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Leong KSW, Derraik JGB, Hofman PL, Cutfield WS. Antibiotics, gut microbiome and obesity. Clin Endocrinol (Oxf) 2018; 88:185-200. [PMID: 29023853 DOI: 10.1111/cen.13495] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/09/2017] [Indexed: 12/13/2022]
Abstract
Antibiotics have been hailed by many as "miracle drugs" that have been effectively treating infectious diseases for over a century, leading to a marked reduction in morbidity and mortality. However, with the increasing use of antibiotics, we are now faced not only with the increasing threat of antibiotic resistance, but also with a rising concern about potential long-term effects of antibiotics on human health, including the development of obesity. The obesity pandemic continues to increase, a problem that affects both adults and children alike. Disruptions to the gut microbiome have been linked to a multitude of adverse conditions, including obesity, type 2 diabetes, inflammatory bowel diseases, anxiety, autism, allergies, and autoimmune diseases. This review focuses on the association between antibiotics and obesity, and the role of the gut microbiome. There is strong evidence supporting the role of antibiotics in the development of obesity in well-controlled animal models. However, evidence for this link in humans is still inconclusive, and we need further well-designed clinical trials to clarify this association.
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Affiliation(s)
- Karen S W Leong
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - José G B Derraik
- Liggins Institute, University of Auckland, Auckland, New Zealand
- A Better Start - National Science Challenge, University of Auckland, Auckland, New Zealand
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Paul L Hofman
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Wayne S Cutfield
- Liggins Institute, University of Auckland, Auckland, New Zealand
- A Better Start - National Science Challenge, University of Auckland, Auckland, New Zealand
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52
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Yuksekdag Z, Cinar Acar B, Aslim B, Tukenmez U. β-Glucosidase activity and bioconversion of isoflavone glycosides to aglycones by potential probiotic bacteria. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2018. [DOI: 10.1080/10942912.2017.1382506] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Zehranur Yuksekdag
- Faculty of Science, Department of Biology, Gazi University, Ankara, Turkey
| | - Berat Cinar Acar
- Faculty of Science, Department of Biology, Gazi University, Ankara, Turkey
| | - Belma Aslim
- Faculty of Science, Department of Biology, Gazi University, Ankara, Turkey
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53
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Itani T, Ayoub Moubareck C, Melki I, Rousseau C, Mangin I, Butel MJ, Karam-Sarkis D. Preterm infants with necrotising enterocolitis demonstrate an unbalanced gut microbiota. Acta Paediatr 2018; 107:40-47. [PMID: 28921627 DOI: 10.1111/apa.14078] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/21/2017] [Accepted: 09/13/2017] [Indexed: 02/04/2023]
Abstract
AIM This Lebanese study tested the hypothesis that differences would exist in the gut microbiota of preterm infants with and without necrotising enterocolitis (NEC), as reported in Western countries. METHODS This study compared 11 infants with NEC and 11 controls, all born at 27-35 weeks, in three neonatal intensive care units between January 2013 and March 2015. Faecal samples were collected at key time points, and microbiota was analysed by culture, quantitative PCR (qPCR) and temperature temporal gel electrophoresis (TTGE). RESULTS The cultures revealed that all preterm infants were poorly colonised and harboured no more than seven species. Prior to NEC diagnosis, significant differences were observed by qPCR with a higher colonisation by staphylococci (p = 0.034) and lower colonisations by enterococci (p = 0.039) and lactobacilli (p = 0.048) in the NEC group compared to the healthy controls. Throughout the study, virtually all of the infants were colonised by Enterobacteriaceae at high levels. TTGE analysis revealed no particular clusterisation, showing high interindividual variability. CONCLUSION The NEC infants were poorly colonised with no more than seven species, and the controls had a more diversified and balanced gut microbiota. Understanding NEC aetiology better could lead to more effective prophylactic interventions and a reduced incidence.
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Affiliation(s)
- Tarek Itani
- Microbiology Laboratory; Faculty of Pharmacy; Saint-Joseph University; Beirut Lebanon
| | - Carole Ayoub Moubareck
- Microbiology Laboratory; Faculty of Pharmacy; Saint-Joseph University; Beirut Lebanon
- College of Natural and Health Sciences; Zayed University; Dubai UAE
| | - Imad Melki
- Hôtel Dieu de France Hospital; Beirut Lebanon
| | - Clotilde Rousseau
- Department Risk in pregnancy; Hospital University; Paris Descartes University; Sorbonne Paris Cité; Paris France
- Microbiology; Saint-Louis Hospital; APHP; Paris France
| | - Irène Mangin
- Department Risk in pregnancy; Hospital University; Paris Descartes University; Sorbonne Paris Cité; Paris France
- Laboratoire MIEL; Conservatoire national des arts et métiers; Paris France
| | - Marie-José Butel
- Department Risk in pregnancy; Hospital University; Paris Descartes University; Sorbonne Paris Cité; Paris France
| | - Dolla Karam-Sarkis
- Microbiology Laboratory; Faculty of Pharmacy; Saint-Joseph University; Beirut Lebanon
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54
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Esaiassen E, Hjerde E, Cavanagh JP, Pedersen T, Andresen JH, Rettedal SI, Støen R, Nakstad B, Willassen NP, Klingenberg C. Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants. Front Pediatr 2018; 6:347. [PMID: 30505830 PMCID: PMC6250747 DOI: 10.3389/fped.2018.00347] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/26/2018] [Indexed: 12/15/2022] Open
Abstract
Objectives: In 2014 probiotic supplementation (Lactobacillus acidophilus and Bifidobacterium longum subspecies infantis; InfloranⓇ) was introduced as standard of care to prevent necrotizing enterocolitis (NEC) in extremely preterm infants in Norway. We aimed to evaluate the influence of probiotics and antibiotic therapy on the developing gut microbiota and antibiotic resistome in extremely preterm infants, and to compare with very preterm infants and term infants not given probiotics. Study design: A prospective, observational multicenter study in six tertiary-care neonatal units. We enrolled 76 infants; 31 probiotic-supplemented extremely preterm infants <28 weeks gestation, 35 very preterm infants 28-31 weeks gestation not given probiotics and 10 healthy full-term control infants. Taxonomic composition and collection of antibiotic resistance genes (resistome) in fecal samples, collected at 7 and 28 days and 4 months age, were analyzed using shotgun-metagenome sequencing. Results: Median (IQR) birth weight was 835 (680-945) g and 1,290 (1,150-1,445) g in preterm infants exposed and not exposed to probiotics, respectively. Two extremely preterm infants receiving probiotic developed NEC requiring surgery. At 7 days of age we found higher median relative abundance of Bifidobacterium in probiotic supplemented infants (64.7%) compared to non-supplemented preterm infants (0.0%) and term control infants (43.9%). Lactobacillus was only detected in small amounts in all groups, but the relative abundance increased up to 4 months. Extremely preterm infants receiving probiotics had also much higher antibiotic exposure, still overall microbial diversity and resistome was not different than in more mature infants at 4 weeks and 4 months. Conclusion: Probiotic supplementation may induce colonization resistance and alleviate harmful effects of antibiotics on the gut microbiota and antibiotic resistome. Clinical Trial Registration: Clinicaltrials.gov: NCT02197468. https://clinicaltrials.gov/ct2/show/NCT02197468.
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Affiliation(s)
- Eirin Esaiassen
- Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry, Norstruct, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jorunn Pauline Cavanagh
- Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway
| | - Tanja Pedersen
- Department of Paediatrics, Haukeland University Hospital, Bergen, Norway
| | - Jannicke H Andresen
- Department of Neonatal Intensive Care, Oslo University Hospital, Oslo, Norway
| | - Siren I Rettedal
- Department of Paediatrics, Stavanger University Hospital, Stavanger, Norway
| | - Ragnhild Støen
- Department of Paediatrics, St. Olavs University Hospital, Trondheim, Norway.,Department of Laboratory Medicine, Children's and Women's Health, University of Science and Technology, Trondheim, Norway
| | - Britt Nakstad
- Department of Paediatric and Adolescents Medicine, Akershus University Hospital, Nordbyhagen, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Nils P Willassen
- Department of Chemistry, Norstruct, UiT The Arctic University of Norway, Tromsø, Norway
| | - Claus Klingenberg
- Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway
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55
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Grier A, Qiu X, Bandyopadhyay S, Holden-Wiltse J, Kessler HA, Gill AL, Hamilton B, Huyck H, Misra S, Mariani TJ, Ryan RM, Scholer L, Scheible KM, Lee YH, Caserta MT, Pryhuber GS, Gill SR. Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth. MICROBIOME 2017; 5:158. [PMID: 29228972 PMCID: PMC5725645 DOI: 10.1186/s40168-017-0377-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/23/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Identification of factors that influence the neonatal gut microbiome is urgently needed to guide clinical practices that support growth of healthy preterm infants. Here, we examined the influence of nutrition and common practices on the gut microbiota and growth in a cohort of preterm infants. RESULTS With weekly gut microbiota samples spanning postmenstrual age (PMA) 24 to 46 weeks, we developed two models to test associations between the microbiota, nutrition and growth: a categorical model with three successive microbiota phases (P1, P2, and P3) and a model with two periods (early and late PMA) defined by microbiota composition and PMA, respectively. The more significant associations with phase led us to use a phase-based framework for the majority of our analyses. Phase transitions were characterized by rapid shifts in the microbiota, with transition out of P1 occurring nearly simultaneously with the change from meconium to normal stool. The rate of phase progression was positively associated with gestational age at birth, and delayed transition to a P3 microbiota was associated with growth failure. We found distinct bacterial metabolic functions in P1-3 and significant associations between nutrition, microbiota phase, and infant growth. CONCLUSION The phase-dependent impact of nutrition on infant growth along with phase-specific metabolic functions suggests a pioneering potential for improving growth outcomes by tailoring nutrient intake to microbiota phase.
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MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Breast Feeding
- Cohort Studies
- DNA, Bacterial
- Feces/microbiology
- Female
- Gastrointestinal Microbiome
- Gestational Age
- Humans
- Infant
- Infant Health
- Infant, Newborn
- Infant, Premature/growth & development
- Infant, Premature/physiology
- Infant, Premature, Diseases/diet therapy
- Infant, Premature, Diseases/prevention & control
- Male
- Meconium/microbiology
- Nutritional Status
- RNA, Ribosomal, 16S
- Sequence Analysis, DNA
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Affiliation(s)
- Alex Grier
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sanjukta Bandyopadhyay
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Haeja A Kessler
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Ann L Gill
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Brooke Hamilton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Heidie Huyck
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sara Misra
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Rita M Ryan
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Lori Scholer
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Kristin M Scheible
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Yi-Horng Lee
- Division of Pediatric Surgery, Department of Surgery, Robert Wood Johnson University Hospital, New Brunswick, NJ, USA
| | - Mary T Caserta
- Division of Infectious Disease, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Steven R Gill
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
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56
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Nash AK, Auchtung TA, Wong MC, Smith DP, Gesell JR, Ross MC, Stewart CJ, Metcalf GA, Muzny DM, Gibbs RA, Ajami NJ, Petrosino JF. The gut mycobiome of the Human Microbiome Project healthy cohort. MICROBIOME 2017; 5:153. [PMID: 29178920 PMCID: PMC5702186 DOI: 10.1186/s40168-017-0373-4] [Citation(s) in RCA: 519] [Impact Index Per Article: 74.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 11/14/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene. RESULTS Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents. CONCLUSIONS Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.
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Affiliation(s)
- Andrea K. Nash
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Thomas A. Auchtung
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Matthew C. Wong
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Daniel P. Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Jonathan R. Gesell
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Matthew C. Ross
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Christopher J. Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Ginger A. Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Nadim J. Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
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57
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Lebeer S, Bron PA, Marco ML, Van Pijkeren JP, O'Connell Motherway M, Hill C, Pot B, Roos S, Klaenhammer T. Identification of probiotic effector molecules: present state and future perspectives. Curr Opin Biotechnol 2017; 49:217-223. [PMID: 29153882 DOI: 10.1016/j.copbio.2017.10.007] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/24/2017] [Accepted: 10/31/2017] [Indexed: 01/01/2023]
Abstract
Comprehension of underlying mechanisms of probiotic action will support rationale selection of probiotic strains and targeted clinical study design with a higher likelihood of success. This will consequently contribute to better substantiation of health claims. Here, we aim to provide a perspective from a microbiology point of view that such comprehensive understanding is not straightforward. We show examples of well-documented probiotic effector molecules in Lactobacillus and Bifidobacterium strains, including surface-located molecules such as specific pili, S-layer proteins, exopolysaccharides, muropeptides, as well as more widely produced metabolites such as tryptophan-related and histamine-related metabolites, CpG-rich DNA, and various enzymes such as lactase and bile salt hydrolases. We also present recent advances in genetic tool development, microbiome analyses and model systems, as well as perspectives on how the field could further progress. This opinion is based on a discussion group organized at the annual meeting of the International Scientific Association on Probiotics and Prebiotics (ISAPP) in June 2017.
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Affiliation(s)
- Sarah Lebeer
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
| | | | - Maria L Marco
- Department of Food Science & Technology, University of California, Davis, USA
| | | | - Mary O'Connell Motherway
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Colin Hill
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Western Road, Cork, Ireland
| | - Bruno Pot
- Yakult R&D, Europe, Almere, The Netherlands; Vrije Universiteit Brussels, Belgium
| | - Stefan Roos
- Swedish University of Agricultural Sciences & BioGaia AB, Sweden
| | - Todd Klaenhammer
- Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, USA
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Bazanella M, Maier TV, Clavel T, Lagkouvardos I, Lucio M, Maldonado-Gòmez MX, Autran C, Walter J, Bode L, Schmitt-Kopplin P, Haller D. Randomized controlled trial on the impact of early-life intervention with bifidobacteria on the healthy infant fecal microbiota and metabolome. Am J Clin Nutr 2017; 106:1274-1286. [PMID: 28877893 DOI: 10.3945/ajcn.117.157529] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/08/2017] [Indexed: 11/14/2022] Open
Abstract
Background: Early-life colonization of the intestinal tract is a dynamic process influenced by numerous factors. The impact of probiotic-supplemented infant formula on the composition and function of the infant gut microbiota is not well defined.Objective: We sought to determine the effects of a bifidobacteria-containing formula on the healthy human intestinal microbiome during the first year of life.Design: A double-blind, randomized, placebo-controlled study of newborn infants assigned to a standard whey-based formula containing a total of 107 colony-forming units (CFU)/g of Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, B. longum subspecies infantis (intervention), or to a control formula without bifidobacteria (placebo). Breastfed controls were included. Diversity and composition of fecal microbiota were determined by 16S ribosomal RNA gene amplicon sequencing, and metabolite profiles were analyzed by ultrahigh-performance liquid chromatography-mass spectrometry over a period of 2 y.Results: Infants (n = 106) were randomly assigned to either the interventional (n = 48) or placebo (n = 49) group; 9 infants were exclusively breastfed throughout the entire intervention period of 12 mo. Infants exposed to bifidobacteria-supplemented formula showed decreased occurrence of Bacteroides and Blautia spp. associated with changes in lipids and unknown metabolites at month 1. Microbiota and metabolite profiles of intervention and placebo groups converged during the study period, and long-term colonization (24 mo) of the supplemented Bifidobacterium strains was not detected. Significant differences in microbiota and metabolites were detected between infants fed breast milk and those fed formula (P < 0.005) and between infants birthed vaginally and those birthed by cesarean delivery (P < 0.005). No significant differences were observed between infant feeding groups regarding growth, antibiotic uptake, or other health variables (P > 0.05).Conclusion: The supplementation of bifidobacteria to infant diet can modulate the occurrence of specific bacteria and metabolites during early life with no detectable long-term effects. This trial was registered at germanctr.de as DRKS00003660.
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Affiliation(s)
| | - Tanja V Maier
- Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Oberschleißheim, Germany
| | | | | | - Marianna Lucio
- Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Oberschleißheim, Germany
| | | | - Chloe Autran
- Divisions of Neonatology and Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MoMICoRE), University of California, San Diego, La Jolla, CA
| | - Jens Walter
- Chair for Nutrition, Microbes and Gastrointestinal Health, University of Alberta, Edmonton, Alberta, Canada; and
| | - Lars Bode
- Divisions of Neonatology and Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MoMICoRE), University of California, San Diego, La Jolla, CA
| | - Philippe Schmitt-Kopplin
- Chair of Analytical Food Chemistry, Technical University of Munich, Freising, Germany.,Research Unit Analytical Biogeochemistry, Helmholtz Center Munich, Oberschleißheim, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, .,ZIEL - Institute for Food & Health, and
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59
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Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Fofanova T, Nelson A, Skeath T, Perry JD, Petrosino JF, Berrington JE, Cummings SP. Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. MICROBIOME 2017; 5:75. [PMID: 28701177 PMCID: PMC5508794 DOI: 10.1186/s40168-017-0295-1] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/29/2017] [Indexed: 05/28/2023]
Abstract
BACKGROUND Late onset sepsis (LOS) in preterm infants is associated with considerable morbidity and mortality. While studies have implicated gut bacteria in the aetiology of the disease, functional analysis and mechanistic insights are generally lacking. We performed temporal bacterial (n = 613) and metabolomic (n = 63) profiling on extensively sampled stool from 7 infants with LOS and 28 matched healthy (no LOS or NEC) controls. RESULTS The bacteria isolated in diagnostic blood culture usually corresponded to the dominant bacterial genera in the gut microbiome. Longitudinal changes were monitored based on preterm gut community types (PGCTs), where control infants had an increased number of PGCTs compared to LOS infants (P = 0.011). PGCT 6, characterised by Bifidobacteria dominance, was only present in control infants. Metabolite profiles differed between LOS and control infants at diagnosis and 7 days later, but not 7 days prior to diagnosis. Bifidobacteria was positively correlated with control metabolites, including raffinose, sucrose, and acetic acid. CONCLUSIONS Using multi-omic analysis, we show that the gut microbiome is involved in the pathogenesis of LOS. While the causative agent of LOS varies, it is usually abundant in the gut. Bifidobacteria dominance was associated with control infants, and the presence of this organism may directly protect, or act as a marker for protection, against gut epithelial translocation. While the metabolomic data is preliminary, the findings support that gut development and protection in preterm infants is associated with increased in prebiotic oligosaccharides (e.g. raffinose) and the growth of beneficial bacteria (e.g. Bifidobacterium).
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Affiliation(s)
- Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Nicholas D Embleton
- Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP.77030, UK
| | - Emma C L Marrs
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tatiana Fofanova
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Tom Skeath
- Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP.77030, UK
| | - John D Perry
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, UK
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Janet E Berrington
- Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP.77030, UK
| | - Stephen P Cummings
- School of Science and Engineering, Teesside University, Middlesbrough, TS1 3BX, UK
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Laforest-Lapointe I, Arrieta MC. Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective. Front Immunol 2017; 8:788. [PMID: 28740492 PMCID: PMC5502328 DOI: 10.3389/fimmu.2017.00788] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/22/2017] [Indexed: 12/24/2022] Open
Abstract
Alterations in gut microbial colonization during early life have been reported in infants that later developed asthma, allergies, type 1 diabetes, as well as in inflammatory bowel disease patients, previous to disease flares. Mechanistic studies in animal models have established that microbial alterations influence disease pathogenesis via changes in immune system maturation. Strong evidence points to the presence of a window of opportunity in early life, during which changes in gut microbial colonization can result in immune dysregulation that predisposes susceptible hosts to disease. Although the ecological patterns of microbial succession in the first year of life have been partly defined in specific human cohorts, the taxonomic and functional features, and diversity thresholds that characterize these microbial alterations are, for the most part, unknown. In this review, we summarize the most important links between the temporal mosaics of gut microbial colonization and the age-dependent immune functions that rely on them. We also highlight the importance of applying ecology theory to design studies that explore the interactions between this complex ecosystem and the host immune system. Focusing research efforts on understanding the importance of temporally structured patterns of diversity, keystone groups, and inter-kingdom microbial interactions for ecosystem functions has great potential to enable the development of biologically sound interventions aimed at maintaining and/or improving immune system development and preventing disease.
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Affiliation(s)
- Isabelle Laforest-Lapointe
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
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61
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Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 2017; 41:453-478. [PMID: 28333226 PMCID: PMC5812509 DOI: 10.1093/femsre/fuw046] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
| | | | - Beata Anna Raczkowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), 46020 Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Paterna, 46980 Valencia, Spain
- These authors contributed equally to this work
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Corresponding author: Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain. Tel: (+34) 915854872; E-mail:
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
- These authors contributed equally to this work
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Stewart CJ, Embleton ND, Clements E, Luna PN, Smith DP, Fofanova TY, Nelson A, Taylor G, Orr CH, Petrosino JF, Berrington JE, Cummings SP. Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants. Front Microbiol 2017. [PMID: 28634475 PMCID: PMC5459931 DOI: 10.3389/fmicb.2017.01008] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The short and long-term impact of birth mode on the developing gut microbiome in neonates has potential implications for the health of infants. In term infants, the microbiome immediately following birth across multiple body sites corresponds to birth mode, with increased Bacteroides in vaginally delivered infants. We aimed to determine the impact of birth mode of the preterm gut microbiome over the first 100 days of life and following neonatal intensive care unit (NICU) discharge. In total, 867 stool samples from 46 preterm infants (21 cesarean and 25 vaginal), median gestational age 27 weeks, were sequenced (V4 region 16S rRNA gene, Illumina MiSeq). Of these, 776 samples passed quality filtering and were included in the analysis. The overall longitudinal alpha-diversity and within infant beta-diversity was comparable between cesarean and vaginally delivered infants. Vaginally delivered infants kept significantly more OTUs from 2 months of life and following NICU discharge, but OTUs lost, gained, and regained were not different based on birth mode. Furthermore, the temporal progression of dominant genera was comparable between birth modes and no significant difference was found for any genera following adjustment for covariates. Lastly, preterm gut community types (PGCTs) showed some moderate differences in very early life, but progressed toward a comparable pattern by week 5. No PGCT was significantly associated with cesarean or vaginal birth. Unlike term infants, birth mode was not significantly associated with changes in microbial diversity, composition, specific taxa, or overall microbial development in preterm infants. This may result from the dominating effects of NICU exposures including the universal use of antibiotics immediately following birth and/or the lack of Bacteroides colonizing preterm infants.
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Affiliation(s)
- Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Nicholas D Embleton
- Newcastle Neonatal ServiceRoyal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Elizabeth Clements
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Pamela N Luna
- Department of Statistics, Rice University, HoustonTX, United States
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Tatiana Y Fofanova
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon Tyne, United Kingdom
| | - Gillian Taylor
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Caroline H Orr
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Janet E Berrington
- Newcastle Neonatal ServiceRoyal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Stephen P Cummings
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
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63
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Moya-Pérez A, Luczynski P, Renes IB, Wang S, Borre Y, Anthony Ryan C, Knol J, Stanton C, Dinan TG, Cryan JF. Intervention strategies for cesarean section-induced alterations in the microbiota-gut-brain axis. Nutr Rev 2017; 75:225-240. [PMID: 28379454 PMCID: PMC5410982 DOI: 10.1093/nutrit/nuw069] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microbial colonization of the gastrointestinal tract is an essential process that modulates host physiology and immunity. Recently, researchers have begun to understand how and when these microorganisms colonize the gut and the early-life factors that impact their natural ecological establishment. The vertical transmission of maternal microbes to the offspring is a critical factor for host immune and metabolic development. Increasing evidence also points to a role in the wiring of the gut-brain axis. This process may be altered by various factors such as mode of delivery, gestational age at birth, the use of antibiotics in early life, infant feeding, and hygiene practices. In fact, these early exposures that impact the intestinal microbiota have been associated with the development of diseases such as obesity, type 1 diabetes, asthma, allergies, and even neurodevelopmental disorders. The present review summarizes the impact of cesarean birth on the gut microbiome and the health status of the developing infant and discusses possible preventative and restorative strategies to compensate for early-life microbial perturbations.
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Affiliation(s)
- Angela Moya-Pérez
- A. Moya-Pérez, P. Luczynski, Y. Borre, C.A. Ryan, C. Stanton, T.G. Dinan, and J.F. Cryan are with the APC Microbiome Institute; C.A. Ryan is with the Department of Paediatrics and Child Health; T.G. Dinan is with the Department of Psychiatry and Neurobehavioural Science; and J.F. Cryan is with the Department of Anatomy and Neuroscience; University College Cork, Cork, Ireland. I.B. Renes and J. Knol are with Nutricia Research, Utrecht, the Netherlands. S. Wang is with Nutricia Research, Singapore. J. Knol is with the Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands. C. Stanton is with the Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
| | - Pauline Luczynski
- A. Moya-Pérez, P. Luczynski, Y. Borre, C.A. Ryan, C. Stanton, T.G. Dinan, and J.F. Cryan are with the APC Microbiome Institute; C.A. Ryan is with the Department of Paediatrics and Child Health; T.G. Dinan is with the Department of Psychiatry and Neurobehavioural Science; and J.F. Cryan is with the Department of Anatomy and Neuroscience; University College Cork, Cork, Ireland. I.B. Renes and J. Knol are with Nutricia Research, Utrecht, the Netherlands. S. Wang is with Nutricia Research, Singapore. J. Knol is with the Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands. C. Stanton is with the Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
| | - Ingrid B. Renes
- A. Moya-Pérez, P. Luczynski, Y. Borre, C.A. Ryan, C. Stanton, T.G. Dinan, and J.F. Cryan are with the APC Microbiome Institute; C.A. Ryan is with the Department of Paediatrics and Child Health; T.G. Dinan is with the Department of Psychiatry and Neurobehavioural Science; and J.F. Cryan is with the Department of Anatomy and Neuroscience; University College Cork, Cork, Ireland. I.B. Renes and J. Knol are with Nutricia Research, Utrecht, the Netherlands. S. Wang is with Nutricia Research, Singapore. J. Knol is with the Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands. C. Stanton is with the Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
| | - Shugui Wang
- A. Moya-Pérez, P. Luczynski, Y. Borre, C.A. Ryan, C. Stanton, T.G. Dinan, and J.F. Cryan are with the APC Microbiome Institute; C.A. Ryan is with the Department of Paediatrics and Child Health; T.G. Dinan is with the Department of Psychiatry and Neurobehavioural Science; and J.F. Cryan is with the Department of Anatomy and Neuroscience; University College Cork, Cork, Ireland. I.B. Renes and J. Knol are with Nutricia Research, Utrecht, the Netherlands. S. Wang is with Nutricia Research, Singapore. J. Knol is with the Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands. C. Stanton is with the Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
| | - Yuliya Borre
- A. Moya-Pérez, P. Luczynski, Y. Borre, C.A. Ryan, C. Stanton, T.G. Dinan, and J.F. Cryan are with the APC Microbiome Institute; C.A. Ryan is with the Department of Paediatrics and Child Health; T.G. Dinan is with the Department of Psychiatry and Neurobehavioural Science; and J.F. Cryan is with the Department of Anatomy and Neuroscience; University College Cork, Cork, Ireland. I.B. Renes and J. Knol are with Nutricia Research, Utrecht, the Netherlands. S. Wang is with Nutricia Research, Singapore. J. Knol is with the Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands. C. Stanton is with the Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
| | - C. Anthony Ryan
- A. Moya-Pérez, P. Luczynski, Y. Borre, C.A. Ryan, C. Stanton, T.G. Dinan, and J.F. Cryan are with the APC Microbiome Institute; C.A. Ryan is with the Department of Paediatrics and Child Health; T.G. Dinan is with the Department of Psychiatry and Neurobehavioural Science; and J.F. Cryan is with the Department of Anatomy and Neuroscience; University College Cork, Cork, Ireland. I.B. Renes and J. Knol are with Nutricia Research, Utrecht, the Netherlands. S. Wang is with Nutricia Research, Singapore. J. Knol is with the Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands. C. Stanton is with the Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
| | - Jan Knol
- A. Moya-Pérez, P. Luczynski, Y. Borre, C.A. Ryan, C. Stanton, T.G. Dinan, and J.F. Cryan are with the APC Microbiome Institute; C.A. Ryan is with the Department of Paediatrics and Child Health; T.G. Dinan is with the Department of Psychiatry and Neurobehavioural Science; and J.F. Cryan is with the Department of Anatomy and Neuroscience; University College Cork, Cork, Ireland. I.B. Renes and J. Knol are with Nutricia Research, Utrecht, the Netherlands. S. Wang is with Nutricia Research, Singapore. J. Knol is with the Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands. C. Stanton is with the Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
| | - Catherine Stanton
- A. Moya-Pérez, P. Luczynski, Y. Borre, C.A. Ryan, C. Stanton, T.G. Dinan, and J.F. Cryan are with the APC Microbiome Institute; C.A. Ryan is with the Department of Paediatrics and Child Health; T.G. Dinan is with the Department of Psychiatry and Neurobehavioural Science; and J.F. Cryan is with the Department of Anatomy and Neuroscience; University College Cork, Cork, Ireland. I.B. Renes and J. Knol are with Nutricia Research, Utrecht, the Netherlands. S. Wang is with Nutricia Research, Singapore. J. Knol is with the Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands. C. Stanton is with the Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
| | - Timothy G. Dinan
- A. Moya-Pérez, P. Luczynski, Y. Borre, C.A. Ryan, C. Stanton, T.G. Dinan, and J.F. Cryan are with the APC Microbiome Institute; C.A. Ryan is with the Department of Paediatrics and Child Health; T.G. Dinan is with the Department of Psychiatry and Neurobehavioural Science; and J.F. Cryan is with the Department of Anatomy and Neuroscience; University College Cork, Cork, Ireland. I.B. Renes and J. Knol are with Nutricia Research, Utrecht, the Netherlands. S. Wang is with Nutricia Research, Singapore. J. Knol is with the Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands. C. Stanton is with the Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
| | - John F. Cryan
- A. Moya-Pérez, P. Luczynski, Y. Borre, C.A. Ryan, C. Stanton, T.G. Dinan, and J.F. Cryan are with the APC Microbiome Institute; C.A. Ryan is with the Department of Paediatrics and Child Health; T.G. Dinan is with the Department of Psychiatry and Neurobehavioural Science; and J.F. Cryan is with the Department of Anatomy and Neuroscience; University College Cork, Cork, Ireland. I.B. Renes and J. Knol are with Nutricia Research, Utrecht, the Netherlands. S. Wang is with Nutricia Research, Singapore. J. Knol is with the Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands. C. Stanton is with the Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
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Stewart CJ, Embleton ND, Clements E, Luna PN, Smith DP, Fofanova TY, Nelson A, Taylor G, Orr CH, Petrosino JF, Berrington JE, Cummings SP. Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants. Front Microbiol 2017. [PMID: 28634475 DOI: 10.3389/fmicb.2017.01008/full] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
The short and long-term impact of birth mode on the developing gut microbiome in neonates has potential implications for the health of infants. In term infants, the microbiome immediately following birth across multiple body sites corresponds to birth mode, with increased Bacteroides in vaginally delivered infants. We aimed to determine the impact of birth mode of the preterm gut microbiome over the first 100 days of life and following neonatal intensive care unit (NICU) discharge. In total, 867 stool samples from 46 preterm infants (21 cesarean and 25 vaginal), median gestational age 27 weeks, were sequenced (V4 region 16S rRNA gene, Illumina MiSeq). Of these, 776 samples passed quality filtering and were included in the analysis. The overall longitudinal alpha-diversity and within infant beta-diversity was comparable between cesarean and vaginally delivered infants. Vaginally delivered infants kept significantly more OTUs from 2 months of life and following NICU discharge, but OTUs lost, gained, and regained were not different based on birth mode. Furthermore, the temporal progression of dominant genera was comparable between birth modes and no significant difference was found for any genera following adjustment for covariates. Lastly, preterm gut community types (PGCTs) showed some moderate differences in very early life, but progressed toward a comparable pattern by week 5. No PGCT was significantly associated with cesarean or vaginal birth. Unlike term infants, birth mode was not significantly associated with changes in microbial diversity, composition, specific taxa, or overall microbial development in preterm infants. This may result from the dominating effects of NICU exposures including the universal use of antibiotics immediately following birth and/or the lack of Bacteroides colonizing preterm infants.
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Affiliation(s)
- Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Nicholas D Embleton
- Newcastle Neonatal ServiceRoyal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Elizabeth Clements
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Pamela N Luna
- Department of Statistics, Rice University, HoustonTX, United States
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Tatiana Y Fofanova
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon Tyne, United Kingdom
| | - Gillian Taylor
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Caroline H Orr
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Janet E Berrington
- Newcastle Neonatal ServiceRoyal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Stephen P Cummings
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
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65
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Molloy EJ, Curstedt T, Halliday HL, Hallman M, Saugstad OD, Speer CP. Sharing Progress in Neonatal (SPIN) Brain, Gut, Heart, and Lung. Neonatology 2017; 111:384-387. [PMID: 28538232 DOI: 10.1159/000464316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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66
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Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Nelson A, Abdulkadir B, Skeath T, Petrosino JF, Perry JD, Berrington JE, Cummings SP. Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease. MICROBIOME 2016; 4:67. [PMID: 28034304 PMCID: PMC5200962 DOI: 10.1186/s40168-016-0216-8] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 12/01/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND The preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <32 weeks gestation, we selected 7 infants who developed NEC (defined rigorously) and 28 matched controls. We performed detailed temporal bacterial (n = 641) and metabolomic (n = 75) profiling of the gut microbiome throughout the disease. RESULTS A core community of Klebsiella, Escherichia, Staphyloccocus, and Enterococcus was present in all samples. Gut microbiota profiles grouped into six distinct clusters, termed preterm gut community types (PGCTs). Each PGCT reflected dominance by the core operational taxonomic units (OTUs), except of PGCT 6, which had high diversity and was dominant in bifidobacteria. While PGCTs 1-5 were present in infants prior to NEC diagnosis, PGCT 6 was comprised exclusively of healthy samples. NEC infants had significantly more PGCT transitions prior to diagnosis. Metabolomic profiling identified significant pathways associated with NEC onset, with metabolites involved in linoleate metabolism significantly associated with NEC diagnosis. Notably, metabolites associated with NEC were the lowest in PGCT 6. CONCLUSIONS This is the first study to integrate sequence and metabolomic stool analysis in preterm neonates, demonstrating that NEC does not have a uniform microbial signature. However, a diverse gut microbiome with a high abundance of bifidobacteria may protect preterm infants from disease. These results may inform biomarker development and improve understanding of gut-mediated mechanisms of NEC.
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MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- DNA, Bacterial/analysis
- DNA, Ribosomal/analysis
- Enterocolitis, Necrotizing/metabolism
- Enterocolitis, Necrotizing/microbiology
- Feces/microbiology
- Female
- Gastrointestinal Microbiome
- Humans
- Infant, Newborn
- Infant, Premature
- Infant, Premature, Diseases/metabolism
- Infant, Premature, Diseases/microbiology
- Linoleic Acid/metabolism
- Longitudinal Studies
- Male
- Metabolic Networks and Pathways
- Phylogeny
- Proteomics/methods
- RNA, Ribosomal, 16S/analysis
- Sequence Analysis, DNA/methods
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Affiliation(s)
- Christopher J Stewart
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Alkek Center for Metagenomics and Microbiome Research, Houston, Texas, 77030, USA.
| | - Nicholas D Embleton
- Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, United Kingdom
| | - Emma C L Marrs
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, United Kingdom
| | - Daniel P Smith
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Alkek Center for Metagenomics and Microbiome Research, Houston, Texas, 77030, USA
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - Bashir Abdulkadir
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - Tom Skeath
- Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, United Kingdom
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Alkek Center for Metagenomics and Microbiome Research, Houston, Texas, 77030, USA
| | - John D Perry
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne, NE7 7DN, United Kingdom
| | - Janet E Berrington
- Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, United Kingdom
| | - Stephen P Cummings
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
- School of Science and Engineering, Teesside University, Middlesbrough, TS1 3BX, United Kingdom
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67
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Zhang SF, Tang ZS, Tong L, Tao XX, Suo QF, Xu XM. Effects of clostridium butyricum and bifidobacterium on BTLA expression on CD4 + T cells and lymphocyte differentiation in late preterm infants. Microb Pathog 2016; 100:112-118. [PMID: 27622346 DOI: 10.1016/j.micpath.2016.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Probiotics is recognized to promote growth performance and immune function via balancing the intestinal microflora. Live clostridium butyricum and bifidobacterium combined powder (LCBBCP) has been widely to treat intestinal dysbacteriosis in newborns in China. This study was undertaken to investigate the effects of the combined probiotics on the expression of B and T lymphocyte attenuator (BTLA) on CD4+ T cells and the differentiation of lymphocyte subsets in late preterm infants. METHODS Eighty eligible late preterm infants were equally randomized into LCBBCP therapy group (oral LCBBCP dissolved in formula milk before intake) and control group (treated with simple formula milk for preterm infants) by random digit table. Flow cytometry was used to determine the expression level of BTLA on CD4+ T cells and the percentage of individual subpopulation of lymphocytes in peripheral-blood mononuclear cells (PBMCs) obtained from the late preterm infants in both groups. RESULTS BTLA protein expression on CD4+ T cells showed no significant change in LCBBCP therapy group before and after intervention, yet was rapidly and significantly down-regulated in the controls. The percentage of increased CD4+ T cells, decreased CD8+ T cells and increased ratio of CD4+/CD8+ T cell proportion were seen in both groups after treatment, yet the increasing or decreasing extent in LCBBCP therapy group was more obvious than in control group. The proportion of NK cells and B lymphocytes remained no significant difference between the two groups before and after therapy. CONCLUSIONS LCBBCP appears capable of facilitating the activation, proliferation and differentiation of T lymphocytes, which is beneficial to improving immunity in late preterm infants. The continuous high expression of BTLA on CD4+ T cells in LCBBCP therapy group may be involved in the inhibiting of excessive activation of T lymphocytes. Our findings may lay a basis for further clinical evaluation of the efficacies and wider clinical recommendation of probiotics containing live clostridium butyricum and bifidobacterium for late preterm infants.
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Affiliation(s)
- Shi-Fa Zhang
- Department of Pediatrics, Yijishan Hospital, Wannan Medical College, Wuhu 241001, Anhui, China
| | - Zong-Sheng Tang
- Department of Central Laboratory, Yijishan Hospital, Wannan Medical College, Wuhu 241001, Anhui, China.
| | - Ling Tong
- Department of Pediatrics, Yijishan Hospital, Wannan Medical College, Wuhu 241001, Anhui, China
| | - Xiang-Xiang Tao
- Office of Educational Administration, Wannan Medical College, Wuhu 241001, Anhui, China
| | - Qi-Feng Suo
- Department of Central Laboratory, Yijishan Hospital, Wannan Medical College, Wuhu 241001, Anhui, China
| | - Xue-Mei Xu
- Department of Pediatrics, Yijishan Hospital, Wannan Medical College, Wuhu 241001, Anhui, China
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