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Román L, Melis-Arcos F, Pröschle T, Saa PA, Garrido D. Genome-scale metabolic modeling of the human milk oligosaccharide utilization by Bifidobacterium longum subsp. infantis. mSystems 2024; 9:e0071523. [PMID: 38363147 PMCID: PMC10949479 DOI: 10.1128/msystems.00715-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024] Open
Abstract
Bifidobacterium longum subsp. infantis is a representative and dominant species in the infant gut and is considered a beneficial microbe. This organism displays multiple adaptations to thrive in the infant gut, regarded as a model for human milk oligosaccharides (HMOs) utilization. These carbohydrates are abundant in breast milk and include different molecules based on lactose. They contain fucose, sialic acid, and N-acetylglucosamine. Bifidobacterium metabolism is complex, and a systems view of relevant metabolic pathways and exchange metabolites during HMO consumption is missing. To address this limitation, a refined genome-scale network reconstruction of this bacterium is presented using a previous reconstruction of B. infantis ATCC 15967 as a template. The latter was expanded based on an extensive revision of genome annotations, current literature, and transcriptomic data integration. The metabolic reconstruction (iLR578) accounted for 578 genes, 1,047 reactions, and 924 metabolites. Starting from this reconstruction, we built context-specific genome-scale metabolic models using RNA-seq data from cultures growing in lactose and three HMOs. The models revealed notable differences in HMO metabolism depending on the functional characteristics of the substrates. Particularly, fucosyl-lactose showed a divergent metabolism due to a fucose moiety. High yields of lactate and acetate were predicted under growth rate maximization in all conditions, whereas formate, ethanol, and 1,2-propanediol were substantially lower. Similar results were also obtained under near-optimal growth on each substrate when varying the empirically observed acetate-to-lactate production ratio. Model predictions displayed reasonable agreement between central carbon metabolism fluxes and expression data across all conditions. Flux coupling analysis revealed additional connections between succinate exchange and arginine and sulfate metabolism and a strong coupling between central carbon reactions and adenine metabolism. More importantly, specific networks of coupled reactions under each carbon source were derived and analyzed. Overall, the presented network reconstruction constitutes a valuable platform for probing the metabolism of this prominent infant gut bifidobacteria.IMPORTANCEThis work presents a detailed reconstruction of the metabolism of Bifidobacterium longum subsp. infantis, a prominent member of the infant gut microbiome, providing a systems view of its metabolism of human milk oligosaccharides.
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Affiliation(s)
- Loreto Román
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Melis-Arcos
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tomás Pröschle
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pedro A. Saa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Mathematical and Computational Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, Santiago, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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Lou YC, Chen L, Borges AL, West-Roberts J, Firek BA, Morowitz MJ, Banfield JF. Infant gut DNA bacteriophage strain persistence during the first 3 years of life. Cell Host Microbe 2024; 32:35-47.e6. [PMID: 38096814 DOI: 10.1016/j.chom.2023.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024]
Abstract
Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we establish a large phage sequence database and use strain-resolved analyses to investigate DNA phage succession in infants throughout the first 3 years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years and are more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment are more likely to persist than non-recoded phages and generally display an increase in in-frame reassigned stop codons over 3 years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.
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Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - LinXing Chen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94709, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob West-Roberts
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brian A Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA.
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Díaz R, Garrido D. Screening competition and cross-feeding interactions during utilization of human milk oligosaccharides by gut microbes. Microbiome Res Rep 2024; 3:12. [PMID: 38455082 PMCID: PMC10917614 DOI: 10.20517/mrr.2023.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 03/09/2024]
Abstract
Background: The infant gut microbiome is a complex community that influences short- and long-term health. Its assembly and composition are governed by variables such as the feeding type. Breast milk provides infants an important supply of human milk oligosaccharides (HMO), a broad family of carbohydrates comprising neutral, fucosylated, and sialylated molecules. There is a positive association between HMOs and the overrepresentation of Bifidobacterium species in the infant gut, which is sustained by multiple molecular determinants present in the genomes of these species. Infant-gut-associated Bifidobacterium species usually share a similar niche and display similar HMO inclinations, suggesting they compete for these resources. There is also strong evidence of cross-feeding interactions between HMO-derived molecules and bifidobacteria. Methods: In this study, we screened for unidirectional and bidirectional interactions between Bifidobacterium and other species using individual HMO. Bifidobacterium bifidum and Bacteroides thetaiotaomicron increased the growth of several other species when their supernatants were used, probably mediated by the partial degradation of HMO. In contrast, Bifidobacterium longum subsp. infantis. supernatants did not exhibit positive growth. Results: Bifidobacterium species compete for lacto-N-tetraose, which is associated with reduced bidirectional growth. The outcome of these interactions was HMO-dependent, in which the two species could compete for one substrate but cross-feed on another. 2'-fucosyllactose and lacto-N-neotetraose are associated with several positive interactions that generally originate from the partial degradation of these HMOs. Conclusion: This study presents evidence for complex interactions during HMO utilization, which can be cooperative or competitive, depending on the nature of the HMO. This information could be useful for understanding how breast milk supports the growth of some Bifidobacterium species, shaping the ecology of this important microbial community.
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Affiliation(s)
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Santiago 7820436, Chile
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Zhang A, de Ángel Solá D, Acevedo Flores M, Cao L, Wang L, Kim JG, Tarr PI, Warner BB, Rosario Matos N, Wang L. Infants exposed in utero to Hurricane Maria have gut microbiomes with reduced diversity and altered metabolic capacity. mSphere 2023; 8:e0013423. [PMID: 37754563 PMCID: PMC10597457 DOI: 10.1128/msphere.00134-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/10/2023] [Indexed: 09/28/2023] Open
Abstract
The gut microbiome is a potentially important mechanism that links prenatal disaster exposures with increased disease risks. However, whether prenatal disaster exposures are associated with alterations in the infant's gut microbiome remains unknown. We established a birth cohort study named Hurricane as the Origin of Later Alterations in Microbiome (HOLA) after Hurricane Maria struck Puerto Rico in 2017. We enrolled vaginally born Latino term infants aged 2 to 6 months, including n = 29 infants who were exposed in utero to Hurricane Maria in Puerto Rico and n = 34 infants who were conceived at least 5 months after the hurricane as controls. Shotgun metagenomic sequencing was performed on infant stool swabs. Infants exposed in utero to Hurricane Maria had a reduced diversity in their gut microbiome compared to the control infants, which was mainly seen in the exclusively formula-fed group (P = 0.02). Four bacterial species, including Bacteroides vulgatus, Clostridium innocuum, Bifidobacterium pseudocatenulatum, and Clostridium neonatale, were depleted in the exposure group compared to the control group. Compositional differences in the microbial community and metabolic genes between the exposure and control groups were significant, which were driven by the formula feeding group (P = 0.02 for the microbial community and P = 0.008 for the metabolic genes). Metabolic modules involved in carbohydrate metabolism were reduced in the exposure group. Prenatal maternal exposure to Hurricane Maria was associated with a reduced gut commensal and an altered microbial composition and metabolic potential in the offspring's gut. Breastfeeding can adjust the composition of the gut microbiomes of exposed infants. IMPORTANCE Climate change is a serious issue that is affecting human health. With more frequent and intense weather disasters due to climate change, there is an urgent need to evaluate and understand the impacts of prenatal disaster exposures on the offspring. The prenatal stage is a particularly vulnerable stage for disease origination. However, the impact of prenatal weather disaster exposures on the offspring's gut microbiome has not been evaluated. Our HOLA study starts to fill this knowledge gap and provides novel insights into the microbiome as a mechanism that links prenatal disaster exposures with elevated disease risks. Our major finding that reduced microbial diversity and altered metabolic capacity are associated with prenatal hurricane exposures warrants further studies to evaluate the impact of weather disasters on the unborn.
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Affiliation(s)
- Ai Zhang
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - David de Ángel Solá
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Midnela Acevedo Flores
- Department of Pediatrics and Obstetrics and Gynecology, San Juan City Hospital Research Unit, San Juan Hospital, San Juan, Puerto Rico
| | - Lijuan Cao
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Leran Wang
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Josh G. Kim
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Barbara B. Warner
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Nicolás Rosario Matos
- Department of Pediatrics and Obstetrics and Gynecology, San Juan City Hospital Research Unit, San Juan Hospital, San Juan, Puerto Rico
| | - Leyao Wang
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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Bakshi S, Paswan VK, Yadav SP, Bhinchhar BK, Kharkwal S, Rose H, Kanetkar P, Kumar V, Al-Zamani ZAS, Bunkar DS. A comprehensive review on infant formula: nutritional and functional constituents, recent trends in processing and its impact on infants' gut microbiota. Front Nutr 2023; 10:1194679. [PMID: 37415910 PMCID: PMC10320619 DOI: 10.3389/fnut.2023.1194679] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Human milk is considered the most valuable form of nutrition for infants for their growth, development and function. So far, there are still some cases where feeding human milk is not feasible. As a result, the market for infant formula is widely increasing, and formula feeding become an alternative or substitute for breastfeeding. The nutritional value of the formula can be improved by adding functional bioactive compounds like probiotics, prebiotics, human milk oligosaccharides, vitamins, minerals, taurine, inositol, osteopontin, lactoferrin, gangliosides, carnitine etc. For processing of infant formula, diverse thermal and non-thermal technologies have been employed. Infant formula can be either in powdered form, which requires reconstitution with water or in ready-to-feed liquid form, among which powder form is readily available, shelf-stable and vastly marketed. Infants' gut microbiota is a complex ecosystem and the nutrient composition of infant formula is recognized to have a lasting effect on it. Likewise, the gut microbiota establishment closely parallels with host immune development and growth. Therefore, it must be contemplated as an important factor for consideration while developing formulas. In this review, we have focused on the formulation and manufacturing of safe and nutritious infant formula equivalent to human milk or aligning with the infant's needs and its ultimate impact on infants' gut microbiota.
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Affiliation(s)
- Shiva Bakshi
- Department of Dairy Science and Food Technology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Vinod Kumar Paswan
- Department of Dairy Science and Food Technology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Satya Prakash Yadav
- Department of Dairy Science and Food Technology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Basant Kumar Bhinchhar
- Department of Livestock Production Management, Sri Karan Narendra Agriculture University, Jobner, India
| | - Sheela Kharkwal
- Department of Agriculture Economics, Sri Karan Narendra Agriculture University, Jobner, India
| | - Hency Rose
- Division of Dairy Technology, ICAR—National Dairy Research Institute, Karnal, India
| | - Prajasattak Kanetkar
- Department of Dairy Science and Food Technology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Vishal Kumar
- Department of Dairy Science and Food Technology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Zakarya Ali Saleh Al-Zamani
- Department of Dairy Science and Food Technology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
- Department of Food Technology and Science, Faculty of Agriculture and Veterinary Medicine, Ibb University, Ibb, Yemen
| | - Durga Shankar Bunkar
- Department of Dairy Science and Food Technology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
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Shankar A, Das DJ, Nayar S, Thomas S. Deciphering effect of maternal postpartum antibiotic prophylaxis on infant gut microbiome: a whole metagenomic analysis. Future Microbiol 2023. [PMID: 37204286 DOI: 10.2217/fmb-2022-0200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Aim: To analyze the impact of postpartum antibiotic (Ab) prophylaxis on the infant gut microbiome. Materials & methods: Whole metagenomic analysis was performed on breast milk and infant fecal samples collected from mother-infant pairs who belonged to two groups: an Ab group comprising mothers who had received a single course of Abs in the immediate postpartum period and a non-Ab group comprising mothers who had not received Abs. Results: The characteristic presence of Citrobacter werkmanii, an emerging multidrug-resistant uropathogen, and a higher relative abundance of genes encoding resistance to specific Abs were noted in samples from the Ab group compared with those from the non-Ab group. Conclusion: Policies regarding prophylactic Ab prescription across government and private health sectors in the postpartum period need to be strengthened.
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Affiliation(s)
- Aparna Shankar
- Department of Pathogen Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Devika J Das
- Department of Pathogen Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Seema Nayar
- Department of Microbiology, Government Medical College, Thiruvananthapuram, Kerala, 695011, India
| | - Sabu Thomas
- Department of Pathogen Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
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Rahman T, Sarwar PF, Potter C, Comstock SS, Klepac-Ceraj V. Role of human milk oligosaccharide metabolizing bacteria in the development of atopic dermatitis/eczema. Front Pediatr 2023; 11:1090048. [PMID: 37020647 PMCID: PMC10069630 DOI: 10.3389/fped.2023.1090048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/23/2023] [Indexed: 04/07/2023] Open
Abstract
Despite affecting up to 20% of infants in the United States, there is no cure for atopic dermatitis (AD), also known as eczema. Atopy usually manifests during the first six months of an infant's life and is one predictor of later allergic health problems. A diet of human milk may offer protection against developing atopic dermatitis. One milk component, human milk oligosaccharides (HMOs), plays an important role as a prebiotic in establishing the infant gut microbiome and has immunomodulatory effects on the infant immune system. The purpose of this review is to summarize the available information about bacterial members of the intestinal microbiota capable of metabolizing HMOs, the bacterial genes or metabolic products present in the intestinal tract during early life, and the relationship of these genes and metabolic products to the development of AD/eczema in infants. We find that specific HMO metabolism gene sets and the metabolites produced by HMO metabolizing bacteria may enable the protective role of human milk against the development of atopy because of interactions with the immune system. We also identify areas for additional research to further elucidate the relationship between the human milk metabolizing bacteria and atopy. Detailed metagenomic studies of the infant gut microbiota and its associated metabolomes are essential for characterizing the potential impact of human milk-feeding on the development of atopic dermatitis.
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Affiliation(s)
- Trisha Rahman
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Prioty F. Sarwar
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Cassie Potter
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Sarah S. Comstock
- Department of Food Science & Human Nutrition, Michigan State University, East Lansing, MI, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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Lagkouvardos I, Intze E, Schaubeck M, Rooney JP, Hecht C, Piloquet H, Clavel T. Early life gut microbiota profiles linked to synbiotic formula effects: a randomized clinical trial in European infants. Am J Clin Nutr 2023; 117:326-39. [PMID: 36811568 DOI: 10.1016/j.ajcnut.2022.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/05/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Microbial colonization of the gastrointestinal tract after birth is an essential event that influences infant health with life-long consequences. Therefore, it is important to investigate strategies to positively modulate colonization in early life. OBJECTIVES This randomized, controlled intervention study included 540 infants to investigate the effects of a synbiotic intervention formula (IF) containing Limosilactobacillus fermentum CECT5716 and galacto-oligosaccharides on the fecal microbiome. METHODS The fecal microbiota from infants was analyzed by 16S rRNA amplicon sequencing at 4, 12, and 24 months of age. Metabolites (e.g., short-chain fatty acids) and other milieu parameters (e.g., pH, humidity, and IgA) were also measured in stool samples. RESULTS Microbiota profiles changed with age, with major differences in diversity and composition. Significant effects of the synbiotic IF compared with control formula (CF) were visible at month 4, including higher occurrence of Bifidobacterium spp. and Lactobacillaceae and lower occurrence of Blautia spp., as well as Ruminoccocus gnavus and relatives. This was accompanied by lower fecal pH and concentrations of butyrate. After de novo clustering at 4 months of age, overall phylogenetic profiles of the infants receiving IF were closer to reference profiles of those fed with human milk than infants fed CF. The changes owing to IF were associated with fecal microbiota states characterized by lower occurrence of Bacteroides compared with higher levels of Firmicutes (valid name Bacillota), Proteobacteria (valid name Pseudomonadota), and Bifidobacterium at 4 months of age. These microbiota states were linked to higher prevalence of infants born by Cesarean section. CONCLUSIONS The synbiotic intervention influenced fecal microbiota and milieu parameters at an early age depending on the overall microbiota profiles of the infants, sharing a few similarities with breastfed infants. This trial was registered at clinicaltrials.gov as NCT02221687.
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Lundgren SN, Madan JC, Karagas MR, Morrison HG, Christensen BC, Hoen AG. Human milk-associated bacterial communities associate with the infant gut microbiome over the first year of life. Front Microbiol 2023; 14:1164553. [PMID: 37138613 PMCID: PMC10149717 DOI: 10.3389/fmicb.2023.1164553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction Microbial communities inhabiting the human infant gut are important for immune system development and lifelong health. One critical exposure affecting the bacterial colonization of the infant gut is consumption of human milk, which contains diverse microbial communities and prebiotics. We hypothesized that human milk-associated microbial profiles are associated with those of the infant gut. Methods Maternal-infant dyads enrolled in the New Hampshire Birth Cohort Study (n = 189 dyads) contributed breast milk and infant stool samples collected approximately at 6 weeks, 4 months, 6 months, 9 months, and 12 months postpartum (n = 572 samples). Microbial DNA was extracted from milk and stool and the V4-V5 region of the bacterial 16S rRNA gene was sequenced. Results Clustering analysis identified three breast milk microbiome types (BMTs), characterized by differences in Streptococcus, Staphylococcus, Pseudomonas, Acinetobacter, and microbial diversity. Four 6-week infant gut microbiome types (6wIGMTs) were identified, differing in abundances of Bifidobacterium, Bacteroides, Clostridium, Streptococcus, and Escherichia/Shigella, while two 12-month IGMTs (12mIGMTs) differed primarily by Bacteroides presence. At 6 weeks, BMT was associated with 6wIGMT (Fisher's exact test value of p = 0.039); this association was strongest among infants delivered by Cesarean section (Fisher's exact test value of p = 0.0028). The strongest correlations between overall breast milk and infant stool microbial community structures were observed when comparing breast milk samples to infant stool samples collected at a subsequent time point, e.g., the 6-week breast milk microbiome associated with the 6-month infant gut microbiome (Mantel test Z-statistic = 0.53, value of p = 0.001). Streptoccous and Veillonella species abundance were correlated in 6-week milk and infant stool, and 4- and 6-month milk Pantoea species were associated with infant stool Lachnospiraceae genera at 9 and 12 months. Discussion We identified clusters of human milk and infant stool microbial communities that were associated in maternal-infant dyads at 6 weeks of life and found that milk microbial communities were more strongly associated with infant gut microbial communities in infants delivered operatively and after a lag period. These results suggest that milk microbial communities have a long-term effect on the infant gut microbiome both through sharing of microbes and other molecular mechanisms.
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Affiliation(s)
- Sara N. Lundgren
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
| | - Juliette C. Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
- Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH, United States
- Department of Psychiatry, Children’s Hospital at Dartmouth, Lebanon, NH, United States
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
| | - Hilary G. Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
- *Correspondence: Brock C. Christensen,
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
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Vatanen T, Jabbar KS, Ruohtula T, Honkanen J, Avila-Pacheco J, Siljander H, Stražar M, Oikarinen S, Hyöty H, Ilonen J, Mitchell CM, Yassour M, Virtanen SM, Clish CB, Plichta DR, Vlamakis H, Knip M, Xavier RJ. Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism. Cell 2022; 185:4921-4936.e15. [PMID: 36563663 PMCID: PMC9869402 DOI: 10.1016/j.cell.2022.11.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular-but not extensively hydrolyzed-formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.
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Affiliation(s)
- Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - Terhi Ruohtula
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Jarno Honkanen
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
| | | | - Heli Siljander
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland; Centre for Military Medicine, Finnish Defence Forces, Riihimäki, Finland
| | - Martin Stražar
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sami Oikarinen
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Heikki Hyöty
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Caroline M Mitchell
- Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Moran Yassour
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel; The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suvi M Virtanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland; Center for Child Health Research and Development and Innovation Center, Tampere University Hospital, Tampere, Finland
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Damian R Plichta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA
| | - Mikael Knip
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; New Children's Hospital, Helsinki University Hospital, Helsinki, Finland; Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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11
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Ma J, Palmer DJ, Geddes D, Lai CT, Stinson L. Human Milk Microbiome and Microbiome-Related Products: Potential Modulators of Infant Growth. Nutrients 2022; 14. [PMID: 36501178 DOI: 10.3390/nu14235148] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Infant growth trajectory may influence later-life obesity. Human milk provides a wide range of nutritional and bioactive components that are vital for infant growth. Compared to formula-fed infants, breastfed infants are less likely to develop later-onset obesity, highlighting the potential role of bioactive components present in human milk. Components of particular interest are the human milk microbiota, human milk oligosaccharides (HMOs), short-chain fatty acids (SCFAs), and antimicrobial proteins, each of which influence the infant gut microbiome, which in turn has been associated with infant body composition. SCFAs and antimicrobial proteins from human milk may also systemically influence infant metabolism. Although inconsistent, multiple studies have reported associations between HMOs and infant growth, while studies on other bioactive components in relation to infant growth are sparse. Moreover, these microbiome-related components may interact with each other within the mammary gland. Here, we review the evidence around the impact of human milk microbes, HMOs, SCFAs, and antimicrobial proteins on infant growth. Breastfeeding is a unique window of opportunity to promote optimal infant growth, with aberrant growth trajectories potentially creating short- and long-term public health burdens. Therefore, it is important to understand how bioactive components of human milk influence infant growth.
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12
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Feng C, Tian L, Hong H, Wang Q, Zhan X, Luo Y, Tan Y. In Vitro Gut Fermentation of Whey Protein Hydrolysate: An Evaluation of Its Potential Modulation on Infant Gut Microbiome. Nutrients 2022; 14. [PMID: 35405988 DOI: 10.3390/nu14071374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 11/17/2022] Open
Abstract
Whey protein and its hydrolysate are ubiquitously consumed as nutritional supplements. This study aimed to evaluate the potential effect of whey protein hydrolysate (WPH) on the infant gut microbiome, which is more variable than that of adults. Colonic fermentation was simulated through a static digestion model and fecal culture fermentation, using feces from normal infants aged from 1−3 years old. During in vitro gut fermentation, measurements of short-chain fatty acids (SCFA) concentrations and 16S rRNA amplicon sequencing were performed. Additionally, the growth curves of cultivated probiotics were analyzed to evaluate the prebiotic potential of WPH. Besides the decline of pH in fermentation, the addition of WPH induced a significant increase in the SCFA production and also the relative abundance of Proteobacteria, Bacteroides, and Streptococcus (p < 0.05). The lower ratio of Firmicutes/Bacteroidetes in WPH-supplemented samples indicated the positive modulation of WPH on the gut microbiota, which could benefit the energy balance and metabolism of infants. The stimulation effect of WPH on the probiotics (particularly Lactobacillus acidophilus NCFM) during cultivation implied the prebiotic potential as well. Our findings shed light on WPH as a valuable dietary supplement with not only enriched resources of essential amino acids but also the potential to restore the infant gut microbiome.
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13
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Komatsu Y, Kumakura D, Seto N, Izumi H, Takeda Y, Ohnishi Y, Nakaoka S, Aizawa T. Dynamic Associations of Milk Components With the Infant Gut Microbiome and Fecal Metabolites in a Mother-Infant Model by Microbiome, NMR Metabolomic, and Time-Series Clustering Analyses. Front Nutr 2022; 8:813690. [PMID: 35071301 PMCID: PMC8780135 DOI: 10.3389/fnut.2021.813690] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background: The gut microbiome and fecal metabolites of breastfed infants changes during lactation, and are influenced by breast milk components. This study aimed to investigate dynamic associations of milk components with the infant gut microbiome and fecal metabolites throughout the lactation period in a mother–infant model. Methods: One month after delivery, breast milk and subsequent infant feces were collected in a pair for 5 months from a mother and an exclusively breastfed infant. Composition of the fecal microbiome was determined with 16S rRNA sequencing. Low-molecular-weight metabolites, including human milk oligosaccharides (HMOs), and antibacterial proteins were measured in feces and milk using 1H NMR metabolomics and enzyme-linked immunosorbent assays. The association of milk bioactive components with the infant gut microbiome and fecal metabolites was determined with Python clustering and correlation analyses. Results: The HMOs in milk did not fluctuate throughout the lactation period. However, they began to disappear in infant feces at the beginning of month 4. Notably, at this time-point, a bifidobacterium species switching (from B. breve to B. longum subsp. infantis) occurred, accompanied by fluctuations in several metabolites including acetate and butyrate in infant feces. Conclusions: Milk bioactive components, such as HMOs, might play different roles in the exclusively breastfed infants depending on the lactation period.
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Affiliation(s)
- Yosuke Komatsu
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Health Care and Nutritional Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Japan.,Center for Food and Medical Innovation Promotion, Institute for the Promotion of Business-Regional Collaboration of Hokkaido University, Sapporo, Japan
| | - Daiki Kumakura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Namiko Seto
- Health Care and Nutritional Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Japan
| | - Hirohisa Izumi
- Health Care and Nutritional Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Japan.,Center for Food and Medical Innovation Promotion, Institute for the Promotion of Business-Regional Collaboration of Hokkaido University, Sapporo, Japan
| | - Yasuhiro Takeda
- Health Care and Nutritional Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Japan.,Center for Food and Medical Innovation Promotion, Institute for the Promotion of Business-Regional Collaboration of Hokkaido University, Sapporo, Japan
| | - Yuki Ohnishi
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Department of Advanced Transdisciplinary Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Shinji Nakaoka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Department of Advanced Transdisciplinary Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Tomoyasu Aizawa
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Department of Advanced Transdisciplinary Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
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14
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Homann CM, Rossel CAJ, Dizzell S, Bervoets L, Simioni J, Li J, Gunn E, Surette MG, de Souza RJ, Mommers M, Hutton EK, Morrison KM, Penders J, van Best N, Stearns JC. Infants' First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts. Nutrients 2021; 13:nu13082639. [PMID: 34444798 PMCID: PMC8400337 DOI: 10.3390/nu13082639] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/11/2022] Open
Abstract
The introduction of solid foods is an important dietary event during infancy that causes profound shifts in the gut microbial composition towards a more adult-like state. Infant gut bacterial dynamics, especially in relation to nutritional intake remain understudied. Over 2 weeks surrounding the time of solid food introduction, the day-to-day dynamics in the gut microbiomes of 24 healthy, full-term infants from the Baby, Food & Mi and LucKi-Gut cohort studies were investigated in relation to their dietary intake. Microbial richness (observed species) and diversity (Shannon index) increased over time and were positively associated with dietary diversity. Microbial community structure (Bray–Curtis dissimilarity) was determined predominantly by individual and age (days). The extent of change in community structure in the introductory period was negatively associated with daily dietary diversity. High daily dietary diversity stabilized the gut microbiome. Bifidobacterial taxa were positively associated, while taxa of the genus Veillonella, that may be the same species, were negatively associated with dietary diversity in both cohorts. This study furthers our understanding of the impact of solid food introduction on gut microbiome development in early life. Dietary diversity seems to have the greatest impact on the gut microbiome as solids are introduced.
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Affiliation(s)
- Chiara-Maria Homann
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; (C.-M.H.); (S.D.); (M.G.S.)
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4K1, Canada; (E.G.); (K.M.M.)
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Connor A. J. Rossel
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands; (C.A.J.R.); (L.B.); (J.P.)
| | - Sara Dizzell
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; (C.-M.H.); (S.D.); (M.G.S.)
| | - Liene Bervoets
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands; (C.A.J.R.); (L.B.); (J.P.)
| | - Julia Simioni
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, ON L8S 4K1, Canada; (J.S.); (J.L.); (E.K.H.)
| | - Jenifer Li
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, ON L8S 4K1, Canada; (J.S.); (J.L.); (E.K.H.)
- McMaster Midwifery Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Elizabeth Gunn
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4K1, Canada; (E.G.); (K.M.M.)
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Michael G. Surette
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; (C.-M.H.); (S.D.); (M.G.S.)
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Russell J. de Souza
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, ON L8S 4K1, Canada;
- Population Health Research Institute, Hamilton Health Sciences Corporation, Hamilton, ON L8L 2X2, Canada
| | - Monique Mommers
- Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | - Eileen K. Hutton
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, ON L8S 4K1, Canada; (J.S.); (J.L.); (E.K.H.)
- McMaster Midwifery Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Katherine M. Morrison
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4K1, Canada; (E.G.); (K.M.M.)
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - John Penders
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands; (C.A.J.R.); (L.B.); (J.P.)
- InVivo Planetary Health: An Affiliate of the World Universities Network (WUN), West New York, NJ 10704, USA
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre, 6229 ER Maastricht, The Netherlands
| | - Niels van Best
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands; (C.A.J.R.); (L.B.); (J.P.)
- InVivo Planetary Health: An Affiliate of the World Universities Network (WUN), West New York, NJ 10704, USA
- Institute of Medical Microbiology, RWTH University Hospital Aachen, RWTH University, 52074 Aachen, Germany
- Correspondence: (N.v.B.); (J.C.S.)
| | - Jennifer C. Stearns
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; (C.-M.H.); (S.D.); (M.G.S.)
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada
- Correspondence: (N.v.B.); (J.C.S.)
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15
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Tarracchini C, Milani C, Lugli GA, Mancabelli L, Fontana F, Alessandri G, Longhi G, Anzalone R, Viappiani A, Turroni F, van Sinderen D, Ventura M. Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon. Microb Genom 2021; 7. [PMID: 34319225 PMCID: PMC8477406 DOI: 10.1099/mgen.0.000609] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Members of the Bifidobacterium longum species have been shown to possess adaptive abilities to allow colonization of different mammalian hosts, including humans, primates and domesticated mammalian species, such as dogs, horses, cattle and pigs. To date, three subspecies have formally been recognized to belong to this bifidobacterial taxon, i.e. B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. Although B. longum subsp. longum is widely distributed in the human gut irrespective of host age, B. longum subsp. infantis appears to play a significant role as a prominent member of the gut microbiota of breast-fed infants. Nevertheless, despite the considerable scientific relevance of these taxa and the vast body of genomic data now available, an accurate dissection of the genetic features that comprehensively characterize the B. longum species and its subspecies is still missing. In the current study, we employed 261 publicly available B. longum genome sequences, combined with those of 11 new isolates, to investigate genomic diversity of this taxon through comparative genomic and phylogenomic approaches. These analyses allowed us to highlight a remarkable intra-species genetic and physiological diversity. Notably, characterization of the genome content of members of B. longum subsp. infantis subspecies suggested that this taxon may have acquired genetic features for increased competitiveness in the gut environment of suckling hosts. Furthermore, specific B. longum subsp. infantis genomic features appear to be responsible for enhanced horizontal gene transfer (HGT) occurrences, underpinning an intriguing dedication toward acquisition of foreign DNA by HGT events.
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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.,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
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio Srl, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio Srl, Parma, Italy
| | | | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Ireland 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.,Microbiome Research Hub, University of Parma, Parma, Italy
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16
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Dimitratos SM, Brown H, Shafizadeh T, Kazi S, Altmann T, Ostrer B. Symptomatic relief from at-home use of activated Bifidobacterium infantis EVC001 probiotic in infants: results from a consumer survey on the effects on diaper rash, colic symptoms, and sleep. Benef Microbes 2021; 12:27-34. [PMID: 34057053 DOI: 10.3920/bm2020.0229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The gut microbiome during infancy is directly involved in the digestion of human milk, development of the immune system, and long-term health outcomes. Gut dysbiosis in early life has been linked to multiple short-term ailments, from diaper dermatitis and poor stooling habits, to poor sleep and fussiness, with mixed results in the scientific literature on the efficacy of probiotics for symptom resolution. Despite the growing interest in probiotics for consumer use, observed symptomatic relief is rarely documented. This study aims to evaluate observed symptomatic relief from at-home use of activated Bifidobacterium infantis EVC001 in infants. Consumer feedback was collected over a 2-year period via a 30-day post-purchase online survey of B. infantis EVC001 (Evivo®) customers. Outcome measures included observed changes in diaper rash, symptoms of colic, and sleep behaviours in infants fed B. infantis EVC001. A total of 1,621 respondents completed the survey. Before purchasing B. infantis EVC001, the majority of respondents visited the product website, researched infant probiotics online, or consulted with their doctor or other healthcare professional. Of the participants whose infants had ever experienced diaper rash, 72% (n=448) reported improvements, and 57% of those reported complete resolution of this problem. Of those who responded to questions about gassiness/fussiness, naptime sleep, and night-time sleep behaviours, 63% (n=984), 33% (n=520), and 52% (n=806) reported resolution or improvements, respectively. Although clinical data regarding probiotic use are often inconclusive for symptom resolution, home use of B. infantis EVC001 in infants improved diaper rash, gassiness/fussiness, and sleep quality within the first week of use in a significant number of respondents who engaged in a voluntary post-purchase survey. These outcomes may be a result of the unique genetic capacity of B. infantis EVC001 to colonise the infant gut highlighting the importance of strain selection in evaluating the effects of probiotic products.
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Affiliation(s)
- S M Dimitratos
- Department of Nutrition, University of California, Davis, Davis, CA 95616, USA
| | - H Brown
- Evolve BioSystems, Inc, Davis, CA 95618, USA
| | | | - S Kazi
- Evolve BioSystems, Inc, Davis, CA 95618, USA
| | - T Altmann
- Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.,Calabasas Pediatrics Wellness Center, Calabasas, CA 91302, USA
| | - B Ostrer
- Evolve BioSystems, Inc, Davis, CA 95618, USA
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17
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Fan HY, Tung YT, Yang YCSH, Hsu JB, Lee CY, Chang TH, Su ECY, Hsieh RH, Chen YC. Maternal Vegetable and Fruit Consumption during Pregnancy and Its Effects on Infant Gut Microbiome. Nutrients 2021; 13:1559. [PMID: 34063157 PMCID: PMC8148194 DOI: 10.3390/nu13051559] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/20/2022] Open
Abstract
Maternal nutrition intake during pregnancy may affect the mother-to-child transmission of bacteria, resulting in gut microflora changes in the offspring, with long-term health consequences in later life. Longitudinal human studies are lacking, as only a small amount of studies showing the effect of nutrition intake during pregnancy on the gut microbiome of infants have been performed, and these studies have been mainly conducted on animals. This pilot study explores the effects of high or low fruit and vegetable gestational intake on the infant microbiome. We enrolled pregnant women with a complete 3-day dietary record and received postpartum follow-up. The 16S rRNA gene sequence was used to characterize the infant gut microbiome at 2 months (n = 39). Principal coordinate analysis ordination revealed that the infant gut microbiome clustered differently for high and low maternal fruit and vegetable consumption (p < 0.001). The linear discriminant analysis effect size and feature selection identified 6 and 17 taxa from both the high and low fruit and vegetable consumption groups. Among the 23 abundant taxa, we observed that six maternal intake nutrients were associated with nine taxa (e.g., Erysipelatoclostridium, Isobaculum, Lachnospiraceae, Betaproteobacteria, Burkholderiaceae, Sutterella, Clostridia, Clostridiales, and Lachnoclostridium). The amount of gestational fruit and vegetable consumption is associated with distinct changes in the infant gut microbiome at 2 months of age. Therefore, strategies involving increased fruit and vegetable consumption during pregnancy should be employed for modifying the gut microbiome early in life.
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Affiliation(s)
- Hsien-Yu Fan
- Department of Family Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan;
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yu-Tang Tung
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan;
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Yu-Chen S. H. Yang
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei 110, Taiwan;
| | - Justin BoKai Hsu
- Department of Medical Research, Taipei Medical University Hospital, Taipei 110, Taiwan;
| | - Cheng-Yang Lee
- Office of Information Technology, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.L.); (T.-H.C.)
| | - Tzu-Hao Chang
- Office of Information Technology, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.L.); (T.-H.C.)
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan;
| | - Emily Chia-Yu Su
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan;
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Rong-Hong Hsieh
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan;
| | - Yang-Ching Chen
- Department of Family Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan;
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan;
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan;
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
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18
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Sindi AS, Geddes DT, Wlodek ME, Muhlhausler BS, Payne MS, Stinson LF. Can we modulate the breastfed infant gut microbiota through maternal diet? FEMS Microbiol Rev 2021; 45:6133472. [PMID: 33571360 DOI: 10.1093/femsre/fuab011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
Initial colonisation of the infant gut is robustly influenced by regular ingestion of human milk, a substance that contains microbes, microbial metabolites, immune proteins, and oligosaccharides. Numerous factors have been identified as potential determinants of the human milk and infant gut microbiota, including maternal diet; however, there is limited data on the influence of maternal diet during lactation on either of these. Here, we review the processes thought to contribute to human milk and infant gut bacterial colonisation and provide a basis for considering the role of maternal dietary patterns during lactation in shaping infant gut microbial composition and function. Although only one observational study has directly investigated the influence of maternal diet during lactation on the infant gut microbiome, data from animal studies suggests that modulation of the maternal gut microbiota, via diet or probiotics, may influence the mammary or milk microbiota. Additionally, evidence from human studies suggests that the maternal diet during pregnancy may affect the gut microbiota of the breastfed infant. Together, there is a plausible hypothesis that maternal diet during lactation may influence the infant gut microbiota. If substantiated in further studies, this may present a potential window of opportunity for modulating the infant gut microbiome in early life.
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Affiliation(s)
- Azhar S Sindi
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Western Australia, Australia.,College of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Donna T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Mary E Wlodek
- Department of Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Beverly S Muhlhausler
- CSIRO, Adelaide, South Australia, Australia.,School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew S Payne
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Western Australia, Australia
| | - Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
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19
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Mueller NT, Differding MK, Østbye T, Hoyo C, Benjamin-Neelon SE. Association of birth mode of delivery with infant faecal microbiota, potential pathobionts, and short chain fatty acids: a longitudinal study over the first year of life. BJOG 2021; 128:1293-1303. [PMID: 33338292 DOI: 10.1111/1471-0528.16633] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Caesarean section (CS) interrupts mother-to-newborn microbial transfer at birth. Beyond the neonatal period, the impact of CS on offspring gut microbiota and their short-chain fatty acids (SCFAs) remains unclear. Here, we examine birth delivery mode (CS versus vaginal delivery) with the infant gut microbiota and faecal SCFAs measured 3 and 12 months after birth. DESIGN Longitudinal study. SETTING North Carolina. POPULATION In 2013-15, we enrolled pregnant women and followed up their offspring for 12 months. We asked a subset of participants, enrolled over a 3-month period, to provide faecal samples at the 3- and 12-month follow-up visits. METHODS AND MAIN OUTCOMES We sequenced the 16S rRNA V4 region with Illumina MiSeq and quantified SCFA concentrations using gas chromatography. We examined delivery mode with differential abundance of microbiota amplicon sequence variants (ASVs) using beta-binomial regression and faecal SCFAs using linear regression. We adjusted models for confounders. RESULTS Of the 70 infants in our sample, 25 (36%) were delivered by CS. Compared with vaginal delivery, CS was associated with differential abundance of 14 infant bacterial ASVs at 3 months and 13 ASVs at 12 months (all FDR P < 0.05). Of note, CS infants had a higher abundance of the potential pathobionts Clostridium neonatale (P = 0.04) and Clostridium perfringens (P = 0.04) and a lower abundance of potentially beneficial Bifidobacterium and Bacteroides spp. (both P < 0.05) at 3 months. Other ASVs were differentially abundant at 12 months. Infants delivered by CS also had higher faecal butyrate concentration at 3 months (P < 0.005) but not at 12 months. CONCLUSIONS Caesarean section was associated with increased butyrate excretion, decreased Bifidobacterium and Bacteroides spp., and more colonisation of the infant gut by pathobionts at 3 months of age. CS was also associated with altered gut microbiota composition, but not faecal SCFAs, at 12 months. TWEETABLE ABSTRACT Caesarean section delivery was associated with increased butyrate excretion, decreased Bifidobacterium, and increased colonisation of the infant gut by pathobionts at 3 months of age.
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Affiliation(s)
- N T Mueller
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
| | - M K Differding
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - T Østbye
- Department of Family Medicine and Community Health, Duke University, Durham, NC, USA
| | - C Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - S E Benjamin-Neelon
- Department of Health, Behavior and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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20
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Grech A, Collins CE, Holmes A, Lal R, Duncanson K, Taylor R, Gordon A. Maternal exposures and the infant gut microbiome: a systematic review with meta-analysis. Gut Microbes 2021; 13:1-30. [PMID: 33978558 PMCID: PMC8276657 DOI: 10.1080/19490976.2021.1897210] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/12/2021] [Accepted: 02/22/2021] [Indexed: 02/04/2023] Open
Abstract
Early life, including the establishment of the intestinal microbiome, represents a critical window of growth and development. Postnatal factors affecting the microbiome, including mode of delivery, feeding type, and antibiotic exposure have been widely investigated, but questions remain regarding the influence of exposures in utero on infant gut microbiome assembly. This systematic review aimed to synthesize evidence on exposures before birth, which affect the early intestinal microbiome. Five databases were searched in August 2019 for studies exploring pre-pregnancy or pregnancy 'exposure' data in relation to the infant microbiome. Of 1,441 publications identified, 76 were included. Factors reported influencing microbiome composition and diversity included maternal antibiotic and probiotic uses, dietary intake, pre-pregnancy body mass index (BMI), gestational weight gain (GWG), diabetes, mood, and others. Eleven studies contributed to three meta-analyses quantifying associations between maternal intrapartum antibiotic exposure (IAP), BMI and GWG, and infant microbiome alpha diversity (Shannon Index). IAP, maternal overweight/obesity and excessive GWG were all associated with reduced diversity. Most studies were observational, few included early recruitment or longitudinal follow-up, and the timing, frequency, and methodologies related to stool sampling and analysis were variable. Standardization and collaboration are imperative to enhance understanding in this complex and rapidly evolving area.
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Affiliation(s)
- Allison Grech
- Central Clinical School, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales(NSW), Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia
| | - Clare E Collins
- School of Health Sciences, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Physical Activity and Nutrition, University of Newcastle, Callaghan, NSW, Australia
| | - Andrew Holmes
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Camperdown, NSW, Australia
| | - Ravin Lal
- Central Clinical School, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales(NSW), Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia
| | - Kerith Duncanson
- School of Health Sciences, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
| | - Rachael Taylor
- School of Health Sciences, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Physical Activity and Nutrition, University of Newcastle, Callaghan, NSW, Australia
| | - Adrienne Gordon
- Central Clinical School, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales(NSW), Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia
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21
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Babakobi MD, Reshef L, Gihaz S, Belgorodsky B, Fishman A, Bujanover Y, Gophna U. Effect of Maternal Diet and Milk Lipid Composition on the Infant Gut and Maternal Milk Microbiomes. Nutrients 2020; 12:E2539. [PMID: 32825705 DOI: 10.3390/nu12092539] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022] Open
Abstract
Inter-subject variability in human milk microbiome is well known; however, its origins and possible relationship to the mother’s diet are still debated. We investigated associations between maternal nutrition, milk fatty acids composition and microbiomes in mother–infant dyads. Breast milk and infant fecal samples were collected across three time points (one week, one month and three months postpartum) from 22 mother–infant pairs. Food frequency questionnaires for the months of pregnancy and three months postpartum were collected. Milk fatty acids were analyzed by GC–MS and the microbiome in breast milk and infant feces was determined by 16S rRNA sequencing. Statistical interactions were computed using Spearman’s method and corrected for multiple comparisons. We found significant negative correlation between Streptococcus relative abundance in maternal milk and intake of unsaturated fatty acids and folic acid at one month postpartum. At three months postpartum, vitamin B-12 consumption was significantly associated with a single operational taxonomic unit belonging to Streptococcus. Comparison between milk microbiome and lipid composition showed, one-month postpartum, significant negative correlation between Streptococcus relative abundance and the abundance of oleic acid. Additional correlations were detected between Staphylococcus hominis and two medium-chain saturated fatty acids. Our results reinforce the hypothesis that maternal nutrition may affect milk microbiome.
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22
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Ahlborn N, Young W, Mullaney J, Samuelsson LM. In Vitro Fermentation of Sheep and Cow Milk Using Infant Fecal Bacteria. Nutrients 2020; 12:E1802. [PMID: 32560419 PMCID: PMC7353214 DOI: 10.3390/nu12061802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 12/15/2022] Open
Abstract
While human milk is the optimal food for infants, formulas that contain ruminant milk can have an important role where breastfeeding is not possible. In this regard, cow milk is most commonly used. However, recent years have brought interest in other ruminant milk. While many similarities exist between ruminant milk, there are likely enough compositional differences to promote different effects in the infant. This may include effects on different bacteria in the large bowel, leading to different metabolites in the gut. In this study sheep and cow milk were digested using an in vitro infant digestive model, followed by fecal fermentation using cultures inoculated with fecal material from two infants of one month and five months of age. The effects of the cow and sheep milk on the fecal microbiota, short-chain fatty acids (SCFA), and other metabolites were investigated. Significant differences in microbial, SCFA, and metabolite composition were observed between fermentation of sheep and cow milk using fecal inoculum from a one-month-old infant, but comparatively minimal differences using fecal inoculum from a five-month-old infant. These results show that sheep milk and cow milk can have differential effects on the gut microbiota, while demonstrating the individuality of the gut microbiome.
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Affiliation(s)
- Natalie Ahlborn
- AgResearch Ltd., Grasslands Research Centre, Palmerston North 4442, New Zealand; (N.A.); (W.Y.); (J.M.)
- Faculty of Life Sciences, Rhine-Waal University of Applied Sciences, 47533 Kleve, Germany
| | - Wayne Young
- AgResearch Ltd., Grasslands Research Centre, Palmerston North 4442, New Zealand; (N.A.); (W.Y.); (J.M.)
- Riddet Institute, Massey University, Palmerston North 4474, New Zealand
- High Value Nutrition, National Science Challenges, The Liggins Institute at the University of Auckland, Auckland 1010, New Zealand
| | - Jane Mullaney
- AgResearch Ltd., Grasslands Research Centre, Palmerston North 4442, New Zealand; (N.A.); (W.Y.); (J.M.)
- Riddet Institute, Massey University, Palmerston North 4474, New Zealand
- High Value Nutrition, National Science Challenges, The Liggins Institute at the University of Auckland, Auckland 1010, New Zealand
| | - Linda M. Samuelsson
- AgResearch Ltd., Grasslands Research Centre, Palmerston North 4442, New Zealand; (N.A.); (W.Y.); (J.M.)
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23
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Wang Z, Neupane A, Vo R, White J, Wang X, Marzano SYL. Comparing Gut Microbiome in Mothers' Own Breast Milk- and Formula-Fed Moderate-Late Preterm Infants. Front Microbiol 2020; 11:891. [PMID: 32528425 PMCID: PMC7264382 DOI: 10.3389/fmicb.2020.00891] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/16/2020] [Indexed: 12/26/2022] Open
Abstract
Gut microbiome plays an important role in adult human health and diseases. However, how nutritional factors shape the initial colonization of gut bacteria in infants, especially in preterm infants, is still not completely known. In this study, we compared the effects of feeding with mothers' own breast milk (MBM) and formula on the initial composition and gene expression of gut bacteria in moderate-late preterm infants. Fecal samples were collected from ten formula-fed and ten MBM healthy infants born between 32 and 37 weeks' gestation after they reached full-volume enteral feedings. Total DNAs were extracted from fecal samples for amplicon sequencing of 16S ribosomal RNA (rRNA) gene and total RNA with rRNA depletion for metatranscriptome RNA-Seq 16S rRNA gene amplicon sequencing results showed that the alpha-diversity was similar between the MBM- and formula-fed preterm infants, but the beta-diversity showed a significant difference in composition (p = 0.002). The most abundant taxa were Veillonella (18.4%) and Escherichia/Shigella (15.2%) in MBM infants, whereas the most abundant taxa of formula-fed infants were Streptococcus (18.6%) and Klebsiella (17.4%). The genera Propionibacterium, Streptococcus, and Finegoldia and order Clostridiales had significantly higher relative abundance in the MBM group than the formula group, whereas bacteria under family Enterobacteriaceae, genera Enterococcus and Veillonella, and class Bacilli were more abundant in the formula group. In general, microbiomes from both diet groups exhibited high functional levels of catalytic activity and metabolic processing when analyzed for gene ontology using a comparative metatranscriptome approach. Statistically, the microbial genes in the MBM group had an upregulation in expression related to glycine reductase, periplasmic acid stress response in Enterobacteria, acid resistance mechanisms, and L-fucose utilization. In contrast, the formula-fed group had upregulations in genes associated with methionine and valine degradation functions. Our data suggest that the nutritional source plays a role in shaping the moderate-late preterm gut microbiome as evidenced by the differences in bacterial composition and gene expression profiles in the fecal samples. The MBM group enriched Propionibacterium. Glycine reductase was highly upregulated in the microbiota from MBM along with the upregulated acid stress tolerance genes, suggesting that the intensity of fermentation process was enhanced.
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Affiliation(s)
- Ziyi Wang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Richard Vo
- Department of Pediatrics, Sanford Children’s Hospital, Sanford USD Medical Center, Sioux Falls, SD, United States
- Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
| | - Jessica White
- Department of Pediatrics, Sanford Children’s Hospital, Sanford USD Medical Center, Sioux Falls, SD, United States
- Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
| | - Xiuqing Wang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Shin-Yi Lee Marzano
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
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24
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Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C, Wilmes P. Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life. Front Microbiol 2017; 8:738. [PMID: 28512451 PMCID: PMC5411419 DOI: 10.3389/fmicb.2017.00738] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/10/2017] [Indexed: 12/26/2022] Open
Abstract
Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.
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Affiliation(s)
- Linda Wampach
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Angela Hogan
- Integrated BioBank of LuxembourgLuxembourg, Luxembourg
| | - Emilie E L Muller
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Luisa W Hugerth
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of TechnologyStockholm, Sweden
| | - Lutz Bindl
- Centre Hospitalier de LuxembourgLuxembourg, Luxembourg
| | - Jean Bottu
- Centre Hospitalier de LuxembourgLuxembourg, Luxembourg
| | - Anders F Andersson
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of TechnologyStockholm, Sweden
| | - Carine de Beaufort
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg.,Centre Hospitalier de LuxembourgLuxembourg, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
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25
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Thompson AL, Monteagudo-Mera A, Cadenas MB, Lampl ML, Azcarate-Peril MA. Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome. Front Cell Infect Microbiol 2015; 5:3. [PMID: 25705611 PMCID: PMC4318912 DOI: 10.3389/fcimb.2015.00003] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/05/2015] [Indexed: 01/14/2023] Open
Abstract
The development of the infant intestinal microbiome in response to dietary and other exposures may shape long-term metabolic and immune function. We examined differences in the community structure and function of the intestinal microbiome between four feeding groups, exclusively breastfed infants before introduction of solid foods (EBF), non-exclusively breastfed infants before introduction of solid foods (non-EBF), EBF infants after introduction of solid foods (EBF+S), and non-EBF infants after introduction of solid foods (non-EBF+S), and tested whether out-of-home daycare attendance was associated with differences in relative abundance of gut bacteria. Bacterial 16S rRNA amplicon sequencing was performed on 49 stool samples collected longitudinally from a cohort of 9 infants (5 male, 4 female). PICRUSt metabolic inference analysis was used to identify metabolic impacts of feeding practices on the infant gut microbiome. Sequencing data identified significant differences across groups defined by feeding and daycare attendance. Non-EBF and daycare-attending infants had higher diversity and species richness than EBF and non-daycare attending infants. The gut microbiome of EBF infants showed increased proportions of Bifidobacterium and lower abundance of Bacteroidetes and Clostridiales than non-EBF infants. PICRUSt analysis indicated that introduction of solid foods had a marginal impact on the microbiome of EBF infants (24 enzymes overrepresented in EBF+S infants). In contrast, over 200 bacterial gene categories were overrepresented in non-EBF+S compared to non-EBF infants including several bacterial methyl-accepting chemotaxis proteins (MCP) involved in signal transduction. The identified differences between EBF and non-EBF infants suggest that breast milk may provide the gut microbiome with a greater plasticity (despite having a lower phylogenetic diversity) that eases the transition into solid foods.
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Affiliation(s)
- Amanda L. Thompson
- Department of Anthropology, University of North CarolinaChapel Hill, NC, USA
| | - Andrea Monteagudo-Mera
- Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North CarolinaChapel Hill, NC, USA
| | - Maria B. Cadenas
- Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North CarolinaChapel Hill, NC, USA
| | - Michelle L. Lampl
- Department of Anthropology and Center for the Study of Human Health, Emory UniversityAtlanta, GA, USA
| | - M. A. Azcarate-Peril
- Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North CarolinaChapel Hill, NC, USA
- Department of Cell Biology and Physiology, School of Medicine, University of North CarolinaChapel Hill, NC, USA
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