The bacterial communities of the small intestine and stool in children with short bowel syndrome
Open accessAbstract
Short bowel syndrome (SBS) presents an increasing problem in pediatrics. SBS often results from surgical resection of necrotic bowel following necrotizing enterocolitis or treatment of anatomic gastrointestinal defects. SBS is associated with significant morbidity and mortality, and creates substantial burdens for patients, families, and the health system. Recent reports have demonstrated that the fecal microbiome of children with SBS is significantly different from healthy control and severe intestinal microbial imbalances is associated with poor growth. We hypothesized that children with SBS and adverse clinical features such as PN dependent, shorter bowel length and lack of ileocecal valve would demonstrate more gut dysbiosis compare with the SBS non-PN dependent. An improved understanding of SBS pathogenesis would enhance management and potentially suggest new interventions. We studied microbial communities of SBS and control non-SBS patients from the jejunum, obtained endoscopically or by ostomy aspiration, and stool. We enrolled SBS patients who did and did not require parenteral nutrition (PN), as a surrogate marker for the seriousness of their disease. We studied the microbiota using high-throughput DNA sequencing of 16S rRNA genes and statistical analyses. We found that microbial diversity was significantly greater in jejunal aspirate than in stool samples in SBS patients, unlike non-SBS patients; that SBS patients receiving enteral feeds had greater diversity, and that SBS patients on PN and enteral feeds had lower differences in diversity in jejunal vs. stool samples. We found a trend toward increased diversity in patients with an intact ileocecal valve, and found that certain taxa were more abundant in the certain sample types, and in SBS patients vs. non-SBS patients. SBS patients have lower microbial diversity, especially patients with more severe disease, patients requiring PN, and those lacking an ileocecal valve. SBS patients, particularly those with more complex characteristics, exhibit differences in their intestinal microbiota. Particular individual taxa were over- and under-represented in patients with more unfavorable disease. While diminished diversity and alterations in microbiota composition are likely consequences of SBS, future efforts aimed at increasing microbial diversity and interventions targeting specific microbiota characteristics might constitute a testable approach to ameliorate some clinical SBS clinical consequences.
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Children with shorter remnant bowel (<35 cm) had greater reliance on parenteral nutrition, impaired linear growth, and a microbiota enriched in Proteobacteria, while those with longer remnant bowel had relatively higher proportions of Firmicutes.
“children with shorter remnant bowel (<35 cm) had greater reliance on PN, impaired linear growth, and a microbiota enriched in Proteobacteria, while those with longer remnant bowel showed relatively higher proportions of Firmicutes [6,7,8,9].”
From Pre-, Pro-, Post- and Synbiotics in Pediatric Short Bowel Syndrome: A Narrative Review of Current Evidence (2026) · cites this paper as [9]
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Experimental — accuracy not yet measuredReliance on parenteral nutrition and reduction in enteral feeding contribute to intestinal flora alterations by decreasing microbial diversity and encouraging pathogenic strains such as Enterobacteriaceae.
“Reliance on PN and reduction in enteral feeding are other key contributors to intestinal flora alterations: as PN bypasses the intestine, fewer nutrients can reach the gut lumen, thus leading to a decreased microbial diversity and encouragement of pathogenic strains such as Enterobacteriaceae [9,10].”
From Pre-, Pro-, Post- and Synbiotics in Pediatric Short Bowel Syndrome: A Narrative Review of Current Evidence (2026) · cites this paper as [9]
The Discussion (page not provided) reports less diverse jejunal microbiota in children with short bowel syndrome receiving PN than in those receiving only enteral nutrition. The Results (page not provided) report higher abundance of some unclassified Enterobacteriaceae in jejunal samples from patients receiving PN. But the Discussion explicitly says it cannot determine whether PN decreased diversity; the paper does not establish the proposed nutrient-bypass mechanism or that PN encourages pathogenic strains. (LLM, conf=0.88)
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“In fact, it has been demonstrated that children with shorter remnant bowel ( 35 cm) had greater reliance on PN, impaired linear growth, and a microbiota enriched in Proteobacteria, while those with longer remnant bowel showed relatively higher proportions of Firmicutes [6–9].”
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- Authors
- Zeichner, S. L., Mongodin, E. F., Hittle, L., Huang, S.-H., & Torres, C.
- Affiliations
- University of Virginia (US)
- University of Maryland, Baltimore (US)
- George Washington University (US)
- Children's National (US)
- Corresponding author
- Zeichner, Steven L.
- Torres, Clarivet
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2019-05-16
- Volume
- 14
- Issue
- 5
- Pages
- e0215351
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC6521997
- OpenAlex
- W2945667030
- Cited by
- 31
- References
- 59
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 4 · 2023: 4 · 2022: 2 · 2021: 5 · 2020: 4 · 2019: 1
- FWCI
- 0.99
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institute of Diabetes and Digestive and Kidney Diseases (DK105355)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Clinical Nutrition and Gastroenterology
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Keywords
- short bowel syndrome, gut microbiota, microbial diversity, fecal microbiota, parenteral nutrition dependence, ileocecal valve, enteral nutrition, necrotizing enterocolitis, pediatric patients, dysbiosis
- MeSH terms
- Bacteria, Child, Child, Preschool, Feces, Female, Humans, Intestine, Small, Male, Prospective Studies, RNA, Ribosomal, 16S, Short Bowel Syndrome, Case-Control Studies, Sequence Analysis, DNA, High-Throughput Nucleotide Sequencing
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