive. As such, PCR amplicon-based sequencing approaches have been developed and continue to be refined for mycobiome analyses. Genomic targets that have been utilized include the 18S and 28S rDNA sequences, and the internal transcribed spacer regions (ITS1 and ITS2) of the rDNA locus [12]. The ITS regions of the fungal genome are highly variable and capable of providing identification at the species level, but taxonomic characterization of fungi remains challenging as the reference databases available for fungi are far from comprehensive, with up to 20% of sequences annotated incorrectly [13]. Thus, mycobiome characterization may be biased by the marker gene region sequenced and Page 2 of 10 the reference database used. Until improved reference databases are available and new marker gene sequences that more universally distinguish fungi are identified, methods combining broad DNA amplicon surveys with a targeted approach, such as quantitative PCR and/or culturing, will likely be needed to gain robust and accurate mycobiome characterization [14]. Given these challenges, throughout this review we note the particular approach employed by each study to characterize mycobiota. Herein, we focus on the current state of mycobiota research in infants, including culture-based, targeted and broad survey-based genomic approaches, with a focus on two aspects of infant mycobiota research, namely factors influencing early-life mycobiota and potential links between early fungal exposures and health outcomes. Because research on t (...truncated)