Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

Mihai Pop, Alan W Walker, Joseph Paulson, Brianna Lindsay, Martin Antonio, M Anowar Hossain, Joseph Oundo, Boubou Tamboura, Volker Mai, Irina Astrovskaya, Hector Bravo, Richard Rance, Mark Stares, Myron M Levine, Sandra Panchalingam, Karen Kotloff, Usman N Ikumapayi, Chinelo Ebruke, Mitchell Adeyemi, Dilruba Ahmed & 15 others Firoz Ahmed, Meer Alam, Ruhul Amin, Sabbir Siddiqui, John B Ochieng, Emmanuel Ouma, Jane Juma, Euince Mailu, Richard Omore, J Glenn Morris, Robert F Breiman, Debasish Saha, Julian Parkhill, James P Nataro, O Colin Stine

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Abstract

BACKGROUND: Diarrheal diseases continue to contribute significantly to morbidity and mortality in infants and young children in developing countries. There is an urgent need to better understand the contributions of novel, potentially uncultured, diarrheal pathogens to severe diarrheal disease, as well as distortions in normal gut microbiota composition that might facilitate severe disease.

RESULTS: We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. Our study includes 992 children from four low-income countries in West and East Africa, and Southeast Asia. Known pathogens, as well as bacteria currently not considered as important diarrhea-causing pathogens, are positively associated with MSD, and these include Escherichia/Shigella, and Granulicatella species, and Streptococcus mitis/pneumoniae groups. In both cases and controls, there tend to be distinct negative correlations between facultative anaerobic lineages and obligate anaerobic lineages. Overall genus-level microbiota composition exhibit a shift in controls from low to high levels of Prevotella and in MSD cases from high to low levels of Escherichia/Shigella in younger versus older children; however, there was significant variation among many genera by both site and age.

CONCLUSIONS: Our findings expand the current understanding of microbiota-associated diarrhea pathogenicity in young children from developing countries. Our findings are necessarily based on correlative analyses and must be further validated through epidemiological and molecular techniques.

Original languageEnglish
Article numberR76
JournalGenome Biology
Volume15
Issue number6
DOIs
Publication statusPublished - 27 Jun 2014

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intestinal microorganisms
Diarrhea
diarrhea
income
Microbiota
diarrheal disease
pathogen
Escherichia
Shigella
Developing Countries
developing world
Granulicatella
developing countries
pathogens
Streptococcus mitis
pneumonia
Prevotella
infant mortality
pathogenicity
morbidity

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Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. / Pop, Mihai; Walker, Alan W; Paulson, Joseph; Lindsay, Brianna; Antonio, Martin; Hossain, M Anowar; Oundo, Joseph; Tamboura, Boubou; Mai, Volker; Astrovskaya, Irina; Bravo, Hector; Rance, Richard; Stares, Mark; Levine, Myron M; Panchalingam, Sandra; Kotloff, Karen; Ikumapayi, Usman N; Ebruke, Chinelo; Adeyemi, Mitchell; Ahmed, Dilruba; Ahmed, Firoz; Alam, Meer; Amin, Ruhul; Siddiqui, Sabbir; Ochieng, John B; Ouma, Emmanuel; Juma, Jane; Mailu, Euince; Omore, Richard; Morris, J Glenn; Breiman, Robert F; Saha, Debasish; Parkhill, Julian; Nataro, James P; Stine, O Colin.

In: Genome Biology, Vol. 15, No. 6, R76, 27.06.2014.

Research output: Contribution to journalArticle

Pop, M, Walker, AW, Paulson, J, Lindsay, B, Antonio, M, Hossain, MA, Oundo, J, Tamboura, B, Mai, V, Astrovskaya, I, Bravo, H, Rance, R, Stares, M, Levine, MM, Panchalingam, S, Kotloff, K, Ikumapayi, UN, Ebruke, C, Adeyemi, M, Ahmed, D, Ahmed, F, Alam, M, Amin, R, Siddiqui, S, Ochieng, JB, Ouma, E, Juma, J, Mailu, E, Omore, R, Morris, JG, Breiman, RF, Saha, D, Parkhill, J, Nataro, JP & Stine, OC 2014, 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition' Genome Biology, vol. 15, no. 6, R76. https://doi.org/10.1186/gb-2014-15-6-r76
Pop, Mihai ; Walker, Alan W ; Paulson, Joseph ; Lindsay, Brianna ; Antonio, Martin ; Hossain, M Anowar ; Oundo, Joseph ; Tamboura, Boubou ; Mai, Volker ; Astrovskaya, Irina ; Bravo, Hector ; Rance, Richard ; Stares, Mark ; Levine, Myron M ; Panchalingam, Sandra ; Kotloff, Karen ; Ikumapayi, Usman N ; Ebruke, Chinelo ; Adeyemi, Mitchell ; Ahmed, Dilruba ; Ahmed, Firoz ; Alam, Meer ; Amin, Ruhul ; Siddiqui, Sabbir ; Ochieng, John B ; Ouma, Emmanuel ; Juma, Jane ; Mailu, Euince ; Omore, Richard ; Morris, J Glenn ; Breiman, Robert F ; Saha, Debasish ; Parkhill, Julian ; Nataro, James P ; Stine, O Colin. / Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. In: Genome Biology. 2014 ; Vol. 15, No. 6.
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abstract = "BACKGROUND: Diarrheal diseases continue to contribute significantly to morbidity and mortality in infants and young children in developing countries. There is an urgent need to better understand the contributions of novel, potentially uncultured, diarrheal pathogens to severe diarrheal disease, as well as distortions in normal gut microbiota composition that might facilitate severe disease.RESULTS: We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. Our study includes 992 children from four low-income countries in West and East Africa, and Southeast Asia. Known pathogens, as well as bacteria currently not considered as important diarrhea-causing pathogens, are positively associated with MSD, and these include Escherichia/Shigella, and Granulicatella species, and Streptococcus mitis/pneumoniae groups. In both cases and controls, there tend to be distinct negative correlations between facultative anaerobic lineages and obligate anaerobic lineages. Overall genus-level microbiota composition exhibit a shift in controls from low to high levels of Prevotella and in MSD cases from high to low levels of Escherichia/Shigella in younger versus older children; however, there was significant variation among many genera by both site and age.CONCLUSIONS: Our findings expand the current understanding of microbiota-associated diarrhea pathogenicity in young children from developing countries. Our findings are necessarily based on correlative analyses and must be further validated through epidemiological and molecular techniques.",
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TY - JOUR

T1 - Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

AU - Pop, Mihai

AU - Walker, Alan W

AU - Paulson, Joseph

AU - Lindsay, Brianna

AU - Antonio, Martin

AU - Hossain, M Anowar

AU - Oundo, Joseph

AU - Tamboura, Boubou

AU - Mai, Volker

AU - Astrovskaya, Irina

AU - Bravo, Hector

AU - Rance, Richard

AU - Stares, Mark

AU - Levine, Myron M

AU - Panchalingam, Sandra

AU - Kotloff, Karen

AU - Ikumapayi, Usman N

AU - Ebruke, Chinelo

AU - Adeyemi, Mitchell

AU - Ahmed, Dilruba

AU - Ahmed, Firoz

AU - Alam, Meer

AU - Amin, Ruhul

AU - Siddiqui, Sabbir

AU - Ochieng, John B

AU - Ouma, Emmanuel

AU - Juma, Jane

AU - Mailu, Euince

AU - Omore, Richard

AU - Morris, J Glenn

AU - Breiman, Robert F

AU - Saha, Debasish

AU - Parkhill, Julian

AU - Nataro, James P

AU - Stine, O Colin

PY - 2014/6/27

Y1 - 2014/6/27

N2 - BACKGROUND: Diarrheal diseases continue to contribute significantly to morbidity and mortality in infants and young children in developing countries. There is an urgent need to better understand the contributions of novel, potentially uncultured, diarrheal pathogens to severe diarrheal disease, as well as distortions in normal gut microbiota composition that might facilitate severe disease.RESULTS: We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. Our study includes 992 children from four low-income countries in West and East Africa, and Southeast Asia. Known pathogens, as well as bacteria currently not considered as important diarrhea-causing pathogens, are positively associated with MSD, and these include Escherichia/Shigella, and Granulicatella species, and Streptococcus mitis/pneumoniae groups. In both cases and controls, there tend to be distinct negative correlations between facultative anaerobic lineages and obligate anaerobic lineages. Overall genus-level microbiota composition exhibit a shift in controls from low to high levels of Prevotella and in MSD cases from high to low levels of Escherichia/Shigella in younger versus older children; however, there was significant variation among many genera by both site and age.CONCLUSIONS: Our findings expand the current understanding of microbiota-associated diarrhea pathogenicity in young children from developing countries. Our findings are necessarily based on correlative analyses and must be further validated through epidemiological and molecular techniques.

AB - BACKGROUND: Diarrheal diseases continue to contribute significantly to morbidity and mortality in infants and young children in developing countries. There is an urgent need to better understand the contributions of novel, potentially uncultured, diarrheal pathogens to severe diarrheal disease, as well as distortions in normal gut microbiota composition that might facilitate severe disease.RESULTS: We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. Our study includes 992 children from four low-income countries in West and East Africa, and Southeast Asia. Known pathogens, as well as bacteria currently not considered as important diarrhea-causing pathogens, are positively associated with MSD, and these include Escherichia/Shigella, and Granulicatella species, and Streptococcus mitis/pneumoniae groups. In both cases and controls, there tend to be distinct negative correlations between facultative anaerobic lineages and obligate anaerobic lineages. Overall genus-level microbiota composition exhibit a shift in controls from low to high levels of Prevotella and in MSD cases from high to low levels of Escherichia/Shigella in younger versus older children; however, there was significant variation among many genera by both site and age.CONCLUSIONS: Our findings expand the current understanding of microbiota-associated diarrhea pathogenicity in young children from developing countries. Our findings are necessarily based on correlative analyses and must be further validated through epidemiological and molecular techniques.

U2 - 10.1186/gb-2014-15-6-r76

DO - 10.1186/gb-2014-15-6-r76

M3 - Article

VL - 15

JO - Genome Biology

JF - Genome Biology

SN - 1474-760X

IS - 6

M1 - R76

ER -