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Title: Effects of microbiota-directed foods in gnotobiotic animals and undernourished children

Abstract

To examine the contributions of impaired gut microbial community development to childhood undernutrition, we combined metabolomic and proteomic analyses of plasma samples with metagenomic analyses of fecal samples to characterize the biological state of Bangladeshi children with severe acute malnutrition (SAM) as they transitioned, after standard treatment, to moderate acute malnutrition (MAM) with persistent microbiota immaturity. Host and microbial effects of microbiota-directed complementary food (MDCF) prototypes targeting weaning-phase bacterial taxa underrepresented in SAM and MAM microbiota were characterized in gnotobiotic mice and gnotobiotic piglets colonized with age- and growth-discriminatory bacteria. A randomized, double-blind controlled feeding study identified a lead MDCF that changes the abundances of targeted bacteria and increases plasma biomarkers and mediators of growth, bone formation, neurodevelopment, and immune function in children with MAM.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2]; ORCiD logo [3]; ORCiD logo [4];  [5];  [5];  [5] more »;  [1];  [1];  [6];  [6];  [6];  [7];  [8];  [8];  [8];  [8];  [8];  [8];  [8];  [8];  [1];  [8];  [1] « less
+ Show Author Affiliations
  1. Washington Univ., St. Louis, MO (United States)
  2. Aix-Marseille Univ., and CNRS/IN2P3, Marseille (France); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. {Bob} L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  5. Duke Univ., Durham, NC (United States)
  6. Sanford Burnham Prebys Medical Discovery Inst., La Jolla, CA (United States); Russian Academy of Sciences (RAS), Moscow (Russian Federation)
  7. Sanford Burnham Prebys Medical Discovery Inst., La Jolla, CA (United States)
  8. International Centre for Diarrhoeal Disease Research (Bangladesh)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1546507
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Science
Additional Journal Information:
Journal Volume: 365; Journal Issue: 6449; Journal ID: ISSN 0036-8075
Publisher:
AAAS
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Gehrig, Jeanette, Venkatesh, Siddarth, Chang, Hao-Wei, Hibberd, Matthew C., Kung, Vanderlene, Cheng, Jiye, Chen, Robert, Subramanian, Sathish, Cowardin, Carrie, Meier, Martin, O'Donnell, David, Talcott, Michael, Spears, Larry, Semenkovich, Clay, Henrissat, Bernard, Giannone, Richard J., Hettich, Robert, Ilkayeva, Olga, Muehlbauer, Michael, Newgard, Christopher, Sawyer, Christopher, Head, Richard, Rodionov, Dmitry A., Arzamasov, Aleksandr, Leyn, Semen, Osterman, Andrei L., Hossain, Md Iqbal, Islam, Munirul, Choudhury, Nuzhat, Sarker, Shafiqul, Huq, Sayeeda, Mahmud, Imteaz, Mostafa, Ishita, Mahfuz, Mustafa, Barratt, Michael J., Ahmed, Tahmeed, and Gordon, Jeffrey I.. Effects of microbiota-directed foods in gnotobiotic animals and undernourished children. United States: N. p., 2019. Web. doi:10.1126/science.aau4732.
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Gehrig, Jeanette, Venkatesh, Siddarth, Chang, Hao-Wei, Hibberd, Matthew C., Kung, Vanderlene, Cheng, Jiye, Chen, Robert, Subramanian, Sathish, Cowardin, Carrie, Meier, Martin, O'Donnell, David, Talcott, Michael, Spears, Larry, Semenkovich, Clay, Henrissat, Bernard, Giannone, Richard J., Hettich, Robert, Ilkayeva, Olga, Muehlbauer, Michael, Newgard, Christopher, Sawyer, Christopher, Head, Richard, Rodionov, Dmitry A., Arzamasov, Aleksandr, Leyn, Semen, Osterman, Andrei L., Hossain, Md Iqbal, Islam, Munirul, Choudhury, Nuzhat, Sarker, Shafiqul, Huq, Sayeeda, Mahmud, Imteaz, Mostafa, Ishita, Mahfuz, Mustafa, Barratt, Michael J., Ahmed, Tahmeed, & Gordon, Jeffrey I.. Effects of microbiota-directed foods in gnotobiotic animals and undernourished children. United States. https://doi.org/10.1126/science.aau4732
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Gehrig, Jeanette, Venkatesh, Siddarth, Chang, Hao-Wei, Hibberd, Matthew C., Kung, Vanderlene, Cheng, Jiye, Chen, Robert, Subramanian, Sathish, Cowardin, Carrie, Meier, Martin, O'Donnell, David, Talcott, Michael, Spears, Larry, Semenkovich, Clay, Henrissat, Bernard, Giannone, Richard J., Hettich, Robert, Ilkayeva, Olga, Muehlbauer, Michael, Newgard, Christopher, Sawyer, Christopher, Head, Richard, Rodionov, Dmitry A., Arzamasov, Aleksandr, Leyn, Semen, Osterman, Andrei L., Hossain, Md Iqbal, Islam, Munirul, Choudhury, Nuzhat, Sarker, Shafiqul, Huq, Sayeeda, Mahmud, Imteaz, Mostafa, Ishita, Mahfuz, Mustafa, Barratt, Michael J., Ahmed, Tahmeed, and Gordon, Jeffrey I.. Fri . "Effects of microbiota-directed foods in gnotobiotic animals and undernourished children". United States. https://doi.org/10.1126/science.aau4732. https://www.osti.gov/servlets/purl/1546507.
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@article{osti_1546507,
title = {Effects of microbiota-directed foods in gnotobiotic animals and undernourished children},
author = {Gehrig, Jeanette and Venkatesh, Siddarth and Chang, Hao-Wei and Hibberd, Matthew C. and Kung, Vanderlene and Cheng, Jiye and Chen, Robert and Subramanian, Sathish and Cowardin, Carrie and Meier, Martin and O'Donnell, David and Talcott, Michael and Spears, Larry and Semenkovich, Clay and Henrissat, Bernard and Giannone, Richard J. and Hettich, Robert and Ilkayeva, Olga and Muehlbauer, Michael and Newgard, Christopher and Sawyer, Christopher and Head, Richard and Rodionov, Dmitry A. and Arzamasov, Aleksandr and Leyn, Semen and Osterman, Andrei L. and Hossain, Md Iqbal and Islam, Munirul and Choudhury, Nuzhat and Sarker, Shafiqul and Huq, Sayeeda and Mahmud, Imteaz and Mostafa, Ishita and Mahfuz, Mustafa and Barratt, Michael J. and Ahmed, Tahmeed and Gordon, Jeffrey I.},
abstractNote = {To examine the contributions of impaired gut microbial community development to childhood undernutrition, we combined metabolomic and proteomic analyses of plasma samples with metagenomic analyses of fecal samples to characterize the biological state of Bangladeshi children with severe acute malnutrition (SAM) as they transitioned, after standard treatment, to moderate acute malnutrition (MAM) with persistent microbiota immaturity. Host and microbial effects of microbiota-directed complementary food (MDCF) prototypes targeting weaning-phase bacterial taxa underrepresented in SAM and MAM microbiota were characterized in gnotobiotic mice and gnotobiotic piglets colonized with age- and growth-discriminatory bacteria. A randomized, double-blind controlled feeding study identified a lead MDCF that changes the abundances of targeted bacteria and increases plasma biomarkers and mediators of growth, bone formation, neurodevelopment, and immune function in children with MAM.},
doi = {10.1126/science.aau4732},
journal = {Science},
number = 6449,
volume = 365,
place = {United States},
year = {2019},
month = {7}
}
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https://doi.org/10.1126/science.aau4732
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Figures / Tables:

Fig. 1 Fig. 1: Longitudinal study of Bangladeshi children with SAM treated with therapeutic foods. (A) Study design. (B) Anthropometry and MAZ scores. Gray bars represent the three time points at which blood samples were collected. (C) Summary of MAZ scores for children with SAM (WHZ < –3; n = 96 fecalmore » samples) and subsequently (post-SAM) MAM (WHZ > –3 and <–2; n = 151 fecal samples), plus healthy children aged 6 to 24 months living in the same area in which the SAM study was conducted (n = 450 fecal samples). Mean values for WHZ, WAZ, HAZ, and MAZ ± SEM are plotted on the x axes of (B) and (C). ****P < 0.0001 (one-way ANOVA followed by Tukey’s multiple comparisons test).« less
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Works referenced in this record:

Spatiotemporal Regulation of Hsp90–Ligand Complex Leads to Immune Activation
journal, May 2016

Inflammation Dampened by Gelatinase A Cleavage of Monocyte Chemoattractant Protein-3
journal, August 2000

Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition
journal, February 2016

GAGE: generally applicable gene set enrichment for pathway analysis
journal, January 2009

mTOR Signaling in Growth, Metabolism, and Disease
journal, April 2017

Transgenic Overexpression of Pregnancy-Associated Plasma Protein-A Increases the Somatic Growth and Skeletal Muscle Mass in Mice
journal, December 2007

  • Rehage, Mark; Mohan, Subburaman; Wergedal, Jon E.
  • Endocrinology, Vol. 148, Issue 12
  • DOI: 10.1210/en.2007-0274

Potential role for TL1A, the new TNF-family member and potent costimulator of IFN-γ, in mucosal inflammation
journal, July 2004

Avoiding the pitfalls of gene set enrichment analysis with SetRank
journal, March 2017

  • Simillion, Cedric; Liechti, Robin; Lischer, Heidi E. L.
  • BMC Bioinformatics, Vol. 18, Issue 1
  • DOI: 10.1186/s12859-017-1571-6

Obesity and malnutrition similarly alter the renin–angiotensin system and inflammation in mice and human adipose
journal, October 2017

  • Pinheiro, Thales de Almeida; Barcala-Jorge, Antônio Sérgio; Andrade, João Marcus Oliveira
  • The Journal of Nutritional Biochemistry, Vol. 48
  • DOI: 10.1016/j.jnutbio.2017.06.008

Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children
journal, February 2016

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000

  • Kanehisa, Minoru; Goto, Susumu
  • Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30
  • DOI: 10.1093/nar/28.1.27

Notch signaling mediates crosstalk between endothelial cells and macrophages via Dll4 and IL6 in cardiac microvascular inflammation
journal, March 2016

Plasma biomarker proteins for detection of human growth hormone administration in athletes
journal, August 2017

The Tryptophan Metabolite 3-Hydroxyanthranilic Acid Plays Anti-Inflammatory and Neuroprotective Roles During Inflammation
journal, September 2011

  • Krause, Daniela; Suh, Hyeon-Sook; Tarassishin, Leonid
  • The American Journal of Pathology, Vol. 179, Issue 3
  • DOI: 10.1016/j.ajpath.2011.05.048

Downregulation of Fetuin-B and Zinc-a2-glycoprotein is Linked to Impaired Fatty Acid Metabolism in Liver Cells
journal, January 2012

  • Choi, Jung-Won; Liu, Hao; Mukherjee, Rajib
  • Cellular Physiology and Biochemistry, Vol. 30, Issue 2
  • DOI: 10.1159/000339065

The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature
journal, June 2010

  • Zhao, Jianhua; Li, Mingyao; Bradfield, Jonathan P.
  • BMC Medical Genetics, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2350-11-96

Physiology and pathophysiology of IGFBP-1 and IGFBP-2 – Consensus and dissent on metabolic control and malignant potential
journal, October 2015

  • Hoeflich, Andreas; Russo, Vincenzo C.
  • Best Practice & Research Clinical Endocrinology & Metabolism, Vol. 29, Issue 5
  • DOI: 10.1016/j.beem.2015.07.002

NF-κB, inflammation, immunity and cancer: coming of age
journal, January 2018

  • Taniguchi, Koji; Karin, Michael
  • Nature Reviews Immunology, Vol. 18, Issue 5
  • DOI: 10.1038/nri.2017.142

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
journal, November 2013

Advances in human proteomics at high scale with the SOMAscan proteomics platform
journal, June 2012

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
journal, May 2015

Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice
journal, May 2016

  • Planer, Joseph D.; Peng, Yangqing; Kau, Andrew L.
  • Nature, Vol. 534, Issue 7606
  • DOI: 10.1038/nature17940

Fast and sensitive protein alignment using DIAMOND
journal, November 2014

  • Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
  • Nature Methods, Vol. 12, Issue 1
  • DOI: 10.1038/nmeth.3176

GDF 15 is a heart‐derived hormone that regulates body growth
journal, June 2017

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides
journal, October 2015

Bifidobacteria can protect from enteropathogenic infection through production of acetate
journal, January 2011

  • Fukuda, Shinji; Toh, Hidehiro; Hase, Koji
  • Nature, Vol. 469, Issue 7331
  • DOI: 10.1038/nature09646

The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008

  • Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
  • BMC Genomics, Vol. 9, Issue 1, Article No. 75
  • DOI: 10.1186/1471-2164-9-75

Lack of fibulin-3 causes early aging and herniation, but not macular degeneration in mice
journal, September 2007

  • McLaughlin, Precious J.; Bakall, Benjamin; Choi, Jiwon
  • Human Molecular Genetics, Vol. 16, Issue 24
  • DOI: 10.1093/hmg/ddm264

A systematic review of complementary feeding practices in South Asian infants and young children: the Bangladesh perspective
journal, July 2017

Prokka: rapid prokaryotic genome annotation
journal, March 2014

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012

  • Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
  • Journal of Computational Biology, Vol. 19, Issue 5
  • DOI: 10.1089/cmb.2012.0021

Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis
journal, February 2008

  • Masuda, Takeshi; Tomita, Masaru; Ishihama, Yasushi
  • Journal of Proteome Research, Vol. 7, Issue 2
  • DOI: 10.1021/pr700658q

Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition
journal, February 2016

Persistent gut microbiota immaturity in malnourished Bangladeshi children
journal, June 2014

  • Subramanian, Sathish; Huq, Sayeeda; Yatsunenko, Tanya
  • Nature, Vol. 510, Issue 7505
  • DOI: 10.1038/nature13421

Fatty acid synthesis configures the plasma membrane for inflammation in diabetes
journal, November 2016

Stanniocalcin-1 Potently Inhibits the Proteolytic Activity of the Metalloproteinase Pregnancy-associated Plasma Protein-A
journal, July 2015

  • Kløverpris, Søren; Mikkelsen, Jakob H.; Pedersen, Josefine H.
  • Journal of Biological Chemistry, Vol. 290, Issue 36
  • DOI: 10.1074/jbc.M115.650143

Assessment of Variability in the SOMAscan Assay
journal, October 2017

IGF-Binding Proteins: Why Do They Exist and Why Are There So Many?
journal, April 2018

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome
journal, November 2008

  • Sela, D. A.; Chapman, J.; Adeuya, A.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 48
  • DOI: 10.1073/pnas.0809584105

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering
journal, August 2009

  • Ma, Ze-Qiang; Dasari, Surendra; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 8, Issue 8
  • DOI: 10.1021/pr900360j

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

  • Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.f.303

Necrotic but not apoptotic cell death releases heat shock proteins, which deliver a partial maturation signal to dendritic cells and activate the NF-κB pathway
journal, November 2000

  • Basu, Sreyashi; Binder, Robert J.; Suto, Ryuichiro
  • International Immunology, Vol. 12, Issue 11
  • DOI: 10.1093/intimm/12.11.1539

Distinct structural requirements for CDON and BOC in the promotion of Hedgehog signaling
journal, June 2015

Overexpression of Human Stanniocalcin Affects Growth and Reproduction in Transgenic Mice
journal, March 2002

Identification of Metabolic Signatures Linked to Anti-Inflammatory Effects of Faecalibacterium prausnitzii
journal, April 2015

PAPP-A, IGFBP-4 and IGF-II are secreted by human adipose tissue cultures in a depot-specific manner
journal, December 2016

  • Gude, Mette Faurholdt; Hjortebjerg, Rikke; Oxvig, Claus
  • European Journal of Endocrinology, Vol. 175, Issue 6
  • DOI: 10.1530/EJE-16-0569

Eggs in Early Complementary Feeding and Child Growth: A Randomized Controlled Trial
journal, June 2017

  • Iannotti, Lora L.; Lutter, Chessa K.; Stewart, Christine P.
  • Pediatrics, Vol. 140, Issue 1
  • DOI: 10.1542/peds.2016-3459

The Notch Ligand DLL4 Defines a Capability of Human Dendritic Cells in Regulating Th1 and Th17 Differentiation
journal, December 2015

Vulnerability of the fetal primate brain to moderate reduction in maternal global nutrient availability
journal, January 2011

  • Antonow-Schlorke, I.; Schwab, M.; Cox, L. A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 7
  • DOI: 10.1073/pnas.1009838108

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013

  • Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1226

MyriMatch:  Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis
journal, February 2007

  • Tabb, David L.; Fernando, Christopher G.; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 6, Issue 2
  • DOI: 10.1021/pr0604054

Fetuin B Is a Secreted Hepatocyte Factor Linking Steatosis to Impaired Glucose Metabolism
journal, December 2015

Severe Acute Malnutrition in Childhood: Hormonal and Metabolic Status at Presentation, Response to Treatment, and Predictors of Mortality
journal, June 2014

  • Bartz, Sarah; Mody, Aaloke; Hornik, Christoph
  • The Journal of Clinical Endocrinology & Metabolism, Vol. 99, Issue 6
  • DOI: 10.1210/jc.2013-4018

Home-Based Treatment of Malnourished Malawian Children with Locally Produced or Imported Ready-to-Use Food
journal, January 2004

  • Sandige, Heidi; Ndekha, MacDonald J.; Briend, André
  • Journal of Pediatric Gastroenterology and Nutrition, Vol. 39, Issue 2
  • DOI: 10.1097/00005176-200408000-00003

Pregnancy-Associated Plasma Protein-A Increases Osteoblast Proliferation in Vitro and Bone Formation in Vivo
journal, December 2006

  • Qin, Xuezhong; Wergedal, Jon E.; Rehage, Mark
  • Endocrinology, Vol. 147, Issue 12
  • DOI: 10.1210/en.2006-1055

TL1A Synergizes with IL-12 and IL-18 to Enhance IFN-γ Production in Human T Cells and NK Cells
journal, May 2004

  • Papadakis, Konstantinos A.; Prehn, John L.; Landers, Carol
  • The Journal of Immunology, Vol. 172, Issue 11
  • DOI: 10.4049/jimmunol.172.11.7002

RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements
journal, July 2005

  • Abreu-Goodger, C.; Merino, E.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki445

LC/MS/MS Method for Quantitative Determination of Long-Chain Fatty Acyl-CoAs
journal, May 2005

  • Magnes, Christoph; Sinner, Frank M.; Regittnig, Werner
  • Analytical Chemistry, Vol. 77, Issue 9
  • DOI: 10.1021/ac048314i

Versatile and open software for comparing large genomes
journal, January 2004

  • Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L.
  • Genome Biology, Vol. 5, Issue 2, R12
  • DOI: 10.1186/gb-2004-5-2-r12

Lactobacillus reuteri induces gut intraepithelial CD4 + CD8αα + T cells
journal, August 2017

  • Cervantes-Barragan, Luisa; Chai, Jiani N.; Tianero, Ma. Diarey
  • Science, Vol. 357, Issue 6353
  • DOI: 10.1126/science.aah5825

Cutadapt removes adapter sequences from high-throughput sequencing reads
journal, May 2011

The first 1000 cultured species of the human gastrointestinal microbiota
journal, September 2014

  • Rajilić-Stojanović, Mirjana; de Vos, Willem M.
  • FEMS Microbiology Reviews, Vol. 38, Issue 5
  • DOI: 10.1111/1574-6976.12075

Construction and Optimization of a Heterologous Pathway for Protocatechuate Catabolism in Escherichia coli Enables Bioconversion of Model Aromatic Compounds
journal, July 2017

  • Clarkson, Sonya M.; Giannone, Richard J.; Kridelbaugh, Donna M.
  • Applied and Environmental Microbiology, Vol. 83, Issue 18
  • DOI: 10.1128/AEM.01313-17

A Laboratory-Developed TaqMan Array Card for Simultaneous Detection of 19 Enteropathogens
journal, November 2012

  • Liu, J.; Gratz, J.; Amour, C.
  • Journal of Clinical Microbiology, Vol. 51, Issue 2
  • DOI: 10.1128/JCM.02658-12

Investigating Deep Phylogenetic Relationships among Cyanobacteria and Plastids by Small Subunit rRNA Sequence Analysis
journal, July 1999

Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein
journal, January 2013

  • Russell, Wendy R.; Duncan, Sylvia H.; Scobbie, Lorraine
  • Molecular Nutrition & Food Research, Vol. 57, Issue 3
  • DOI: 10.1002/mnfr.201200594

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
journal, May 2012

  • Yu, Guangchuang; Wang, Li-Gen; Han, Yanyan
  • OMICS: A Journal of Integrative Biology, Vol. 16, Issue 5
  • DOI: 10.1089/omi.2011.0118

Stunting Is Characterized by Chronic Inflammation in Zimbabwean Infants
journal, February 2014

Nutrition of Children and Women in Bangladesh: Trends and Directions for the Future
journal, July 2012

  • Ahmed, Tahmeed; Ireen, Santhia; Ahmed, AM Shamsir
  • Journal of Health, Population and Nutrition, Vol. 30, Issue 1
  • DOI: 10.3329/jhpn.v30i1.11268

Beyond antibodies: New affinity reagents to unlock the proteome
journal, February 2014

Compensatory Responses to Pyruvate Carboxylase Suppression in Islet β-Cells: PRESERVATION OF GLUCOSE-STIMULATED INSULIN SECRETION
journal, June 2006

  • Jensen, Mette V.; Joseph, Jamie W.; Ilkayeva, Olga
  • Journal of Biological Chemistry, Vol. 281, Issue 31
  • DOI: 10.1074/jbc.M604350200

The effects of micronutrient deficiencies on bacterial species from the human gut microbiota
journal, May 2017

An important regulatory role for CD4+CD8   T cells in the intestinal epithelial layer in the prevention of inflammatory bowel disease
journal, April 2003

  • Das, G.; Augustine, M. M.; Das, J.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 9
  • DOI: 10.1073/pnas.0831037100

A sparse covarying unit that describes healthy and impaired human gut microbiota development
journal, July 2019

  • Raman, Arjun S.; Gehrig, Jeanette L.; Venkatesh, Siddarth
  • Science, Vol. 365, Issue 6449
  • DOI: 10.1126/science.aau4735

Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel
journal, September 2015

Search and clustering orders of magnitude faster than BLAST
journal, August 2010

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria
journal, January 2013

  • Novichkov, Pavel S.; Kazakov, Alexey E.; Ravcheev, Dmitry A.
  • BMC Genomics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2164-14-745

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice
journal, March 2011

  • Goodman, A. L.; Kallstrom, G.; Faith, J. J.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 15
  • DOI: 10.1073/pnas.1102938108

Mortality in severely malnourished children with diarrhoea and use of a standardised management protocol
journal, June 1999

WISP-3 functions as a ligand and promotes superoxide dismutase activity
journal, March 2006

  • Davis, Leila; Chen, Yi; Sen, Malini
  • Biochemical and Biophysical Research Communications, Vol. 342, Issue 1
  • DOI: 10.1016/j.bbrc.2006.01.132

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
journal, October 2008

  • Sokol, H.; Pigneur, B.; Watterlot, L.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 43
  • DOI: 10.1073/pnas.0804812105

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
journal, September 2005

A Branched-Chain Amino Acid-Related Metabolic Signature that Differentiates Obese and Lean Humans and Contributes to Insulin Resistance
journal, April 2009

CD4 CTL: Living up to the challenge
journal, November 2013

Bifidobacterium longum subspecies infantis: champion colonizer of the infant gut
journal, October 2014

  • Underwood, Mark A.; German, J. Bruce; Lebrilla, Carlito B.
  • Pediatric Research, Vol. 77, Issue 1-2
  • DOI: 10.1038/pr.2014.156

Tissue adaptation of regulatory and intraepithelial CD4+ T cells controls gut inflammation
journal, June 2016

  • Sujino, T.; London, M.; Hoytema van Konijnenburg, D. P.
  • Science, Vol. 352, Issue 6293
  • DOI: 10.1126/science.aaf3892

limma powers differential expression analyses for RNA-sequencing and microarray studies
journal, January 2015

  • Ritchie, Matthew E.; Phipson, Belinda; Wu, Di
  • Nucleic Acids Research, Vol. 43, Issue 7
  • DOI: 10.1093/nar/gkv007

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
journal, October 2017

  • Steinegger, Martin; Söding, Johannes
  • Nature Biotechnology, Vol. 35, Issue 11
  • DOI: 10.1038/nbt.3988

Ready-to-Use Therapeutic Food Made From Locally Available Food Ingredients Is Well Accepted by Children Having Severe Acute Malnutrition in Bangladesh
journal, August 2017

  • Choudhury, Nuzhat; Ahmed, Tahmeed; Hossain, Md Iqbal
  • Food and Nutrition Bulletin, Vol. 39, Issue 1
  • DOI: 10.1177/0379572117743929

Phylogeny of human intestinal bacteria that activate the dietary lignan secoisolariciresinol diglucoside: SDG-converting human intestinal bacteria
journal, March 2006

Gut microbiota induce IGF-1 and promote bone formation and growth
journal, November 2016

  • Yan, Jing; Herzog, Jeremy W.; Tsang, Kelly
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 47
  • DOI: 10.1073/pnas.1607235113

Heat Shock Protein 90 Mediates Efficient Antigen Cross Presentation through the Scavenger Receptor Expressed by Endothelial Cells-I
journal, August 2010

  • Murshid, Ayesha; Gong, Jianlin; Calderwood, Stuart K.
  • The Journal of Immunology, Vol. 185, Issue 5
  • DOI: 10.4049/jimmunol.0903635

Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function
journal, May 2015

Plasma growth differentiation factor 15 is associated with weight loss and mortality in cancer patients: GDF15 in cancer-related weight loss
journal, April 2015

  • Lerner, Lorena; Hayes, Teresa G.; Tao, Nianjun
  • Journal of Cachexia, Sarcopenia and Muscle, Vol. 6, Issue 4
  • DOI: 10.1002/jcsm.12033

Physiological role of bone morphogenetic proteins in osteogenesis
journal, February 2006

  • Kugimiya, Fumitaka; Ohba, Shinsuke; Nakamura, Kozo
  • Journal of Bone and Mineral Metabolism, Vol. 24, Issue 2
  • DOI: 10.1007/s00774-005-0653-0

The MAL-ED Cohort Study in Mirpur, Bangladesh
journal, November 2014

  • Ahmed, Tahmeed; Mahfuz, Mustafa; Islam, Md Munirul
  • Clinical Infectious Diseases, Vol. 59, Issue suppl_4
  • DOI: 10.1093/cid/ciu458

Assessment of Environmental Enteropathy in the MAL-ED Cohort Study: Theoretical and Analytic Framework
journal, November 2014

  • Kosek, Margaret; Guerrant, Richard L.; Kang, Gagandeep
  • Clinical Infectious Diseases, Vol. 59, Issue suppl_4
  • DOI: 10.1093/cid/ciu457

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journal, June 2016

  • Vassilyadi, Photios; Harding, Scott V.; Hazell, Tom J.
  • Pediatric Research, Vol. 80, Issue 5
  • DOI: 10.1038/pr.2016.135

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journal, January 2015

A new transcriptional role for matrix metalloproteinase-12 in antiviral immunity
journal, April 2014

  • Marchant, David J.; Bellac, Caroline L.; Moraes, Theo J.
  • Nature Medicine, Vol. 20, Issue 5
  • DOI: 10.1038/nm.3508

Quantification of Bone Microarchitecture with the Structure Model Index
journal, January 1997

  • Hildebrand, Tor; RÜEgsegger, Peter
  • Computer Methods in Biomechanics and Biomedical Engineering, Vol. 1, Issue 1
  • DOI: 10.1080/01495739708936692

Serum growth hormone-binding protein in obesity: effect of a short- term, very low calorie diet and diet-induced weight loss
journal, April 1996

  • Rasmussen, M. H.
  • Journal of Clinical Endocrinology & Metabolism, Vol. 81, Issue 4
  • DOI: 10.1210/jc.81.4.1519

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014

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journal, March 2008

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journal, March 2017

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journal, February 2021

  • Kangale, Luis Johnson; Levasseur, Anthony; Raoult, Didier
  • Microbiology Resource Announcements, Vol. 10, Issue 5
  • DOI: 10.1128/mra.00297-20

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journal, January 2021

  • Yoshida, Koki; Zhang, Ruixuan; Garcia, Kimberly G.
  • Microbiology Resource Announcements, Vol. 10, Issue 1
  • DOI: 10.1128/mra.01323-20

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journal, March 2021

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  • Simillion, Cedric André Marie; Liechti, Robin; Lischer, Heidi E. L.
  • BioMed Central
  • DOI: 10.7892/boris.98173

Tissue adaptation of regulatory and intraepithelial CD4+ T cells controls gut inflammation
text, January 2016

  • Sujino, T.; London, M.; Hoytema Van Konijnenburg, D. P.
  • American Association for the Advancement of Science
  • DOI: 10.5167/uzh-125907

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journal, November 2015

Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein
journal, January 2013

  • Russell, Wendy R.; Duncan, Sylvia H.; Scobbie, Lorraine
  • Molecular Nutrition & Food Research, Vol. 57, Issue 3
  • DOI: 10.1002/mnfr.201200594

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journal, February 2014

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journal, September 2011

  • Krause, Daniela; Suh, Hyeon-Sook; Tarassishin, Leonid
  • The American Journal of Pathology, Vol. 179, Issue 3
  • DOI: 10.1016/j.ajpath.2011.05.048

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journal, April 2017

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journal, January 2018

  • Taniguchi, Koji; Karin, Michael
  • Nature Reviews Immunology, Vol. 18, Issue 5
  • DOI: 10.1038/nri.2017.142

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journal, November 2008

  • Sela, D. A.; Chapman, J.; Adeuya, A.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 48
  • DOI: 10.1073/pnas.0809584105

An important regulatory role for CD4+CD8   T cells in the intestinal epithelial layer in the prevention of inflammatory bowel disease
journal, April 2003

  • Das, G.; Augustine, M. M.; Das, J.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 9
  • DOI: 10.1073/pnas.0831037100

Vulnerability of the fetal primate brain to moderate reduction in maternal global nutrient availability
journal, January 2011

  • Antonow-Schlorke, I.; Schwab, M.; Cox, L. A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 7
  • DOI: 10.1073/pnas.1009838108

Gut microbiota induce IGF-1 and promote bone formation and growth
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  • Yan, Jing; Herzog, Jeremy W.; Tsang, Kelly
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 47
  • DOI: 10.1073/pnas.1607235113

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013

  • Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1226

Home-Based Treatment of Malnourished Malawian Children with Locally Produced or Imported Ready-to-Use Food
journal, January 2004

  • Sandige, Heidi; Ndekha, MacDonald J.; Briend, André
  • Journal of Pediatric Gastroenterology and Nutrition, Vol. 39, Issue 2
  • DOI: 10.1097/00005176-200408000-00003

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journal, March 2017

  • Simillion, Cedric; Liechti, Robin; Lischer, Heidi E. L.
  • BMC Bioinformatics, Vol. 18, Issue 1
  • DOI: 10.1186/s12859-017-1571-6

Severe Acute Malnutrition in Childhood: Hormonal and Metabolic Status at Presentation, Response to Treatment, and Predictors of Mortality
journal, June 2014

  • Bartz, Sarah; Mody, Aaloke; Hornik, Christoph
  • The Journal of Clinical Endocrinology & Metabolism, Vol. 99, Issue 6
  • DOI: 10.1210/jc.2013-4018

Eggs in Early Complementary Feeding and Child Growth: A Randomized Controlled Trial
journal, June 2017

  • Iannotti, Lora L.; Lutter, Chessa K.; Stewart, Christine P.
  • Pediatrics, Vol. 140, Issue 1
  • DOI: 10.1542/peds.2016-3459

Nutrition of Children and Women in Bangladesh: Trends and Directions for the Future
journal, July 2012

  • Ahmed, Tahmeed; Ireen, Santhia; Ahmed, AM Shamsir
  • Journal of Health, Population and Nutrition, Vol. 30, Issue 1
  • DOI: 10.3329/jhpn.v30i1.11268
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