Development of necrotising enterocolitis (NEC) is considered to be dependent on the bacterial colonisation of the gut. With little concordance between published data and a recent study failing to detect a common strain in infants with NEC, more questions than answers are arising about our understanding of this complex disease

Bloch, Sune

Friis, Morten

Friis-Hansen, Lennart Jan

Martin-Bertelsen, Tomas

Nielsen, Michelle C.

Rye-Jørgensen, Niklas

Sørensen, Mads Sølvsten

Winther, Ole

English

Christopher James Stewart

Stephen Paul Cummings

MUCC (Crossref)

Citation: Stewart, Christopher and Cummings, Stephen (2015) Gut bacteria and necrotizing 
enterocolitis: cause or effect? Trends in Microbiology, 23 (6). pp. 332-333. ISSN 0966-842X 
Published by: Elsevier
URL:  http://dx.doi.org/10.1016/j.tim.2015.04.005 
<http://dx.doi.org/10.1016/j.tim.2015.04.005>
This  version  was  downloaded  from  Northumbria  Research  Link: 
http://nrl.northumbria.ac.uk/22371/
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required.)
Gut bacteria and necrotizing enterocolitis: cause or effect? 
 
Christopher James Stewart, Northumbria University, Newcastle upon Tyne, UK. Email: 
Christopher.stewart@northumbria.ac.uk. Twitter: CJStewart7. 
Stephen Paul Cummings Northumbria University, Newcastle upon Tyne, UK. Corresponding 
author. Email: Stephen.cummings@northumbria.ac.uk 
 
Key words: Necrotising enterocolitis, Preterm, Gut microbiome, Metagenomics 
 
 
Main Article 
Necrotising enterocolitis (NEC) is multifactorial disease process which affects the gut, most 
typically the terminal ileum, and occurs almost exclusively in babies born significantly 
preterm (<32 weeks gestation). The main risk factors for NEC include gestational age, birth 
weight and feeding with infant formula, that are in turn associated with the immaturity of 
both the gut and the immune system. The gut bacteria have a significant role in developing 
barrier function, integrity, and mucosal and systemic immune function in the neonate. They 
also ‘educate’ the gut associated lymphoid tissue, allowing the infant’s immune system to 
tolerate the presence of its microbiota [1]. As NEC does not occur in a sterile environment 
(e.g. in utero or germ free animal models), it may be that in some preterm infants this 
habituation by the immune system to the gut microbial community may be undermined 
initiating an exaggerated inflammation cascade that results in NEC [2].   
Over the past four decades, researchers, driven by improvements in methodology, have 
trawled through microbiological datasets to determine the role of the preterm gut microbiota 
in NEC and in particular, whether the presence of specific bacteria are correlated with the 
disease. There are conflicting reports in the literature, with some studies showing no 
association of the gut microbiota with incidence of NEC [3], whereas others studies identify 
particular taxa (i.e. Klebsiella; Clostridium) correlated with an increased risk of disease [4]. 
Many early molecular studies demonstrated differing abundances of bacteria in stool prior to 
NEC diagnosis, but were confounded by low and non-optimal sampling [5]. It is important to 
note that many studies of the gut microbiota present data where all NEC cases within an 
experimental cohort are pooled. Analyses such as these, while simple to understand, are 
misleading as any increase in a particular taxa are unlikely to be shared across all NEC 
infants. More recently, improved sampling coupled to advances in sequencing technology, 
have highlighted the diverse and individual nature of the gut microbiota both within infants 
on a single neonatal intensive care unit (NICU), but also between different NICUs [6].  
The recent study by Raveh-Sadka et al. [7] is a powerful demonstration of how, using newly 
developed methodologies, it is possible to resolve sequence data from gut associated 
microbial communities into genomes. Using this approach they began to tease out the 
complexity of these microbial communities and their contribution, if any, to NEC. The study 
carried out metagenomic sequencing on 55 stool samples from 10 infants (6 NEC, 4 controls) 
during an NEC outbreak 2.5 times the average case in the NICU (Magee-Women’s Hospital 
of the University of Pittsburgh Medical Centre). The study showed that there was no 
evidence for a common genomically distinct pathogenic agent causing NEC. An important 
unknown in any outbreak of NEC within in a NICU, is whether a single pathogenic strain is 
cross-colonising infants. While a review of NEC outbreaks failed to determine a consistent 
pattern of colonisation [8], it is plausible that identical strains could be found in infants 
diagnosed with NEC. However, Raveh-Sadka et al. showed that in their cohort each 
individual infant had a distinct bacterial profile down to strain level. They were also able to 
explore strains of individual taxa. In this case, Enterococcus faecalis present in several of the 
babies. They were able to show each infant had its own pattern of specific strains which in 
turn threw up some fascinating questions, around the ecology of E. faecalis. For example, 
what was the size and diversity of the community from which these strains are derived? How 
might they disperse and colonise the host? What are the barriers to colonisation within the 
NICU? Are they able to competitively exclude other strains? Does dominance of a particular 
strain reflect strong selective pressures modulated by the host’s genetic background and the 
microbial community resident in the gut? Given that E. faecalis has been implicated in 
beneficially modulating the immune response in neonates [9] these questions may have 
clinical as well as fundamental significance. The ability to resolve the community to bacterial 
strain level also demonstrated how different strains of the bacterium Veillonella responded to 
antibiotics with one strain being replaced by a second.  This may help explain why some 
microbiome studies on preterm gut communities showed no significant changes to antibiotic 
administration at the level of family or genus [10].  It also highlights the limitations of 
sequence based studies on 16S rRNA gene diversity that cannot resolve the community to 
strain level.  
Aside from bacterial colonisation in NEC, Raveh-Sadka et al. presented some intriguing and 
novel findings relating to the preterm gut microbiome. One aspect the authors explored was 
the potential capabilities for mobile elements such as plasmids and phages to move around 
the NICU, potentially contributing to NEC. Comparable to the results for strain level 
analysis, identical sequences were found within infants overtime and there were few cases 
where plasmids and phages were detected in different infants. However, there were no 
identical mobile elements that were shared between NEC infants.  
With more questions than answers arising from a decade of molecular research into the role 
of the preterm gut microbiome in NEC, the study by Raveh-Sadka et al. clearly demonstrates 
the opportunities that rapidly evolving sequencing technologies offer to understand this 
complex multi-factorial disease. In the short and medium term genome-resolved 
metagenomics will help better frame our research questions and identify potential interactions 
between microbial components of a community and its environment that are not otherwise 
visible. In the longer term unpicking the complexity of NEC will require greater collaboration 
and agreement on methodologies and the exploitation of bio-banks of stool, urine, serum, and 
resected tissue samples from preterm infants to help overcome issues around small disease 
cohorts. Moreover, researchers will need to exploit system based approaches including 
metabolomics and proteomics, of both microbial community and the host to more 
comprehensively characterise the mechanisms of NEC.  
 
References 
1. Bevins, C.L. et al. (2011) The potter’s wheel: the host’s role in sculpting its 
microbiota. Cell. Mol. Life Sci. 68, 3675–3685 
2. Berrington, J.E. et al. (2013) Gut microbiota in preterm infants: assessment and 
relevance to health and disease? Arch. Dis. Child. Fetal Neonatal Ed. 98:F286-F290 
doi:10.1136/archdischild-2012-302134  
3. Normann, E, et al. (2013) Intestinal microbial profiles in extremely preterm infants 
with and without necrotizing enterocolitis. Acta Paediat. 102. 129–136. 
4. Sim, K. et al. (2015) Dysbiosis anticipating necrotizing enterocolitis in very 
premature infants. Clin. Infect. Dis. 60, 389-397 
5. Stewart, C.J. et al. (2012) The preterm gut microbiota: changes associated with 
necrotizing enterocolitis and infection. Acta. Paediat. 101, 1121–1127. 
6. Taft, D.H. et al. (2014) Intestinal microbiota of preterm infants differ over time and 
between hospitals. Microbiome 2, 36 doi.org/10.1186/2049-2618-2-36 
7. Raveh-Sadka, T. et al. (2015) Gut bacteria are rarely shared by co-hospitalized 
premature infants, regardless of necrotizing enterocolitis development. eLife 4, 
e05477 
8. Boccia, D. et al. (2001) Nosocomial necrotising enterocolitis outbreaks: epidemiology 
and control measures. Eur J. Ped., 160, 385-391 
9. Wang, S. et al. (2014) Enterococcus faecalis from Healthy infants modulates 
inflammation through MAPK signalling pathways. PLoS ONE 9, e97523. 
doi:10.1371/journal.pone.0097523  
10. Stewart, C.J. et al. (2013) Development of the preterm gut microbiome in twins at risk 
of necrotising enterocolitis and sepsis. PLoS ONE 8, e73465. 
doi:10.1371/journal.pone.0073465 
 
 


Gut bacteria and necrotizing enterocolitis: cause or effect?

Copenhagen University Research Information System

Differential gene expression in the otic capsule and the middle ear-an annotation of bone-related signaling genes

Stewart, Christopher

Cummings, Stephen

Teeside University's Research Repository

Northumbria Research Link
Citation:  Stewart,  Christopher  and  Cummings,  Stephen  (2015)  Gut  bacteria  and  necrotizing 
enterocolitis: cause or effect? Trends in Microbiology, 23 (6). pp. 332-333. ISSN 0966-842X 
Published by: Elsevier
URL: http://dx.doi.org/10.1016/j.tim.2015.04.005 <http://dx.doi.org/10.1016/j.tim.2015.04.005>
This version was downloaded from Northumbria Research Link: http://nrl.northumbria.ac.uk/22371/
Northumbria University has developed Northumbria Research Link (NRL) to enable users to access 
the University’s research output. Copyright © and moral rights for items on NRL are retained by the 
individual author(s) and/or other copyright owners.  Single copies of full items can be reproduced, 
displayed or performed, and given to third parties in any format or medium for personal research or 
study, educational, or not-for-profit purposes without prior permission or charge, provided the authors, 
title and full bibliographic details are given, as well as a hyperlink and/or URL to the original metadata 
page. The content must not be changed in any way. Full items must not be sold commercially in any  
format or medium without formal permission of the copyright holder.  The full policy is available online: 
http://nrl.northumbria.ac.uk/pol  i cies.html  
This  document  may differ  from the  final,  published version of  the research  and has been made 
available online in accordance with publisher policies. To read and/or cite from the published version 
of the research, please visit the publisher’s website (a subscription may be required.)
                        
Gut bacteria and necrotizing enterocolitis: cause or effect? 
 
Christopher James Stewart, Northumbria University, Newcastle upon Tyne, UK. Email: 
Christopher.stewart@northumbria.ac.uk. Twitter: CJStewart7. 
Stephen Paul Cummings Northumbria University, Newcastle upon Tyne, UK. Corresponding 
author. Email: Stephen.cummings@northumbria.ac.uk 
 
Key words: Necrotising enterocolitis, Preterm, Gut microbiome, Metagenomics 
 
 
Main Article 
Necrotising enterocolitis (NEC) is multifactorial disease process which affects the gut, most 
typically the terminal ileum, and occurs almost exclusively in babies born significantly 
preterm (<32 weeks gestation). The main risk factors for NEC include gestational age, birth 
weight and feeding with infant formula, that are in turn associated with the immaturity of 
both the gut and the immune system. The gut bacteria have a significant role in developing 
barrier function, integrity, and mucosal and systemic immune function in the neonate. They 
also ‘educate’ the gut associated lymphoid tissue, allowing the infant’s immune system to 
tolerate the presence of its microbiota [1]. As NEC does not occur in a sterile environment 
(e.g. in utero or germ free animal models), it may be that in some preterm infants this 
habituation by the immune system to the gut microbial community may be undermined 
initiating an exaggerated inflammation cascade that results in NEC [2].   
Over the past four decades, researchers, driven by improvements in methodology, have 
trawled through microbiological datasets to determine the role of the preterm gut microbiota 
in NEC and in particular, whether the presence of specific bacteria are correlated with the 
disease. There are conflicting reports in the literature, with some studies showing no 
association of the gut microbiota with incidence of NEC [3], whereas others studies identify 
particular taxa (i.e. Klebsiella; Clostridium) correlated with an increased risk of disease [4]. 
Many early molecular studies demonstrated differing abundances of bacteria in stool prior to 
NEC diagnosis, but were confounded by low and non-optimal sampling [5]. It is important to 
note that many studies of the gut microbiota present data where all NEC cases within an 
experimental cohort are pooled. Analyses such as these, while simple to understand, are 
misleading as any increase in a particular taxa are unlikely to be shared across all NEC 
infants. More recently, improved sampling coupled to advances in sequencing technology, 
have highlighted the diverse and individual nature of the gut microbiota both within infants 
on a single neonatal intensive care unit (NICU), but also between different NICUs [6].  
The recent study by Raveh-Sadka et al. [7] is a powerful demonstration of how, using newly 
developed methodologies, it is possible to resolve sequence data from gut associated 
microbial communities into genomes. Using this approach they began to tease out the 
complexity of these microbial communities and their contribution, if any, to NEC. The study 
carried out metagenomic sequencing on 55 stool samples from 10 infants (6 NEC, 4 controls) 
during an NEC outbreak 2.5 times the average case in the NICU (Magee-Women’s Hospital 
of the University of Pittsburgh Medical Centre). The study showed that there was no 
evidence for a common genomically distinct pathogenic agent causing NEC. An important 
unknown in any outbreak of NEC within in a NICU, is whether a single pathogenic strain is 
cross-colonising infants. While a review of NEC outbreaks failed to determine a consistent 
pattern of colonisation [8], it is plausible that identical strains could be found in infants 
diagnosed with NEC. However, Raveh-Sadka et al. showed that in their cohort each 
individual infant had a distinct bacterial profile down to strain level. They were also able to 
explore strains of individual taxa. In this case, Enterococcus faecalis present in several of the 
babies. They were able to show each infant had its own pattern of specific strains which in 
turn threw up some fascinating questions, around the ecology of E. faecalis. For example, 
what was the size and diversity of the community from which these strains are derived? How 
might they disperse and colonise the host? What are the barriers to colonisation within the 
NICU? Are they able to competitively exclude other strains? Does dominance of a particular 
strain reflect strong selective pressures modulated by the host’s genetic background and the 
microbial community resident in the gut? Given that E. faecalis has been implicated in 
beneficially modulating the immune response in neonates [9] these questions may have 
clinical as well as fundamental significance. The ability to resolve the community to bacterial 
strain level also demonstrated how different strains of the bacterium Veillonella responded to 
antibiotics with one strain being replaced by a second.  This may help explain why some 
microbiome studies on preterm gut communities showed no significant changes to antibiotic 
administration at the level of family or genus [10].  It also highlights the limitations of 
sequence based studies on 16S rRNA gene diversity that cannot resolve the community to 
strain level.  
Aside from bacterial colonisation in NEC, Raveh-Sadka et al. presented some intriguing and 
novel findings relating to the preterm gut microbiome. One aspect the authors explored was 
the potential capabilities for mobile elements such as plasmids and phages to move around 
the NICU, potentially contributing to NEC. Comparable to the results for strain level 
analysis, identical sequences were found within infants overtime and there were few cases 
where plasmids and phages were detected in different infants. However, there were no 
identical mobile elements that were shared between NEC infants.  
With more questions than answers arising from a decade of molecular research into the role 
of the preterm gut microbiome in NEC, the study by Raveh-Sadka et al. clearly demonstrates 
the opportunities that rapidly evolving sequencing technologies offer to understand this 
complex multi-factorial disease. In the short and medium term genome-resolved 
metagenomics will help better frame our research questions and identify potential interactions 
between microbial components of a community and its environment that are not otherwise 
visible. In the longer term unpicking the complexity of NEC will require greater collaboration 
and agreement on methodologies and the exploitation of bio-banks of stool, urine, serum, and 
resected tissue samples from preterm infants to help overcome issues around small disease 
cohorts. Moreover, researchers will need to exploit system based approaches including 
metabolomics and proteomics, of both microbial community and the host to more 
comprehensively characterise the mechanisms of NEC.  
 
References 
1. Bevins, C.L. et al. (2011) The potter’s wheel: the host’s role in sculpting its 
microbiota. Cell. Mol. Life Sci. 68, 3675–3685 
2. Berrington, J.E. et al. (2013) Gut microbiota in preterm infants: assessment and 
relevance to health and disease? Arch. Dis. Child. Fetal Neonatal Ed. 98:F286-F290 
doi:10.1136/archdischild-2012-302134  
3. Normann, E, et al. (2013) Intestinal microbial profiles in extremely preterm infants 
with and without necrotizing enterocolitis. Acta Paediat. 102. 129–136. 
4. Sim, K. et al. (2015) Dysbiosis anticipating necrotizing enterocolitis in very 
premature infants. Clin. Infect. Dis. 60, 389-397 
5. Stewart, C.J. et al. (2012) The preterm gut microbiota: changes associated with 
necrotizing enterocolitis and infection. Acta. Paediat. 101, 1121–1127. 
6. Taft, D.H. et al. (2014) Intestinal microbiota of preterm infants differ over time and 
between hospitals. Microbiome 2, 36 doi.org/10.1186/2049-2618-2-36 
7. Raveh-Sadka, T. et al. (2015) Gut bacteria are rarely shared by co-hospitalized 
premature infants, regardless of necrotizing enterocolitis development. eLife 4, 
e05477 
8. Boccia, D. et al. (2001) Nosocomial necrotising enterocolitis outbreaks: epidemiology 
and control measures. Eur J. Ped., 160, 385-391 
9. Wang, S. et al. (2014) Enterococcus faecalis from Healthy infants modulates 
inflammation through MAPK signalling pathways. PLoS ONE 9, e97523. 
doi:10.1371/journal.pone.0097523  
10. Stewart, C.J. et al. (2013) Development of the preterm gut microbiome in twins at risk 
of necrotising enterocolitis and sepsis. PLoS ONE 8, e73465. 
doi:10.1371/journal.pone.0073465 
 
 


Hypothesis: A number of bone-related genes may be responsible for the unique suppression of perilabyrinthine bone remodeling. Background: Bone remodeling is highly inhibited around the inner ear space most likely because of osteoprotegerin (OPG), which is a well-known potent inhibitor of osteoclast formation and function. However, other signaling molecules may also be responsible for the inhibition of bone remodeling within the otic capsule. Methods: Microarray technology was used to determine bone-related genes differentially expressed between the lining tissues of the otic capsule (spiral ligament and stria vascularis) and the lining tissues from the middle ear of the rat. Data was analyzed with statistical bioinformatics tools. Gene expression levels of selected genes were validated using quantitative polymerase chain reaction. Results: A total of 413 genes were identified when young inner bulla (growing) were compared with young otic capsule and 358 genes were identified when adult inner bulla (quiescent) were compared with adult otic capsule. Fourteen genes were involved in bone metabolism of which four genes have been previously discussed in the literature of perilabyrinthine bone biology. Conclusion: The gene expression of the otic capsule was significantly different from that of the middle ear. This study identified a number of differentially expressed bone-related mRNAs of potential significance and confirmed the OPG/receptor activator of nuclear factor kappa-B (RANK)/RANK ligand (RANKL) pathway as the key signaling system for the unique behavior of bone cells within the otic capsule. No differentially expressed up-or downstream messengers in the OPG/RANK/RANKL pathway were found

Friis-Hansen, Lennart

Rye-Jorgensen, Niklas

Sorensen, Mads S.

Online Research Database In Technology

Differential Gene Expression in the Otic Capsule and the Middle Ear-An Annotation of Bone-Related Signaling Genes

Crossref

Trends in Microbiology

and necrotizing enterocolitis: cause or effect? Christopher James Stewart, Northumbria University, Newcastle upon Tyne,

Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis.

Dysbiosis anticipating necrotizing enterocolitis in very premature infants.

Enterococcus faecalis from Healthy infants modulates inflammation through MAPK signalling pathways.

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife 4,

Gut microbiota in preterm infants: assessment and relevance to health and disease?

Intestinal microbial profiles in extremely preterm infants with and without necrotizing enterocolitis.

Intestinal microbiota of preterm infants differ over time and between hospitals.

Nosocomial necrotising enterocolitis outbreaks: epidemiology and control measures.

The potter’s wheel: the host’s role in sculpting its microbiota.

The preterm gut microbiota: changes associated with necrotizing enterocolitis and infection.

http://nrl.northumbria.ac.uk/22371/3/Spotlight_article_%25283%2529.pdf

Gut bacteria and necrotizing enterocolitis: cause or effect?

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