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Zhao J, Guo Y, Jiang Q, Lan H, Hung WL, Lynch B. Bifidobacterium longum subsp. infantis YLGB-1496-Toxicological evaluation. J Appl Toxicol 2024. [PMID: 39252460 DOI: 10.1002/jat.4688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 09/11/2024]
Abstract
Bifidobacterium infantis YLGB-1496, originally isolated from breast milk from a Taiwanese mother, is under study for use as a probiotic. As part of safety assessment, an Ames, in vivo mouse micronucleus, and in vivo mouse spermatocyte chromosome aberration assay were conducted along with a 13-week oral rat toxicity study. B. infantis YLGB-1496 had no activity in any of the genotoxicity assays. Administration of the bacteria to Sprague-Dawley rats at doses ranging from 0 to 1.5 g/kg bw/day had no treatment-related effects on any of the endpoints measured. There appear to be no concerns for translocation or pathogenicity of B. infantis YLGB-1496 based on extensive experience with the species in general. The results of the current investigations support potential use of B. infantis YLGB-1496 as a probiotic in infant formula.
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Affiliation(s)
- Jian Zhao
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing, China
| | - Yueyi Guo
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing, China
| | - Qiuyue Jiang
- National Center of Technology Innovation for Dairy, Hohhot, China
| | - Hanglian Lan
- National Center of Technology Innovation for Dairy, Hohhot, China
| | - Wei-Lian Hung
- National Center of Technology Innovation for Dairy, Hohhot, China
| | - Barry Lynch
- Intertek Health Sciences Inc., Mississauga, ON, Canada
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2
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Shao Y, Garcia-Mauriño C, Clare S, Dawson NJR, Mu A, Adoum A, Harcourt K, Liu J, Browne HP, Stares MD, Rodger A, Brocklehurst P, Field N, Lawley TD. Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly. Nat Microbiol 2024:10.1038/s41564-024-01804-9. [PMID: 39242817 DOI: 10.1038/s41564-024-01804-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 08/05/2024] [Indexed: 09/09/2024]
Abstract
Human microbiota assembly commences at birth, seeded by both maternal and environmental microorganisms. Ecological theory postulates that primary colonizers dictate microbial community assembly outcomes, yet such microbial priority effects in the human gut remain underexplored. Here using longitudinal faecal metagenomics, we characterized neonatal microbiota assembly for a cohort of 1,288 neonates from the UK. We show that the pioneering neonatal gut microbiota can be stratified into one of three distinct community states, each dominated by a single microbial species and influenced by clinical and host factors, such as maternal age, ethnicity and parity. A community state dominated by Enterococcus faecalis displayed stochastic microbiota assembly with persistent high pathogen loads into infancy. In contrast, community states dominated by Bifidobacterium, specifically B. longum and particularly B. breve, exhibited a stable assembly trajectory and long-term pathogen colonization resistance, probably due to strain-specific functional adaptions to a breast milk-rich neonatal diet. Consistent with our human cohort observation, B. breve demonstrated priority effects and conferred pathogen colonization resistance in a germ-free mouse model. Our findings solidify the crucial role of Bifidobacteria as primary colonizers in shaping the microbiota assembly and functions in early life.
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Affiliation(s)
- Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
| | | | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Nicholas J R Dawson
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Andre Mu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Anne Adoum
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Katherine Harcourt
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Junyan Liu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Mark D Stares
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Alison Rodger
- Institute for Global Health, University College London, London, UK
| | - Peter Brocklehurst
- Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - Nigel Field
- Institute for Global Health, University College London, London, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
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3
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Houngbédji M, Jespersen JS, Wilfrid Padonou S, Jespersen L. Cereal-based fermented foods as microbiota-directed products for improved child nutrition and health in sub-Saharan Africa. Crit Rev Food Sci Nutr 2024:1-22. [PMID: 38973125 DOI: 10.1080/10408398.2024.2365342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Several strategies, programs and policies have long been developed and implemented to alleviate child malnutrition in sub-Saharan African countries. However, stunting and wasting still persist at an alarming rate, suggesting that alternative strategies are needed to induce faster progress toward the 2030 SDGs targets of reducing malnutrition. Gut microbiota-directed intervention is now being recognized as an unconventional powerful approach to mitigate malnutrition and improve overall child health. In an African setting, manufactured probiotic and synbiotic foods or supplements may not be successful owing to the non-affordability and high attachment of African populations to their food tradition. This review analyses the potential of indigenous fermented cereal-based products including porridges, doughs, beverages, bread- and yoghurt-like products, to be used as microbiota-directed foods for over 6 months children. The discussion includes relevant strategies to effectively enhance the beneficial effects of these products on gut microbiota composition for improved child health and nutrition in sub-Saharan Africa. Characterization of probiotic features and general safety of food processing in sub-Saharan Africa as well as randomized clinical studies are still lacking to fully ascertain the health effects and suitability of these fermented foods in preventing and treating child malnutrition and diarrhea.
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Affiliation(s)
- Marcel Houngbédji
- Laboratoire de Sciences et Technologies des Aliments, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Jéricho, Cotonou, Benin
- Laboratoire de Sciences et Technologie des Aliments, des Bioressources et de Nutrition Humaine, Université Nationale d'Agriculture, Sakété, Bénin
| | | | - Sègla Wilfrid Padonou
- Laboratoire de Sciences et Technologies des Aliments, Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Jéricho, Cotonou, Benin
- Laboratoire de Sciences et Technologie des Aliments, des Bioressources et de Nutrition Humaine, Université Nationale d'Agriculture, Sakété, Bénin
| | - Lene Jespersen
- Department of Food Science, University of Copenhagen, Copenhagen, Frederiksberg C, Denmark
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Arzamasov AA, Rodionov DA, Hibberd MC, Guruge JL, Kazanov MD, Leyn SA, Kent JE, Sejane K, Bode L, Barratt MJ, Gordon JI, Osterman AL. Integrative genomic reconstruction of carbohydrate utilization networks in bifidobacteria: global trends, local variability, and dietary adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602360. [PMID: 39005317 PMCID: PMC11245093 DOI: 10.1101/2024.07.06.602360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Bifidobacteria are among the earliest colonizers of the human gut, conferring numerous health benefits. While multiple Bifidobacterium strains are used as probiotics, accumulating evidence suggests that the individual responses to probiotic supplementation may vary, likely due to a variety of factors, including strain type(s), gut community composition, dietary habits of the consumer, and other health/lifestyle conditions. Given the saccharolytic nature of bifidobacteria, the carbohydrate composition of the diet is one of the primary factors dictating the colonization efficiency of Bifidobacterium strains. Therefore, a comprehensive understanding of bifidobacterial glycan metabolism at the strain level is necessary to rationally design probiotic or synbiotic formulations that combine bacterial strains with glycans that match their nutrient preferences. In this study, we systematically reconstructed 66 pathways involved in the utilization of mono-, di-, oligo-, and polysaccharides by analyzing the representation of 565 curated metabolic functional roles (catabolic enzymes, transporters, transcriptional regulators) in 2973 non-redundant cultured Bifidobacterium isolates and metagenome-assembled genomes (MAGs). Our analysis uncovered substantial heterogeneity in the predicted glycan utilization capabilities at the species and strain level and revealed the presence of a yet undescribed phenotypically distinct subspecies-level clade within the Bifidobacterium longum species. We also identified Bangladeshi isolates harboring unique gene clusters tentatively implicated in the breakdown of xyloglucan and human milk oligosaccharides. Predicted carbohydrate utilization phenotypes were experimentally characterized and validated. Our large-scale genomic analysis considerably expands the knowledge of carbohydrate metabolism in bifidobacteria and provides a foundation for rationally designing single- or multi-strain probiotic formulations of a given bifidobacterial species as well as synbiotic combinations of bifidobacterial strains matched with their preferred carbohydrate substrates.
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Affiliation(s)
- Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janaki L Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey, 34956
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - James E Kent
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Kristija Sejane
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA
| | - Lars Bode
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), and the Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
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Aihetanmu S, Liang Z, Zhang X, Luo B, Zhang H, Huang J, Tian F, Sun H, Ni Y. Genetic specialization of key bifidobacterial phylotypes in multiple mother-infant dyad cohorts from geographically isolated populations. Front Microbiol 2024; 15:1399743. [PMID: 39021621 PMCID: PMC11251887 DOI: 10.3389/fmicb.2024.1399743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/10/2024] [Indexed: 07/20/2024] Open
Abstract
Little has been known about symbiotic relationships and host specificity for symbionts in the human gut microbiome so far. Bifidobacteria are a paragon of the symbiotic bacteria biota in the human gut. In this study, we characterized the population genetic structure of three bifidobacteria species from 58 healthy mother-infant pairs of three ethnic groups in China, geographically isolated, by Rep-PCR, multi-locus sequence analysis (MLSA), and in vitro carbohydrate utilization. One hundred strains tested were incorporated into 50 sequence types (STs), of which 29 STs, 17 STs, and 4 STs belong to B. longum subsp. longum, B. breve, and B. animalis subsp. lactis, respectively. The conspecific strains from the same mother-child pair were genetically very similar, supporting the vertical transmission of Bifidobacterium phylotypes from mother to offspring. In particular, results based on allele profiles and phylogeny showed that B. longum subsp. longum and B. breve exhibited considerable intraspecies genetic heterogeneity across three ethnic groups, and strains were clustered into ethnicity-specific lineages. Yet almost all strains of B. animalis subsp. lactis were incorporated into the same phylogenetic clade, regardless of ethnic origin. Our findings support the hypothesis of co-evolution between human gut symbionts and their respective populations, which is closely linked to the lifestyle of specific bacterial lineages. Hence, the natural and evolutionary history of Bifidobacterium species would be an additional consideration when selecting bifidobacterial strains for industrial and therapeutic applications.
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Affiliation(s)
| | - Zhixuan Liang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Xueling Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Baolong Luo
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Huimin Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Jian Huang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Fengwei Tian
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hailong Sun
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Yongqing Ni
- School of Food Science and Technology, Shihezi University, Shihezi, China
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Loutet MG, Narimani A, Qamar H, Yonemitsu C, Pell LG, Mahmud AA, Ahmed T, Bode L, Bassani DG, Roth DE. Associations between human milk oligosaccharides and infant growth in a Bangladeshi mother-infant cohort. Pediatr Res 2024; 96:356-364. [PMID: 38052861 PMCID: PMC11343707 DOI: 10.1038/s41390-023-02927-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND We aimed to estimate associations between human milk oligosaccharides (HMOs) and infant growth (length-for-age (LAZ) and weight-for-length (WLZ) z-scores) at 12 months postnatal age. METHODS In this secondary analysis of data from a maternal vitamin D trial in Dhaka, Bangladesh (N = 192), absolute concentrations of HMOs were measured in 13 ± 1 week(s) postpartum milk samples, infant anthropometric measurements were obtained soon after birth and at 12 months postpartum, and infant feeding was classified during 6 months postpartum. Associations between individual HMOs or HMO groups and LAZ or WLZ were estimated by multivariable linear regression adjusting for infant feeding pattern, maternal secretor status, and other potential confounders. RESULTS The concentrations of 6'sialyllactose, lacto-N-neotetraose, and the non-fucosylated non-sialylated HMOs were inversely associated with LAZ at 12 months of age, whereas the fucosylated non-sialylated HMO concentration was positively associated with LAZ at 12 months. These associations were robust in analyses restricted to infants who were primarily exclusively/predominantly fed human milk during the first 3 (or 6) months. CONCLUSIONS Since HMOs are both positively and negatively associated with postnatal growth, there is a need for randomized trials to estimate the causal benefits and risks of exogenously administered HMOs on infant growth and other health outcomes. IMPACT 6'sialyllactose, lacto-N-neotetraose, and the non-fucosylated non-sialylated human milk oligosaccharides (HMOs) were inversely associated with length-for-age z-scores (LAZ) at 12 months, whereas the fucosylated non-sialylated HMO concentration was positively associated with LAZ at 12 months among Bangladeshi infants. Associations between individual and grouped HMOs with infant length growth at 12 months were as strong or stronger in analyses restricted to infants who were exclusively or predominantly fed human milk up to 3 (or 6) months. Randomized trials are needed to characterize the effects of specific HMOs on infant growth, particularly in countries where postnatal linear growth faltering is common.
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Affiliation(s)
- Miranda G Loutet
- The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- The University of Toronto, Toronto, ON, M5S 1A1, Canada.
| | - Arash Narimani
- The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Huma Qamar
- The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | | | - Lisa G Pell
- The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | | | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, icddr,b, Dhaka, Bangladesh
| | - Lars Bode
- University of California San Diego, San Diego, CA, USA
| | - Diego G Bassani
- The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Daniel E Roth
- The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- The University of Toronto, Toronto, ON, M5S 1A1, Canada
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Qi Q, Wang L, Zhu Y, Li S, Gebremedhin MA, Wang B, Zhu Z, Zeng L. Unraveling the Microbial Symphony: Impact of Antibiotics and Probiotics on Infant Gut Ecology and Antibiotic Resistance in the First Six Months of Life. Antibiotics (Basel) 2024; 13:602. [PMID: 39061284 PMCID: PMC11274100 DOI: 10.3390/antibiotics13070602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/24/2024] [Accepted: 06/05/2024] [Indexed: 07/28/2024] Open
Abstract
We aimed to examine the effects of antibiotic and probiotic usage on the gut microbiota structure and the presence of antibiotic-resistance genes (ARGs) in infants during the first six months of life. Questionnaires and fecal samples were collected within three days of birth, two months, and six months to assess antibiotic and probiotic exposure. Gut microbiotas were sequenced via 16S rRNA, and ARGs were conducted by qPCR, including beta-lactam (mecA, blaTEM), tetracycline (tetM), fluoroquinolone (qnrS), aminoglycoside (aac(6')-Ib), and macrolide (ermB). Infants were categorized by antibiotic and probiotic usage and stratified by delivery mode, microbial composition, and ARG abundances were compared, and potential correlations were explored. A total of 189 fecal samples were analyzed in this study. The gut microbiota diversity (Chao1 index) was significantly lower in the "only probiotics" (PRO) group compared to the "neither antibiotics nor probiotics" (CON) group at six months for the CS stratification (p = 0.029). Compositionally, the abundance of core genus Bifidobacterium_pseudocatenulatum was less abundant for the antibiotic during delivery (IAP) group than that in the CON group within the first three days (p = 0.009), while core genus Enterococcus_faecium was more abundant in the PRO than that in the CON group (p = 0.021) at two months. ARGs were highly detected, with Enterococcus hosting tetM and Escherichia associated with blaTEM within three days of birth, though no correlation was found between Bifidobacterium and ARGs. These findings emphasized the critical importance of carefully managing antibiotic and probiotic exposures in early life, with implications for promoting lifelong health through preserving a healthy infant gut ecosystem.
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Affiliation(s)
- Qi Qi
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
| | - Liang Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
| | - Yingze Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
| | - Shaoru Li
- Experimental Teaching Center, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China;
| | - Mitslal Abrha Gebremedhin
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
| | - Baozhu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
- Department of Health, Northwest Women’s and Children’s Hospital, Xi’an 710003, China
| | - Zhonghai Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
| | - Lingxia Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
- Center for Chronic Disease Control and Prevention, Global Health Institution, Xi’an Jiaotong University, Xi’an 710061, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi’an 710061, China
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8
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Hermes GDA, Rasmussen C, Wellejus A. Variation in the Conservation of Species-Specific Gene Sets for HMO Degradation and Its Effects on HMO Utilization in Bifidobacteria. Nutrients 2024; 16:1893. [PMID: 38931248 PMCID: PMC11206791 DOI: 10.3390/nu16121893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Human milk provides essential nutrients for infants but also consists of human milk oligosaccharides (HMOs), which are resistant to digestion by the infant. Bifidobacteria are among the first colonizers, providing various health benefits for the host. This is largely facilitated by their ability to efficiently metabolize HMOs in a species-specific way. Nevertheless, these abilities can vary significantly by strain, and our understanding of the mechanisms applied by different strains from the same species remains incomplete. Therefore, we assessed the effects of strain-level genomic variation in HMO utilization genes on growth on HMOs in 130 strains from 10 species of human associated bifidobacteria. Our findings highlight the extent of genetic diversity between strains of the same species and demonstrate the effects on species-specific HMO utilization, which in most species is largely retained through the conservation of a core set of genes or the presence of redundant pathways. These data will help to refine our understanding of the genetic factors that contribute to the persistence of individual strains and will provide a better mechanistic rationale for the development and optimization of new early-life microbiota-modulating products to improve infant health.
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Affiliation(s)
- Gerben D. A. Hermes
- Human Health Research, Human Health Biosolutions, Novonesis, Kogle Alle 6, 2970 Hoersholm, Denmark (A.W.)
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9
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Yuan C, Chen S, Sun R, Ren L, Zhao T, Wu M, Zhang A. Thymol improves the growth performance of blue foxes by regulating the gut microbiota. Front Microbiol 2024; 15:1368293. [PMID: 38946897 PMCID: PMC11212683 DOI: 10.3389/fmicb.2024.1368293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/07/2024] [Indexed: 07/02/2024] Open
Abstract
Introduction The drawbacks of using antibiotics as feed additives for blue foxes have gradually become apparent; moreover, thymol has wide-spectrum antimicrobial activity and has the potential to replace antibiotics in various animals. However, there are few reports on the effects of thymol on blue foxes. Methods This study aimed to investigate the effects of different concentrations of thymol on the growth performance, apparent nutrient digestibility, serum biochemical indicators, intestinal morphology, and gut microbiota of blue foxes. Twenty-four male blue foxes (120 ± 5 d) of similar weight (6.05 ± 0.16 kg) were randomly divided into 4 groups. 0, 100, 200, and 300 mg/kg thymol were added to the basal diets of groups C, L, M, and H, respectively. Results Compared with those in the C group, the addition of 100 mg/kg thymol to the diet significantly increased organic matter (OM) digestibility, crude protein (CP) digestibility, immunoglobulin (Ig) A, IgM, the VH of the duodenum, the CD of the jejunum, the VH of the ileum, and the VH/CD of the ileum (P < 0.05) and strongly significantly increased IgG (P < 0.01). The addition of 200 mg/kg thymol to the diet increased the VH/CD of the duodenum (P < 0.05). The addition of 300 mg/kg thymol to the diet significantly increased the VH and CD of the jejunum (P < 0.05). The addition of 200 mg/kg and 300 mg/kg thymol to the diets increased the final weight (FW) (P < 0.05). Adding 100 mg/kg thymol significantly increased the levels of interleukin-4 (IL-4) and catalase (CAT) compared with those in the other groups (P < 0.05). 16S rRNA gene detection revealed that thymol can change the abundances of Bifidobacterium, Fusobacterium, Allobaculum, Streptococcus, Megasphaera, and Lactobacillus in the gut. Conclusion The addition of thymol to diets can increase the abundance of Bifidobacterium, Fusobacterium, and Allobaculum, which may contribute to improving the growth performance of blue foxes.
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Affiliation(s)
| | | | | | | | | | | | - Aiwu Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
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10
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Muñoz-Fernandez SS, Garcez FB, Alencar JCG, Bastos AA, Morley JE, Cederholm T, Aprahamian I, de Souza HP, Avelino-Silva TJ, Bindels LB, Ribeiro SML. Gut microbiota disturbances in hospitalized older adults with malnutrition and clinical outcomes. Nutrition 2024; 122:112369. [PMID: 38422755 DOI: 10.1016/j.nut.2024.112369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE Malnutrition is one of the most threatening conditions in geriatric populations. The gut microbiota has an important role in the host's metabolic and muscular health: however, its interplay with disease-related malnutrition is not well understood. We aimed to identify the association of malnutrition with the gut microbiota and predict clinical outcomes in hospitalized acutely ill older adults. METHODS We performed a secondary longitudinal analysis in 108 geriatric patients from a prospective cohort evaluated at admission and 72 h of hospitalization. We collected clinical, demographic, nutritional, and 16S rRNA gene-sequenced gut microbiota data. Microbiota diversity, overall composition, and differential abundance were calculated and compared between patients with and without malnutrition. Microbiota features associated with malnutrition were used to predict clinical outcomes. RESULTS Patients with malnutrition (51%) had a different microbiota composition compared to those who were well-nourished during hospitalization (ANOSIM R = 0.079, P = 0.003). Patients with severe malnutrition showed poorer α-diversity at admission (Shannon P = 0.012, Simpson P = 0.018) and follow-up (Shannon P = 0.023, Chao1 P = 0.008). Differential abundance of Lachnospiraceae NK4A136 group, Subdoligranulum, and Faecalibacterium prausnitzii were significantly lower and inversely associated with malnutrition, while Corynebacterium, Ruminococcaceae Incertae Sedis, and Fusobacterium were significantly increased and positively associated with malnutrition. Corynebacterium, Ruminococcaceae Incertae Sedis, and the overall composition were important predictors of critical care in patients with malnutrition during hospitalization. CONCLUSION Older adults with malnutrition, especially in a severe stage, may be subject to substantial gut microbial disturbances during hospitalization. The gut microbiota profile of patients with malnutrition might help us to predict worse clinical outcomes.
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Affiliation(s)
- Shirley S Muñoz-Fernandez
- Nutrition Department, School of Public Health, University of São Paulo, São Paulo, Sao Paulo, Brazil.
| | - Flavia B Garcez
- Laboratorio de Investigacao Medica em Envelhecimento (LIM 66), Servico de Geriatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Sao Paulo, Brazil; Departamento de Medicina, Hospital Universitario, Universidade Federal de Sergipe, Aracaju, Sergipe, Brazil
| | - Julio C G Alencar
- Disciplina de Emergencias Clínicas, Departamento de Clínica Medica, Faculty of Medicine, University of São Paulo, São Paulo, Sao Paulo, Brazil
| | - Amália A Bastos
- Nutrition Department, School of Public Health, University of São Paulo, São Paulo, Sao Paulo, Brazil
| | - John E Morley
- Division of Geriatric Medicine, School of Medicine, Saint Louis University, St. Louis, Missouri, USA
| | - Tommy Cederholm
- Department of Public Health and Caring Sciences, Clinical Nutrition and Metabolism, Uppsala University, Uppsala, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Ivan Aprahamian
- Division of Geriatrics, Department of Internal Medicine, Jundiaí Medical School, Group of Investigation on Multimorbidity and Mental Health in Aging (GIMMA), Jundiaí, Sao Paulo, Brazil
| | - Heraldo P de Souza
- Disciplina de Emergencias Clínicas, Departamento de Clínica Medica, Faculty of Medicine, University of São Paulo, São Paulo, Sao Paulo, Brazil
| | - Thiago J Avelino-Silva
- Laboratorio de Investigacao Medica em Envelhecimento (LIM 66), Servico de Geriatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Sao Paulo, Brazil
| | - Laure B Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Sandra M L Ribeiro
- Nutrition Department, School of Public Health, University of São Paulo, São Paulo, Sao Paulo, Brazil; School of Arts, Science, and Humanity, University of São Paulo, São Paulo, Sao Paulo, Brazil
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11
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Wong CB, Huang H, Ning Y, Xiao J. 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. Microorganisms 2024; 12:1014. [PMID: 38792843 PMCID: PMC11124435 DOI: 10.3390/microorganisms12051014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
A healthy gut microbiome is crucial for the immune system and overall development of infants. Bifidobacterium has been known to be a predominant species in the infant gut; however, an emerging concern is the apparent loss of this genus, in particular, Bifidobacterium longum subsp. infantis (B. infantis) in the gut microbiome of infants in industrialized nations, underscoring the importance of restoring this beneficial bacterium. With the growing understanding of the gut microbiome, probiotics, especially infant-type human-residential bifidobacteria (HRB) strains like B. infantis, are gaining prominence for their unique ability to utilize HMOs and positively influence infant health. This article delves into the physiology of a probiotic strain, B. infantis M-63, its symbiotic relationship with HMOs, and its potential in improving gastrointestinal and allergic conditions in infants and children. Moreover, this article critically assesses the role of HMOs and the emerging trend of supplementing infant formulas with the prebiotic HMOs, which serve as fuel for beneficial gut bacteria, thereby emulating the protective effects of breastfeeding. The review highlights the potential of combining B. infantis M-63 with HMOs as a feasible strategy to improve health outcomes in infants and children, acknowledging the complexities and requirements for further research in this area.
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Affiliation(s)
- Chyn Boon Wong
- International Division, Morinaga Milk Industry Co., Ltd., 5-2, Higashi Shimbashi 1-Chome, Minato-ku, Tokyo 105-7122, Japan
| | - Huidong Huang
- Nutrition Research Institute, Junlebao Dairy Group Co., Ltd., 36 Shitong Road, Shijiazhuang 050221, China
| | - Yibing Ning
- Nutrition Research Institute, Junlebao Dairy Group Co., Ltd., 36 Shitong Road, Shijiazhuang 050221, China
| | - Jinzhong Xiao
- Morinaga Milk Industry (Shanghai) Co., Ltd., Room 509 Longemont Yes Tower, No. 369 Kaixuan Road, Changning District, Shanghai 200050, China
- Department of Microbiota Research, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Research Center for Probiotics, Department of Nutrition and Health, China Agricultural University, Beijing 100093, China
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12
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Bogza A, King IL, Maurice CF. Worming into infancy: Exploring helminth-microbiome interactions in early life. Cell Host Microbe 2024; 32:639-650. [PMID: 38723604 DOI: 10.1016/j.chom.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 06/06/2024]
Abstract
There is rapidly growing awareness of microbiome assembly and function in early-life gut health. Although many factors, such as antibiotic use and highly processed diets, impinge on this process, most research has focused on people residing in high-income countries. However, much of the world's population lives in low- and middle-income countries (LMICs), where, in addition to erratic antibiotic use and suboptimal diets, these groups experience unique challenges. Indeed, many children in LMICs are infected with intestinal helminths. Although helminth infections are strongly associated with diverse developmental co-morbidities and induce profound microbiome changes, few studies have directly examined whether intersecting pathways between these components of the holobiont shape health outcomes in early life. Here, we summarize microbial colonization within the first years of human life, how helminth-mediated changes to the gut microbiome may affect postnatal growth, and why more research on this relationship may improve health across the lifespan.
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Affiliation(s)
- Andrei Bogza
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada; Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Irah L King
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada; Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
| | - Corinne F Maurice
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada.
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13
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Nobili A, Pane M, Skvortsova M, Ben Salem M, Morgenthaler S, Jamieson E, Di Stefano M, Bathrellou E, Mamalaki E, Ramos-Garcia V, Kuligowski J, Vasileiadis M, Georgiadis P, Falcone M, Refinetti P. Innovative Biomarkers for Obesity and Type 1 Diabetes Based on Bifidobacterium and Metabolomic Profiling. Microorganisms 2024; 12:931. [PMID: 38792760 PMCID: PMC11124356 DOI: 10.3390/microorganisms12050931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
The role of Bifidobacterium species and microbial metabolites such as short-chain fatty acids (SCFAs) and human milk oligosaccharides in controlling intestinal inflammation and the pathogenesis of obesity and type 1 diabetes (T1D) has been largely studied in recent years. This paper discusses the discovery of signature biomarkers for obesity and T1D based on data from a novel test for profiling several Bifidobacterium species, combined with metabolomic analysis. Through the NUTRISHIELD clinical study, a total of 98 children were recruited: 40 healthy controls, 40 type 1 diabetics, and 18 obese children. Bifidobacterium profiles were assessed in stool samples through an innovative test allowing high taxonomic resolution and precise quantification, while SCFAs and branched amino acids were measured in urine samples through gas chromatography-mass spectrometry (GC-MS). KIDMED questionnaires were used to evaluate the children's dietary habits and correlate them with the Bifidobacterium and metabolomic profiles. We found that B. longum subs. infantis and B. breve were higher in individuals with obesity, while B. bifidum and B. longum subs. longum were lower compared to healthy individuals. In individuals with T1D, alterations were found at the metabolic level, with an overall increase in the level of the most measured metabolites. The high taxonomic resolution of the Bifidobacterium test used meant strong correlations between the concentrations of valine and isoleucine, and the relative abundance of some Bifidobacterium species such as B. longum subs. infantis, B. breve, and B. bifidum could be observed.
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Affiliation(s)
- Angelica Nobili
- Autoimmune Pathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (A.N.); (M.D.S.); (M.F.)
| | - Marco Pane
- Probiotical Research, 28100 Novara, Italy;
| | - Mariya Skvortsova
- REM Analytics SA, 1870 Monthey, Switzerland; (M.S.); (M.B.S.); (S.M.); (E.J.)
| | - Meryam Ben Salem
- REM Analytics SA, 1870 Monthey, Switzerland; (M.S.); (M.B.S.); (S.M.); (E.J.)
| | - Stephan Morgenthaler
- REM Analytics SA, 1870 Monthey, Switzerland; (M.S.); (M.B.S.); (S.M.); (E.J.)
- Department of Mathematics, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Emily Jamieson
- REM Analytics SA, 1870 Monthey, Switzerland; (M.S.); (M.B.S.); (S.M.); (E.J.)
| | - Marina Di Stefano
- Autoimmune Pathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (A.N.); (M.D.S.); (M.F.)
| | - Eirini Bathrellou
- Department of Nutrition and Dietetics, Harokopio University, 17676 Athens, Greece; (E.B.); (E.M.)
| | - Eirini Mamalaki
- Department of Nutrition and Dietetics, Harokopio University, 17676 Athens, Greece; (E.B.); (E.M.)
| | - Victoria Ramos-Garcia
- Neonatal Research Group, Health Research Institute La Fe, 46026 Valencia, Spain; (V.R.-G.); (J.K.)
| | - Julia Kuligowski
- Neonatal Research Group, Health Research Institute La Fe, 46026 Valencia, Spain; (V.R.-G.); (J.K.)
| | | | | | - Marika Falcone
- Autoimmune Pathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (A.N.); (M.D.S.); (M.F.)
| | - Paulo Refinetti
- REM Analytics SA, 1870 Monthey, Switzerland; (M.S.); (M.B.S.); (S.M.); (E.J.)
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14
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Hardjo J, Selene NB. Stunting and Gut Microbiota: A Literature Review. Pediatr Gastroenterol Hepatol Nutr 2024; 27:137-145. [PMID: 38818278 PMCID: PMC11134181 DOI: 10.5223/pghn.2024.27.3.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/07/2023] [Accepted: 01/02/2024] [Indexed: 06/01/2024] Open
Abstract
Stunting, a condition characterized by impaired growth and development in children, remains a major public health concern worldwide. Over the past decade, emerging evidence has shed light on the potential role of gut microbiota modulation in stunting. Gut microbiota dysbiosis has been linked to impaired nutrient absorption, chronic inflammation, altered short-chain fatty acid production, and perturbed hormonal and signaling pathways, all of which may hinder optimal growth in children. This review aims to provide a comprehensive analysis of existing research exploring the bidirectional relationship between stunting and the gut microbiota. Although stunting can alter the gut microbial community, microbiota dysbiosis may exacerbate it, forming a vicious cycle that sustains the condition. The need for effective preventive and therapeutic strategies targeting the gut microbiota to combat stunting is also discussed. Nutritional interventions, probiotics, and prebiotics are among the most promising approaches to modulate the gut microbiota and potentially ameliorate stunting outcomes. Ultimately, a better understanding of the gut microbiota-stunting nexus is vital for guiding evidence-based interventions that can improve the growth and development trajectory of children worldwide, making substantial strides toward reducing the burden of stunting in vulnerable populations.
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Affiliation(s)
- Jessy Hardjo
- Department of Emergency Medicine, General Hospital Ploso, East Java, Indonesia
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15
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Lui JC. Gut microbiota in regulation of childhood bone growth. Exp Physiol 2024; 109:662-671. [PMID: 38156734 PMCID: PMC11061630 DOI: 10.1113/ep091620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Childhood stunting and wasting, or decreased linear and ponderal growth associated with undernutrition, continue to be a major global public health challenge. Although many of the current therapeutic and dietary interventions have significantly reduced childhood mortality caused by undernutrition, there remain great inefficacies in improving childhood stunting. Longitudinal bone growth in children is governed by different genetic, nutritional and other environmental factors acting systemically on the endocrine system and locally at the growth plate. Recent studies have shown that this intricate interplay between nutritional and hormonal regulation of the growth plate could involve the gut microbiota, highlighting the importance of a holistic approach in tackling childhood undernutrition. In this review, I focus on the mechanistic insights provided by these recent advances in gut microbiota research and discuss ongoing development of microbiota-based therapeutics in humans, which could be the missing link in solving undernutrition and childhood stunting.
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Affiliation(s)
- Julian C. Lui
- Section on Growth and DevelopmentNational Institute of Child Health and Human DevelopmentBethesdaMarylandUSA
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16
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Shennon I, Wilson BC, Behling AH, Portlock T, Haque R, Forrester T, Nelson CA, O'Sullivan JM. The infant gut microbiome and cognitive development in malnutrition. Clin Nutr 2024; 43:1181-1189. [PMID: 38608404 DOI: 10.1016/j.clnu.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 03/11/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
Malnutrition affects 195 million children under the age of five worldwide with long term effects that include impaired cognitive development. Brain development occurs rapidly over the first 36 months of life. Whilst seemingly independent, changes to the brain and gut microbiome are linked by metabolites, hormones, and neurotransmitters as part of the gut-brain axis. In the context of severe malnutrition, the composition of the gut microbiome and the repertoire of biochemicals exchanged via the gut-brain axis vary when compared to healthy individuals. These effects are primarily due to the recognized interacting determinants, macro- and micronutrient deficiencies, infection, infestations and toxins related to poor sanitation, and a dearth of psycho-social stimulation. The standard of care for the treatment of severe acute malnutrition is focused on nutritional repletion and weight restoration through the provision of macro- and micronutrients, the latter usually in excess of recommended dietary allowances (RDA). However, existing formulations and supplements have not been designed to specifically address key recovery requirements for brain and gut microbiome development. Animal model studies indicate that treatments targeting the gut microbiome could improve brain development. Despite this, research on humans targeting the gut microbiome with the aim of restoring brain functionality are scarce. We conclude that there is a need for assessment of cognition and the use of various tools that permit visualization of the brain anatomy and function (e.g., Magnetic resonance imaging (MRI), functional near-infrared spectroscopy (fNIRS), electroencephalogram (EEG)) to understand how interventions targeting the gut microbiome impact brain development.
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Affiliation(s)
- Inoli Shennon
- The Liggins Institute, The University of Auckland, Auckland 1023, New Zealand
| | - Brooke C Wilson
- The Liggins Institute, The University of Auckland, Auckland 1023, New Zealand
| | - Anna H Behling
- The Liggins Institute, The University of Auckland, Auckland 1023, New Zealand
| | - Theo Portlock
- The Liggins Institute, The University of Auckland, Auckland 1023, New Zealand
| | - Rashidul Haque
- Infectious Disease Division, International Centre for Diarrheal Disease Research, Bangladesh
| | - Terrence Forrester
- UWI Solutions for Developing Countries, The University of the West Indies, Mona, Kingston 7, Jamaica
| | - Charles A Nelson
- Department of Pediatrics, Division of Developmental Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Harvard Graduate School of Education, Cambridge, MA, USA
| | - Justin M O'Sullivan
- The Liggins Institute, The University of Auckland, Auckland 1023, New Zealand; The Maurice Wilkins Centre, The University of Auckland, Auckland 1010, New Zealand; MRC Lifecourse Epidemiology Unit, University of Southampton, University Road, Southampton SO17 1BJ, UK; Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore.
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17
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Hilliard MA, Sela DA. Transmission and Persistence of Infant Gut-Associated Bifidobacteria. Microorganisms 2024; 12:879. [PMID: 38792709 PMCID: PMC11124121 DOI: 10.3390/microorganisms12050879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Bifidobacterium infantis are the primary colonizers of the infant gut, yet scientific research addressing the transmission of the genus Bifidobacterium to infants remains incomplete. This review examines microbial reservoirs of infant-type Bifidobacterium that potentially contribute to infant gut colonization. Accordingly, strain inheritance from mother to infant via the fecal-oral route is likely contingent on the bifidobacterial strain and phenotype, whereas transmission via the vaginal microbiota may be restricted to Bifidobacterium breve. Additional reservoirs include breastmilk, horizontal transfer from the environment, and potentially in utero transfer. Given that diet is a strong predictor of Bifidobacterium colonization in early life and the absence of Bifidobacterium is observed regardless of breastfeeding, it is likely that additional factors are responsible for bifidobacterial colonization early in life.
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Affiliation(s)
- Margaret A. Hilliard
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA;
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - David A. Sela
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA;
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
- Department of Nutrition, University of Massachusetts, Amherst, MA 01003, USA
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
- Department of Microbiology & Physiological Systems and Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
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18
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Serrano Matos YA, Cano J, Shafiq H, Williams C, Sunny J, Cowardin CA. Colonization during a key developmental window reveals microbiota-dependent shifts in growth and immunity during undernutrition. MICROBIOME 2024; 12:71. [PMID: 38589975 PMCID: PMC11003143 DOI: 10.1186/s40168-024-01783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Childhood undernutrition is a major global health challenge with devastating lifelong consequences. Linear growth stunting due to undernutrition has been linked to poor health outcomes, and mothers who experience growth stunting in childhood are more likely to give birth to stunted children later in life. Based on these findings, we hypothesized that intergenerational colonization of mice with microbiota from human donors with undernutrition may recapitulate certain immune and growth changes observed in this disorder. RESULTS To test this hypothesis, we developed a gnotobiotic murine model of undernutrition using microbiota from human infants with healthy or stunted growth trajectories. Intergenerational colonization with microbiota derived from children with growth stunting lead to less linear growth and the development of immune features of undernutrition and enteropathy, including intestinal villus blunting, lower liver IGF-1 and accumulation of intraepithelial lymphocytes and plasma cells in the small intestine. In contrast, colonization after weaning lead to fewer host phenotypic changes between these distinct microbial communities. CONCLUSIONS These results are broadly consistent with previous findings demonstrating that exposure of the immune system to microbial products during the weaning phase is a critical determinant of later life immune function. Overall, our results suggest intergenerational colonization with human microbiota samples is a useful approach with which to investigate microbiota-dependent changes in growth and immunity in early life. Murine models that capture the intergenerational and multifactorial nature of undernutrition are critical to understanding the underlying biology of this disorder. Video Abstract.
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Affiliation(s)
- Yadeliz A Serrano Matos
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jasmine Cano
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hamna Shafiq
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Claire Williams
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Julee Sunny
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Carrie A Cowardin
- Division of Pediatric Gastroenterology & Hepatology, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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19
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Walter J. Establishing microbiome causality to tackle malnutrition. Nat Microbiol 2024; 9:884-885. [PMID: 38503976 DOI: 10.1038/s41564-024-01653-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Affiliation(s)
- Jens Walter
- APC Microbiome Ireland, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
- Department of Medicine, University College Cork, Cork, Ireland.
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20
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Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition. Nat Microbiol 2024; 9:922-937. [PMID: 38503977 PMCID: PMC10994852 DOI: 10.1038/s41564-024-01628-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 03/21/2024]
Abstract
Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies.
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Affiliation(s)
- Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Kali M Pruss
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Clara Kao
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marie Crane
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Chemistry, University of California, Davis, CA, USA
| | - Nikita P Balcazo
- Department of Chemistry, University of California, Davis, CA, USA
| | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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21
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Li W, Liang H, He W, Gao X, Wu Z, Hu T, Lin X, Wang M, Zhong Y, Zhang H, Ge L, Jin X, Xiao L, Zou Y. Genomic and functional diversity of cultivated Bifidobacterium from human gut microbiota. Heliyon 2024; 10:e27270. [PMID: 38463766 PMCID: PMC10923715 DOI: 10.1016/j.heliyon.2024.e27270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 02/14/2024] [Accepted: 02/27/2024] [Indexed: 03/12/2024] Open
Abstract
The genus Bifidobacterium widely exists in human gut and has been increasingly used as the adjuvant probiotics for the prevention and treatment of diseases. However, the functional differences of Bifidobacterium genomes from different regions of the world remain unclear. We here describe an extensive study on the genomic characteristics and function annotations of 1512 genomes (clustered to 849 non-redundant genomes) of Bifidobacterium cultured from human gut. The distribution of some carbohydrate-active enzymes varied among different Bifidobacterium species and continents. More than 36% of the genomes of B. pseudocatenulatum harbored biosynthetic gene clusters of lanthipeptide-class-iv. 99.76% of the cultivated genomes of Bifidobacterium harbored genes of bile salt hydrolase. Most genomes of B. adolescentis, and all genomes of B. dentium harbored genes involved in gamma-aminobutyric acid synthesis. B. longum subsp. infantis were characterized harboring most genes related to human milk oligosaccharide utilization. Significant differences between the distribution of antibiotic resistance genes among different species and continents revealed the importance to use antibiotics precisely in the clinical treatment. Phages infecting Bifidobacterium and horizontal gene transfers occurring in genomes of Bifidobacterium were dependent on species and region sources, and might help Bifidobacterium adapt to the environment. In addition, the distribution of Bifidobacterium in human gut was found varied from different regions of the world. This study represents a comprehensive view of characteristics and functions of genomes of cultivated Bifidobacterium from human gut, and enables clinical advances in the future.
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Affiliation(s)
- Wenxi Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- BGI Research, Shenzhen, 518083, China
| | | | - Wenxin He
- BGI Research, Shenzhen, 518083, China
| | | | - Zhinan Wu
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Xiaoqian Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- BGI Research, Shenzhen, 518083, China
| | - Mengmeng Wang
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiyi Zhong
- BGI Research, Shenzhen, 518083, China
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Haifeng Zhang
- BGI Research, Shenzhen, 518083, China
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Lan Ge
- BGI Research, Shenzhen, 518083, China
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Qingdao, 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
- BGI Research, Qingdao, 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, China
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22
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Gough EK, Edens TJ, Carr L, Robertson RC, Mutasa K, Ntozini R, Chasekwa B, Geum HM, Baharmand I, Gill SK, Mutasa B, Mbuya MNN, Majo FD, Tavengwa N, Francis F, Tome J, Evans C, Kosek M, Prendergast AJ, Manges AR. Bifidobacterium longum modifies a nutritional intervention for stunting in Zimbabwean infants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.18.24301438. [PMID: 38293149 PMCID: PMC10827232 DOI: 10.1101/2024.01.18.24301438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Child stunting is an indicator of chronic undernutrition and reduced human capital. However, it remains a poorly understood public health problem. Small-quantity lipid-based nutrient supplements (SQ-LNS) have been widely tested to reduce stunting, but have modest effects. The infant intestinal microbiome may contribute to stunting, and is partly shaped by mother and infant histo-blood group antigens (HBGA). We investigated whether mother-infant fucosyltransferase status, which governs HBGA, and the infant gut microbiome modified the impact of SQ-LNS on stunting at age 18 months among Zimbabwean infants in the SHINE Trial ( NCT01824940 ). We found that mother-infant fucosyltransferase discordance and Bifidobacterium longum reduced SQ-LNS efficacy. Infant age-related microbiome shifts in B. longum subspecies dominance from infantis , a proficient human milk oligosaccharide utilizer, to suis or longum , proficient plant-polysaccharide utilizers, were partly influenced by discordance in mother-infant FUT2+/FUT3- phenotype, suggesting that a "younger" microbiome at initiation of SQ-LNS reduces its benefits on stunting.
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23
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Addae HY, Apprey C, Kwarteng A. Gut Microbiome-Targeted Nutrition Interventions and Growth among Children in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis. Curr Dev Nutr 2024; 8:102085. [PMID: 38455707 PMCID: PMC10918490 DOI: 10.1016/j.cdnut.2024.102085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 03/09/2024] Open
Abstract
Background Childhood malnutrition is a public health challenge of much interest and concern globally. However, a perturbed gut microbiome (GM) may limit some nutrition interventions' effects among healthy children with undernutrition. Objectives This review aimed to evaluate the effects of GM-targeted nutrition interventions on growth outcomes among children (0-59 mo) using published studies in low- and middle-income countries. Methods The methods were guided by the Cochrane methodology. The literature search was conducted to include articles published from inception to July 2023 in PubMed, Google Scholar, and Cochrane Databases. We identified and included 35 studies among 11,047 children. The analysis was conducted considering various growth parameters in the qualitative synthesis and weight gain (kg) in the meta-analysis. Results In the qualitative synthesis, 55.6% of prebiotics, 66.7% of probiotics, 71.4% of synbiotics, and 28.6% of "microbiome complementary feed" studies had significant effects on growth outcomes. Also, prebiotics had more studies with significant effects among healthy children, whereas probiotics, synbiotics, and "microbiome complementary feeds" had more studies with significant effects among children with undernutrition. Nineteen studies were included in the meta-analyses, of which 7 (36.8%) measured GM outcomes. The meta-analysis showed that prebiotics exhibited heterogeneity but had significant effects on weight in the intervention as compared with the control (mean difference [MD]: 0.14 kg; 95% CI: 0.02, 0.25; I2 = 63%, P = 0.02; 4 studies, n = 932). Probiotics had significant effects on weight in the intervention (MD: 0.15 kg; 95% CI: 0.06, 0.25; I2 = 42%, P = 0.05; 8 studies, n = 2437) as compared to the control. However, synbiotics (MD: 0.26 kg; 95% CI: -0.04, 0.56; I2 = 41%, P = 0.17; 4 studies, n = 1896] and "microbiome complementary feed" (MD: -0.03 kg; 95% CI: -0.18, 0.11; I2 = 0%, P = 0.60; 3 studies, n = 733] had no significant effects on weight in the intervention as compared with control. Conclusions Although probiotics and synbiotics may be effective at enhancing growth among children, the selection of interventions should be contingent upon health status.This trial was registered at www.crd.york.ac.uk/prospero/ as CRD42023434109.
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Affiliation(s)
- Hammond Yaw Addae
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
- Nursing Department, Nursing and Midwifery Training College, Kpembe, Ghana
| | - Charles Apprey
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, KNUST, Kumasi, Ghana
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24
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Gunjur A, Shao Y, Rozday T, Klein O, Mu A, Haak BW, Markman B, Kee D, Carlino MS, Underhill C, Frentzas S, Michael M, Gao B, Palmer J, Cebon J, Behren A, Adams DJ, Lawley TD. A gut microbial signature for combination immune checkpoint blockade across cancer types. Nat Med 2024; 30:797-809. [PMID: 38429524 PMCID: PMC10957475 DOI: 10.1038/s41591-024-02823-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 01/12/2024] [Indexed: 03/03/2024]
Abstract
Immune checkpoint blockade (ICB) targeting programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte protein 4 (CTLA-4) can induce remarkable, yet unpredictable, responses across a variety of cancers. Studies suggest that there is a relationship between a cancer patient's gut microbiota composition and clinical response to ICB; however, defining microbiome-based biomarkers that generalize across cohorts has been challenging. This may relate to previous efforts quantifying microbiota to species (or higher taxonomic rank) abundances, whereas microbial functions are often strain specific. Here, we performed deep shotgun metagenomic sequencing of baseline fecal samples from a unique, richly annotated phase 2 trial cohort of patients with diverse rare cancers treated with combination ICB (n = 106 discovery cohort). We demonstrate that strain-resolved microbial abundances improve machine learning predictions of ICB response and 12-month progression-free survival relative to models built using species-rank quantifications or comprehensive pretreatment clinical factors. Through a meta-analysis of gut metagenomes from a further six comparable studies (n = 364 validation cohort), we found cross-cancer (and cross-country) validity of strain-response signatures, but only when the training and test cohorts used concordant ICB regimens (anti-PD-1 monotherapy or combination anti-PD-1 plus anti-CTLA-4). This suggests that future development of gut microbiome diagnostics or therapeutics should be tailored according to ICB treatment regimen rather than according to cancer type.
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Affiliation(s)
- Ashray Gunjur
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK.
| | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Timothy Rozday
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Oliver Klein
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Andre Mu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Bastiaan W Haak
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Amsterdam, Netherlands
| | - Ben Markman
- Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
- Department of Medical Oncology, Alfred Health, Melbourne, Victoria, Australia
- School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Damien Kee
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Rare Cancer Laboratory, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Matteo S Carlino
- Department of Medical Oncology, Blacktown and Westmead Hospitals, Sydney, New South Wales, Australia
- Melanoma Institute of Australia, University of Sydney, Sydney, New South Wales, Australia
| | - Craig Underhill
- Border Medical Oncology and Haematology Research Unit, Albury-Wodonga Regional Cancer Centre, Albury-Wodonga, New South Wales, Australia
- Rural Medical School, University of New South Wales, Albury, New South Wales, Australia
| | - Sophia Frentzas
- Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
| | - Michael Michael
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Bo Gao
- Department of Medical Oncology, Blacktown and Westmead Hospitals, Sydney, New South Wales, Australia
| | - Jodie Palmer
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Jonathan Cebon
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
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25
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Alam J, Fahim SM, Islam MR, Alam MA, Gazi MA, Ahmed T. Effects of L-Carnitine Supplementation on the Rate of Weight Gain and Biomarkers of Environmental Enteric Dysfunction in Children with Severe Acute Malnutrition: A Double-Blind Randomized Controlled Clinical Trial. J Nutr 2024; 154:949-961. [PMID: 38331348 DOI: 10.1016/j.tjnut.2024.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Severe acute malnutrition (SAM) is a major public health concern among low- and middle-income countries, where the majority of the children encountering this acute form of malnutrition suffer from environmental enteric dysfunction (EED). However, evidence regarding the effects of L-carnitine supplementation on the rate of weight gain and EED biomarkers in malnourished children is limited. OBJECTIVES We aimed to investigate the role of L-carnitine supplementation on the rate of weight gain, duration of hospital stays, and EED biomarkers among children with SAM. METHODS A prospective, double-blind, placebo-controlled, randomized clinical trial was conducted at the Nutritional Rehabilitation Unit (NRU) of Dhaka Hospital, International Centre for Diarrheal Disease Research, Bangladesh. Children with SAM aged 9-24 mo were randomly assigned to receive commercial L-carnitine syrup (100 mg/kg/d) or placebo for 15 d in addition to standard of care. A total of 98 children with Weight-for-Length-z-score (WLZ) < -3 Standard deviation were enrolled between October 2021 and March 2023. Analyses were conducted on an intention-to-treat basis. RESULTS The primary outcome variable, "rate of weight gain," was comparable between L-carnitine and placebo groups (2.09 ± 2.23 compared with 2.07 ± 2.70; P = 0.973), which was consistent even after adjusting for potential covariates (age, sex, Weight-for-Age z-score, asset index, and WASH practices) through linear regression [ß: 0.37; 95% confidence interval (CI): -0.63,1.37; P = 0.465]. The average hospital stay was ∼4 d. The results of adjusted median regression showed that following intervention, there was no significant difference in the EED biomarkers among the treatment arms; Myeloperoxidase (ng/mL) [ß: -1342.29; 95% CI: -2817.35, 132.77; P = 0.074], Neopterin (nmol/L) [ß: -153.33; 95% CI: -556.58, 249.91; P = 0.452], alpha-1-antitrypsin (mg/mL) [ß: 0.05; 95% CI: -0.15, 0.25; P = 0.627]. Initial L-carnitine (μmol/L) levels (median, interquartile range) for L-carnitine compared with placebo were 54.84 (36.0, 112.9) and 59.74 (45.7, 96.0), whereas levels after intervention were 102.05 (60.9, 182.1) and 105.02 (73.1, 203.7). CONCLUSIONS Although our study findings suggest that L-carnitine bears no additional effect on SAM, we recommend clinical trials with a longer duration of supplementation, possibly with other combinations of interventions, to investigate further into this topic of interest. This trial was registered at clinicaltrials.gov as NCT05083637.
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Affiliation(s)
- Jinat Alam
- Nutrition Research Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh.
| | - Shah Mohammad Fahim
- Nutrition Research Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Md Ridwan Islam
- Nutrition Research Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Md Ashraful Alam
- Nutrition Research Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh; Poche Centre for Indigenous Health, University of Queensland, Brisbane Qld, Australia
| | - Md Amran Gazi
- Nutrition Research Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- Nutrition Research Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh; Office of the Executive Director, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh; Department of Global Health, University of Washington, Seattle, WA, United States; Department of Public Health Nutrition, James P Grant School of Public Health, BRAC University, Dhaka, Bangladesh
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26
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Tarracchini C, Milani C, Lugli GA, Mancabelli L, Turroni F, van Sinderen D, Ventura M. The infant gut microbiota as the cornerstone for future gastrointestinal health. ADVANCES IN APPLIED MICROBIOLOGY 2024; 126:93-119. [PMID: 38637108 DOI: 10.1016/bs.aambs.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The early postnatal period represents a critical window of time for the establishment and maturation of the human gut microbiota. The gut microbiota undergoes dramatic developmental changes during the first year of life, being influenced by a variety of external factors, with diet being a major player. Indeed, the introduction of complementary feeding provides novel nutritive substrates and triggers a shift from milk-adapted gut microbiota toward an adult-like bacterial composition, which is characterized by an enhancement in diversity and proportions of fiber-degrading bacterial genera like Ruminococcus, Prevotella, Eubacterium, and Bacteroides genera. Inadequate gut microbiota development in early life is frequently associated with concomitant and future adverse health conditions. Thus, understanding the processes that govern initial colonization and establishment of microbes in the gastrointestinal tract is of great importance. This review summarizes the actual understanding of the assembly and development of the microbial community associated with the infant gut, emphasizing the importance of mother-to-infant vertical transmission events as a fundamental arrival route for the first colonizers.
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Affiliation(s)
- Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy.
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27
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Bakshani CR, Crouch LI. Human milk oligosaccharides and Bifidobacterium species. Trends Microbiol 2024; 32:118-119. [PMID: 38087708 DOI: 10.1016/j.tim.2023.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 02/09/2024]
Abstract
Several bacterial species initially colonise the infant gut, but are outcompeted. Human milk oligosaccharides (HMOs) in breast milk create an environment for Bifidobacterium to flourish. Laursen and Roager recently showed a clear link between breast milk and the dominance of Bifidobacterium longum subsp. infantis in the infant gut.
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Affiliation(s)
- Cassie R Bakshani
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Lucy I Crouch
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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28
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Li D, Chen Y, Wan M, Mei F, Wang F, Gu P, Zhang X, Wei R, Zeng Y, Zheng H, Chen B, Xiong Q, Xue T, Guan T, Guo J, Tian Y, Zeng LY, Liu Z, Yuan H, Yang L, Liu H, Dai L, Yu Y, Qiu Y, Wu P, Win S, Than TA, Wei R, Schnabl B, Kaplowitz N, Jiang Y, Ma Q, Chen P. Oral magnesium prevents acetaminophen-induced acute liver injury by modulating microbial metabolism. Cell Host Microbe 2024; 32:48-62.e9. [PMID: 38056458 DOI: 10.1016/j.chom.2023.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/10/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
Acetaminophen overuse is a common cause of acute liver failure (ALF). During ALF, toxins are metabolized by enzymes such as CYP2E1 and transformed into reactive species, leading to oxidative damage and liver failure. Here, we found that oral magnesium (Mg) alleviated acetaminophen-induced ALF through metabolic changes in gut microbiota that inhibit CYP2E1. The gut microbiota from Mg-supplemented humans prevented acetaminophen-induced ALF in mice. Mg exposure modulated Bifidobacterium metabolism and enriched indole-3-carboxylic acid (I3C) levels. Formate C-acetyltransferase (pflB) was identified as a key Bifidobacterium enzyme involved in I3C generation. Accordingly, a Bifidobacterium pflB knockout showed diminished I3C generation and reduced the beneficial effects of Mg. Conversely, treatment with I3C or an engineered bacteria overexpressing Bifidobacterium pflB protected against ALF. Mechanistically, I3C bound and inactivated CYP2E1, thus suppressing formation of harmful reactive intermediates and diminishing hepatocyte oxidative damage. These findings highlight how interactions between Mg and gut microbiota may help combat ALF.
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Affiliation(s)
- Dongping Li
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yu Chen
- Department of Gastroenterology, The Seventh Affiliated Hospital of Southern Medical University, Foshan 528244, China
| | - Meijuan Wan
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Fengyi Mei
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Fangzhao Wang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Peng Gu
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xianglong Zhang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Rongjuan Wei
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yunong Zeng
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hanzhao Zheng
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Bangguo Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qingquan Xiong
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tao Xue
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tianshan Guan
- Department of Gastroenterology, The Seventh Affiliated Hospital of Southern Medical University, Foshan 528244, China
| | - Jiayin Guo
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuanxin Tian
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Li-Yan Zeng
- School of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zhanguo Liu
- Department of Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Hang Yuan
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ling Yang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hongbin Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yao Yu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yifeng Qiu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Peng Wu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Sanda Win
- Research Center for Liver Disease, Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Tin Aung Than
- Research Center for Liver Disease, Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Riqing Wei
- Department of Biopharmaceutics, Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Bernd Schnabl
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA MC0063, USA
| | - Neil Kaplowitz
- Research Center for Liver Disease, Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Yong Jiang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Qiang Ma
- Department of Biopharmaceutics, Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
| | - Peng Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Department of Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
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29
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Zhou T, Xiao L, Zuo Z, Zhao F. MAMI: a comprehensive database of mother-infant microbiome and probiotic resources. Nucleic Acids Res 2024; 52:D738-D746. [PMID: 37819042 PMCID: PMC10767955 DOI: 10.1093/nar/gkad813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/04/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Extensive evidence has demonstrated that the human microbiome and probiotics confer great impacts on human health, particularly during critical developmental stages such as pregnancy and infancy when microbial communities undergo remarkable changes and maturation. However, a major challenge in understanding the microbial community structure and interactions between mothers and infants lies in the current lack of comprehensive microbiome databases specifically focused on maternal and infant health. To address this gap, we have developed an extensive database called MAMI (Microbiome Atlas of Mothers and Infants) that archives data on the maternal and neonatal microbiome, as well as abundant resources on edible probiotic strains. By leveraging this resource, we can gain profound insights into the dynamics of microbial communities, contributing to lifelong wellness for both mothers and infants through precise modulation of the developing microbiota. The functionalities incorporated into MAMI provide a unique perspective on the study of the mother-infant microbiome, which not only advance microbiome-based scientific research but also enhance clinical practice. MAMI is publicly available at https://bioinfo.biols.ac.cn/mami/.
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Affiliation(s)
- Tian Zhou
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Liwen Xiao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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30
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Hibberd MC, Webber DM, Rodionov DA, Henrissat S, Chen RY, Zhou C, Lynn HM, Wang Y, Chang HW, Lee EM, Lelwala-Guruge J, Kazanov MD, Arzamasov AA, Leyn SA, Lombard V, Terrapon N, Henrissat B, Castillo JJ, Couture G, Bacalzo NP, Chen Y, Lebrilla CB, Mostafa I, Das S, Mahfuz M, Barratt MJ, Osterman AL, Ahmed T, Gordon JI. Bioactive glycans in a microbiome-directed food for children with malnutrition. Nature 2024; 625:157-165. [PMID: 38093016 PMCID: PMC10764277 DOI: 10.1038/s41586-023-06838-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/06/2023] [Indexed: 12/26/2023]
Abstract
Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1-4. Here we analyse biospecimens from a randomized, controlled trial of a microbiome-directed complementary food (MDCF-2) that produced superior rates of weight gain compared with a calorically more dense conventional ready-to-use supplementary food in 12-18-month-old Bangladeshi children with moderate acute malnutrition4. We reconstructed 1,000 bacterial genomes (metagenome-assembled genomes (MAGs)) from the faecal microbiomes of trial participants, identified 75 MAGs of which the abundances were positively associated with ponderal growth (change in weight-for-length Z score (WLZ)), characterized changes in MAG gene expression as a function of treatment type and WLZ response, and quantified carbohydrate structures in MDCF-2 and faeces. The results reveal that two Prevotella copri MAGs that are positively associated with WLZ are the principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilizing the component glycans of MDCF-2. The predicted specificities of carbohydrate-active enzymes expressed by their polysaccharide-utilization loci are correlated with (1) the in vitro growth of Bangladeshi P. copri strains, possessing varying degrees of polysaccharide-utilization loci and genomic conservation with these MAGs, in defined medium containing different purified glycans representative of those in MDCF-2, and (2) the levels of faecal carbohydrate structures in the trial participants. These associations suggest that identifying bioactive glycan structures in MDCFs metabolized by growth-associated bacterial taxa will help to guide recommendations about their use in children with acute malnutrition and enable the development of additional formulations.
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Affiliation(s)
- Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Janaki Lelwala-Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Nikita P Bacalzo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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31
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Li L, Chen J, Sun H, Niu Q, Zhao Y, Yang X, Sun Q. Orm2 Deficiency Aggravates High-Fat Diet-Induced Obesity through Gut Microbial Dysbiosis and Intestinal Inflammation. Mol Nutr Food Res 2024; 68:e2300236. [PMID: 37853937 DOI: 10.1002/mnfr.202300236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/09/2023] [Indexed: 10/20/2023]
Abstract
SCOPE Orosomucoid 2 (Orm2) is a hepatocyte-secreted protein that plays a crucial role in regulating obesity-type metabolic disease and immunity. The imbalance of gut microbiota is one of the causes of obesity, but the mechanism of the relationship between Orm2 and gut microbiota in obesity remains unclear. METHODS AND RESULTS Orm2-/- (Orm2 knockout) mice on a normal diet developed spontaneous obesity and metabolic disturbances at the 20th week. Through 16S rRNA gene sequencing, the study finds that the gut microbiota of Orm2-/- mice has a different microbial composition compared to wild type (WT) mice. Furthermore, a high-fat diet (HFD) for 16 weeks exacerbates obesity in Orm2-/- mice. Lack of Orm2 promotes dysregulation of gut microbiota under the HFD, especially a reduction of Clostridium spp. Supplementation with Clostridium butyricum alleviates obesity and alters the gut microbial composition in WT mice, but has minimal effects on Orm2-/- mice. In contrast, co-housing of Orm2-/- mice with WT mice rescues Orm2-/- obesity by reducing pathogenic bacteria and mitigating intestinal inflammation. CONCLUSION These findings suggest Orm2 deficiency exacerbates HFD-induced gut microbiota disturbance and intestinal inflammation, providing a novel insight into the complex bacterial flora but not a single probiotic administration in the therapeutic strategy of obesity.
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Affiliation(s)
- Li Li
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jionghao Chen
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haoming Sun
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qiang Niu
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yan Zhao
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojun Yang
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qingzhu Sun
- Department of Animal Science, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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32
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Browne HP, Iqbal NT, Osman M, Tigoi C, Lawley TD, Gordon JI, Ahmed T, Kariuki S. Boosting microbiome science worldwide could save millions of children's lives. Nature 2024; 625:237-240. [PMID: 38191714 PMCID: PMC10810019 DOI: 10.1038/d41586-024-00017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Studies of the microbes living on and in our bodies are conducted mainly in a few rich countries, squandering opportunities to improve the health of people globally.
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33
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Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI. Prevotella copri-related effects of a therapeutic food for malnutrition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553030. [PMID: 37645712 PMCID: PMC10461977 DOI: 10.1101/2023.08.11.553030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Preclinical and clinical studies are providing evidence that the healthy growth of infants and children reflects, in part, healthy development of their gut microbiomes1-5. This process of microbial community assembly and functional maturation is perturbed in children with acute malnutrition. Gnotobiotic animals, colonized with microbial communities from children with severe and moderate acute malnutrition, have been used to develop microbiome-directed complementary food (MDCF) formulations for repairing the microbiomes of these children during the weaning period5. Bangladeshi children with moderate acute malnutrition (MAM) participating in a previously reported 3-month-long randomized controlled clinical study of one such formulation, MDCF-2, exhibited significantly improved weight gain compared to a commonly used nutritional intervention despite the lower caloric density of the MDCF6. Characterizing the 'metagenome assembled genomes' (MAGs) of bacterial strains present in the microbiomes of study participants revealed a significant correlation between accelerated ponderal growth and the expression by two Prevotella copri MAGs of metabolic pathways involved in processing of MDCF-2 glycans1. To provide a direct test of these relationships, we have now performed 'reverse translation' experiments using a gnotobiotic mouse model of mother-to-offspring microbiome transmission. Mice were colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains cultured from Bangladeshi infants/children in the study population, with or without P. copri isolates resembling the MAGs. By combining analyses of microbial community assembly, gene expression and processing of glycan constituents of MDCF-2 with single nucleus RNA-Seq and mass spectrometric analyses of the intestine, we establish a principal role for P. copri in mediating metabolism of MDCF-2 glycans, characterize its interactions with other consortium members including Bifidobacterium longum subsp. infantis, and demonstrate the effects of P. copri-containing consortia in mediating weight gain and modulating the activities of metabolic pathways involved in lipid, amino acid, carbohydrate plus other facets of energy metabolism within epithelial cells positioned at different locations in intestinal crypts and villi. Together, the results provide insights into structure/function relationships between MDCF-2 and members of the gut communities of malnourished children; they also have implications for developing future prebiotic, probiotic and/or synbiotic therapeutics for microbiome restoration in children with already manifest malnutrition, or who are at risk for this pervasive health challenge.
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Affiliation(s)
- Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Evan M. Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Kali M. Pruss
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Robert Y. Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Clara Kao
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Hannah M. Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Daniel M. Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Marie Crane
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Juan J. Castillo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Nikita P. Balcazo
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | | | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710 USA
| | - Michael J. Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
| | - Christopher B. Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27710 USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710 USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710 USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710 USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
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Capeding MRZ, Phee LCM, Ming C, Noti M, Vidal K, Le Carrou G, Frézal A, Moll JM, Vogt JK, Myers PN, Nielsen BH, Boulangé CL, Samuel TM, Berger B, Cercamondi CI. Safety, efficacy, and impact on gut microbial ecology of a Bifidobacterium longum subspecies infantis LMG11588 supplementation in healthy term infants: a randomized, double-blind, controlled trial in the Philippines. Front Nutr 2023; 10:1319873. [PMID: 38162520 PMCID: PMC10755859 DOI: 10.3389/fnut.2023.1319873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Bifidobacterium longum subspecies infantis (B. infantis) may play a key role in infant gut development. This trial evaluated safety, tolerability, and efficacy of B. infantis LMG11588 supplementation. Methods This randomized, placebo-controlled, double-blind study conducted in the Philippines included healthy breastfed and/or formula-fed infants (14-21 days old) randomized for 8 weeks to a control group (CG; n = 77), or any of two B. infantis experimental groups (EGs): low (Lo-EG; 1*108 CFU/day; n = 75) or high dose (Hi-EG; 1.8*1010 CFU/day; n = 76). Primary endpoint was weight gain; secondary endpoints included stooling patterns, gastrointestinal symptoms, adverse events, fecal microbiome, biomarkers, pH, and organic acids. Results Non-inferiority in weight gain was demonstrated for Hi-EG and Lo-EG vs. CG. Overall, probiotic supplementation promoted mushy-soft stools, fewer regurgitation episodes, and increased fecal acetate production, which was more pronounced in the exclusively breastfed infants (EBF) and positively correlated with B. infantis abundance. In EBF, fecal pro-inflammatory cytokines (IL-1 beta, IL-8) were reduced. Strain-level metagenomic analysis allowed attributing the increased abundance of B. infantis in EGs versus CG, to LMG11588 probiotic colonization. Colonization by autochthonous B. infantis strains was similar between groups. Discussion B. infantis LMG11588 supplementation was associated with normal infant growth, was safe and well-tolerated and promoted a Bifidobacterium-rich microbiota driven by B. infantis LMG11588 colonization without disturbing the natural dispersal of autochthonous B. infantis strains. In EBF, supplementation stimulated microbial metabolic activity and beneficially modulated enteric inflammation.
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Affiliation(s)
| | | | - Chang Ming
- Biostatistics & Data, Nestlé Research, Lausanne, Switzerland
| | - Mario Noti
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Karine Vidal
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Gilles Le Carrou
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - A. Frézal
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | | | | | | | - Claire L. Boulangé
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Tinu Mary Samuel
- Nestlé Product Technology Center – Nutrition, Société des Produits Nestlé S.A., Vevey, Switzerland
| | - Bernard Berger
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Colin Ivano Cercamondi
- Nestlé Product Technology Center – Nutrition, Société des Produits Nestlé S.A., Vevey, Switzerland
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Zhang C, Yu L, Ma C, Jiang S, Zhang Y, Wang S, Tian F, Xue Y, Zhao J, Zhang H, Liu L, Chen W, Huang S, Zhang J, Zhai Q. A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation. Cell Host Microbe 2023; 31:1989-2006.e8. [PMID: 37992712 DOI: 10.1016/j.chom.2023.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 09/01/2023] [Accepted: 10/11/2023] [Indexed: 11/24/2023]
Abstract
Impaired gastrointestinal motility is associated with gut dysbiosis. Probiotics, such as Bifidobacteria, can improve this bowel disorder; however, efficacy is strain-dependent. We determine that a genetic factor, the abfA cluster governing arabinan utilization, in Bifidobacterium longum impacts treatment efficacy against functional constipation (FC). In mice with FC, B. longum, but not an abfA mutant, improved gastrointestinal transit time, an affect that was dependent upon dietary arabinan. abfA genes were identified in other commensal bacteria, whose effects in ameliorating murine FC were similarly abfA-dependent. In a double-blind, randomized, placebo-controlled clinical trial, supplementation with abfA-cluster-carrying B. longum, but not an abfA-deficient strain, enriched arabinan-utilization residents, increased beneficial metabolites, and improved FC symptoms. Across human cohorts, abfA-cluster abundance can predict FC, and transplantation of abfA cluster-enriched human microbiota to FC-induced germ-free mice improved gut motility. Collectively, these findings demonstrate a role for microbial abfA cluster in ameliorating FC, establishing principles for genomics-directed probiotic therapies.
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Affiliation(s)
- Chengcheng Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Chenchen Ma
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, China
| | - Shuaiming Jiang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, China
| | - Yufeng Zhang
- Faculty of Dentistry, University of Hong Kong, Hong Kong SAR, China
| | - Shunhe Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuzheng Xue
- Department of Gastroenterology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shi Huang
- Faculty of Dentistry, University of Hong Kong, Hong Kong SAR, China.
| | - Jiachao Zhang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, China.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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36
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Doran BA, Chen RY, Giba H, Behera V, Barat B, Sundararajan A, Lin H, Sidebottom A, Pamer EG, Raman AS. An evolution-based framework for describing human gut bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569969. [PMID: 38105970 PMCID: PMC10723311 DOI: 10.1101/2023.12.04.569969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The human gut microbiome contains many bacterial strains of the same species ('strain-level variants'). Describing strains in a biologically meaningful way rather than purely taxonomically is an important goal but challenging due to the genetic complexity of strain-level variation. Here, we measured patterns of co-evolution across >7,000 strains spanning the bacterial tree-of-life. Using these patterns as a prior for studying hundreds of gut commensal strains that we isolated, sequenced, and metabolically profiled revealed widespread structure beneath the phylogenetic level of species. Defining strains by their co-evolutionary signatures enabled predicting their metabolic phenotypes and engineering consortia from strain genome content alone. Our findings demonstrate a biologically relevant organization to strain-level variation and motivate a new schema for describing bacterial strains based on their evolutionary history.
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Affiliation(s)
- Benjamin A. Doran
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637
| | - Robert Y. Chen
- Department of Psychiatry, University of Washington, Seattle, WA, 98195
| | - Hannah Giba
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637
- Department of Pathology, University of Chicago, Chicago, IL, 60637
| | - Vivek Behera
- Department of Medicine, University of Chicago, Chicago, IL, 60637
| | - Bidisha Barat
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637
| | | | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637
| | - Ashley Sidebottom
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637
| | - Eric G. Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637
- Department of Medicine, University of Chicago, Chicago, IL, 60637
| | - Arjun S. Raman
- Duchossois Family Institute, University of Chicago, Chicago, IL, 60637
- Department of Pathology, University of Chicago, Chicago, IL, 60637
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL, 60637
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37
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Ji J, Jin W, Liu S, Jiao Z, Li X. Probiotics, prebiotics, and postbiotics in health and disease. MedComm (Beijing) 2023; 4:e420. [PMID: 37929014 PMCID: PMC10625129 DOI: 10.1002/mco2.420] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023] Open
Abstract
The gut microbiota and its homeostasis play a crucial role in human health. However, for some diseases related to the gut microbiota, current traditional medicines can only relieve symptoms, and it is difficult to solve the root causes or even cause side effects like disturbances in the gut microbiota. Increasing clinical studies and evidences have demonstrated that probiotics, prebiotics, and postbiotics can prevent and treat various diseases, but currently they can only be used as dietary supplements rather than medicines, which restricts the application of probiotics in the field of medicine. Here, this review analyzes the importance of gut microbiota in human health and the current problems of traditional medicines, and systematically summarizes the effectiveness and mechanisms of probiotics, prebiotics, and postbiotics in maintaining health and treating diseases based on animal models and clinical trials. And based on current research outcomes and development trends in this field, the challenges and prospects of their clinical application in maintaining health, alleviating and treating diseases are analyzed. It is hoped to promote the application of probiotics, prebiotics, and postbiotics in disease treatment and open up new frontiers in probiotic research.
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Affiliation(s)
- Jing Ji
- MOE Key Laboratory of Cell Activities and Stress AdaptationsSchool of Life SciencesLanzhou UniversityLanzhouGansuChina
| | - Weilin Jin
- Institute of Cancer NeuroscienceMedical Frontier Innovation Research CenterThe First Hospital of Lanzhou UniversityThe First Clinical Medical College of Lanzhou UniversityLanzhouGansuChina
| | - Shuang‐Jiang Liu
- State Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Zuoyi Jiao
- Cuiying Biomedical Research CenterThe Second Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Xiangkai Li
- MOE Key Laboratory of Cell Activities and Stress AdaptationsSchool of Life SciencesLanzhou UniversityLanzhouGansuChina
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38
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Laursen MF, Roager HM. Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy. THE ISME JOURNAL 2023; 17:2452-2457. [PMID: 37816852 PMCID: PMC10689826 DOI: 10.1038/s41396-023-01525-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/12/2023]
Abstract
Despite the significant role of the gut microbiota in infant health and development, little is known about the ecological processes determining gut microbial community assembly. According to ecology theory, the timing and order of arrival of microbial species into an ecosystem affect microbial community assembly, a phenomenon termed priority effects. Bifidobacterium species are recognized as highly abundant early colonizers of the infant's gut, partly due to their ability to selectively utilize human milk oligosaccharides (HMOs) from breast milk. However, the role of priority effects in Bifidobacterium community assembly remains unclear. Here, we investigated the Bifidobacterium community assembly in the gut of 25 breastfed Danish infants longitudinally sampled throughout the first 6 months of life. Our results showed that the breastfed infants were often initially, but temporarily, dominated by suboptimal HMO-utilizing Bifidobacterium taxa, such as B. longum subsp. longum, before more efficient HMO-utilizers such as B. longum subsp. infantis, replaced the first colonizer as the dominant Bifidobacterium taxon. Subsequently, we validated this observation using gnotobiotic mice sequentially colonized with B. longum subsp. longum and B. longum subsp. infantis or vice versa, with or without supplementation of HMOs in the drinking water. The results showed that in the absence of HMOs, order of arrival determined dominance. Yet, when mice were supplemented with HMOs the strength of priority effects diminished, and B. longum subsp. infantis dominated regardless of colonization order. Our data demonstrate that the arrival order of Bifidobacterium taxa and the deterministic force of breast milk-derived HMOs, dictate Bifidobacterium community assembly in the infant's gut.
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Affiliation(s)
- Martin F Laursen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark.
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39
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Odenwald MA, Lin H, Lehmann C, Dylla NP, Cole CG, Mostad JD, Pappas TE, Ramaswamy R, Moran A, Hutchison AL, Stutz MR, Dela Cruz M, Adler E, Boissiere J, Khalid M, Cantoral J, Haro F, Oliveira RA, Waligurski E, Cotter TG, Light SH, Beavis KG, Sundararajan A, Sidebottom AM, Reddy KG, Paul S, Pillai A, Te HS, Rinella ME, Charlton MR, Pamer EG, Aronsohn AI. Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease. Nat Microbiol 2023; 8:2033-2049. [PMID: 37845315 PMCID: PMC11059310 DOI: 10.1038/s41564-023-01493-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/08/2023] [Indexed: 10/18/2023]
Abstract
Progression of chronic liver disease is precipitated by hepatocyte loss, inflammation and fibrosis. This process results in the loss of critical hepatic functions, increasing morbidity and the risk of infection. Medical interventions that treat complications of hepatic failure, including antibiotic administration for systemic infections and lactulose treatment for hepatic encephalopathy, can impact gut microbiome composition and metabolite production. Here, using shotgun metagenomic sequencing and targeted metabolomic analyses on 847 faecal samples from 262 patients with acute or chronic liver disease, we demonstrate that patients hospitalized for liver disease have reduced microbiome diversity and a paucity of bioactive metabolites, including short-chain fatty acids and bile acid derivatives, that impact immune defences and epithelial barrier integrity. We find that patients treated with the orally administered but non-absorbable disaccharide lactulose have increased densities of intestinal bifidobacteria and reduced incidence of systemic infections and mortality. Bifidobacteria metabolize lactulose, produce high concentrations of acetate and acidify the gut lumen in humans and mice, which, in combination, can reduce the growth of antibiotic-resistant bacteria such as vancomycin-resistant Enterococcus faecium in vitro. Our studies suggest that lactulose and bifidobacteria serve as a synbiotic to reduce rates of infection in patients with severe liver disease.
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Affiliation(s)
- Matthew A Odenwald
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA.
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Christopher Lehmann
- Department of Medicine, Section of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, USA
| | - Nicholas P Dylla
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Cody G Cole
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Jake D Mostad
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Téa E Pappas
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | - Angelica Moran
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Alan L Hutchison
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Matthew R Stutz
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Cook County Health, Chicago, IL, USA
| | - Mark Dela Cruz
- Section of Cardiology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Emerald Adler
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Jaye Boissiere
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Maryam Khalid
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Jackelyn Cantoral
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Fidel Haro
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Rita A Oliveira
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Thomas G Cotter
- Division of Digestive and Liver Diseases, UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel H Light
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | | | | | - K Gautham Reddy
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Sonali Paul
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Anjana Pillai
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Helen S Te
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Mary E Rinella
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Michael R Charlton
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Andrew I Aronsohn
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL, USA
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40
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Abstract
PURPOSE OF REVIEW In this review, we discuss recent research that has furthered our understanding of microbiome development during childhood, the role of the microbiome in infections during this life stage, and emerging opportunities for microbiome-based therapies for infection prevention or treatment in children. RECENT FINDINGS The microbiome is highly dynamic during childhood and shaped by a variety of host and environmental factors. In turn, the microbiome influences risk and severity of a broad range of infections during childhood, with recent studies highlighting potential roles in respiratory, gastrointestinal, and systemic infections. The microbiome exerts this influence through both direct interactions with potential pathogens and indirectly through modulation of host immune responses. The elucidation of some of these mechanisms by recent studies and the development of effective microbiome-based therapies for adults with recurrent Clostridioides difficile infection highlight the enormous promise that targeting the microbiome has for reducing the burden of infectious diseases during childhood. SUMMARY The microbiome has emerged as a key modifier of infection susceptibility and severity among children. Further research is needed to define the roles of microbes other than bacteria and to elucidate the mechanisms underlying microbiome-host and microbiome-pathogen interactions of importance to infectious diseases in children.
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Affiliation(s)
- Jillian H. Hurst
- Department of Pediatrics, Division of Infectious Diseases, Duke University School of Medicine, Durham, NC
- Duke Microbiome Center, Duke University School of Medicine, Durham, NC
| | - Sarah M. Heston
- Department of Pediatrics, Division of Infectious Diseases, Duke University School of Medicine, Durham, NC
- Duke Microbiome Center, Duke University School of Medicine, Durham, NC
| | - Matthew S. Kelly
- Department of Pediatrics, Division of Infectious Diseases, Duke University School of Medicine, Durham, NC
- Duke Microbiome Center, Duke University School of Medicine, Durham, NC
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Melsaether C, Høtoft D, Wellejus A, Hermes GDA, Damholt A. Seeding the Infant Gut in Early Life-Effects of Maternal and Infant Seeding with Probiotics on Strain Transfer, Microbiota, and Gastrointestinal Symptoms in Healthy Breastfed Infants. Nutrients 2023; 15:4000. [PMID: 37764787 PMCID: PMC10538230 DOI: 10.3390/nu15184000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
We investigated the effects of two dosing regimens of two multi-strain probiotic products on the gut microbiota of breastfed infants, including the transfer of the dosed strains and clinical outcomes. In forty-seven dyads, infants were either exposed through maternal intake (MS) of Lactobacillus acidophilus LA-5, Bifidobacterium animalis subsp. lactis BB-12, Lacticaseibacillus rhamnosus LGG, and Bifidobacterium longum subsp. infantis Bifin02 from gestational week thirty-three until four weeks after birth (n = 24) or dosed directly (IS) with the same strains except for LA-5 starting within 24 h after birth until day 28 (n = 23). Infant stool samples were collected on day 0, 14, 28, and 42 after birth. Gastrointestinal symptoms were assessed by parents using an electronic diary. Microbiota composition was determined using 16S rRNA sequencing, and strain recovery was analyzed by qPCR. Notably, 100% of the IS infants were colonized with Bifin02 after 14 days as opposed to only 25% of the MS infants. Mean stool frequency was significantly lower in IS infants compared to MS infants and IS infants had softer stools on day 14, 28, and 42. A significantly steeper slope of progression of inconsolable crying and fussing was observed in MS infants compared to IS infants. In conclusion, direct infant seeding induced a faster increase in fecal bifidobacteria abundancy and Bifin02 recovery compared to dosed through the maternal intake.
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Affiliation(s)
- Cathrine Melsaether
- Chr. Hansen A/S, Boege Alle 10-12, 2970 Hoersholm, Denmark; (A.W.); (G.D.A.H.); (A.D.)
| | - Diana Høtoft
- Department of Gynecology and Obstetrics, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark;
| | - Anja Wellejus
- Chr. Hansen A/S, Boege Alle 10-12, 2970 Hoersholm, Denmark; (A.W.); (G.D.A.H.); (A.D.)
| | - Gerben D. A. Hermes
- Chr. Hansen A/S, Boege Alle 10-12, 2970 Hoersholm, Denmark; (A.W.); (G.D.A.H.); (A.D.)
| | - Anders Damholt
- Chr. Hansen A/S, Boege Alle 10-12, 2970 Hoersholm, Denmark; (A.W.); (G.D.A.H.); (A.D.)
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42
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Odiase E, Frank DN, Young BE, Robertson CE, Kofonow JM, Davis KN, Berman LM, Krebs NF, Tang M. The Gut Microbiota Differ in Exclusively Breastfed and Formula-Fed United States Infants and are Associated with Growth Status. J Nutr 2023; 153:2612-2621. [PMID: 37506974 PMCID: PMC10517231 DOI: 10.1016/j.tjnut.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Evidence regarding the effects of infant feeding type (exclusive breastfeeding compared with exclusive formula feeding) on the gut microbiota and how it impacts infant growth status is limited. OBJECTIVES The primary objective was to compare gut microbiota by feeding type and characterize the associations between gut microbiota and infant growth status. METHODS Stool samples from healthy, full-term infants (4-5 mo-old) who were either exclusively breastfed (BF) or exclusively formula-fed (FF) in Denver, CO, United States were collected, and fecal 16S ribosomal ribonucleic acid gene-based profiling was conducted. Length and weight were measured at the time of stool collection. Length-for-age z-score, weight-for-age z-scores (WAZ), and weight-for-length z-scores were calculated based on the World Health Organization standards. Associations between gut microbial taxa and anthropometric z-scores were assessed by Spearman's rank correlation test. RESULTS A total of 115 infants (BF n = 54; FF n = 61) were included in this study. Feeding type (BF compared with FF) was the most significant tested variable on gut microbiota composition (P < 1 × 10-⁶), followed by mode of delivery and race. Significant differences were observed in α-diversity, β-diversity, and relative abundances of individual taxa between BF and FF. BF infants had lower α-diversity than FF infants. Abundances of Bifidobacterium and Lactobacillus were greater in the breastfeeding group. FF infants had a higher relative abundance of unclassified Ruminococcaceae (P < 0.001), which was associated with a higher WAZ (P < 0.001) and length-for-age z-score (P < 0.01). Lactobacillus was inversely associated with WAZ (P < 0.05). CONCLUSIONS Feeding type is the main driver of gut microbiota differences in young infants. The gut microbiota differences based on feeding type (exclusive breast- or formula feeding) were associated with observed differences in growth status. This trial was registered at clinicaltrials.gov as NCT02142647, NCT01693406, and NCT04137445.
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Affiliation(s)
- Eunice Odiase
- Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, University of Virginia, Charlottesville, VA, 22904, USA
| | - Daniel N Frank
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bridget E Young
- University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Charles E Robertson
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jennifer M Kofonow
- Division of Infectious Disease, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kathryn N Davis
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lillian M Berman
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nancy F Krebs
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Minghua Tang
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Ma Y, Liu X, Zhang X, Yu Y, Li Y, Song M, Wang J. Efficient Mining of Anticancer Peptides from Gut Metagenome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300107. [PMID: 37382183 PMCID: PMC10477861 DOI: 10.1002/advs.202300107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/03/2023] [Indexed: 06/30/2023]
Abstract
The gut microbiome plays a crucial role in modulating host health and disease. It serves as a vast reservoir of functional molecules that hold great potential for clinical applications. One specific area of interest is identifying anticancer peptides (ACPs) for innovative cancer therapies. However, ACPs discovery is hindered by a heavy reliance on experimental methodologies. To overcome this limitation, we here employed a novel approach by leveraging the overlap between ACPs and antimicrobial peptides (AMPs). By combining well-established AMP prediction methods with mining techniques in metagenomic cohorts, a total of 40 potential ACPs is identified. Out of the identified ACPs, 39 demonstrated inhibitory effects against at least one cancer cell line, exhibiting significant differences from known ACPs. Moreover, the therapeutic potential of the two most promising peptides in a mouse xenograft cancer model is evaluated. Encouragingly, the peptides exhibit effective tumor inhibition without any detectable toxic effects. Interestingly, both peptides display uncommon secondary structures, highlighting its distinctive characteristics. This findings highlight the efficacy of the multi-center mining approach, which effectively uncovers novel ACPs from the gut microbiome. This approach has significant implications for expanding treatment options not only for CRC, but also for other cancer types.
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Affiliation(s)
- Yue Ma
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of Sciences100101BeijingP. R. China
- University of Chinese Academy of SciencesBeijing100049P. R. China
- Max Planck Institute for Evolutionary Biology24306PlönGermany
| | - Xiaolin Liu
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of Sciences100101BeijingP. R. China
- University of Chinese Academy of SciencesBeijing100049P. R. China
- Max Planck Institute for Evolutionary Biology24306PlönGermany
| | - Xuan Zhang
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of Sciences100101BeijingP. R. China
| | - Ying Yu
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of Sciences100101BeijingP. R. China
| | - Yujing Li
- State Key Laboratory of Membrane BiologyInstitute of ZoologyChinese Academy of Sciences100101BeijingP. R. China
- Institute for Stem Cell and RegenerationChinese Academy of Sciences100101BeijingP. R. China
- Beijing Institute for Stem Cell and Regenerative Medicine100101BeijingP. R. China
| | - Moshi Song
- State Key Laboratory of Membrane BiologyInstitute of ZoologyChinese Academy of Sciences100101BeijingP. R. China
- Institute for Stem Cell and RegenerationChinese Academy of Sciences100101BeijingP. R. China
- Beijing Institute for Stem Cell and Regenerative Medicine100101BeijingP. R. China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of Sciences100101BeijingP. R. China
- University of Chinese Academy of SciencesBeijing100049P. R. China
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44
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Shiver AL, Sun J, Culver R, Violette A, Wynter C, Nieckarz M, Mattiello SP, Sekhon PK, Friess L, Carlson HK, Wong D, Higginbottom S, Weglarz M, Wang W, Knapp BD, Guiberson E, Sanchez J, Huang PH, Garcia PA, Buie CR, Good B, DeFelice B, Cava F, Scaria J, Sonnenburg J, Sinderen DV, Deutschbauer AM, Huang KC. A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555234. [PMID: 37693407 PMCID: PMC10491234 DOI: 10.1101/2023.08.29.555234] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Bifidobacteria commonly represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest as a probiotic therapy, predicting the nutritional requirements and health-promoting effects of Bifidobacteria is challenging due to major knowledge gaps. To overcome these deficiencies, we used large-scale genetics to create a compendium of mutant fitness in Bifidobacterium breve (Bb). We generated a high density, randomly barcoded transposon insertion pool in Bb, and used this pool to determine Bb fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. To enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1462 genes. We leveraged these tools to improve models of metabolic pathways, reveal unexpected host- and diet-specific requirements for colonization, and connect the production of immunomodulatory molecules to growth benefits. These resources will greatly reduce the barrier to future investigations of this important beneficial microbe.
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Affiliation(s)
- Anthony L. Shiver
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Rebecca Culver
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Arvie Violette
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Charles Wynter
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Marta Nieckarz
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Samara Paula Mattiello
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- College of Mathematics and Science, The University of Tennessee Southern, Pulaski TN 38478, USA
| | - Prabhjot Kaur Sekhon
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Lisa Friess
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Hans K. Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel Wong
- Department of Applied Physics, Stanford University, Stanford CA 94305, USA
| | - Steven Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Meredith Weglarz
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, California, USA
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, Stanford CA 94305, USA
| | | | - Emma Guiberson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Po-Hsun Huang
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Paulo A. Garcia
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Cullen R. Buie
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Benjamin Good
- Department of Applied Physics, Stanford University, Stanford CA 94305, USA
| | | | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Justin Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Douwe Van Sinderen
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
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Jones HJ, Bourke CD, Swann JR, Robertson RC. Malnourished Microbes: Host-Microbiome Interactions in Child Undernutrition. Annu Rev Nutr 2023; 43:327-353. [PMID: 37207356 DOI: 10.1146/annurev-nutr-061121-091234] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Childhood undernutrition is a major global health burden that is only partially resolved by nutritional interventions. Both chronic and acute forms of child undernutrition are characterized by derangements in multiple biological systems including metabolism, immunity, and endocrine systems. A growing body of evidence supports a role of the gut microbiome in mediating these pathways influencing early life growth. Observational studies report alterations in the gut microbiome of undernourished children, while preclinical studies suggest that this can trigger intestinal enteropathy, alter host metabolism, and disrupt immune-mediated resistance against enteropathogens, each of which contribute to poor early life growth. Here, we compile evidence from preclinical and clinical studies and describe the emerging pathophysiological pathways by which the early life gut microbiome influences host metabolism, immunity, intestinal function, endocrine regulation, and other pathways contributing to child undernutrition. We discuss emerging microbiome-directed therapies and consider future research directions to identify and target microbiome-sensitive pathways in child undernutrition.
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Affiliation(s)
- Helen J Jones
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
| | - Claire D Bourke
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
| | - Jonathan R Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ruairi C Robertson
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
- Microenvironment and Immunity Unit, INSERM U1224, Institut Pasteur, Université Paris Cité, Paris, France
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46
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Mancabelli L, Milani C, Fontana F, Liotto N, Tabasso C, Perrone M, Lugli GA, Tarracchini C, Alessandri G, Viappiani A, Bernasconi S, Roggero P, Mosca F, Turroni F, Ventura M. A pilot study to disentangle the infant gut microbiota composition and identification of bacteria correlates with high fat mass. MICROBIOME RESEARCH REPORTS 2023; 2:23. [PMID: 38046821 PMCID: PMC10688801 DOI: 10.20517/mrr.2023.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/28/2023] [Accepted: 06/13/2023] [Indexed: 12/05/2023]
Abstract
Background: At birth, the human intestine is colonized by a complex community of microorganisms known as gut microbiota. These complex microbial communities that inhabit the gut microbiota are thought to play a key role in maintaining host physiological homeostasis. For this reason, correct colonization of the gastrointestinal tract in the early stages of life could be fundamental for human health. Furthermore, alterations of the infant microbiota are correlated with the development of human inflammatory diseases and disorders. In this context, the possible relationships between intestinal microbiota and body composition during infancy are of great interest. Methods: In this study, we have performed a pilot study based on 16S rRNA gene profiling and metagenomic approaches on repeatedly measured data on time involving a cohort of 41 Italian newborns, which is aimed to investigate the possible correlation between body fat mass percentage (FM%) and the infant gut microbiota composition. Results and conclusion: The taxonomical analysis of the stool microbiota of each infant included in the cohort allowed the identification of a specific correlation between intestinal bacteria, such as Bifidobacterium and Veillonella, and the increase in FM%. Moreover, the analysis of the infant microbiome's metabolic capabilities suggested that the intestinal microbiome functionally impacts the human host and its possible influence on host physiology.
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Affiliation(s)
- Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma 43125, Italy
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, Parma 43124, Italy
| | - Christian Milani
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, Parma 43124, Italy
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Nadia Liotto
- NICU, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Chiara Tabasso
- NICU, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Michela Perrone
- NICU, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | | | - Sergio Bernasconi
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, Parma 43124, Italy
| | - Paola Roggero
- NICU, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Fabio Mosca
- NICU, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Francesca Turroni
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, Parma 43124, Italy
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Marco Ventura
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, Parma 43124, Italy
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
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Fontaine F, Turjeman S, Callens K, Koren O. The intersection of undernutrition, microbiome, and child development in the first years of life. Nat Commun 2023; 14:3554. [PMID: 37322020 PMCID: PMC10272168 DOI: 10.1038/s41467-023-39285-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
Undernutrition affects about one out of five children worldwide. It is associated with impaired growth, neurodevelopment deficits, and increased infectious morbidity and mortality. Undernutrition, however, cannot be solely attributed to a lack of food or nutrient deficiency but rather results from a complex mix of biological and environmental factors. Recent research has shown that the gut microbiome is intimately involved in the metabolism of dietary components, in growth, in the training of the immune system, and in healthy development. In this review, we look at these features in the first three years of life, which is a critical window for both microbiome establishment and maturation and child development. We also discuss the potential of the microbiome in undernutrition interventions, which could increase efficacy and improve child health outcomes.
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Affiliation(s)
- Fanette Fontaine
- Food and Agriculture Organization of the United Nations, Rome, Italy
- Université Paris- Cité, 75006, Paris, France
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Karel Callens
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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48
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Zhao G, Xie L, Wu Y, Wang B, Teng W, Sun Z, Kao Q, Liu W, Pi X, Ma H. Effects of urbanization and lifestyle habits on the intestinal microbiota of adolescents in eastern China. Front Microbiol 2023; 14:989303. [PMID: 37378282 PMCID: PMC10291051 DOI: 10.3389/fmicb.2023.989303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Introduction Owing to urbanization, living habits have changed widely, leading to alterations in the intestinal microbiota of urban residents. However, there are few studies on the characteristics of intestinal microbiota of adolescents living in different urbanized areas in China. Methods A total of 302 fecal samples collected from adolescent students in eastern China were examined. 16S rRNA high-throughput sequencing was used to identify the fecal microbiota. These data were combined with questionnaire survey results to investigate the effect of urbanization on the intestinal microbiota of adolescents in eastern China. Moreover, the role of lifestyle habits in this relationship was also evaluated. Results The results revealed significant differences in the structure of the intestinal microbiota among adolescents living in regions with different levels of urbanization. Adolescents living in urban regions had a significantly higher proportion of Bacteroides (p < 0.001, FDR = 0.004), whereas those living in towns and rural regions had higher proportions of Bifidobacterium (p < 0.001, FDR < 0.001) and Prevotella (p < 0.05, FDR = 0.019). The diversity of the intestinal microbiota was higher in urban residents than in adolescents living in towns and rural regions (p < 0.05). In addition, the differences in intestinal microbiota across individuals living in cities, towns, and rural regions were related to dietary preferences, flavor preferences, and sleep and exercise durations. Adolescents who ate more meat had more Dorea (LDA = 3.622, p = 0.04), while the abundance of Escherichia-Shigella is higher among adolescents who ate more condiments (LDA = 4.285, p = 0.02). The abundance of Dialister was significantly increased in adolescents with longer sleep durations (LDA = 4.066, p = 0.03). Adolescents who exercised for a long duration had more Faecalibacterium than those who exercised for a shorter duration (LDA = 4.303, p = 0.04). Discussion Our research has preliminarily demonstrated that there were differences in the composition of Gut microbiome in stool samples of adolescents living in different urbanized areas, and provide a scientific basis for the maintenance of a healthy intentional microbota in adolescences.
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Affiliation(s)
- Gang Zhao
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Lu Xie
- School of Public Health, Hangzhou Normal University, Hangzhou, China
| | - Yan Wu
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Bing Wang
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Weilin Teng
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Zhou Sun
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Qingjun Kao
- Department of Infectious Disease Control and Prevention, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Wei Liu
- Zhejiang Academy of Agriculture Sciences, Institute of Plant Protection and Microbiology, Hangzhou, China
| | - Xionge Pi
- Zhejiang Academy of Agriculture Sciences, Institute of Plant Protection and Microbiology, Hangzhou, China
| | - Haiyan Ma
- School of Public Health, Hangzhou Normal University, Hangzhou, China
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49
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Crouch LI. N-glycan breakdown by bacterial CAZymes. Essays Biochem 2023; 67:373-385. [PMID: 37067180 PMCID: PMC10154615 DOI: 10.1042/ebc20220256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 04/18/2023]
Abstract
The modification of proteins by N-glycans is ubiquitous to most organisms and they have multiple biological functions, including protecting the adjoining protein from degradation and facilitating communication or adhesion between cells, for example. Microbes have evolved CAZymes to deconstruct different types of N-glycans and some of these have been characterised from microbes originating from different niches, both commensals and pathogens. The specificity of these CAZymes provides clues as to how different microbes breakdown these substrates and possibly cross-feed them. Discovery of CAZymes highly specific for N-glycans also provides new tools and options for modifying glycoproteins.
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Affiliation(s)
- Lucy I Crouch
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, U.K
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50
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Holowka T, van Duin D, Bartelt LA. Impact of childhood malnutrition and intestinal microbiota on MDR infections. JAC Antimicrob Resist 2023; 5:dlad051. [PMID: 37102119 PMCID: PMC10125725 DOI: 10.1093/jacamr/dlad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
The global burden of infection from MDR organisms (MDROs) disproportionately affects children residing in low- and middle-income countries and those with increased healthcare exposure. These populations have high rates of malnutrition making them increasingly vulnerable to infection with intestinal-derived pathogens. Malnourished children experience increased incidence of intestinal carriage and invasive infection with intestinal-derived MDROs including ESBL- and carbapenemase-producing Enterobacterales. However, the relationship between malnutrition and MDRO infection remains to be clearly defined. Impairment in intestinal barrier function and innate and adaptive immunity in malnutrition increases the risk for infection with intestinal-derived pathogens, and there is an increasing appreciation of the role of the intestinal microbiota in this process. Current evidence from human studies and animal models suggests that diet and the intestinal microbiota influence each other to determine nutritional status, with important implications for infectious outcomes. These insights are crucial to developing microbiota-targeted strategies aimed at reversing the growing burden of MDRO infections in malnourished populations worldwide.
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Affiliation(s)
- Thomas Holowka
- Division of Infectious Diseases, Department of Medicine, University of North Carolina School of Medicine, 130 Mason Farm Rd, CB #7030, Chapel Hill, NC 27599, USA
| | - David van Duin
- Division of Infectious Diseases, Department of Medicine, University of North Carolina School of Medicine, 130 Mason Farm Rd, CB #7030, Chapel Hill, NC 27599, USA
| | - Luther A Bartelt
- Division of Infectious Diseases, Department of Medicine, University of North Carolina School of Medicine, 130 Mason Farm Rd, CB #7030, Chapel Hill, NC 27599, USA
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