Researchers at Bambino Gesù Children’s Hospital in Rome have reported a detailed picture of gut microbial disruption in five newborns treated for complex surgical, gastrointestinal, and urological conditions, including Hirschsprung’s disease. The case series, published in Frontiers in Medicine, found a consistent reduction in beneficial commensal bacteria—particularly Bifidobacterium and Lactobacillus species—alongside an increased abundance of potential opportunistic pathogens, mainly belonging to the phylum Proteobacteria. The authors describe these patterns as common signatures of dysbiosis, together with potential disease-specific microbial patterns, while stressing that the small sample size prevents generalizable conclusions.
The study set out to investigate alterations in the gut microbiota (GM) of newborns with complex clinical conditions and to explore how early-life factors—delivery mode, feeding practices, antibiotic therapy, preterm birth, surgery, and hospitalization—might shape microbial colonization. During the first year of life, the gut microbiota is relatively unstable and influenced by these factors, and surgical interventions and complex congenital conditions may further alter microbial colonization, potentially contributing to complications and systemic inflammation. The researchers compared each patient’s microbial profile with that of 30 healthy, age-matched controls drawn from a hospital biobank, divided into two cohorts of 15 children aged 0–1 month and 15 children aged 2–12 months. The controls were full-term, had no history of gastrointestinal diseases, were not hospitalized, and were not undergoing antibiotic therapy.
The five patients presented markedly different clinical pictures. Patient 1, a preterm male born at 34 weeks’ gestation, had a type IV congenital laryngeal cleft requiring intubation, gastric bipartition surgery at 11 days of age, and later tracheoesophageal reconstruction and tracheostomy; his postoperative course was complicated by gastric perforation, pneumothorax, and repeated infectious episodes involving Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Stenotrophomonas maltophilia. Patient 2, born extremely preterm at 24 weeks and 6 days, had a large patent ductus arteriosus and an ileostomy after previous necrotizing enterocolitis, and underwent ileocolostomy at 89 days of age. Patient 3, a term male with trisomy 21, developed neonatal intestinal obstruction and was diagnosed with aganglionic megacolon (Hirschsprung’s disease), managed conservatively with rectal irrigations. Patient 4, a term female, also received a diagnosis of megacolon and Hirschsprung’s disease confirmed by rectal suction biopsy. Patient 5, a term male, had posterior urethral valves with severe bilateral grade V vesicoureteral reflux and experienced urinary and bloodstream infections with S. aureus and Klebsiella pneumoniae.
Stool samples were collected postsurgery from four of the five patients, and stoma samples were also collected: upper and lower gastric stoma contents for case 1 and an ileostomy sample for case 2. The team used 16S rRNA gene sequencing of the V3–V4 hypervariable region, sequencing on an Illumina MiSeq platform and processing the data with QIIME 2 and the DADA2 plugin, with taxonomic assignment against the Greengenes2 reference database. In addition, the researchers assigned each patient a microbial dysbiosis index (MDI) by comparing gut microbial profiles with those of age- and gender-matched controls, using three fecal samples collected on three different days. Dysbiosis was classified as mild below 25 percent, moderate between 25 and 35 percent, and high above 35 percent quadratic dissimilarity. The authors emphasize that the MDI was used exclusively as an exploratory measure, not as a diagnostic parameter.
Case 1’s microbiota was analyzed in both stool and gastrostomy contents at one and two months after surgery. At the first time point, the stool profile showed a higher prevalence of Firmicutes—80 percent of the Firmicutes_D subgroup—than in controls, with Staphylococcus reaching 70.9 percent of the profile compared with 8.1 percent in controls, while Bifidobacterium was 3.7 percent against 19.4 percent in controls and Lactobacillus was 3.4 percent. Two months later, the fecal profile shifted: Firmicutes fell to 34.6 percent, while Bacteroidota rose to 13.2 percent, Proteobacteria to 17.2 percent, and Actinobacteriota to 6.3 percent, with increases in Pseudomonas (4.9 percent) and Escherichia (9.4 percent). The gastric stoma content showed a high prevalence of Firmicutes and Proteobacteria and a low prevalence of Actinobacteriota at both time points, with Staphylococcus rising to 75.7 percent at the second measurement. Notably, serum lipopolysaccharide (LPS) testing—performed for two of the five patients at clinician request—showed that higher LPS levels coincided with the higher Proteobacteria prevalence at the second time point: 7.32 EU/mL compared with 4.99 EU/mL, both above the reported physiological reference range of 0.01–1.0 EU/mL.
Case 2’s ileostomy-derived profile was dominated by Firmicutes (77.5 percent Firmicutes_D and 18.7 percent Firmicutes_A), with Staphylococcus at 70.9 percent and Clostridioides difficile at 19.8 percent of the species-level profile, while Bifidobacterium and Akkermansia muciniphila were each below 0.1 percent, Bacteroidota was 0.2 percent, and Actinobacteriota was undetectable—marked departures from the control profiles, in which Bifidobacterium accounted for 32.8 percent. Serum LPS in this patient was also elevated at 5.1 EU/mL. The authors note that microbial diversity in neonatal ileostomy content has generally been observed to be low, dominated by Proteobacteria and Firmicutes with low Bacteroidota abundance, and that prior work on small bowel resection reported a reduced Bacteroidetes population and an increased Firmicutes-to-Bacteroidetes ratio. For cases 1 and 2, they identify intestinal dysbiosis as a possible signature in neonates undergoing surgery, associated with deficient Bacteroides and Bifidobacterium populations and an abundance of Escherichia and Pseudomonas, together with high serum LPS levels that can be correlated with Gram-negative bacterial abundance and possible peripheral inflammation.
The two Hirschsprung’s disease cases showed distinct but overlapping patterns. Case 3’s profile showed an overabundance of Firmicutes (59.6 percent Firmicutes_D) and Proteobacteria (39.3 percent) compared with controls, driven by increases in Streptococcus (48.8 percent), Lactobacillus (7.2 percent), and particularly Escherichia (39.2 percent versus 6.1 percent in controls), alongside decreases in Bacteroidota and Actinobacteriota, with Bifidobacterium at just 0.8 percent against 32.8 percent in controls. Three stool samples yielded a high dysbiosis index of 36 percent. The authors relate these findings to prior reports of intestinal dysbiosis in Hirschsprung’s disease, including reductions in beneficial taxa such as Bacteroides and Bifidobacterium and overabundance of Escherichia, and to characterizations of Hirschsprung-associated enterocolitis marked by Proteobacteria and Firmicutes overabundance and Bacteroidota reduction.
Case 5, the infant with posterior urethral valves, showed an increase in Firmicutes (40.7 percent Firmicutes_A and 31.4 percent Firmicutes_D) and Proteobacteria (19.9 percent) and a decrease in Bacteroidota (6.7 percent) and Actinobacteriota (1.3 percent) relative to controls. The Proteobacteria fraction included increases in Klebsiella (13.5 percent), Proteus (7 percent), Escherichia (2.3 percent), and Pseudomonas (0.9 percent), and the three-sample dysbiosis index was 37 percent. The authors connect this to previous observations in neonates with complex urological conditions, where a decrease in short-chain fatty acid–producing bacteria such as Bifidobacterium and an increase in potential pathogens such as Enterobacteriaceae have been reported, with the gut microbiota dominated by aerobic taxa such as Klebsiella and Proteus species and a decrease in anaerobic taxa.
The authors are careful to frame these microbial shifts within their clinical context. They note that surgery may be associated with alterations in the gut microbial community, including a reduction in potentially beneficial taxa such as Bifidobacterium and changes in the relative abundance of taxa including Pseudomonas and Escherichia, but that these shifts should not be considered specific signatures of surgery or disease alone, since they may be influenced by multiple clinical and environmental factors. Gastrostomy may influence gastric colonization through bacterial growth on the catheter and reflux of gastric contents, and Staphylococcus epidermidis overgrowth may relate to preterm birth, which is usually associated with higher abundance of Proteobacteria and coagulase-negative staphylococci. Lower abundances of beneficial species such as Lactobacillus, Ruminococcus, and Bifidobacterium have been associated with immunological impairment in preterm neonates, and prolonged antibiotic therapy in newborns may disrupt intestinal homeostasis and promote antibiotic-resistant pathogens, increasing the risks of necrotizing enterocolitis, late-onset sepsis, and death.
The study’s limitations are substantial and acknowledged by the authors. The sample of five neonates does not allow generalizable conclusions and may not capture the full variability of gut microbiota alterations in this setting. The heterogeneity of surgical conditions—gastrostomy, ileostomy, Hirschsprung’s disease, and bowel resection—and of baseline characteristics such as prematurity, antibiotic exposure, and nutritional regimens may have influenced microbial profiles independently of surgery, and distinguishing surgery-specific changes from those related to prematurity, hospitalization, or underlying disease is difficult. Sample collection timing was not uniform among patients, introducing variability related to postoperative time and clinical status. Nevertheless, the team concludes that consistent microbial signatures emerged across different pathological conditions, marked by loss of beneficial commensals and overgrowth of potential opportunistic pathogens, underscoring the importance of monitoring microbiota composition in these vulnerable newborns and the need for larger, longitudinal studies to evaluate the long-term impact of dysbiosis and the potential role of microbiota-targeted interventions.
Subject of Research: Gut microbiota dysbiosis in neonates with complex surgical, gastrointestinal, and urological conditions
Article Title: Gut microbiota composition and dysbiosis signatures associated with complex gastrointestinal and urological conditions in neonates: a case series study
Article References: Riccardo, M., De Rose, D. U., Stefania, P., Marangelo, C., Salvatori, G., Fusaro, F., Conforti, A., Capolupo, I., Putignani, L., & Dotta, A. (2026). Gut microbiota composition and dysbiosis signatures associated with complex gastrointestinal and urological conditions in neonates: a case series study. Frontiers in Medicine, 13, Article 1917675. https://doi.org/10.3389/fmed.2026.1917675
Image Credits: AI Generated
DOI: 10.3389/fmed.2026.1917675
Keywords: gut microbiota, neonates, dysbiosis, Hirschsprung's disease, Proteobacteria, Bifidobacterium, case series, 16S rRNA sequencing, preterm birth, antibiotic exposure, lipopolysaccharide, pediatric surgery
News Source: Morgan Morrow. (October 29, 2026). Gut Dysbiosis Signatures Found in Five Newborns With Complex Surgical and Urological Conditions. Scienmag.
