- Email: [email protected]
Intimate Crosstalk in Lower Airways at the Beginning of Life
Cell Host & Microbe
In Translation Intimate Crosstalk in Lower Airways at the Beginning of Life Erika von Mutius1,2,3,* 1Dr.
von Hauner Children’s Hospital, Ludwig Maximilian University, Munich, Germany for Asthma and Allergy Prevention, Helmholtz Centre, Munich, Germany 3Member of the German Center for Lung Research, Munich, Germany *Correspondence: [email protected] https://doi.org/10.1016/j.chom.2018.11.014 2Institute
The early life formation of the immunological and microbial environment of the human lower airways remains unknown. In this issue of Cell Host & Microbe, Pattaroni et al. (2018) shed light on this critical period, which is important for maturation or dysregulation of the microbiome and immune responses and disease development. The role of the microbiome for human health and disease is a matter of intense research and debate. Investigators address this fundamental question with a variety of approaches: experimental studies in animals, mostly mice, under pathogen- and germ-free conditions; 16S rRNA-based and metagenomic sequencing of human samples; and culture-based approaches and mathematical modeling to question and mirror the intricate interplay of microbial communities and the host’s response. For human studies, the accessibility of the diseased organ is of key importance. In skin diseases such as atopic dermatitis, the compositional structure and metabolic function of the skin microbiome, its external and internal determinants, and its crosstalk with the host’s local and systemic immune responses can be studied by means of skin swabs and biopsies in lesional and non-affected areas (Eyerich et al., 2018). For the gut microbiome, which has been proposed to play a key role for the development of intestinal, behavioral, neurological, and respiratory conditions, fecal samples can be collected with relative ease, even if they will not fully reflect microbial processes in more upstream parts of the digestive tract and at mucosal surfaces (Gilbert et al., 2018). The upper respiratory tract is accessible even in young infants, where maturation of the nasopharyngeal microbiome has been elegantly shown to determine the risk of viral infections (Hakansson et al., 2018). Yet, the study of the lower respiratory tract microbiome is a challenging endeavor. The human respiratory tract is a spatially complex branching ecosystem
where, in adults, airways divide at least 23 times, yielding an alveolar surface area that is 30 times that of the skin and about double that of the gastrointestinal tract (Hasleton, 1972; Helander and €ndriks, 2014). The healthy respiratory Fa tract is a low-nutrient environment for microbes that is lined by a thin and selectively bacteriostatic layer of lipid-rich surfactant, which prevents collapse (Wu et al., 2003). Many studies in adults have relied on specimen collected during bronchoscopies by either bronchoalveolar lavage, brushings, or biopsies, in which the procedure can be performed under local anesthesia. Children do not tolerate such intervention, and therefore, pediatric bronchoscopies necessitate general anesthesia, which is ethically not justifiable in healthy children. To obtain spontaneous and induced sputum, expectorations is an alternative non-invasive route to collect lower respiratory tract specimen, but preschool children do not cough up expectorations but rather swallow them. Therefore, an ethically acceptable means of studying the lower respiratory tract microbiome is the use of endotracheal aspirates via suctioning a patient’s endotracheal tube. This approach has yielded interesting results in the study of the dynamics of respiratory microbiota in critically ill adult patients (Panzer et al., 2018). Pattaroni and colleagues have applied this method to very young children (Pattaroni et al., 2018). They present the findings of their comprehensive study aiming at identifying the early-life bacterial colonization pattern of the lower airways in relation to the maturating im-
758 Cell Host & Microbe 24, December 12, 2018 ª 2018 Elsevier Inc.
mune system early in life in this issue of Cell Host & Microbe. Pattaroni et al. (2018) studied more than 40 infants aged 1 day to 1 year, about half of them undergoing endotracheal intubation for elective surgery and 60% being preterm infants. About two-thirds were studied in the neonatal period within 28 days of birth. Three microbiota profiles were identified. The first two clusters were dominated by either Staphylococcus or Ureaplasma genera, while the third cluster exhibited a balanced composition, including Streptococcus, Neisseria, Prevotella, Porphyromonas, Veillonella, and Fusobacteria genera. The highest diversity (Shannon Index) was observed in samples of the mixed cluster but did not differ between the Staphylococcus and Ureaplasma clusters. All three clusters were detected within the 3 first postnatal days. The Ureaplasma and Staphylococcus clusters were absent in infants older than 7 weeks postnatal age, whereas the mixed cluster was detectable in samples from infants across the whole first year of life. Gestational age had the strongest effect on microbiota composition: none of the samples collected from infants born before 30 weeks of gestational age were in the mixed cluster. Delivery mode significantly contributed to 28% of the variance in the preterm model but had no effect in the term population. To evaluate the impact of these microbial communities on the host, their virulence potential was evaluated via the PICRUSt algorithm. IgA protease activity was among the most increased virulence functions in samples from term children. This correlated with a significant
Cell Host & Microbe
In Translation enrichment in the IgA production pathway by gestational age when analyzing the infant’s own gene expression data in a subset of 16 subjects with additional host transcriptomic data. These findings suggest that lower airways of preterm and term infants represent distinct ecosystems with differential selective pressures upon bacterial colonization. In term infants, the matched increased expression of genes linked to the IgA pathway and the predicted increased expression of microbial genes to combat IgA is highly suggestive of a crosstalk between the airway microbiota and the immune system. When interpreting the findings, one must bear in mind that intubation yielding endotracheal aspirates is performed in sick children, either transiently in elective surgery or for longer time periods in prematurely born infants. Infants may necessitate elective surgery for illnesses unrelated to respiratory health, such as fractures or malformations, or for potentially related diseases such as enlarged adenoids. Intubated preterm infants born at low gestational ages (weeks 25–29), such as the infants included in this study, often suffer from numerous conditions. The most immediate problem is the neonatal respiratory distress syndrome (NRDS), which arises at or shortly after birth and affects more than 75% of neonates born before 29 weeks of gestation (Hiles et al., 2017). NRDS is caused by physiological and structural pulmonary immaturity with insufficient levels of pulmonary surfactant, which compromises alveolar integrity and hampers normal gas exchange. NRDS is treated with surfactant replacement and respiratory support. Long-term ventilator support
will in turn often result in chronic lung disease and bronchopulmonary dysplasia. Moreover, preterm neonates are at risk of life-threatening bacterial infections such as septicaemia and necrotizing enterocolitis, which necessitate highdose and often prolonged intravenous antibiotic treatment. It is therefore not surprising that gestational age and thereby the distinction between preterm and term infants divided the microbial compositional structure of the lower airway samples into distinct preterm and term clusters. Within the preterm, but not term, population, delivery mode mattered, which might be attributable to neonatal intensive care environments where disinfection is routine, thereby potentially hampering further postnatal colonization. The lack of further follow up of enrolled infants limits the ability to understand the role of the identified microbial clusters and related functions for development of disease. However, this is the first study to give us insight into the early-life formation of the immunological and microbial environment of the human lower airways, a period in life that is equally critical for further maturation or dysregulation of the human microbiome and immune responses, respectively. The findings suggest an intimate crosstalk between the microbiome and the immune response at mucosal surfaces, which pertain to the IgA pathway as early as in the first year of life.
Massachusetts Medical Society for serving as a member of the editorial board at the New England Journal of Medicine. REFERENCES Eyerich, K., Brown, S.J., Perez White, B.E., Tanaka, R.J., Bissonette, R., Dhar, S., Bieber, T., Hijnen, D.J., Guttman-Yassky, E., Irvine, A., et al. (2018). Human and computational models of atopic dermatitis: a review and perspectives by an expert panel of the International Eczema Council. J. Allergy Clin. Immunol. S0091-6749(18) 31573-2. Gilbert, J.A., Blaser, M.J., Caporaso, J.G., Jansson, J.K., Lynch, S.V., and Knight, R. (2018). Current understanding of the human microbiome. Nat. Med. 24, 392–400. Hakansson, A.P., Orihuela, C.J., and Bogaert, D. (2018). Bacterial-host interactions: physiology and pathophysiology of respiratory infection. Physiol. Rev. 98, 781–811. Hasleton, P.S. (1972). The internal surface area of the adult human lung. J. Anat. 112, 391–400. €ndriks, L. (2014). Surface Helander, H.F., and Fa area of the digestive tract - revisited. Scand. J. Gastroenterol. 49, 681–689. Hiles, M., Culpan, A.M., Watts, C., Munyombwe, T., and Wolstenhulme, S. (2017). Neonatal respiratory distress syndrome: chest X-ray or lung ultrasound? A systematic review. Ultrasound 25, 80–91. Panzer, A.R., Lynch, S.V., Langelier, C., Christie, J.D., McCauley, K., Nelson, M., Cheung, C.K., Benowitz, N.L., Cohen, M.J., and Calfee, C.S. (2018). Lung microbiota is related to smoking status and to development of acute respiratory distress syndrome in critically ill trauma patients. Am. J. Respir. Crit. Care Med. 197, 621–631.
DECLARATION OF INTERESTS
Pattaroni, C., Watzenboeck, M.L., Schneidegger, S., Kieser, S., Wong, N.C., Bernasconi, E., Pernot, J., Mercier, L., Knapp, S., Nicod, L.P., et al. (2018). Early-life formation of the microbial and immunological environment of human airways. Cell Host Microb 24, this issue, 857–865.
Dr. von Mutius received fees for serving as an Advisory Board member from OM Pharma SA and University of Utrecht, as well as speaker fees from Boehringer Ingelheim International GmbH. Also, she has been receiving honoraria from
Wu, H., Kuzmenko, A., Wan, S., Schaffer, L., Weiss, A., Fisher, J.H., Kim, K.S., and McCormack, F.X. (2003). Surfactant proteins A and D inhibit the growth of Gram-negative bacteria by increasing membrane permeability. J. Clin. Invest. 111, 1589– 1602.
Cell Host & Microbe 24, December 12, 2018 759
In Translation Intimate Crosstalk in Lower Airways at the Beginning of Life Erika von Mutius1,2,3,* 1Dr.
von Hauner Children’s Hospital, Ludwig Maximilian University, Munich, Germany for Asthma and Allergy Prevention, Helmholtz Centre, Munich, Germany 3Member of the German Center for Lung Research, Munich, Germany *Correspondence: [email protected] https://doi.org/10.1016/j.chom.2018.11.014 2Institute
The early life formation of the immunological and microbial environment of the human lower airways remains unknown. In this issue of Cell Host & Microbe, Pattaroni et al. (2018) shed light on this critical period, which is important for maturation or dysregulation of the microbiome and immune responses and disease development. The role of the microbiome for human health and disease is a matter of intense research and debate. Investigators address this fundamental question with a variety of approaches: experimental studies in animals, mostly mice, under pathogen- and germ-free conditions; 16S rRNA-based and metagenomic sequencing of human samples; and culture-based approaches and mathematical modeling to question and mirror the intricate interplay of microbial communities and the host’s response. For human studies, the accessibility of the diseased organ is of key importance. In skin diseases such as atopic dermatitis, the compositional structure and metabolic function of the skin microbiome, its external and internal determinants, and its crosstalk with the host’s local and systemic immune responses can be studied by means of skin swabs and biopsies in lesional and non-affected areas (Eyerich et al., 2018). For the gut microbiome, which has been proposed to play a key role for the development of intestinal, behavioral, neurological, and respiratory conditions, fecal samples can be collected with relative ease, even if they will not fully reflect microbial processes in more upstream parts of the digestive tract and at mucosal surfaces (Gilbert et al., 2018). The upper respiratory tract is accessible even in young infants, where maturation of the nasopharyngeal microbiome has been elegantly shown to determine the risk of viral infections (Hakansson et al., 2018). Yet, the study of the lower respiratory tract microbiome is a challenging endeavor. The human respiratory tract is a spatially complex branching ecosystem
where, in adults, airways divide at least 23 times, yielding an alveolar surface area that is 30 times that of the skin and about double that of the gastrointestinal tract (Hasleton, 1972; Helander and €ndriks, 2014). The healthy respiratory Fa tract is a low-nutrient environment for microbes that is lined by a thin and selectively bacteriostatic layer of lipid-rich surfactant, which prevents collapse (Wu et al., 2003). Many studies in adults have relied on specimen collected during bronchoscopies by either bronchoalveolar lavage, brushings, or biopsies, in which the procedure can be performed under local anesthesia. Children do not tolerate such intervention, and therefore, pediatric bronchoscopies necessitate general anesthesia, which is ethically not justifiable in healthy children. To obtain spontaneous and induced sputum, expectorations is an alternative non-invasive route to collect lower respiratory tract specimen, but preschool children do not cough up expectorations but rather swallow them. Therefore, an ethically acceptable means of studying the lower respiratory tract microbiome is the use of endotracheal aspirates via suctioning a patient’s endotracheal tube. This approach has yielded interesting results in the study of the dynamics of respiratory microbiota in critically ill adult patients (Panzer et al., 2018). Pattaroni and colleagues have applied this method to very young children (Pattaroni et al., 2018). They present the findings of their comprehensive study aiming at identifying the early-life bacterial colonization pattern of the lower airways in relation to the maturating im-
758 Cell Host & Microbe 24, December 12, 2018 ª 2018 Elsevier Inc.
mune system early in life in this issue of Cell Host & Microbe. Pattaroni et al. (2018) studied more than 40 infants aged 1 day to 1 year, about half of them undergoing endotracheal intubation for elective surgery and 60% being preterm infants. About two-thirds were studied in the neonatal period within 28 days of birth. Three microbiota profiles were identified. The first two clusters were dominated by either Staphylococcus or Ureaplasma genera, while the third cluster exhibited a balanced composition, including Streptococcus, Neisseria, Prevotella, Porphyromonas, Veillonella, and Fusobacteria genera. The highest diversity (Shannon Index) was observed in samples of the mixed cluster but did not differ between the Staphylococcus and Ureaplasma clusters. All three clusters were detected within the 3 first postnatal days. The Ureaplasma and Staphylococcus clusters were absent in infants older than 7 weeks postnatal age, whereas the mixed cluster was detectable in samples from infants across the whole first year of life. Gestational age had the strongest effect on microbiota composition: none of the samples collected from infants born before 30 weeks of gestational age were in the mixed cluster. Delivery mode significantly contributed to 28% of the variance in the preterm model but had no effect in the term population. To evaluate the impact of these microbial communities on the host, their virulence potential was evaluated via the PICRUSt algorithm. IgA protease activity was among the most increased virulence functions in samples from term children. This correlated with a significant
Cell Host & Microbe
In Translation enrichment in the IgA production pathway by gestational age when analyzing the infant’s own gene expression data in a subset of 16 subjects with additional host transcriptomic data. These findings suggest that lower airways of preterm and term infants represent distinct ecosystems with differential selective pressures upon bacterial colonization. In term infants, the matched increased expression of genes linked to the IgA pathway and the predicted increased expression of microbial genes to combat IgA is highly suggestive of a crosstalk between the airway microbiota and the immune system. When interpreting the findings, one must bear in mind that intubation yielding endotracheal aspirates is performed in sick children, either transiently in elective surgery or for longer time periods in prematurely born infants. Infants may necessitate elective surgery for illnesses unrelated to respiratory health, such as fractures or malformations, or for potentially related diseases such as enlarged adenoids. Intubated preterm infants born at low gestational ages (weeks 25–29), such as the infants included in this study, often suffer from numerous conditions. The most immediate problem is the neonatal respiratory distress syndrome (NRDS), which arises at or shortly after birth and affects more than 75% of neonates born before 29 weeks of gestation (Hiles et al., 2017). NRDS is caused by physiological and structural pulmonary immaturity with insufficient levels of pulmonary surfactant, which compromises alveolar integrity and hampers normal gas exchange. NRDS is treated with surfactant replacement and respiratory support. Long-term ventilator support
will in turn often result in chronic lung disease and bronchopulmonary dysplasia. Moreover, preterm neonates are at risk of life-threatening bacterial infections such as septicaemia and necrotizing enterocolitis, which necessitate highdose and often prolonged intravenous antibiotic treatment. It is therefore not surprising that gestational age and thereby the distinction between preterm and term infants divided the microbial compositional structure of the lower airway samples into distinct preterm and term clusters. Within the preterm, but not term, population, delivery mode mattered, which might be attributable to neonatal intensive care environments where disinfection is routine, thereby potentially hampering further postnatal colonization. The lack of further follow up of enrolled infants limits the ability to understand the role of the identified microbial clusters and related functions for development of disease. However, this is the first study to give us insight into the early-life formation of the immunological and microbial environment of the human lower airways, a period in life that is equally critical for further maturation or dysregulation of the human microbiome and immune responses, respectively. The findings suggest an intimate crosstalk between the microbiome and the immune response at mucosal surfaces, which pertain to the IgA pathway as early as in the first year of life.
Massachusetts Medical Society for serving as a member of the editorial board at the New England Journal of Medicine. REFERENCES Eyerich, K., Brown, S.J., Perez White, B.E., Tanaka, R.J., Bissonette, R., Dhar, S., Bieber, T., Hijnen, D.J., Guttman-Yassky, E., Irvine, A., et al. (2018). Human and computational models of atopic dermatitis: a review and perspectives by an expert panel of the International Eczema Council. J. Allergy Clin. Immunol. S0091-6749(18) 31573-2. Gilbert, J.A., Blaser, M.J., Caporaso, J.G., Jansson, J.K., Lynch, S.V., and Knight, R. (2018). Current understanding of the human microbiome. Nat. Med. 24, 392–400. Hakansson, A.P., Orihuela, C.J., and Bogaert, D. (2018). Bacterial-host interactions: physiology and pathophysiology of respiratory infection. Physiol. Rev. 98, 781–811. Hasleton, P.S. (1972). The internal surface area of the adult human lung. J. Anat. 112, 391–400. €ndriks, L. (2014). Surface Helander, H.F., and Fa area of the digestive tract - revisited. Scand. J. Gastroenterol. 49, 681–689. Hiles, M., Culpan, A.M., Watts, C., Munyombwe, T., and Wolstenhulme, S. (2017). Neonatal respiratory distress syndrome: chest X-ray or lung ultrasound? A systematic review. Ultrasound 25, 80–91. Panzer, A.R., Lynch, S.V., Langelier, C., Christie, J.D., McCauley, K., Nelson, M., Cheung, C.K., Benowitz, N.L., Cohen, M.J., and Calfee, C.S. (2018). Lung microbiota is related to smoking status and to development of acute respiratory distress syndrome in critically ill trauma patients. Am. J. Respir. Crit. Care Med. 197, 621–631.
DECLARATION OF INTERESTS
Pattaroni, C., Watzenboeck, M.L., Schneidegger, S., Kieser, S., Wong, N.C., Bernasconi, E., Pernot, J., Mercier, L., Knapp, S., Nicod, L.P., et al. (2018). Early-life formation of the microbial and immunological environment of human airways. Cell Host Microb 24, this issue, 857–865.
Dr. von Mutius received fees for serving as an Advisory Board member from OM Pharma SA and University of Utrecht, as well as speaker fees from Boehringer Ingelheim International GmbH. Also, she has been receiving honoraria from
Wu, H., Kuzmenko, A., Wan, S., Schaffer, L., Weiss, A., Fisher, J.H., Kim, K.S., and McCormack, F.X. (2003). Surfactant proteins A and D inhibit the growth of Gram-negative bacteria by increasing membrane permeability. J. Clin. Invest. 111, 1589– 1602.
Cell Host & Microbe 24, December 12, 2018 759