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Rafiq T, Stearns JC, Shanmuganathan M, Azab SM, Anand SS, Thabane L, Beyene J, Williams NC, Morrison KM, Teo KK, Britz-McKibbin P, de Souza RJ. Integrative multiomics analysis of infant gut microbiome and serum metabolome reveals key molecular biomarkers of early onset childhood obesity. Heliyon 2023; 9:e16651. [PMID: 37332914 PMCID: PMC10272340 DOI: 10.1016/j.heliyon.2023.e16651] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023] Open
Abstract
Evidence supports a complex interplay of gut microbiome and host metabolism as regulators of obesity. The metabolic phenotype and microbial metabolism of host diet may also contribute to greater obesity risk in children early in life. This study aimed to identify features that discriminated overweight/obese from normal weight infants by integrating gut microbiome and serum metabolome profiles. This prospective analysis included 50 South Asian children living in Canada, selected from the SouTh Asian biRth cohorT (START). Serum metabolites were measured by multisegment injection-capillary electrophoresis-mass spectrometry and the relative abundance of bacterial 16S rRNA gene amplicon sequence variant was evaluated at 1 year. Cumulative body mass index (BMIAUC) and skinfold thickness (SSFAUC) scores were calculated from birth to 3 years as the total area under the growth curve (AUC). BMIAUC and/or SSFAUC >85th percentile was used to define overweight/obesity. Data Integration Analysis for Biomarker discovery using Latent cOmponent (DIABLO) was used to identify discriminant features associated with childhood overweight/obesity. The associations between identified features and anthropometric measures were examined using logistic regression. Circulating metabolites including glutamic acid, acetylcarnitine, carnitine, and threonine were positively, whereas γ-aminobutyric acid (GABA), symmetric dimethylarginine (SDMA), and asymmetric dimethylarginine (ADMA) were negatively associated with childhood overweight/obesity. The abundance of the Pseudobutyrivibrio and Lactobacillus genera were positively, and Clostridium sensu stricto 1 and Akkermansia were negatively associated with childhood overweight/obesity. Integrative analysis revealed that Akkermansia was positively whereas Lactobacillus was inversely correlated with GABA and SDMA, and Pseudobutyrivibrio was inversely correlated with GABA. This study provides insights into metabolic and microbial signatures which may regulate satiety, energy metabolism, inflammatory processes, and/or gut barrier function, and therefore, obesity trajectories in childhood. Understanding the functional capacity of these molecular features and potentially modifiable risk factors such as dietary exposures early in life may offer a novel approach for preventing childhood obesity.
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Affiliation(s)
- Talha Rafiq
- Medical Sciences Graduate Program, Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
- Population Health Research Institute, Hamilton Health Sciences, McMaster University, Hamilton, ON L8L 2X2, Canada
| | - Jennifer C. Stearns
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Meera Shanmuganathan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Sandi M. Azab
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
- Department of Pharmacognosy, Alexandria University, Alexandria 21521, Egypt
| | - Sonia S. Anand
- Population Health Research Institute, Hamilton Health Sciences, McMaster University, Hamilton, ON L8L 2X2, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
- Department of Health Research Methods, Evidence & Impact, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Lehana Thabane
- Department of Health Research Methods, Evidence & Impact, McMaster University, Hamilton, ON L8S 4L8, Canada
- Biostatistics Unit, Father Sean O’Sullivan Research Centre, The Research Institute, St Joseph’s Healthcare Hamilton, Hamilton, ON L8N 4A6, Canada
- Faculty of Health Sciences, University of Johannesburg, Johannesburg 524, South Africa
| | - Joseph Beyene
- Department of Health Research Methods, Evidence & Impact, McMaster University, Hamilton, ON L8S 4L8, Canada
| | | | - Katherine M. Morrison
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Koon K. Teo
- Population Health Research Institute, Hamilton Health Sciences, McMaster University, Hamilton, ON L8L 2X2, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
- Department of Health Research Methods, Evidence & Impact, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Russell J. de Souza
- Population Health Research Institute, Hamilton Health Sciences, McMaster University, Hamilton, ON L8L 2X2, Canada
- Department of Health Research Methods, Evidence & Impact, McMaster University, Hamilton, ON L8S 4L8, Canada
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Stennett RN, Adamo KB, Anand SS, Bajaj HS, Bangdiwala SI, Desai D, Gerstein HC, Kandasamy S, Khan F, Lear SA, McDonald SD, Pocsai T, Ritvo P, Rogge A, Schulze KM, Sherifali D, Stearns JC, Wahi G, Williams NC, Zulyniak MA, de Souza RJ. A culturally tailored personaliseD nutrition intErvention in South ASIan women at risk of Gestational Diabetes Mellitus (DESI-GDM): a randomised controlled trial protocol. BMJ Open 2023; 13:e072353. [PMID: 37130668 PMCID: PMC10163497 DOI: 10.1136/bmjopen-2023-072353] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/14/2023] [Indexed: 05/04/2023] Open
Abstract
INTRODUCTION South Asians are more likely to develop gestational diabetes mellitus (GDM) than white Europeans. Diet and lifestyle modifications may prevent GDM and reduce undesirable outcomes in both the mother and offspring. Our study seeks to evaluate the effectiveness and participant acceptability of a culturally tailored, personalised nutrition intervention on the glucose area under the curve (AUC) after a 2-hour 75 g oral glucose tolerance test (OGTT) in pregnant women of South Asian ancestry with GDM risk factors. METHODS AND ANALYSIS A total of 190 South Asian pregnant women with at least 2 of the following GDM risk factors-prepregnancy body mass index>23, age>29, poor-quality diet, family history of type 2 diabetes in a first-degree relative or GDM in a previous pregnancy will be enrolled during gestational weeks 12-18, and randomly assigned in a 1:1 ratio to: (1) usual care, plus weekly text messages to encourage walking and paper handouts or (2) a personalised nutrition plan developed and delivered by a culturally congruent dietitian and health coach; and FitBit to track steps. The intervention lasts 6-16 weeks, depending on week of recruitment. The primary outcome is the glucose AUC from a three-sample 75 g OGTT 24-28 weeks' gestation. The secondary outcome is GDM diagnosis, based on Born-in-Bradford criteria (fasting glucose>5.2 mmol/L or 2 hours post load>7.2 mmol/L). ETHICS AND DISSEMINATION The study has been approved by the Hamilton Integrated Research Ethics Board (HiREB #10942). Findings will be disseminated among academics and policy-makers through scientific publications along with community-orientated strategies. TRIAL REGISTRATION NUMBER NCT03607799.
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Affiliation(s)
- Rosain N Stennett
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kristi B Adamo
- School of Human Kinetics, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Sonia S Anand
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
| | | | - Shrikant I Bangdiwala
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Dipika Desai
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Hertzel C Gerstein
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Sujane Kandasamy
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Farah Khan
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Scott A Lear
- Population Health Research Institute, Hamilton, Ontario, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sarah D McDonald
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Obstetrics & Gynecology, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Division of Maternal-Fetal Medicine, Faculty of Medicine, McMaster University, Hamilton, Ontario, Canada
- Department of Radiology, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Tayler Pocsai
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Paul Ritvo
- Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - Andrea Rogge
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Karleen M Schulze
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Diana Sherifali
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- School of Nursing, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer C Stearns
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Department of Obstetrics & Gynecology, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Gita Wahi
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | - Michael A Zulyniak
- Food Science and Nutrition, University of Leeds, Leeds, West Yorkshire, UK
| | - Russell J de Souza
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
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Guitor AK, Yousuf EI, Raphenya AR, Hutton EK, Morrison KM, McArthur AG, Wright GD, Stearns JC. Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation. Microbiome 2022; 10:136. [PMID: 36008821 PMCID: PMC9414150 DOI: 10.1186/s40168-022-01327-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/14/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Probiotic use in preterm infants can mitigate the impact of antibiotic exposure and reduce rates of certain illnesses; however, the benefit on the gut resistome, the collection of antibiotic resistance genes, requires further investigation. We hypothesized that probiotic supplementation of early preterm infants (born < 32-week gestation) while in hospital reduces the prevalence of antibiotic resistance genes associated with pathogenic bacteria in the gut. We used a targeted capture approach to compare the resistome from stool samples collected at the term corrected age of 40 weeks for two groups of preterm infants (those that routinely received a multi-strain probiotic during hospitalization and those that did not) with samples from full-term infants at 10 days of age to identify if preterm birth or probiotic supplementation impacted the resistome. We also compared the two groups of preterm infants up to 5 months of age to identify persistent antibiotic resistance genes. RESULTS At the term corrected age, or 10 days of age for the full-term infants, we found over 80 antibiotic resistance genes in the preterm infants that did not receive probiotics that were not identified in either the full-term or probiotic-supplemented preterm infants. More genes associated with antibiotic inactivation mechanisms were identified in preterm infants unexposed to probiotics at this collection time-point compared to the other infants. We further linked these genes to mobile genetic elements and Enterobacteriaceae, which were also abundant in their gut microbiomes. Various genes associated with aminoglycoside and beta-lactam resistance, commonly found in pathogenic bacteria, were retained for up to 5 months in the preterm infants that did not receive probiotics. CONCLUSIONS This pilot survey of preterm infants shows that probiotics administered after preterm birth during hospitalization reduced the diversity and prevented persistence of antibiotic resistance genes in the gut microbiome. The benefits of probiotic use on the microbiome and the resistome should be further explored in larger groups of infants. Due to its high sensitivity and lower sequencing cost, our targeted capture approach can facilitate these surveys to further address the implications of resistance genes persisting into infancy without the need for large-scale metagenomic sequencing. Video Abstract.
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Affiliation(s)
- Allison K Guitor
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Efrah I Yousuf
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Eileen K Hutton
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Katherine M Morrison
- Department of Pediatrics, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Jennifer C Stearns
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada.
- Department of Medicine, McMaster University, Hamilton, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.
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Allain T, DeMichele E, Stearns JC, Yunker W, Buret AG. Role of Oral Microbiota Biofilms in Recurrent Tonsillitis and Sleep‐Disordered Breathing in Children. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Warren Yunker
- Department of SurgeryCumming School of MedicineUniversity of CalgaryCalgaryAB
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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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Vazquez-Moreno M, Perez-Herrera A, Locia-Morales D, Dizzel S, Meyre D, Stearns JC, Cruz M. Association of gut microbiome with fasting triglycerides, fasting insulin and obesity status in Mexican children. Pediatr Obes 2021; 16:e12748. [PMID: 33191616 DOI: 10.1111/ijpo.12748] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/13/2020] [Accepted: 10/23/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND The association of gut microbiota with obesity and its cardio-metabolic complications in paediatric populations is still controversial. OBJECTIVE We investigated the association of obesity and cardio-metabolic traits with gut microbiota on 167 and 163 children with normal weight and obesity from Mexico City and Oaxaca, Mexico. METHODS Anthropometric and biochemical traits were measured. The microbial communities were determined by high-throughput sequencing of bacterial 16S rRNA gene v3-v4 region. RESULTS The gut microbial community structure was associated with obesity and fasting plasma insulin (FPI) in Mexico City (PObesity = 0.012, PFPI = 0.0003) and Oaxaca (PObesity = 0.034, PFPI = 0.016), and with triglycerides (TG) in Oaxaca (P = .0002). The Firmicutes/Bacteroidetes ratio was positively associated with TG in Oaxaca (P = .003). Firmicutes and Bacteroidetes phyla were positively and negatively associated with obesity (Mexico City: PFirmicutes = 0.013, PBacteroidetes = 0.009) and TG (Oaxaca: PFirmicutes = 0.002, PBacteroidetes = 0.004). In Oaxaca, Verrucomicrobia was negatively associated with obesity (P = .004). In Mexico City, the bacterial genus Fusicatenibacter, Romboutsia, Ruminococcaceae, Ruminiclostridium, Blautia, Clostridium, Anaerostipes and Intestinibacter were associated with obesity and FPI, while in Oaxaca, Bacteroides, Alistipes and Clostridium were associated with TG. CONCLUSION The gut microbial community structure in children is associated with obesity and FPI in Mexico City, and with obesity, FPI and TG in Oaxaca.
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Affiliation(s)
- Miguel Vazquez-Moreno
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Aleyda Perez-Herrera
- Consejo Nacional de Ciencia y Tecnología, Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Oaxaca, Oaxaca, Mexico
| | - Daniel Locia-Morales
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Sara Dizzel
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - David Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer C Stearns
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.,Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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De Souza RJ, Bilodeau NM, Gordon K, Davis AD, Stearns JC, Cranmer-Byng M, Gasparelli K, Davis Hill L, Anand SS. Entsisewata’karí:teke (You Will Be Healthy Again): Clinical Outcomes of Returning to a Traditional Haudenosaunee Diet. IJIH 2021. [DOI: 10.32799/ijih.v16i2.33098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Haudenosaunee Peoples of eastern North America have a strong agricultural tradition and culture associated with maize horticulture. Traditional foodways and diet were disrupted after the people were dispossessed from traditional lands maintained prior to colonization. As a result, Haudenosaunee have been disconnected from their traditional diet and lifestyle, and chronic diseases such as diabetes and obesity are increasing. Healthy Roots was developed in Six Nations of the Grand River territory by Haudenosaunee community members. It started as a 90-day challenge, in which participants adhere to a diet of traditional foods found in Haudenosaunee territories pre-European contact. The community decided to formally evaluate the impact of the diet in a pilot pre–post intervention study of 22 participants in 2016/17. We investigated the effects of the 3-month dietary intervention on physical measurements, ectopic fat (including visceral and liver adipose tissue), serum lipids, and hemoglobin A1c among Haudenosaunee participants in Six Nations. We provided biweekly Haudenosaunee food boxes, and offered workshops, cooking classes, and individual support from a dietitian. The intervention reduced body weight, body circumferences including waist circumference, hemoglobin A1c, and MRI-detected hepatic fat fraction. There were no adverse events. Engagement in the program was high and trends favoured improved well-being. The intervention shows great potential as a mechanism for improving physical health and restoring cultural connectedness and identity. The implications for improving mental health and community cohesion are also important areas to consider in future research.
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Yousuf EI, Carvalho M, Dizzell SE, Kim S, Gunn E, Twiss J, Giglia L, Stuart C, Hutton EK, Morrison KM, Stearns JC. Persistence of Suspected Probiotic Organisms in Preterm Infant Gut Microbiota Weeks After Probiotic Supplementation in the NICU. Front Microbiol 2020; 11:574137. [PMID: 33117319 PMCID: PMC7552907 DOI: 10.3389/fmicb.2020.574137] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 06/19/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022] Open
Abstract
Probiotics are becoming a prevalent supplement to prevent necrotizing enterocolitis in infants born preterm. However, little is known about the ability of these live bacterial supplements to colonize the gut or how they affect endogenous bacterial strains and the overall gut community. We capitalized on a natural experiment resulting from a policy change that introduced the use of probiotics to preterm infants in a single Neonatal Intensive Care Unit. We used amplicon sequence variants (ASVs) derived from the v3 region of the 16S rRNA gene to compare the prevalence and abundance of Bifidobacterium and Lactobacillus in the gut of preterm infants who were and were not exposed to a probiotic supplement in-hospital. Infants were followed to 5 months corrected age. In the probiotic-exposed infants, ASVs belonging to species of Bifidobacterium appeared at high relative abundance during probiotic supplementation and persisted for up to 5 months. In regression models that controlled for the confounding effects of age and antibiotic exposure, probiotic-exposed infants had a higher abundance of the suspected probiotic bifidobacteria than unexposed infants. Conversely, the relative abundance of Lactobacillus was similar between preterm groups over time. Lactobacillus abundance was inversely related to antibiotic exposure. Furthermore, the overall gut microbial community of the probiotic-exposed preterm infants at term corrected age clustered more closely to samples collected from 10-day old full-term infants than to samples from unexposed preterm infants at term age. In conclusion, routine in-hospital administration of probiotics to preterm infants resulted in the potential for colonization of the gut with probiotic organisms post-discharge and effects on the gut microbiome as a whole. Further research is needed to fully discriminate probiotic bacterial strains from endogenous strains and to explore their functional role in the gut microbiome and in infant health.
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Affiliation(s)
- Efrah I Yousuf
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada.,Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON, Canada
| | - Marilia Carvalho
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, ON, Canada
| | - Sara E Dizzell
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, ON, Canada
| | - Stephanie Kim
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada.,Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON, Canada
| | - Elizabeth Gunn
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada.,Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON, Canada
| | - Jennifer Twiss
- Department of Pediatrics, Division of Neonatology, McMaster University, Hamilton, ON, Canada
| | - Lucy Giglia
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Connie Stuart
- Neonatal Follow Up Clinic, McMaster Children's Hospital, Hamilton, ON, Canada
| | - Eileen K Hutton
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON, Canada.,Department of Obstetrics & Gynecology, McMaster University, Hamilton, ON, Canada
| | - Katherine M Morrison
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada.,Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON, Canada
| | - Jennifer C Stearns
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON, Canada.,Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
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9
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Wessels JM, Lajoie J, Cooper MIJH, Omollo K, Felker AM, Vitali D, Dupont HA, Nguyen PV, Mueller K, Vahedi F, Kimani J, Oyugi J, Cheruiyot J, Mungai JN, Deshiere A, Tremblay MJ, Mazzulli T, Stearns JC, Ashkar AA, Fowke KR, Surette MG, Kaushic C. Medroxyprogesterone acetate alters the vaginal microbiota and microenvironment in women and increases susceptibility to HIV-1 in humanized mice. Dis Model Mech 2019; 12:dmm.039669. [PMID: 31537512 PMCID: PMC6826019 DOI: 10.1242/dmm.039669] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 03/19/2019] [Accepted: 09/11/2019] [Indexed: 12/20/2022] Open
Abstract
The hormonal contraceptive medroxyprogesterone acetate (MPA) is associated with increased risk of human immunodeficiency virus (HIV), via incompletely understood mechanisms. Increased diversity in the vaginal microbiota modulates genital inflammation and is associated with increased HIV-1 acquisition. However, the effect of MPA on diversity of the vaginal microbiota is relatively unknown. In a cohort of female Kenyan sex workers, negative for sexually transmitted infections (STIs), with Nugent scores <7 (N=58 of 370 screened), MPA correlated with significantly increased diversity of the vaginal microbiota as assessed by 16S rRNA gene sequencing. MPA was also significantly associated with decreased levels of estrogen in the plasma, and low vaginal glycogen and α-amylase, factors implicated in vaginal colonization by lactobacilli, bacteria that are believed to protect against STIs. In a humanized mouse model, MPA treatment was associated with low serum estrogen, low glycogen and enhanced HIV-1 susceptibility. The mechanism by which the MPA-mediated changes in the vaginal microbiota may contribute to HIV-1 susceptibility in humans appears to be independent of inflammatory cytokines and/or activated T cells. Altogether, these results suggest MPA-induced hypo-estrogenism may alter key metabolic components that are necessary for vaginal colonization by certain bacterial species including lactobacilli, and allow for greater bacterial diversity in the vaginal microbiota. This article has an associated First Person interview with the first author of the paper. Summary: MPA may increase susceptibility to HIV-1 in sex workers through the suppression of endogenous estrogen, reducing vaginal glycogen and α-amylase levels, which increases bacterial diversity, potentially reducing protective bacterial species such as lactobacilli.
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Affiliation(s)
- Jocelyn M Wessels
- McMaster Immunology Research Centre, Michael G. DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Julie Lajoie
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada.,Department of Medical Microbiology, University of Nairobi, P.O. BOX 30197-00100, Nairobi, Kenya
| | - Maeve I J Hay Cooper
- McMaster Immunology Research Centre, Michael G. DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Kenneth Omollo
- Department of Medical Microbiology, University of Nairobi, P.O. BOX 30197-00100, Nairobi, Kenya
| | - Allison M Felker
- McMaster Immunology Research Centre, Michael G. DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Danielle Vitali
- McMaster Immunology Research Centre, Michael G. DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Haley A Dupont
- McMaster Immunology Research Centre, Michael G. DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Philip V Nguyen
- McMaster Immunology Research Centre, Michael G. DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Kristen Mueller
- McMaster Immunology Research Centre, Michael G. DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Fatemeh Vahedi
- McMaster Immunology Research Centre, Michael G. DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Joshua Kimani
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada.,Department of Medical Microbiology, University of Nairobi, P.O. BOX 30197-00100, Nairobi, Kenya.,Kenyan AIDS Control Program, P.O. Box 19361 - 00202, Nairobi, Kenya
| | - Julius Oyugi
- Department of Medical Microbiology, University of Nairobi, P.O. BOX 30197-00100, Nairobi, Kenya
| | | | - John N Mungai
- Kenyan AIDS Control Program, P.O. Box 19361 - 00202, Nairobi, Kenya
| | - Alexandre Deshiere
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, Québec City, Québec G1V 4G2, Canada.,Department of Microbiology and Immunology Medical Biology, Université Laval, Québec City, Québec G1V 0A6, Canada
| | - Michel J Tremblay
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, Québec City, Québec G1V 4G2, Canada.,Department of Microbiology and Immunology Medical Biology, Université Laval, Québec City, Québec G1V 0A6, Canada
| | - Tony Mazzulli
- Public Health Laboratories, Public Health Ontario, Toronto, Ontario M5G 1V2, Canada.,Mount Sinai Hospital/University Health Network, Department of Microbiology, Toronto, Ontario M5G 1X5, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jennifer C Stearns
- Department of Medicine, Farncombe Family Digestive Health Institute, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Ali A Ashkar
- McMaster Immunology Research Centre, Michael G. DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Keith R Fowke
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada.,Department of Medical Microbiology, University of Nairobi, P.O. BOX 30197-00100, Nairobi, Kenya
| | - Michael G Surette
- Department of Medicine, Farncombe Family Digestive Health Institute, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,McMaster Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Charu Kaushic
- McMaster Immunology Research Centre, Michael G. DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, Ontario L8S 4K1, Canada .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada.,McMaster Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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10
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Foley KP, Zlitni S, Denou E, Duggan BM, Chan RW, Stearns JC, Schertzer JD. Long term but not short term exposure to obesity related microbiota promotes host insulin resistance. Nat Commun 2018; 9:4681. [PMID: 30409977 PMCID: PMC6224578 DOI: 10.1038/s41467-018-07146-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 10/15/2018] [Indexed: 12/21/2022] Open
Abstract
The intestinal microbiota and insulin sensitivity are rapidly altered after ingestion of obesogenic diets. We find that changes in the composition of the fecal microbiota precede changes in glucose tolerance when mice are fed obesogenic, low fiber, high fat diets (HFDs). Antibiotics alter glycemia during the first week of certain HFDs, but antibiotics show a more robust improvement in glycemic control in mice with protracted obesity caused by long-term feeding of multiple HFDs. Microbiota transmissible dysglycemia and glucose intolerance only occur when germ-free mice are exposed to obesity-related microbes for more than 45 days. We find that sufficient host exposure time to microbiota derived from HFD-fed mice allows microbial factors to contribute to insulin resistance, independently from increased adiposity in mice. Our results are consistent with intestinal microbiota contributing to chronic insulin resistance and dysglycemia during prolonged obesity, despite rapid diet-induced changes in the taxonomic composition of the fecal microbiota. Gut microbiota impact host metabolism and gut microbiome composition reflects dietary habits. Here the authors show that, in animals fed obesogenic diets, changes in gut microbiota precede changes in glucose homeostasis. Importantly, long term exposure of the host to the changed microbiota is required to impair glucose homeostasis.
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Affiliation(s)
- Kevin P Foley
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, L8N 3Z5, ON, Canada
| | - Soumaya Zlitni
- Departments of Genetics and Medicine, Stanford University, Stanford, 94305, California, USA
| | - Emmanuel Denou
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, L8N 3Z5, ON, Canada
| | - Brittany M Duggan
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, L8N 3Z5, ON, Canada
| | - Rebecca W Chan
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, L8N 3Z5, ON, Canada
| | - Jennifer C Stearns
- Department of Medicine, McMaster University, Hamilton, L8N 3Z5, ON, Canada
| | - Jonathan D Schertzer
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, L8N 3Z5, ON, Canada.
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11
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Jarde A, Lewis-Mikhael AM, Moayyedi P, Stearns JC, Collins SM, Beyene J, McDonald SD. Pregnancy outcomes in women taking probiotics or prebiotics: a systematic review and meta-analysis. BMC Pregnancy Childbirth 2018; 18:14. [PMID: 29310610 PMCID: PMC5759212 DOI: 10.1186/s12884-017-1629-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [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: 06/05/2017] [Accepted: 12/14/2017] [Indexed: 12/15/2022] Open
Abstract
Background Probiotics are living microorganisms that, when administered in adequate amounts, confer a health benefit. It has been speculated that probiotics might help prevent preterm birth, but in two previous systematic reviews possible major increases in this risk have been suggested. Our objective was to perform a systematic review and meta-analysis of the risk of preterm birth and other adverse pregnancy outcomes in pregnant women taking probiotics, prebiotics or synbiotics. Methods We searched six electronic databases (MEDLINE, EMBASE, CINAHL, Cochrane Central Register of Controlled Trials, Web of Science’s Core collection and BIOSIS Preview) up to September 2016 and contacted authors for additional data. We included randomized controlled trials in which women with a singleton pregnancy received a probiotic, prebiotic or synbiotic intervention. Two independent reviewers extracted data using a piloted form and assessed the risk of bias using the Cochrane risk of bias tool. We used random-effects meta-analyses to pool the results. Results We identified 2574 publications, screened 1449 non-duplicate titles and abstracts and read 160 full text articles. The 49 publications that met our inclusion criteria represented 27 studies. No study used synbiotics, one used prebiotics and the rest used probiotics. Being randomized to take probiotics during pregnancy neither increased nor decreased the risk of preterm birth < 34 weeks (RR 1.03, 95% CI 0.29–3.64, I2 0%, 1017 women in 5 studies), preterm birth < 37 weeks (RR 1.08, 95% CI 0.71–1.63, I2 0%, 2484 women in 11 studies), or most of our secondary outcomes, including gestational diabetes mellitus. Conclusions We found no evidence that taking probiotics or prebiotics during pregnancy either increases or decreases the risk of preterm birth or other infant and maternal adverse pregnancy outcomes. Trial registration We prospectively published the protocol for this study in the PROSPERO database (CRD42016048129). Electronic supplementary material The online version of this article (10.1186/s12884-017-1629-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Jarde
- Department of Obstetrics and Gynecology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
| | - Anne-Mary Lewis-Mikhael
- Department of Obstetrics and Gynecology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Paul Moayyedi
- Department of Medicine, Gastroenterology Division, McMaster University, Hamilton, ON, Canada
| | - Jennifer C Stearns
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Stephen M Collins
- Farncombe Family Digestive Health Research Institute, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Joseph Beyene
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
| | - Sarah D McDonald
- Department of Obstetrics and Gynecology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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12
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Abstract
Microbiome research of host-associated communities has been advanced recently through improvements in sequencing technologies and bioinformatic methods. Traditional microbiological culture, when combined with molecular techniques, can provide a sensitive platform to comprehensively study the airway microbiota. Here we describe the culture methods necessary to capture a large proportion of the airway microbiota and molecular methods for profiling bacterial communities through the 16S rRNA gene, which, when combined, offer a more complete picture of the diversity of airway microbial communities than either method alone.
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Affiliation(s)
- Fiona J Whelan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Laura Rossi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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13
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Stearns JC, Simioni J, Gunn E, McDonald H, Holloway AC, Thabane L, Mousseau A, Schertzer JD, Ratcliffe EM, Rossi L, Surette MG, Morrison KM, Hutton EK. Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants. Sci Rep 2017; 7:16527. [PMID: 29184093 PMCID: PMC5705725 DOI: 10.1038/s41598-017-16606-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/10/2017] [Indexed: 01/15/2023] Open
Abstract
Early life microbial colonization and succession is critically important to healthy development with impacts on metabolic and immunologic processes throughout life. A longitudinal prospective cohort was recruited from midwifery practices to include infants born at full term gestation to women with uncomplicated pregnancies. Here we compare bacterial community succession in infants born vaginally, with no exposure to antibiotics (n = 53), with infants who were exposed to intrapartum antibiotic prophylaxis (IAP) for Group B Streptococcus (GBS; n = 14), and infants born by C-section (n = 7). Molecular profiles of the 16 S rRNA genes indicate that there is a delay in the expansion of Bifidobacterium, which was the dominate infant gut colonizer, over the first 12 weeks and a persistence of Escherichia when IAP for GBS exposure is present during vaginal labour. Longer duration of IAP exposure increased the magnitude of the effect on Bifidobacterium populations, suggesting a longer delay in microbial community maturation. As with prior studies, we found altered gut colonisation following C-section that included a notable lack of Bacteroidetes. This study found that exposure of infants to IAP for GBS during vaginal birth affected aspects of gut microbial ecology that, although dramatic at early time points, disappeared by 12 weeks of age in most infants.
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Affiliation(s)
- Jennifer C Stearns
- Department of Medicine, McMaster University, Hamilton, Canada. .,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.
| | - Julia Simioni
- Midwifery Education Program, McMaster University, Hamilton, Canada
| | - Elizabeth Gunn
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - Helen McDonald
- Midwifery Education Program, McMaster University, Hamilton, Canada
| | - Alison C Holloway
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, Canada
| | - Lehana Thabane
- Department of Clinical Epidemiology & Biostatistics, McMaster University, Hamilton, Canada
| | - Andrea Mousseau
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, Canada
| | - Jonathan D Schertzer
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.,Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Elyanne M Ratcliffe
- Department of Pediatrics, McMaster University, Hamilton, Canada.,Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Laura Rossi
- Department of Medicine, McMaster University, Hamilton, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
| | - Michael G Surette
- Department of Medicine, McMaster University, Hamilton, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.,Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Canada
| | | | - Eileen K Hutton
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, Canada
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14
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Cavallari JF, Fullerton MD, Duggan BM, Foley KP, Denou E, Smith BK, Desjardins EM, Henriksbo BD, Kim KJ, Tuinema BR, Stearns JC, Prescott D, Rosenstiel P, Coombes BK, Steinberg GR, Schertzer JD. Muramyl Dipeptide-Based Postbiotics Mitigate Obesity-Induced Insulin Resistance via IRF4. Cell Metab 2017; 25:1063-1074.e3. [PMID: 28434881 DOI: 10.1016/j.cmet.2017.03.021] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/08/2017] [Accepted: 03/24/2017] [Indexed: 12/16/2022]
Abstract
Intestinal dysbiosis contributes to obesity and insulin resistance, but intervening with antibiotics, prebiotics, or probiotics can be limited by specificity or sustained changes in microbial composition. Postbiotics include bacterial components such as lipopolysaccharides, which have been shown to promote insulin resistance during metabolic endotoxemia. We found that bacterial cell wall-derived muramyl dipeptide (MDP) is an insulin-sensitizing postbiotic that requires NOD2. Injecting MDP lowered adipose inflammation and reduced glucose intolerance in obese mice without causing weight loss or altering the composition of the microbiome. MDP reduced hepatic insulin resistance during obesity and low-level endotoxemia. NOD1-activating muropeptides worsened glucose tolerance. IRF4 distinguished opposing glycemic responses to different types of peptidoglycan and was required for MDP/NOD2-induced insulin sensitization and lower metabolic tissue inflammation during obesity and endotoxemia. IRF4 was dispensable for exacerbated glucose intolerance via NOD1. Mifamurtide, an MDP-based drug with orphan drug status, was an insulin sensitizer at clinically relevant doses in obese mice.
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Affiliation(s)
- Joseph F Cavallari
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Morgan D Fullerton
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Brittany M Duggan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Kevin P Foley
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Emmanuel Denou
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Brennan K Smith
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Eric M Desjardins
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Brandyn D Henriksbo
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Kalvin J Kim
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Brian R Tuinema
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Jennifer C Stearns
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8N 3Z5, Canada; Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - David Prescott
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology (IKMB), University of Kiel, Schittenhelmstrasse 12, 24105 Kiel, Germany
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Gregory R Steinberg
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Jonathan D Schertzer
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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15
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Stearns JC, Zulyniak MA, de Souza RJ, Campbell NC, Fontes M, Shaikh M, Sears MR, Becker AB, Mandhane PJ, Subbarao P, Turvey SE, Gupta M, Beyene J, Surette MG, Anand SS. Ethnic and diet-related differences in the healthy infant microbiome. Genome Med 2017; 9:32. [PMID: 28356137 PMCID: PMC5372248 DOI: 10.1186/s13073-017-0421-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [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: 06/22/2016] [Accepted: 03/04/2017] [Indexed: 12/12/2022] Open
Abstract
Background The infant gut is rapidly colonized by microorganisms soon after birth, and the composition of the microbiota is dynamic in the first year of life. Although a stable microbiome may not be established until 1 to 3 years after birth, the infant gut microbiota appears to be an important predictor of health outcomes in later life. Methods We obtained stool at one year of age from 173 white Caucasian and 182 South Asian infants from two Canadian birth cohorts to gain insight into how maternal and early infancy exposures influence the development of the gut microbiota. We investigated whether the infant gut microbiota differed by ethnicity (referring to groups of people who have certain racial, cultural, religious, or other traits in common) and by breastfeeding status, while accounting for variations in maternal and infant exposures (such as maternal antibiotic use, gestational diabetes, vegetarianism, infant milk diet, time of introduction of solid food, infant birth weight, and weight gain in the first year). Results We demonstrate that ethnicity and infant feeding practices independently influence the infant gut microbiome at 1 year, and that ethnic differences can be mapped to alpha diversity as well as a higher abundance of lactic acid bacteria in South Asians and a higher abundance of genera within the order Clostridiales in white Caucasians. Conclusions The infant gut microbiome is influenced by ethnicity and breastfeeding in the first year of life. Ethnic differences in the gut microbiome may reflect maternal/infant dietary differences and whether these differences are associated with future cardiometabolic outcomes can only be determined after prospective follow-up. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0421-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer C Stearns
- Department of Medicine, McMaster University, Hamilton, ON, Canada. .,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada.
| | | | - Russell J de Souza
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | | | - Michelle Fontes
- Department of Medicine, McMaster University, Hamilton, ON, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Mateen Shaikh
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Malcolm R Sears
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Allan B Becker
- Department of Immunology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Piushkumar J Mandhane
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Padmaja Subbarao
- Hospital for Sick Children & Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Stuart E Turvey
- BC Children's Hospital and Child and Family Research Institute, Department of Paediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Milan Gupta
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Joseph Beyene
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Michael G Surette
- Department of Medicine, McMaster University, Hamilton, ON, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Sonia S Anand
- Department of Medicine, McMaster University, Hamilton, ON, Canada.,Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
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16
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Simioni J, Hutton EK, Gunn E, Holloway AC, Stearns JC, McDonald H, Mousseau A, Schertzer JD, Ratcliffe EM, Thabane L, Surette MG, Morrison KM. A comparison of intestinal microbiota in a population of low-risk infants exposed and not exposed to intrapartum antibiotics: The Baby & Microbiota of the Intestine cohort study protocol. BMC Pediatr 2016; 16:183. [PMID: 27832763 PMCID: PMC5103394 DOI: 10.1186/s12887-016-0724-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 11/02/2016] [Indexed: 02/08/2023] Open
Abstract
Background The intestinal microbiota influences metabolic, nutritional, and immunologic processes and has been associated with a broad range of adverse health outcomes including asthma, obesity and Type 2 diabetes. Early life exposures may alter the course of gut microbial colonization leading to differences in metabolic and immune regulation throughout life. Although approximately 50 % of low-risk full-term infants born in Canada are exposed to intrapartum antibiotics, little is known about the influence of this common prophylactic treatment on the developing neonatal intestinal microbiota. The purpose of this study is to describe the intestinal microbiome over the first 3 years of life among healthy, breastfed infants born to women with low-risk pregnancies at full term gestation and to determine if at 1 year of age, the intestinal microbiome of infants exposed to intrapartum antibiotics differs in type and quantity from the infants that are not exposed. Methods A prospectively followed cohort of 240 mother-infant pairs will be formed by enrolling eligible pregnant women from midwifery practices in the City of Hamilton and surrounding area in Ontario, Canada. Participants will be followed until the age of 3 years. Women are eligible to participate in the study if they are considered to be low-risk, planning a vaginal birth and able to communicate in English. Women are excluded if they have a multiple pregnancy or a preterm birth. Study questionnaires are completed, anthropometric measures are taken and biological samples are acquired including eight infant stool samples between 3 days and 3 years of age. Discussion Our experience to date indicates that midwifery practices and clients are keen to participate in this research. The midwifery client population is likely to have high rates of breastfeeding and low rates of intervention, allowing us to examine the comparative development of the microbiome in a relatively healthy and homogenous population. Results from this study will make an important contribution to the growing understanding of the patterns of intestinal microbiome colonization in the early years of life and may have implications for best practices to support the establishment of the microbiome at birth. Electronic supplementary material The online version of this article (doi:10.1186/s12887-016-0724-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia Simioni
- Midwifery Education Program, McMaster University, Hamilton, ON, Canada
| | - Eileen K Hutton
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, ON, Canada
| | - Elizabeth Gunn
- Department of Pediatrics, McMaster University, HSC 3A59 1280 Main St W, L8N 3Z5, Hamilton, ON, Canada
| | - Alison C Holloway
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, ON, Canada
| | - Jennifer C Stearns
- Department of Medicine, McMaster University, Hamilton, ON, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Helen McDonald
- Midwifery Education Program, McMaster University, Hamilton, ON, Canada
| | - Andrea Mousseau
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, ON, Canada
| | - Jonathan D Schertzer
- Department of Pediatrics, McMaster University, HSC 3A59 1280 Main St W, L8N 3Z5, Hamilton, ON, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Elyanne M Ratcliffe
- Department of Pediatrics, McMaster University, HSC 3A59 1280 Main St W, L8N 3Z5, Hamilton, ON, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Lehana Thabane
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada.,Centre for Evaluation of Medicines, St. Joseph's Healthcare Hamilton, Hamilton, ON, Canada
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Katherine M Morrison
- Department of Pediatrics, McMaster University, HSC 3A59 1280 Main St W, L8N 3Z5, Hamilton, ON, Canada.
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17
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Pirbaglou M, Katz J, de Souza RJ, Stearns JC, Motamed M, Ritvo P. Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials. Nutr Res 2016; 36:889-898. [PMID: 27632908 DOI: 10.1016/j.nutres.2016.06.009] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/14/2016] [Accepted: 06/17/2016] [Indexed: 12/15/2022]
Abstract
Gastrointestinal microbiota, consisting of microbial communities in the gastrointestinal tract, play an important role in digestive, metabolic, and immune functioning. Preclinical studies on rodents have linked behavioral and neurochemical changes in the central nervous system with deficits or alterations in these bacterial communities. Moreover, probiotic supplementation in rodents has been shown to markedly change behavior, with correlated changes in central neurochemistry. While such studies have documented behavioral and mood-related supplementation effects, the significance of these effects in humans, especially in relation to anxiety and depression symptoms, are relatively unknown. Thus, the purpose of this paper was to systematically evaluate current literature on the impact of probiotic supplementation on anxiety and depression symptoms in humans. To this end, multiple databases, including Medline, PsycINFO, PubMed, Scopus, and Web of Science were searched for randomized controlled trials published between January 1990 and January 2016. Search results led to a total of 10 randomized controlled trials (4 in clinically diagnosed and 6 in non-clinical samples) that provided limited support for the use of some probiotics in reducing human anxiety and depression. Despite methodological limitations of the included trials and the complex nature of gut-brain interactions, results suggest the detection of apparent psychological benefits from probiotic supplementation. Nevertheless a better understanding of developmental, modulatory, and metagenomic influences on the GI microbiota, specifically as they relate to mood and mental health, represent strong priorities for future research in this area.
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Affiliation(s)
- Meysam Pirbaglou
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - Joel Katz
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada; Department of Psychology, York University, Toronto, Ontario, Canada
| | - Russell J de Souza
- Department of Clinical Epidemiology & Biostatistics, McMaster University, Hamilton, Ontario, Canada
| | | | - Mehras Motamed
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - Paul Ritvo
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada; Department of Psychology, York University, Toronto, Ontario, Canada; University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
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18
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Stearns JC, Davidson CJ, McKeon S, Whelan FJ, Fontes ME, Schryvers AB, Bowdish DME, Kellner JD, Surette MG. Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. ISME J 2015; 9:1268. [PMID: 25897775 DOI: 10.1038/ismej.2015.49] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Stearns JC, Davidson CJ, McKeon S, Whelan FJ, Fontes ME, Schryvers AB, Bowdish DME, Kellner JD, Surette MG. Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. ISME J 2015; 9:1246-59. [PMID: 25575312 DOI: 10.1038/ismej.2014.250] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 01/24/2023]
Abstract
The upper respiratory tract (URT) is a crucial site for host defense, as it is home to bacterial communities that both modulate host immune defense and serve as a reservoir of potential pathogens. Young children are at high risk of respiratory illness, yet the composition of their URT microbiota is not well understood. Microbial profiling of the respiratory tract has traditionally focused on culturing common respiratory pathogens, whereas recent culture-independent microbiome profiling can only report the relative abundance of bacterial populations. In the current study, we used both molecular profiling of the bacterial 16S rRNA gene and laboratory culture to examine the bacterial diversity from the oropharynx and nasopharynx of 51 healthy children with a median age of 1.1 years (range 1-4.5 years) along with 19 accompanying parents. The resulting profiles suggest that in young children the nasopharyngeal microbiota, much like the gastrointestinal tract microbiome, changes from an immature state, where it is colonized by a few dominant taxa, to a more diverse state as it matures to resemble the adult microbiota. Importantly, this difference in bacterial diversity between adults and children accompanies a change in bacterial load of three orders of magnitude. This indicates that the bacterial communities in the nasopharynx of young children have a fundamentally different structure from those in adults and suggests that maturation of this community occurs sometime during the first few years of life, a period that includes ages at which children are at the highest risk for respiratory disease.
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Affiliation(s)
| | - Carla J Davidson
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Suzanne McKeon
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Fiona J Whelan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Michelle E Fontes
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Anthony B Schryvers
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Dawn M E Bowdish
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - James D Kellner
- 1] Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada [2] Department of Paediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Michael G Surette
- 1] Department of Medicine, McMaster University, Hamilton, Ontario, Canada [2] Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada [3] Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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20
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Stearns JC, Woody OZ, McConkey BJ, Glick BR. Effects of bacterial ACC deaminase on Brassica napus gene expression. Mol Plant Microbe Interact 2012; 25:668-676. [PMID: 22352713 DOI: 10.1094/mpmi-08-11-0213] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Plants in association with plant growth-promoting rhizobacteria can benefit from lower plant ethylene levels through the action of the bacterial enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. This enzyme cleaves the immediate biosynthetic precursor of ethylene, ACC. Ethylene is responsible for many aspects of plant growth and development but, under stressful conditions, it exacerbates stress symptoms. The ACC deaminase-containing bacterium Pseudomonas putida UW4 is a potent plant growth-promoting strain and, as such, was used to elaborate the detailed role of bacterial ACC deaminase in Brassica napus (canola) plant growth promotion. Transcriptional changes in bacterially treated canola plants were investigated with the use of an Arabidopsis thaliana oligonucleotide microarray. A heterologous approach was necessary because there are few tools available at present to measure global expression changes in nonmodel organisms, specifically with the sensitivity of microarrays. The results indicate that the transcription of genes involved in plant hormone regulation, secondary metabolism, and stress response was altered in plants by the presence of the bacterium, whereas the upregulation of genes for auxin response factors and the downregulation of stress response genes was observed only in the presence of bacterial ACC deaminase. These results support the suggestion that there is a direct link between ethylene and the auxin response, which has been suggested from physiological studies, and provide more evidence for the stress-reducing benefits of ACC deaminase-expressing plant growth-promoting bacteria.
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Stearns JC, Lynch MDJ, Senadheera DB, Tenenbaum HC, Goldberg MB, Cvitkovitch DG, Croitoru K, Moreno-Hagelsieb G, Neufeld JD. Bacterial biogeography of the human digestive tract. Sci Rep 2011; 1:170. [PMID: 22355685 PMCID: PMC3240969 DOI: 10.1038/srep00170] [Citation(s) in RCA: 284] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 11/07/2011] [Indexed: 02/08/2023] Open
Abstract
We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated >32 million paired-end sequences of bacterial 16S rRNA genes (V3 region) representing >95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with >99% Good's coverage for all samples. The highest OTU richness and phylogenetic diversity was found in the mouth samples. The microbial communities of multiple biopsy sites within the colon were highly similar within individuals and largely distinct from those in stool. Within an individual, OTU overlap among broad site definitions (mouth, stomach/duodenum, colon and stool) ranged from 32–110 OTUs, 25 of which were common to all individuals and included OTUs affiliated with Faecalibacterium prasnitzii and the TM7 phylum. This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease.
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Affiliation(s)
- Jennifer C Stearns
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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22
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Sauder LA, Engel K, Stearns JC, Masella AP, Pawliszyn R, Neufeld JD. Aquarium nitrification revisited: Thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters. PLoS One 2011; 6:e23281. [PMID: 21858055 PMCID: PMC3156731 DOI: 10.1371/journal.pone.0023281] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 07/11/2011] [Indexed: 01/25/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS) indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology.
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Affiliation(s)
- Laura A. Sauder
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | | | - Andre P. Masella
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Richard Pawliszyn
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Josh D. Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- * E-mail:
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23
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Glick BR, Stearns JC. Making phytoremediation work better: maximizing a plant's growth potential in the midst of adversity. Int J Phytoremediation 2011; 13 Suppl 1:4-16. [PMID: 22046748 DOI: 10.1080/15226514.2011.568533] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
While a number of different plants can either breakdown a variety of organic contaminants or hyperaccumulate metals from the environment, even the most efficient of those plants is typically inhibited by the presence of the toxicant(s). The plant stress that is induced by the presence of various environmental toxicants typically limits a plant's growth and ultimately its ability to phytoremediate the toxicant(s). Here, it is argued that the simple strategy of adding plant growth-promoting bacteria (preferably endophytes) that reduce plant ethylene levels by ACC deaminase activity and have the ability to synthesize the phytohoromone IAA, and are used to phytoremediate various toxicants can significantly (and often dramatically) increase both plant growth and phytoremediation activity in the presence of those toxicants.
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Affiliation(s)
- Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
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Stearns JC, Shah S, Greenberg BM, Dixon DG, Glick BR. Tolerance of transgenic canola expressing 1-aminocyclopropane-1-carboxylic acid deaminase to growth inhibition by nickel. Plant Physiol Biochem 2005; 43:701-8. [PMID: 16023358 DOI: 10.1016/j.plaphy.2005.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Accepted: 05/09/2005] [Indexed: 05/03/2023]
Abstract
Plant growth-promoting bacteria are useful to phytoremediation strategies in that they confer advantages to plants in contaminated soil. When plant growth-promoting bacteria contain the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, the bacterial cell acts as a sink for ACC, the immediate biosynthetic precursor of the plant growth regulator ethylene thereby lowering plant ethylene levels and decreasing the negative effects of various environmental stresses. In an effort to gain the advantages provided by bacterial ACC deaminase in the phytoremediation of metals from the environment two transgenic canola lines with the gene for this enzyme were generated and tested. In these transgenic canola plants, expression of the ACC deaminase gene is driven by either tandem constitutive cauliflower mosaic virus (CaMV) 35S promoters or the root specific rolD promoter from Agrobacterium rhizogenes. Following the growth of transgenic and non-transformed canola in nickel contaminated soil, it was observed that the rolD plants demonstrate significantly increased tolerance to nickel compared to the non-transformed control plants.
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Affiliation(s)
- Jennifer C Stearns
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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25
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Abstract
The plant hormone ethylene is an essential signaling molecule involved in many plant processes including: germination, flower development, fruit ripening and responses to many environmental stimuli. Moreover, large increases in ethylene levels occur during plant stress responses, fruit ripening and flower wilting. Manipulation of ethylene biosynthesis or perception allows us to modulate these processes and thereby create plants with more robust and/or desirable traits, giving us a glimpse into the role of ethylene in the plant. Here, recent and landmark advances in genetic alteration of members of the ethylene pathway in plants and the physiological consequences of these alterations are examined.
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