No studies have examined the relationships between bacterial communities along sites of the upper aerodigestive tract of an individual subject. Our objective was to perform an intrasubject and intersite analysis to determine the contributions of two upper mucosal sites (mouth and nose) as source communities for the bacterial microbiome of lower sites (lungs and stom- ach). Oral wash, bronchoalveolar lavage (BAL)fluid, nasal swab, and gastric aspirate samples were collected from 28 healthy subjects. Extensive analysis of controls and serial intrasubject BALfluid samples demonstrated that sampling of the lungs by bronchoscopy was not confounded by oral microbiome contamination. By quantitative PCR, the oral cavity and stomach con- tained the highest bacterial signal levels and the nasal cavity and lungs contained much lower levels. Pyrosequencing of 16S rRNA gene amplicon libraries generated from these samples showed that the oral and gastric compartments had the greatest species richness, which was significantly greater in both than the richness measured in the lungs and nasal cavity. The bacterial communities of the lungs were significantly different from those of the mouth, nose, and stomach, while the greatest similarity was between the oral and gastric communities. However, the bacterial communities of healthy lungs shared significant member- ship with the mouth, but not the nose, and marked subject-subject variation was noted. In summary, microbial immigration from the oral cavity appears to be the significant source of the lung microbiome during health, but unlike the stomach, the lungs exhibit evidence of selective elimination of Prevotellabacteria derived from the upper airways. IMPORTANCE We have demonstrated that the bacterial communities of the healthy lung overlapped those found in the mouth but were found at lower concentrations, with lower membership and a different community composition. The nasal microbiome, which was distinct from the oral microbiome, appeared to contribute little to the composition of the lung microbiome in healthy subjects. Our studies of the nasal, oral, lung, and stomach microbiomes within an individual illustrate the microbiological conti- nuity of the aerodigestive tract in healthy adults and provide culture-independent microbiological support for the concept that microaspiration is common in healthy individuals.

Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals

Although the notion that “the normal lung is free from bacteria” remains common in textbooks, it is virtually always stated without citation or argument. The lungs are constantly exposed to diverse communities of microbes from the oropharynx and other sources, and over the past decade, novel culture-independent techniques of microbial identification have revealed that the lungs, previously considered sterile in health, harbor diverse communities of microbes. In this review, we describe the topography and population dynamics of the respiratory tract, both in health and as altered by acute and chronic lung disease. We provide a survey of current techniques of sampling, sequencing, and analysis of respiratory microbiota and review technical challenges and controversies in the field. We review and synthesize what is known about lung microbiota in various diseases and identify key lessons learned across disease states.

/pdf/the-microbiome-and-the-respiratory-tract-1m3z2yp28b.pdf

The Microbiome and the Respiratory Tract

### 1.1 Background

Patients with cough frequently present to clinicians working in both primary and secondary care.1,2 Acute cough, which often follows an upper respiratory tract infection, may be initially disruptive but is usually self-limiting and rarely needs significant medical intervention. Chronic cough is often the key symptom of many important chronic respiratory diseases but may be the sole presenting feature of a number of extrapulmonary conditions, in particular upper airway and gastrointestinal disease. Even with a clear diagnosis, cough can be difficult to control and, for the patient, can be associated with impaired quality of life.3,4 Sessions dedicated to cough at respiratory meetings are popular, suggesting that the pathophysiology, evaluation, and successful treatment of cough remain topics of keen interest to many medical practitioners.

### 1.2 Need and purpose of BTS recommendations on the management of cough

The American College of Chest Physicians (ACCP) and the European Respiratory Society (ERS)5,6 have each endorsed their own set of guidelines on the management of cough; however, criticism7 of their content and breadth suggest the need for further concise recommendations. The British Thoracic Society guidelines cover not only chronic cough but also acute cough and the organisational issues of cough clinics. International differences in delivery of respiratory health care and management strategies support the notion that such guidelines would be desirable. The British Thoracic Society Standards of Care Committee agreed to the development of a Working Group tasked with the job of producing a set of guidelines for the management of cough with the following key objectives:

https://thorax.bmj.com/content/thoraxjnl/61/suppl_1/i1.full.pdf

Recommendations for the management of cough in adults

Fig. 1.— 
Overview of the evaluation of chronic cough in an adult. ACE-I: angiotensin converting enzyme inhibitor; PEF: peak expiratory flow; PNDS: post-nasal drip syndrome; GORD: gastro-oesophageal reflux disease.





Fig. 2.— 
Therapeutic algorithm. ACE: angiotensin-converting enzyme; GORD: gastro-oesophageal reflux disease.





Fig. 3.— 
Investigational algorithm. CT: computed tomography.





Fig. 4.— 
Diagnostic algorithm for the approach to children with chronic cough. ENT: ear, nose and throat; PFT: pulmonary function testing; BAL: bronchoalveolar lavage; CT: computed tomography; tbc: total blood count; CMV: cytomegalovirus; PCR: polymerase chain reaction; MRI: magnetic resonance imaging; NO: nitric oxide; BHR: bronchial hyperresponsiveness.





CONTENTS



Chronic cough, here defined as a cough of >8 weeks duration, is a common and frequently debilitating symptom 1, 2 that is often viewed as an intractable problem. However, theexperience of specialist cough clinics is that a very high success rate, in the order of 90%, can be achieved (table 1⇓) 3–15. The key to successful management is to establish a diagnosis and to treat the cause of cough. Truly idiopathic cough is rare and misdiagnosis common, particularly because of the failure to recognise that cough is often provoked from sites outside the airway. These guidelines aim to distil the lessons from these reports and provide a framework for a logical care pathway for patients with this highly disabling symptom.

View this table:

Table 1— 
Commonest causes of chronic cough in patients investigated in specialist clinics



There are three common causes of chronic cough that arise from three different anatomical areas. This varied presentation explains the major reason for the success of multidisciplinary cough clinics compared with general clinics 16. As asthma, reflux and rhinitis are the realms of different specialists who have little experience in the diagnosis of conditions outside their expertise, a patient with chronic cough may not undergo full evaluation. This problem is exacerbated by the frequently atypical presentation of …

https://erj.ersjournals.com/content/erj/24/3/481.full.pdf

The diagnosis and management of chronic cough

The principles of respiratory microbiology are being re-evaluated and re-written, starting with the debunked myth of lung sterility. The “terrain” of the respiratory ecosystem differs—anatomically and physiologically—from that of other mucosal sites, and changes dramatically in illness, when the dynamic homeostasis between host and microbiome is disrupted. Researchers are only just beginning to understand the contribution of viruses, phages, and fungi to the lung microbiome; thus, we have restricted our discussion to the bacterial microbiota of the lungs.

The Lung Microbiome: New Principles for Respiratory Bacteriology in Health and Disease.

A new multiparametric device (RBC-7) was used for recording cough in ambulatory children over a 24 hour period. The number of coughs and the pattern of coughing can easily be studied with the aid of a personal computer and dedicated computer software. Forty one 'normal' children were recorded, identified from a primary school with the aid of a questionnaire. They were free from any respiratory infection for one month, and had a normal examination and spirometry immediately before recording. Cough frequency was 11.3, range 1 to 34, cough episodes per 24 hours. This was unaffected by passive smoking or the presence of furry pets in the home. Nocturnal and prolonged coughing was unusual in these children. The device was highly acceptable to the children, and no adverse effects were reported. Such objective data on cough outside the laboratory setting are unique, help to determine what is normal, and may help in the diagnosis and assessment of many respiratory diseases.

https://adc.bmj.com/content/archdischild/74/6/531.full.pdf

A Bush

Papers

How much coughing is normal