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Coker MO, Laue HE, Hoen AG, Hilliard M, Dade E, Li Z, Palys T, Morrison HG, Baker E, Karagas MR, Madan JC. Infant Feeding Alters the Longitudinal Impact of Birth Mode on the Development of the Gut Microbiota in the First Year of Life. Front Microbiol 2021; 12:642197. [PMID: 33897650 PMCID: PMC8059768 DOI: 10.3389/fmicb.2021.642197] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
Cesarean-delivered (CD) infants harbor a distinct gut microbiome from vaginally delivered (VD) infants, however, during infancy, the most important driver of infant gut microbial colonization is infant feeding. Earlier studies have shown that breastfeeding is associated with higher levels of health-promoting bacteria such and Bifidobacterium and Bacteroides via modulation of the immune system, and production of metabolites. As the infant gut matures and solid foods are introduced, it is unclear whether longer duration of breast feeding restore loss of beneficial taxa within the intestinal microbiota of operatively delivered infants. Within the New Hampshire Birth Cohort Study, we evaluated the longitudinal effect of delivery mode and infant feeding on the taxonomic composition and functional capacity of developing gut microbiota in the First year of life. Microbiota of 500 stool samples collected between 6 weeks and 12 months of age (from 229 infants) were characterized by 16S ribosomal RNA sequencing. Shotgun metagenomic sequencing was also performed on 350 samples collected at either 6 weeks or 12 months of age. Among infant participants, 28% were cesarean-delivered (CD) infants and most (95%) initiated breastfeeding within the first six months of life, with 26% exclusively breastfed and 69% mixed-fed (breast milk and formula), in addition to complementary foods by age 1. Alpha (within-sample) diversity was significantly lower in CD infants compared to vaginally delivered (VD) infants (P < 0.05) throughout the study period. Bacterial community composition clustering by both delivery mode and feeding duration at 1 year of age revealed that CD infants who were breast fed for < 6 months were more dissimilar to VD infants than CD infants who breast fed for ≥ 6 months. We observed that breastfeeding modified the longitudinal impact of delivery mode on the taxonomic composition of the microbiota by 1 year of age, with an observed increase in abundance of Bacteroides fragilis and Lactobacillus with longer duration of breastfeeding among CD infants while there was an increase in Faecalibacterium for VD infants. Our findings confirm that duration of breastfeeding plays a critical role in restoring a health-promoting microbiome, call for further investigations regarding the association between breast milk exposure and health outcomes in early life.
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Affiliation(s)
- Modupe O. Coker
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
- School of Dental Medicine, School of Public Health at Rutgers, Newark, NJ, United States
| | - Hannah E. Laue
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Anne G. Hoen
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
- Center for Molecular Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, United States
| | - Margaret Hilliard
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Erika Dade
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Zhigang Li
- Department of Biostatistics, University of Florida, Gainsville, FL, United States
| | - Thomas Palys
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, United States
| | - Hilary G. Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
| | - Emily Baker
- Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH, United States
| | - Margaret R. Karagas
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
- Center for Molecular Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, United States
| | - Juliette C. Madan
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, United States
- Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH, United States
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Antosca K, Hoen AG, Palys T, Hilliard M, Morrison HG, Coker M, Madan J, Karagas MR. Reliability of stool microbiome methods for DNA yields and sequencing among infants and young children. Microbiologyopen 2020; 9:e1018. [PMID: 32166902 PMCID: PMC7221451 DOI: 10.1002/mbo3.1018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/04/2020] [Accepted: 02/11/2020] [Indexed: 12/15/2022] Open
Abstract
With the emergence of large‐scale epidemiologic human microbiome studies, there is a need to understand the reproducibility of microbial DNA sequencing and the impact of specimen collection and processing methods on measures of microbial community composition and structure, with reproducibility studies in infants and young children particularly lacking. Here, we examined batch‐to‐batch variability and reliability of collection, handling, and processing protocols, testing replicate stool samples from infants and young children using Illumina MiSeq sequencing of the bacterial 16S rRNA gene V4‐V5 hypervariable region, evaluating 33 conditions with different protocols and extraction methods. We detected no evidence of batch effects in replicate DNA samples or extractions from the same stool sample. Variability in DNA yield and alpha diversity was observed between the different collection, handling, and processing protocols. However, across all protocols, subject variability was the dominant contributor to microbiome structure, with comparatively little impact of the protocol used. While collection method and DNA extraction kit may affect DNA yield, and correspondingly alpha diversity, our findings suggest that characterization of the structure and composition of the fecal microbiome of infants and young children are reliably measurable by standardized collection, handling, and processing protocols and DNA extraction methods within an individual longitudinal study.
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Affiliation(s)
- Katherine Antosca
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.,Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Anne G Hoen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.,Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.,Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Lebanon, NH, USA
| | - Thomas Palys
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.,Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Margaret Hilliard
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Modupe Coker
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Juliette Madan
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.,Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.,Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Lebanon, NH, USA.,Division of Neonatology, Department of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.,Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.,Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Lebanon, NH, USA
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Beltman ME, Mullen MP, Elia G, Hilliard M, Diskin MG, Evans AC, Crowe MA. Global proteomic characterization of uterine histotroph recovered from beef heifers yielding good quality and degenerate day 7 embryos. Domest Anim Endocrinol 2014; 46:49-57. [PMID: 24210454 DOI: 10.1016/j.domaniend.2013.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/02/2013] [Accepted: 10/08/2013] [Indexed: 12/29/2022]
Abstract
The objective was to analyze the proteomic composition of uterine flushes collected from beef heifers on day 7 after insemination. Estrus was synchronized in crossbred beef heifers by using a protocol with a controlled intravaginal drug releasing device. Heifers detected in standing estrus (within 24-48 h after removal of controlled intravaginal drug releasing device) were inseminated (estrus = day 0) with frozen-thawed semen from a single ejaculate of a bull with proven fertility. Heifers from which an embryo was recovered (after slaughter on day 7) were classified as either having a viable embryo (morula/blastocyst stage) or a degenerate embryo (arrested at the 2- to 16-cell stage). The overall recovery rate (viable and degenerate combined) was 64%. Global liquid chromatography coupled to tandem mass spectrometry proteomic analysis of the histotroph collected identified 40 high-confidence proteins present on day 7; 26 proteins in the viable group, 10 in the degenerate group, and 4 shared between both groups. Five proteins (platelet-activating factor acetylhydrolase IB subunit γ [PAFAH1B3], tubulin α-1D chain, tubulin β-4A chain, cytochrome C, and dihydropyrimidinase-related protein-2) were unique or more abundant in the histotroph collected from animals with a viable embryo, and 1 protein (S100-A4) was more abundant in the histotroph collected from animals with a degenerate embryo. Of interest, PAFAH1B3, detected only in histotroph from the group yielding viable embryos, belongs to the group of platelet-activating factors that are known to be important for the development of the pre-implantation embryo in other species. To our knowledge this is the first report of PAFAH1B3 in relation to bovine early embryonic development.
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Affiliation(s)
- M E Beltman
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - M P Mullen
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Teagasc, Animal and Bioscience Research Centre, Animal & Grassland Research and Innovation Centre, Athenry, County Galway, Ireland
| | - G Elia
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - M Hilliard
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; National Institute for Bioprocessing Research & Training, Blackrock, County Dublin, Ireland
| | - M G Diskin
- Teagasc, Animal and Bioscience Research Centre, Animal & Grassland Research and Innovation Centre, Athenry, County Galway, Ireland
| | - A C Evans
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - M A Crowe
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Teagasc, Animal and Bioscience Research Centre, Animal & Grassland Research and Innovation Centre, Athenry, County Galway, Ireland; Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Sample S, Hilliard M. 410: Does a Mobile Voice-Over Internet Protocol Communications System Improve Emergency Department Efficiency? Ann Emerg Med 2008. [DOI: 10.1016/j.annemergmed.2008.06.438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Molloy ES, Morgan MP, Doherty GA, McDonnell B, Hilliard M, O'Byrne J, Fitzgerald DJ, McCarthy GM. Mechanism of basic calcium phosphate crystal-stimulated cyclo-oxygenase-1 up-regulation in osteoarthritic synovial fibroblasts. Rheumatology (Oxford) 2008; 47:965-71. [DOI: 10.1093/rheumatology/ken144] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Abstract
BACKGROUND In 1995, a program was begun at the University of South Alabama (USA) to improve the reporting of medical risk factors on birth certificates. METHODS Data on medical risk factors for USA Hospital and the remainder of the state for 1994 and 1996 were examined to observe the effects of the USA Medical Center program. RESULTS The number of medical risk factors reported changed markedly between 1994 and 1996 for most items and changed hardly at all for the remainder of the state. The changes for selected factors from 1994 to 1996 were as follows: anemia, 19 (0.4% of all birth certificates) to 489 (12.3%); acute or chronic lung disease, 1 (<0.1%) to 405 (10.2%); cardiac disease, 10 (0.2%) to 99 (2.5%); diabetes, 111 (2.6%) to 160 (4.0%); genital herpes, 3 (0.1%) to 81 (2.0%); and hemoglobinopathy, 0 (0%) to 166 (4.2%). Changes in other factors were similar. CONCLUSIONS The USA Medical Center program has significantly increased the frequency and percent of birth certificates indicating medical risk factors.
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Affiliation(s)
- L A Woolbright
- Alabama Department of Public Health, Center for Health Statistics, Montgomery 36103, USA
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Loftus SK, Chen Y, Gooden G, Ryan JF, Birznieks G, Hilliard M, Baxevanis AD, Bittner M, Meltzer P, Trent J, Pavan W. Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis. Proc Natl Acad Sci U S A 1999; 96:9277-80. [PMID: 10430933 PMCID: PMC17770 DOI: 10.1073/pnas.96.16.9277] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With cDNA microarrays, it is now possible to compare the expression of many genes simultaneously. To maximize the likelihood of finding genes whose expression is altered under the experimental conditions, it would be advantageous to be able to select clones for tissue-appropriate cDNA sets. We have taken advantage of the extensive sequence information in the dbEST expressed sequence tag (EST) database to identify a neural crest-derived melanocyte cDNA set for microarray analysis. Analysis of characterized genes with dbEST identified one library that contained ESTs representing 21 neural crest-expressed genes (library 198). The distribution of the ESTs corresponding to these genes was biased toward being derived from library 198. This is in contrast to the EST distribution profile for a set of control genes, characterized to be more ubiquitously expressed in multiple tissues (P < 1 x 10(-9)). From library 198, a subset of 852 clustered ESTs were selected that have a library distribution profile similar to that of the 21 neural crest-expressed genes. Microarray analysis demonstrated the majority of the neural crest-selected 852 ESTs (Mel1 array) were differentially expressed in melanoma cell lines compared with a non-neural crest kidney epithelial cell line (P < 1 x 10(-8)). This was not observed with an array of 1,238 ESTs that was selected without library origin bias (P = 0.204). This study presents an approach for selecting tissue-appropriate cDNAs that can be used to examine the expression profiles of developmental processes and diseases.
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Affiliation(s)
- S K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
Chronic intracerebroventricular (i.c.v.) infusion of 3.2 micrograms/day of nerve growth factor (NGF) in normal rats elevated choline acetyltransferase (ChAT) activity of the striatum, medial septum, and basal forebrain and improved performance of a conditioned taste aversion (CTA) task. Relative to bovine serum albumin (BSA) or Cytochrome C treatments, NGF treatment facilitated acquisition and prolonged extinction of a lithium chloride (LiCl)-induced saccharin aversion. This facilitation was evident at saccharin/LiCl intervals ranging up to 1 h. Also, NGF treatment did not increase reactivity to LiCl-induced illness and neither shifted detection thresholds nor altered hedonic reactions to taste stimuli, indicating that NGF did not produce simple changes in sensory function. NGF treatments that elevate ChAT also facilitate memory of CTA in normal, adult rats.
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Affiliation(s)
- W J Lipinski
- Department of Psychology, Eastern Michigan University, Ypsilanti 48197, USA
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Bazzicalupo P, Hilliard M, Lewis E, De Riso L, Sebastiano M, Ristoratore F. Neurons and genes involved in chemical sensitivity in nematodes. Parasite 1994. [DOI: 10.1051/parasite/199401s1058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Di Marco N, Hilliard M. Comparisons of associate, diploma and baccalaureate degree nurses' state board, quality of patient care, competency rating, supervisor rating, subordinates' satisfaction with supervision and self-report job satisfaction scores. Int J Nurs Stud 1978; 15:163-70. [PMID: 251539 DOI: 10.1016/0020-7489(78)90002-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Hilliard M. A PRELIMINARY REPORT ON GLANDULAR THERAPY IN GYNAECOLOGICAL CONDITIONS. Can Med Assoc J 1937; 37:223-228. [PMID: 20320723 PMCID: PMC536077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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