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Wilde J, Slack E, Foster KR. Host control of the microbiome: Mechanisms, evolution, and disease. Science 2024; 385:eadi3338. [PMID: 39024451 DOI: 10.1126/science.adi3338] [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: 04/19/2023] [Accepted: 05/29/2024] [Indexed: 07/20/2024]
Abstract
Many species, including humans, host communities of symbiotic microbes. There is a vast literature on the ways these microbiomes affect hosts, but here we argue for an increased focus on how hosts affect their microbiomes. Hosts exert control over their symbionts through diverse mechanisms, including immunity, barrier function, physiological homeostasis, and transit. These mechanisms enable hosts to shape the ecology and evolution of microbiomes and generate natural selection for microbial traits that benefit the host. Our microbiomes result from a perpetual tension between host control and symbiont evolution, and we can leverage the host's evolved abilities to regulate the microbiota to prevent and treat disease. The study of host control will be central to our ability to both understand and manipulate microbiotas for better health.
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Affiliation(s)
- Jacob Wilde
- Department of Biology, University of Oxford, Oxford, UK
| | - Emma Slack
- Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Basel Institute for Child Health, Basel, Switzerland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
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Cohen A, Turjeman S, Levin R, Tal S, Koren O. Comparison of canine colostrum and milk using a multi-omics approach. Anim Microbiome 2024; 6:19. [PMID: 38650014 PMCID: PMC11034113 DOI: 10.1186/s42523-024-00309-4] [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: 09/04/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND A mother's milk is considered the gold standard of nutrition in neonates and is a source of cytokines, immunoglobulins, growth factors, and other important components, yet little is known about the components of canine milk, specifically colostrum, and the knowledge related to its microbial and metabolic profiles is particularly underwhelming. In this study, we characterized canine colostrum and milk microbiota and metabolome for several breeds of dogs and examined profile shifts as milk matures in the first 8 days post-whelping. RESULTS Through untargeted metabolomics, we identified 63 named metabolites that were significantly differentially abundant between days 1 and 8 of lactation. Surprisingly, the microbial compositions of the colostrum and milk, characterized using 16S rRNA gene sequencing, were largely similar, with only two differentiating genera. The shifts observed, mainly increases in several sugars and amino sugars over time and shifts in amino acid metabolites, align with shifts observed in human milk samples and track with puppy development. CONCLUSION Like human milk, canine milk composition is dynamic, and shifts are well correlated with developing puppies' needs. Such a study of the metabolic profile of canine milk, and its relation to the microbial community, provides insights into the changing needs of the neonate, as well as the ideal nutrition profile for optimal functionality. This information will add to the existing knowledge base of canine milk composition with the prospect of creating a quality, tailored milk substitute or supplement for puppies.
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Affiliation(s)
- Alisa Cohen
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Rachel Levin
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Smadar Tal
- Koret School of Veterinary Medicine, The Hebrew University Veterinary Teaching Hospital, Hebrew University of Jerusalem, Rehovot, Israel
- Tel-Hai Academic College, Upper Galilee, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
- Kyung Hee University, Seoul, the Republic of Korea.
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Li S, You X, Rani A, Özcan E, Sela DA. Bifidobacterium infantis utilizes N-acetylglucosamine-containing human milk oligosaccharides as a nitrogen source. Gut Microbes 2023; 15:2244721. [PMID: 37609905 PMCID: PMC10448974 DOI: 10.1080/19490976.2023.2244721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023] Open
Abstract
Bifidobacterium longum subsp. infantis (B. infantis) utilizes oligosaccharides secreted in human milk as a carbohydrate source. These human milk oligosaccharides (HMOs) integrate the nitrogenous residue N-acetylglucosamine (NAG), although HMO nitrogen utilization has not been described to date. Herein, we characterize the B. infantis nitrogen utilization phenotype on two NAG-containing HMO species, LNT and LNnT. This was characterized through in vitro growth kinetics, incorporation of isotopically labeled NAG nitrogen into the proteome, as well as modulation of intracellular 2-oxoglutarate levels while utilizing HMO nitrogen. Further support is provided by comparative transcriptomics and proteomics that identified global regulatory networks deployed during HMO nitrogen utilization. The aggregate data demonstrate that B. infantis strains utilize HMO nitrogen with the potential to significantly impact fundamental and clinical studies, as well as enable applications.
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Affiliation(s)
- Shuqi Li
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Xiaomeng You
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Asha Rani
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Ezgi Özcan
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - David A. Sela
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
- Department of Nutrition, University of Massachusetts Amherst, Amherst, MA, USA
- Department of Microbiology & Physiological Systems and Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA
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Ingribelli E, Modrackova N, Tejnecky V, Killer J, Schwab C, Neuzil-Bunesova V. Culture-dependent screening of endospore-forming clostridia in infant feces. BMC Microbiol 2023; 23:347. [PMID: 37978420 PMCID: PMC10655253 DOI: 10.1186/s12866-023-03104-4] [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: 03/09/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Only a few studies dealt with the occurrence of endospore-forming clostridia in the microbiota of infants without obvious health complications. METHODS A methodology pipeline was developed to determine the occurrence of endospore formers in infant feces. Twenty-four fecal samples (FS) were collected from one infant in monthly intervals and were subjected to variable chemical and heat treatment in combination with culture-dependent analysis. Isolates were identified by MALDI-TOF mass spectrometry, 16S rRNA gene sequencing, and characterized with biochemical assays. RESULTS More than 800 isolates were obtained, and a total of 21 Eubacteriales taxa belonging to the Clostridiaceae, Lachnospiraceae, Oscillospiraceae, and Peptostreptococcaceae families were detected. Clostridium perfringens, C. paraputrificum, C. tertium, C. symbiosum, C. butyricum, and C. ramosum were the most frequently identified species compared to the rarely detected Enterocloster bolteae, C. baratii, and C. jeddahense. Furthermore, the methodology enabled the subsequent cultivation of less frequently detectable gut taxa such as Flavonifractor plautii, Intestinibacter bartlettii, Eisenbergiella tayi, and Eubacterium tenue. The isolates showed phenotypic variability regarding enzymatic activity, fermentation profiles, and butyrate production. CONCLUSIONS Taken together, this approach suggests and challenges a cultivation-based pipeline that allows the investigation of the population of endospore formers in complex ecosystems such as the human gastrointestinal tract.
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Affiliation(s)
- Eugenio Ingribelli
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Prague, Czechia
| | - Nikol Modrackova
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Prague, Czechia
| | - Vaclav Tejnecky
- Department of Soil Science and Soil Protection, Czech University of Life Sciences Prague, Prague, Czechia
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Prague, Czechia
- Institute of Animal Physiology and Genetics v.v.i, the Czech Academy of Sciences, Prague, Czechia
| | - Clarissa Schwab
- Biological and Chemical Engineering, Aarhus University, Aarhus C, Denmark
| | - Vera Neuzil-Bunesova
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Prague, Czechia.
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Charton E, Henry G, Cahu A, Le Gouar Y, Dahirel P, Moughan PJ, Montoya CA, Bellanger A, Dupont D, Le Huërou-Luron I, Deglaire A. Ileal Digestibility of Nitrogen and Amino Acids in Human Milk and an Infant Formula as Determined in Neonatal Minipiglets. J Nutr 2023; 153:1063-1074. [PMID: 36868512 DOI: 10.1016/j.tjnut.2023.02.025] [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: 11/11/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Infant formula (IF) has to provide at least the same amount of amino acids (AAs) as human milk (HM). AA digestibility in HM and IF was not studied extensively, with no data available for tryptophan digestibility. OBJECTIVES The present study aimed to measure the true ileal digestibility (TID) of total nitrogen and AAs in HM and IF to estimate AA bioavailability using Yucatan mini-piglets as an infant model. METHODS Twenty-four 19-day-old piglets (males and females) received either HM or IF for 6 days or a protein-free diet for 3 days, with cobalt-EDTA as an indigestible marker. Diets were fed hourly over 6 h before euthanasia and digesta collection. Total N, AA, and marker contents in diets and digesta were measured to determine the TID. Unidimensional statistical analyses were conducted. RESULTS Dietary N content was not different between HM and IF, while true protein was lower in HM (-4 g/L) due to a 7-fold higher non-protein N content in HM. The TID of total N was lower (P < 0.001) for HM (91.3 ± 1.24%) than for IF (98.0 ± 0.810%), while the TID of amino acid nitrogen (AAN) was not different (average of 97.4 ± 0.655%, P = 0.272). HM and IF had similar (P > 0.05) TID for most of the AAs including tryptophan (96.7 ± 0.950%, P = 0.079), except for some AAs (lysine, phenylalanine, threonine, valine, alanine, proline, and serine), with small significant difference (P < 0.05). The first limiting AA was the aromatic AAs, and the digestible indispensable AA score (DIAAS) was higher for HM (DIAASHM = 101) than for IF (DIAASIF = 83). CONCLUSION HM, compared to IF, had a lower TID for total N only, whereas the TID of AAN and most AAs, including Trp, was high and similar. A larger proportion of non-protein N is transferred to the microbiota with HM, which is of physiological relevance, although this fraction is poorly considered for IF manufacturing.
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Affiliation(s)
- Elise Charton
- STLO, Institut Agro, INRAE, Rennes, France; Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint Gilles, France
| | | | - Armelle Cahu
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint Gilles, France
| | | | - Patrice Dahirel
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint Gilles, France
| | - Paul J Moughan
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Carlos A Montoya
- Riddet Institute, Massey University, Palmerston North, New Zealand; Smart Foods Innovation and Bioproducts, AgResearch Limited, Palmerston North, New Zealand
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You X, Rani A, Özcan E, Lyu Y, Sela DA. Bifidobacterium longum subsp. infantis utilizes human milk urea to recycle nitrogen within the infant gut microbiome. Gut Microbes 2023; 15:2192546. [PMID: 36967532 PMCID: PMC10054289 DOI: 10.1080/19490976.2023.2192546] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Human milk guides the structure and function of microbial commensal communities that colonize the nursing infant gut. Indigestible molecules dissolved in human milk establish a microbiome often dominated by bifidobacteria capable of utilizing these substrates. Interestingly, urea accounts for ~15% of total human milk nitrogen, representing a potential reservoir for microbiota that may be salvaged for critical metabolic operations during lactation and neonatal development. Accordingly, B. infantis strains are competent for urea nitrogen utilization, constituting a previously hypothetical phenotype in commensal bacteria hosted by humans. Urease gene expression, downstream nitrogen metabolic pathways, and enzymatic activity are induced during urea utilization to yield elevated ammonia concentrations. Moreover, biosynthetic networks relevant to infant nutrition and development are transcriptionally responsive to urea utilization including branched chain and other essential amino acids. Importantly, isotopically labeled urea nitrogen is broadly distributed throughout the expressed B. infantis proteome. This incisively demonstrates that the previously inaccessible urea nitrogen is incorporated into microbial products available for infant host utilization. In aggregate, B. infantis possesses the requisite phenotypic foundation to participate in human milk urea nitrogen recycling within its infant host and thus may be a key contributor to nitrogen homeostasis early in life.
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Affiliation(s)
- Xiaomeng You
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Asha Rani
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Ezgi Özcan
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Yang Lyu
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - David A Sela
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
- Department of Nutrition, University of Massachusetts, Amherst, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Charton E, Bourgeois A, Bellanger A, Le-Gouar Y, Dahirel P, Romé V, Randuineau G, Cahu A, Moughan PJ, Montoya CA, Blat S, Dupont D, Deglaire A, Le Huërou-Luron I. Infant nutrition affects the microbiota-gut-brain axis: Comparison of human milk vs. infant formula feeding in the piglet model. Front Nutr 2022; 9:976042. [PMID: 36211510 PMCID: PMC9532976 DOI: 10.3389/fnut.2022.976042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Early nutrition plays a dominant role in infant development and health. It is now understood that the infant diet impacts the gut microbiota and its relationship with gut function and brain development. However, its impact on the microbiota-gut-brain axis has not been studied in an integrative way. The objective here was to evaluate the effects of human milk (HM) or cow’s milk based infant formula (IF) on the relationships between gut microbiota and the collective host intestinal-brain axis. Eighteen 10-day-old Yucatan mini-piglets were fed with HM or IF. Intestinal and fecal microbiota composition, intestinal phenotypic parameters, and the expression of genes involved in several gut and brain functions were determined. Unidimensional analyses were performed, followed by multifactorial analyses to evaluate the relationships among all the variables across the microbiota-gut-brain axis. Compared to IF, HM decreased the α-diversity of colonic and fecal microbiota and modified their composition. Piglets fed HM had a significantly higher ileal and colonic paracellular permeability assessed by ex vivo analysis, a lower expression of genes encoding tight junction proteins, and a higher expression of genes encoding pro-inflammatory and anti-inflammatory immune activity. In addition, the expression of genes involved in endocrine function, tryptophan metabolism and nutrient transport was modified mostly in the colon. These diet-induced intestinal modifications were associated with changes in the brain tissue expression of genes encoding the blood-brain barrier, endocrine function and short chain fatty acid receptors, mostly in hypothalamic and striatal areas. The integrative approach underlined specific groups of bacteria (Veillonellaceae, Enterobacteriaceae, Lachnospiraceae, Rikenellaceae, and Prevotellaceae) associated with changes in the gut-brain axis. There is a clear influence of the infant diet, even over a short dietary intervention period, on establishment of the microbiota-gut-brain axis.
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Affiliation(s)
- Elise Charton
- STLO, INRAE, Institut Agro, Rennes, France
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
| | | | | | | | - Patrice Dahirel
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
| | - Véronique Romé
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
| | | | - Armelle Cahu
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
| | - Paul J. Moughan
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Carlos A. Montoya
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Smart Foods and Bioproducts Innovation Centre of Excellence, AgResearch Limited, Palmerston North, New Zealand
| | - Sophie Blat
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
| | | | | | - Isabelle Le Huërou-Luron
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
- *Correspondence: Isabelle Le Huërou-Luron,
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Urine Metabolomic Profile of Breast- versus Formula-Fed Neonates Using a Synbiotic-Enriched Formula. Int J Mol Sci 2022; 23:ijms231810476. [PMID: 36142388 PMCID: PMC9499619 DOI: 10.3390/ijms231810476] [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: 07/31/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to compare the urine metabolic fingerprint of healthy neonates exclusively breastfed with that of neonates fed with a synbiotic-enriched formula (Rontamil® Complete 1) at four time points (the 3rd and 15th days of life and the 2nd and 3rd months). The determination of urine metabolic fingerprint was performed using NMR metabolomics. Multivariate data analyses were performed with SIMCA-P 15.0 software and R language. Non-distinct profiles for both groups (breastfeeding and synbiotic formula) for the two first time points (3rd and 15th days of life) were detected, whereas after the 2nd month of life, a discrimination trend was observed between the two groups, which was further confirmed at the 3rd month of life. A clear discrimination of the synbiotic formula samples was evident when comparing the metabolites taken in the first days of life (3rd day) with those taken in the 2nd and 3rd months of life. In both cases, OPLS-DA models explained more than 75% of the metabolic variance. Non-distinct metabolomic profiles were obtained between breastfed and synbiotic-formula-fed neonates up to the 15th day of life. Discrimination trends were observed only after the 2nd month of the study, which could be attributed to breastfeeding variations and the consequent dynamic profile of urine metabolites compared to the stable ingredients of the synbiotic formula.
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Hu H, Tan Y, Li C, Chen J, Kou Y, Xu ZZ, Liu Y, Tan Y, Dai L. StrainPanDA: Linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data. IMETA 2022; 1:e41. [PMID: 38868710 PMCID: PMC10989911 DOI: 10.1002/imt2.41] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/20/2022] [Accepted: 06/28/2022] [Indexed: 06/14/2024]
Abstract
Microbial strains of variable functional capacities coexist in microbiomes. Current bioinformatics methods of strain analysis cannot provide the direct linkage between strain composition and their gene contents from metagenomic data. Here we present Strain-level Pangenome Decomposition Analysis (StrainPanDA), a novel method that uses the pangenome coverage profile of multiple metagenomic samples to simultaneously reconstruct the composition and gene content variation of coexisting strains in microbial communities. We systematically validate the accuracy and robustness of StrainPanDA using synthetic data sets. To demonstrate the power of gene-centric strain profiling, we then apply StrainPanDA to analyze the gut microbiome samples of infants, as well as patients treated with fecal microbiota transplantation. We show that the linked reconstruction of strain composition and gene content profiles is critical for understanding the relationship between microbial adaptation and strain-specific functions (e.g., nutrient utilization and pathogenicity). Finally, StrainPanDA has minimal requirements for computing resources and can be scaled to process multiple species in a community in parallel. In short, StrainPanDA can be applied to metagenomic data sets to detect the association between molecular functions and microbial/host phenotypes to formulate testable hypotheses and gain novel biological insights at the strain or subspecies level.
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Affiliation(s)
- Han Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
- Bioinformatics DepartmentXbiome, Scientific Research Building, Tsinghua High‐Tech ParkShenzhenChina
| | - Yuxiang Tan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Chenhao Li
- Center for Computational and Integrative BiologyMassachusetts General Hospital and Harvard Medical School, Richard B. Simches Research CenterBostonMassachusettsUSA
| | - Junyu Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Yan Kou
- Bioinformatics DepartmentXbiome, Scientific Research Building, Tsinghua High‐Tech ParkShenzhenChina
| | - Zhenjiang Zech Xu
- Department of Food Science and Technology, State Key Laboratory of Food Science and TechnologyNanchang UniversityNanchangChina
| | - Yang‐Yu Liu
- Channing Division of Network Medicine, Department of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Yan Tan
- Bioinformatics DepartmentXbiome, Scientific Research Building, Tsinghua High‐Tech ParkShenzhenChina
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
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