1
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Deek RA, Ma S, Lewis J, Li H. Statistical and computational methods for integrating microbiome, host genomics, and metabolomics data. eLife 2024; 13:e88956. [PMID: 38832759 PMCID: PMC11149933 DOI: 10.7554/elife.88956] [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: 04/26/2023] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Large-scale microbiome studies are progressively utilizing multiomics designs, which include the collection of microbiome samples together with host genomics and metabolomics data. Despite the increasing number of data sources, there remains a bottleneck in understanding the relationships between different data modalities due to the limited number of statistical and computational methods for analyzing such data. Furthermore, little is known about the portability of general methods to the metagenomic setting and few specialized techniques have been developed. In this review, we summarize and implement some of the commonly used methods. We apply these methods to real data sets where shotgun metagenomic sequencing and metabolomics data are available for microbiome multiomics data integration analysis. We compare results across methods, highlight strengths and limitations of each, and discuss areas where statistical and computational innovation is needed.
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Affiliation(s)
- Rebecca A Deek
- Department of Biostatistics, University of PittsburghPittsburghUnited States
| | - Siyuan Ma
- Department of Biostatistics, Vanderbilt School of MedicineNashvilleUnited States
| | - James Lewis
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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2
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Shad A, Rewell SSJ, Macowan M, Gandasasmita N, Wang J, Chen K, Marsland B, O'Brien TJ, Li J, Semple BD. Modelling lung infection with Klebsiella pneumoniae after murine traumatic brain injury. J Neuroinflammation 2024; 21:122. [PMID: 38720343 PMCID: PMC11080247 DOI: 10.1186/s12974-024-03093-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/05/2024] [Indexed: 05/12/2024] Open
Abstract
Pneumonia is a common comorbidity in patients with severe traumatic brain injury (TBI), and is associated with increased morbidity and mortality. In this study, we established a model of intratracheal Klebsiella pneumoniae administration in young adult male and female mice, at 4 days following an experimental TBI, to investigate how K. pneumoniae infection influences acute post-TBI outcomes. A dose-response curve determined the optimal dose of K. pneumoniae for inoculation (1 x 10^6 colony forming units), and administration at 4 days post-TBI resulted in transient body weight loss and sickness behaviors (hypoactivity and acute dyspnea). K. pneumoniae infection led to an increase in pro-inflammatory cytokines in serum and bronchoalveolar lavage fluid at 24 h post-infection, in both TBI and sham (uninjured) mice. By 7 days, when myeloperoxidase + neutrophil numbers had returned to baseline in all groups, lung histopathology was observed with an increase in airspace size in TBI + K. pneumoniae mice compared to TBI + vehicle mice. In the brain, increased neuroinflammatory gene expression was observed acutely in response to TBI, with an exacerbated increase in Ccl2 and Hmox1 in TBI + K. pneumoniae mice compared to either TBI or K. pneumoniae alone. However, the presence of neuroinflammatory immune cells in the injured brain, and the extent of damage to cortical and hippocampal brain tissue, was comparable between K. pneumoniae and vehicle-treated mice by 7 days. Examination of the fecal microbiome across a time course did not reveal any pronounced effects of either injury or K. pneumoniae on bacterial diversity or abundance. Together, these findings demonstrate that K. pneumoniae lung infection after TBI induces an acute and transient inflammatory response, primarily localized to the lungs with some systemic effects. However, this infection had minimal impact on secondary injury processes in the brain following TBI. Future studies are needed to evaluate the potential longer-term consequences of this dual-hit insult.
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Affiliation(s)
- Ali Shad
- Department of Neuroscience, The School of Translational Medicine, Monash University, Level 6 Alfred Centre, 99 Commercial Rd, Melbourne, VIC, 3004 VIC, Australia
- Alfred Health, Prahran, VIC, Australia
| | - Sarah S J Rewell
- Department of Neuroscience, The School of Translational Medicine, Monash University, Level 6 Alfred Centre, 99 Commercial Rd, Melbourne, VIC, 3004 VIC, Australia
- Alfred Health, Prahran, VIC, Australia
| | - Matthew Macowan
- Department of Immunology, The School of Translational Medicine, Monash University, Melbourne, VIC, Australia
- GIN Discovery Program, The School of Translational Medicine, Monash University, Melbourne, VIC, Australia
| | - Natasha Gandasasmita
- Department of Neuroscience, The School of Translational Medicine, Monash University, Level 6 Alfred Centre, 99 Commercial Rd, Melbourne, VIC, 3004 VIC, Australia
| | - Jiping Wang
- Department of Microbiology, Monash Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ke Chen
- Department of Microbiology, Monash Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ben Marsland
- Department of Immunology, The School of Translational Medicine, Monash University, Melbourne, VIC, Australia
- GIN Discovery Program, The School of Translational Medicine, Monash University, Melbourne, VIC, Australia
| | - Terence J O'Brien
- Department of Neuroscience, The School of Translational Medicine, Monash University, Level 6 Alfred Centre, 99 Commercial Rd, Melbourne, VIC, 3004 VIC, Australia
- Alfred Health, Prahran, VIC, Australia
- GIN Discovery Program, The School of Translational Medicine, Monash University, Melbourne, VIC, Australia
- Department of Medicine (Royal Melbourne Hospital), University of Melbourne, Parkville, VIC, Australia
| | - Jian Li
- Department of Microbiology, Monash Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Bridgette D Semple
- Department of Neuroscience, The School of Translational Medicine, Monash University, Level 6 Alfred Centre, 99 Commercial Rd, Melbourne, VIC, 3004 VIC, Australia.
- Alfred Health, Prahran, VIC, Australia.
- Department of Medicine (Royal Melbourne Hospital), University of Melbourne, Parkville, VIC, Australia.
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3
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Lipinksi JH, Ranjan P, Dickson RP, O’Dwyer DN. The Lung Microbiome. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1269-1275. [PMID: 38560811 PMCID: PMC11073614 DOI: 10.4049/jimmunol.2300716] [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: 10/25/2023] [Accepted: 01/01/2024] [Indexed: 04/04/2024]
Abstract
Although the lungs were once considered a sterile environment, advances in sequencing technology have revealed dynamic, low-biomass communities in the respiratory tract, even in health. Key features of these communities-composition, diversity, and burden-are consistently altered in lung disease, associate with host physiology and immunity, and can predict clinical outcomes. Although initial studies of the lung microbiome were descriptive, recent studies have leveraged advances in technology to identify metabolically active microbes and potential associations with their immunomodulatory by-products and lung disease. In this brief review, we discuss novel insights in airway disease and parenchymal lung disease, exploring host-microbiome interactions in disease pathogenesis. We also discuss complex interactions between gut and oropharyngeal microbiota and lung immunobiology. Our advancing knowledge of the lung microbiome will provide disease targets in acute and chronic lung disease and may facilitate the development of new therapeutic strategies.
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Affiliation(s)
- Jay H. Lipinksi
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Piyush Ranjan
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Dept. of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Robert P. Dickson
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Dept. of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI, USA
| | - David N. O’Dwyer
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
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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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Thorsen J, Li XJ, Peng S, Sunde RB, Shah SA, Bhattacharyya M, Poulsen CS, Poulsen CE, Leal Rodriguez C, Widdowson M, Neumann AU, Trivedi U, Chawes B, Bønnelykke K, Bisgaard H, Sørensen SJ, Stokholm J. The airway microbiota of neonates colonized with asthma-associated pathogenic bacteria. Nat Commun 2023; 14:6668. [PMID: 37863895 PMCID: PMC10589220 DOI: 10.1038/s41467-023-42309-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
Culture techniques have associated colonization with pathogenic bacteria in the airways of neonates with later risk of childhood asthma, whereas more recent studies utilizing sequencing techniques have shown the same phenomenon with specific anaerobic taxa. Here, we analyze nasopharyngeal swabs from 1 month neonates in the COPSAC2000 prospective birth cohort by 16S rRNA gene sequencing of the V3-V4 region in relation to asthma risk throughout childhood. Results are compared with previous culture results from hypopharyngeal aspirates from the same cohort and with hypopharyngeal sequencing data from the later COPSAC2010 cohort. Nasopharyngeal relative abundance values of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis are associated with the same species in the hypopharyngeal cultures. A combined pathogen score of these bacteria's abundance values is associated with persistent wheeze/asthma by age 7. No other taxa are associated. Compared to the hypopharyngeal aspirates from the COPSAC2010 cohort, the anaerobes Veillonella and Prevotella, which have previously been implicated in asthma development, are less commonly detected in the COPSAC2000 nasopharyngeal samples, but correlate with the pathogen score, hinting at latent community structures that bridge current and previous results. These findings have implications for future asthma prevention efforts.
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Affiliation(s)
- Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Xuan Ji Li
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Shuang Peng
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Bjersand Sunde
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark
| | - Shiraz A Shah
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Madhumita Bhattacharyya
- Chair of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | - Casper Sahl Poulsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Christina Egeø Poulsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Cristina Leal Rodriguez
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Michael Widdowson
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Avidan Uriel Neumann
- Chair of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Munich, Munich, Germany
| | - Urvish Trivedi
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark.
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark.
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Pérez-Cobas AE, Rodríguez-Beltrán J, Baquero F, Coque TM. Ecology of the respiratory tract microbiome. Trends Microbiol 2023; 31:972-984. [PMID: 37173205 DOI: 10.1016/j.tim.2023.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/05/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023]
Abstract
A thriving multi-kingdom microbial ecosystem inhabits the respiratory tract: the respiratory tract microbiome (RTM). In recent years, the contribution of the RTM to human health has become a crucial research aspect. However, research into the key ecological processes, such as robustness, resilience, and microbial interaction networks, has only recently started. This review leans on an ecological framework to interpret the human RTM and determine how the ecosystem functions and assembles. Specifically, the review illustrates the ecological RTM models and discusses microbiome establishment, community structure, diversity stability, and critical microbial interactions. Lastly, the review outlines the RTM responses to ecological disturbances, as well as the promising approaches for restoring ecological balance.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain; CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain.
| | - Jerónimo Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain; CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain; CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
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Shibata R, Zhu Z, Kyo M, Ooka T, Freishtat RJ, Mansbach JM, Pérez-Losada M, Camargo CA, Hasegawa K. Nasopharyngeal fungal subtypes of infant bronchiolitis and disease severity risk. EBioMedicine 2023; 95:104742. [PMID: 37536062 PMCID: PMC10415709 DOI: 10.1016/j.ebiom.2023.104742] [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: 04/25/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Bronchiolitis is a leading cause of infant hospitalization. Recent research suggests the heterogeneity within bronchiolitis and the relationship of airway viruses and bacteria with bronchiolitis severity. However, little is known about the pathobiological role of fungi. We aimed to identify bronchiolitis mycotypes by integrating fungus and virus data, and determine their association with bronchiolitis severity and biological characteristics. METHODS In a multicentre prospective cohort study of 398 infants (age <1 year, male 59%) hospitalized for bronchiolitis, we applied clustering approaches to identify mycotypes by integrating nasopharyngeal fungus (detected in RNA-sequencing data) and virus data (respiratory syncytial virus [RSV], rhinovirus [RV]) at hospitalization. We examined their association with bronchiolitis severity-defined by positive pressure ventilation (PPV) use and biological characteristics by nasopharyngeal metatranscriptome and transcriptome data. RESULTS In infants hospitalized for bronchiolitis, we identified four mycotypes: A) fungiM.restrictavirusRSV/RV, B) fungiM.restrictavirusRSV, C) fungiM.globosavirusRSV/RV, D) funginot-detectedvirusRSV/RV mycotypes. Compared to mycotype A infants (the largest subtype, n = 211), mycotype C infants (n = 85) had a significantly lower risk of PPV use (7% vs. 1%, adjOR, 0.21; 95% CI, 0.02-0.90; p = 0.033), while the risk of PPV use was not significantly different in mycotype B or D. In the metatranscriptome and transcriptome data, mycotype C had similar bacterial composition and microbial functions yet dysregulated pathways (e.g., Fc γ receptor-mediated phagocytosis pathway and chemokine signaling pathway; FDR <0.05). INTERPRETATION In this multicentre cohort, fungus-virus clustering identified distinct mycotypes of infant bronchiolitis with differential severity risks and unique biological characteristics. FUNDING This study was supported by the National Institutes of Health.
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Affiliation(s)
- Ryohei Shibata
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michihito Kyo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tadao Ooka
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Health Science, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA; Division of Emergency Medicine, Children's National Hospital, Washington, DC, USA; Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, The George Washington University, Washington, DC, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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Wang X, Shao Z, Zhu M, Li B, You M, Chen X. The correlation of the intestinal with pharyngeal microbiota in early neonates. Front Microbiol 2023; 14:1225352. [PMID: 37601350 PMCID: PMC10434775 DOI: 10.3389/fmicb.2023.1225352] [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: 05/19/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction The gut-lung axis has long been recognized as an important mechanism affecting intestinal and lung immunity. Still, few studies have examined the correlation between the intestinal and pharyngeal microbiota in early neonates, especially when feeding patterns are one of the main drivers of microbiota development. Methods To explore the composition and function of intestinal and pharyngeal microbiota and to analyze the effect of limited formula feeding on the initial microbiota colonization in early full-term neonates, we characterized the stool and oropharyngeal microbiota of 20 healthy full-term newborns sampled on days 0 and 5-7 after birth using 16S rRNA gene sequencing. Based on the sequencing results, a comparison was made of the compositions and functions of the intestinal and oropharyngeal microbiota for analysis. Results and discussion At the phylum level, Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most abundant in both niches. At the genus level, the species of pioneer bacteria were rich in the intestine and oropharynx but low in abundance on day 0. On days 5-7, Bifidobacterium (25.40%) and Escherichia-Shigella (22.16%) were dominant in the intestine, while Streptococcus (38.40%) and Staphylococcus (23.13%) were dominant in the oropharynx. There were eight core bacteria genera in the intestine and oropharynx on days 5-7, which were Bifidobacterium, Escherichia-Shigella, Staphylococcus, Streptococcus, Bacteroides, Parabacteroides, Rothia, and Acinetobacter. As indicated by PICRUSt analysis, on days 5-7, the intestinal microbiota was more predictive than the oropharyngeal microbiota in transcription, metabolism, cell motility, cellular processes and signaling, and organismal system function in the KEGG pathway. Compared to exclusive breastfeeding, limited formula feeding (40-60%) had no significant effect on the neonatal intestinal and oropharyngeal microbiota composition during the initial colonization period. Our results suggest that the initial colonization of microbiota is closely related to the ecological niche environment in the intestine and oropharynx, with their core microbiota being closely correlated. We found that early limited formula feeding could not significantly affect the initial colonization of microbiota in the intestine and oropharynx.
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Affiliation(s)
- Xuejuan Wang
- Department of Neonatal, Shanghai Pudong New Area Health Maternal and Child Health Hospital, Shanghai, China
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhiying Shao
- Department of Neonatal, Shanghai Pudong New Area Health Maternal and Child Health Hospital, Shanghai, China
| | - Minrong Zhu
- Department of Neonatal, Shanghai Pudong New Area Health Maternal and Child Health Hospital, Shanghai, China
| | - Bingjie Li
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mingyu You
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoqing Chen
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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9
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Lloyd CM, Saglani S. Early-life respiratory infections and developmental immunity determine lifelong lung health. Nat Immunol 2023; 24:1234-1243. [PMID: 37414905 DOI: 10.1038/s41590-023-01550-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Respiratory infections are common in infants and young children. However, the immune system develops and matures as the child grows, thus the effects of infection during this time of dynamic change may have long-term consequences. The infant immune system develops in conjunction with the seeding of the microbiome at the respiratory mucosal surface, at a time that the lungs themselves are maturing. We are now recognizing that any disturbance of this developmental trajectory can have implications for lifelong lung health. Here, we outline our current understanding of the molecular mechanisms underlying relationships between immune and structural cells in the lung with the local microorganisms. We highlight the importance of gaining greater clarity as to what constitutes a healthy respiratory ecosystem and how environmental exposures influencing this network will aid efforts to mitigate harmful effects and restore lung immune health.
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Affiliation(s)
- Clare M Lloyd
- National Heart and Lung Institute, Faculty of Medicine, Imperial College, London, UK.
| | - Sejal Saglani
- National Heart and Lung Institute, Faculty of Medicine, Imperial College, London, UK.
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Lin L, Yi X, Liu H, Meng R, Li S, Liu X, Yang J, Xu Y, Li C, Wang Y, Xiao N, Li H, Liu Z, Xiang Z, Shu W, Guan WJ, Zheng XY, Sun J, Wang Z. The airway microbiome mediates the interaction between environmental exposure and respiratory health in humans. Nat Med 2023:10.1038/s41591-023-02424-2. [PMID: 37349537 DOI: 10.1038/s41591-023-02424-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Exposure to environmental pollution influences respiratory health. The role of the airway microbial ecosystem underlying the interaction of exposure and respiratory health remains unclear. Here, through a province-wide chronic obstructive pulmonary disease surveillance program, we conducted a population-based survey of bacterial (n = 1,651) and fungal (n = 719) taxa and metagenomes (n = 1,128) from induced sputum of 1,651 household members in Guangdong, China. We found that cigarette smoking and higher PM2.5 concentration were associated with lung function impairment through the mediation of bacterial and fungal communities, respectively, and that exposure was associated with an enhanced inter-kingdom microbial interaction resembling the pattern seen in chronic obstructive pulmonary disease. Enrichment of Neisseria was associated with a 2.25-fold increased risk of high respiratory symptom burden, coupled with an elevation in Aspergillus, in association with occupational pollution. We developed an individualized microbiome-based health index, which covaried with exposure, respiratory symptoms and diseases, with potential generalizability to global datasets. Our results may inform environmental risk prevention and guide interventions that harness airway microbiome.
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Affiliation(s)
- Lifeng Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Haiyue Liu
- Xiamen Key Laboratory of Genetic Testing, Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Ruilin Meng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Saiqiang Li
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiaomin Liu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Junhao Yang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yanjun Xu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Chuan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ye Wang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ni Xiao
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huimin Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zuheng Liu
- Xiamen Key Laboratory of Cardiac Electrophysiology, Department of Cardiology, Xiamen Institute of Cardiovascular Diseases, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Zhiming Xiang
- Department of Radiology, Panyu Central Hospital, Guangzhou, China
| | - Wensheng Shu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Department of Thoracic Surgery, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xue-Yan Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
| | - Jiufeng Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China.
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11
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Doron I, Kusakabe T, Iliev ID. Immunoglobulins at the interface of the gut mycobiota and anti-fungal immunity. Semin Immunol 2023; 67:101757. [PMID: 37003056 PMCID: PMC10192079 DOI: 10.1016/j.smim.2023.101757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The dynamic and complex community of microbes that colonizes the intestines is composed of bacteria, fungi, and viruses. At the mucosal surfaces, immunoglobulins play a key role in protection against bacterial and fungal pathogens, and their toxins. Secretory immunoglobulin A (sIgA) is the most abundantly produced antibody at the mucosal surfaces, while Immunoglobulin G (IgG) isotypes play a critical role in systemic protection. IgA and IgG antibodies with reactivity to commensal fungi play an important role in shaping the mycobiota and host antifungal immunity. In this article, we review the latest evidence that establishes a connection between commensal fungi and B cell-mediated antifungal immunity as an additional layer of protection against fungal infections and inflammation.
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Affiliation(s)
- Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Takato Kusakabe
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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12
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Huynh M, Crane MJ, Jamieson AM. The lung, the niche, and the microbe: Exploring the lung microbiome in cancer and immunity. Front Immunol 2023; 13:1094110. [PMID: 36733391 PMCID: PMC9888758 DOI: 10.3389/fimmu.2022.1094110] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
The lung is a complex and unique organ system whose biology is strongly influenced by environmental exposure, oxygen abundance, connection to extrapulmonary systems via a dense capillary network, and an array of immune cells that reside in the tissue at steady state. The lung also harbors a low biomass community of commensal microorganisms that are dynamic during both health and disease with the capacity to modulate regulatory immune responses during diseases such as cancer. Lung cancer is the third most common cancer worldwide with the highest mortality rate amongst cancers due to the difficulty of an early diagnosis. This review discusses the current body of work addressing the interactions between the lung microbiota and the immune system, and how these two components of the pulmonary system are linked to lung cancer development and outcomes. Bringing in lessons from broader studies examining the effects of the gut microbiota on cancer outcomes, we highlight many challenges and gaps in this nascent field.
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Affiliation(s)
| | | | - Amanda M. Jamieson
- Department of Molecular Microbiology & Immunology, Brown University, Providence, RI, United States
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13
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Pirini F, Cortesi M, Tumedei MM, Zanoni M, Ravaioli S, Bravaccini S. Tumor resident microbiota and response to therapies: An insight on tissue bacterial microbiota. Front Cell Dev Biol 2023; 10:1048360. [PMID: 36684442 PMCID: PMC9845623 DOI: 10.3389/fcell.2022.1048360] [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: 09/19/2022] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
The role of the intestinal microbiota in the promotion, progression, and response to therapies is gaining importance, but recent studies confirm the presence of microbiota also in the tumor, thus becoming a component of the tumor microenvironment. There is not much knowledge on the characteristics and mechanisms of action of the tumor resident microbiota, but there are already indications of its involvement in conditioning the response to therapies. In this review, we discuss recent publications on the interaction between microbiota and anticancer treatments, mechanisms of resistance and possible strategies for manipulating the microbiota that could improve treatments in a personalized medicine perspective.
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14
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Jaswal K, Todd OA, Behnsen J. Neglected gut microbiome: interactions of the non-bacterial gut microbiota with enteric pathogens. Gut Microbes 2023; 15:2226916. [PMID: 37365731 DOI: 10.1080/19490976.2023.2226916] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
A diverse array of commensal microorganisms inhabits the human intestinal tract. The most abundant and most studied members of this microbial community are undoubtedly bacteria. Their important role in gut physiology, defense against pathogens, and immune system education has been well documented over the last decades. However, the gut microbiome is not restricted to bacteria. It encompasses the entire breadth of microbial life: viruses, archaea, fungi, protists, and parasitic worms can also be found in the gut. While less studied than bacteria, their divergent but important roles during health and disease have become increasingly more appreciated. This review focuses on these understudied members of the gut microbiome. We will detail the composition and development of these microbial communities and will specifically highlight their functional interactions with enteric pathogens, such as species of the family Enterobacteriaceae. The interactions can be direct through physical interactions, or indirect through secreted metabolites or modulation of the immune response. We will present general concepts and specific examples of how non-bacterial gut communities modulate bacterial pathogenesis and present an outlook for future gut microbiome research that includes these communities.
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Affiliation(s)
- Kanchan Jaswal
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Olivia A Todd
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
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15
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Chen Z, Tian Y, Wang Y, Zhao H, Chen C, Zhang F. Profile of the Lower Respiratory Tract Microbiome in Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome and Lung Disease. Front Microbiol 2022; 13:888996. [PMID: 35814692 PMCID: PMC9260662 DOI: 10.3389/fmicb.2022.888996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022] Open
Abstract
Once an human immunodeficiency virus (HIV)-infected individual enters the onset period, a variety of opportunistic infections may occur, affecting various systems and organs throughout the body, due to the considerable reduction in the body’s immune function. The objectives of this study were to explore the relationship between immune status and microbial communities in the lungs of individuals with HIV infection. A total of 88 patients with lung disease [80 (91%) HIV-positive and 8 (9%) HIV-negative] were enrolled in our study between January and July 2018, and 88 bronchoalveolar lavage fluid (BALF) samples were obtained during bronchoscopy. In this cross-sectional study, we investigated differences in the pulmonary microbiome of patients with HIV who had different immune statuses. The diversity of bacteria in the lungs of HIV-positive individuals was lower than that in HIV-negative individuals (p < 0.05). There was a significant difference in the composition and distribution of bacteria and fungi between the HIV-positive and HIV-negative groups (p < 0.01). The number of fungal species in the BALF of HIV-positive patients was higher than in HIV-negative patients. The diversity of bacteria and fungi in the BALF of HIV-positive patients increased with decreasing CD4 T-cell counts. Linear regression analysis showed that Pneumocystis (R2 = 6.4e−03, p < 0.05), Cryptosphaeria (R2 = 7.2e−01, p < 0.05), Candida (R2 = 3.9e−02, p < 0.05), and Trichosporon (R2 = 7.7e−01, p < 0.05) were negatively correlated with CD4 counts (F-test, p < 0.05). The samples collected from HIV-positive patients exhibited a different pattern relative to those from the HIV-negative group. Differences in host immune status cause differences in the diversity and structure of lower respiratory tract microorganisms.
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Affiliation(s)
- Zhen Chen
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Ya Tian
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Wang
- Affiliated Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Hongxin Zhao
- Affiliated Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Chen Chen
- Affiliated Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Chen Chen,
| | - Fujie Zhang
- Affiliated Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Fujie Zhang,
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16
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Gamal A, Elshaer M, Alabdely M, Kadry A, McCormick TS, Ghannoum M. The Mycobiome: Cancer Pathogenesis, Diagnosis, and Therapy. Cancers (Basel) 2022; 14:2875. [PMID: 35740541 PMCID: PMC9221014 DOI: 10.3390/cancers14122875] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
Cancer is among the leading causes of death globally. Despite advances in cancer research, a full understanding of the exact cause has not been established. Recent data have shown that the microbiome has an important relationship with cancer on various levels, including cancer pathogenesis, diagnosis and prognosis, and treatment. Since most studies have focused only on the role of bacteria in this process, in this article we review the role of fungi-another important group of the microbiome, the totality of which is referred to as the "mycobiome"-in the development of cancer and how it can impact responses to anticancer medications. Furthermore, we provide recent evidence that shows how the different microbial communities interact and affect each other at gastrointestinal and non-gastrointestinal sites, including the skin, thereby emphasizing the importance of investigating the microbiome beyond bacteria.
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Affiliation(s)
- Ahmed Gamal
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
| | - Mohammed Elshaer
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Mayyadah Alabdely
- Department of Internal Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA;
| | - Ahmed Kadry
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
- Department of Dermatology and Venereology, Al-Azhar University, Cairo 11651, Egypt
| | - Thomas S. McCormick
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
| | - Mahmoud Ghannoum
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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