Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer
Authors: Francis Ka Leung Chan
Joseph Jao Yiu Sung
William Ka Kei Wu
Sunny Hei Wong
Rudin Zhenwei Dai
Siew Chien Ng
Olabisi Oluwabukola Coker
Jun Yu
Geicho Nakatsu
Journal: Gut (2019)
Discipline: CLINICAL MEDICINE
Keywords: colorectal cancer; fungi; gut microbiota; pathogen.
Affiliations: State Key Laboratory of Digestive Disease, Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong., Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong.

Abstract:  Objectives: Bacteriome and virome alterations are associated with colorectal cancer (CRC). Nevertheless, the gut fungal microbiota in CRC remains largely unexplored. We aimed to characterise enteric mycobiome in CRC. Design: Faecal shotgun metagenomic sequences of 184 patients with CRC, 197 patients with adenoma and 204 control subjects from Hong Kong were analysed (discovery cohort: 73 patients with CRC and 92 control subjects; validation cohort: 111 patients with CRC, 197 patients with adenoma and 112 controls from Hong Kong). CRC-associated fungal markers and ecological changes were also validated in additional independent cohorts of 90 patients with CRC, 42 patients with adenoma and 66 control subjects of published repository sequences from Germany and France. Assignment of taxonomies was performed by exact k-mer alignment against an integrated microbial reference genome database. Results: Principal component analysis revealed separate clusters for CRC and control (p&lt;0.0001), with distinct mycobiomes in early-stage and late-stage CRC (p=0.0048). Basidiomycota:Ascomycota ratio was higher in CRC (p=0.0042), with increase in Malasseziomycetes (p&lt;0.0001) and decrease in Saccharomycetes (p&lt;0.0001) and Pneumocystidomycetes (p=0.0017). Abundances of 14 fungal biomarkers distinguished CRC from controls with an area under the receiver-operating characteristic curve (AUC) of 0.93 and validated AUCs of 0.82 and 0.74 in independent Chinese cohort V1 and European cohort V2, respectively. Further ecological analysis revealed higher numbers of co-occurring fungal intrakingdom and co-exclusive bacterial-fungal correlations in CRC (p&lt;0.0001). Moreover, co-occurrence interactions between fungi and bacteria, mostly contributed by fungal Ascomycota and bacterial Proteobacteria in control, were reverted to co-exclusive interplay in CRC (p=0.00045). Conclusions: This study revealed CRC-associated mycobiome dysbiosis characterised by altered fungal composition and ecology, signifying that the gut mycobiome might play a role in CRC. 

Retracted: No

PubPeer comments:
 Assessment: The authors focus here on the fungal metagenome part in faeces of patients with colorectal cancer and other pathologies. Yet, the reported species sound extremely unusual for gut content, to list: Kwoniella mangrovensis (plant associated), Moniliophthora perniciosa (plant associated), Aspergillus ochracereoseus (environmental), Talaromyces islandicus (crop spoilage), Metarhizium acridum (insect pathogen), Grosmannia clavigera (plant pathogen), Thielaviopsis punctulata (plant pathogen), Erysiphe necator (plant pathogen), Blumeria graminis (plant pathogen), and more. Due to the imbalance in sequencing efforts in different areas (e.g. more focus on clinically or agriculturally important samples), it is more likely that these are wrongly identified by the k-mer based tool, which are prone of false-positive identifying if unsuitable reference databases are used. Supporting analysis: To show that these identifications are most likely false-positive results, I used the other standard way of confirmation to check the abundance of some example organisms. We downloaded one of the used bioprojects, PRJEB10878 (from reference #14 within the manuscript). In addition I downloaded some of the fungal genomes, which were supposedly present (Thielaviopsis punctulata CR-DP1, Talaromyces islandicus WF-38-12, Moniliophthora perniciosa FA553, Metarhizium acridum CQMa_10, Kwoniella mangroviensis CBS_10435, Grosmannia clavigera kw1407, Erysiphe necator strain c, Aspergillus ochraceoroseus IBT 24754, Blumeria graminis f. sp. Tritici, Debaryomyces fabryi CBS 789). I used bowtie2 to map the reads of bioproject PRJEB10878 to these genomes. In only one case (ERR1018185 to the genome of Aspergillus ochraceoroseus) the concordantly mapped reads exceeded 10.000 (37785), with on average only 300 reads mapping per sample. If sample ERR1018185 is excluded, this drops to a maximum of 3695, with an average of 235 reads, down to sample ERR1018312 (and multiple others) with 0 reads mapping to any of these genomes. This number is probably insufficient to conclude that any of these fungi are present, especially considering that most of these reads are probably rRNA derived. ,