Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge

Abstract

See Covering the Cover synopsis on page 1193. BACKGROUND & AIMS: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and on recovery. METHODS: We performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 patients with coronavirus disease 2019 (COVID-19) in Hong Kong, from February 5 through May 12, 2020. Fecal samples were collected 2 to 3 times per week from time of hospitalization until discharge. We compared fecal mycobiome compositions of patients with COVID-19 with those from 9 subjects with community-acquired pneumonia and 30 healthy individuals (controls). We assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples. RESULTS: Patients with COVID-19 had significant alterations in their fecal mycobiomes compared with controls, characterized by enrichment of Candia albicans and a highly heterogeneous mycobiome configuration, at time of hospitalization. Although fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from those of controls during times of hospitalization, 8 of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition, through the last sample collected. The diversity of the fecal mycobiome of the last sample collected from patients with COVID-19 was 2.5-fold higher than that of controls (P < .05). Samples collected at all timepoints from patients with COVID-19 had increased proportions of opportunistic fungal pathogens, Candida albicans, Candida auris, and Aspergillus flavus compared with controls. Two respiratory-associated fungal pathogens, A. flavus and

Gastrointestinal symptoms associated with COVID-19: impact on the gut microbiome

“…During the hospitalization time, were detected in COVID-19 patients; Bacteroides dorei, Bacteroides thetaiotaomicron, Bacteroides massiliensis, and Bacteroides ovatus, which downregulate the expression of ACE2 in the murine gut, correlating inversely with SARS-CoV-2 load in fecal samples. 71 This study opens the doors to possible interventions for gut microbiota in hospitalized patients to reduce the severity of COVID-19. Another study of just 10 patients showed that the gut bacteria was associated with fecal SARS-CoV-2 load.…”

“…70 Another small study of 15 patients hospitalized in Hong Kong has served to establish a gut microbiome profile in association with COVID-19 severity and changes in fecal shedding of SARS-CoV-2. 71 Through the application of in-depth shotgun metagenomics analysis, the authors investigated longitudinal changes of the gut microbiome in COVID-19. The abundance of Coprobacillus, Clostridium ramosum, and Clostridium hathewayi correlated with COVID-19 severity, and it was observed an inverse correlation between the abundance of Faecalibacterium prausnitzii (an anti-inflammatory bacterium).…”

Temporal Landscape of Human Gut RNA and DNA Viromes in SARS-CoV-2 Infection and Severity

“…In addition, COVID-19 patients had higher abundances of eukaryotic-and environmentderived viruses whereas non-COVID-19 subjects harbored more bacteriophages in feces. Such viral changes might be a consequence of SARS-CoV-2 infection along with its impact on the GI tract and the resident holistic microbiota ecology [8,15,16]. Overall, dysbiosis in gut RNA and DNA virome persisted in COVID-19 patients during disease course and after disease resolution indicating a potential long-lasting detrimental effect to the host after SARS-CoV-2 infection.…”

“…With the advancement of high-throughput sequencing technology, the highly individual-speci c viromes consisting of members causing acute disease or chronically colonizing in asymptomatic individuals are increasingly being uncovered [13,14]. We have previously demonstrated that the gut microbiome was signi cantly perturbed in COVID- 19 and associated with disease severity and symptoms [8,15,16]. Given the coresidence and co-evolutionary nature of virome and bacterial microbiome in human gut, we herein hypothesize that the gut virome in patients with COVID-19 is altered as well and human baseline virome may be associated with immune defense and severity to SARS-CoV-2 infection.…”

<p>Dynamic Interplay Between Microbiota and Mucosal Immunity in Early Shaping of Asthma and its Implication for the COVID-19 Pandemic</p>

“…132 Consistent with this report, the gut microbiome of COVID-19 patients was documented with an enrichment of opportunistic bacteria (Clostridium, Actinomyces, and Bacteroides) and fungi (Candida albicans, Candida auris, and Aspergillus flavus) and depletion of beneficial commensals, such as Eubacterium, Faecalibacterium prausnitzii, and Lachnospiraceae. 133 More importantly, the severity of the symptoms related to COVID-19 was linked to an expansion of pathogenic Clostridium and reduction of Alistipes and Bacteroides commensals. Limited information with regard to respiratory microbes have been documented in COVID-19 with the general consensus that opportunistic fungal and bacterial infections are widespread in the lungs of patients suffering from this disease.…”