The Human Mycobiome: An ISAPP mini-symposium

ISAPP announces an open registration mini-symposium on the human mycobiome to be held July 1, 2021 at 10 AM-noon EDT.

Although the contribution of the intestinal microbiome in human physiology is well-studied, the specific role of intestinal fungi, the gut mycobiome, is not well understood. Yet they may play an important role in shaping host development and health. For example, the evidence that fungi are involved in development of chronic inflammatory diseases is building. Further, a healthy gut microbiome is likely a major line of defense against the detrimental spread of fungi from the intestinal environment to other parts of the body, or unwanted establishment of fungi in the gut itself. This mini-symposium features six short lectures that will explore different aspects of the human mycobiome, including research, clinical and industry perspectives.

Mini-symposium schedule, July 1, 2021

10:00-10:05 AM EDT Welcome. Eamonn Quigley/Mary Ellen Sanders ISAPP
10:05-10:25 Overview of the human mycobiome. Pauline Scanlan University College Cork, Ireland


Characterizing gut mycobiota from healthy adults: conventional vs vegetarian diets. Heather Hallen-Adams University of Nebraska – Lincoln
10:45-11:05 Gut mycobiota in immunity and IBD. Iliyan D Iliev Cornell University, Ithaca, NY
11:05-11:25 Mycobiome of infants in a type-1 diabetes prospective cohort.  Joseph Petrosino Baylor College of Medicine

Houston, TX

11:25-11:35 A clinician’s perspective on gut fungi. Eamonn Quigley Houston Methodist,

Weill Cornell Medical College, TX

11:35-11:40 Importance of the mycobiome: industry perspective. Roy Montijn TNO, Microbiology & Systems Biology, The Netherlands
11:40-noon Q&A

The webinar is free and open to all — registration is required.

ISAPP provides guidance on use of probiotics and prebiotics in time of COVID-19

By ISAPP board of directors

Summary: No probiotics or prebiotics have been shown to prevent or treat COVID-19 or inhibit the growth of SARSCoV-2. We recommend placebo-controlled trials be conducted, which have been undertaken by some research groups. If being used in clinical practice in advance of such evidence, we recommend a registry be organized to collect data on interventions and outcomes.  

Many people active in the probiotic and prebiotic fields have been approached regarding their recommendations for using these interventions in an attempt to prevent or treat COVID-19. Here, the ISAPP board of directors provides some basic facts on this topic.

What is known. Some human trials have shown that specific probiotics can reduce the incidence and duration of common upper respiratory tract infections, especially in children (Hao et al. 2015; Luoto et al. 2014), but also with some evidence for adults (King et al. 2014) and nursing home residents (Van Puyenbroeck et al. 2012; Wang et al. 2018). However, not all evidence is of high quality and more trials are needed to confirm these findings, as well as determine the optimal strain(s), dosing regimens, time and duration of intervention. Further, we do not know how relevant these studies are for COVID-19, as the outcomes are for probiotic impact on upper respiratory tract infections, whereas COVID-19 is also a lower respiratory tract infection and inflammatory disease.

There is less information on the use of prebiotics for addressing respiratory issues than there is for probiotics, as they are used mainly to improve gut health. However, there is evidence supporting the use of galactans and fructans in infant formulae to reduce upper respiratory infections (Shahramian et al. 2018; Arslanoglu et al. 2008). A meta-analysis of synbiotics also showed promise in repressing respiratory infections (Chan et al. 2020).

Mechanistic underpinnings. Is there scientific evidence to suggest that probiotics or prebiotics could impact SARS-CoV-2? Data are very limited. Some laboratory studies have suggested that certain probiotics have anti-viral effects including against other forms of coronavirus (Chai et al. 2013). Other studies indicate the potential to interfere with the main host receptor of the SARS-CoV-2 virus, the angiotensin converting enzyme 2 (ACE2). For example, during milk fermentation, some lactobacilli have been shown to release peptides with high affinity for ACE (Li et al. 2019). Recently, Paenibacillus bacteria were shown to naturally produce carboxypeptidases homologous to ACE2 in structure and function (Minato et al. 2020). In mice, intranasal inoculation of Limosilactobacillus reuteri (formerly Lactobacillus reuteri) F275 (ATCC 23272) has been shown to have protective effects against lethal infection from a pneumonia virus of mice (PVM) (Garcia-Crespo et al. 2013). These data point towards immunomodulatory effects involving rapid, transient neutrophil recruitment in association with proinflammatory mediators but not Th1 cytokines. A recent study demonstrated that TLR4 signaling was crucial for the effects of preventive intranasal treatment with probiotic Lacticaseibacillus rhamnosus (formerly Lactobacillus rhamnosus) GG in a neonatal mouse model of influenza infection (Kumova et al., 2019). Whether these or other immunomodulatory effects, following local or oral administration, could be relevant to SARS-CoV-2 infections in humans is at present not known.

Our immune systems have evolved to respond to continual exposure to live microbes. Belkaid and Hand (2016) state: “The microbiota plays a fundamental role on the induction, training, and function of the host immune system. In return, the immune system has largely evolved as a means to maintain the symbiotic relationship of the host with these highly diverse and evolving microbes.” This suggests a mechanism whereby exposure to dietary microbes, including probiotics, could positively impact immune function (Sugimura et al. 2015; Jespersen et al. 2015).

The role of the gut in COVID-19. Many COVID-19 patients present with gastrointestinal symptoms and also suffer from sepsis that may originate in the gut. This could be an important element in the development and outcome of the disease. Though results from studies vary, it is evident that gastrointestinal symptoms, loss of taste, and diarrhea, in particular, can be features of the infection and may occur in the absence of overt respiratory symptoms. There is a suggestion that gastrointestinal symptoms are associated with a more severe disease course. Angiotensin converting enzyme 2 and virus nucleocapsid protein have been detected in gastrointestinal epithelial cells, and infectious virus particles have been isolated from feces. In some patients, viral RNA may be detectable in feces when nasopharyngeal samples are negative. The significance of these findings in terms of disease transmission is unknown but, in theory, do provide an opportunity for microbiome-modulating interventions that may have anti-viral effects (Cheung et al. 2020; Tian et al. 2020; Han et al. 2020).

A preprint (not peer reviewed) has recently been released, titled ‘Gut microbiota may underlie the predisposition of healthy individuals to COVID-19’ (Gao et al. 2020) suggesting that this could be an interesting research direction and worthy of further discussion. A review of China National Health Commission and National Administration of Traditional Chinese Medicine guidelines also suggested probiotic use, although more work on specific strains is needed (Mak et al. 2020).

Are probiotics or prebiotics safe? Currently marketed probiotics and prebiotics are available primarily as foods and food/dietary supplements, not as drugs to treat or prevent disease. Assuming they are manufactured in a manner consistent with applicable regulations, they should be safe for the generally healthy population and can be consumed during this time.

Baud et al. (in press) presented a case for probiotics and prebiotics to be part of the management of COVID-19. Although not fully aligned with ISAPP’s official position, readers may find the points made and references cited of interest.

Conclusion. We reiterate, currently no probiotics or prebiotics have been shown to prevent or treat COVID-19 or inhibit the growth of SARSCoV-2.


Connecting with the ISAPP community: Continuing to advance the science of probiotics and prebiotics

By Mary Ellen Sanders PhD, executive science officer, ISAPP

On behalf of the ISAPP board of directors, I am reaching out to the ISAPP community to say we hope you are doing well and taking all the necessary steps in your local communities to remain healthy. At present, the global ISAPP community is physically distant but digitally close, and it is important for us to remain connected and strong.

ISAPP’s activities are as important as ever during this time of increased attention to health, and ISAPP is continuing to uphold its commitment to (1) stewardship, (2) advancing the science, and (3) working with stakeholders. Although our annual meeting, which some of you may have initially planned to attend, has been cancelled, other ISAPP activities are continuing or expanding as follows:


  • Building on an important topic for our annual meeting, ISAPP is working to develop a strategic approach to communicating the science on probiotics, prebiotics, fermented foods, synbiotics, and postbiotics.
  • The ISAPP board of directors is pleased that our founding board members, Profs. Gregor Reid and Glenn Gibson, have agreed to remain on the board until the 2021 meeting, in particular to help with long-range planning. New academic board members will also be elected, thereby expanding the board. Working together, we will bring fresh insights, strategies and global reach.
  • The board is considering how best to approach our cancelled meeting. In lieu of re-scheduling this year’s in-person meeting, we are planning to have virtual content covering some of the originally scheduled topics. Some discussion group topics will be carried over to the 2021 meeting, while others will be addressed virtually. We will communicate further on this soon.
  • Our newsletter will continue on a monthly basis.
  • Blog postings, which are aimed at either consumers or scientists, remain timely and popular – with new contributions posted on average every 2-3 weeks. Authored by board members and other experts in the field, these blogs provide a forum for opinions and observations on current issues and controversies as well as insights on global fermented foods, critical regulatory actions, and other relevant topics.
  • ISAPP filed comments on March 17 with the American Gastroenterological Association in response to their draft recommendations for probiotic use in GI conditions.
  • Spearheaded by former ISAPP IAC representative to the board, Dr. Roberta Grimaldi, ISAPP has subtitled several of the most popular ISAPP videos in different languages, including Dutch, French, Spanish, Russian, Japanese, Italian and Indonesian. The first of these should be posted by end of April.
  • The ISAPP-Students and Fellows Association has launched a blog program to provide perspectives by young scientists on issues of importance to the probiotic and prebiotic fields. They have also submitted a manuscript to Frontiers in Microbiology discussing a toolkit needed for their future in science: “Future of probiotics and prebiotics: an early career researchers’ perspective”.
  • Three consensus panels have been conducted since May of 2019. A manuscript arising from the synbiotics panel, chaired by Prof. Kelly Swanson, is in press with Nature Reviews Gastroenterology and Hepatology. The paper summarizing the consensus panel on fermented foods, chaired by Profs. Robert Hutkins and Maria Marco, is almost ready for submission to Nature Reviews Gastroenterology and Hepatology. A manuscript from the consensus panel on postbiotics, chaired by Prof. Seppo Salminen, is currently being written. All three papers are expected to provide clarity to the field with regard to definition of terms, current evidence for health benefits, and impact on stakeholders.
  • In addition to the three consensus panel papers in progress, several different ISAPP endeavors are at different stages of publication:
    • ISAPP vice president, Prof. Dan Merenstein, and executive science officer, Dr. Mary Ellen Sanders, worked with biostatistician and frequent ISAPP contributor, Prof. Dan Tancredi, to summarize evidence for clinical endpoints for probiotics, to be published in the Journal of Family Physicians. This paper, titled “Probiotics as a Tx resource in primary care”. The paper is currently in press.
    • Several ISAPP board members and other participants in a 2019 meeting discussion group recently submitted to Current Developments in Nutrition a paper titled “Dietary Recommendation on Adequate Intake of Live Microbes: A Path Forward”.
    • Marla Cunningham, the current IAC representative to the ISAPP board, has led an effort to compile results from the IAC Learning Forum from the 2019 ISAPP meeting on the topic of matrix effects impacting probiotic and prebiotic functionality. Manuscript in preparation.
    • Colin Hill and I represented ISAPP on a paper under review at Nutrients initiated by IPA-Europe titled “Criteria to qualify microorganisms as ‘probiotic’ in foods and dietary supplements”. This paper consolidates and fleshes out minimum criteria for use of the term ‘probiotic’ published by different groups, including the 2002 FAO/WHO working group, the 2014 ISAPP consensus paper on probiotics, and the 2018 ISAPP discussion group on global harmonization.
    • Glenn Gibson and Marla Cunningham are coordinating a paper titled “The future of probiotics and prebiotics in human health” as an output from their 2019 discussion group.

See here for all published ISAPP papers.

ISAPP board members, 2019 annual meeting

Messages about probiotics and COVID-19

With many conflicting and confusing health messages circulating during this global pandemic, including some criticisms of our field as well as some unsupported claims made by certain individuals and companies, ISAPP will remain an important touchstone for scientifically accurate information. Focusing on health effects is key to demonstrating probiotic and prebiotic efficacy, and we acknowledge that human studies are the ultimate measure of efficacy, but also, elucidating mechanisms of action help us understand how these interventions interface with the immune system and other mediators of health.  Currently, there is some evidence that certain probiotics/prebiotics can reduce the risk of viral infections (discussed in other blog posts here and here), but it is important to remember that they have not been studied specifically for COVID-19 prevention or treatment. This must be acknowledged when communicating with the wider community.

We greatly appreciate the continued support of our IAC members. The ISAPP Board, colleagues, and SFA will continue to chart a course forward in preparation for life after the pandemic. Our intent is to emerge from these experiences more connected and purposeful than ever. We welcome suggestions on how collectively we can endure and strengthen the science and communications that remain foundations of our field.