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Gut microbiota is associated with host characteristics such as age, sex, immune condition or frailty and is thought to be a key player in numerous human diseases. Nevertheless, its association with outcome in critically ill patients has been poorly investigated. The aim of this study is to assess the association between gut microbiota composition and Day-28 mortality in critically ill patients. Methods Rectal swab at admission of every patient admitted to intensive care unit (ICU) between October and November 2019 was frozen at − 80 °C. DNA extraction was performed thanks to QIAamp ®  PowerFecal ®  Pro DNA kit (QIAgen ® ). V3–V4 regions of 16SRNA and ITS2 coding genes were amplified by PCR. Sequencing (2x250 bp paired-end) was performed on MiSeq sequencer (Illumina ® ). DADA2 pipeline on R software was used for bioinformatics analyses. Risk factors for Day-28 mortality were investigated by logistic regression. Results Fifty-seven patients were consecutively admitted to ICU of whom 13/57 (23%) deceased and 44/57 (77%) survived. Bacteriobiota  α -diversity was lower among non-survivors than survivors (Shannon and Simpson index respectively,  p  &lt; 0.001 and  p  = 0.001) as was mycobiota  α -diversity (respectively  p  = 0.03 and  p  = 0.03). Both gut bacteriobiota and mycobiota Shannon index were independently associated with Day-28 mortality in multivariate analysis (respectively OR: 0.19, 97.5 CI [0.04–0.60],  p  &lt; 0.01 and OR: 0.29, 97.5 CI [0.09–0.75],  p  = 0.02). Bacteriobiota  β -diversity was significantly different between survivors and non-survivors ( p  = 0.05) but not mycobiota  β -diversity ( p  = 0.57). Non-survivors had a higher abundance of  Staphylococcus haemolyticus ,  Clostridiales  sp.,  Campylobacter ureolyticus ,  Akkermansia  sp.,  Malassezia sympodialis ,  Malassezia dermatis  and  Saccharomyces cerevisiae , whereas survivors had a higher abundance of  Collinsella aerofaciens ,  Blautia  sp.,  Streptococcus  sp.,  Faecalibacterium prausnitzii  and  Bifidobacterium  sp. Conclusion The gut bacteriobiota and mycobiota  α  diversities are independently associated with Day-28 mortality in critically ill patients. The causal nature of this interference and, if so, the underlying mechanisms should be further investigated to assess if gut microbiota modulation could be a future therapeutic approach.

Gut bacteriobiota and mycobiota are both associated with Day-28 mortality among critically ill patients