{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:11:38Z","timestamp":1787026298648,"version":"build-2736575974"},"reference-count":31,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T00:00:00Z","timestamp":1757548800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"\n Introduction<\/jats:title>\n Necrotizing enterocolitis (NEC) is an inflammatory bowel disease that primarily affects preterm infants. Predisposing risk factors for NEC include prematurity, formula feeding, anemia, and sepsis. To date, no studies have investigated the gut microbiota of preterm infants with NEC in India.<\/jats:p>\n <\/jats:sec>\n \n Method<\/jats:title>\n In the current study, shotgun metagenomic sequencing was performed on fecal samples from premature infants with NEC and healthy preterm infants (n = 24). Sequencing was conducted using the NovaSeq X Plus platform, generating 2 \u00d7 150 bp paired-end reads. The infants were matched based on gestational age and postnatal age.<\/jats:p>\n <\/jats:sec>\n \n Result<\/jats:title>\n \n The median time to NEC diagnosis was 9 days (range: 1\u201330 days). Taxonomic analysis revealed a high prevalence of\n Enterobacteriaceae<\/jats:italic>\n at the family level, with the genera\n Klebsiella<\/jats:italic>\n and\n Escherichia<\/jats:italic>\n particularly prominent in neonates with NEC. No statistically significant differences in alpha or beta diversity were observed between stool samples from infants with and without NEC. Linear regression analysis demonstrated that\n Enterobacteriaceae<\/jats:italic>\n were significantly more abundant in stool samples from infants with NEC than without NEC (q &lt; 0.05). Differential abundance analysis using Linear Discriminant Analysis Effect Size (LEfSe) identified\n Klebsiella pneumoniae<\/jats:italic>\n and\n Escherichia coli<\/jats:italic>\n as enriched in the gut microbiota of preterm infants with NEC. Functional analysis revealed an increase in genes associated with lipopolysaccharide (LPS) O-antigen, the type IV secretion system (T4SS), the L-rhamnose pathway, quorum sensing, and iron transporters, including ABC transporters, in stool samples from infants with NEC.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n \n The high prevalence of\n Enterobacteriaceae<\/jats:italic>\n and enrichment of LPS O-antigen and T4SS genes may be associated with NEC in Indian preterm infants.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fcimb.2025.1649384","type":"journal-article","created":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T05:25:39Z","timestamp":1757568339000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Characterization of gut microbiota signatures in Indian preterm infants with necrotizing enterocolitis: a shotgun metagenomic approach"],"prefix":"10.3389","volume":"15","author":[{"given":"Prabavathi","family":"Devarajalu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Savita Verma","family":"Attri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jogender","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sourabh","family":"Dutta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayakanthan","family":"Kabeerdoss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,9,11]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1186\/s12887-020-02231-5","article-title":"Global incidence of Necrotizing Enterocolitis: a systematic review and Meta-analysis","volume":"20","author":"Alsaied","year":"2020","journal-title":"BMC Pediatr."},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0105046","article-title":"Mucosa-associated bacterial diversity in necrotizing enterocolitis","volume":"9","author":"Brower-Sinning","year":"2014","journal-title":"PloS One"},{"key":"B3","doi-asserted-by":"publisher","first-page":"4027","DOI":"10.1093\/bioinformatics\/btac438","article-title":"microbiomeMarker: an R\/Bioconductor package for microbiome marker identification and visualization","volume":"38","author":"Cao","year":"2022","journal-title":"Bioinformatics"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000377","article-title":"Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors","volume":"6","author":"Chen","year":"2020","journal-title":"Microbial Genomics"},{"key":"B5","unstructured":"Transmission dynamics and control of multidrug-resistant Klebsiella pneumoniae in neonates in a developing country\n \n \n \n Crellen\n T.\n \n \n Turner\n P.\n \n \n Pol\n S.\n \n \n Baker\n S.\n \n \n Nguyen\n T. 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