Common Lung Microbiome Identified among Mechanically Ventilated Surgical Patients

Smith, Ashley D.; Zhang, Yan; Barber, Robert C.; Minshall, Christian T.; Huebinger, Ryan M.; Allen, Michael S.

doi:10.1371/journal.pone.0166313

Cited by 12 publications

(16 citation statements)

References 31 publications

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“…The bacterium Ruegeria pomeroyi is more abundant in corals with white patch syndrome or skeletal growth anomalies than in healthy corals (Sere et al, 2013 ; Li et al, 2015 ). The genus Thauera , of the class Betaproteobacteria , has been detected in sediments, sludge, soils, and wastewater treatment plants (Liu et al, 2013 ), and it has been recently reported in research on human (Smith et al, 2016 ; Xu et al, 2017 ). Xu et al ( 2017 ) observed that Thauera was significantly more abundant in individuals with substance use disorders than in healthy individuals.…”

Section: Discussionmentioning

confidence: 99%

Dietary l-arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut Microbiota in Broiler Chickens Challenged by Clostridium perfringens

Zhang

et al. 2018

Front. Microbiol.

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Our previous reports suggested that Dietary l-arginine supplementation attenuated gut injury of broiler chickens infected with Clostridium perfringens by enhancing intestinal immune responses, absorption and barrier function, but its effect on the gut microbiome of broiler chickens remains unclear. This experiment aimed at evaluating the effects of Dietary l-arginine supplementation on the gut bacterial community composition and function of broiler chickens challenged with C. perfringens. In total, 105 1-day-old male Arbor Acres broiler chickens were assigned to three groups: Control (CTL), C. perfringens-challenged (CP), and C. perfringens-challenged and fed diet supplemented with 0.3% l-arginine (ARGCP) groups. The challenge led to macroscopic and histomorphological gut lesions, decreased villus height and increased the number of Observed species, Shannon, Chao1 and ACE indices of ileal microbiota, whereas l-arginine addition reversed these changes. Moreover, the three treatments harbored distinct microbial communities (ANOSIM, P < 0.05). At the genus level, 24 taxa (e.g., Nitrosomonas spp., Coxiella spp., Ruegeria spp., and Thauera spp.) were significantly more abundant in CP group than in CTL group (P < 0.05), whereas the levels of 23 genera of them were significantly decreased by l-arginine supplementation (P < 0.05). The abundances of only 3 genera were different between CTL and ARGCP groups (P < 0.05). At the species level, the challenge promoted the relative abundance of Nitrospira sp. enrichment culture clone M1-9, Bradyrhizobium elkanii, Nitrospira bacterium SG8-3, and Pseudomonas veronii, which was reversed by l-arginine supplementation (P < 0.05). Furthermore, the challenge decreased the levels of Lactobacillus gasseri (P < 0.05). Predictive functional profiling of microbial communities by PICRUSt showed that compared with CP group, ARGCP group had enriched pathways relating to membrane transport, replication and repair, translation and nucleotide metabolism and suppressed functions corresponding to amino acid and lipid metabolisms (P < 0.05). The relative abundances of KEGG pathways in l-arginine-fed broilers were almost equal to those of the controls. In conclusion, l-arginine alleviated the gut injury and normalized the ileal microbiota of C. perfringens-challenged chickens to resemble that of unchallenged controls in terms of microbial composition and functionality.

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Section: Discussionmentioning

confidence: 99%

Dietary l-arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut Microbiota in Broiler Chickens Challenged by Clostridium perfringens

Zhang

et al. 2018

Front. Microbiol.

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“…Characteristics of each sample group regarding age, gender, prior antibiotic administration, reason for BAL, and days post injury for BAL collection are listed in Table 1 . Sequence analysis of 6 of the C- samples were previously reported in Smith et al [ 24 ]. Samples were selected sequentially based upon the diagnosis of the pathology laboratory.…”

Section: Resultsmentioning

confidence: 99%

“…As described previously [ 24 ], upon collection, a portion of the raw BAL fluid was retained for research analysis and stored in a polypropylene tube at 4°C. The remaining BAL fluid was submitted to the Parkland Memorial Hospital Clinical Pathology Laboratory for microbiological identification as part of the standard of care.…”

Section: Methodsmentioning

confidence: 99%

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Variations of the lung microbiome and immune response in mechanically ventilated surgical patients

et al. 2018

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Mechanically ventilated surgical patients have a variety of bacterial flora that are often undetectable by traditional culture methods. The source of infection in many of these patients remains unclear. To address this clinical problem, the microbiome profile and host inflammatory response in bronchoalveolar lavage samples from the surgical intensive care unit were examined relative to clinical pathology diagnoses. The hypothesis was tested that clinical diagnosis of respiratory tract flora were similar to culture positive lavage samples in both microbiome and inflammatory profile. Bronchoalveolar lavage samples were collected in the surgical intensive care unit as standard of care for intubated individuals with a clinical pulmonary infection score of >6 or who were expected to be intubated for >48 hours. Cytokine analysis was conducted with the Bioplex Pro Human Th17 cytokine panel. The microbiome of the samples was sequenced for the 16S rRNA region using the Ion Torrent. Microbiome diversity analysis showed the culture-positive samples had the lowest levels of diversity and culture negative with the highest based upon the Shannon-Wiener index (culture positive: 0.77 ± 0.36, respiratory tract flora: 2.06 ± 0.73, culture negative: 3.97 ± 0.65). Culture-negative samples were not dominated by a single bacterial genera. Lavages classified as respiratory tract flora were more similar to the culture-positive in the microbiome profile. A comparison of cytokine expression between groups showed increased levels of cytokines (IFN-g, IL-17F, IL-1B, IL-31, TNF-a) in culture-positive and respiratory tract flora groups. Culture-positive samples exhibited a more robust immune response and reduced diversity of bacterial genera. Lower cytokine levels in culture-negative samples, despite a greater number of bacterial species, suggest a resident nonpathogenic bacterial community may be indicative of a normal pulmonary environment. Respiratory tract flora samples were most similar to the culture-positive samples and may warrant classification as culture-positive when considering clinical treatment.

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“…Trying to identify the best methodology, we believed it was crucial to use different comparators or positive controls: an internal bacterial positive control (mock population) and conventional microbiology. Because many studies did not do so, it seems hard to interpret the results of many studies revealing bacterial genus or species which are usually not identi ed in respiratory samples [32] [33]. It is thereby impossible to determine which methodology or primer set give the most reliable results.…”

Section: Discussionmentioning

confidence: 99%

16s rRNA Lung Microbiota Study in Mechanically Ventilated Patient: A Pilot Study

Fromentin¹,

Bridier‐Nahmias²,

LeGoff³

et al. 2020

Preprint

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BackgroundCharacterization of the respiratory tract bacterial microbiota is in its infancy when compared to the gut microbiota knowledge. As key methodological steps can directly affect the accuracy of the results, it is crucial to determine a robust methodology in order to limit bias.Two different pairs of primers 515F-806R targeting the V4 hypervariable region of the 16SrRNA gene, “S-V4” for “Stringent V4” primer pair and “R-V4” for “Relaxed V4” primer pair, are respectively used in two ongoing international projects “the Human microbiome project” and “the Earth microbiome project”. We compared two methods of sample processing using these two different primer pairs for bacterial microbiota analyses of respiratory samples from critically-ill ventilated patients. For the later, Illumina 250 paired-end sequencing was done on a MiSeq platform after DNA extraction using mechanical lysis (bead-beating) and NucliSENS easyMAG. The concordance with conventional microbiology is the criterion of choice to determine the optimal method.ResultsTwenty samples from seven patients and four controls were sequenced. The two primer pair provided highly different results. Only 54% of the samples had a similar microbial composition with both pairs of primers. “S-V4” gave the best agreement with the conventional microbiology for ETA: 89% as compared to 44% for the “R-V4” primer pair. The main difference related to Enterobacteriaceae, which were concordant between conventional cultures and microbiota analyses using “S-V4”. Enterobacteriaceae detection was poor for “R-V4”. Among patients with VAP, a decrease in alpha diversity in ETA was observed. The mean of pairwise Unifrac distance was higher inside this group of patients at the time of VAP diagnosis as compared to control patients.ConclusionAccuracy of the bacterial lung microbiota composition was highly correlated to the pair of primers used for amplification of the 16s rRNA hypervariable sequence. Comparison of microbiota results obtained by sequencing and conventional microbiology allowed us to select the best option for further studies. This work validates our methodology based on 16SrRNA gene amplification with 515F-806R “S-V4” primer pair associated to Illumina® MiSeq 250 paired-end sequencing.

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Common Lung Microbiome Identified among Mechanically Ventilated Surgical Patients

Cited by 12 publications

References 31 publications

Dietary l-arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut Microbiota in Broiler Chickens Challenged by Clostridium perfringens

Dietary l-arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut Microbiota in Broiler Chickens Challenged by Clostridium perfringens

Variations of the lung microbiome and immune response in mechanically ventilated surgical patients

16s rRNA Lung Microbiota Study in Mechanically Ventilated Patient: A Pilot Study

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Common Lung Microbiome Identified among Mechanically Ventilated Surgical Patients

Cited by 12 publications

References 31 publications

Dietary l-arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut Microbiota in Broiler Chickens Challenged by Clostridium perfringens

Dietary l-arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut Microbiota in Broiler Chickens Challenged by Clostridium perfringens

Variations of the lung microbiome and immune response in mechanically ventilated surgical patients

16s rRNA&nbsp;Lung Microbiota Study in Mechanically Ventilated Patient: A Pilot Study

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16s rRNA Lung Microbiota Study in Mechanically Ventilated Patient: A Pilot Study