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

Bassis, Christine M.; Erb-Downward, John R.; Dickson, Robert P.; Freeman, Christine M.; Schmidt, Thomas M.; Young, Vincent B.; Beck, James M.; Curtis, Jeffrey L.; Huffnagle, Gary B.

doi:10.1128/mbio.00037-15

Cited by 629 publications

(652 citation statements)

References 45 publications

(82 reference statements)

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“…A culture-based study in healthy adults supports this finding, as the bronchial fraction had a greater diversity and higher concentrations of normal respiratory flora than the alveolar fraction (Rasmussen et al, 2001). In a second microbiome study, sequential BAL specimens were obtained from two lobes, with no significant difference in bacterial community composition, and the authors concluded that sampling of the lungs by bronchoscopy was not confounded by oral microbiome contamination (Bassis et al, 2015). In our study, generally more bacteria were recovered from the first lavage when measured by proportions with lower-airway infection or mean growth scores.…”

supporting

confidence: 56%

“…ml 21 ), suggesting colonization of the lower airways rather than contamination. The healthy lung is no longer considered to be sterile, with evidence suggesting it may harbour its own unique microbiome (Bassis et al, 2015;Charlson et al, 2011). Bacterial communities from the healthy lung largely reflect upper respiratory tract (URT) organisms, in particular from the oral rather than the nasal cavity, with Streptococcus being among the prominent genera (Bassis et al, 2015;Charlson et al, 2011).…”

mentioning

confidence: 99%

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Respiratory bacterial culture from two sequential bronchoalveolar lavages of the same lobe in children with chronic cough

Hare

Marsh

Smith‐Vaughan

et al. 2015

Journal of Medical Microbiology

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Identification of bacteria causing lower-airway infections is important to determine appropriate antimicrobial therapy. Flexible bronchoscopy with bronchoalveolar lavage (BAL) is used to obtain lower-airway specimens in young children. The first lavage (lavage-1) is typically used for bacterial culture. However, no studies in children have compared the detection of cultivable bacteria from sequential lavages of the same lobe. BAL fluid was collected from two sequential lavages of the same lobe in 79 children enrolled in our prospective studies of chronic cough. The respiratory bacteria Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus and Haemophilus parainfluenzae were isolated and identified using standard published methods. H. influenzae was differentiated from Haemophilus haemolyticus using PCR assays. Lower-airway infection was defined as $10 4 c.f.u. ml 21 BAL fluid. We compared cultivable bacteria from lavage-1 with those from the second lavage (lavage-2) using the k statistic. Lower-airway infections by any pathogen were detected in 46 % of first lavages and 39 % of second lavages. Detection was similar in both lavages for all pathogens; the k statistic was 0.7-0.8 for all bacteria except H. parainfluenzae. Of all infections detected in either lavage, 90 % were detected in lavage-1 and 78 % in lavage-2. However, culture of lavage-2 identified infections that would have been missed in 8 % of children, including infections by additional Streptococcus pneumoniae serotypes. Our findings support the continued use of lavage-1 for bacterial culture; however, culture of lavage-2 may yield additional identifications of bacterial pathogens in lower-airway infections.

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supporting

confidence: 56%

mentioning

confidence: 99%

Respiratory bacterial culture from two sequential bronchoalveolar lavages of the same lobe in children with chronic cough

Hare

Marsh

Smith‐Vaughan

et al. 2015

Journal of Medical Microbiology

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“…The microbiome harbored by the bronchial tree and the oropharynx have a close similarity in the healthy subject, mainly due to aspiration of oropharyngeal secretions during sleep (8,9). The local environment of the bronchial tree and the lung is able to modify the microbiome after the aspiration of secretions, however, as shown by the higher relative abundance of specific OTUs part of the Prevotella genus in respiratory samples (9).…”

Section: The Respiratory Microbiomementioning

confidence: 99%

Microbiome in chronic obstructive pulmonary disease

Monsó¹

2017

Ann. Transl. Med.

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The introduction of culture-independent techniques for the microbiological analysis of respiratory samples has confirmed that the respiratory system hosts a large number of microorganisms, which include a wide range of bacteria. The regular exposure to tobacco smoke changes the microbiome in healthy smokers, first in the oropharynx, increasing the presence of a restricted number of genera which attain high relative abundance, a pattern that may be considered as dysbiosis. In chronic obstructive pulmonary disease (COPD), microbiome analyses of sputum samples have demonstrated an important decline in bacterial diversity, with a change to a restricted flora with an overrepresentation of the Proteobacteria phylum, which include most of the bacteria commonly considered as potentially pathogenic microorganisms, paralleled by a decline in the relative abundance of microorganisms part of the Firmicutes phylum. In exacerbations, specific bacteria overrepresented in microbiome analyses and potentially causal of the acute episode may not be recovered by sputum culture, while colonizing microorganisms grow easily, in spite that their relative abundance have not changed from previous stability. This situation has been described in patients showing chronic colonization by Pseudomonas aeruginosa, who suffer from exacerbations that in most cases are due to other PPMs, in spite of the persistence of positive cultures for the colonizing Pseudomonas strains.Interaction between different microorganisms can be addressed through microbiome analyses, and functional metagenomics, that describes the genomic potential of the community, has shown that, in spite that the bronchial microbiome as a whole may not change significantly, clear changes in carbohydrate metabolism, cancer, cell growth and death, transport and catabolism pathways often appear during exacerbations. These functional changes may be important because through them the resident community as a whole show its power to modify important metabolic patterns.

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“…While for decades we could rest assured that the only microbially colonised niches seemed to be our digestive system and the skin, there is now hardly any part of our bodies indeed not inhabited by microbes. This includes nasal and auditory cavities, hair follicles and sweat glands, the respiratory and the urogenital tract systems and might even include dormant remainders of infections circulating in our blood system (Bassis et al 2015;Callewaert et al 2014;Costello et al 2009;Potgieter et al 2015;Thomas-White et al 2016). In short, apparently anything that can be reached and attached to in the human body becomes colonised by bacteria.…”

mentioning

confidence: 99%