JID for Clinicians: Influences of the human gut microbiome, impact of diet on C. diff outcomes and more

IDSA’s Journal of Infectious Diseases has launched a monthly roundup of JID papers with direct relevance to clinicians. Read on to learn more about the role of the gut microbiome in HIV-associated atherosclerosis, the link between pathogen outgrowth in the gastrointestinal tract and bacterial infections in infancy, and other research ready to inform clinical practice. (Titles and summaries are adapted from the June 2025 issue of JID.)

Distinct Gut Microbiota Signatures Associated With Progression of Atherosclerosis in People Living With Human Immunodeficiency Virus

Companion editorial: The Gut Microbiome: Another Piece in the Puzzle of HIV-Associated Atherosclerosis

This prospective 96-week, longitudinal study investigates the longitudinal associations between gut microbiota dynamics and the progression of carotid intima-media thickness in individuals with HIV. Subclinical atherosclerosis progression was consistently linked with Agathobacter and Ruminococcus 2, whereas non-progression was consistently associated with Prevotella 7. This study suggests that progression of HIV-associated atherosclerosis is associated with distinctive signatures in the gut microbiota. 

Fecal Microbiota and Volatile Metabolome Pattern Alterations Precede Late-Onset Meningitis in Preterm Neonates

Companion editorial: Oops, the Microbes Did It Again: Gut Dysbiosis Precedes Late-Onset Meningitis

Analogous to late-onset sepsis, this study presents data indicating the fecal microbiota and volatile metabolome are altered in preterm infants (born < 30 weeks’ gestation) prior to late-onset meningitis. Compared to controls, a prediction model based on six bacterial genera and species could accurately predict late-onset meningitis one-three days before clinical onset with an AUC of 0.88, whereas the volatile metabolome was only moderately associated with preclinical late-onset meningitis.

Microbiome and Metabolome Restoration After Administration of Fecal Microbiota, Live-jslm (REBYOTA) for Preventing Recurrent Clostridioides difficile Infection

Available data indicate that microbiota-based biotherapeutics such as fecal microbiota, live-jslm (RBL) effectively prevent some recurrent Clostridioides difficile infection, but the mechanisms of response require further study. Before RBL administration, Gammaproteobacteria and Bacilli dominated the microbiota community, and primary bile acids were more prevalent than secondary BAs. Clinical response after RBL administration correlated with shifts to predominantly Bacteroidia and Clostridia and increased secondary BAs.

The Impact of Diet on Clostridioides difficile Infection: A Review

C. difficile’s metabolism and pathogenesis are strongly influenced by nutrient availability from the host and gut commensals. This review aims to enrich the understanding of dietary components that impact C. difficile metabolism and pathogenesis, as well as provide limitations in the current science to support future inquiry to develop nonpharmacologic approaches to prevent and treat C. difficile infection.

Molecular Epidemiology and Clinical Characterization of Carbapenemase-Producing Enterobacter Species From an International Cohort

Despite the global public health threat posed by carbapenem-resistant Enterobacter spp., clinical and molecular epidemiological studies on international Enterobacter spp. isolates remain scarce. Further analysis of the CRACKLE-2 study (ClinicalTrials.gov, NCT03646227) revealed E. xiangfangensis and E. hoffmannii are common species among international carbapenemase-producing Enterobacter spp., potentially linked to the clonal spread of a few predominant clones that have acquired fluoroquinolone resistance and carbapenemase-encoding plasmids.