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Pol S, Kallonen T, Mäklin T, Sar P, Hopkins J, Soeng S, Miliya T, Ling CL, Bentley SD, Corander J, Turner P. Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing. mBio 2024; 15:e0078424. [PMID: 38682956 DOI: 10.1128/mbio.00784-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The nasopharynx is an important reservoir of disease-associated and antimicrobial-resistant bacterial species. This proof-of-concept study assessed the utility of a combined culture, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and targeted metagenomic sequencing workflow for the study of the pediatric nasopharyngeal bacterial microbiota. Nasopharyngeal swabs and clinical metadata were collected from Cambodian children during a hospital outpatient visit and then biweekly for 12 weeks. Swabs were cultured on chocolate and blood-gentamicin agar, and all colony morphotypes were identified by MALDI-TOF MS. Metagenomic sequencing was done on a scrape of all colonies from a chocolate agar culture and processed using the mSWEEP pipeline. One hundred one children were enrolled, yielding 620 swabs. MALDI-TOF MS identified 106 bacterial species/40 genera: 20 species accounted for 88.5% (2,190/2,474) of isolates. Colonization by Moraxella catarrhalis (92.1% of children on ≥1 swab), Haemophilus influenzae (87.1%), and Streptococcus pneumoniae (83.2%) was particularly common. In S. pneumoniae-colonized children, a median of two serotypes [inter-quartile range (IQR) 1-2, range 1-4] was detected. For the 21 bacterial species included in the mSWEEP database and identifiable by MALDI-TOF, detection by culture + MALDI-TOF MS and culture + mSWEEP was highly concordant with a median species-level agreement of 96.9% (IQR 86.8%-98.8%). mSWEEP revealed highly dynamic lineage-level colonization patterns for S. pneumoniae which were quite different to those for S. aureus. A combined culture, MALDI-TOF MS, targeted metagenomic sequencing approach for the exploration of the young child nasopharyngeal microbiome was technically feasible, and each component yielded complementary data. IMPORTANCE The human upper respiratory tract is an important source of disease-causing and antibiotic-resistant bacteria. However, understanding the interactions and stability of these bacterial populations is technically challenging. We used a combination of approaches to determine colonization patterns over a 3-month period in 101 Cambodian children. The combined approach was feasible to implement, and each component gave complementary data to enable a better understanding of the complex patterns of bacterial colonization.
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Affiliation(s)
- Sreymom Pol
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Tommi Mäklin
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Poda Sar
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Jill Hopkins
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Sona Soeng
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Clare L Ling
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | | | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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Dombrowska-Pali A, Wiktorczyk-Kapischke N, Chrustek A, Olszewska-Słonina D, Gospodarek-Komkowska E, Socha MW. Human Milk Microbiome-A Review of Scientific Reports. Nutrients 2024; 16:1420. [PMID: 38794658 PMCID: PMC11124344 DOI: 10.3390/nu16101420] [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: 04/05/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
One of the most important bioactive components of breast milk are free breast milk oligosaccharides, which are a source of energy for commensal intestinal microorganisms, stimulating the growth of Bifidobacterium, Lactobacillus, and Bacteroides in a child's digestive tract. There is some evidence that maternal, perinatal, and environmental-cultural factors influence the modulation of the breast milk microbiome. This review summarizes research that has examined the composition of the breast milk microbiome and the factors that may influence it. The manuscript highlights the potential importance of the breast milk microbiome for the future development and health of children. The origin of bacteria in breast milk is thought to include the mother's digestive tract (entero-mammary tract), bacterial exposure to the breast during breastfeeding, and the retrograde flow of breast milk from the infant's mouth to the woman's milk ducts. Unfortunately, despite increasingly more precise methods for assessing microorganisms in human milk, the topic of the human milk microbiome is still quite limited and requires scientific research that takes into account various conditions.
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Affiliation(s)
- Agnieszka Dombrowska-Pali
- Department of Perinatology, Gynecology and Gynecologic Oncology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Łukasiewicza 1, 85-821 Bydgoszcz, Poland;
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Curie-Skłodowskiej 9, 85-094 Bydgoszcz, Poland; (N.W.-K.); (E.G.-K.)
| | - Agnieszka Chrustek
- Department of Pathobiochemistry and Clinical Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Curie-Skłodowskiej 9, 85-094 Bydgoszcz, Poland; (A.C.); (D.O.-S.)
| | - Dorota Olszewska-Słonina
- Department of Pathobiochemistry and Clinical Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Curie-Skłodowskiej 9, 85-094 Bydgoszcz, Poland; (A.C.); (D.O.-S.)
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Curie-Skłodowskiej 9, 85-094 Bydgoszcz, Poland; (N.W.-K.); (E.G.-K.)
| | - Maciej W. Socha
- Department of Perinatology, Gynecology and Gynecologic Oncology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Łukasiewicza 1, 85-821 Bydgoszcz, Poland;
- Department of Obstetrics and Gynecology, St. Adalberts’s Hospital in Gdańsk, Copernicus Healthcare Entity LLC, Jana Pawła II 50, 80-462 Gdańsk, Poland
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Perdijk O, Azzoni R, Marsland BJ. The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract. Physiol Rev 2024; 104:835-879. [PMID: 38059886 DOI: 10.1152/physrev.00020.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/07/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
The last decade of microbiome research has highlighted its fundamental role in systemic immune and metabolic homeostasis. The microbiome plays a prominent role during gestation and into early life, when maternal lifestyle factors shape immune development of the newborn. Breast milk further shapes gut colonization, supporting the development of tolerance to commensal bacteria and harmless antigens while preventing outgrowth of pathogens. Environmental microbial and lifestyle factors that disrupt this process can dysregulate immune homeostasis, predisposing infants to atopic disease and childhood asthma. In health, the low-biomass lung microbiome, together with inhaled environmental microbial constituents, establishes the immunological set point that is necessary to maintain pulmonary immune defense. However, in disease perturbations to immunological and physiological processes allow the upper respiratory tract to act as a reservoir of pathogenic bacteria, which can colonize the diseased lung and cause severe inflammation. Studying these host-microbe interactions in respiratory diseases holds great promise to stratify patients for suitable treatment regimens and biomarker discovery to predict disease progression. Preclinical studies show that commensal gut microbes are in a constant flux of cell division and death, releasing microbial constituents, metabolic by-products, and vesicles that shape the immune system and can protect against respiratory diseases. The next major advances may come from testing and utilizing these microbial factors for clinical benefit and exploiting the predictive power of the microbiome by employing multiomics analysis approaches.
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Affiliation(s)
- Olaf Perdijk
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Rossana Azzoni
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
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Olson M, Toffoli S, Vander Wyst KB, Zhou F, Reifsnider E, Petrov ME, Whisner CM. Associations of Infant Feeding, Sleep, and Weight Gain with the Toddler Gut Microbiome. Microorganisms 2024; 12:549. [PMID: 38543600 PMCID: PMC10972346 DOI: 10.3390/microorganisms12030549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/02/2024] [Accepted: 03/08/2024] [Indexed: 05/05/2024] Open
Abstract
This study examines how feeding, sleep, and growth during infancy impact the gut microbiome (GM) in toddlers. The research was conducted on toddlers (n = 36), born to Latina women of low-income with obesity. Their mothers completed retrospective feeding and sleeping questionnaires at 1, 6, and 12 months; at 36 months, fecal samples were collected. Sequencing of the 16S rRNA gene (V4 region) revealed that breastfeeding for at least 1 month and the introduction of solids before 6 months differentiated the GM in toddlerhood (Bray-Curtis, pseudo-F = 1.805, p = 0.018, and pseudo-F = 1.651, p = 0.044, respectively). Sleep had an effect across time; at 1 and 6 months of age, a lower proportion of nighttime sleep (relative to 24 h total sleep) was associated with a richer GM at three years of age (Shannon H = 4.395, p = 0.036 and OTU H = 5.559, p = 0.018, respectively). Toddlers experiencing rapid weight gain from birth to 6 months had lower phylogenetic diversity (Faith PD H = 3.633, p = 0.057). These findings suggest that early life nutrition, sleeping patterns, and growth rate in infancy may influence the GM composition. Further verification of these results with objective sleep data and a larger sample is needed.
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Affiliation(s)
- Magdalena Olson
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (M.O.); (S.T.); (K.B.V.W.); (F.Z.)
- Center for Health Through Microbiomes, The Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Samantha Toffoli
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (M.O.); (S.T.); (K.B.V.W.); (F.Z.)
| | - Kiley B. Vander Wyst
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (M.O.); (S.T.); (K.B.V.W.); (F.Z.)
| | - Fang Zhou
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (M.O.); (S.T.); (K.B.V.W.); (F.Z.)
| | - Elizabeth Reifsnider
- Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ 85004, USA; (E.R.); (M.E.P.)
| | - Megan E. Petrov
- Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ 85004, USA; (E.R.); (M.E.P.)
| | - Corrie M. Whisner
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; (M.O.); (S.T.); (K.B.V.W.); (F.Z.)
- Center for Health Through Microbiomes, The Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
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Galeana-Cadena D, Gómez-García IA, Lopez-Salinas KG, Irineo-Moreno V, Jiménez-Juárez F, Tapia-García AR, Boyzo-Cortes CA, Matías-Martínez MB, Jiménez-Alvarez L, Zúñiga J, Camarena A. Winds of change a tale of: asthma and microbiome. Front Microbiol 2023; 14:1295215. [PMID: 38146448 PMCID: PMC10749662 DOI: 10.3389/fmicb.2023.1295215] [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: 09/15/2023] [Accepted: 11/15/2023] [Indexed: 12/27/2023] Open
Abstract
The role of the microbiome in asthma is highlighted, considering its influence on immune responses and its connection to alterations in asthmatic patients. In this context, we review the variables influencing asthma phenotypes from a microbiome perspective and provide insights into the microbiome's role in asthma pathogenesis. Previous cohort studies in patients with asthma have shown that the presence of genera such as Bifidobacterium, Lactobacillus, Faecalibacterium, and Bacteroides in the gut microbiome has been associated with protection against the disease. While, the presence of other genera such as Haemophilus, Streptococcus, Staphylococcus, and Moraxella in the respiratory microbiome has been implicated in asthma pathogenesis, indicating a potential link between microbial dysbiosis and the development of asthma. Furthermore, respiratory infections have been demonstrated to impact the composition of the upper respiratory tract microbiota, increasing susceptibility to bacterial diseases and potentially triggering asthma exacerbations. By understanding the interplay between the microbiome and asthma, valuable insights into disease mechanisms can be gained, potentially leading to the development of novel therapeutic approaches.
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Affiliation(s)
- David Galeana-Cadena
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Itzel Alejandra Gómez-García
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Karen Gabriel Lopez-Salinas
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Valeria Irineo-Moreno
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Fabiola Jiménez-Juárez
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Alan Rodrigo Tapia-García
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Red de Medicina para la Educación, el Desarrollo y la Investigación Científica de Iztacala, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Alberto Boyzo-Cortes
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Melvin Barish Matías-Martínez
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Luis Jiménez-Alvarez
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Joaquín Zúñiga
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Angel Camarena
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
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Shen D, Wang K, Fathi MA, Li Y, Win-Shwe TT, Li C. A succession of pulmonary microbiota in broilers during the growth cycle. Poult Sci 2023; 102:102884. [PMID: 37423015 PMCID: PMC10466298 DOI: 10.1016/j.psj.2023.102884] [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: 04/03/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/11/2023] Open
Abstract
Respiratory health problems in poultry production are frequent and knotty and thus attract the attention of farmers and researchers. The breakthrough of gene sequencing technology has revealed that healthy lungs harbor rich microbiota, whose succession and homeostasis are closely related to lung health status, suggesting a new idea to explore the mechanism of lung injury in broilers with pulmonary microbiota as the entry point. This study aimed to investigate the succession of pulmonary microbiota in healthy broilers during the growth cycle. Fixed and molecular samples were collected from the lungs of healthy broilers at 1, 3, 14, 21, 28, and 42 d of age. Lung tissue morphology was observed by hematoxylin and eosin staining, and the changes in the composition and diversity of pulmonary microbiota were analyzed using 16S rRNA gene sequencing. The results showed that lung index peaked at 3 d, then decreased with age. No significant change was observed in the α diversity of pulmonary microbiota, while the β diversity changed regularly with age during the broilers' growth cycle. The relative abundance of dominant bacteria of Firmicutes and their subordinate Lactobacillus increased with age, while the abundance of Proteobacteria decreased with age. The correlation analysis between the abundance of differential bacteria and predicted function showed that dominant bacteria of Firmicutes, Proteobacteria and Lactobacillus were significantly correlated with most functional abundance, indicating that they may involve in lung functional development and physiological activities of broilers. Collectively, these findings suggest that the lung has been colonized with abundant microbiota in broilers when they were just hatched, and their composition changed regularly with day age. The dominant bacteria, Firmicutes, Proteobacteria, and Lactobacillus, play crucial roles in lung function development and physiological activities. It paves the way for further research on the mechanism of pulmonary microbiota-mediated lung injury in broilers.
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Affiliation(s)
- Dan Shen
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Wang
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Mohamed Ahmed Fathi
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Animal Production Research Institute, Agricultural Research Centre, Dokki, Giza 12618, Egypt
| | - Yansen Li
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tin-Tin Win-Shwe
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Chunmei Li
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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Claassen-Weitz S, Gardner-Lubbe S, Xia Y, Mwaikono KS, Mounaud SH, Nierman WC, Workman L, Zar HJ, Nicol MP. Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort. MICROBIOME 2023; 11:127. [PMID: 37271810 PMCID: PMC10240772 DOI: 10.1186/s40168-023-01563-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/30/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Bacteria colonizing the nasopharynx play a key role as gatekeepers of respiratory health. Yet, dynamics of early life nasopharyngeal (NP) bacterial profiles remain understudied in low- and middle-income countries (LMICs), where children have a high prevalence of risk factors for lower respiratory tract infection. We investigated longitudinal changes in NP bacterial profiles, and associated exposures, among healthy infants from low-income households in South Africa. METHODS We used short fragment (V4 region) 16S rRNA gene amplicon sequencing to characterize NP bacterial profiles from 103 infants in a South African birth cohort, at monthly intervals from birth through the first 12 months of life and six monthly thereafter until 30 months. RESULTS Corynebacterium and Staphylococcus were dominant colonizers at 1 month of life; however, these were rapidly replaced by Moraxella- or Haemophilus-dominated profiles by 4 months. This succession was almost universal and largely independent of a broad range of exposures. Warm weather (summer), lower gestational age, maternal smoking, no day-care attendance, antibiotic exposure, or low height-for-age z score at 12 months were associated with higher alpha and beta diversity. Summer was also associated with higher relative abundances of Staphylococcus, Streptococcus, Neisseria, or anaerobic gram-negative bacteria, whilst spring and winter were associated with higher relative abundances of Haemophilus or Corynebacterium, respectively. Maternal smoking was associated with higher relative abundances of Porphyromonas. Antibiotic therapy (or isoniazid prophylaxis for tuberculosis) was associated with higher relative abundance of anerobic taxa (Porphyromonas, Fusobacterium, and Prevotella) and with lower relative abundances of health associated-taxa Corynebacterium and Dolosigranulum. HIV-exposure was associated with higher relative abundances of Klebsiella or Veillonella and lower relative abundances of an unclassified genus within the family Lachnospiraceae. CONCLUSIONS In this intensively sampled cohort, there was rapid and predictable replacement of early profiles dominated by health-associated Corynebacterium and Dolosigranulum with those dominated by Moraxella and Haemophilus, independent of exposures. Season and antibiotic exposure were key determinants of NP bacterial profiles. Understudied but highly prevalent exposures prevalent in LMICs, including maternal smoking and HIV-exposure, were associated with NP bacterial profiles. Video Abstract.
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Affiliation(s)
- Shantelle Claassen-Weitz
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sugnet Gardner-Lubbe
- Department of Statistics and Actuarial Science, Faculty of Economic and Management Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Yao Xia
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Center for Artificial Intelligence and Machine Learning, School of Science, Edith Cowan University, Joondalup, Australia
| | - Kilaza S. Mwaikono
- Computational Biology Group and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Department of Science and Laboratory Technology, Dar Es Salaam Institute of Technology, Dar Es Salaam, Tanzania
| | | | | | - Lesley Workman
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P. Nicol
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
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Tran TH, Roberts AQ, Escapa IF, Gao W, Segre JA, Kong HH, Conlan S, Kelly MS, Lemon KP. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543719. [PMID: 37333201 PMCID: PMC10274666 DOI: 10.1101/2023.06.05.543719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.
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Affiliation(s)
- Tommy H. Tran
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ari Q. Roberts
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel F. Escapa
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Julie A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Katherine P. Lemon
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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Chung CJ, Hermes BM, Gupta Y, Ibrahim S, Belheouane M, Baines JF. Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling. Anim Microbiome 2023; 5:31. [PMID: 37264412 DOI: 10.1186/s42523-023-00250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Mammalian lungs comprise a complex microbial ecosystem that interacts with host physiology. Previous research demonstrates that the environment significantly contributes to bacterial community structure in the upper and lower respiratory tract. However, the influence of host genetics on the makeup of lung microbiota remains ambiguous, largely due to technical difficulties related to sampling, as well as challenges inherent to investigating low biomass communities. Thus, innovative approaches are warranted to clarify host-microbe interactions in the mammalian lung. RESULTS Here, we aimed to characterize host genomic regions associated with lung bacterial traits in an advanced intercross mouse line (AIL). By performing quantitative microbial profiling (QMP) using the highly precise method of droplet digital PCR (ddPCR), we refined 16S rRNA gene amplicon-based traits to identify and map candidate lung-resident taxa using a QTL mapping approach. In addition, the two abundant core taxa Lactobacillus and Pelomonas were chosen for independent microbial phenotyping using genus-specific primers. In total, this revealed seven significant loci involving eight bacterial traits. The narrow confidence intervals afforded by the AIL population allowed us to identify several promising candidate genes related to immune and inflammatory responses, cell apoptosis, DNA repair, and lung functioning and disease susceptibility. Interestingly, one genomic region associated with Lactobacillus abundance contains the well-known anti-inflammatory cytokine Il10, which we confirmed through the analysis of Il10 knockout mice. CONCLUSIONS Our study provides the first evidence for a role of host genetic variation contributing to variation in the lung microbiota. This was in large part made possible through the careful curation of 16S rRNA gene amplicon data and the incorporation of a QMP-based methods. This approach to evaluating the low biomass lung environment opens new avenues for advancing lung microbiome research using animal models.
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Affiliation(s)
- C J Chung
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - B M Hermes
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - Y Gupta
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - S Ibrahim
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Meriem Belheouane
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
- Research Center Borstel, Evolution of the Resistome, Leibniz Lung Center, Parkallee 1-40, 23845, Borstel, Germany.
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
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10
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Fu ZY, Huang C, Lei L, Chen LC, Wei LJ, Zhou J, Tao M, Quan MT, Huang Y. The effect of oropharyngeal colostrum administration on the clinical outcomes of premature infants: A meta-analysis. Int J Nurs Stud 2023; 144:104527. [PMID: 37295286 DOI: 10.1016/j.ijnurstu.2023.104527] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Preterm complications are now the second leading cause of death in children under five years of age. Colostrum is essential to prevent infection and promote maturation in preterm infants. Guidelines recommend that preterm infants be fed colostrum by the oral and pharyngeal routes as early as possible after birth to provide immune protection; however, due to disease and an uncoordinated sucking and swallowing function, it is challenging to provide colostrum through the oropharyngeal route, which limits the immune protection it provides. OBJECTIVE To update the existing meta-analysis, evaluate the effect of oropharyngeal colostrum administration on related outcomes in preterm infants and explore the optimal frequency and duration of oropharyngeal colostrum administration through subgroup analysis. METHODS The Cochrane Library, PubMed, Web of Science, ScienceDirect, and Ovid databases were searched for randomized control trials (RCTs) of oropharyngeal colostrum administration for preterm infants. Two researchers screened the literature strictly according to the inclusion and exclusion criteria and evaluated the quality. Primary data and data from the included literature were extracted. Finally, the data were statistically analyzed by the Review Manager 5.3 software. RESULTS A total of 1736 preterm infants were included in 16 RCTs. The meta-analysis showed that the incidence of necrotizing enterocolitis, late-onset sepsis, feeding intolerance, and death was lower, the time to full enteral feeding was shorter, and the day of recovery to birth weight was earlier in the intervention group (oropharyngeal colostrum administration group) than in the control group, and this difference was statistically significant. Subgroup analysis: Frequency of oropharyngeal colostrum administration: The incidence of necrotizing enterocolitis and late-onset sepsis in the once every 4 h group was lower than that in the control group, and the time to complete enteral feeding was shorter. Duration of oropharyngeal colostrum administration: In the 1-3 days group and 4-7 days group, the time to full enteral feeding in the intervention group was shorter. In the 8-10 days group, the incidence of necrotizing enterocolitis and late-onset sepsis was lower in the intervention group. CONCLUSIONS Oropharyngeal colostrum administration can reduce the incidence of necrotizing enterocolitis, late-onset sepsis, feeding intolerance and mortality, shorten the time to full enteral feeding, and lead to a faster recovery to birth weight in preterm infants. The appropriate oropharyngeal colostrum administration frequency may be 4 h, and the optimal duration may be 8-10 days. Therefore, it is recommended that clinical medical staff implement oropharyngeal colostrum administration for premature infants based on existing evidence. TWEETABLE ABSTRACT Oropharyngeal colostrum administration can reduce the incidence of complications in preterm infants and shorten the time to full enteral feeding.
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Affiliation(s)
- Zhen Yan Fu
- Nursing Department, Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China; Department of Neonatology, Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Chi Huang
- Department of Neonatology, Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Lei Lei
- Department of Neonatology, Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Li Cheng Chen
- Department of Neonatology, Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Li Juan Wei
- Department of Neonatology, Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Jiao Zhou
- Department of Neonatology, Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Ming Tao
- Nursing Department, Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Ming Tao Quan
- School of Nursing, Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Yi Huang
- Nursing Department, Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China.
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11
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Oddi S, Mantziari A, Huber P, Binetti A, Salminen S, Collado MC, Vinderola G. Human Milk Microbiota Profile Affected by Prematurity in Argentinian Lactating Women. Microorganisms 2023; 11:microorganisms11041090. [PMID: 37110513 PMCID: PMC10145235 DOI: 10.3390/microorganisms11041090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/10/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
To study (16S rRNA-sequencing) the impact of gestational and corrected ages on the microbiota profile of human milk (HM) of mothers that delivered full-term and pre-term children, HM samples were obtained and classified according to the gestational age as group T (full-term births ≥37 weeks), and group P (pre-term births <37 weeks). Group P was longitudinally followed, and the samples were collected at the full-term corrected gestational age: when the chronological age plus the gestational age were ≥37 weeks (PT group). The HM microbiota composition differed depending on the gestational age (T vs. P). Group T had lower levels of Staphylococcus and higher levels of Rothia and Streptococcus, as compared to group P. The alpha Simpson diversity value was higher in group T than in P, whereas no differences were found between groups T and PT, suggesting a microbial evolution of the composition of group P towards group T over chronological age. Full-term delivery was associated with a greater diversity of microbes in HM. The microbial composition of pre-term HM, at the corrected age, did not show significant differences, as compared to the samples obtained from the full-term group, suggesting that it would be appropriate to consider the corrected age in terms of the composition and the diversity of the milk in future studies.
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Affiliation(s)
- Sofía Oddi
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Anastasia Mantziari
- Functional Foods Forum, Faculty of Medicine, University of Turku, 20520 Turku, Finland
| | - Paula Huber
- Laboratorio de Plancton, Instituto Nacional de Limnología (INALI, UNL-CONICET), Universidad Nacional del Litoral, Santa Fe 3000, Argentina
- Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos 13565-905, SP, Brazil
| | - Ana Binetti
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, 20520 Turku, Finland
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Valencia, Spain
| | - Gabriel Vinderola
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
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12
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Aziz M, Palmer A, Iversen S, Salazar JE, Pham T, Roach K, Becker K, Kaspar U, Price LB, Baig S, Stegger M, Andersen PS, Liu CM. Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome. Sci Rep 2023; 13:6110. [PMID: 37059715 PMCID: PMC10103046 DOI: 10.1038/s41598-023-32709-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting murJ, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 104 D. pigrum 16S rRNA gene copies per swab. This assay adds a reliable and rapid D. pigrum detection tool to the microbiome researcher toolkit investigating the role of generalist and specialist bacteria in the nasal environment.
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Affiliation(s)
- Maliha Aziz
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Amber Palmer
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Søren Iversen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Juan E Salazar
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Tony Pham
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Kelsey Roach
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Ursula Kaspar
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Lance B Price
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Sharmin Baig
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Paal Skytt Andersen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Cindy M Liu
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, 800 22nd Street NW, Washington, DC, 20052, USA.
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13
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Brackenborough K, Ellis H, Flight WG. Respiratory Viruses and Cystic Fibrosis. Semin Respir Crit Care Med 2023; 44:196-208. [PMID: 36535663 DOI: 10.1055/s-0042-1758728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The threat of respiratory virus infection to human health and well-being has been clearly highlighted by the coronavirus disease 2019 (COVID-19) pandemic. For people with cystic fibrosis (CF), the clinical significance of viral infections long predated the emergence of severe acute respiratory syndrome coronavirus 2. This article reviews the epidemiology, diagnosis, and treatment of respiratory virus infection in the context of CF as well as the current understanding of interactions between viruses and other microorganisms in the CF lung. The incidence of respiratory virus infection in CF varies by age with young children typically experiencing more frequent episodes than adolescents and adults. At all ages, respiratory viruses are very common in CF and are associated with pulmonary exacerbations. Respiratory viruses are identified at up to 69% of exacerbations, while viruses are also frequently detected during clinical stability. The full impact of COVID-19 in CF is yet to be established. Early studies found that rates of COVID-19 were lower in CF cohorts than in the general population. The reasons for this are unclear but may be related to the effects of shielding, infection control practices, maintenance CF therapies, or the inflammatory milieu in the CF lung. Observational studies have consistently identified that prior solid organ transplantation is a key risk factor for poor outcomes from COVID-19 in CF. Several key priorities for future research are highlighted. First, the impact of highly effective CFTR modulator therapy on the epidemiology and pathophysiology of viral infections in CF requires investigation. Second, the impact of respiratory viruses on the development and dynamics of the CF lung microbiota is poorly understood and viral infection may have important interactions with bacteria and fungi in the airway. Finally, bacteriophages represent a key focus of future investigation both for their role in transmission of antimicrobial resistance and as a promising treatment modality for multiresistant pathogens.
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Affiliation(s)
- Kate Brackenborough
- Oxford Centre for Respiratory Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - Huw Ellis
- Oxford Centre for Respiratory Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - William G Flight
- Oxford Centre for Respiratory Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom.,Research and Development, GlaxoSmithKline plc, Brentford, United Kingdom
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14
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Di Simone SK, Rudloff I, Nold-Petry CA, Forster SC, Nold MF. Understanding respiratory microbiome-immune system interactions in health and disease. Sci Transl Med 2023; 15:eabq5126. [PMID: 36630485 DOI: 10.1126/scitranslmed.abq5126] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Interactions between the developing microbiome and maturing immune system in early life are critical for establishment of a homeostasis beneficial to both host and commensals. The lung harbors a diverse community of microbes associated with health and local or systemic disease. We discuss how early life colonization and community changes correlate with immune development and health and disease throughout infancy, childhood, and adult life. We highlight key advances in microbiology, immunology, and computational biology that allow investigation of the functional relevance of interactions between the respiratory microbiome and host immune system, which may unlock the potential for microbiome-based therapeutics.
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Affiliation(s)
- Sara K Di Simone
- Department of Paediatrics, Monash University, Melbourne 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne 3168, Australia.,Centre for Innate Immunity and Infectious Disease, Hudson Institute of Medical Research, Melbourne 3168, Australia
| | - Ina Rudloff
- Department of Paediatrics, Monash University, Melbourne 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne 3168, Australia
| | - Claudia A Nold-Petry
- Department of Paediatrics, Monash University, Melbourne 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne 3168, Australia
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Disease, Hudson Institute of Medical Research, Melbourne 3168, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne 3168, Australia
| | - Marcel F Nold
- Department of Paediatrics, Monash University, Melbourne 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne 3168, Australia.,Monash Newborn, Monash Children's Hospital, Melbourne 3168, Australia
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15
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Abushawish A, Haro K, Hoshina T, Kitajima N, Kusuhara K. Environmental factors related to differences in the microbiota in the upper respiratory tract in young children: Focusing on the impact of early nursery attendance. Front Pediatr 2023; 11:1015872. [PMID: 36798144 PMCID: PMC9927022 DOI: 10.3389/fped.2023.1015872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Microbial colonization of the upper respiratory tract (URT) during the first years of life differs significantly according to environmental factors. We investigated the association between early nursery attendance, URT infection (URTI) and drugs used for its treatment and the differences in the URT microbiota. METHODS This prospective study included 33 young children (11 and 22 with and without nursery attendance during their infancy, respectively). URT secretions were collected from the nasopharynx of these children at 2, 4, 6, 12, 18 and 24 months old. Clinical information after the latest sampling, including histories of URTI and the uses of antibiotics or cold medicines, was collected from all children. URT bacteria were identified by a clone library analysis of the 16S rRNA gene. RESULTS In the diversity of URT microbiota using the Shannon index, we did not detect any associations between variations in the URT microbiota and environmental factors (nursery attendance, development of URTIs, or the uses of antibiotics or cold medicines). However, in a clustering analysis, the proportion of the samples classified as Corynebacterium propinquum-dominant cluster was significantly lower in children ≥6 months old with nursery attendance than in those without nursery attendance. In addition, the URT microbiota was significantly different between samples from children ≥6 months old with and without a history of ≥3 URTI episodes after the first sampling. Furthermore, the URT microbiota was also significantly different between samples from these children with and without antibiotic use between the previous and present samplings. CONCLUSION Early nursery attendance and its related factors, including the frequency of URTI and antibiotic treatment, may be associated with the differences in the URT flora in young children.
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Affiliation(s)
- Asmaa Abushawish
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kaoru Haro
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan.,Department of Pediatrics, Sato Children's Clinic, Kitakyushu, Japan
| | - Takayuki Hoshina
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Naoko Kitajima
- Department of Pediatrics, Onga Nakama Medical Association, Onga Hospital, Onga, Japan
| | - Koichi Kusuhara
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
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16
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Chen W, Yin G, Chen Y, Wang L, Wang Y, Zhao C, Wang W, Ye J. Analysis of factors that influence the occurrence of otitis media with effusion in pediatric patients with adenoid hypertrophy. Front Pediatr 2023; 11:1098067. [PMID: 36911018 PMCID: PMC9992982 DOI: 10.3389/fped.2023.1098067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Objective Adenoid hypertrophy (AH) and otitis media with effusion (OME) are common pediatric otolaryngological diseases and often occur concurrently. The purpose of this study was to comprehensively analyze the factors that influence the occurrence of OME pediatric patients with AH. Methods Patients younger than 12 years with AH, who were hospitalized for treatment at Beijing Tsinghua Changgung Hospital in Beijing, China, between March 2018 and February 2022 were enrolled. The patients were divided into an AH group and an AH + OME group based on the presence of OME. The authors collected the following clinical data for univariable analysis: sex; age; body mass index (BMI); comorbid nasal congestion/rhinorrhea, recurrent tonsillitis, or allergic rhinitis (AR); adenoid and tonsil grade; tonsillar hypertrophy; food/drug allergy; history of adenoidectomy and congenital diseases; breastfeeding status; preterm birth; exposure to environmental tobacco smoke (ETS); family history of adenotonsillectomy, otitis media, and AR; main data of polysomnography and oropharyngeal conditional pathogen culture data of some patients. Univariate analysis was performed as a basis for logistic regression analysis. Results A total of 511 children (329 boys and 182 girls) were included, their mean age was 5.37 ± 2.10 years. Of them, 407 (79.6%) were in the AH group and 104 (20.4%) in the AH + OME group. Univariate analysis revealed statistically significant differences in age, BMI, adenoid grade, AR, breastfeeding status, and ETS exposure between the two groups. Multivariate stepwise logistic regression analysis showed that age, adenoid grade, AR, breastfeeding status, and ETS influenced the occurrence of OME in pediatric patients with AH. The risk of OME decreased with increasing age. High adenoid grade, ETS exposure, and comorbid AR were risk factors for OME in pediatric patients with AH, but breastfeeding was a protective factor. The final analytical results of the oropharyngeal conditional pathogen culture data showed that Streptococcus pneumoniae positivity was associated with OME in AH. Conclusion The pathogenesis of AH with OME is complex. Young age, high adenoid grade, ETS exposure, non-breastfed status, comorbid AR, and the presence of S. pneumoniae in the oropharynx are risk factors for OME in pediatric patients with AH.
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Affiliation(s)
- Wenjing Chen
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Guoping Yin
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yijing Chen
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Lijun Wang
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yingying Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Chunmei Zhao
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Wan Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Jingying Ye
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
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17
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Farooq S, Khatri S. Life Course of Asthma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1426:43-76. [PMID: 37464116 DOI: 10.1007/978-3-031-32259-4_3] [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: 07/20/2023]
Abstract
Asthma is a heterogeneous chronic airway disease that can vary over a lifetime. Although broad categories of asthma by severity and type have been constructed, there remains a tremendous opportunity to discover an approach to managing asthma with additional factors in mind. Many in the field have suggested and are pursuing a novel paradigm shift in how asthma might be better managed, considering the life course of exposures, management priorities, and predicted trajectory of lung function growth. This approach will require a more holistic view of prenatal, postnatal, adolescence, hormonal and gender aspects, and the aging process. In addition, the environment, externally and internally, including in one's genetic code and epigenetic changes, are factors that affect how asthma progresses or becomes more stable in individuals. This chapter focuses on the various influences that may, to differing degrees, affect people with asthma, which can develop at any time in their lives. Shifting the paradigm of thought and strategies for care and advocating for public policies and health delivery that focus on this philosophy is paramount to advance asthma care for all.
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Affiliation(s)
- Sobia Farooq
- National Heart, Lung, and Blood Institute, CMO Division of Lung Diseases, Bethesda, MD, USA
| | - Sumita Khatri
- National Heart, Lung, and Blood Institute, CMO Division of Lung Diseases, Bethesda, MD, USA.
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18
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Karampatsas K, Faal A, Jaiteh M, Garcia-Perez I, Aller S, Shaw AG, Kopytek A, Witney AA, Le Doare K. Gastrointestinal, vaginal, nasopharyngeal, and breast milk microbiota profiles and breast milk metabolomic changes in Gambian infants over the first two months of lactation: A prospective cohort study. Medicine (Baltimore) 2022; 101:e31419. [PMID: 36401392 PMCID: PMC9678627 DOI: 10.1097/md.0000000000031419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Microbiota composition in breast milk affects intestinal and respiratory microbiota colonization and the mucosal immune system's development in infants. The metabolomic content of breast milk is thought to interact with the microbiota and may influence developing infant immunity. One hundred seven Gambian mothers and their healthy, vaginally delivered, exclusively breastfed infants were included in our study. We analyzed 32 breast milk samples, 51 maternal rectovaginal swabs and 30 infants' rectal swabs at birth. We also analyzed 9 breast milk samples and 18 infants' nasopharyngeal swabs 60 days post-delivery. We used 16S rRNA gene sequencing to determine the microbiota composition. Metabolomic profiling analysis was performed on colostrum and mature breast milk samples using a multiplatform approach combining 1-H Nuclear Magnetic Resonance Spectroscopy and Gas Chromatography-Mass Spectrometry. Bacterial communities were distinct in composition and diversity across different sample types. Breast milk composition changed over the first 60 days of lactation. α-1,4- and α-1,3-fucosylated human milk oligosaccharides, and other 33 key metabolites in breast milk (monosaccharides, sugar alcohols and fatty acids) increased between birth and day 60 of life. This study's results indicate that infant gut and respiratory microbiota are unique bacterial communities, distinct from maternal gut and breast milk, respectively. Breast milk microbiota composition and metabolomic profile change throughout lactation. These changes may contribute to the infant's immunological, metabolic, and neurological development and could consist the basis for future interventions to correct disrupted early life microbial colonization.
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Affiliation(s)
- Konstantinos Karampatsas
- Centre for Neonatal and Paediatric Infection, St George’s, University of London, London, UK
- * Correspondence: Konstantinos Karampatsas, Institute for Infection and Immunity, St George’s, University of London, Jenner Wing, Level 2, SW17 0RE London, UK (e-mail: )
| | - Amadou Faal
- Medical Research Council The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Mustapha Jaiteh
- Medical Research Council The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Isabel Garcia-Perez
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Sean Aller
- Centre for Neonatal and Paediatric Infection, St George’s, University of London, London, UK
| | - Alexander G. Shaw
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Aleksandra Kopytek
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Adam A. Witney
- Centre for Neonatal and Paediatric Infection, St George’s, University of London, London, UK
| | - Kirsty Le Doare
- Centre for Neonatal and Paediatric Infection, St George’s, University of London, London, UK
- Medical Research Council The Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Medical Research Council Uganda, Virus Research Institute, Uganda
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Odom-Mabey AR, Gill CJ, Pieciak R, Ismail A, Thea D, MacLeod WB, Johnson WE, Lapidot R. Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.14041.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Previous studies of infants born to HIV-positive mothers have linked HIV exposure to poor outcomes from gastrointestinal and respiratory illnesses, and to overall increased mortality rates. The mechanism behind this is unknown, but it is possible that differences in the nasopharyngeal (NP) microbiome between HIV-unexposed and HIV-exposed infants could play a role in perpetuating some outcomes. Methods: We conducted a longitudinal analysis of 170 NP swabs of healthy HIV-exposed, uninfected (HEU; n=10) infants and their HIV(+) mothers and HIV-unexposed, uninfected (HUU; n=10) infants and their HIV(-) mothers. These swabs were identified from a sample library collected in Lusaka, Zambia between 2015 and 2016. Using 16S rRNA gene sequencing, we characterized the maturation of the microbiome over the first 14 weeks of life to determine what quantifiable differences exist between HEU and HUU infants, and what patterns are reflected in the mothers' NP microbiomes. Results: In both HEU and HUU infants, Staphylococcus and Corynebacterium began as primary colonizers of the NP microbiome but were in time replaced by Dolosigranulum, Streptococcus, Moraxella and Haemophilus. When studying differences between infants, the microbe Staphylococcus haemolyticus indicated a distinctive high association with HIV exposure at birth, even when accounting for the interaction between HIV exposure status and time of sampling. When comparing infants to their mothers with paired analyses, HEU infants’ NP microbiome composition was only slightly different from their HIV(+) mothers at birth or 14 weeks, including in their carriage of S. pneumoniae, H. influenzae, and S. haemolyticus. Conclusions: Our analyses indicate that the HEU infants in our study exhibit subtle differences in the NP microbial composition throughout the sampling interval. Given our results and the sampling limitations of our study, we believe that further research must be conducted in order to confidently understand the relationship between HIV exposure and infants’ NP microbiomes.
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Rotem R, Hirsch A, Barg M, Mor P, Michaelson-Cohen R, Rottenstreich M. Trial of labor following cesarean in preterm deliveries: success rates and maternal and neonatal outcomes: a multicenter retrospective study. Arch Gynecol Obstet 2022:10.1007/s00404-022-06746-3. [PMID: 36068361 DOI: 10.1007/s00404-022-06746-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/12/2022] [Indexed: 11/02/2022]
Abstract
PURPOSE To evaluate the rates of vaginal birth after cesarean (VBAC) among parturients attempting preterm trial of labor following a cesarean delivery (TOLAC) vs. term TOLAC. METHODS A multicenter historic cohort study was conducted at two university-affiliated centers between August 2005 and March 2021. Parturients in their second delivery, attempting TOLAC after a single low segment transverse cesarean delivery were included. We retrospectively examined computerized medical records of all preterm (< 37 weeks) and term (37-42 weeks) births. Multifetal gestations and postterm deliveries (≥ 42 weeks) were excluded. A univariate analysis was conducted, followed by a multivariate analysis. RESULTS 4865 second deliveries following previous cesarean were identified: 212 (4.4%) preterm and 4653 (95.6%) term. Hypertensive disorders, diabetes and fertility treatments were significantly more prevalent in the preterm group. VBAC rate was significantly lower in preterm group (57.5 vs 79.7%., p < 0.01), including both spontaneous and vaginal-assisted deliveries. In multivariate analysis, preterm TOLAC was independently associated with TOLAC failure [adjusted odds ratio 2.24, [95% confidence interval 1.62-3.09]. Overall, maternal outcomes were favorable. Rates of uterine rupture, re-laparotomy and postpartum hemorrhage were comparable between groups. Neonatal outcomes were less favorable among the preterm group; however, preterm vs. term TOLAC was not associated with low 5 min Apgar score (aOR 1.76, 95% CI 0.92-3.40). CONCLUSION In our study, VBAC rates were lower in preterm compared to term deliveries. Maternal outcomes were comparable. Neonatal outcomes were less favorable in the preterm group, more likely due to prematurity than delivery mode.
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Affiliation(s)
- Reut Rotem
- Department of Obstetrics and Gynecology, Shaare Zedek Medical Center, Hebrew University Faculty of Medicine, POB 3235, 91031, Jerusalem, Israel
| | - Ayala Hirsch
- Department of Obstetrics and Gynecology, Shaare Zedek Medical Center, Hebrew University Faculty of Medicine, POB 3235, 91031, Jerusalem, Israel
| | - Moshe Barg
- Department of Obstetrics and Gynecology, Shaare Zedek Medical Center, Hebrew University Faculty of Medicine, POB 3235, 91031, Jerusalem, Israel
| | - Pnina Mor
- Department of Obstetrics and Gynecology, Shaare Zedek Medical Center, Hebrew University Faculty of Medicine, POB 3235, 91031, Jerusalem, Israel.,Medical Genetics Institute, Shaare Zedek Medical Center, Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Rachel Michaelson-Cohen
- Department of Obstetrics and Gynecology, Shaare Zedek Medical Center, Hebrew University Faculty of Medicine, POB 3235, 91031, Jerusalem, Israel. .,Medical Genetics Institute, Shaare Zedek Medical Center, Hebrew University Faculty of Medicine, Jerusalem, Israel.
| | - Misgav Rottenstreich
- Department of Obstetrics and Gynecology, Shaare Zedek Medical Center, Hebrew University Faculty of Medicine, POB 3235, 91031, Jerusalem, Israel.,Department of Nursing, Jerusalem College of Technology, Jerusalem, Israel
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Rosas-Salazar C, Shilts MH, Tang ZZ, Hong Q, Turi KN, Snyder BM, Wiggins DA, Lynch CE, Gebretsadik T, Peebles RS, Anderson LJ, Das SR, Hartert TV. Exclusive breast-feeding, the early-life microbiome and immune response, and common childhood respiratory illnesses. J Allergy Clin Immunol 2022; 150:612-621. [PMID: 35283139 PMCID: PMC9463089 DOI: 10.1016/j.jaci.2022.02.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND The impact of breast-feeding on certain childhood respiratory illnesses remains controversial. OBJECTIVE We sought to examine the effect of exclusive breast-feeding on the early-life upper respiratory tract (URT) and gut microbiome, the URT immune response in infancy, and the risk of common pediatric respiratory diseases. METHODS We analyzed data from a birth cohort of healthy infants with prospective ascertainment of breast-feeding patterns and common pediatric pulmonary and atopic outcomes. In a subset of infants, we also characterized the URT and gut microbiome using 16S ribosomal RNA sequencing and measured 9 URT cytokines using magnetic bead-based assays. RESULTS Of the 1949 infants enrolled, 1495 (76.71%) had 4-year data. In adjusted analyses, exclusive breast-feeding (1) had an inverse dose-response on the ⍺-diversity of the early-life URT and gut microbiome, (2) was positively associated with the URT levels of IFN-α, IFN-γ, and IL-17A in infancy, and (3) had a protective dose-response on the development of a lower respiratory tract infection in infancy, 4-year current asthma, and 4-year ever allergic rhinitis (odds ratio [95% CI] for each 4 weeks of exclusive breast-feeding, 0.95 [0.91-0.99], 0.95 [0.90-0.99], and 0.95 [0.92-0.99], respectively). In exploratory analyses, we also found that the protective association of exclusive breast-feeding on 4-year current asthma was mediated through its impact on the gut microbiome (P = .03). CONCLUSIONS Our results support a protective causal role of exclusive breast-feeding in the risk of developing a lower respiratory tract infection in infancy and asthma and allergic rhinitis in childhood. They also shed light on potential mechanisms of these associations, including the effect of exclusive breast-feeding on the gut microbiome.
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Affiliation(s)
| | - Meghan H Shilts
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wis
| | - Qilin Hong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wis
| | - Kedir N Turi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Brittney M Snyder
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Derek A Wiggins
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Christian E Lynch
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Tebeb Gebretsadik
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tenn
| | - R Stokes Peebles
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Larry J Anderson
- Department of Pediatrics, Emory University and Children's Healthcare of Atlanta, Atlanta, Ga
| | - Suman R Das
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn; Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tenn.
| | - Tina V Hartert
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
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22
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Kloepfer KM, McCauley KE, Kirjavainen PV. The Microbiome as a Gateway to Prevention of Allergic Disease Development. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY: IN PRACTICE 2022; 10:2195-2204. [PMID: 35718258 DOI: 10.1016/j.jaip.2022.05.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 12/18/2022]
Abstract
Allergic diseases exclusively affect tissues that face environmental challenges and harbor endogenous bacterial microbiota. The microbes inhabiting the affected tissues may not be mere bystanders in this process but actively affect the risk of allergic sensitization, disease development, and exacerbation or abatement of symptoms. Experimental evidence provides several plausible means by which the human microbiota could influence the development of allergic diseases including, but not limited to, effects on antigen presentation and induction of tolerance and allergen permeation by endorsing or disrupting epithelial barrier integrity. Epidemiological evidence attests to the significance of age-appropriate, nonpathogenic microbiota development in skin, gastrointestinal tract, and airways for protection against allergic disease development. Thus, there exist potential targets for preventive actions either in the prenatal or postnatal period. These could include maternal dietary interventions, antibiotic stewardship for both the mother and infant, reducing elective cesarean deliveries, and understanding barriers to breastfeeding and timing of food diversification. In here, we will review the current understanding and evidence of allergy-associated human microbiota patterns, their role in the development of allergic diseases, and how we could harness these associations to our benefit against allergies.
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23
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Recurrent Acute Otitis Media Environmental Risk Factors: A Literature Review from the Microbiota Point of View. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2030046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Acute otitis media (AOM) constitutes a multifactorial disease, as several host and environmental factors contribute to its occurrence. Prevention of AOM represents one of the most important goals in pediatrics, both in developing countries, in which complications, mortality, and deafness remain possible consequences of the disease, compared to in developed countries, in which this condition has an important burden in terms of medical, social, and economical implications. The strategies for AOM prevention are based on reducing the burden of risk factors, through the application of behavioral, environmental, and therapeutic interventions. The introduction of culture-independent techniques has allowed high-throughput investigation of entire bacterial communities, providing novel insights into the pathogenesis of middle ear diseases through the identification of potential protective bacteria. The upper respiratory tract (URT) is a pivotal region in AOM pathogenesis, as it could act as a source of pathogens than of protective microorganisms for the middle ear (ME). Due to its direct connection with the external ambient, the URT is particularly exposed to the influence of environmental agents. The aim of this review was to evaluate AOM environmental risk factors and their impact on URT microbial communities, and to investigate AOM pathogenesis from the microbiota perspective.
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Wang L, DeWan AT. Microbiome links breastfeeding and asthma protection: a cohort study helps elucidate this underlying player. J Allergy Clin Immunol 2022; 150:587-588. [DOI: 10.1016/j.jaci.2022.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022]
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Rocafort M, Henares D, Brotons P, Launes C, Fernandez de Sevilla M, Fumado V, Barrabeig I, Arias S, Redin A, Ponomarenko J, Mele M, Millat-Martinez P, Claverol J, Balanza N, Mira A, Garcia-Garcia JJ, Bassat Q, Jordan I, Muñoz-Almagro C. Impact of COVID-19 Lockdown on the Nasopharyngeal Microbiota of Children and Adults Self-Confined at Home. Viruses 2022; 14:v14071521. [PMID: 35891502 PMCID: PMC9315980 DOI: 10.3390/v14071521] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 01/25/2023] Open
Abstract
The increased incidence of COVID-19 cases and deaths in Spain in March 2020 led to the declaration by the Spanish government of a state of emergency imposing strict confinement measures on the population. The objective of this study was to characterize the nasopharyngeal microbiota of children and adults and its relation to SARS-CoV-2 infection and COVID-19 severity during the pandemic lockdown in Spain. This cross-sectional study included family households located in metropolitan Barcelona, Spain, with one adult with a previous confirmed COVID-19 episode and one or more exposed co-habiting child contacts. Nasopharyngeal swabs were used to determine SARS-CoV-2 infection status, characterize the nasopharyngeal microbiota and determine common respiratory DNA/RNA viral co-infections. A total of 173 adult cases and 470 exposed children were included. Overall, a predominance of Corynebacterium and Dolosigranulum and a limited abundance of common pathobionts including Haemophilus and Streptococcus were found both among adults and children. Children with current SARS-CoV-2 infection presented higher bacterial richness and increased Fusobacterium, Streptococcus and Prevotella abundance than non-infected children. Among adults, persistent SARS-CoV-2 RNA was associated with an increased abundance of an unclassified member of the Actinomycetales order. COVID-19 severity was associated with increased Staphylococcus and reduced Dolosigranulum abundance. The stringent COVID-19 lockdown in Spain had a significant impact on the nasopharyngeal microbiota of children, reflected in the limited abundance of common respiratory pathobionts and the predominance of Corynebacterium, regardless of SARS-CoV-2 detection. COVID-19 severity in adults was associated with decreased nasopharynx levels of healthy commensal bacteria.
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Affiliation(s)
- Muntsa Rocafort
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
| | - Desiree Henares
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Medicine Department, Universitat Internacional de Catalunya, Sant Cugat, 08195 Barcelona, Spain
| | - Cristian Launes
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Mariona Fernandez de Sevilla
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Victoria Fumado
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Irene Barrabeig
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Epidemiological Surveillance Unit, Department of Health, Generalitat de Catalunya, 08907 Barcelona, Spain
| | - Sara Arias
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
| | - Alba Redin
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- Medicine Department, Universitat Internacional de Catalunya, Sant Cugat, 08195 Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Maria Mele
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Pere Millat-Martinez
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
| | - Joana Claverol
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
| | - Nuria Balanza
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
| | - Alex Mira
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Department of Health and Genomics, Center for Advanced Research in Public Health, Fundacion para el Fomento de la Investigacion Sanitaria y Biomedica de la Comunitat Valenciana (FISABIO), 46020 Valencia, Spain
| | - Juan J. Garcia-Garcia
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Quique Bassat
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça Maputo 1929, Mozambique
| | - Iolanda Jordan
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Medicine Department, Universitat Internacional de Catalunya, Sant Cugat, 08195 Barcelona, Spain
- Correspondence: ; Tel.: +34-673302405; Fax: +34-932803626
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Nasal Microbiota, Olfactory Health, Neurological Disorders and Aging—A Review. Microorganisms 2022; 10:microorganisms10071405. [PMID: 35889124 PMCID: PMC9320618 DOI: 10.3390/microorganisms10071405] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/07/2023] Open
Abstract
The nasal region is one of the distinct environments for the survival of various microbiota. The human microbial niche begins to inhabit the human body right from birth, and the microbiota survive as commensals or opportunistic pathogens throughout the life of humans in their bodies in various habitats. These microbial communities help to maintain a healthy microenvironment by preventing the attack of pathogens and being involved in immune regulation. Any dysbiosis of microbiota residing in the mucosal surfaces, such as the nasal passages, guts, and genital regions, causes immune modulation and severe infections. The coexistence of microorganisms in the mucosal layers of respiratory passage, resulting in infections due to their co-abundance and interactions, and the background molecular mechanisms responsible for such interactions, need to be considered for investigation. Additional clinical evaluations can explain the interactions among the nasal microbiota, nasal dysbiosis and neurodegenerative diseases (NDs). The respiratory airways usually act as a substratum place for the microbes and can act as the base for respiratory tract infections. The microbial metabolites and the microbes can cross the blood–brain barrier and may cause NDs, such as Parkinson’s disease (PD), Alzheimer’s disease (AD), and multiple sclerosis (MS). The scientific investigations on the potential role of the nasal microbiota in olfactory functions and the relationship between their dysfunction and neurological diseases are limited. Recently, the consequences of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in patients with neurological diseases are under exploration. The crosstalk between the gut and the nasal microbiota is highly influential, because their mucosal regions are the prominent microbial niche and are connected to the olfaction, immune regulation, and homeostasis of the central nervous system. Diet is one of the major factors, which strongly influences the mucosal membranes of the airways, gut, and lung. Unhealthy diet practices cause dysbiosis in gut microbiota and the mucosal barrier. The current review summarizes the interrelationship between the nasal microbiota dysbiosis, resulting olfactory dysfunctions, and the progression of NDs during aging and the involvement of coronavirus disease 2019 in provoking the NDs.
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Stricker S, Hain T, Chao CM, Rudloff S. Respiratory and Intestinal Microbiota in Pediatric Lung Diseases-Current Evidence of the Gut-Lung Axis. Int J Mol Sci 2022; 23:ijms23126791. [PMID: 35743234 PMCID: PMC9224356 DOI: 10.3390/ijms23126791] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/07/2023] Open
Abstract
The intestinal microbiota is known to influence local immune homeostasis in the gut and to shape the developing immune system towards elimination of pathogens and tolerance towards self-antigens. Even though the lung was considered sterile for a long time, recent evidence using next-generation sequencing techniques confirmed that the lower airways possess their own local microbiota. Since then, there has been growing evidence that the local respiratory and intestinal microbiota play a role in acute and chronic pediatric lung diseases. The concept of the so-called gut–lung axis describing the mutual influence of local microbiota on distal immune mechanisms was established. The mechanisms by which the intestinal microbiota modulates the systemic immune response include the production of short-chain fatty acids (SCFA) and signaling through pattern recognition receptors (PRR) and segmented filamentous bacteria. Those factors influence the secretion of pro- and anti-inflammatory cytokines by immune cells and further modulate differentiation and recruitment of T cells to the lung. This article does not only aim at reviewing recent mechanistic evidence from animal studies regarding the gut–lung axis, but also summarizes current knowledge from observational studies and human trials investigating the role of the respiratory and intestinal microbiota and their modulation by pre-, pro-, and synbiotics in pediatric lung diseases.
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Affiliation(s)
- Sebastian Stricker
- Department of Pediatrics, Justus Liebig University Giessen, 35392 Giessen, Germany;
- Correspondence: ; Tel.: +49-641-985-56617
| | - Torsten Hain
- Institute of Medical Microbiology, Justus Liebig University Giessen, 35392 Giessen, Germany;
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Cho-Ming Chao
- Department of Pediatrics, University Medical Center Rostock, 18057 Rostock, Germany;
| | - Silvia Rudloff
- Department of Pediatrics, Justus Liebig University Giessen, 35392 Giessen, Germany;
- Department of Nutritional Science, Justus Liebig University Giessen, 35392 Giessen, Germany
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Lapidot R, Faits T, Ismail A, Allam M, Khumalo Z, MacLeod W, Kwenda G, Mupila Z, Nakazwe R, Segrè D, Johnson WE, Thea DM, Mwananyanda L, Gill CJ. Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study. Gates Open Res 2022. [DOI: 10.12688/gatesopenres.13561.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background: Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or a consequence of it, is unknown. In order to answer this question, longitudinal studies are needed. Methods: We conducted an analysis of a longitudinal prospective cohort study of 1,981 Zambian mother-infant pairs who underwent NP sampling from 1-week through 14-weeks of age at 2-3-week intervals. Ten of the infants in the cohort who developed LRTI were matched 1:3 with healthy comparators. We completed 16S rRNA gene sequencing on the samples each of these infants contributed, as well as from baseline samples of the infants’ mothers, and characterized the normal maturation of the healthy infant NP microbiome, compared to infants who developed LRTI. Results: The infant NP microbiome maturation was characterized by transitioning from Staphylococcus dominant to respiratory-genera dominant profiles during the first three months of life, similar to what is described in the literature. Interestingly, infants who developed LRTI had NP dysbiosis before infection, in most cases as early as the first week of life. Dysbiosis was characterized by the presence of Novosphingobium, Delftia, high relative abundance of Anaerobacillus, Bacillus, and low relative abundance of Dolosigranulum, compared to the healthy controls. Mothers of infants with LRTI also had low relative abundance of Dolosigranulum in their baseline samples compared to mothers of infants that did not develop an LRTI. Conclusions: Our results suggest that NP microbiome dysbiosis precedes LRTI in young infants and may be present in their mothers as well. Early dysbiosis may play a role in the causal pathway leading to LRTI or could be a marker of other pathogenic forces that directly lead to LRTI.
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Barnes MVC, Openshaw PJM, Thwaites RS. Mucosal Immune Responses to Respiratory Syncytial Virus. Cells 2022; 11:cells11071153. [PMID: 35406717 PMCID: PMC8997753 DOI: 10.3390/cells11071153] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/30/2022] Open
Abstract
Despite over half a century of research, respiratory syncytial virus (RSV)-induced bronchiolitis remains a major cause of hospitalisation in infancy, while vaccines and specific therapies still await development. Our understanding of mucosal immune responses to RSV continues to evolve, but recent studies again highlight the role of Type-2 immune responses in RSV disease and hint at the possibility that it dampens Type-1 antiviral immunity. Other immunoregulatory pathways implicated in RSV disease highlight the importance of focussing on localised mucosal responses in the respiratory mucosa, as befits a virus that is essentially confined to the ciliated respiratory epithelium. In this review, we discuss studies of mucosal immune cell infiltration and production of inflammatory mediators in RSV bronchiolitis and relate these studies to observations from peripheral blood. We also discuss the advantages and limitations of studying the nasal mucosa in a disease that is most severe in the lower airway. A fresh focus on studies of RSV pathogenesis in the airway mucosa is set to revolutionise our understanding of this common and important infection.
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Song Y, Hou J, Kwok JSL, Weng H, Tang MF, Wang MH, Leung ASY, Tao KP, Wong GWK, Chan RWY, Tsui SKW, Leung TF. Whole-Genome Shotgun Sequencing for Nasopharyngeal Microbiome in Pre-school Children With Recurrent Wheezing. Front Microbiol 2022; 12:792556. [PMID: 35250904 PMCID: PMC8889122 DOI: 10.3389/fmicb.2021.792556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/21/2021] [Indexed: 12/20/2022] Open
Abstract
Microbiome mediates early life immune deviation in asthma development. Recurrent wheeze (RW) in pre-school years is a risk factor for asthma diagnosis in school-age children. Dysbiosis exists in asthmatic airways, while its origin in pre-school years and relationship to RW is not clearly defined. This study investigated metagenomics of nasopharyngeal microbiome in pre-school children with RW. We applied whole-genome shotgun sequencing and human rhinovirus (HRV) detection on nasopharyngeal samples collected from three groups of pre-school children: (i) RW group: 16 children at-risk for asthma who were hospitalized for RW, (ii) inpatient control (IC): 18 subjects admitted for upper respiratory infection, and (iii) community control (CC): 36 children without respiratory syndromes. Sequence reads were analyzed by MetaPhlAn2 and HUMAnN2 algorithm for taxonomic and functional identification. Linear discriminant analysis effect size (LEfSe) analysis was used to identify discriminative features. We identified that Moraxella catarrhalis and Dolosigranulum pigrum were predominant species in nasopharynx. RW had lower alpha diversity (Shannon diversity index) than CC (0.48 vs. 1.07; Padj = 0.039), characterized by predominant Proteobacteria. LEfSe analysis revealed D. pigrum was the only discriminative species across groups (LDA = 5.57, P = 0.002), with its relative abundance in RW, IC, and CC being 9.6, 14.2, and 37.3%, respectively (P < 0.05). LEfSe identified five (ribo)nucleotides biosynthesis pathways to be group discriminating. Adjusting for HRV status, pre-school children with RW have lower nasopharyngeal biodiversity, which is associated with Proteobacteria predominance and lower abundance of D. pigrum. Along with discriminative pathways found in RW and CC, these microbial biomarkers help to understand RW pathogenesis.
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Affiliation(s)
- Yuping Song
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Jinpao Hou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Jamie Sui Lam Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Haoyi Weng
- Jockey Club School of Public Health and Primary Care, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Man Fung Tang
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Maggie Haitian Wang
- Jockey Club School of Public Health and Primary Care, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Agnes Sze Yin Leung
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Kin Pong Tao
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,The Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Gary Wing Kin Wong
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Renee Wan Yi Chan
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,The Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Stephen Kwok Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Ting Fan Leung
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,The Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
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Kelly MS, Plunkett C, Yu Y, Aquino JN, Patel SM, Hurst JH, Young RR, Smieja M, Steenhoff AP, Arscott-Mills T, Feemster KA, Boiditswe S, Leburu T, Mazhani T, Patel MZ, Rawls JF, Jawahar J, Shah SS, Polage CR, Cunningham CK, Seed PC. Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy. THE ISME JOURNAL 2022; 16:655-665. [PMID: 34511605 PMCID: PMC8857224 DOI: 10.1038/s41396-021-01108-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/22/2021] [Accepted: 09/03/2021] [Indexed: 02/08/2023]
Abstract
Streptococcus pneumoniae (pneumococcus) is a leading cause of severe infections among children and adults. Interactions between commensal microbes in the upper respiratory tract and S. pneumoniae are poorly described. In this study, we sought to identify interspecies interactions that modify the risk of S. pneumoniae colonization during infancy and to describe development of the upper respiratory microbiome during infancy in a sub-Saharan African setting. We collected nasopharyngeal swabs monthly (0-6 months of age) or bimonthly (6-12 months of age) from 179 mother-infant dyads in Botswana. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and identified S. pneumoniae colonization using a species-specific PCR assay. We detect S. pneumoniae colonization in 144 (80%) infants at a median age of 71 days and identify a strong negative association between the relative abundance of the bacterial genera Corynebacterium within the infant nasopharyngeal microbiome and the risk of S. pneumoniae colonization. Using in vitro cultivation experiments, we demonstrate growth inhibition of S. pneumoniae by secreted factors from strains of several Corynebacterium species isolated from these infants. Finally, we demonstrate that antibiotic exposures and the winter season are associated with a decline in the relative abundance of Corynebacterium within the nasopharyngeal microbiome, while breastfeeding is associated with an increase in the Corynebacterium relative abundance. Our findings provide novel insights into the interspecies interactions that contribute to colonization resistance to S. pneumoniae and suggest that the nasopharyngeal microbiome may be a previously unrecognized mechanism by which environmental factors influence the risk of pneumococcal infections during childhood. Moreover, this work lays the foundation for future studies seeking to use targeted manipulation of the nasopharyngeal microbiome to prevent infections caused by S. pneumoniae.
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Affiliation(s)
- Matthew S. Kelly
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana ,grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Catherine Plunkett
- grid.16753.360000 0001 2299 3507Division of Pediatric Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - Yahe Yu
- grid.40803.3f0000 0001 2173 6074Department of Mathematics, North Carolina State University, Raleigh, NC USA
| | - Jhoanna N. Aquino
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Sweta M. Patel
- grid.26009.3d0000 0004 1936 7961Division of Pulmonary Allergy, and Critical Care Medicine, Duke University, Durham, NC USA
| | - Jillian H. Hurst
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Rebecca R. Young
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Marek Smieja
- grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada
| | - Andrew P. Steenhoff
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana ,grid.239552.a0000 0001 0680 8770Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.239552.a0000 0001 0680 8770Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Tonya Arscott-Mills
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana ,grid.239552.a0000 0001 0680 8770Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Kristen A. Feemster
- grid.239552.a0000 0001 0680 8770Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Sefelani Boiditswe
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Tirayaone Leburu
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Tiny Mazhani
- grid.7621.20000 0004 0635 5486University of Botswana School of Medicine, Gaborone, Botswana
| | - Mohamed Z. Patel
- grid.7621.20000 0004 0635 5486University of Botswana School of Medicine, Gaborone, Botswana
| | - John F. Rawls
- grid.26009.3d0000 0004 1936 7961Department of Molecular Genetics and Microbiology, Duke University, Durham, NC USA
| | - Jayanth Jawahar
- grid.26009.3d0000 0004 1936 7961Department of Molecular Genetics and Microbiology, Duke University, Durham, NC USA
| | - Samir S. Shah
- grid.239573.90000 0000 9025 8099Divisions of Hospital Medicine and Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Christopher R. Polage
- grid.26009.3d0000 0004 1936 7961Department of Pathology, Duke University, Durham, NC USA
| | - Coleen K. Cunningham
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Patrick C. Seed
- grid.16753.360000 0001 2299 3507Division of Pediatric Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
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Govers C, Calder PC, Savelkoul HFJ, Albers R, van Neerven RJJ. Ingestion, Immunity, and Infection: Nutrition and Viral Respiratory Tract Infections. Front Immunol 2022; 13:841532. [PMID: 35296080 PMCID: PMC8918570 DOI: 10.3389/fimmu.2022.841532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/02/2022] [Indexed: 12/12/2022] Open
Abstract
Respiratory infections place a heavy burden on the health care system, particularly in the winter months. Individuals with a vulnerable immune system, such as very young children and the elderly, and those with an immune deficiency, are at increased risk of contracting a respiratory infection. Most respiratory infections are relatively mild and affect the upper respiratory tract only, but other infections can be more serious. These can lead to pneumonia and be life-threatening in vulnerable groups. Rather than focus entirely on treating the symptoms of infectious disease, optimizing immune responsiveness to the pathogens causing these infections may help steer towards a more favorable outcome. Nutrition may have a role in such prevention through different immune supporting mechanisms. Nutrition contributes to the normal functioning of the immune system, with various nutrients acting as energy sources and building blocks during the immune response. Many micronutrients (vitamins and minerals) act as regulators of molecular responses of immune cells to infection. It is well described that chronic undernutrition as well as specific micronutrient deficiencies impair many aspects of the immune response and make individuals more susceptible to infectious diseases, especially in the respiratory and gastrointestinal tracts. In addition, other dietary components such as proteins, pre-, pro- and synbiotics, and also animal- and plant-derived bioactive components can further support the immune system. Both the innate and adaptive defense systems contribute to active antiviral respiratory tract immunity. The initial response to viral airway infections is through recognition by the innate immune system of viral components leading to activation of adaptive immune cells in the form of cytotoxic T cells, the production of neutralizing antibodies and the induction of memory T and B cell responses. The aim of this review is to describe the effects of a range different dietary components on anti-infective innate as well as adaptive immune responses and to propose mechanisms by which they may interact with the immune system in the respiratory tract.
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Affiliation(s)
- Coen Govers
- Cell Biology and Immunology, Wageningen University and Research, Wageningen, Netherlands
| | - Philip C. Calder
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust and University of Southampton, Southampton, United Kingdom
| | - Huub F. J. Savelkoul
- Cell Biology and Immunology, Wageningen University and Research, Wageningen, Netherlands
| | | | - R. J. Joost van Neerven
- Cell Biology and Immunology, Wageningen University and Research, Wageningen, Netherlands
- Research & Development, FrieslandCampina, Amersfoort, Netherlands
- *Correspondence: R. J. Joost van Neerven,
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The hidden universe of human milk microbiome: origin, composition, determinants, role, and future perspectives. Eur J Pediatr 2022; 181:1811-1820. [PMID: 35124754 PMCID: PMC9056486 DOI: 10.1007/s00431-022-04383-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/14/2022]
Abstract
UNLABELLED Although traditionally considered sterile, human milk is currently recognized as an alive ecosystem that harbors not only bacteria, but also viruses, fungi and yeasts, and minor genera, collectively known as the human milk microbiome (HMM). The seeding of HMM is a complex phenomenon whose dynamics are still a matter of research. Many factors contribute to its determination, both maternal, neonatal, environmental, and related to human milk itself. The transmission of microorganisms to the infant through breastfeeding may impact its present and future health, mainly shaping the GI tract microbiome and immune system. The existence and persistence of HMM as a conserved feature among different species may also have an evolutionary meaning, which will become apparent only in evolutionary times. CONCLUSION The complexities of HMM warrant further research in order to deepen our knowledge on its origin, determinants, and impact on infants' health. The practical and translational implications of research on HMM (e.g., reconstitution of donor human milk through inoculation of infant's own mother milk, modulation of HMM through maternal dietary supplementation) should not be overlooked. WHAT IS KNOWN • Human milk harbors a wide variety of microorganisms, ranging from bacteria to viruses, fungi and yeasts, and minor genera. • Human milk microbiome is shaped over time by many factors: maternal, neonatal, environmental, and related to human milk itself. • The transmission of microorganisms through breastfeeding may impact the infant's present and future health. WHAT IS NEW • We provide an overview on human milk microbiome, hopefully encouraging physicians to consider it among the other better-known breastfeeding benefits. • Further studies, with standardized and rigorous study designs to enhance accuracy and reproducibility of the results, are needed to deepen our knowledge of the human milk microbiota and its role in newborn and infant's health.
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Narendrakumar L, Ray A. Respiratory tract microbiome and pneumonia. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 192:97-124. [DOI: 10.1016/bs.pmbts.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Emilie V, Aline F, Bernard T, Billen F, Georges D, Cécile C. Variations in facial conformation are associated with differences in nasal microbiota in healthy dogs. BMC Vet Res 2021; 17:361. [PMID: 34819074 PMCID: PMC8611846 DOI: 10.1186/s12917-021-03055-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/19/2021] [Indexed: 11/10/2022] Open
Abstract
Background Extrinsic and intrinsic factors have been shown to influence nasal microbiota (NM) in humans. Very few studies investigated the association between nasal microbiota and factors such as facial/body conformation, age, and environment in dogs. The objectives are to investigate variations in NM in healthy dogs with different facial and body conformations. A total of 46 dogs of different age, living environment and from 3 different breed groups were recruited: 22 meso−/dolichocephalic medium to large breed dogs, 12 brachycephalic dogs and 12 terrier breeds. The nasal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V1-V3 regions) amplicons. Results We showed major differences in the NM composition together with increased richness and α-diversity in brachycephalic dogs, compared to meso−/dolichocephalic medium to large dogs and dogs from terrier breeds. Conclusion Healthy brachycephalic breeds and their unique facial conformation is associated with a distinct NM profile. Description of the NM in healthy dogs serves as a foundation for future researches assessing the changes associated with disease and the modulation of NM communities as a potential treatment.
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Affiliation(s)
- Vangrinsven Emilie
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Quartier Vallée 2, Avenue de Cureghem 3, 4000, Liège, Belgium.
| | - Fastrès Aline
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Quartier Vallée 2, Avenue de Cureghem 3, 4000, Liège, Belgium
| | - Taminiau Bernard
- Department of Food Sciences - Microbiology, Faculty of Veterinary Medicine, University of Liège, Quartier Vallée 2, Avenue de Cureghem 3, 4000, Liège, Belgium
| | - Frédéric Billen
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Quartier Vallée 2, Avenue de Cureghem 3, 4000, Liège, Belgium
| | - Daube Georges
- Department of Food Sciences - Microbiology, Faculty of Veterinary Medicine, University of Liège, Quartier Vallée 2, Avenue de Cureghem 3, 4000, Liège, Belgium
| | - Clercx Cécile
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Quartier Vallée 2, Avenue de Cureghem 3, 4000, Liège, Belgium
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Short- and Long-Term Implications of Human Milk Microbiota on Maternal and Child Health. Int J Mol Sci 2021; 22:ijms222111866. [PMID: 34769296 PMCID: PMC8584477 DOI: 10.3390/ijms222111866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/14/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
Human milk (HM) is considered the most complete food for infants as its nutritional composition is specifically designed to meet infant nutritional requirements during early life. HM also provides numerous biologically active components, such as polyunsaturated fatty acids, milk fat globules, IgA, gangliosides or polyamines, among others; in addition, HM has a “bifidogenic effect”, a prebiotic effect, as a result of the low concentration of proteins and phosphates, as well as the presence of lactoferrin, lactose, nucleotides and oligosaccharides. Recently, has been a growing interest in HM as a potential source of probiotics and commensal bacteria to the infant gut, which might, in turn, influence both the gut colonization and maturation of infant immune system. Our review aims to address practical approaches to the detection of microbial communities in human breast milk samples, delving into their origin, composition and functions. Furthermore, we will summarize the current knowledge of how HM microbiota dysbiosis acts as a short- and long-term predictor of maternal and infant health. Finally, we also provide a critical view of the role of breast milk-related bacteria as a novel probiotic strategy in the prevention and treatment of maternal and offspring diseases.
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Kang HM, Kang JH. Effects of nasopharyngeal microbiota in respiratory infections and allergies. Clin Exp Pediatr 2021; 64:543-551. [PMID: 33872488 PMCID: PMC8566799 DOI: 10.3345/cep.2020.01452] [Citation(s) in RCA: 7] [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] [Received: 08/27/2020] [Accepted: 04/02/2021] [Indexed: 11/27/2022] Open
Abstract
The human microbiome, which consists of a collective cluster of commensal, symbiotic, and pathogenic microorganisms living in the human body, plays a key role in host health and immunity. The human nasal cavity harbors commensal bacteria that suppress the colonization of opportunistic pathogens. However, dysbiosis of the nasal microbial community is associated with many diseases, such as acute respiratory infections including otitis media, sinusitis and bronchitis and allergic respiratory diseases including asthma. The nasopharyngeal acquisition of pneumococcus, which exists as a pathobiont in the nasal cavity, is the initial step in virtually all pneumococcal diseases. Although the factors influencing nasal colonization and elimination are not fully understood, the adhesion of opportunistic pathogens to nasopharyngeal mucosa receptors and the eliciting of immune responses in the host are implicated in addition to bacterial microbiota properties and colonization resistance dynamics. Probiotics or synbiotic interventions may show promising and effective roles in the adjunctive treatment of dysbiosis; however, more studies are needed to characterize how these interventions can be applied in clinical practice in the future.
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Affiliation(s)
- Hyun Mi Kang
- Division of Pediatric Infectious Diseases, Departments of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin Han Kang
- Division of Pediatric Infectious Diseases, Departments of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Henares D, Brotons P, de Sevilla MF, Fernandez-Lopez A, Hernandez-Bou S, Perez-Argüello A, Mira A, Muñoz-Almagro C, Cabrera-Rubio R. Differential nasopharyngeal microbiota composition in children according to respiratory health status. Microb Genom 2021; 7. [PMID: 34699345 PMCID: PMC8627214 DOI: 10.1099/mgen.0.000661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Acute respiratory infections (ARIs) constitute one of the leading causes of antibiotic administration, hospitalization and death among children <5 years old. The upper respiratory tract microbiota has been suggested to explain differential susceptibility to ARIs and modulate ARI severity. The aim of the present study was to investigate the relation of nasopharyngeal microbiota and other microbiological parameters with respiratory health and disease, and to assess nasopharyngeal microbiota diagnostic utility for discriminating between different respiratory health statuses. We conducted a prospective case-control study at Hospital Sant Joan de Deu (Barcelona, Spain) from 2014 to 2018. This study included three groups of children <18 years with gradual decrease of ARI severity: cases with invasive pneumococcal disease (IPD) (representative of lower respiratory tract infections and systemic infections), symptomatic controls with mild viral upper respiratory tract infections (URTI), and healthy/asymptomatic controls according to an approximate case-control ratio 1:2. Nasopharyngeal samples were collected from participants for detection, quantification and serotyping of pneumococcal DNA, viral DNA/RNA detection and 16S rRNA gene sequencing. Microbiological parameters were included on case-control classification models. A total of 140 subjects were recruited (IPD=27, URTI=48, healthy/asymptomatic control=65). Children's nasopharyngeal microbiota composition varied according to respiratory health status and infection severity. The IPD group was characterized by overrepresentation of Streptococcus pneumoniae, higher frequency of invasive pneumococcal serotypes, increased rate of viral infection and underrepresentation of potential protective bacterial species such as Dolosigranulum pigrum and Moraxella lincolnii. Microbiota-based classification models differentiated cases from controls with moderately high accuracy. These results demonstrate the close relationship existing between a child's nasopharyngeal microbiota and respiratory health, and provide initial evidence of the potential of microbiota-based diagnostics for differential diagnosis of severe ARIs using non-invasive samples.
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Affiliation(s)
- Desiree Henares
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariona F de Sevilla
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, Barcelona, Spain
| | | | | | | | - Alex Mira
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Health and Genomics, Center for Advanced Research in Public Health, FISABIO, Valencia, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre (TEAGASC), Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, County Cork, Ireland
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Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, Gao W, Bomar L, Tran TH, Jones DS, Minot S, Roberts RJ, Johnston CD, Lemon KP. Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. mSystems 2021; 6:e0042521. [PMID: 34546072 PMCID: PMC8547433 DOI: 10.1128/msystems.00425-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.
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Affiliation(s)
| | - Silvio D. Brugger
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Isabel Fernandez Escapa
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Sean L. Cotton
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Sara M. Eslami
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Lindsey Bomar
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Tommy H. Tran
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Dakota S. Jones
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Samuel Minot
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Christopher D. Johnston
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Katherine P. Lemon
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Section of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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40
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Chronic Rhinosinusitis and Alzheimer's Disease-A Possible Role for the Nasal Microbiome in Causing Neurodegeneration in the Elderly. Int J Mol Sci 2021; 22:ijms222011207. [PMID: 34681867 PMCID: PMC8541405 DOI: 10.3390/ijms222011207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/08/2021] [Accepted: 10/14/2021] [Indexed: 12/25/2022] Open
Abstract
Among millions of sufferers of chronic rhinosinusitis (CRS), the challenge is not only constantly coping with CRS-related symptoms, such as congested nose, sinus pain, and headaches, but also various complications, such as attention difficulties and possible depression. These complications suggest that neural activity in the central nervous system may be altered in those patients, leading to unexpected conditions, such as neurodegeneration in elderly patients. Recently, some studies linked the presence of CRS and cognitive impairments that could further develop into Alzheimer’s disease (AD). AD is the leading cause of dementia in the elderly and is characterised by progressive memory loss, cognitive behavioural deficits, and significant personality changes. The microbiome, especially those in the gut, has been recognised as a human organ and plays an important role in the development of various conditions, including AD. However, less attention has been paid to the microbiome in the nasal cavity. Increased nasal inflammatory responses due to CRS may be an initial event that changes local microbiome homeostasis, which may further affect neuronal integrity in the central nervous system resulting in AD. Evidence suggests a potential of β-amyloid deposition starting in olfactory neurons, which is then expanded from the nasal cavity to the central nervous system. In this paper, we reviewed currently available evidence that suggests this potential mechanism to advise the need to investigate the link between these two conditions.
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De Boeck I, Wittouck S, Martens K, Spacova I, Cauwenberghs E, Allonsius CN, Jörissen J, Wuyts S, Van Beeck W, Dillen J, Bron PA, Steelant B, Hellings PW, Vanderveken OM, Lebeer S. The nasal mutualist Dolosigranulum pigrum AMBR11 supports homeostasis via multiple mechanisms. iScience 2021; 24:102978. [PMID: 34485860 PMCID: PMC8403741 DOI: 10.1016/j.isci.2021.102978] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 12/21/2022] Open
Abstract
Comparing the nasal microbiome of healthy individuals and chronic rhinosinusitis (CRS) patients revealed Dolosigranulum pigrum as a species clearly associated with nasal health, although isolates obtained from healthy individuals are scarce. In this study, we explored the properties of this understudied lactic acid bacterium by integrating comparative genomics, habitat mining, cultivation, and functional characterization of interaction capacities. Mining 10.000 samples from the Earth Microbiome Project of 17 habitat types revealed that Dolosigranulum is mainly associated with the human nasal cavity. D. pigrum AMBR11 isolated from the nose of a healthy individual exerted antimicrobial activity against Staphylococcus aureus, decreased proinflammatory cytokine production in airway epithelial cells, and Galleria mellonella larvae mortality induced by this important nasal pathobiont. Furthermore, the strain protected the nasal barrier function in a mouse model using interleukin-4 as disruptive cytokine. Hence, D. pigrum AMBR11 is a mutualist with high potential as topical live biotherapeutic product.
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Affiliation(s)
- Ilke De Boeck
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Stijn Wittouck
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Katleen Martens
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Unit, Herestraat 49, 3000 Leuven, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Eline Cauwenberghs
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Camille Nina Allonsius
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Jennifer Jörissen
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Sander Wuyts
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Wannes Van Beeck
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Jelle Dillen
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Peter A. Bron
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Brecht Steelant
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Unit, Herestraat 49, 3000 Leuven, Belgium
| | - Peter W. Hellings
- KU Leuven Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Unit, Herestraat 49, 3000 Leuven, Belgium
- Clinical Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Olivier M. Vanderveken
- Faculty of Medicine and Health Sciences, Translational Neurosciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
- ENT, Head and Neck Surgery and Communication Disorders, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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Serotype Distribution of Streptococcus pneumoniae Carriage in Six-Month-Old Infants: A Cross-sectional Study During 2017-18, Tehran, Iran. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2021. [DOI: 10.5812/pedinfect.112705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: Streptococcus pneumoniae is recognized as one of the main pathogens inducing several invasive and non-invasive infections in children. Objective: The present study aimed to evaluate the serotype distribution of S. pneumoniae in six–month–old carriers. Methods: This study encompassed 600 six-month-old healthy infants whose pharyngeal swap samples were collected and then cultured to isolate S. pneumoniae. Twenty- five different serotypes were defined on positive culture samples by multiplex PCR. Results: In this study, 13 cases (2.2%) were positive S. pneumonia. The most common isolated serotypes of S. pneumoniae were serotypes 23F (n = 6, 1%) and 3 (n = 3, 0.5%), respectively. Notably, the most frequent serotype in formula-fed infants (n = 300) was Serotype 23F (n = 5, 1.7%); however, Serotype 3 (n = 3, 1%) was the most frequent one in breastfed participants (n = 300). According to the findings, the overall coverage of PCV10, PCV13, and PPSV23 on the S. pneumoniae serotypes at the age of six months was 50%, 73%, and 85%, respectively. Conclusions: At this age, the type of feeding could not significantly affect the frequency rate of S. pneumoniae colonization, while the serotype distributions in the two breastfed and formula-fed groups were different.
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43
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Nesbitt H, Burke C, Haghi M. Manipulation of the Upper Respiratory Microbiota to Reduce Incidence and Severity of Upper Respiratory Viral Infections: A Literature Review. Front Microbiol 2021; 12:713703. [PMID: 34512591 PMCID: PMC8432964 DOI: 10.3389/fmicb.2021.713703] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/06/2021] [Indexed: 12/12/2022] Open
Abstract
There is a high incidence of upper respiratory viral infections in the human population, with infection severity being unique to each individual. Upper respiratory viruses have been associated previously with secondary bacterial infection, however, several cross-sectional studies analyzed in the literature indicate that an inverse relationship can also occur. Pathobiont abundance and/or bacterial dysbiosis can impair epithelial integrity and predispose an individual to viral infection. In this review we describe common commensal microorganisms that have the capacity to reduce the abundance of pathobionts and maintain bacterial symbiosis in the upper respiratory tract and discuss the potential and limitations of localized probiotic formulations of commensal bacteria to reduce the incidence and severity of viral infections.
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Affiliation(s)
- Henry Nesbitt
- Discipline of Pharmacy, Graduate School Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Catherine Burke
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Mehra Haghi
- Discipline of Pharmacy, Graduate School Health, University of Technology Sydney, Sydney, NSW, Australia
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44
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Hasrat R, Kool J, de Steenhuijsen Piters WAA, Chu MLJN, Kuiling S, Groot JA, van Logchem EM, Fuentes S, Franz E, Bogaert D, Bosch T. Benchmarking laboratory processes to characterise low-biomass respiratory microbiota. Sci Rep 2021; 11:17148. [PMID: 34433845 PMCID: PMC8387476 DOI: 10.1038/s41598-021-96556-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/11/2021] [Indexed: 11/10/2022] Open
Abstract
The low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray–Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.
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Affiliation(s)
- Raiza Hasrat
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Jolanda Kool
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Sjoerd Kuiling
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - James A Groot
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Elske M van Logchem
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, 3508 AB, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands.,University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands.
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Yang F, Gao Y, Zhao H, Li J, Cheng X, Meng L, Dong P, Yang H, Chen S, Zhu J. Revealing the distribution characteristics of antibiotic resistance genes and bacterial communities in animal-aerosol-human in a chicken farm: From One-Health perspective. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112687. [PMID: 34438267 DOI: 10.1016/j.ecoenv.2021.112687] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/07/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Antibiotics in breeding industry can enter the environment through multiple pathways, thus accelerating the emergence and spread of antibiotic resistance genes (ARGs), among which aerosol transmission is easily achieved and often overlooked. To elucidate the role of aerosols in this situation, the present study investigated the distribution characteristics of 107 ARG subtypes (targeting to eight different ARG types) and nine mobile genetic elements (MGEs) and bacterial community in animal (chicken cloaca), environment (aerosols) and human (nasopharynx) of a chicken farm (n = 42) in Henan Province. In total, 116 ARG subtypes and MGEs were identified in the poultry farm. The total bacterial concentration of aerosols inside the chicken house (3.117 × 104 CFU/m3) exceeded the corresponding limit. The microbial communities in the samples of cloaca swab (C) and the workers' nasopharyngeal swab (N) were closer, while the abundance distribution of ARGs/ MGEs in cloacal swab (C) and aerosol (AI) in chicken house were much similar. There were certain consistency of the microbial community structure and the distribution of ARGs among the three groups of chicken cloaca, air aerosol, and workers' nasopharynx. Our results highlighted that animal breeding does have a certain impact on the surrounding environment and human, and aerosols play an important role in this process.
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Affiliation(s)
- Fan Yang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yanling Gao
- Henan Vocational College of Agriculture, Zhengzhou 450001, Henan, China
| | - Hongcheng Zhao
- Qingpu District Center for Disease Control and Prevention, Shanghai 201799, China
| | - Jinlei Li
- Henan Institute of Veterinary Drug and Feed Control, Zhengzhou 450001, Henan, China
| | - Xuemin Cheng
- College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Lei Meng
- Henan Institute of Veterinary Drug and Feed Control, Zhengzhou 450001, Henan, China
| | - Peng Dong
- Henan Institute of Veterinary Drug and Feed Control, Zhengzhou 450001, Henan, China
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Shuaiyin Chen
- College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China.
| | - Jingyuan Zhu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China.
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Elgamal Z, Singh P, Geraghty P. The Upper Airway Microbiota, Environmental Exposures, Inflammation, and Disease. ACTA ACUST UNITED AC 2021; 57:medicina57080823. [PMID: 34441029 PMCID: PMC8402057 DOI: 10.3390/medicina57080823] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Along with playing vital roles in pathogen exclusion and immune system priming, the upper airways (UAs) and their microbiota are essential for myriad physiological functions such as conditioning and transferring inhaled air. Dysbiosis, a microbial imbalance, is linked with various diseases and significantly impedes the quality of one’s life. Daily inhaled exposures and/or underlying conditions contribute to adverse changes to the UA microbiota. Such variations in the microbial community exacerbate UA and pulmonary disorders via modulating inflammatory and immune pathways. Hence, exploring the UA microbiota’s role in maintaining homeostasis is imperative. The microbial composition and subsequent relationship with airborne exposures, inflammation, and disease are crucial for strategizing innovating UA diagnostics and therapeutics. The development of a healthy UA microbiota early in life contributes to normal respiratory development and function in the succeeding years. Although different UA cavities present a unique microbial profile, geriatrics have similar microbes across their UAs. This lost community segregation may contribute to inflammation and disease, as it stimulates disadvantageous microbial–microbial and microbial–host interactions. Varying inflammatory profiles are associated with specific microbial compositions, while the same is true for many disease conditions and environmental exposures. A shift in the microbial composition is also detected upon the administration of numerous therapeutics, highlighting other beneficial and adverse side effects. This review examines the role of the UA microbiota in achieving homeostasis, and the impact on the UAs of environmental airborne pollutants, inflammation, and disease.
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Affiliation(s)
- Ziyad Elgamal
- Department of Biomedical Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY 11203, USA
| | - Pratyush Singh
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada;
| | - Patrick Geraghty
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY 11203, USA
- Correspondence: ; Tel.: +1-718-270-3141
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Raya Tonetti F, Tomokiyo M, Ortiz Moyano R, Quilodrán-Vega S, Yamamuro H, Kanmani P, Melnikov V, Kurata S, Kitazawa H, Villena J. The Respiratory Commensal Bacterium Dolosigranulum pigrum 040417 Improves the Innate Immune Response to Streptococcus pneumoniae. Microorganisms 2021; 9:microorganisms9061324. [PMID: 34207076 PMCID: PMC8234606 DOI: 10.3390/microorganisms9061324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 12/24/2022] Open
Abstract
Previously, we demonstrated that the nasal administration of Dolosigranulum pigrum 040417 differentially modulated the respiratory innate immune response triggered by the activation of Toll-like receptor 2 in infant mice. In this work, we aimed to evaluate the beneficial effects of D. pigrum 040417 in the context of Streptococcus pneumoniae infection and characterize the role of alveolar macrophages (AMs) in the immunomodulatory properties of this respiratory commensal bacterium. The nasal administration of D. pigrum 040417 to infant mice significantly increased their resistance to pneumococcal infection, differentially modulated respiratory cytokines production, and reduced lung injuries. These effects were associated to the ability of the 040417 strain to modulate AMs function. Depletion of AMs significantly reduced the capacity of the 040417 strain to improve both the reduction of pathogen loads and the protection against lung tissue damage. We also demonstrated that the immunomodulatory properties of D. pigrum are strain-specific, as D. pigrum 030918 was not able to modulate respiratory immunity or to increase the resistance of mice to an S. pneumoniae infection. These findings enhanced our knowledge regarding the immunological mechanisms involved in modulation of respiratory immunity induced by beneficial respiratory commensal bacteria and suggested that particular strains could be used as next-generation probiotics.
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Affiliation(s)
- Fernanda Raya Tonetti
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán 4000, Argentina; (F.R.T.); (R.O.M.)
| | - Mikado Tomokiyo
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Ramiro Ortiz Moyano
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán 4000, Argentina; (F.R.T.); (R.O.M.)
| | - Sandra Quilodrán-Vega
- Laboratory of Food Microbiology, Faculty of Veterinary Sciences, University of Concepción, Chillán 3780000, Chile;
| | - Hikari Yamamuro
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Paulraj Kanmani
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
| | - Vyacheslav Melnikov
- Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia;
| | - Shoichiro Kurata
- Laboratory of Molecular Genetics, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
- Correspondence: (H.K.); (J.V.)
| | - Julio Villena
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán 4000, Argentina; (F.R.T.); (R.O.M.)
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Correspondence: (H.K.); (J.V.)
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Abstract
The nasopharyngeal microbiome is a dynamic microbial interface of the aerodigestive tract, and a diagnostic window in the fight against respiratory infections and antimicrobial resistance. As its constituent bacteria, viruses and mycobacteria become better understood and sampling accuracy improves, diagnostics of the nasopharynx could guide more personalized care of infections of surrounding areas including the lungs, ears and sinuses. This review will summarize the current literature from a clinical perspective and highlight its growing importance in diagnostics and infectious disease management.
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Affiliation(s)
- Matthew Flynn
- School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
- Otolaryngology Department, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - James Dooley
- School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
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49
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De Boeck I, Spacova I, Vanderveken OM, Lebeer S. Lactic acid bacteria as probiotics for the nose? Microb Biotechnol 2021; 14:859-869. [PMID: 33507624 PMCID: PMC8085937 DOI: 10.1111/1751-7915.13759] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
Several studies have recently pointed towards an increased occurrence and prevalence of several taxa of the lactic acid bacteria (LAB) in the microbiota of the upper respiratory tract (URT) under healthy conditions versus disease. These include several species of the Lactobacillales such as Lacticaseibacillus casei, Lactococcus lactis and Dolosigranulum pigrum. In addition to physiological studies on their potential beneficial functions and their long history of safe use as probiotics in other human body sites, LAB are thus increasingly to be explored as alternative or complementary treatment for URT diseases. This review highlights the importance of lactic acid bacteria in the respiratory tract and their potential as topical probiotics for this body site. We focus on the potential probiotic properties and adaptation factors that are needed for a bacterial strain to optimally exert its beneficial activity in the respiratory tract. Furthermore, we discuss a range of in silico, in vitro and in vivo models needed to obtain better insights into the efficacy and adaptation factors specifically for URT probiotics. Such knowledge will facilitate optimal strain selection in order to conduct rigorous clinical studies with the most suitable probiotic strains. Despite convincing evidence from microbiome association and in vitro studies, the clinical evidence for oral or topical probiotics for common URT diseases such as chronic rhinosinusitis (CRS) needs further substantiation.
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Affiliation(s)
- Ilke De Boeck
- Department of Bioscience EngineeringUniversity of AntwerpGroenenborgerlaan 171AntwerpB‐2020Belgium
| | - Irina Spacova
- Department of Bioscience EngineeringUniversity of AntwerpGroenenborgerlaan 171AntwerpB‐2020Belgium
| | - Olivier M. Vanderveken
- ENT, Head and Neck Surgery and Communication DisordersAntwerp University HospitalEdegemBelgium
- Faculty of Medicine and Health SciencesTranslational NeurosciencesUniversity of AntwerpAntwerpBelgium
| | - Sarah Lebeer
- Department of Bioscience EngineeringUniversity of AntwerpGroenenborgerlaan 171AntwerpB‐2020Belgium
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50
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Renz A, Widerspick L, Dräger A. First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. Metabolites 2021; 11:232. [PMID: 33918864 PMCID: PMC8069353 DOI: 10.3390/metabo11040232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/21/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Dolosigranulum pigrum is a quite recently discovered Gram-positive coccus. It has gained increasing attention due to its negative correlation with Staphylococcus aureus, which is one of the most successful modern pathogens causing severe infections with tremendous morbidity and mortality due to its multiple resistances. As the possible mechanisms behind its inhibition of S. aureus remain unclear, a genome-scale metabolic model (GEM) is of enormous interest and high importance to better study its role in this fight. This article presents the first GEM of D. pigrum, which was curated using automated reconstruction tools and extensive manual curation steps to yield a high-quality GEM. It was evaluated and validated using all currently available experimental data of D. pigrum. With this model, already predicted auxotrophies and biosynthetic pathways could be verified. The model was used to define a minimal medium for further laboratory experiments and to predict various carbon sources' growth capacities. This model will pave the way to better understand D. pigrum's role in the fight against S. aureus.
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Affiliation(s)
- Alina Renz
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany; (A.R.); (L.W.)
- Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
| | - Lina Widerspick
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany; (A.R.); (L.W.)
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany; (A.R.); (L.W.)
- Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), Partner site Tübingen, 72076 Tübingen, Germany
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