Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure

Joann Romano-Keeler, Meghan H. Shilts, Andrey Tovchigrechko, Chunlin Wang, Robert M. Brucker, Daniel J. Moore, Christopher Fonnesbeck, Shufang Meng, Hernan Correa, Harold N. Lovvorn, Yi Wei Tang, Lora V Hooper, Seth R. Bordenstein, Suman R. Das, Jorn Hendrik Weitkamp

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Objective Necrotizing enterocolitis (NEC) is the most common surgical emergency in preterm infants, and pathogenesis associates with changes in the fecal microbiome. As fecal samples incompletely represent microbial communities in intestinal mucosa, we sought to determine the NEC tissue-specific microbiome and assess its contribution to pathogenesis. Design We amplified and sequenced the V1-V3 hypervariable region of the bacterial 16S rRNA gene extracted from intestinal tissue and corresponding fecal samples from 12 surgical patients with NEC and 14 surgical patients without NEC. Low quality and non-bacterial sequences were removed, and taxonomic assignment was made with the Ribosomal Database Project. Operational taxonomic units were clustered at 97%. We tested for differences between NEC and non-NEC samples in microbiome alpha-and beta-diversity and differential abundance of specific taxa between NEC and non-NEC samples. Additional analyses were performed to assess the contribution of other demographic and environmental confounding factors on the infant tissue and fecal microbiome.

Original languageEnglish (US)
Article numbere0206366
JournalPLoS One
Volume13
Issue number10
DOIs
StatePublished - Oct 1 2018

Fingerprint

enterocolitis
Necrotizing Enterocolitis
microbial communities
Microbiota
antibiotics
Tissue
Anti-Bacterial Agents
Enterocolitis
Genes
pathogenesis
Intestinal Mucosa
rRNA Genes
Premature Infants
sampling
Emergencies
intestinal mucosa
Demography
Databases
demographic statistics
ribosomal RNA

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Romano-Keeler, J., Shilts, M. H., Tovchigrechko, A., Wang, C., Brucker, R. M., Moore, D. J., ... Weitkamp, J. H. (2018). Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure. PLoS One, 13(10), [e0206366]. https://doi.org/10.1371/journal.pone.0206366

Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure. / Romano-Keeler, Joann; Shilts, Meghan H.; Tovchigrechko, Andrey; Wang, Chunlin; Brucker, Robert M.; Moore, Daniel J.; Fonnesbeck, Christopher; Meng, Shufang; Correa, Hernan; Lovvorn, Harold N.; Tang, Yi Wei; Hooper, Lora V; Bordenstein, Seth R.; Das, Suman R.; Weitkamp, Jorn Hendrik.

In: PLoS One, Vol. 13, No. 10, e0206366, 01.10.2018.

Research output: Contribution to journalArticle

Romano-Keeler, J, Shilts, MH, Tovchigrechko, A, Wang, C, Brucker, RM, Moore, DJ, Fonnesbeck, C, Meng, S, Correa, H, Lovvorn, HN, Tang, YW, Hooper, LV, Bordenstein, SR, Das, SR & Weitkamp, JH 2018, 'Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure', PLoS One, vol. 13, no. 10, e0206366. https://doi.org/10.1371/journal.pone.0206366
Romano-Keeler, Joann ; Shilts, Meghan H. ; Tovchigrechko, Andrey ; Wang, Chunlin ; Brucker, Robert M. ; Moore, Daniel J. ; Fonnesbeck, Christopher ; Meng, Shufang ; Correa, Hernan ; Lovvorn, Harold N. ; Tang, Yi Wei ; Hooper, Lora V ; Bordenstein, Seth R. ; Das, Suman R. ; Weitkamp, Jorn Hendrik. / Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure. In: PLoS One. 2018 ; Vol. 13, No. 10.
@article{d0b5fe23106f4ee194a0515c13e98177,
title = "Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure",
abstract = "Objective Necrotizing enterocolitis (NEC) is the most common surgical emergency in preterm infants, and pathogenesis associates with changes in the fecal microbiome. As fecal samples incompletely represent microbial communities in intestinal mucosa, we sought to determine the NEC tissue-specific microbiome and assess its contribution to pathogenesis. Design We amplified and sequenced the V1-V3 hypervariable region of the bacterial 16S rRNA gene extracted from intestinal tissue and corresponding fecal samples from 12 surgical patients with NEC and 14 surgical patients without NEC. Low quality and non-bacterial sequences were removed, and taxonomic assignment was made with the Ribosomal Database Project. Operational taxonomic units were clustered at 97{\%}. We tested for differences between NEC and non-NEC samples in microbiome alpha-and beta-diversity and differential abundance of specific taxa between NEC and non-NEC samples. Additional analyses were performed to assess the contribution of other demographic and environmental confounding factors on the infant tissue and fecal microbiome.",
author = "Joann Romano-Keeler and Shilts, {Meghan H.} and Andrey Tovchigrechko and Chunlin Wang and Brucker, {Robert M.} and Moore, {Daniel J.} and Christopher Fonnesbeck and Shufang Meng and Hernan Correa and Lovvorn, {Harold N.} and Tang, {Yi Wei} and Hooper, {Lora V} and Bordenstein, {Seth R.} and Das, {Suman R.} and Weitkamp, {Jorn Hendrik}",
year = "2018",
month = "10",
day = "1",
doi = "10.1371/journal.pone.0206366",
language = "English (US)",
volume = "13",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "10",

}

TY - JOUR

T1 - Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure

AU - Romano-Keeler, Joann

AU - Shilts, Meghan H.

AU - Tovchigrechko, Andrey

AU - Wang, Chunlin

AU - Brucker, Robert M.

AU - Moore, Daniel J.

AU - Fonnesbeck, Christopher

AU - Meng, Shufang

AU - Correa, Hernan

AU - Lovvorn, Harold N.

AU - Tang, Yi Wei

AU - Hooper, Lora V

AU - Bordenstein, Seth R.

AU - Das, Suman R.

AU - Weitkamp, Jorn Hendrik

PY - 2018/10/1

Y1 - 2018/10/1

N2 - Objective Necrotizing enterocolitis (NEC) is the most common surgical emergency in preterm infants, and pathogenesis associates with changes in the fecal microbiome. As fecal samples incompletely represent microbial communities in intestinal mucosa, we sought to determine the NEC tissue-specific microbiome and assess its contribution to pathogenesis. Design We amplified and sequenced the V1-V3 hypervariable region of the bacterial 16S rRNA gene extracted from intestinal tissue and corresponding fecal samples from 12 surgical patients with NEC and 14 surgical patients without NEC. Low quality and non-bacterial sequences were removed, and taxonomic assignment was made with the Ribosomal Database Project. Operational taxonomic units were clustered at 97%. We tested for differences between NEC and non-NEC samples in microbiome alpha-and beta-diversity and differential abundance of specific taxa between NEC and non-NEC samples. Additional analyses were performed to assess the contribution of other demographic and environmental confounding factors on the infant tissue and fecal microbiome.

AB - Objective Necrotizing enterocolitis (NEC) is the most common surgical emergency in preterm infants, and pathogenesis associates with changes in the fecal microbiome. As fecal samples incompletely represent microbial communities in intestinal mucosa, we sought to determine the NEC tissue-specific microbiome and assess its contribution to pathogenesis. Design We amplified and sequenced the V1-V3 hypervariable region of the bacterial 16S rRNA gene extracted from intestinal tissue and corresponding fecal samples from 12 surgical patients with NEC and 14 surgical patients without NEC. Low quality and non-bacterial sequences were removed, and taxonomic assignment was made with the Ribosomal Database Project. Operational taxonomic units were clustered at 97%. We tested for differences between NEC and non-NEC samples in microbiome alpha-and beta-diversity and differential abundance of specific taxa between NEC and non-NEC samples. Additional analyses were performed to assess the contribution of other demographic and environmental confounding factors on the infant tissue and fecal microbiome.

UR - http://www.scopus.com/inward/record.url?scp=85055614581&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85055614581&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0206366

DO - 10.1371/journal.pone.0206366

M3 - Article

C2 - 30365522

AN - SCOPUS:85055614581

VL - 13

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 10

M1 - e0206366

ER -