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Hoskinson C, Medeleanu MV, Reyna ME, Dai DLY, Chowdhury B, Moraes TJ, Mandhane PJ, Simons E, Kozyrskyj AL, Azad MB, Petersen C, Turvey SE, Subbarao P. Antibiotics taken within the first year of life are linked to infant gut microbiome disruption and elevated atopic dermatitis risk. J Allergy Clin Immunol 2024; 154:131-142. [PMID: 38670232 DOI: 10.1016/j.jaci.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/22/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Atopic dermatitis (AD) is the most common chronic inflammatory skin disease in both pediatric and adult populations. The development of AD has been linked to antibiotic usage, which causes perturbation of the microbiome and has been associated with abnormal immune system function. However, imbalances in the gut microbiome itself associated with antibiotic usage have been inconsistently linked to AD. OBJECTIVES This study aimed to elucidate the timing and specific factors mediating the relationship between systemic (oral or intravenous) antibiotic usage and AD. METHODS We used statistical modeling and differential analysis to link CHILD Cohort Study participants' history of antibiotic usage and early-life gut microbiome alterations to AD. RESULTS Here we report that systemic antibiotics during the first year of life, as compared to later, are associated with AD risk (adjusted odds ratio [aOR] = 1.81; 95% CI: 1.28-2.57; P < .001), with an increased number of antibiotic courses corresponding to a dose response-like increased risk of AD risk (1 course: aOR: 1.67; 95% CI: 1.17-2.38; 2 or more courses: aOR: 2.16; 95% CI: 1.30-3.59). Further, we demonstrate that microbiome alterations associated with both AD and systemic antibiotic usage fully mediate the effect of antibiotic usage on the development of AD (βindirect = 0.072; P < .001). Alterations in the 1-year infant gut microbiome of participants who would later develop AD included increased Tyzzerella nexilis, increased monosaccharide utilization, and parallel decreased Bifidobacterium and Eubacterium spp, and fermentative pathways. CONCLUSIONS These findings indicate that early-life antibiotic usage, especially in the first year of life, modulates key gut microbiome components that may be used as markers to predict and possibly prevent the development of AD.
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Affiliation(s)
- Courtney Hoskinson
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Maria V Medeleanu
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Canada; Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Myrtha E Reyna
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Darlene L Y Dai
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Biswajit Chowdhury
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Canada
| | - Theo J Moraes
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Canada
| | | | - Elinor Simons
- Section of Allergy and Immunology, Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anita L Kozyrskyj
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Meghan B Azad
- Section of Allergy and Immunology, Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada; Manitoba Interdisciplinary Lactation Centre, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Charisse Petersen
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Padmaja Subbarao
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Canada; Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada; Department of Medicine, McMaster University, Hamilton, Ontario, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.
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Li D, Luo ZB, Zhu J, Wang JX, Jin ZY, Qi S, Jin M, Quan LH. Ginsenoside F2-Mediated Intestinal Microbiota and Its Metabolite Propionic Acid Positively Impact the Gut-Skin Axis in Atopic Dermatitis Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:339-350. [PMID: 38150707 DOI: 10.1021/acs.jafc.3c06015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Atopic dermatitis (AD) is a complex inflammatory skin disease induced by multiple factors. AD can also cause intestinal inflammation and disorders of the gut microbiota. Ginseng is a kind of edible and medicinal plant; its main active components are ginsenosides. Ginsenosides have a variety of anti-inflammatory effects and regulate the gut microbiota; however, their role in AD and the underlying mechanisms are unclear. In this study, we found that intragastric administration of ginsenoside F2 improved AD-like skin symptoms and reduced inflammatory cell infiltration, serum immunoglobulin E levels, and mRNA expression of inflammatory cytokines in AD mice. 16s rRNA sequencing analysis showed that ginsenoside F2 altered the intestinal microbiota structure and enriched the short-chain fatty acid-producing microbiota in AD mice. Metabolomic analysis revealed that ginsenoside F2 significantly increased the propionic acid (Pa) content of feces and serum in AD mice, which was positively correlated with significant enrichment of Parabacteroides goldsteinii and Lactobacillus plantarum in the intestines. Pa inhibits inflammatory responses in the gut and skin of AD mice through the G-protein-coupled receptor43/NF-κB pathway, thereby improving skin AD symptoms. These results revealed, for the first time, the mechanism by which ginsenoside F2 improves AD through the Pa (a metabolite of intestinal microbiota)-gut-skin axis.
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Affiliation(s)
- Dongxu Li
- College of Integration Science, Yanbian University, Yanji 133002, China
| | - Zhao-Bo Luo
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Jun Zhu
- College of Integration Science, Yanbian University, Yanji 133002, China
| | - Jun-Xia Wang
- Department of Animal Science, College of Agricultural, Yanbian University, Yanji 133002, China
| | - Zheng-Yun Jin
- Department of Animal Science, College of Agricultural, Yanbian University, Yanji 133002, China
| | - Shaobo Qi
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Meiling Jin
- Department of Pharmacology, College of Medicine, Yanbian University, Yanji 133002, China
| | - Lin-Hu Quan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
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Eckermann HA, Meijer J, Cooijmans K, Lahti L, de Weerth C. Daily skin-to-skin contact alters microbiota development in healthy full-term infants. Gut Microbes 2024; 16:2295403. [PMID: 38197254 DOI: 10.1080/19490976.2023.2295403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
The gut microbiota is vital for human body development and function. Its development in early life is influenced by various environmental factors. In this randomized controlled trial, the gut microbiota was obtained as a secondary outcome measure in a study on the effects of one hour of daily skin-to-skin contact (SSC) for five weeks in healthy full-term infants. Specifically, we studied the effects on alpha/beta diversity, volatility, microbiota maturation, and bacterial and gut-brain-axis-related functional abundances in microbiota assessed thrice in the first year. Pregnant Dutch women (n = 116) were randomly assigned to the SSC or care-as-usual groups. The SSC group participants engaged in one hour of daily SSC from birth to five weeks of age. Stool samples were collected at two, five, and 52 weeks and the V4 region was sequenced. We observed significant differences in the microbiota composition, bacterial abundances, and predicted functional pathways between the groups. The SSC group exhibited lower microbiota volatility during early infancy. Microbiota maturation was slower in the SSC group during the first year and our results suggested that breastfeeding duration may have partially mediated this relation. Our findings provide evidence that postpartum SSC may influence microbiota development. Replication is necessary to validate and generalize these results. Future studies should include direct stress measurements and extend microbiota sampling beyond the first year to investigate stress as a mechanism and research SSC's impact on long-term microbiota maturation trajectories.
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Affiliation(s)
- Henrik Andreas Eckermann
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
| | - Jennifer Meijer
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
| | - Kelly Cooijmans
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Carolina de Weerth
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
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Suárez-Martínez C, Santaella-Pascual M, Yagüe-Guirao G, Martínez-Graciá C. Infant gut microbiota colonization: influence of prenatal and postnatal factors, focusing on diet. Front Microbiol 2023; 14:1236254. [PMID: 37675422 PMCID: PMC10478010 DOI: 10.3389/fmicb.2023.1236254] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/08/2023] [Indexed: 09/08/2023] Open
Abstract
Maternal microbiota forms the first infant gut microbial inoculum, and perinatal factors (diet and use of antibiotics during pregnancy) and/or neonatal factors, like intra partum antibiotics, gestational age and mode of delivery, may influence microbial colonization. After birth, when the principal colonization occurs, the microbial diversity increases and converges toward a stable adult-like microbiota by the end of the first 3-5 years of life. However, during the early life, gut microbiota can be disrupted by other postnatal factors like mode of infant feeding, antibiotic usage, and various environmental factors generating a state of dysbiosis. Gut dysbiosis have been reported to increase the risk of necrotizing enterocolitis and some chronic diseases later in life, such as obesity, diabetes, cancer, allergies, and asthma. Therefore, understanding the impact of a correct maternal-to-infant microbial transfer and a good infant early colonization and maturation throughout life would reduce the risk of disease in early and late life. This paper reviews the published evidence on early-life gut microbiota development, as well as the different factors influencing its evolution before, at, and after birth, focusing on diet and nutrition during pregnancy and in the first months of life.
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Affiliation(s)
- Clara Suárez-Martínez
- Food Science and Nutrition Department, Veterinary Faculty, Regional Campus of International Excellence Campus Mare Nostrum, University of Murcia, Murcia, Spain
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
| | - Marina Santaella-Pascual
- Food Science and Nutrition Department, Veterinary Faculty, Regional Campus of International Excellence Campus Mare Nostrum, University of Murcia, Murcia, Spain
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
| | - Genoveva Yagüe-Guirao
- Food Science and Nutrition Department, Veterinary Faculty, Regional Campus of International Excellence Campus Mare Nostrum, University of Murcia, Murcia, Spain
- Microbiology Service, Virgen de La Arrixaca University Hospital, Murcia, Spain
| | - Carmen Martínez-Graciá
- Food Science and Nutrition Department, Veterinary Faculty, Regional Campus of International Excellence Campus Mare Nostrum, University of Murcia, Murcia, Spain
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
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Leo S, Cetiner OF, Pittet LF, Messina NL, Jakob W, Falquet L, Curtis N, Zimmermann P. Metagenomics analysis of the neonatal intestinal resistome. Front Pediatr 2023; 11:1169651. [PMID: 37397142 PMCID: PMC10313230 DOI: 10.3389/fped.2023.1169651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 04/25/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The intestinal microbiome forms a major reservoir for antibiotic resistance genes (ARGs). Little is known about the neonatal intestinal resistome. Objective The objective of this study was to investigate the intestinal resistome and factors that influence the abundance of ARGs in a large cohort of neonates. Methods Shotgun metagenomics was used to analyse the resistome in stool samples collected at 1 week of age from 390 healthy, term-born neonates who did not receive antibiotics. Results Overall, 913 ARGs belonging to 27 classes were identified. The most abundant ARGs were those conferring resistance to tetracyclines, quaternary ammonium compounds, and macrolide-lincosamide-streptogramin-B. Phylogenetic composition was strongly associated with the resistome composition. Other factors that were associated with the abundance of ARGs were delivery mode, gestational age, birth weight, feeding method, and antibiotics in the last trimester of pregnancy. Sex, ethnicity, probiotic use during pregnancy, and intrapartum antibiotics had little effect on the abundance of ARGs. Conclusion Even in the absence of direct antibiotic exposure, the neonatal intestine harbours a high abundance and a variety of ARGs.
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Affiliation(s)
- Stefano Leo
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
| | - Omer F. Cetiner
- Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Laure F. Pittet
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Pediatric Infectious Diseases Unit, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicole L. Messina
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - William Jakob
- Microbiology Laboratory, Fribourg Hospital, Fribourg, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Infectious Diseases Unit, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Petra Zimmermann
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
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Nowrouzian FL, Stadler LS, Östblom A, Lindberg E, Lina G, Adlerberth I, Wold AE. Staphylococcus aureus sequence type (ST) 45, ST30, and ST15 in the gut microbiota of healthy infants - persistence and population counts in relation to ST and virulence gene carriage. Eur J Clin Microbiol Infect Dis 2023; 42:267-276. [PMID: 36689019 PMCID: PMC9899187 DOI: 10.1007/s10096-022-04539-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/14/2022] [Indexed: 01/24/2023]
Abstract
Staphylococcus aureus colonizes the anterior nares, and also the gut, particularly in infants. S. aureus is divided into lineages, termed clonal complexes (CCs), which comprise closely related sequence types (STs). While CC30 and CC45 predominate among nasal commensals, their prevalence among gut-colonizing S. aureus is unknown. Here, 67 gut commensal S. aureus strains from 49 healthy Swedish infants (aged 3 days to 12 months) were subjected to multi-locus sequence typing. The STs of these strains were related to their virulence gene profiles, time of persistence in the microbiota, and fecal population counts. Three STs predominated: ST45 (22% of the strains); ST15 (21%); and ST30 (18%). In a logistic regression, ST45 strains showed higher fecal population counts than the others, independent of virulence gene carriage. The lower fecal counts of ST15 were linked to the carriage of fib genes (encoding fibrinogen-binding proteins), while those of ST30 were linked to fib and sea (enterotoxin A) carriage. While only 11% of the ST15 and ST30 strains were acquired after 2 months of age, this was true of 53% of the ST45 strains (p = 0.008), indicating that the former may be less fit for establishment in a more mature microbiota. None of the ST45 strains was transient (persisting < 3 weeks), and persistent ST45 strains colonized for significantly longer periods than persistent strains of other STs (mean, 34 vs 22 weeks, p = 0.04). Our results suggest that ST45 strains are well-adapted for commensal gut colonization in infants, reflecting yet-unidentified traits of these strains.
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Affiliation(s)
- Forough L Nowrouzian
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10, S-413 46, Gothenburg, Sweden.
| | - Liselott Svensson Stadler
- Culture Collection University of Gothenburg, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Dahlgren's University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Anna Östblom
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10, S-413 46, Gothenburg, Sweden
| | - Erika Lindberg
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10, S-413 46, Gothenburg, Sweden
| | - Gerard Lina
- Centre National de Référence Des Staphylocoques, Hospices Civils de Lyon, CIRI, Université Lyon1, INSERM U1111, CNRS-UMR 5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Ingegerd Adlerberth
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10, S-413 46, Gothenburg, Sweden
| | - Agnes E Wold
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10, S-413 46, Gothenburg, Sweden
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Alsultan A, Walton G, Andrews SC, Clarke SR. Staphylococcus aureus FadB is a dehydrogenase that mediates cholate resistance and survival under human colonic conditions. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36947574 DOI: 10.1099/mic.0.001314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Staphylococcus aureus is a common colonizer of the human gut and in doing so it must be able to resist the actions of the host's innate defences. Bile salts are a class of molecules that possess potent antibacterial activity that control growth. Bacteria that colonize and survive in that niche must be able to resist the action of bile salts, but the mechanisms by which S. aureus does so are poorly understood. Here we show that FadB is a bile-induced oxidoreductase which mediates bile salt resistance and when heterologously expressed in Escherichia coli renders them resistant. Deletion of fadB attenuated survival of S. aureus in a model of the human distal colon.
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Affiliation(s)
- Amjed Alsultan
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6EX, UK
- Present address: Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Al-qadisiyah, Aldewanyiah, Iraq
| | - Gemma Walton
- Food Microbial Sciences Unit, Department of Food and Nutritional Sciences, University of Reading, Whiteknights, Reading, RG6 6AP, UK
| | - Simon C Andrews
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6EX, UK
| | - Simon R Clarke
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6EX, UK
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8
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Abjani F, Madhavan P, Chong PP, Chinna K, Rhodes CA, Lim YAL. Urbanisation and its Associated Factors Affecting Human Gut Microbiota: Where are we Heading to? Ann Hum Biol 2023; 50:137-147. [PMID: 36650931 DOI: 10.1080/03014460.2023.2170464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
ContextThe continuous rise in urbanisation and its associated factors have been reflected in the structure of the human gut ecosystem.ObjectiveThe main focus of the review is to discuss and summarise the major risk factors associated with urbanisation that affects human gut microbiota thus affecting human health.MethodsMultiple medical literature databases, namely PubMed, Google, Google Scholar, and Web of Science were used to find relevant materials for urbanization and its major factors affecting human gut microbiota/microbiome. Both layman and Medical Subject Headings (MeSH) terms were used in the search. Due to the scarcity of the data, no limitation was set on the publication date. Relevant material in the English language which includes case reports, chapters of books, journal articles, online news reports and medical records was included in this review.ResultsBased on the data discussed in the review, it is quite clear that urbanisation and its associated factors have long-standing effects on the human gut microbiota that result in alterations of gut microbial diversity and composition. This is a matter of serious concern as chronic inflammatory diseases are on the rise in urbanised societies.ConclusionA better understanding of the factors associated with urbanisation will help us to identify and implement new biological and social approaches to prevent and treat diseases and improve health globally by deepening our understanding of these relationships and increasing studies across urbanisation gradients.HIGHLIGHTSHuman gut microbiota has been linked to almost every important function, including metabolism, intestinal homeostasis, immune system, biosynthesis of vitamins, brain processes, and its behaviour.However, dysbiosis i.e., alteration in the composition and diversity of gut microbiota is associated with the pathogenesis of many chronic conditions.In the 21st century, urbanisation represents a major demographic shift in developed and developing countries.During this period of urbanisation, humans have been exposed to many environmental exposures, all of which have led to the dysbiosis of human gut microbiota.The main focus of the review is to discuss and summarize the major risk factors associated with urbanisation and how it affects the diversity and composition of gut microbiota which ultimately affects human health.
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Affiliation(s)
- Farhat Abjani
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, Jalan Taylors, 47500 Subang Jaya, Selangor, Malaysia
| | - Priya Madhavan
- School of Medicine, Faculty of Health & Medical Sciences, Taylor's University, Jalan Taylors, 47500 Subang Jaya, Selangor, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, Jalan Taylors, 47500 Subang Jaya, Selangor, Malaysia
| | - Karuthan Chinna
- Faculty of Business and Management, UCSI University 56100 Cheras, Kuala Lumpur, Malaysia
| | - Charles Anthony Rhodes
- Department of Parasitology, University Malaya Medical Centre, 50603 Kuala Lumpur, Federal Territory of Kuala Lumpur, Malaysia
| | - Yvonne Ai Lian Lim
- Department of Parasitology, Faculty of Medicine, University of Malaya. 50603 Kuala Lumpur, Federal Territory of Kuala Lumpur, Malaysia
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Mubanga M, Lundholm C, Rohlin ES, Rejnö G, Brew BK, Almqvist C. Mode of delivery and offspring atopic dermatitis in a Swedish nationwide study. Pediatr Allergy Immunol 2023; 34:e13904. [PMID: 36705040 PMCID: PMC10107099 DOI: 10.1111/pai.13904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND Atopic dermatitis is a common chronic childhood disease associated with significant morbidity and healthcare costs. There is a known association between caesarean section and asthma, but the relationship between caesarean section and offspring atopic dermatitis remains uncertain. METHODS We conducted a register-based nationwide cohort study including children born in Sweden between January 2006 and December 2018. Data on health and socioeconomic variables were extracted from the national registers for children aged ≤5 years. Time-to-event analyses were used to calculate hazard ratios (HR) with 95% confidence intervals (CI) adjusting for confounders and familial factors. RESULTS 1,399,406 children were included (6,029,542 person-years at risk). Atopic dermatitis was observed in 17.2% of the 1,150,896 children born by vaginal delivery and 18.3% of the 248,510 born by caesarean section. The mean age of onset of atopic dermatitis was 2.72 years (SD 1.8). Birth by caesarean section was associated with a higher risk of atopic dermatitis (adj-HR 1.12, 95% CI: 1.10-1.14). A higher risk of atopic dermatitis was found in children born by instrumental vaginal delivery (adj-HR 1.10, 1.07-1.13); emergency caesarean section (adj-HR 1.12, 1.10-1.15), and elective caesarean section (adj-HR 1.13, 1.10-1.16) than uncomplicated vaginal delivery in children <1 year of age. Similar hazards were observed in those ≥1 year of age. In sibling control analysis, greater risks remained in children aged <1 year but not in age ≥1 year. CONCLUSIONS In our study population, it was observed that children born by caesarean section or instrumental vaginal delivery were at higher risk of early childhood atopic dermatitis. Although familial confounding attenuates the risk in children aged ≥1 year, this was not observed in the first year of life.
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Affiliation(s)
- Mwenya Mubanga
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Lundholm
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Elin S Rohlin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Gustaf Rejnö
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Obstetrics and Gynaecology Unit, Stockholm, Sweden
| | - Bronwyn K Brew
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,National Perinatal Epidemiology and Statistics Unit, Centre for Big Data Research in Health and School of Clinical Medicine, University of New South Wales, Sydney, Australia
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
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10
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Perkin MR, Strachan DP. The hygiene hypothesis for allergy - conception and evolution. FRONTIERS IN ALLERGY 2022; 3:1051368. [PMID: 36506644 PMCID: PMC9731379 DOI: 10.3389/falgy.2022.1051368] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
In 1989, a short paper entitled "Hay fever, hygiene and household size" observed that British children from larger families were less likely to develop hay fever and suggested that this could be because early exposure to infection prevents allergy. This sibship size association for hay fever, since replicated many times in Britain and other affluent countries and confirmed by objective measures of atopy, prompted what has come to be known as the "hygiene hypothesis for allergy", although that term was not specifically used in the 1989 paper. The present paper reviews the historical roots of the "hygiene hypothesis" and charts its development over more than 30 years. Initial scepticism among immunologists turned to enthusiasm in the mid-1990s as the Th1/Th2 paradigm for allergic sensitisation emerged from animal experiments and the concept of "immunological old friends" became popular from the early 2000s. From the late 1990s, observations of reduced allergy risk among children of anthroposophic families and those brought up on farms suggested that the sibship size effects formed part of a broader range of "hygiene-related" determinants of allergy. Children from large families with farming exposure have approximately sixfold reduction in prevalence of hay fever, indicating the potential strength and epidemiological importance of these environmental determinants. During the 21st century, a wide range of specific microbial, environmental and lifestyle factors have been investigated as possible underlying mechanisms, but sadly none have emerged as robust explanations for the family size and farming effects. Thus, while the "hygiene hypothesis" led to a fundamental reappraisal of our relationship with our microbial environment and to the concept that early exposure, rather than avoidance, is beneficial for developing a healthy immune system, the underlying mechanism for variations in allergy prevalence with family size remains, in Churchillian terms, "a riddle wrapped in a mystery inside an enigma".
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11
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Gulnaz A, Chang JE, Maeng HJ, Shin KH, Lee KR, Chae YJ. A mechanism-based understanding of altered drug pharmacokinetics by gut microbiota. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2022. [DOI: 10.1007/s40005-022-00600-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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The Changes in Bacterial Microbiome Associated with Immune Disorder in Allergic Respiratory Disease. Microorganisms 2022; 10:microorganisms10102066. [PMID: 36296340 PMCID: PMC9610723 DOI: 10.3390/microorganisms10102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/05/2022] [Accepted: 10/16/2022] [Indexed: 12/02/2022] Open
Abstract
Allergic respiratory disease is a worldwide and increasingly prevalent health problem. Many researchers have identified complex changes in the microbiota of the respiratory and intestinal tracts in patients with allergic respiratory diseases. These affect immune response and influence the progression of disease. However, the diversity of bacterial changes in such cases make it difficult to identify a specific microorganism to target for adjustment. Recent research evidence suggests that common bacterial variations present in allergic respiratory disease are associated with immune disorders. This finding could lead to the discovery of potential therapeutic targets in cases of allergic respiratory disease. In this review, we summarize current knowledge of bacteria changes in cases of allergic respiratory disease, to identify changes commonly associated with immune disorders, and thus provide a theoretical basis for targeting therapies of allergic respiratory disease through effective modulation of key bacteria.
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13
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Davis EC, Castagna VP, Sela DA, Hillard MA, Lindberg S, Mantis NJ, Seppo AE, Järvinen KM. Gut microbiome and breast-feeding: Implications for early immune development. J Allergy Clin Immunol 2022; 150:523-534. [PMID: 36075638 PMCID: PMC9463492 DOI: 10.1016/j.jaci.2022.07.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022]
Abstract
Establishment of the gut microbiome during early life is a complex process with lasting implications for an individual's health. Several factors influence microbial assembly; however, breast-feeding is recognized as one of the most influential drivers of gut microbiome composition during infancy, with potential implications for function. Differences in gut microbial communities between breast-fed and formula-fed infants have been consistently observed and are hypothesized to partially mediate the relationships between breast-feeding and decreased risk for numerous communicable and noncommunicable diseases in early life. Despite decades of research on the gut microbiome of breast-fed infants, there are large scientific gaps in understanding how human milk has evolved to support microbial and immune development. This review will summarize the evidence on how breast-feeding broadly affects the composition and function of the early-life gut microbiome and discuss mechanisms by which specific human milk components shape intestinal bacterial colonization, succession, and function.
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Affiliation(s)
- Erin C Davis
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY
| | | | - David A Sela
- Department of Food Science, University of Massachusetts Amherst, Amherst, Mass; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Mass; Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, Mass
| | - Margaret A Hillard
- Department of Food Science, University of Massachusetts Amherst, Amherst, Mass; Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, Mass
| | - Samantha Lindberg
- Department of Biomedical Sciences, University of Albany, Rensselaer, NY
| | - Nicholas J Mantis
- Division of Infectious Diseases, New York State Department of Health, Albany, NY
| | - Antti E Seppo
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY
| | - Kirsi M Järvinen
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY; Division of Allergy, Immunology, and Rheumatology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY; Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY.
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14
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Obiakor CV, Parks J, Takaro TK, Tun HM, Morales-Lizcano N, Azad MB, Mandhane PJ, Moraes TJ, Simons E, Turvey SE, Subbarao P, Scott JA, Kozyrskyj AL. Early Life Antimicrobial Exposure: Impact on Clostridioides difficile Colonization in Infants. Antibiotics (Basel) 2022; 11:antibiotics11070981. [PMID: 35884235 PMCID: PMC9311587 DOI: 10.3390/antibiotics11070981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022] Open
Abstract
The relationship between antibiotic use and Clostridioides difficile (C. difficile) has been well established in adults and older children but remains unclear and is yet to be fully examined in infant populations. This study aimed to determine the separate and cumulative impact from antibiotics and household cleaning products on C. difficile colonization in infants. This study included 1429 infants at 3–4 months of age and 1728 infants at 12 months of age from the Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort. The levels of infant antimicrobial exposure were obtained from hospital birth charts and standardized questionnaires. Infant gut microbiota was characterized by Illumina 16S ribosomal ribonucleic acid (rRNA) gene sequencing. Analysis of C. difficile was performed using a quantitative polymerase chain reaction (qPCR). Overall, C. difficile colonized 31% and 46% of infants at 3–4 months and 12 months, respectively. At 3–4 months, C. difficile colonization was significantly higher in infants exposed to both antibiotics and higher (above average) usage of household cleaning products (adjusted odds ratio (aOR) 1.50, 95% CI 1.03–2.17; p = 0.032) than in infants who had the least antimicrobial exposure. This higher colonization persisted up to 12 months of age. Our study suggests that cumulative exposure to systemic antibiotics and higher usage of household cleaning products facilitates C. difficile colonization in infants. Further research is needed to understand the future health impacts.
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Affiliation(s)
| | - Jaclyn Parks
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (J.P.); (T.K.T.)
- Cancer Control Research, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Tim K. Takaro
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (J.P.); (T.K.T.)
| | - Hein M. Tun
- School of Public Health, University of Hong Kong, Hong Kong;
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong
| | - Nadia Morales-Lizcano
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; (N.M.-L.); (J.A.S.)
| | - Meghan B. Azad
- Department of Pediatrics & Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada; (M.B.A.); (E.S.)
| | | | - Theo J. Moraes
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; (T.J.M.); (P.S.)
| | - Elinor Simons
- Department of Pediatrics & Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada; (M.B.A.); (E.S.)
| | - Stuart E. Turvey
- Department of Pediatrics, University of British Columbia, Vancouver, BC V6H 0B3, Canada;
| | - Padmaja Subbarao
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; (T.J.M.); (P.S.)
| | - James A. Scott
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; (N.M.-L.); (J.A.S.)
| | - Anita L. Kozyrskyj
- School of Public Health, University of Alberta, Edmonton, AB T6G 1C9, Canada;
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 1C9, Canada;
- Correspondence:
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15
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Christensen ED, Hjelmsø MH, Thorsen J, Shah S, Redgwell T, Poulsen CE, Trivedi U, Russel J, Gupta S, Chawes BL, Bønnelykke K, Sørensen SJ, Rasmussen MA, Bisgaard H, Stokholm J. The developing airway and gut microbiota in early life is influenced by age of older siblings. MICROBIOME 2022; 10:106. [PMID: 35831879 PMCID: PMC9277889 DOI: 10.1186/s40168-022-01305-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/17/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND Growing up with siblings has been linked to numerous health outcomes and is also an important determinant for the developing microbiota. Nonetheless, research into the role of having siblings on the developing microbiota has mainly been incidental. RESULTS Here, we investigate the specific effects of having siblings on the developing airway and gut microbiota using a total of 4497 hypopharyngeal and fecal samples taken from 686 children in the COPSAC2010 cohort, starting at 1 week of age and continuing until 6 years of age. Sibship was evaluated longitudinally and used for stratification. Microbiota composition was assessed using 16S rRNA gene amplicon sequencing of the variable V4 region. We found siblings in the home to be one of the most important determinants of the developing microbiota in both the airway and gut, with significant differences in alpha diversity, beta diversity, and relative abundances of the most abundant taxa, with the specific associations being particularly apparent during the first year of life. The age gap to the closest older sibling was more important than the number of older siblings. The signature of having siblings in the gut microbiota at 1 year was associated with protection against asthma at 6 years of age, while no associations were found for allergy. CONCLUSIONS Having siblings is one of the most important factors influencing a child's developing microbiota, and the specific effects may explain previously established associations between siblings and asthma and infectious diseases. As such, siblings should be considered in all studies involving the developing microbiota, with emphasis on the age gap to the closest older sibling rather than the number of siblings. Video abstract.
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Affiliation(s)
- Emil Dalgaard Christensen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Mathis Hjort Hjelmsø
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shiraz Shah
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Tamsin Redgwell
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Christina Egeø Poulsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Urvish Trivedi
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Shashank Gupta
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Bo L. Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Morten Arendt Rasmussen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark
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16
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Manipulating Microbiota to Treat Atopic Dermatitis: Functions and Therapies. Pathogens 2022; 11:pathogens11060642. [PMID: 35745496 PMCID: PMC9228373 DOI: 10.3390/pathogens11060642] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 12/13/2022] Open
Abstract
Atopic dermatitis (AD) is a globally prevalent skin inflammation with a particular impact on children. Current therapies for AD are challenged by the limited armamentarium and the high heterogeneity of the disease. A novel promising therapeutic target for AD is the microbiota. Numerous studies have highlighted the involvement of the skin and gut microbiota in the pathogenesis of AD. The resident microbiota at these two epithelial tissues can modulate skin barrier functions and host immune responses, thus regulating AD progression. For example, the pathogenic roles of Staphylococcus aureus in the skin are well-established, making this bacterium an attractive target for AD treatment. Targeting the gut microbiota is another therapeutic strategy for AD. Multiple oral supplements with prebiotics, probiotics, postbiotics, and synbiotics have demonstrated promising efficacy in both AD prevention and treatment. In this review, we summarize the association of microbiota dysbiosis in both the skin and gut with AD, and the current knowledge of the functions of commensal microbiota in AD pathogenesis. Furthermore, we discuss the existing therapies in manipulating both the skin and gut commensal microbiota to prevent or treat AD. We also propose potential novel therapies based on the cutting-edge progress in this area.
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17
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Kielenniva K, Ainonen S, Vänni P, Paalanne N, Renko M, Salo J, Tejesvi MV, Pokka T, Pirttilä AM, Tapiainen T. Microbiota of the first-pass meconium and subsequent atopic and allergic disorders in children. Clin Exp Allergy 2022; 52:684-696. [PMID: 35212058 PMCID: PMC9314137 DOI: 10.1111/cea.14117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Some cohort studies have suggested that gut microbiota composition is associated with allergic diseases in children. The microbiota of the first-pass meconium, which forms before birth, represents the first gut microbiota that is easily available for research and little is known about any relationship with allergic disease development. OBJECTIVE We investigated whether the bacterial composition of the first-pass meconium is associated with the development of allergic diseases before 4 years of age. METHODS Prospective birth cohort study. Bacterial composition of first-pass meconium was analysed using bacterial 16S rRNA gene amplicon sequencing. Atopic and allergic diseases were evaluated via online survey or telephone to age 4 years, based on the International Study of Asthma and Allergies in Childhood questionnaire. RESULTS During a 6-week period in 2014, 312 children were born at the Central Finland Central Hospital. Meconium was collected from 212 at a mean of 8-hour age. Outcome data at 4 years were available for 177 (83%) children, and 159 of these had sufficient amplification of bacterial DNA in meconium. Meconium microbiota composition, including diversity indices and relative abundances of the main phyla and genera, was not associated with subsequent atopic eczema, wheezing or cow's milk allergy. Principal components analysis did not identify any clustering of the meconium microbiomes of children with respect to wheezing or cow's milk allergy. CONCLUSIONS We found no evidence that gut microbiota composition of first-pass meconium is associated with atopic manifestations to age 4 years. However, larger studies are needed to fully exclude a relationship.
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Affiliation(s)
- Katja Kielenniva
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Sofia Ainonen
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Petri Vänni
- Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland.,Genobiomics Ltd., Oulu, Finland
| | - Niko Paalanne
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Marjo Renko
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Pediatrics, University of Eastern Finland, Kuopio, Finland
| | - Jarmo Salo
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Mysore V Tejesvi
- Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland.,Genobiomics Ltd., Oulu, Finland
| | - Tytti Pokka
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | | | - Terhi Tapiainen
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
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18
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Widhiati S, Purnomosari D, Wibawa T, Soebono H. The role of gut microbiome in inflammatory skin disorders: A systematic review. Dermatol Reports 2022; 14:9188. [PMID: 35371420 PMCID: PMC8969879 DOI: 10.4081/dr.2022.9188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
The close relationship between the intestine and the skin has been widely stated, seen from gastrointestinal (GI) disorders often accompanied by skin manifestations. Exactly how the gut microbiome is related to skin inflammation and influences the pathophysiology mechanism of skin disorders are still unclear. Many studies have shown a two-way relationship between gut and skin associated with GI health and skin homeostasis and allostasis. This systematic review aimed to explore the associations between the gut microbiome with inflammatory skin disorders, such as acne, psoriasis, atopic dermatitis, and urticaria, and to discover the advanced concept of this relationship. The literature search was limited to any articles published up to December 2020 using PubMed and EBSCOHost. The review followed the PRISMA guidelines for conducting a systematic review. Of the 319 articles screened based on title and abstract, 111 articles underwent full-text screening. Of these, 23 articles met our inclusion criteria, comprising 13 atopic dermatitis (AD), three psoriasis, four acne vulgaris, and four chronic urticaria articles. Acne vulgaris, atopic dermatitis, psoriasis, and chronic urticaria are inflammation skin disorders that were studied recently to ascertain the relationship of these disorders with dysbiosis of the GI microbiome. All acne vulgaris, psoriasis, and chronic urticaria studies stated the association of gut microbiome with skin manifestations. However, the results in atopic dermatitis are still conflicting. Most of the articles agree that Bifidobacterium plays an essential role as anti-inflammation bacteria, and Proteobacteria and Enterobacteria impact inflammation in inflammatory skin disorders.
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Affiliation(s)
- Suci Widhiati
- Departments of Dermatology and Venereology, Faculty of Medicine, Universitas Sebelas Maret/RSUD Dr. Moewardi, Surakarta
| | - Dewajani Purnomosari
- Department of Histology and Cell Biology Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta
| | - Hardyanto Soebono
- Department of Dermatology and Venereology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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19
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Human Milk Oligosaccharides and Bacterial Profile Modulate Infant Body Composition during Exclusive Breastfeeding. Int J Mol Sci 2022; 23:ijms23052865. [PMID: 35270006 PMCID: PMC8911220 DOI: 10.3390/ijms23052865] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/23/2022] [Accepted: 03/02/2022] [Indexed: 02/06/2023] Open
Abstract
Human milk is a complex and variable ecosystem fundamental to the development of newborns. This study aimed to investigate relationships between human milk oligosaccharides (HMO) and human milk bacterial profiles and infant body composition. Human milk samples (n = 60) were collected at two months postpartum. Infant and maternal body composition was measured with bioimpedance spectroscopy. Human milk bacterial profiles were assessed using full-length 16S rRNA gene sequencing and 19 HMOs were quantitated using high-performance liquid chromatography. Relative abundance of human milk bacterial taxa were significantly associated with concentrations of several fucosylated and sialylated HMOs. Individual human milk bacteria and HMO intakes and concentrations were also significantly associated with infant anthropometry, fat-free mass, and adiposity. Furthermore, when data were stratified based on maternal secretor status, some of these relationships differed significantly among infants born to secretor vs non-secretor mothers. In conclusion, in this pilot study the human milk bacterial profile and HMO intakes and concentrations were significantly associated with infant body composition, with associations modified by secretor status. Future research designed to increase the understanding of the mechanisms by which HMO and human milk bacteria modulate infant body composition should include intakes in addition to concentrations.
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20
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Abstract
PURPOSE OF REVIEW This article explores recent findings on the involvement of innate immunity in allergic airways disease, concentrating on allergic rhinitis. RECENT FINDINGS We speculate on the ways in which environmental influences act to initiate inflammation and on how these may have altered in recent decades. Improved understanding of the mechanisms involved may reveal future possibilities for therapy. SUMMARY The complex nature of immunity - both innate and acquired - in airways disease has implications for prevention and for therapy and requires further elucidation.
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Affiliation(s)
- Glenis K Scadding
- Royal National ENT Hospital, University College Hospitals London. Division of Infection and Immunity, University College London
| | - Guy W Scadding
- Allergy and Clinical Immunology, Imperial College, London, UK
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21
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Fungal allergic sensitisation in young rural Zimbabwean children: Gut mycobiome and seroreactivity characteristics. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 2:100082. [PMID: 35028627 PMCID: PMC8714770 DOI: 10.1016/j.crmicr.2021.100082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background The prevalence of allergic diseases has increased over the last few decades, with sensitisation to fungal allergens and gut microbiome dysbiosis implicated in this trend. The fungal community in the gut (mycobiome) has yet to be characterised and related to fungal allergic sensitisation. Thus, we characterised the gut mycobiome and related it to fungal sensitisation and seroreactivity among Zimbabwean children. We further determined the effect of host age, sex, Schistosoma haematobium infection and mycobiome composition on fungal sensitisation and seroreactivity. Methods Using shotgun metagenomic sequencing, we characterised the gut microbiome of stool samples of 116 preschool aged children (PSAC) (≤5 years old, 57(49.1%) male and 59 (50.9%) female). Sensitisation to common fungi in Zimbabwe was assessed using skin prick tests (SPTs). Allergen-specific IgM, IgA, IgG, IgE and IgG4 antibodies were quantified by ELISA. We analysed the relationship between fungal genera and SPT reactivity by ANOVA; fungal genera and IgE antibody reactivity by linear regression; variation in mycobiome abundance with host and environmental factors by PERMANOVA; SPT reactivity and host and environmental factors by logistic regression; seroreactivity and host and environmental factors by ANOVA. Results The mycobiome formed <1% of the sequenced gut microbiome and 228 fungal genera were identified. The most abundant genera detected were Protomyces, Taphrina, and Aspergillus. S.haematobium infection had a significant effect on fungal genera. Prevalence of SPT sensitisation to ≥1 fungal species was 96%, and individuals were frequently sensitised to Saccharomyces cerevisiae. Antibodies were detected in 100% of the population. There was no relationship between mycobiome abundance and IgE titres or IgE/IgG4 ratios for each fungal species; no significant differences between SPT reactivity and abundance of fungal species except for S. cerevisiae; and fungal seroreactivity did not significantly differ with age. There were some sex (m>f for, Epicoccum nigrum and Penicillium chrysogenum) and SPT reactivity -related differences in seroreactivity. Conclusion This is the first comprehensive characterisation of gut mycobiome and fungal allergic sensitisation of rural children in Zimbabwe. Although reported allergic disease is low there is a high percentage of sensitisation. Further studies with larger populations are required to understand the role of the mycobiome in allergic diseases.
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22
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Romano-Keeler J, Sun J. The First 1000 Days: Assembly of the Neonatal Microbiome and Its Impact on Health Outcomes. NEWBORN (CLARKSVILLE, MD.) 2022; 1:219-226. [PMID: 36237439 PMCID: PMC9555117 DOI: 10.5005/jp-journals-11002-0028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Early life microbial colonization is critical for the development of the immune system, postnatal growth, and long-term health and disease. The dynamic and nascent microbiomes of children are highly individualized and are characterized by low bacterial diversity. Any disruptions in microbial colonization can contribute to shifts in normal microbial colonization that persist past the first 1000 days of life and result in intestinal dysbiosis. Here, we focus on microbiome-host interactions during fetal, newborn, and infant microbiome development. We summarize the roles of bacterial communities in fetal development and adverse health outcomes due to dysbiosis. We also discuss how internal and external factors program the microbiome's metabolic machinery as it evolves into an adult-like microbiome. Finally, we discuss the limits of current studies and future directions. Studies on the early-life microbiome will be critical for a better understanding of childhood health and diseases, as well as restorative methods for the prevention and treatment of diseases in adulthood.
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Affiliation(s)
- Joann Romano-Keeler
- Division of Neonatology, Department of Pediatrics, University of Illinois, Chicago, Illinois, United States of America
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, Illinois, United States of America; University of Illinois Cancer Center, Chicago, Illinois, United States of America; Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
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23
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Oemcke LA, Anderson RC, Altermann E, Roy NC, McNabb WC. The Role of Segmented Filamentous Bacteria in Immune Barrier Maturation of the Small Intestine at Weaning. Front Nutr 2021; 8:759137. [PMID: 34869529 PMCID: PMC8637878 DOI: 10.3389/fnut.2021.759137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
The microbiological, physical, chemical, and immunological barriers of the gastrointestinal tract (GIT) begin developing in utero and finish maturing postnatally. Maturation of these barriers is essential for the proper functioning of the GIT. Maturation, particularly of the immunological barrier, involves stimulation by bacteria. Segmented filamentous bacteria (SFB) which are anaerobic, spore-forming commensals have been linked to immune activation. The presence and changes in SFB abundance have been positively correlated to immune markers (cytokines and immunoglobulins) in the rat ileum and stool samples, pre- and post-weaning. The abundance of SFB in infant stool increases from 6 months, peaks around 12 months and plateaus 25 months post-weaning. Changes in SFB abundance at these times correlate positively and negatively with the production of interleukin 17 (IL 17) and immunoglobulin A (IgA), respectively, indicating involvement in immune function and maturation. Additionally, the peak in SFB abundance when a human milk diet was complemented by solid foods hints at a diet effect. SFB genome analysis revealed enzymes involved in metabolic pathways for survival, growth and development, host mucosal attachment and substrate acquisition. This narrative review discusses the current knowledge of SFB and their suggested effects on the small intestine immune system. Referencing the published genomes of rat and mouse SFB, the use of food substrates to modulate SFB abundance is proposed while considering their effects on other microbes. Changes in the immune response caused by the interaction of food substrate with SFB may provide insight into their role in infant immunological barrier maturation.
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Affiliation(s)
- Linda A Oemcke
- Riddet Institute, Massey University, Palmerston North, New Zealand.,School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand.,Smart Foods Innovation Centre of Excellence, AgResearch, Palmerston North, New Zealand
| | - Rachel C Anderson
- Riddet Institute, Massey University, Palmerston North, New Zealand.,Smart Foods Innovation Centre of Excellence, AgResearch, Palmerston North, New Zealand
| | - Eric Altermann
- Riddet Institute, Massey University, Palmerston North, New Zealand.,Consumer Interface Innovation Centre of Excellence, AgResearch, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nicole C Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand.,Department of Human Nutrition, University of Otago, Dunedin, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
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Yao Y, Cai X, Ye Y, Wang F, Chen F, Zheng C. The Role of Microbiota in Infant Health: From Early Life to Adulthood. Front Immunol 2021; 12:708472. [PMID: 34691021 PMCID: PMC8529064 DOI: 10.3389/fimmu.2021.708472] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/17/2021] [Indexed: 12/11/2022] Open
Abstract
From early life to adulthood, the microbiota play a crucial role in the health of the infant. The microbiota in early life are not only a key regulator of infant health but also associated with long-term health. Pregnancy to early life is the golden time for the establishment of the infant microbiota, which is affected by both environmental and genetic factors. Recently, there is an explosion of the studies on the role of microbiota in human diseases, but the application to disease or health is relatively limited because many aspects of human microbiota remain controversial, especially about the infant microbiota. Therefore, a critical and conclusive review is necessary to understand fully the relationship between the microbiota and the health of infant. In this article, we introduce in detail the role of microbiota in the infant from pregnancy to early life to long-term health. The main contents of this article include the relationship between the maternal microbiota and adverse pregnancy outcomes, the establishment of the neonatal microbiota during perinatal period and early life, the composition of the infant gut microbiota, the prediction of the microbiota for long-term health, and the future study directions of microbiota.
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Affiliation(s)
- Yao Yao
- Department of Pharmacy, Women's Hospital School of Medicine Zhejiang University, Hangzhou, China
| | - Xiaoyu Cai
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiqing Ye
- Department of Pharmacy, Women's Hospital School of Medicine Zhejiang University, Hangzhou, China
| | - Fengmei Wang
- Department of Pharmacy, Women's Hospital School of Medicine Zhejiang University, Hangzhou, China
| | - Fengying Chen
- Department of Pharmacy, Women's Hospital School of Medicine Zhejiang University, Hangzhou, China
| | - Caihong Zheng
- Department of Pharmacy, Women's Hospital School of Medicine Zhejiang University, Hangzhou, China
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25
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Association of Cesarean Delivery and Formula Supplementation with the Stool Metabolome of 6-Week-Old Infants. Metabolites 2021; 11:metabo11100702. [PMID: 34677417 PMCID: PMC8540440 DOI: 10.3390/metabo11100702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/15/2022] Open
Abstract
Cesarean delivery and formula feeding have both been implicated as important factors associated with perturbations to the infant gut microbiome. To investigate the functional metabolic response of the infant gut microbial milieu to these factors, we profiled the stool metabolomes of 121 infants from a US pregnancy cohort study at approximately 6 weeks of life and evaluated associations with delivery mode and feeding method. Multivariate analysis of six-week stool metabolomic profiles indicated discrimination by both delivery mode and diet. For diet, exclusively breast-fed infants exhibited metabolomic profiles that were distinct from both exclusively formula-fed and combination-fed infants, which were relatively more similar to each other in metabolomic profile. We also identified individual metabolites that were important for differentiating delivery mode groups and feeding groups and metabolic pathways related to delivery mode and feeding type. We conclude based on previous work and this current study that the microbial communities colonizing the gastrointestinal tracts of infants are not only taxonomically, but also functionally distinct when compared according to delivery mode and feeding groups. Further, different sets of metabolites and metabolic pathways define delivery mode and diet metabotypes.
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26
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Antibiotic-Induced Gut Microbiota Dysbiosis Damages the Intestinal Barrier, Increasing Food Allergy in Adult Mice. Nutrients 2021; 13:nu13103315. [PMID: 34684316 PMCID: PMC8539551 DOI: 10.3390/nu13103315] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/04/2021] [Accepted: 09/14/2021] [Indexed: 12/26/2022] Open
Abstract
(1) Background: The use of antibiotics affects the composition of gut microbiota. Studies have suggested that the colonization of gut microbiota in early life is related to later food allergies. Still, the relationship between altered intestinal microbiota in adulthood and food allergies is unclear. (2) Methods: We established three mouse models to analyze gut microbiota dysbiosis’ impact on the intestinal barrier and determine whether this effect can increase the susceptibility to and severity of food allergy in later life. (3) Results: The antibiotic-induced gut microbiota dysbiosis significantly reduced Lachnospiraceae, Muribaculaceae, and Ruminococcaceae, and increased Enterococcaceae and Clostridiales. At the same time, the metabolic abundance was changed, including decreased short-chain fatty acids and tryptophan, as well as enhanced purine. This change is related to food allergies. After gut microbiota dysbiosis, we sensitized the mice. The content of specific IgE and IgG1 in mice serum was significantly increased, and the inflammatory response was enhanced. The dysbiosis of gut microbiota caused the sensitized mice to have more severe allergic symptoms, ruptured intestinal villi, and a decrease in tight junction proteins (TJs) when re-exposed to the allergen. (4) Conclusions: Antibiotic-induced gut microbiota dysbiosis increases the susceptibility and severity of food allergies. This event may be due to the increased intestinal permeability caused by decreased intestinal tight junction proteins and the increased inflammatory response.
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27
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Qu W, Liu L, Miao L. Exposure to antibiotics during pregnancy alters offspring outcomes. Expert Opin Drug Metab Toxicol 2021; 17:1165-1174. [PMID: 34435921 DOI: 10.1080/17425255.2021.1974000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The composition of microorganisms is closely related to human health. Antibiotic use during pregnancy may have adverse effects on the neonatal gut microbiome and subsequently affect infant health development, leading to childhood atopy and allergic diseases, intestinal, metabolic and brain disorders, and infection. AREAS COVERED This review includes the effect of maternal antibiotic use during pregnancy on potential diseases in animals and human offspring. EXPERT OPINION Exposure to antibiotics during pregnancy alters offspring outcomes. Alterations in the microbiome may potentially lower the risk of a range of problems and may also be a novel therapeutic target in children later in life.
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Affiliation(s)
- Wenhao Qu
- Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, China.,College of Pharmaceutical Science, Soochow University, Suzhou, China
| | - Linsheng Liu
- Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Liyan Miao
- Department of Pharmacy, The First Affiliated Hospital of Soochow University, Suzhou, China.,College of Pharmaceutical Science, Soochow University, Suzhou, China
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28
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Ser HL, Letchumanan V, Goh BH, Wong SH, Lee LH. The Use of Fecal Microbiome Transplant in Treating Human Diseases: Too Early for Poop? Front Microbiol 2021; 12:519836. [PMID: 34054740 PMCID: PMC8155486 DOI: 10.3389/fmicb.2021.519836] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/07/2021] [Indexed: 12/15/2022] Open
Abstract
Fecal microbiome transplant (FMT) has gained popularity over the past few years, given its success in treating several gastrointestinal diseases. At the same time, microbial populations in the gut have been shown to have more physiological effects than we expected as "habitants" of the gut. The imbalance in the gut microbiome or dysbiosis, particularly when there are excessive harmful pathogens, can trigger not just infections but can also result in the development of common diseases, such as cancer and cardiometabolic diseases. By using FMT technology, the dysbiosis of the gut microbiome in patients can be resolved by administering fecal materials from a healthy donor. The current review summarizes the history and current uses of FMT before suggesting potential ideas for its high-quality application in clinical settings.
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Affiliation(s)
- Hooi-Leng Ser
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Vengadesh Letchumanan
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Bey-Hing Goh
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Sunny Hei Wong
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
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29
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Yang J, Wu J, Li Y, Zhang Y, Cho WC, Ju X, van Schothorst EM, Zheng Y. Gut bacteria formation and influencing factors. FEMS Microbiol Ecol 2021; 97:6168382. [PMID: 33705527 DOI: 10.1093/femsec/fiab043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/09/2021] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota plays an important role in human health. In modern life, with the improvement of living conditions, the intake of high-sugar and high-fat diets as well as the large-scale use of antibacterial drugs have an extensive impact on the gut microbiota, even leading to gut microbiota-orchestrating disorders. This review discusses the effects of various factors, including geographic location, age, diet, antibacterial drugs, psychological situation and exercise on gut bacteria, which helps us profoundly to understand the significance of gut bacteria to human health and to find effective solutions to prevent or treat related diseases.
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Affiliation(s)
- Jing Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Chengguan District, Lanzhou 730046, China
| | - Jin'en Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Chengguan District, Lanzhou 730046, China
| | - Yating Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Chengguan District, Lanzhou 730046, China
| | - Yong'e Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Chengguan District, Lanzhou 730046, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong SAR 999077, China
| | - Xianghong Ju
- Department of Veterinary Medicine, College of Agriculture, Guangdong Ocean University, 1 Haida Road, Mazhang District, 524088, China
| | - Evert M van Schothorst
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen 6708WD, The Netherlands
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Chengguan District, Lanzhou 730046, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, 88 Daxuenan Road, Yangzhou 225009, China
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30
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Shaterian N, Abdi F, Ghavidel N, Alidost F. Role of cesarean section in the development of neonatal gut microbiota: A systematic review. Open Med (Wars) 2021; 16:624-639. [PMID: 33869784 PMCID: PMC8035494 DOI: 10.1515/med-2021-0270] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023] Open
Abstract
Background The delivery mode is one of the factors affecting the type of colonization of the human gut. Gut colonization affects all stages of the human life cycle, and the type of gut microbiome can contribute to immune system function, the development of some diseases, and brain development; and it has a significant impact on a newborn’s growth and development. Methods Terms defined as MeSH keywords were searched by the databases, and web search engines such as PubMed, ClinicalTrials.gov, Embase, Scopus, ProQuest, Web of Science, and Google Scholar were searched between 2010 and 2020. The quality of each study was assessed according to the Newcastle–Ottawa scale, and seven eligible and high-quality studies were analyzed. Finding The abundances of Bacteroides and Bifidobacterium during the first 3 months of life; Lactobacillus and Bacteroides during the second 3 months of life; Bacteroides and Bifidobacterium during the second 6 months of life; and Bacteroides, Enterobacter, and Streptococcus after the first year of life were higher in vaginal delivery-born infants. While infants born by cesarean section (CS) had higher abundances of Clostridium and Lactobacillus during the first 3 months of life, Enterococcus and Clostridium during the second 3 months of life, and Lactobacillus and Staphylococcus after the first year of life. Discussion Delivery mode can affect the type of the human intestinal microbiota. The CS-born babies had lower colonization rates of Bifidobacterium and Bacteroides, but they had higher colonization rates of Clostridium, Lactobacillus, Enterobacter, Enterococcus, and Staphylococcus. Given the effect of microbiota colonization on neonatal health, it is therefore recommended to conduct further studies in order to investigate the effect of the colonization on the delivery mode and on baby’s growth and development. Application to practice The aim of this study was to investigate the role of CS in the development of the neonatal gut microbiota.
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Affiliation(s)
- Negin Shaterian
- Student Research Committee, Nursing and Midwifery faculty, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Abdi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Nooshin Ghavidel
- Social Determinants of Health Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Farzane Alidost
- Student Research Committee, School of Nursing and Midwifery, Tehran University of Medical Sciences, Tehran, Iran
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31
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Roswall J, Olsson LM, Kovatcheva-Datchary P, Nilsson S, Tremaroli V, Simon MC, Kiilerich P, Akrami R, Krämer M, Uhlén M, Gummesson A, Kristiansen K, Dahlgren J, Bäckhed F. Developmental trajectory of the healthy human gut microbiota during the first 5 years of life. Cell Host Microbe 2021; 29:765-776.e3. [PMID: 33794185 DOI: 10.1016/j.chom.2021.02.021] [Citation(s) in RCA: 182] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/08/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023]
Abstract
The gut is inhabited by a densely populated ecosystem, the gut microbiota, that is established at birth. However, the succession by which different bacteria are incorporated into the gut microbiota is still relatively unknown. Here, we analyze the microbiota from 471 Swedish children followed from birth to 5 years of age, collecting samples after 4 and 12 months and at 3 and 5 years of age as well as from their mothers at birth using 16S rRNA gene profiling. We also compare their microbiota to an adult Swedish population. Genera follow 4 different colonization patterns during establishment where Methanobrevibacter and Christensenellaceae colonize late and do not reached adult levels at 5 years. These late colonizers correlate with increased alpha diversity in both children and adults. By following the children through age-specific community types, we observe that children have individual dynamics in the gut microbiota development trajectory.
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Affiliation(s)
- Josefine Roswall
- Hallands Hospital Halmstad, Department of Pediatrics, Halmstad, Sweden; Gothenburg Pediatric Growth Research Center, Department of Pediatrics, Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Lisa M Olsson
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Petia Kovatcheva-Datchary
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Staffan Nilsson
- Department of Mathematical Sciences, Chalmers Tekniska Högskola, Gothenburg, Sweden; Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Valentina Tremaroli
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marie-Christine Simon
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Pia Kiilerich
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rozita Akrami
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Manuela Krämer
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mathias Uhlén
- Department of Proteomics, KTH-Royal Institute of Technology, Stockholm, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Anders Gummesson
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark; BGI-Shenzhen, Shenzhen, China
| | - Jovanna Dahlgren
- Gothenburg Pediatric Growth Research Center, Department of Pediatrics, Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Pediatrics, Gothenburg, Sweden
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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32
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Kondori N, Nowrouzian F, Ajdari M, Hesselmar B, Saalman R, Wold AE, Adlerberth I. Candida species as commensal gut colonizers: A study of 133 longitudinally followed Swedish infants. Med Mycol 2021; 58:485-492. [PMID: 31504817 DOI: 10.1093/mmy/myz091] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/04/2019] [Accepted: 08/22/2019] [Indexed: 11/14/2022] Open
Abstract
The gut microbiota harbor a wide range of bacterial species, but also yeasts may be part of this ecosystem. Infants who are being treated in intensive care units are often colonized by Candida species. However, little is known regarding commensal yeast colonization of healthy infants and young children. Here the acquisition of yeast species was studied in a birth-cohort including 133 healthy Swedish infants. A rectal swab sample was obtained on day 3 of life, and fresh fecal samples were obtained at regular intervals up to 3 years of age; the samples were cultured quantitatively for yeasts. Colonization with yeasts increased rapidly in the first months of life, with 73/133 infants (55%) colonized at 6 months of age. The yeast numbers in positive samples decreased from an average of 105 cfu/g in infants aged 0-2 months to 103.5 cfu/g at 3 years of age. Candida albicans was the most frequently isolated species and reached higher population counts than the other species in culture-positive infants. The yeast colonization rate did not differ between infants who were delivered vaginally and those birthed via Caesarean section, whereas breastfed infants showed a lower colonization rate (p < 0.05 for 1 year of age compared to the other infants). The results demonstrate that yeasts, particularly C. albicans and C. parapsilosis (sensu lato), are common commensals in the gut microbiota of healthy infants and young children.
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Affiliation(s)
- Nahid Kondori
- Department of Infectious Diseases, Institution of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Forough Nowrouzian
- Department of Infectious Diseases, Institution of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Marjan Ajdari
- Department of Infectious Diseases, Institution of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Bill Hesselmar
- Department of Infectious Diseases, Institution of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Sweden.,Department of Pediatrics, Institution of Clinical Science, The Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Robert Saalman
- Department of Infectious Diseases, Institution of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Sweden.,Department of Pediatrics, Institution of Clinical Science, The Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Agnes E Wold
- Department of Infectious Diseases, Institution of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Ingegerd Adlerberth
- Department of Infectious Diseases, Institution of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Sweden
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33
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The Association between Early-Life Gut Microbiota and Long-Term Health and Diseases. J Clin Med 2021; 10:jcm10030459. [PMID: 33504109 PMCID: PMC7865818 DOI: 10.3390/jcm10030459] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/12/2021] [Accepted: 01/21/2021] [Indexed: 12/14/2022] Open
Abstract
Early life gut microbiota have been increasingly recognized as major contributors to short and/or long-term human health and diseases. Numerous studies have demonstrated that human gut microbial colonization begins at birth, but continues to develop a succession of taxonomic abundances for two to three years until the gut microbiota reaches adult-like diversity and proportions. Several factors, including gestational age (GA), delivery mode, birth weight, feeding types, antibiotic exposure, maternal microbiome, and diet, influence the diversity, abundance, and function of early life gut microbiota. Gut microbial life is essential for assisting with the digestion of food substances to release nutrients, exerting control over pathogens, stimulating or modulating the immune system, and influencing many systems such as the liver, brain, and endocrine system. Microbial metabolites play multiple roles in these interactions. Furthermore, studies provide evidence supporting that imbalances of the gut microbiota in early life, referred to as dysbiosis, are associated with specific childhood or adult disease outcomes, such as asthma, atopic dermatitis, diabetes, allergic diseases, obesity, cardiovascular diseases (CVD), and neurological disorders. These findings support that the human gut microbiota may play a fundamental role in the risk of acquiring diseases that may be programmed during early life. In fact, it is critical to explore the role of the human gut microbiota in early life.
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Lee YS, Kim JH, Lim DH. Urine Microbe-Derived Extracellular Vesicles in Children With Asthma. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2021; 13:75-87. [PMID: 33191678 PMCID: PMC7680828 DOI: 10.4168/aair.2021.13.1.75] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/30/2022]
Abstract
PURPOSE Several studies have found significant associations between asthma and microbiome. However, it is challenging to obtain-sputum and bronchoalveolar lavage samples from pediatric patients. Thus, we used voided urine to show that urine microbe-derived extracellular vesicles (EVs) in asthma are an available source for clinical research. METHODS Five urine samples were obtained at 2-3-month intervals from each patient with asthma (n = 20), and a single voided urine sample were obtained from each healthy child (n = 20). After isolating EVs, 16S rDNA pyrosequencing was performed. The Chao1 index and principal coordinate analysis (PCoA) were used to assess diversity. To predict microbiota functional capacities, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used based on the Kyoto Encyclopedia of Genes and Genomes pathway database. Eight covariates were included in the EnvFit analysis to identify significant factors in the asthma group. RESULTS The asthma group showed lower Chao1 bacterial richness, and PCoA-based clustering differed significantly. Two phyla, and 13 families and genera were enriched or depleted. Functional profiling revealed significant differences between the asthma and control groups. EnvFit analysis of correlation to age, sex, body mass index, infection, season, asthma phenotype, severity, and symptoms was not significant except for infections associated with visit 1 and the season of visit 2. CONCLUSIONS This study showed that microbe-derived EVs were constantly altered in the urine of children with asthma, consistent with the findings of previous studies indicating microbiome changes in the lung and gut. The urine may reflect the specific pattern of microbiome EVs in children with asthma.
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Affiliation(s)
- Yeong Seok Lee
- Department of Pediatrics, School of Medicine, Inha University, Incheon, Korea
| | - Jeong Hee Kim
- Department of Pediatrics, School of Medicine, Inha University, Incheon, Korea
| | - Dae Hyun Lim
- Department of Pediatrics, School of Medicine, Inha University, Incheon, Korea.
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Gio-Batta M, Sjöberg F, Jonsson K, Barman M, Lundell AC, Adlerberth I, Hesselmar B, Sandberg AS, Wold AE. Fecal short chain fatty acids in children living on farms and a link between valeric acid and protection from eczema. Sci Rep 2020; 10:22449. [PMID: 33384449 PMCID: PMC7775451 DOI: 10.1038/s41598-020-79737-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/10/2020] [Indexed: 12/14/2022] Open
Abstract
Children growing up on farms have low rates of allergy, but the mechanism for this protective effect has not been fully elucidated. Short chain fatty acids (SCFAs) produced by the gut microbiota may play a role in protection from allergy. We measured fecal SCFA levels in samples collected from 28 farming and 37 control children over the first 3 years of life using gas chromatography. Data on diet and other host factors were recorded and allergy was diagnosed at 8 years of age. Among all children, median propionic and butyric acid concentration increased over the first 3 years, and longer SCFAs typically appeared by 1 year of age. Farm children had higher levels of iso-butyric, iso-valeric and valeric acid at 3 years of age than rural controls. In addition, children with elder siblings had higher levels of valeric acid at 3 years of age, and dietary factors also affected SCFA pattern. High levels of valeric acid at 3 years of age were associated with low rate of eczema at 8 years of age. The fecal SCFA pattern in farm children suggests a more rapid maturation of the gut microbiota. Valeric acid or associated microbes may have protective potential against eczema.
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Affiliation(s)
- Monica Gio-Batta
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden.
| | - Fei Sjöberg
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
| | - Karin Jonsson
- Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Malin Barman
- Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Unit of Metals and Health, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna-Carin Lundell
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Ingegerd Adlerberth
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
| | - Bill Hesselmar
- Department of Paediatrics, Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Ann-Sofie Sandberg
- Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Agnes E Wold
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
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Mechanisms Underlying the Skin-Gut Cross Talk in the Development of IgE-Mediated Food Allergy. Nutrients 2020; 12:nu12123830. [PMID: 33333859 PMCID: PMC7765270 DOI: 10.3390/nu12123830] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 02/07/2023] Open
Abstract
Immune-globulin E (IgE)-mediated food allergy is characterized by a variety of clinical entities within the gastrointestinal tract, skin and lungs, and systemically as anaphylaxis. The default response to food antigens, which is antigen specific immune tolerance, requires exposure to the antigen and is already initiated during pregnancy. After birth, tolerance is mostly acquired in the gut after oral ingestion of dietary proteins, whilst exposure to these same proteins via the skin, especially when it is inflamed and has a disrupted barrier, can lead to allergic sensitization. The crosstalk between the skin and the gut, which is involved in the induction of food allergy, is still incompletely understood. In this review, we will focus on mechanisms underlying allergic sensitization (to food antigens) via the skin, leading to gastrointestinal inflammation, and the development of IgE-mediated food allergy. Better understanding of these processes will eventually help to develop new preventive and therapeutic strategies in children.
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Xie T, Wang Y, Zou Z, He J, Yu Y, Liu Y, Bai J. Environmental Tobacco Smoke Exposure and Breastfeeding Duration Influence the Composition and Dynamics of Gut Microbiota in Young Children Aged 0-2 Years. Biol Res Nurs 2020; 23:382-393. [PMID: 33267614 DOI: 10.1177/1099800420975129] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The colonization characteristics of infant gut microbiota are influenced by many factors at various stages, but few studies have explored the longitudinal effects of environmental tobacco smoke exposure and quantitative breastfeeding duration on young children' gut microbiota. We explored the effects of smoke exposure and breastfeeding duration on gut microbiota by following 37 maternal and children pairs in China for 2 years. We collected the demographic information, frequency of smoke exposure, breastfeeding duration, and fecal samples (mothers in the late pregnancy and infants at 6, 12, and 24 months), and analyzed the microbiota results using the V3-V4 gene sequence of 16S rRNA. The diversity of gut microbiota in children was the highest at 24 months and most similar to that in mothers. Breastfeeding duration was positively correlated with Lactobacillus and negatively correlated with Clostridium_sensu_stricto_1. The α diversity of microbiota and the relative abundance of [Ruminococcus]_gnavus_group was higher in the non-smoke exposed group. The higher the smoke exposure, the higher the relative abundance of Megasphaera. Prolonged breastfeeding and reduced smoke exposure are beneficial to the diversity and composition of gut microbiota in young children.
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Affiliation(s)
- Tianqu Xie
- School of Health Sciences, 12390Wuhan University, China
| | - Yuchen Wang
- School of Health Sciences, 12390Wuhan University, China
| | - Zhijie Zou
- School of Health Sciences, 12390Wuhan University, China
| | - Jing He
- School of Health Sciences, 12390Wuhan University, China
| | - Yun Yu
- School of Health Sciences, 12390Wuhan University, China
| | - Yanqun Liu
- School of Health Sciences, 12390Wuhan University, China
| | - Jinbing Bai
- Nell Hodgson Woodruff School of Nursing, 1371Emory University, Atlanta, GA, USA
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38
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Veselovsky VA, Dyachkova MS, Menyaylo EA, Polyaeva PS, Olekhnovich EI, Shitikov EA, Bespiatykh DA, Semashko TA, Kasianov AS, Ilina EN, Danilenko VN, Klimina KM. Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors. Front Immunol 2020; 11:595877. [PMID: 33304352 PMCID: PMC7701253 DOI: 10.3389/fimmu.2020.595877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/20/2020] [Indexed: 01/14/2023] Open
Abstract
As permanent residents of the normal gut microbiota, bifidobacteria have evolved to adapt to the host’s immune response whose priority is to eliminate pathogenic agents. The mechanisms that ensure the survival of commensals during inflammation and maintain the stability of the core component of the normal gut microbiota in such conditions remain poorly understood. We propose a new in vitro approach to study the mechanisms of resistance to immune response factors based on high-throughput sequencing followed by transcriptome analysis. This approach allowed us to detect differentially expressed genes associated with inflammation. In this study, we demonstrated that the presence of the pro-inflammatory cytokines IL-6 and TNFα to the growth medium of the B. longum subsp. longum GT15 strain changes the latter’s growth rate insignificantly while affecting the expression of certain genes. We identified these genes and performed a COG and a KEGG pathway enrichment analysis. Using phylogenetic profiling we predicted the operons of genes whose expression was triggered by the cytokines TNFα and IL-6 in vitro. By mapping the transcription start points, we experimentally validated the predicted operons. Thus, in this study, we predicted the genes involved in a putative signaling pathway underlying the mechanisms of resistance to inflammatory factors in bifidobacteria. Since bifidobacteria are a major component of the human intestinal microbiota exhibiting pronounced anti-inflammatory properties, this study is of great practical and scientific relevance.
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Affiliation(s)
- Vladimir A Veselovsky
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Marina S Dyachkova
- Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Egor A Menyaylo
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Polina S Polyaeva
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Evgenii I Olekhnovich
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Egor A Shitikov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry A Bespiatykh
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana A Semashko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Artem S Kasianov
- Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia.,Laboratory of Plant Genomics, The Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Valeriy N Danilenko
- Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia.,Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | - Ksenia M Klimina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.,Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
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Rabe H, Lundell AC, Sjöberg F, Ljung A, Strömbeck A, Gio-Batta M, Maglio C, Nordström I, Andersson K, Nookaew I, Wold AE, Adlerberth I, Rudin A. Neonatal gut colonization by Bifidobacterium is associated with higher childhood cytokine responses. Gut Microbes 2020; 12:1-14. [PMID: 33274676 PMCID: PMC7747801 DOI: 10.1080/19490976.2020.1847628] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The gut microbiota is a major stimulus for the immune system, and late acquisition of bacteria and/or reduced complexity of the gut flora may delay adaptive immune maturation. However, it is unknown how the gut bacterial colonization pattern in human infants is related to T cell activation during early childhood. We followed 65 Swedish children in the FARMFLORA cohort, from birth up to 3 years of age. In fecal samples collected at several time points during the first year of life, the gut colonization pattern was investigated with the use of both 16S rRNA next generation sequencing (NGS) and culture-based techniques. This was related to production of IL-13, IL-5, IL-6, TNF, IL-1β and IFN-γ by PHA-stimulated fresh mononuclear cells and to proportions of CD4+ T cells that expressed CD45RO at 36 months of age. Both NGS and culture-based techniques showed that colonization by Bifidobacterium at 1 week of age associated with higher production of IL-5, IL-6, IL-13, TNF and IL-1β at 36 months of age. By contrast, gut colonization by Enterococcus, Staphylococcus aureus or Clostridium in early infancy related inversely to induced IL-13, IL-5 and TNF at 3 years of age. Infants with elder siblings produced more cytokines and had a larger fraction of CD45RO+ T cells compared to single children. However, controlling for these factors did not abolish the effect of colonization by Bifidobacterium on immune maturation. Thus, gut colonization in early infancy affects T cell maturation and Bifidobacterium may be especially prone to induce infantile immune maturation.
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Affiliation(s)
- Hardis Rabe
- Institute of Biomedicine, Department of Infectious Diseases, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden,CONTACT Hardis Rabe Institution of Biomedicine, Department of Infectious Diseases, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Anna-Carin Lundell
- Institute of Medicine, Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Fei Sjöberg
- Institute of Biomedicine, Department of Infectious Diseases, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Annika Ljung
- Institute of Biomedicine, Department of Infectious Diseases, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Anna Strömbeck
- Institute of Biomedicine, Department of Microbiology and Immunology, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Monica Gio-Batta
- Institute of Biomedicine, Department of Infectious Diseases, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Cristina Maglio
- Institute of Medicine, Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Inger Nordström
- Institute of Medicine, Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Kerstin Andersson
- Institute of Medicine, Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Agnes E. Wold
- Institute of Biomedicine, Department of Infectious Diseases, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Ingegerd Adlerberth
- Institute of Biomedicine, Department of Infectious Diseases, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Anna Rudin
- Institute of Medicine, Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
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Gorris A, Bustamante G, Mayer KA, Kinaciyan T, Zlabinger GJ. Cesarean section and risk of allergies in Ecuadorian children: A cross-sectional study. IMMUNITY INFLAMMATION AND DISEASE 2020; 8:763-773. [PMID: 33128350 PMCID: PMC7654393 DOI: 10.1002/iid3.368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 10/15/2020] [Indexed: 11/08/2022]
Abstract
BACKGROUND Studies have shown an association between cesarean section (CS) and increased prevalence of childhood allergic diseases. While these observations have been consistent in industrialized countries, evidence from developing countries is limited. OBJECTIVE To assess the association between the mode of delivery and allergic diseases in children aged 3-12 years in Quito, Ecuador. METHODS In this cross-sectional study, parents were surveyed using an anonymous, standardized questionnaire from the International Study of Asthma and Allergies in Childhood project to assess the presence of asthma, allergic rhinitis, atopic dermatitis, and food allergies in their children. The children's age, sex, birthplace, delivery mode (CS/vaginal), socioeconomic status, and ethnicity were recorded. Other parameters included gestational age, breastfeeding, smoking status during pregnancy, and parental allergic diseases. RESULTS After adjusting for confounding factors, children delivered via CS were found to have a higher risk of wheezing (odds ratio [OR] = 4.12, 95% confidence interval [CI]: 1.43-11.89), physician-diagnosed asthma (OR = 24.06; 95% CI: 1.98-292.3), and pimples, or eczema with the itching for 6 months (OR = 2.65; 95% CI: 1.06-6.61) than children delivered vaginally. No association was found between the delivery mode and rhinitis or food allergies. After stratifying by socioeconomic status, CS was only associated with allergic disorders in children of medium/high socioeconomic backgrounds. CONCLUSIONS As seen in industrialized settings, children born by CS in nonindustrialized countries have an increased risk of developing allergic disorders including asthma and dermatitis, compared to those delivered vaginally.
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Affiliation(s)
- Amélie Gorris
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador.,Institute of Immunology, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Gabriela Bustamante
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador.,Program in Health Disparities Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Katharina A Mayer
- Institute of Immunology, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Tamar Kinaciyan
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Gerhard J Zlabinger
- Institute of Immunology, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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42
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Kim G, Bae J, Kim MJ, Kwon H, Park G, Kim SJ, Choe YH, Kim J, Park SH, Choe BH, Shin H, Kang B. Delayed Establishment of Gut Microbiota in Infants Delivered by Cesarean Section. Front Microbiol 2020; 11:2099. [PMID: 33013766 PMCID: PMC7516058 DOI: 10.3389/fmicb.2020.02099] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022] Open
Abstract
The maternal vaginal microbiome is an important source for infant gut microbiome development. However, infants delivered by Cesarean section (CS) do not contact the maternal vaginal microbiome and this delivery method may perturb the early establishment and development of the gut microbiome. The aim of this study was to investigate the early gut microbiota of Korean newborns receiving the same postpartum care services for two weeks after birth by delivery mode using fecal samples collected at days 3, 7, and 14. Early gut microbiota development patterns were examined using 16S rRNA gene-based sequencing from 132 infants either born vaginally (VD, n = 64) or via Cesarean section (CS, n = 68). VD-born neonates showed increased alpha diversity in infant fecal samples collated at days 7 and 14 compared to those from day 3, while those of CS infants did not differ (p < 0.015). Bacterial structures of infants from both groups separated at day 7 (p < 0.001) and day 14 (p < 0.01). The bacterial structure of VD infants gradually changed over time (day 3 vs. day 7, p < 0.012; day 3 vs. day 14, p < 0.001). Day 14 samples of CS infants differed from day 3 and 7 samples (day 3 vs. day 14, p < 0.001). VD infant relative abundance of Bifidobacterium (days 7, 14), Bacteroides (days 7, 14), and Lachnospiraceae (day 7) significantly increased compared to CS infants, with a lower abundance of Enterobacteriaceae (found in all periods of the CS group) (LDA > 3.0). Relative abundances of Bifidobacterium, Lactobacillus, and Staphylococcus were significantly increased in both VD and CS groups at day 14 (LDA > 3.0). Predicted functional analysis showed that VD infants had overrepresented starch/sucrose, amino acid and nucleotide metabolism in gut microbiota with depleted lipopolysaccharide biosynthesis until day 14 compared to CS infants. This study confirmed that delivery mode is the major determinant of neonatal intestinal microbiome establishment and provides a profile of microbiota perturbations in CS infants. Our findings provide preliminary insight for establishing recovery methods to supply the specific microbes missing in CS infants.
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Affiliation(s)
- Gyungcheon Kim
- R&D Institute, BioEleven Co., Ltd., Seoul, South Korea.,Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, South Korea
| | - Jaewoong Bae
- R&D Institute, BioEleven Co., Ltd., Seoul, South Korea
| | - Mi Jin Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hyeji Kwon
- R&D Institute, BioEleven Co., Ltd., Seoul, South Korea
| | - Gwoncheol Park
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, South Korea
| | - Seok-Jin Kim
- R&D Institute, BioEleven Co., Ltd., Seoul, South Korea
| | - Yon Ho Choe
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jisook Kim
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Sook-Hyun Park
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Byung-Ho Choe
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Hakdong Shin
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, South Korea
| | - Ben Kang
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea
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43
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Quin C, Gibson DL. Human behavior, not race or geography, is the strongest predictor of microbial succession in the gut bacteriome of infants. Gut Microbes 2020; 11:1143-1171. [PMID: 32249675 PMCID: PMC7524360 DOI: 10.1080/19490976.2020.1736973] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Colonization of the gastrointestinal tract with microorganisms during infancy represents a critical control point for shaping life-long immune-mediated disease susceptibility. Abnormal colonization or an imbalance of microbes, termed dysbiosis, is implicated in several diseases. Consequently, recent research has aimed at understanding ways to manipulate a dysbiotic microbiome during infancy to resemble a normal, healthy microbiome. However, one of the fundamental issues in microbiome research is characterizing what a "normal" infant microbiome is based on geography, ethnicity and cultural variations. This review provides a comprehensive account of what is currently known about the infant microbiome from a global context. In general, this review shows that the influence of cultural variations in feeding practices, delivery modes and hygiene are the biggest contributors to microbial variability. Despite geography or race, all humans have similar microbial succession during infancy.
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Affiliation(s)
- Candice Quin
- Department of Biology, University of British Columbia, Kelowna, Canada
| | - Deanna L. Gibson
- Department of Biology, University of British Columbia, Kelowna, Canada,Department of Medicine, University of British Columbia, Kelowna, Canada,CONTACT Deanna L. Gibson Department of Biology, University of British Columbia, Okanagan Campus, ASC 386, 3187 University Way, Kelowna, BCV1V 1V7, Canada
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44
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Sjöberg F, Nookaew I, Yazdanshenas S, Gio-Batta M, Adlerberth I, Wold AE. Are all faecal bacteria detected with equal efficiency? A study using next-generation sequencing and quantitative culture of infants' faecal samples. J Microbiol Methods 2020; 177:106018. [PMID: 32795633 DOI: 10.1016/j.mimet.2020.106018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Many species of intestinal bacteria are present in moderate numbers in the faecal microbiota, which is dominated by obligate anaerobes. Little is known regarding the detection sensitivity of next-generation sequencing for these microbes in samples of complex microbiota. METHODS Twenty stool samples from six healthy infants, who were followed from 1 week to 1 year of age, were previously cultured quantitatively for total population counts, as well as for counts of relevant facultative bacteria and a limited selection of obligate anaerobes that are prevalent in the neonatal microbiota. The same samples were analysed by Next-generation sequencing (NGS, pyrosequencing) of the 16S rRNA gene (V1-V3 regions; average read length, 500 nucleotides; average number of reads per sample, 30,000). We used the bacterial culture data to determine the lowest bacterial populations that could be detected by NGS. Different DNA extraction kits (QIAamp DNA Stool Mini, ZR Faecal DNA MiniPrep, and PowerSoil DNA Isolation) were compared for efficacy in extracting DNA from Gram-negative and Gram-positive Type strains. RESULTS NGS yielded one read per 106 CFU/g faeces of the Gram-negative commensal gut bacteria Bacteroides and Enterobacteriaceae, but only one read per 108 CFU/g faeces of Gram-positive bifidobacteria. The Gram-positive facultative bacteria Enterococcus was often undetectable by DNA-based methods despite being present at >106 CFU/g faeces. The DNA extraction kits tested varied considerably in their ability to extract DNA from bacterial samples, and showed considerably lower efficacies in extracting DNA from Gram-positive than from Gram-negative bacteria. CONCLUSIONS NGS has lower sensitivity for detecting Gram-positive bacteria than Gram-negative bacteria, due at least in part to inefficient extraction of DNA from Gram-positive bacteria. Therefore, enzymatic lysis may enhance the yield of DNA and increase the sensitivity of NGS methods for Gram-positive bacteria, and the inclusion of positive and negative controls during DNA extraction is indicated for validation purposes. The differential extraction of DNA from bacterial samples by different DNA extraction kits may limit comparability between studies on the gut microbiota. Finally, quantitative culture methods detect certain bacteria with greater sensitivity than NGS techniques, and thus culture- and DNA-based methods can be used in tandem to define the complex composition of the gut microbiota with greater accuracy.
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Affiliation(s)
- Fei Sjöberg
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden.
| | - Intawat Nookaew
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Shora Yazdanshenas
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Monica Gio-Batta
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Ingegerd Adlerberth
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Agnes E Wold
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
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45
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Klimina KM, Voroshilova VN, Poluektova EU, Veselovsky VA, Yunes RA, Kovtun AS, Kudryavtseva AV, Kasianov AS, Danilenko VN. Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota. Toxins (Basel) 2020; 12:toxins12060388. [PMID: 32545455 PMCID: PMC7354421 DOI: 10.3390/toxins12060388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 01/14/2023] Open
Abstract
The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM.
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Affiliation(s)
- Ksenia M. Klimina
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
- Correspondence:
| | - Viktoriya N. Voroshilova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Elena U. Poluektova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
| | - Vladimir A. Veselovsky
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
| | - Roman A. Yunes
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
| | - Aleksey S. Kovtun
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Artem S. Kasianov
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Valery N. Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
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46
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Yang J, Yao S, Cheng K, Xu L, Hou L, Wei Y, Feng H, Yu X, Zhang X, Tong X, Li Z, Zhao Y. Comparison of Meconium Microbiome in Dizygotic and Monozygotic Twins Born by Caesarean Section (CS). Front Microbiol 2020; 11:1139. [PMID: 32582089 PMCID: PMC7283445 DOI: 10.3389/fmicb.2020.01139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/05/2020] [Indexed: 01/27/2023] Open
Abstract
The early-life microbiota triggers life-long effects on physiological functions and health disorders. Previous studies in adult twins or animal models have revealed associations between host genetics and the harmonious microbiota. However, such associations may be obscured by the fact that each intra-pair of twins will continually encounter various environmental factors as they grow up. Here, we collected the meconium samples from nineteen dizygotic pairs (DZ, n = 38) and nine monozygotic pairs (MZ, n = 18) with cesarean delivery, and 16S rRNA gene sequencing was performed to profile the microbiome at birth. Diversity analysis showed that alpha diversity was not significantly different between two groups, whereas beta diversity of MZ twins was significantly lower than that of either DZ twins or unrelated individuals (i.e., randomly selected individual pairs of non-twinship) (p < 0.05). Two groups had very similar microbial classifications but different relative abundances of certain taxa including more Firmicutes (p = 0.05, Wilcoxon test) at the phylum level and lower abundances of five genera (p < 0.05) in DZ group compared to MZ group, including Rheinheimera, Proteus, SMB53, Sphingobium, and Megamonas. Co-occurrence analysis in each group showed slightly more complicated microbial interactions in DZ than MZ twins, although 22 shared bacterial genera co-existed in two groups, with both Rheinheimera and Megamonas having different centralities in their respective co-occurrence networks. Mean intra-class correlation coefficient (ICC) were also significantly higher for MZ (0.312) compared to DZ twins (0.138) (p < 0.05). The predicted microbial gene functions related to carbohydrate were higher in DZ group, whereas folding, sorting, degradation, cell motility pathways and energy metabolism were markedly over-represented in the microbiota of MZ group. In summary, our study uncovered that microbial diversity and components of the meconium microbiome between DZ and MZ twins were partially consistent with that in singleton neonates by cesarean delivery, but several distinctions related to the heritability supported genetic contributions to intestinal microbiome in early life.
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Affiliation(s)
- Jing Yang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Su Yao
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food & Fermentation Industries Co., Ltd., Beijing, China
| | - Kun Cheng
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food & Fermentation Industries Co., Ltd., Beijing, China
| | - Lili Xu
- Department of Pediatrics, Peking University Third Hospital, Beijing, China
| | - Lingling Hou
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Huijun Feng
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food & Fermentation Industries Co., Ltd., Beijing, China
| | - Xuejian Yu
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food & Fermentation Industries Co., Ltd., Beijing, China
| | - Xin Zhang
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food & Fermentation Industries Co., Ltd., Beijing, China
| | - Xiaomei Tong
- Department of Pediatrics, Peking University Third Hospital, Beijing, China
| | - Zailing Li
- Department of Pediatrics, Peking University Third Hospital, Beijing, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
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47
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Kapourchali FR, Cresci GAM. Early-Life Gut Microbiome-The Importance of Maternal and Infant Factors in Its Establishment. Nutr Clin Pract 2020; 35:386-405. [PMID: 32329544 DOI: 10.1002/ncp.10490] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/10/2020] [Indexed: 12/17/2022] Open
Abstract
The early-life microbiome is gaining appreciation as a major influencer in human development and long-term health. Multiple factors are known to influence the initial colonization, development, and function of the neonatal gut microbiome. In addition, alterations in early-life gut microbial composition is associated with several chronic health conditions such as obesity, asthma, and allergies. In this review, we focus on both maternal and infant factors known to influence early-life gut colonization. Also reviewed is the important role of infant feeding, including evidence-based strategies for maternal and infant supplementation with the goal to protect and/or restore the infant gut microbiome.
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Affiliation(s)
| | - Gail A M Cresci
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Pediatric Gastroenterology, Cleveland Clinic, Cleveland, Ohio, USA.,Center for Human Nutrition, Cleveland Clinic, Cleveland, Ohio, USA
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48
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Zimmermann P, Curtis N. Effect of intrapartum antibiotics on the intestinal microbiota of infants: a systematic review. Arch Dis Child Fetal Neonatal Ed 2020; 105:201-208. [PMID: 31296695 DOI: 10.1136/archdischild-2018-316659] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The use of intrapartum antibiotic prophylaxis (IAP) has become common practice in obstetric medicine and is used in up to 40% of deliveries. Despite its benefits, the risks associated with exposing large numbers of infants to antibiotics, especially long-term effects on health through changes in the microbiota, remain unclear. This systematic review summarises studies that have investigated the effect of IAP on the intestinal microbiota of infants. METHODS A systematic search in Ovid MEDLINE was used to identify original studies that investigated the effect of IAP on the intestinal microbiota in infants. Studies were excluded if: they included preterm infants, the antibiotic regimen was not specified, antibiotics were used for indications other than prophylaxis, probiotics were given to mothers or infants, or antibiotics were given to infants. RESULTS We identified six studies, which investigated a total of 272 infants and included 502 stool samples collected up to 3 months of age. In all the studies, IAP was given for group B streptococcus (GBS) colonisation. Infants who were exposed to GBS IAP had a lower bacterial diversity, a lower relative abundance of Actinobacteria, especially Bifidobacteriaceae, and a larger relative abundance of Proteobacteria in their intestinal microbiota compared with non-exposed infants. Conflicting results were reported for the phyla Bacteroidetes and Firmicutes. CONCLUSIONS GBS IAP has profound effects on the intestinal microbiota of infants by diminishing beneficial commensals. Such changes during the early-life 'critical window' during which the intestinal microbiota and the immune response develop concurrently may have an important influence on immune development. The potential long-term adverse consequences of this on the health of children warrant further investigation.
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Affiliation(s)
- Petra Zimmermann
- Department of Paediatrics, Fribourg Hospital HFR and Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Victoria, Australia.,Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Victoria, Australia.,Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
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49
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Van Daele E, Knol J, Belzer C. Microbial transmission from mother to child: improving infant intestinal microbiota development by identifying the obstacles. Crit Rev Microbiol 2019; 45:613-648. [DOI: 10.1080/1040841x.2019.1680601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Emmy Van Daele
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Gut Biology and Microbiology, Danone Nutricia Research, Utrecht, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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50
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Knight LC, Wang M, Donovan SM, Dilger RN. Early-Life Iron Deficiency and Subsequent Repletion Alters Development of the Colonic Microbiota in the Pig. Front Nutr 2019; 6:120. [PMID: 31440513 PMCID: PMC6692694 DOI: 10.3389/fnut.2019.00120] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/19/2019] [Indexed: 12/26/2022] Open
Abstract
Background: Iron deficiency is the most prevalent micronutrient deficiency worldwide, affecting over two billion people. Early-life iron deficiency may alter the developing microbiota, which may or may not be reversible with subsequent dietary iron repletion. Thus, the aim of this study was to determine whether early-life iron deficiency and subsequent repletion alter colonic microbial composition and fermentation end-product concentrations in pigs. Methods: Forty-two male pigs received either control (CONT, 21.3 mg Fe/L) or iron-deficient (ID, 2.72 mg Fe/L) milk replacer treatments from postnatal day (PND) 2 to 32. Subsequently, 20 pigs continued through a series of age-appropriate, iron-adequate diets from PND 33 to 61. Contents from the ascending colon (AC) and rectum (feces) were collected at PND 32 and/or 61. Assessments included microbiota composition by 16S rRNA sequencing and volatile fatty acid (VFA) concentrations by gas chromatography methods. Data were analyzed using a 1-way ANOVA and PERMANOVA to assess the main effects of early-life iron status on all outcomes. Results: In AC samples, 15 genera differed (P < 0.05) between ID and CONT pigs, while 27 genera differed (P < 0.05) in fecal samples at PND 32. Early-life ID pigs had higher (P = 0.012) relative abundance of Lactobacillus in AC samples compared with CONT pigs. In feces, ID pigs had lower (P < 0.05) relative abundances of Bacteroides and Clostridium from the families of Clostridiaceae, Lachnospiraceae, and Ruminococcaceae. At PND 61, only two genera differed between treatment groups in AC samples, with ID pigs having a higher (P = 0.043) relative abundance of Bifidobacterium and lower (P = 0.047) relative abundance of Prevotella. Beta diversity differed at PND 32 in both AC and feces between CONT and ID pigs but no differences remained at PND 61. At PND 32, the total VFA concentration was higher in ID pigs compared with CONT pigs in both AC (P = 0.003) and feces (P = 0.001), but no differences in VFA concentrations persisted to PND 61. Conclusion: Early-life iron status influenced microbial composition and VFA concentrations within the large intestine, but these differences were largely normalized following subsequent dietary iron repletion.
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Affiliation(s)
- Laura C. Knight
- Piglet Nutrition & Cognition Laboratory, Department of Animal Sciences, University of Illinois, Urbana, IL, United States
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Mei Wang
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL, United States
| | - Sharon M. Donovan
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL, United States
| | - Ryan N. Dilger
- Piglet Nutrition & Cognition Laboratory, Department of Animal Sciences, University of Illinois, Urbana, IL, United States
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
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