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

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106

limma powers differential expression analyses for RNA-sequencing and microarray studies

Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2011.0118 · Cited by 36,259

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887

Cutadapt removes adapter sequences from high-throughput sequencing reads

Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889

KEGG: Kyoto Encyclopedia of Genes and Genomes

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 26,312

Search and clustering orders of magnitude faster than BLAST

Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098

Gut microbiota in human metabolic health and disease

Fan, Y., & Pedersen, O. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0433-9 · Cited by 4,724

The maternal microbiome modulates fetal neurodevelopment in mice

Vuong, H. E., Pronovost, G. N., Williams, D. W., Coley, E. J. L., Siegler, E. L., Qiu, A., Kazantsev, M., Wilson, C. J., Rendon, T., & Hsiao, E. Y. (2020) · Nature · doi:10.1038/s41586-020-2745-3 · Cited by 564

Developmental origins of metabolic diseases

Hoffman, D. J., Powell, T. L., Barrett, E. S., & Hardy, D. B. (2020) · Physiological Reviews · doi:10.1152/physrev.00002.2020 · Cited by 504

Developmental trajectory of the healthy human gut microbiota during the first 5 years of life

Roswall, J., Olsson, L. M., Kovatcheva‐Datchary, P., Nilsson, S., Tremaroli, V., Simon, M., Kiilerich, P., Akrami, R., Kramer, M. M., Uhlén, M., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.021 · Cited by 487

Microbiome-based therapeutics

Sorbara, M. T., & Pamer, E. G. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00667-9 · Cited by 468

Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health

Berding, K., Vlckova, K., Marx, W., Schellekens, H., Stanton, C., Clarke, G., Jacka, F., Dinan, T. G., & Cryan, J. F. (2021) · Advances in Nutrition · doi:10.1093/advances/nmaa181 · Cited by 451

Ketogenic diet for human diseases: the underlying mechanisms and potential for clinical implementations

Zhu, H., Bi, D., Zhang, Y., Kong, C., Du, J., Wu, X., Wei, Q., & Qin, H. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00831-w · Cited by 412

Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions for optimal therapeutic protection

Winkler, E. S., Gilchuk, P., Yu, J., Bailey, A. L., Chen, R. E., Chong, Z., Zost, S. J., Jang, H., Huang, Y., Allen, J. D., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.026 · Cited by 366

The Healthy Microbiome—What Is the Definition of a Healthy Gut Microbiome?

Shanahan, F., Ghosh, T. S., & O’Toole, P. W. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.09.057 · Cited by 383

Vulnerability of the industrialized microbiota

Sonnenburg, J. L., & Sonnenburg, E. D. (2019) · Science · doi:10.1126/science.aaw9255 · Cited by 343

A Microbiota-Directed Food Intervention for Undernourished Children

Chen, R. Y., Mostafa, I., Hibberd, M. C., Das, S., Mahfuz, M., Naila, N. N., Islam, M. M., Huq, S., Alam, M. A., Zaman, M. U., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2023294 · Cited by 306

Vitamins, the gut microbiome and gastrointestinal health in humans

Pham, V. T., Dold, S., Rehman, A., Bird, J. K., & Steinert, R. E. (2021) · Nutrition Research · doi:10.1016/j.nutres.2021.09.001 · Cited by 300

Problems with the concept of gut microbiota dysbiosis

Brüssow, H. (2020) · Microbial Biotechnology · doi:10.1111/1751-7915.13479 · Cited by 250

Gut Microbial Dysbiosis in the Pathogenesis of Gastrointestinal Dysmotility and Metabolic Disorders

Singh, R., Zogg, H., Wei, L., Bartlett, A., Ghoshal, U. C., Rajender, S., & Ro, S. (2020) · Journal of Neurogastroenterology and Motility · doi:10.5056/jnm20149 · Cited by 274

Rethinking healthy eating in light of the gut microbiome

Armet, A. M., Deehan, E. C., O’Sullivan, A. F., Mota, J. F., Field, C. J., Prado, C. M., Lucey, A. J., & Walter, J. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.016 · Cited by 252

Microbiome-based interventions to modulate gut ecology and the immune system

Hitch, T. C. A., Hall, L. J., Walsh, S. K., Leventhal, G. E., Slack, E. M. C., de Wouters, T., Walter, J., & Clavel, T. (2022) · Mucosal Immunology · doi:10.1038/s41385-022-00564-1 · Cited by 268

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

Wylensek, D., Hitch, T. C. A., Riedel, T., Afrizal, A., Kumar, N., Wortmann, E., Liu, T., Devendran, S., Lesker, T. R., Hernández, S. B., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19929-w · Cited by 238

Resistant starch decreases intrahepatic triglycerides in patients with NAFLD via gut microbiome alterations

Ni, Y., Qian, L., Siliceo, S. L., Long, X., Nychas, E., Liu, Y., Ismaiah, M. J., Leung, H., Zhang, L., Gao, Q., et al. (2023) · Cell Metabolism · doi:10.1016/j.cmet.2023.08.002 · Cited by 237

A sparse covarying unit that describes healthy and impaired human gut microbiota development

Raman, A. S., Gehrig, J. L., Venkatesh, S., Chang, H.-W., Hibberd, M. C., Subramanian, S., Kang, G., Bessong, P. O., Lima, A. Â. M., Kosek, M. N., et al. (2019) · Science · doi:10.1126/science.aau4735 · Cited by 218

Of men in mice: the development and application of a humanized gnotobiotic mouse model for microbiome therapeutics

Park, J. C., & Im, S. (2020) · Experimental & Molecular Medicine · doi:10.1038/s12276-020-0473-2 · Cited by 232

Western diets and chronic diseases

Adolph, T. E., & Tilg, H. (2024) · Nature Medicine · doi:10.1038/s41591-024-03165-6 · Cited by 224

Priming for Life: Early Life Nutrition and the Microbiota-Gut-Brain Axis

Ratsika, A., Codagnone, M. G., O’Mahony, S. M., Stanton, C., & Cryan, J. F. (2021) · Nutrients · doi:10.3390/nu13020423 · Cited by 194

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome

Rodionov, D. A., Arzamasov, A. A., Khoroshkin, M., Iablokov, S. N., Leyn, S. A., Peterson, S. N., Novichkov, P. S., & Osterman, A. L. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01316 · Cited by 177

Annual Research Review: Critical windows – the microbiota-gut-brain axis in neurocognitive development

Cowan, C. S. M., Dinan, T. G., & Cryan, J. F. (2020) · Journal of Child Psychology and Psychiatry · doi:10.1111/jcpp.13156 · Cited by 176

Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation

Liu, T., Kern, J. T., Jain, U., Sonnek, N. M., Xiong, S., Simpson, K. F., VanDussen, K. L., Winkler, E. S., Haritunians, T., Malique, A., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.04.004 · Cited by 179

Malnutrition and Gut Microbiota in Children

Iddrisu, I., Monteagudo-Mera, A., Poveda, C. G., Pyle, S., Shahzad, M. A., Andrews, S. C., & Walton, G. (2021) · Nutrients · doi:10.3390/nu13082727 · Cited by 186

Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition

Barratt, M. J., Nuzhat, S., Ahsan, K., Frese, S. A., Arzamasov, A. A., Sarker, S. A., Islam, M. M., Palit, P., Islam, M. R., Hibberd, M. C., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abk1107 · Cited by 166

Duodenal Microbiota in Stunted Undernourished Children with Enteropathy

Chen, R. Y., Kung, V. L., Das, S., Hossain, M. S., Hibberd, M. C., Guruge, J. L., Mahfuz, M., Begum, S., Rahman, M., Fahim, S. M., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa1916004 · Cited by 167

The human gut microbiome and health inequities

Amato, K. R., Arrieta, M., Azad, M. B., Bailey, M. T., Broussard, J. L., Bruggeling, C. E., Claud, E. C., Costello, E. K., Davenport, E., Dutilh, B. E., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2017947118 · Cited by 175

Pursuing Human-Relevant Gut Microbiota-Immune Interactions

Spencer, S. P., Fragiadakis, G. K., & Sonnenburg, J. L. (2019) · Immunity · doi:10.1016/j.immuni.2019.08.002 · Cited by 167

Effects of colon-targeted vitamins on the composition and metabolic activity of the human gut microbiome– a pilot study

Pham, V. T., Fehlbaum, S., Seifert, N., Richard, N., Bruins, M. J., Sybesma, W., Rehman, A., & Steinert, R. E. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1875774 · Cited by 170

Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions

Alexander, M., & Turnbaugh, P. J. (2020) · Immunity · doi:10.1016/j.immuni.2020.07.015 · Cited by 151

Control of immunity via nutritional interventions

Collins, N., & Belkaid, Y. (2022) · Immunity · doi:10.1016/j.immuni.2022.01.004 · Cited by 131

Role of Bifidobacteria on Infant Health

Saturio, S., Nogacka, A. M., Alvarado-Jasso, G. M., Salazar, N., Reyes‐Gavilán, C. G. D. L., Gueimonde, M., & Arboleya, S. (2021) · Microorganisms · doi:10.3390/microorganisms9122415 · Cited by 148

The neurovascular unit and systemic biology in stroke — implications for translation and treatment

Tiedt, S., Buchan, A. M., Dichgans, M., Lizasoaín, I., Moro, M. Á., & Lo, E. H. (2022) · Nature Reviews Neurology · doi:10.1038/s41582-022-00703-z · Cited by 135

Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

Afrizal, A., Jennings, S. A. V., Hitch, T. C. A., Riedel, T., Basic, M., Panyot, A., Treichel, N. S., Hager, F. T., Wong, E. O.-Y., Wolter, B., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.09.011 · Cited by 124

Nonalcoholic Fatty Liver Disease and the Gut-Liver Axis: Exploring an Undernutrition Perspective

Bauer, K. C., Littlejohn, P. T., Ayala, V., Creus-Cuadros, A., & Finlay, B. B. (2022) · Gastroenterology · doi:10.1053/j.gastro.2022.01.058 · Cited by 127

Dietary protein and the intestinal microbiota: An understudied relationship

Bartlett, A., & Kleiner, M. (2022) · iScience · doi:10.1016/j.isci.2022.105313 · Cited by 134

Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth

Consuegra, J., Grenier, T., Bâa-Puyoulet, P., Rahioui, I., Akherraz, H., Gervais, H., Parisot, N., Silva, P. D., Charles, H., Calevro, F., et al. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000681 · Cited by 121

Understanding the mother-breastmilk-infant “triad”

Bode, L., Raman, A. S., MURCH, S. H., Rollins, N. C., & Gordon, J. I. (2020) · Science · doi:10.1126/science.aaw6147 · Cited by 120

Genomic reconstruction of short-chain fatty acid production by the human gut microbiota

Frolova, M. S., Suvorova, I. A., Iablokov, S. N., Petrov, S. N., & Rodionov, D. A. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.949563 · Cited by 122

Vitamins for the Gut Microbiome

Steinert, R. E., Lee, Y. K., & Sybesma, W. (2019) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2019.11.005 · Cited by 115

Microbe-mediated intestinal NOD2 stimulation improves linear growth of undernourished infant mice

Schwarzer, M., Gautam, U. K., Makki, K., Lambert, A., Brabec, T., Joly, A., Šrůtková, D., Poinsot, P., Novotná, T., Geoffroy, S., et al. (2023) · Science · doi:10.1126/science.ade9767 · Cited by 124

Immune-Microbiota Interplay and Colonization Resistance in Infection

Leshem, A., Liwinski, T., & Elinav, E. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.001 · Cited by 117

Microbiota-brain interactions: Moving toward mechanisms in model organisms

Nagpal, J. K., & Cryan, J. F. (2021) · Neuron · doi:10.1016/j.neuron.2021.09.036 · Cited by 110

Mother–infant transmission of human microbiota

Browne, H. P., Shao, Y., & Lawley, T. D. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102173 · Cited by 117

A nonenzymatic method for cleaving polysaccharides to yield oligosaccharides for structural analysis

Amicucci, M. J., Nandita, E., Galermo, A. G., Castillo, J. J., Chen, S., Park, D., Smilowitz, J. T., German, J. B., Mills, D. A., & Lebrilla, C. B. (2020) · Nature Communications · doi:10.1038/s41467-020-17778-1 · Cited by 114

Seasonal shift of the gut microbiome synchronizes host peripheral circadian rhythm for physiological adaptation to a low-fat diet in the giant panda

Huang, G., Wang, L., Li, J., Hou, R., Wang, M., Wang, Z., Qu, Q., Zhou, W., Nie, Y., Hu, Y., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2021.110203 · Cited by 109

Nurturing the Early Life Gut Microbiome and Immune Maturation for Long Term Health

Dogra, S. K., Chung, C. K. C. K., Wang, D., Sakwińska, O., Mottaz, S. C., & Sprenger, N. (2021) · Microorganisms · doi:10.3390/microorganisms9102110 · Cited by 110

Going with the grain: Fiber, cognition, and the microbiota-gut-brain-axis

Berding, K., Carbia, C., & Cryan, J. F. (2021) · Experimental Biology and Medicine · doi:10.1177/1535370221995785 · Cited by 100

Roles of the gut microbiome in weight management

Carmody, R. N., & Bisanz, J. E. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00888-0 · Cited by 113

Reframing anorexia nervosa as a metabo-psychiatric disorder

Bulik, C. M., Carroll, I. M., & Mehler, P. (2021) · Trends in Endocrinology & Metabolism · doi:10.1016/j.tem.2021.07.010 · Cited by 96

A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning

Vatanen, T., Ang, Q. Y., Siegwald, L., Sarker, S. A., Roy, C. I. L., Duboux, S., Delannoy-Bruno, O., Ngom‐Bru, C., Boulangé, C. L., Stražar, M., et al. (2022) · Cell · doi:10.1016/j.cell.2022.10.011 · Cited by 95

The gut microbiome and early-life growth in a population with high prevalence of stunting

Robertson, R. C., Edens, T. J., Carr, L., Mutasa, K., Gough, E. K., Evans, C., Geum, H. M., Baharmand, I., Gill, S. K., Ntozini, R., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36135-6 · Cited by 98

Prevotella species in the human gut is primarily comprised of Prevotella copri, Prevotella stercorea and related lineages

Yeoh, Y. K., Sun, Y., Ip, L., Wang, L., Chan, F. K. L., Miao, Y., & Ng, S. C. (2022) · Scientific Reports · doi:10.1038/s41598-022-12721-4 · Cited by 102

The influence of nutrition on clinical outcomes in children with cancer

Barr, R. D., & Stevens, M. C. G. (2020) · Pediatric Blood & Cancer · doi:10.1002/pbc.28117 · Cited by 92

A systematic review on the role of microbiota in the pathogenesis and treatment of eating disorders

Carbone, E. A., D'Amato, P., Vicchio, G., Fazio, P. D., & Segura‐Garcìa, C. (2020) · European Psychiatry · doi:10.1192/j.eurpsy.2020.109 · Cited by 99

Race in the Microbiome

Benezra, A. (2020) · Science Technology & Human Values · doi:10.1177/0162243920911998 · Cited by 90

A framework for microbiome science in public health

Wilkinson, J. E., Franzosa, E. A., Everett, C., Li, C., trainees, H. R. A., Bae, S., Berzansky, I., Bhosle, A., Bjørnevik, K., Brennan, C. A., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01258-0 · Cited by 92

The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model

Jašarević, E., Hill, E. M., Kane, P. J., Rutt, L., Gyles, T. M., Folts, L. M., Rock, K. D., Howard, C. D., Morrison, K. E., Ravel, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26634-9 · Cited by 86

The gut microbiota mediates protective immunity against tuberculosis via modulation of lncRNA

Yang, F., Yang, Y., Chen, L., Zhang, Z., Liu, L., Zhang, C., Mai, Q., Chen, Z., Chen, Z., Lin, T., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2029997 · Cited by 84

Neonatal intestinal dysbiosis

Underwood, M. A., Mukhopadhyay, S., Lakshminrusimha, S., & Bevins, C. L. (2020) · Journal of Perinatology · doi:10.1038/s41372-020-00829-2 · Cited by 89

Geographic Differences in Gut Microbiota Composition Impact Susceptibility to Enteric Infection

Porras, A. M., Shi, Q., Zhou, H., Callahan, R., Montenegro-Bethancourt, G., Solomons, N., & Brito, I. L. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109457 · Cited by 74

Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data

Gehrig, J. L., Portik, D. M., Driscoll, M. D., Jackson, E., Chakraborty, S., Gratalo, D., Ashby, M., & Valladares, R. B. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000794 · Cited by 80

The future of human malnutrition: rebalancing agency for better nutritional health

Wells, J. C. K., Marphatia, A. A., Amable, G. S., Siervo, M., Friis, H., Miranda, J. J., Haisma, H. H., & Raubenheimer, D. (2021) · Globalization and Health · doi:10.1186/s12992-021-00767-4 · Cited by 103

Dynamic of the human gut microbiome under infectious diarrhea

The, H. C., & Le, S.-N. H. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.01.006 · Cited by 82

Clinical evidence of the role of Methanobrevibacter smithii in severe acute malnutrition

Camara, A., Konaté, S., Alou, M. T., Kodio, A., Togo, A. H., Cortaredona, S., Henrissat, B., Thera, M. A., Doumbo, O. K., Raoult, D., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-84641-8 · Cited by 73

The intersection of undernutrition, microbiome, and child development in the first years of life

Fontaine, F., Turjeman, S., Callens, K., & Koren, O. (2023) · Nature Communications · doi:10.1038/s41467-023-39285-9 · Cited by 84

Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction

Haberman, Y., Iqbal, N. T., Ghandikota, S. K., Mallawaarachchi, I. V., Braun, T., Dexheimer, P. J., Rahman, N., Hadar, R., Sadiq, K., Ahmad, Z., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.01.221 · Cited by 74

Health Benefits of Dietary Fiber for the Management of Inflammatory Bowel Disease

Yusuf, K., Saha, S., & Umar, S. (2022) · Biomedicines · doi:10.3390/biomedicines10061242 · Cited by 76

Microbiome as an immune regulator in health, disease, and therapeutics

Juarez, V. M., Montalbine, A. N., & Singh, A. K. (2022) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2022.114400 · Cited by 77

Dietary Selection Pressures and Their Impact on the Gut Microbiome

Ecklu-Mensah, G., Gilbert, J. A., & Devkota, S. (2021) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2021.07.009 · Cited by 79

Impact of maternal antibodies and microbiota development on the immunogenicity of oral rotavirus vaccine in African, Indian, and European infants

Parker, E. P. K., Bronowski, C., Sindhu, K. N., Babji, S., Benny, B., Carmona‐Vicente, N., Chasweka, N., Chinyama, E., Cunliffe, N. A., Dube, Q., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27074-1 · Cited by 72

Food Insecurity, Malnutrition, and the Microbiome

Christian, V. J., Miller, K. R., & Martindale, R. G. (2020) · Current Nutrition Reports · doi:10.1007/s13668-020-00342-0 · Cited by 71

Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans

Han, N. D., Cheng, J., Delannoy-Bruno, O., Webber, D. M., Terrapon, N., Henrissat, B., Rodionov, D. A., Arzamasov, A. A., Osterman, A. L., Hayashi, D. K., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.004 · Cited by 71

Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities

Keller, L. J., Babin, B. M., Lakemeyer, M., & Bogyo, M. S. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.10.007 · Cited by 72

Bioactive glycans in a microbiome-directed food for children with malnutrition

Hibberd, M. C., Webber, D. M., Rodionov, D. A., Henrissat, S., Chen, R. Y., Zhou, C., Lynn, H. M., Wang, Y., Chang, H.-W., Lee, E. M., et al. (2023) · Nature · doi:10.1038/s41586-023-06838-3 · Cited by 69

Diet-microbiome interactions in cancer treatment: Opportunities and challenges for precision nutrition in cancer

Greathouse, K. L., Wyatt, M., Johnson, A. J., Toy, E. P., Khan, J., Dunn, K., Clegg, D. J., & Reddy, S. (2022) · Neoplasia · doi:10.1016/j.neo.2022.100800 · Cited by 69

Environmental enteric dysfunction: gut and microbiota adaptation in pregnancy and infancy

Cowardin, C. A., Syed, S., Iqbal, N. T., Jamil, Z., Sadiq, K., Iqbal, J., Ali, A., & Moore, S. R. (2022) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-022-00714-7 · Cited by 71

Dietary tryptophan deficiency promotes gut RORγt+ Treg cells at the expense of Gata3+ Treg cells and alters commensal microbiota metabolism

Rankin, L. C., Kaiser, K. A., Santos, K. D. L., Park, H., Uhlemann, A., Gray, D. H. D., & Arpaia, N. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112135 · Cited by 65

Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy

Laursen, M. F., & Roager, H. M. (2023) · The ISME Journal · doi:10.1038/s41396-023-01525-7 · Cited by 63

Gut Microbiota Regulate Astrocytic Functions in the Brain: Possible Therapeutic Consequences

Zhao, Y.-F., Wei, D., & Tang, Y. (2021) · Current Neuropharmacology · doi:10.2174/1570159x19666210215123239 · Cited by 60

Gut microbiome development and childhood undernutrition

Barratt, M. J., Ahmed, T., & Gordon, J. I. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.002 · Cited by 60

The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health

Ang, Q. Y., Alba, D., Upadhyay, V., Bisanz, J. E., Cai, J., Lee, H. L., Barajas, E., Wei, G., Noecker, C. A., Patterson, A. D., et al. (2021) · eLife · doi:10.7554/elife.70349 · Cited by 60

A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes

Darnaud, M., Vadder, F. D., Bogeat, P., Boucinha, L., Bulteau, A., Bunescu, A., Couturier, C., Delgado, A., Dugua, H., Elie, C., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26963-9 · Cited by 56

Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome

Whelan, K., Alexander, M., Gaïani, C., Lunken, G., Holmes, A. J., Staudacher, H. M., Theis, S., & Marco, M. L. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01831-6 · Cited by 67

Combined Prebiotic and Microbial Intervention Improves Oral Cholera Vaccination Responses in a Mouse Model of Childhood Undernutrition

Luccia, B. D., Ahern, P. P., Griffin, N. W., Cheng, J., Guruge, J. L., Byrne, A. E., Rodionov, D. A., Leyn, S. A., Osterman, A. L., Ahmed, T., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.04.008 · Cited by 60

Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition

Chang, H.-W., Lee, E. M., Wang, Y., Zhou, C., Pruss, K. M., Henrissat, S., Chen, R. Y., Kao, C.-Y., Hibberd, M. C., Lynn, H. M., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01628-7 · Cited by 60

The roles and potential of lentil prebiotic carbohydrates in human and plant health

Johnson, N., Johnson, C. R., Thavarajah, P., Kumar, S., & Thavarajah, D. (2020) · Plants People Planet · doi:10.1002/ppp3.10103 · Cited by 57

Studies of xenobiotic-induced gut microbiota dysbiosis: from correlation to mechanisms

Chi, L., Tu, P., Ru, H., & Lü, K. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1921912 · Cited by 60

The impact of maternal and early life malnutrition on health: a diet-microbe perspective

Forgie, A. J., Drall, K. M., Bourque, S. L., Field, C. J., Kozyrskyj, A. L., & Willing, B. P. (2020) · BMC Medicine · doi:10.1186/s12916-020-01584-z · Cited by 59

Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments

Moustafa, M. A. M., Chel, H. M., Thu, M. J., Bawm, S., Htun, L. L., Win, M. M., Oo, Z. M., Ohsawa, N., Lahdenperä, M., Mohamed, W. M. A., et al. (2021) · Scientific Reports · doi:10.1038/s41598-020-80537-1 · Cited by 58

TREM2 deficiency reprograms intestinal macrophages and microbiota to enhance anti–PD-1 tumor immunotherapy

Di Luccia, B., Molgora, M., Khantakova, D., Jaeger, N., Chang, H.-W., Czepielewski, R. S., Helmink, B. A., Onufer, E. J., Fachi, J. L., Bhattarai, B., et al. (2024) · Science Immunology · doi:10.1126/sciimmunol.adi5374 · Cited by 59

Probiotics in the New Era of Human Milk Oligosaccharides (HMOs): HMO Utilization and Beneficial Effects of Bifidobacterium longum subsp. infantis M-63 on Infant Health

Wong, C. B., Huang, H., Ning, Y., & Xiao, J. (2024) · Microorganisms · doi:10.3390/microorganisms12051014 · Cited by 58

MASI: microbiota—active substance interactions database

Zeng, X. L., Yang, X., Fan, J., Tan, Y. C., Ju, L., Shen, W. X., Wang, Y., Wang, X., Chen, W., Ju, D., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa924 · Cited by 54

Human Milk Oligosaccharide Compositions Illustrate Global Variations in Early Nutrition

Vinjamuri, A., Davis, J. C. C., Totten, S. M., Wu, L. D., Klein, L. D., Martin, M., Quinn, E. A., Scelza, B., Breakey, A., Gurven, M., et al. (2022) · The Journal of Nutrition · doi:10.1093/jn/nxac027 · Cited by 53

Identifying determinants of bacterial fitness in a model of human gut microbial succession

Feng, L., Raman, A. S., Hibberd, M. C., Cheng, J., Griffin, N. W., Peng, Y., Leyn, S. A., Rodionov, D. A., Osterman, A. L., & Gordon, J. I. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1918951117 · Cited by 53

When a pandemic and an epidemic collide: COVID-19, gut microbiota, and the double burden of malnutrition

Littlejohn, P. T., & Finlay, B. B. (2021) · BMC Medicine · doi:10.1186/s12916-021-01910-z · Cited by 53

A comprehensive review of mung bean proteins: Extraction, characterization, biological potential, techno‐functional properties, modifications, and applications

Li, S., Feng, X., Hao, X., Zhu, Y., Zou, L., Chen, X., & Yao, Y. (2023) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.13183 · Cited by 57

Impact of international travel and diarrhea on gut microbiome and resistome dynamics

Boolchandani, M., Blake, K. S., Tilley, D. H., Cabada, M. M., Schwartz, D. J., Patel, S., Morales, M. L., Meza, R. A., Soto, G. M., Isidean, S. D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34862-w · Cited by 54

Characterizing the relationship between gut microbiota development and healthy growth

Chang, H.-W. (2021) · Open Scholarship Institutional Repository (Washington University in St. Louis) · doi:10.7936/mf7m-8004

A microbiota-directed complementary food intervention in 12–18-month-old Bangladeshi children improves linear growth

Mostafa, I., Hibberd, M. C., Hartman, S. J., Rahman, M. H. H., Mahfuz, M., Hasan, S. M. T., Ashorn, P., Barratt, M. J., Ahmed, T., & Gordon, J. I. (2024) · EBioMedicine · doi:10.1016/j.ebiom.2024.105166 · Cited by 48

A Microbiota-Directed Food Intervention for Undernourished Children

Chen, R. Y., Mostafa, I., Hibberd, M. C., Das, S., Mahfuz, M., Naila, N. N., Islam, M. M., Huq, S., Alam, M. A., Zaman, M. U., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2023294 · Cited by 306

Computational and mathematical modeling of microbial community and host responses to microbiota-directed complementary foods administered to children with acute malnutrition.

Hartman, S. (2025) · Open Scholarship Institutional Repository (Washington University in St. Louis) · doi:10.7936/k6wz-gm42

Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function

Wang, Y., Chang, H.-W., Cheng, J., Webber, D. M., Lynn, H. M., Hibberd, M. C., Kao, C.-Y., Mostafa, I., Ahmed, T., Barratt, M. J., et al. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2523178122 · Cited by 3