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Trauma Surg Acute Care Open. 2017 Oct 23;2(1):e000108. doi: 10.1136/tsaco-2017-000108. eCollection 2017.

Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury.

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Department of Surgery, San Francisco General Hospital, University of California San Francisco, California, USA.
Department of Surgery, Denver Health and Hospital Authority, University of Colorado, Denver, Colorado, USA.
Division of Pulmonary and Critical Care Medicine, Departments of Medicine and Anesthesia, University of California San Francisco, California, USA.
Division of Gastroenterology, Department of Medicine, University of California San Francisco, California, USA.



Recent studies have demonstrated the vital influence of commensal microbial communities on human health. The central role of the gut in the response to injury is well described; however, no prior studies have used culture-independent profiling techniques to characterize the gut microbiome after severe trauma. We hypothesized that in critically injured patients, the gut microbiome would undergo significant compositional changes in the first 72 hours after injury.


Trauma stool samples were prospectively collected via digital rectal examination at the time of presentation (0 hour). Patients admitted to the intensive care unit (n=12) had additional stool samples collected at 24 hours and/or 72 hours. Uninjured patients served as controls (n=10). DNA was extracted from stool samples and 16S rRNA-targeted PCR amplification was performed; amplicons were sequenced and binned into operational taxonomic units (OTUs; 97% sequence similarity). Diversity was analyzed using principle coordinates analyses, and negative binomial regression was used to determine significantly enriched OTUs.


Critically injured patients had a median Injury Severity Score of 27 and suffered polytrauma. At baseline (0 hour), there were no detectable differences in gut microbial community diversity between injured and uninjured patients. Injured patients developed changes in gut microbiome composition within 72 hours, characterized by significant alterations in phylogenetic composition and taxon relative abundance. Members of the bacterial orders Bacteroidales, Fusobacteriales and Verrucomicrobiales were depleted during 72 hours, whereas Clostridiales and Enterococcus members enriched significantly.


In this initial study of the gut microbiome after trauma, we demonstrate that significant changes in phylogenetic composition and relative abundance occur in the first 72 hours after injury. This rapid change in intestinal microbiota represents a critical phenomenon that may influence outcomes after severe trauma. A better understanding of the nature of these postinjury changes may lead to the ability to intervene in otherwise pathological clinical trajectories.

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critical illness; inflammatory response; microbiome; trauma and sepsis

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