1
|
Tejeda-Garibay S, Zhao L, Hum NR, Pimentel M, Diep AL, Amiri B, Sindi SS, Weilhammer DR, Loots GG, Hoyer KK. Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro. Microbiol Spectr 2024; 12:e0297823. [PMID: 38832766 PMCID: PMC11218535 DOI: 10.1128/spectrum.02978-23] [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: 07/31/2023] [Accepted: 03/19/2024] [Indexed: 06/05/2024] Open
Abstract
Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia, leading to inappropriate antibiotic treatment. The soil Bacillus subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides, while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2×GYE (GYE) and Columbia colistin and nalidixic acid with 5% sheep's blood agar inhibited the growth of Coccidioides, but microbiota grown on chocolate agar did not. Partial depletion of the microbiota through antibiotic disk diffusion revealed diminished inhibition and comparable growth of Coccidioides to controls. To characterize the bacteria grown and identify potential candidates contributing to the inhibition of Coccidioides, 16S rRNA sequencing was performed on tracheal and intestinal agar cultures and murine lung extracts. We found that the host bacteria likely responsible for this inhibition primarily included Lactobacillus and Staphylococcus. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo. IMPORTANCE Coccidioidomycosis is caused by a fungal pathogen that invades the host lungs, causing respiratory distress. In 2019, 20,003 cases of Valley fever were reported to the CDC. However, this number likely vastly underrepresents the true number of Valley fever cases, as many go undetected due to poor testing strategies and a lack of diagnostic models. Valley fever is also often misdiagnosed as bacterial pneumonia, resulting in 60%-80% of patients being treated with antibiotics prior to an accurate diagnosis. Misdiagnosis contributes to a growing problem of antibiotic resistance and antibiotic-induced microbiome dysbiosis; the implications for disease outcomes are currently unknown. About 5%-10% of symptomatic Valley fever patients develop chronic pulmonary disease. Valley fever causes a significant financial burden and a reduced quality of life. Little is known regarding what factors contribute to the development of chronic infections and treatments for the disease are limited.
Collapse
Affiliation(s)
- Susana Tejeda-Garibay
- Quantitative and Systems Biology, Graduate Program, University of California, Merced, Merced, California, USA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Lihong Zhao
- Department of Applied Mathematics, University of California, Merced, Merced, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
| | - Nicholas R. Hum
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Maria Pimentel
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, Merced, California, USA
| | - Anh L. Diep
- Quantitative and Systems Biology, Graduate Program, University of California, Merced, Merced, California, USA
| | - Beheshta Amiri
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Suzanne S. Sindi
- Department of Applied Mathematics, University of California, Merced, Merced, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
| | - Dina R. Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Gabriela G. Loots
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
- />Department of Orthopaedic Surgery, Lawrence J. Ellison Musculoskeletal Research Center, University of California Davis Health, Sacramento, California, USA
| | - Katrina K. Hoyer
- Quantitative and Systems Biology, Graduate Program, University of California, Merced, Merced, California, USA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, Merced, California, USA
| |
Collapse
|
2
|
Grassi L, Asfahl KL, Van den Bossche S, Maenhout I, Sass A, Vande Weygaerde Y, Van Braeckel E, Verhasselt B, Boelens J, Tunney MM, Dandekar AA, Coenye T, Crabbé A. Antibiofilm activity of Prevotella species from the cystic fibrosis lung microbiota against Pseudomonas aeruginosa. Biofilm 2024; 7:100206. [PMID: 38975276 PMCID: PMC11225020 DOI: 10.1016/j.bioflm.2024.100206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/06/2024] [Accepted: 06/06/2024] [Indexed: 07/09/2024] Open
Abstract
It is increasingly recognized that interspecies interactions may modulate the pathogenicity of Pseudomonas aeruginosa during chronic lung infections. Nevertheless, while the interaction between P. aeruginosa and pathogenic microorganisms co-infecting the lungs has been widely investigated, little is known about the influence of other members of the lung microbiota on the infection process. In this study, we focused on investigating the impact of Prevotella species isolated from the sputum of people with cystic fibrosis (pwCF) on biofilm formation and virulence factor production by P. aeruginosa. Screening of a representative collection of Prevotella species recovered from clinical samples showed that several members of this genus (8 out 10 isolates) were able to significantly reduce biofilm formation of P. aeruginosa PAO1, without impact on growth. Among the tested isolates, the strongest biofilm-inhibitory activity was observed for Prevotella intermedia and Prevotella nigrescens, which caused a reduction of up to 90% in the total biofilm biomass of several P. aeruginosa isolates from pwCF. In addition, a strain-specific effect of P. nigrescens on the ability of P. aeruginosa to produce proteases and pyocyanin was observed, with significant alterations in the levels of these virulence factors detected in LasR mutant strains. Overall, these results suggest that non-pathogenic bacteria from the lung microbiota may regulate pathogenicity traits of P. aeruginosa, and possibly affect the outcome of chronic lung infections.
Collapse
Affiliation(s)
- Lucia Grassi
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Kyle L. Asfahl
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | - Ine Maenhout
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Yannick Vande Weygaerde
- Cystic Fibrosis Reference Centre, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Eva Van Braeckel
- Cystic Fibrosis Reference Centre, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Paediatrics, Ghent University, Ghent, Belgium
| | - Bruno Verhasselt
- Laboratory of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jerina Boelens
- Laboratory of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Michael M. Tunney
- School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Ajai A. Dandekar
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
3
|
Tejeda-Garibay S, Zhao L, Hum NR, Pimentel M, Diep AL, Amiri B, Sindi SS, Weilhammer DR, Loots GG, Hoyer KK. Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563655. [PMID: 37961490 PMCID: PMC10634762 DOI: 10.1101/2023.10.23.563655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia leading to inappropriate antibiotic treatment. Soil bacteria B. subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2xGYE (GYE) and CNA w/ 5% sheep's blood agar (5%SB-CNA) inhibited the growth of Coccidioides, but that grown on chocolate agar does not. Partial depletion of the microbiota through antibiotic disk diffusion revealed that microbiota depletion leads to diminished inhibition and comparable growth of Coccidioides growth to controls. To characterize the bacteria grown and narrow down potential candidates contributing to the inhibition of Coccidioides, 16s rRNA sequencing of tracheal and intestinal agar cultures and murine lung extracts was performed. The identity of host bacteria that may be responsible for this inhibition was revealed. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo.
Collapse
Affiliation(s)
- Susana Tejeda-Garibay
- Quantitative and Systems Biology, Graduate Program, University of California Merced, CA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Lihong Zhao
- Department of Applied Mathematics, University of California, Merced, CA
- Health Sciences Research Institute, University of California Merced, Merced, CA
| | - Nicholas R Hum
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Maria Pimentel
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, CA
| | - Anh L Diep
- Quantitative and Systems Biology, Graduate Program, University of California Merced, CA
| | - Beheshta Amiri
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Suzanne S Sindi
- Department of Applied Mathematics, University of California, Merced, CA
- Health Sciences Research Institute, University of California Merced, Merced, CA
| | - Dina R Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Gabriela G Loots
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
- University of California Davis Health, Department of Orthopaedic Surgery, Lawrence J. Ellison Musculo-skeletal Research Center, 2700 Stockton Blvd, Sacramento, CA 95817, CA
| | - Katrina K Hoyer
- Quantitative and Systems Biology, Graduate Program, University of California Merced, CA
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, CA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
- Health Sciences Research Institute, University of California Merced, Merced, CA
| |
Collapse
|
4
|
Li S, Lian WH, Han JR, Ali M, Lin ZL, Liu YH, Li L, Zhang DY, Jiang XZ, Li WJ, Dong L. Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis. NPJ Biofilms Microbiomes 2023; 9:67. [PMID: 37736746 PMCID: PMC10516943 DOI: 10.1038/s41522-023-00439-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.
Collapse
Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
- School of Life Science, Jiaying University, Meizhou, 514015, China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Dong-Ya Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Xian-Zhi Jiang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
| |
Collapse
|
5
|
Kristensen M, de Koff EM, Chu ML, Groendijk S, Tramper-Stranders GA, de Winter-de Groot KM, Janssens HM, Tiddens HA, van Westreenen M, Sanders EAM, Arets BHGM, van der Ent CK, Prevaes SMPJ, Bogaert D. 16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients. Microbiol Spectr 2023; 11:e0405722. [PMID: 37199622 PMCID: PMC10269535 DOI: 10.1128/spectrum.04057-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
16S-based sequencing provides broader information on the respiratory microbial community than conventional culturing. However, it (often) lacks species- and strain-level information. To overcome this issue, we used 16S rRNA-based sequencing results from 246 nasopharyngeal samples obtained from 20 infants with cystic fibrosis (CF) and 43 healthy infants, which were all 0 to 6 months old, and compared them to both standard (blind) diagnostic culturing and a 16S-sequencing-informed "targeted" reculturing approach. Using routine culturing, we almost uniquely detected Moraxella catarrhalis, Staphylococcus aureus, and Haemophilus influenzae (42%, 38%, and 33% of samples, respectively). Using the targeted reculturing approach, we were able to reculture 47% of the top-5 operational taxonomical units (OTUs) in the sequencing profiles. In total, we identified 60 species from 30 genera with a median of 3 species per sample (range, 1 to 8). We also identified up to 10 species per identified genus. The success of reculturing the top-5 genera present from the sequencing profile depended on the genus. In the case of Corynebacterium being in the top 5, we recultured them in 79% of samples, whereas for Staphylococcus, this value was only 25%. The success of reculturing was also correlated with the relative abundance of those genera in the corresponding sequencing profile. In conclusion, revisiting samples using 16S-based sequencing profiles to guide a targeted culturing approach led to the detection of more potential pathogens per sample than conventional culturing and may therefore be useful in the identification and, consequently, treatment of bacteria considered relevant for the deterioration or exacerbation of disease in patients like those with CF. IMPORTANCE Early and effective treatment of pulmonary infections in cystic fibrosis is vital to prevent chronic lung damage. Although microbial diagnostics and treatment decisions are still based on conventional culture methods, research is gradually focusing more on microbiome and metagenomic-based approaches. This study compared the results of both methods and proposed a way to combine the best of both worlds. Many species can relatively easily be recultured based on the 16S-based sequencing profile, and it provides more in-depth information about the microbial composition of a sample than that obtained through routine (blind) diagnostic culturing. Still, well-known pathogens can be missed by both routine diagnostic culture methods as well as by targeted reculture methods, sometimes even when they are highly abundant, which may be a consequence of either sample storage conditions or antibiotic treatment at the time of sampling.
Collapse
Affiliation(s)
- Maartje Kristensen
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emma M. de Koff
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Mei Ling Chu
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Simone Groendijk
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Karin M. de Winter-de Groot
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hettie M. Janssens
- Department of Pediatric Pulmonology and Allergology, Sophia Children’s Hospital, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Harm A. Tiddens
- Department of Pediatric Pulmonology and Allergology, Sophia Children’s Hospital, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mireille van Westreenen
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elisabeth A. M. Sanders
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Bert H. G. M. Arets
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cornelis K. van der Ent
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sabine M. P. J. Prevaes
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Debby Bogaert
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
6
|
Thornton CS, Parkins MD. Microbial Epidemiology of the Cystic Fibrosis Airways: Past, Present, and Future. Semin Respir Crit Care Med 2023; 44:269-286. [PMID: 36623820 DOI: 10.1055/s-0042-1758732] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Progressive obstructive lung disease secondary to chronic airway infection, coupled with impaired host immunity, is the leading cause of morbidity and mortality in cystic fibrosis (CF). Classical pathogens found in the airways of persons with CF (pwCF) include Pseudomonas aeruginosa, Staphylococcus aureus, the Burkholderia cepacia complex, Achromobacter species, and Haemophilus influenzae. While traditional respiratory-tract surveillance culturing has focused on this limited range of pathogens, the use of both comprehensive culture and culture-independent molecular approaches have demonstrated complex highly personalized microbial communities. Loss of bacterial community diversity and richness, counteracted with relative increases in dominant taxa by traditional CF pathogens such as Burkholderia or Pseudomonas, have long been considered the hallmark of disease progression. Acquisition of these classic pathogens is viewed as a harbinger of advanced disease and postulated to be driven in part by recurrent and frequent antibiotic exposure driven by frequent acute pulmonary exacerbations. Recently, CF transmembrane conductance regulator (CFTR) modulators, small molecules designed to potentiate or restore diminished protein levels/function, have been successfully developed and have profoundly influenced disease course. Despite the multitude of clinical benefits, structural lung damage and consequent chronic airway infection persist in pwCF. In this article, we review the microbial epidemiology of pwCF, focus on our evolving understanding of these infections in the era of modulators, and identify future challenges in infection surveillance and clinical management.
Collapse
Affiliation(s)
- Christina S Thornton
- Department of Medicine, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Michael D Parkins
- Department of Medicine, Cumming School of Medicine, University of Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta, Canada
| |
Collapse
|
7
|
Gamal-AbdelNaser A, Mohammed WS, ElHefnawi M, AbdAllah M, Elsharkawy A, Zahran FM. The oral microbiome of treated and untreated chronic HCV infection: A preliminary study. Oral Dis 2023; 29:843-852. [PMID: 34396636 DOI: 10.1111/odi.14007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Chronic hepatitis C virus (HCV) infection is a debilitating disease that is lately treated using direct-acting antivirals (DAAs). Changes in the oral microbiome were detected in other liver diseases; however, oral microbiome was never investigated in patients having chronic HCV infection, whether pre- or post-treatment. MATERIALS AND METHODS This case-control preliminary study enrolled three equal groups: Group (I): untreated HCV patients; group (II): HCV patients who achieved viral clearance after DAA administration; and group (III): healthy controls. For each participant, a buccal swab was harvested and its 16S rRNA was sequenced. RESULTS The oral microbiome of chronic HCV patients had a significantly distinct bacterial community compared to healthy controls, characterized by high diversity and abundance of certain pathogenic species. These changes resemble that of oral lichen planus patients. After treatment by DAAs, the oral microbiome shifted to a community with partial similarity to both the diseased and the healthy ones. CONCLUSIONS Chronic HCV is associated with dysbiotic oral microbiome having abundant pathogenic bacteria. With HCV clearance by DAAs, the oral microbiome shifts to approach the healthy composition.
Collapse
Affiliation(s)
- Ayat Gamal-AbdelNaser
- Department of Oral Medicine and Periodontology, Faculty of Dentistry, Cairo University, Cairo, Egypt
| | - Waleed S Mohammed
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Mahmoud ElHefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics & Systems Department, National Research Centre, Giza, Egypt
| | - Mohamed AbdAllah
- Medical Research Division, National Research Centre, Giza, Egypt
| | - Aisha Elsharkawy
- Endemic Medicine and Hepatogastroentrology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Fat'heya M Zahran
- Department of Oral Medicine and Periodontology, Faculty of Dentistry, Cairo University, Cairo, Egypt
| |
Collapse
|
8
|
Stinson LF, Ma J, Sindi AS, Geddes DT. Methodological approaches for studying the human milk microbiome. Nutr Rev 2022; 81:705-715. [PMID: 36130405 DOI: 10.1093/nutrit/nuac082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human milk contains a low-biomass, low-diversity microbiome, consisting largely of bacteria. This community is of great research interest in the context of infant health and maternal and mammary health. However, this sample type presents many unique methodological challenges. In particular, there are numerous technical considerations relating to sample collection and storage, DNA extraction and sequencing, viability, and contamination. Failure to properly address these challenges may lead to distortion of bacterial DNA profiles generated from human milk samples, ultimately leading to spurious conclusions. Here, these technical challenges are discussed, and various methodological approaches used to address them are analyzed. Data were collected from studies in which a breadth of methodological approaches were used, and recommendations for robust and reproducible analysis of the human milk microbiome are proposed. Such methods will ensure high-quality data are produced in this field, ultimately supporting better research outcomes for mothers and infants.
Collapse
Affiliation(s)
- Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Jie Ma
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Azhar S Sindi
- Division of Obstetrics and Gynaecology, School of Medicine, The University of Western Australia, Perth, Australia.,is with the College of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Donna T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| |
Collapse
|
9
|
Thornton CS, Acosta N, Surette MG, Parkins MD. Exploring the Cystic Fibrosis Lung Microbiome: Making the Most of a Sticky Situation. J Pediatric Infect Dis Soc 2022; 11:S13-S22. [PMID: 36069903 PMCID: PMC9451016 DOI: 10.1093/jpids/piac036] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/16/2022] [Indexed: 01/02/2023]
Abstract
Chronic lower respiratory tract infections are a leading contributor to morbidity and mortality in persons with cystic fibrosis (pwCF). Traditional respiratory tract surveillance culturing has focused on a limited range of classic pathogens; however, comprehensive culture and culture-independent molecular approaches have demonstrated complex communities highly unique to each individual. Microbial community structure evolves through the lifetime of pwCF and is associated with baseline disease state and rates of disease progression including occurrence of pulmonary exacerbations. While molecular analysis of the airway microbiome has provided insight into these dynamics, challenges remain including discerning not only "who is there" but "what they are doing" in relation to disease progression. Moreover, the microbiome can be leveraged as a multi-modal biomarker for both disease activity and prognostication. In this article, we review our evolving understanding of the role these communities play in pwCF and identify challenges in translating microbiome data to clinical practice.
Collapse
Affiliation(s)
- Christina S Thornton
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA,Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada,Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Michael D Parkins
- Corresponding Author: Michael D. Parkins, MD, MSc, FRCPC, Associate Professor, Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada; Department of Medicine, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada; Snyder Institute for Chronic Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada. E-mail:
| |
Collapse
|
10
|
Culture-dependent evaluation of the respiratory microbiome in children with cystic fibrosis. EUREKA: HEALTH SCIENCES 2022. [DOI: 10.21303/2504-5679.2022.002568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The study aimed to assess the regional peculiarities of the respiratory profile of children with cystic fibrosis (CF) in the Dnipro region (Ukraine).
Methods. Children living in the Dnipro region and aged younger than 18 years old with molecular-genetic confirmation of CF were enrolled in the study. Lung colonization was evaluated using a culture-dependent method. Sputum, mucus from the posterior pharyngeal wall and bronchoalveolar lavage fluid (BALF) were utilized.
Results. The Firmicutes phylum was the most common and occupied 54.00 % of the general proportion. On the other hand, the Proteobacteria phylum demonstrated overexpression in CF airways and kept the second rank with 28.87 %.
Sorensen's species similarity coefficient showed an allied affinity between the microbial burden of oropharyngeal samples with nasopharyngeal and sputum, QS = 0.61 and 0.91, respectively. However, the species composition within the nasal cavity was distinct from sputum and BALF (QS=0.47).
The primary pathogens in childhood were S. aureus, H. influenza, P. aeruginosa and A. fumigatus. In contrast to gram-negative non-fermenters (GNNF), the prevalence of S. aureus isolates by age had a non-linear character. The commensal microbiota changed negatively with age. Among children under 12 years, the Streptococcus genus was identified in 23.08 % of the samples, but among the age category older than 15 – only in 9.22 %.
11.06 % of S. aureus had small colony variants (SCVs) morphotypes. Isolates of P. aeruginosa with the properties of SCVs were also found in children who underwent prolonged antimicrobial treatment. However, the most prominent was the mucoid phenotype – 34.31 % of isolates.
Conclusions. Along with conventional microbiological properties, obligate pathobionts in children with CF exhibited changes, resulting in difficulties in identification. These included auxotrophic modification into SCVs and mucoid transformation.
The culture-dependent technique gives crucial data about the profile of pathogens usually associated with CF, although it is sufficiently limited
Collapse
|
11
|
Constantino-Teles P, Jouault A, Touqui L, Saliba AM. Role of Host and Bacterial Lipids in Pseudomonas aeruginosa Respiratory Infections. Front Immunol 2022; 13:931027. [PMID: 35860265 PMCID: PMC9289105 DOI: 10.3389/fimmu.2022.931027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa is one of the most common agents of respiratory infections and has been associated with high morbidity and mortality rates. The ability of P. aeruginosa to cause severe respiratory infections results from the coordinated action of a variety of virulence factors that promote bacterial persistence in the lungs. Several of these P. aeruginosa virulence mechanisms are mediated by bacterial lipids, mainly lipopolysaccharide, rhamnolipid, and outer membrane vesicles. Other mechanisms arise from the activity of P. aeruginosa enzymes, particularly ExoU, phospholipase C, and lipoxygenase A, which modulate host lipid signaling pathways. Moreover, host phospholipases, such as cPLA2α and sPLA2, are also activated during the infectious process and play important roles in P. aeruginosa pathogenesis. These mechanisms affect key points of the P. aeruginosa-host interaction, such as: i) biofilm formation that contributes to bacterial colonization and survival, ii) invasion of tissue barriers that allows bacterial dissemination, iii) modulation of inflammatory responses, and iv) escape from host defenses. In this mini-review, we present the lipid-based mechanism that interferes with the establishment of P. aeruginosa in the lungs and discuss how bacterial and host lipids can impact the outcome of P. aeruginosa respiratory infections.
Collapse
Affiliation(s)
- Pamella Constantino-Teles
- Department of Microbiology, Immunology and Parasitology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Albane Jouault
- Sorbonne Université, Centre de Recherche Saint-Antoine, Inserm, Institut Pasteur, Mucoviscidose et Bronchopathies Chroniques, Département Santé Globale, Paris, France
| | - Lhousseine Touqui
- Sorbonne Université, Centre de Recherche Saint-Antoine, Inserm, Institut Pasteur, Mucoviscidose et Bronchopathies Chroniques, Département Santé Globale, Paris, France
| | - Alessandra Mattos Saliba
- Department of Microbiology, Immunology and Parasitology, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro, Brazil
- *Correspondence: Alessandra Mattos Saliba,
| |
Collapse
|
12
|
Mirzaei R, Sabokroo N, Ahmadyousefi Y, Motamedi H, Karampoor S. Immunometabolism in biofilm infection: lessons from cancer. Mol Med 2022; 28:10. [PMID: 35093033 PMCID: PMC8800364 DOI: 10.1186/s10020-022-00435-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Biofilm is a community of bacteria embedded in an extracellular matrix, which can colonize different human cells and tissues and subvert the host immune reactions by preventing immune detection and polarizing the immune reactions towards an anti-inflammatory state, promoting the persistence of biofilm-embedded bacteria in the host. MAIN BODY OF THE MANUSCRIPT It is now well established that the function of immune cells is ultimately mediated by cellular metabolism. The immune cells are stimulated to regulate their immune functions upon sensing danger signals. Recent studies have determined that immune cells often display distinct metabolic alterations that impair their immune responses when triggered. Such metabolic reprogramming and its physiological implications are well established in cancer situations. In bacterial infections, immuno-metabolic evaluations have primarily focused on macrophages and neutrophils in the planktonic growth mode. CONCLUSION Based on differences in inflammatory reactions of macrophages and neutrophils in planktonic- versus biofilm-associated bacterial infections, studies must also consider the metabolic functions of immune cells against biofilm infections. The profound characterization of the metabolic and immune cell reactions could offer exciting novel targets for antibiofilm therapy.
Collapse
Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Niloofar Sabokroo
- Department of Microbiology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Yaghoub Ahmadyousefi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, Iran
- Research Center for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hamid Motamedi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
13
|
Muggeo A, Perotin JM, Brisebarre A, Dury S, Dormoy V, Launois C, Ancel J, Mulette P, de Champs C, Deslée G, Guillard T. Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease. Front Microbiol 2022; 12:781797. [PMID: 34970242 PMCID: PMC8712763 DOI: 10.3389/fmicb.2021.781797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease characterized by airflow limitation. This chronic respiratory disease represents the third leading cause of death worldwide. Alteration of the airway microbiota has been reported to be associated with exacerbation frequency in COPD, but its role on the symptoms in patients at stable state is still incompletely described. This study aimed to determine whether bacteria isolated in sputum can be associated with the clinical features of COPD patients within stable state. Our study highlights, for the first time, that altered microbiota with Enterobacterales is associated with pejorative clinical symptoms in stable COPD patients. The airway microbiota of 38 patients was analyzed using an extended culture approach and mass spectrometry identification. Cluster analysis by principal coordinate analysis of the bacterial communities showed that the patients could be classified into three distinct clusters in our cohort. The clusters showed no differences in proportions of the phylum, but one of them was associated with a high prevalence of Enterobacterales (71.4% in cluster 1 vs. 0% in cluster 3), loss of microbiota diversity, and higher bacterial load (107 vs. 105 CFU/ml, respectively) and characterized by predominant cough and impact on mental health. These novel findings, supported by further studies, could lead to modifying the processing of COPD sputum in the everyday practice of clinical microbiology laboratories.
Collapse
Affiliation(s)
- Anaëlle Muggeo
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Laboratory of Bacteriology-Virology-Hospital Hygiene-Parasitology-Mycology, Reims University Hospital, Reims, France
| | - Jeanne-Marie Perotin
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Audrey Brisebarre
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France
| | - Sandra Dury
- Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Valérian Dormoy
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France
| | - Claire Launois
- Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Julien Ancel
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Pauline Mulette
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Christophe de Champs
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Laboratory of Bacteriology-Virology-Hospital Hygiene-Parasitology-Mycology, Reims University Hospital, Reims, France
| | - Gaëtan Deslée
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Thomas Guillard
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Laboratory of Bacteriology-Virology-Hospital Hygiene-Parasitology-Mycology, Reims University Hospital, Reims, France
| |
Collapse
|
14
|
D’Anna SE, Maniscalco M, Cappello F, Carone M, Motta A, Balbi B, Ricciardolo FLM, Caramori G, Di Stefano A. Bacterial and viral infections and related inflammatory responses in chronic obstructive pulmonary disease. Ann Med 2021; 53:135-150. [PMID: 32997525 PMCID: PMC7877965 DOI: 10.1080/07853890.2020.1831050] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/25/2020] [Indexed: 12/24/2022] Open
Abstract
In chronic obstructive pulmonary disease (COPD) patients, bacterial and viral infections play a relevant role in worsening lung function and, therefore, favour disease progression. The inflammatory response to lung infections may become a specific indication of the bacterial and viral infections. We here review data on the bacterial-viral infections and related airways and lung parenchyma inflammation in stable and exacerbated COPD, focussing our attention on the prevalent molecular pathways in these different clinical conditions. The roles of macrophages, autophagy and NETosis are also briefly discussed in the context of lung infections in COPD. Controlling their combined response may restore a balanced lung homeostasis, reducing the risk of lung function decline. KEY MESSAGE Bacteria and viruses can influence the responses of the innate and adaptive immune system in the lung of chronic obstructive pulmonary disease (COPD) patients. The relationship between viruses and bacterial colonization, and the consequences of the imbalance of these components can modulate the inflammatory state of the COPD lung. The complex actions involving immune trigger cells, which activate innate and cell-mediated inflammatory responses, could be responsible for the clinical consequences of irreversible airflow limitation, lung remodelling and emphysema in COPD patients.
Collapse
Affiliation(s)
| | - Mauro Maniscalco
- Divisione di Pneumologia, Istituti Clinici Scientifici Maugeri, IRCCS, Telese, Italy
| | - Francesco Cappello
- Dipartimento di Biomedicina, Neuroscienze e Diagnostica avanzata (BIND), Istituto di Anatomia Umana e Istologia Università degli Studi di Palermo, Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Mauro Carone
- UOC Pulmonology and Pulmonary Rehabilitation, Istituti Clinici Scientifici Maugeri, IRCCS di Bari, Bari, Italy
| | - Andrea Motta
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Italy
| | - Bruno Balbi
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell’Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, IRCCS, Veruno, Italy
| | - Fabio L. M. Ricciardolo
- Dipartimento di Scienze Cliniche e Biologiche, Università di Torino, AOU San Luigi Gonzaga, Torino, Italy
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini morfologiche e funzionali (BIOMORF), Università degli studi di Messina, Italy
| | - Antonino Di Stefano
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell’Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, IRCCS, Veruno, Italy
| |
Collapse
|
15
|
Ali F, Das S, Hossain TJ, Chowdhury SI, Zedny SA, Das T, Ahmed Chowdhury MN, Uddin MS. Production optimization, stability and oil emulsifying potential of biosurfactants from selected bacteria isolated from oil-contaminated sites. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211003. [PMID: 34659780 PMCID: PMC8511774 DOI: 10.1098/rsos.211003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Oil pollution is of increasing concern for environmental safety and the use of microbial surfactants in oil remediation has become inevitable for their efficacy and ecofriendly nature. In this work, biosurfactants of bacteria isolated from oil-contaminated soil have been characterized. Four potent biosurfactant-producing strains (SD4, SD11, SD12 and SD13) were selected from 27 isolates based on drop collapse assay and emulsification index, and identified as species belonging to Bacillus, Burkholderia, Providencia and Klebsiella, revealed from their 16S rRNA gene-based analysis. Detailed morphological and biochemical characteristics of each selected isolate were determined. Their growth conditions for maximum biosurfactant production were optimized and found quite similar among the four isolates with a pH of 3.0 and temperature 37°C after 6 or 7 days of growth on kerosene. The biosurfactants of SD4, SD11 and SD12 appeared to be glycolipids and that of SD13 a lipopeptide. Emulsification activity of most of the biosurfactants was stable at low and high temperatures (4-100°C), a wide range of pH (2-10) and salt concentrations (2-7% NaCl). Each biosurfactant showed antimicrobial activity against two or more pathogenic bacteria. The biosurfactants were well-capable of emulsifying kerosene, diesel and soya bean, and could efficiently degrade diesel.
Collapse
Affiliation(s)
- Ferdausi Ali
- Department of Microbiology, University of Chittagong, Chattogram 4331, Bangladesh
| | - Sharup Das
- Department of Microbiology, University of Chittagong, Chattogram 4331, Bangladesh
| | - Tanim Jabid Hossain
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram 4331, Bangladesh
| | - Sumaiya Islam Chowdhury
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram 4331, Bangladesh
| | - Subrina Akter Zedny
- Department of Microbiology, University of Chittagong, Chattogram 4331, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram 4331, Bangladesh
| | - Tuhin Das
- Department of Microbiology, University of Chittagong, Chattogram 4331, Bangladesh
| | | | - Mohammad Seraj Uddin
- Department of Microbiology, University of Chittagong, Chattogram 4331, Bangladesh
| |
Collapse
|
16
|
Ratjen F, VanDevanter DR. Retracing changes in cystic fibrosis understanding and management over the past twenty years. J Cyst Fibros 2021; 21:3-9. [PMID: 34602342 DOI: 10.1016/j.jcf.2021.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Felix Ratjen
- Division of Respiratory Medicine, Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Canada
| | - Donald R VanDevanter
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH USA.
| |
Collapse
|
17
|
Bharwani A, Szamosi JC, Taylor VH, Lee Y, Bala A, Mansur R, Subramaniapillai M, Surette M, McIntyre RS. Changes in the gut microbiome associated with infliximab in patients with bipolar disorder. Brain Behav 2021; 11:e2259. [PMID: 34152099 PMCID: PMC8413825 DOI: 10.1002/brb3.2259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Available information exists supporting the gut-brain axis, but additional information is needed to explore how the gut microbiome changes when exposed to mood disorder treatments. We sought to explore the effects of a novel treatment for bipolar disorder (BD), infliximab, on the gut microbiome. METHODS Participants with a primary diagnosis of BD (n = 15) who participated in a 12-week, randomized placebo-controlled trial evaluating the efficacy of adjunctive infliximab in the treatment of BD were recruited and followed. Stool samples were collected prior to randomization and at 12 weeks. 16S rRNA sequencing was employed in order to analyze the gut microbial community profile. RESULTS A total of 17 participants were randomized to infliximab (n = 9; mean [SD] age, 47.6 [10.3] years; 8 female) or to placebo (n = 8; mean [SD] age, 45.9 [10.7] years; 7 female) but two participants from the infliximab group were lost to follow-up post randomization. Across all time points, there were no differences in the diversity on either Shannon or Simpson's Diversity indices. Comparison of Aitchison distances revealed a lack of clustering of the microbiota by time point, but did reveal a small overall effect of treatment that was not significantly different at individual time points. There were also no effects of either time or treatment on differential abundance at either the amplicon sequence variant or genus level. CONCLUSIONS These observations indicate that no community-wide changes in the microbiota diversity and profile were detected after the use of infliximab treatment.
Collapse
Affiliation(s)
- Aadil Bharwani
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jake C Szamosi
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Valerie H Taylor
- Department of Psychiatry, Foothills Medical Centre, University of Calgary, Calgary, Alberta, Canada
| | - Yena Lee
- Mood Disorders Psychopharmacology Unit, University Health Network, Toronto, Ontario, Canada
| | - Asem Bala
- Department of Psychiatry, Foothills Medical Centre, University of Calgary, Calgary, Alberta, Canada
| | - Rodrigo Mansur
- Mood Disorders Psychopharmacology Unit, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Mehala Subramaniapillai
- Mood Disorders Psychopharmacology Unit, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Michael Surette
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Roger S McIntyre
- Mood Disorders Psychopharmacology Unit, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
18
|
Cooke NCA, Bala A, Allard JP, Hota S, Poutanen S, Taylor VH. The safety and efficacy of fecal microbiota transplantation in a population with bipolar disorder during depressive episodes: study protocol for a pilot randomized controlled trial. Pilot Feasibility Stud 2021; 7:142. [PMID: 34261526 PMCID: PMC8278713 DOI: 10.1186/s40814-021-00882-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Background Bipolar disorder (BD) is a chronic, debilitating illness with significant medical morbidity, often secondary to current treatments, and a high recurrence rate. This burden of disease reflects limitations in the tolerability and efficacy of current treatments. There is a compelling body of evidence linking the gut microbiota to mental illness, and while microbial manipulation via probiotic use has been studied as a therapeutic in BD, targeted trials of fecal microbiota transplantation (FMT) have not been conducted in this population. Methods and design We describe a pilot randomized controlled trial of FMT in participants with BD depression to assess the feasibility, efficacy, safety, and tolerability of this intervention. Individuals between 18 and 65 years of age will be enrolled in the study if they meet diagnostic criteria for a major depressive episode of at least moderate severity in the context of a BD diagnosis and have not responded to treatment for BD. Participants will be randomized 1:1 to receive either screened and processed donor stool (allogenic FMT) or their own stool (autologous FMT) via colonoscopy and monitored for 24 weeks post intervention. Depressive and manic symptoms, treatment acceptability, and gastrointestinal and other side effects are assessed at baseline (prior to randomization) and weekly. Stool samples to assess microbiome composition are obtained at baseline and 3 and 6 months. Discussion Currently, FMT represents a novel therapeutic option for treating BD depression. This protocol allows for the assessment of the feasibility, efficacy, acceptability, and safety of an intervention aimed at changing the microbiome in those with BD. Results from this pilot study will guide the development of larger trials of FMT for BD depression and may give more insight into how the gut microbiome are altered in those with BD depression. Trial registration Clinical Trials Gov NCT03279224
Collapse
Affiliation(s)
- Noah C A Cooke
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Asem Bala
- Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Johane P Allard
- Department of Medicine, Toronto General Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Susy Hota
- Infection Prevention and Control Department, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Susan Poutanen
- Departments of Microbiology and Medicine, University Health Network and Sinai Health, University of Toronto, Toronto, Canada
| | - Valerie H Taylor
- Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada. .,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
| |
Collapse
|
19
|
Reid BM, Horne R, Donzella B, Szamosi JC, Coe CL, Foster JA, Gunnar MR. Microbiota-immune alterations in adolescents following early life adversity: A proof of concept study. Dev Psychobiol 2021; 63:851-863. [PMID: 33249563 DOI: 10.1002/dev.22061] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/17/2020] [Accepted: 10/23/2020] [Indexed: 12/21/2022]
Abstract
Early adverse care has long-term impacts on physical and mental health. The influence of rearing conditions on the infant's gut microbiota and its relationship with developmental health has become more evident. The microbiome is essential for normal growth and metabolism, and the signaling from the gut to the brain may underlie individual differences in resilience later in life. Microbial diversity and composition were determined using 16S rRNA gene amplicon sequencing in fecal samples from 17 adolescents adopted internationally from orphanages into the United States and 18 adolescents reared in birth families who had similar educational and income levels. Analyses focused on diversity of the microbial community structure and differences in the abundance of specific bacterial taxa. Blood samples were used to immunophenotype the numbers of several T-cell subsets and cytomegalovirus (CMV) seropositivity. Negative binomial regression analysis revealed several operational taxonomic units that were significantly different based on early rearing conditions and CMV seropositivity. There were significant associations between the relative abundance of certain taxa, the percentages of T-cell subsets in circulation, and CMV seropositivity. These findings demonstrate a possible link between the gut microbiota and associations with immune alterations initiated by early life adversity.
Collapse
Affiliation(s)
- Brie M Reid
- Institute of Child Development, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Rachael Horne
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, USA
| | - Bonny Donzella
- Institute of Child Development, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Jake C Szamosi
- Department of Medicine and Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, USA
| | | | - Jane A Foster
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, USA
| | - Megan R Gunnar
- Institute of Child Development, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| |
Collapse
|
20
|
Bonifacio JPP, Schmolke M. Visualization of Respiratory Commensal Bacteria in Context of Their Natural Host Environment. Front Microbiol 2021; 12:678389. [PMID: 34149669 PMCID: PMC8212125 DOI: 10.3389/fmicb.2021.678389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Commensal microbes are an integral component of mammalian physiology. 16S rRNA gene-specific next generation sequencing from DNA of total organs, swabs or lavages has revolutionized the characterization of bacterial communities in virtually every ecological niche of the body. Culturomics, next allowed the isolation and characterization of commensal bacteria in the lab and the establishment of artificial communities of bacteria, which were eventually reintroduced in model organisms. Spatial organization of microbiota within a given host environment is critical to the physiological or pathological phenotypes provoked by commensal microbiota. In situ hybridization (ISH) is a complementary technique to sequencing and culturing to visualize the presence of individual bacterial operational taxonomic unit (OTUs) in context of the colonized organ. We recently applied highly sensitive in situ RNA hybridization to detection of commensal bacteria in low abundance respiratory tract samples of mice housed under specific pathogen free conditions. This technique allows species-specific detection of living bacteria using RNAScopeTM technology, while preserving the natural environment of the organ. We here provide a detailed step-by-step protocol describing the detection of commensal lung bacteria in respiratory tissue.
Collapse
Affiliation(s)
- Joao P P Bonifacio
- Microbiology and Molecular Medicine Department, University of Geneva, Geneva, Switzerland
| | - Mirco Schmolke
- Microbiology and Molecular Medicine Department, University of Geneva, Geneva, Switzerland
| |
Collapse
|
21
|
Lamoureux C, Guilloux CA, Beauruelle C, Gouriou S, Ramel S, Dirou A, Le Bihan J, Revert K, Ropars T, Lagrafeuille R, Vallet S, Le Berre R, Nowak E, Héry-Arnaud G. An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches. Sci Rep 2021; 11:6845. [PMID: 33767218 PMCID: PMC7994387 DOI: 10.1038/s41598-021-85592-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
Strict anaerobes are undeniably important residents of the cystic fibrosis (CF) lung but are still unknowns. The main objectives of this study were to describe anaerobic bacteria diversity in CF airway microbiota and to evaluate the association with lung function. An observational study was conducted during eight months. A hundred and one patients were enrolled in the study, and 150 sputum samples were collected using a sterile sample kit designed to preserve anaerobic conditions. An extended-culture approach on 112 sputa and a molecular approach (quantitative PCR targeting three of the main anaerobic genera in CF lung: Prevotella, Veillonella, and Fusobacterium) on 141 sputa were developed. On culture, 91.1% of sputa were positive for at least one anaerobic bacterial species, with an average of six anaerobic species detected per sputum. Thirty-one anaerobic genera and 69 species were found, which is the largest anaerobe diversity ever reported in CF lungs. Better lung function (defined as Forced Expiratory Volume in one second > 70%) was significantly associated with higher quantification of Veillonella. These results raise the question of the potential impact of anaerobes on lung function.
Collapse
Affiliation(s)
- Claudie Lamoureux
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | | | - Clémence Beauruelle
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | | | - Sophie Ramel
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Anne Dirou
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Jean Le Bihan
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Krista Revert
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Thomas Ropars
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | | | - Sophie Vallet
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | - Rozenn Le Berre
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Pulmonary and Internal Medicine, Brest University Hospital, Brest, France
| | - Emmanuel Nowak
- INSERM CIC 1412, Brest University Hospital, Brest, France
| | - Geneviève Héry-Arnaud
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France. .,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France.
| |
Collapse
|
22
|
Abstract
Cystic fibrosis (CF) is the most common, lethal genetic disease among the Caucasian population. The leading cause of mortality is recurrent acute exacerbations resulting in chronic airway inflammation and subsequent downward progression of pulmonary function. Traditionally, these periods of clinical deterioration have been associated with several principal pathogens. However, a growing body of literature has demonstrated a polymicrobial lower respiratory community compromised of facultative and obligate anaerobes. Despite the understanding of a complex bacterial milieu in CF patient airways, specific roles of anaerobes in disease progression have not been established. In this paper, we first present a brief review of the anaerobic microorganisms that have been identified within CF lower respiratory airways. Next, we discuss the potential contribution of these organisms to CF disease progression, in part by pathogenic potential and also through synergistic interaction with principal pathogens. Finally, we propose a variety of clinical scenarios in which these anaerobic organisms indirectly facilitate principal CF pathogens by modulating host defense and contribute to treatment failure by antibiotic inactivation. These mechanisms may affect patient clinical outcomes and contribute to further disease progression.
Collapse
|
23
|
Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures. Sci Rep 2021; 11:3963. [PMID: 33597669 PMCID: PMC7889618 DOI: 10.1038/s41598-021-83524-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/01/2021] [Indexed: 12/18/2022] Open
Abstract
Studying respiratory illness-specific microbial signatures and their interaction with other micro-residents could provide a better understanding of lung microbial ecology. Each respiratory illness has a specific disease etiology, however, so far no study has revealed disease—specific microbial markers. The present study was designed to determine disease-specific microbial features and their interactions with other residents in chronic obstructive pulmonary diseases (stable and exacerbated), sarcoidosis, and interstitial lung diseases. Broncho-alveolar lavage samples (n = 43) were analyzed by SSU rRNA gene sequencing to study the alveolar microbiome in these diseases. A predominance of Proteobacteria followed by Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria was observed in all the disease subsets. Shannon diversity was significantly higher in stable COPD when compared to exacerbated chronic obstructive pulmonary disease (ECOPD) (p = 0.0061), and ILD patient samples (p = 0.037). The lung microbiome of the patients with stable COPD was more diverse in comparison to ECOPD and ILD patients (p < 0.001). Lefse analysis identified 40 disease—differentiating microbial features (LDA score (log10) > 4). Species network analysis indicated a significant correlation (p < 0.05) of diseases specific microbial signature with other lung microbiome members. The current study strengthens the proposed hypothesis that each respiratory illness has unique microbial signatures. These microbial signatures could be used as diagnostic markers to differentiate among various respiratory illnesses.
Collapse
|
24
|
Fromentin M, Ricard JD, Roux D. Respiratory microbiome in mechanically ventilated patients: a narrative review. Intensive Care Med 2021; 47:292-306. [PMID: 33559707 PMCID: PMC7871139 DOI: 10.1007/s00134-020-06338-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
The respiratory microbiome has been less explored than the gut microbiome. Despite the speculated importance of dysbiosis of the microbiome in ventilator-associated pneumonia (VAP) and acute respiratory distress syndrome (ARDS), only few studies have been performed in invasively ventilated ICU patients. And only the results of small cohorts have been published. An overlap exists between bacterial populations observed in the lower respiratory tract and the oropharyngeal tract. The bacterial microbiota is characterized by relatively abundant bacteria difficult to cultivate by standard methods. Under mechanical ventilation, a dysbiosis occurs with a drop overtime in diversity. During VAP development, lung dysbiosis is characterized by a shift towards a dominant bacterial pathogen (mostly Proteobacteria) whereas enrichment of gut-associated bacteria mainly Enterobacteriaceae is the specific feature discriminating ARDS patients. However, the role of this dysbiosis in VAP and ARDS pathogenesis is not yet fully understood. A more in-depth analysis of the interplay between bacteria, virus and fungi and a better understanding of the host-microbiome interaction could provide a more comprehensive view of the role of the microbiome in VAP and ARDS pathogenesis. Priority should be given to validate a consensual and robust methodology for respiratory microbiome research and to conduct longitudinal studies. A deeper understanding of microbial interplay should be a valuable guide for care of ARDS and VAP preventive/therapeutic strategies. We present a review on the current knowledge and expose perspectives and potential clinical applications of respiratory microbiome research in mechanically ventilated patients.
Collapse
Affiliation(s)
- Mélanie Fromentin
- Anesthesiology and Intensive Care Department, AP-HP, Hôpital Cochin, 75014, Paris, France.,UMR1137 IAME, INSERM, Université de Paris, 75018, Paris, France
| | - Jean-Damien Ricard
- Médecine Intensive Réanimation, DMU ESPRIT, AP-HP, Hôpital Louis Mourier, 92700, Colombes, France.,UMR1137 IAME, INSERM, Université de Paris, 75018, Paris, France
| | - Damien Roux
- Médecine Intensive Réanimation, DMU ESPRIT, AP-HP, Hôpital Louis Mourier, 92700, Colombes, France. .,UMR1137 IAME, INSERM, Université de Paris, 75018, Paris, France.
| |
Collapse
|
25
|
Moossavi S, Fontes ME, Rossi L, Fusch G, Surette MG, Azad MB. Capturing the diversity of the human milk microbiota through culture-enriched molecular profiling: a feasibility study. FEMS Microbiol Lett 2021; 368:6070652. [PMID: 33417698 DOI: 10.1093/femsle/fnab001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Previous human milk studies have confirmed the existence of a highly diverse bacterial community using culture-independent and targeted culture-dependent techniques. However, culture-enriched molecular profiling of milk microbiota has not been done. Additionally, the impact of storage conditions and milk fractionation on microbiota composition is not understood. In this feasibility study, we optimized and applied culture-enriched molecular profiling to study culturable milk microbiota in eight milk samples collected from mothers of infants admitted to a neonatal intensive care unit. Fresh samples were immediately plated or stored at -80°C for 2 weeks (short-term frozen). Long-term samples were stored at -20°C for >6 months. Samples were cultured using 10 different culture media and incubated both aerobically and anaerobically. We successfully isolated major milk bacteria, including Streptococcus, Staphylococcus and Bifidobacterium, from fresh milk samples, but were unable to culture any bacteria from the long-term frozen samples. Short-term freezing shifted the composition of viable milk bacteria from the original composition in fresh samples. Nevertheless, the inter-individual variability of milk microbiota composition was observed even after short-term storage. There was no major difference in the overall milk microbiota composition between milk fractions in this feasibility study. This is among the first studies on culture-enriched molecular profiling of the milk microbiota demonstrating the effect of storage and fractionation on milk microbiota composition.
Collapse
Affiliation(s)
- Shirin Moossavi
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.,Manitoba Interdisciplinary Lactation Centre (MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada.,Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 14117-13135, Iran.,Microbiome and Microbial Ecology Interest Group (MMEIG), Universal Scientific Education and Research Network (USERN), Calgary, AB T2N 4Z1, Canada
| | - Michelle E Fontes
- Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Laura Rossi
- Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Gerhard Fusch
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Michael G Surette
- Department of Medicine and Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Meghan B Azad
- Manitoba Interdisciplinary Lactation Centre (MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada.,Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| |
Collapse
|
26
|
Khasnobish A, Takayasu L, Watanabe KI, Nguyen TTT, Arakawa K, Hotta O, Joh K, Nakano A, Hosomi S, Hattori M, Suda W, Morita H. Dysbiosis in the Salivary Microbiome Associated with IgA Nephropathy-A Japanese Cohort Study. Microbes Environ 2021; 36. [PMID: 34078780 PMCID: PMC8209455 DOI: 10.1264/jsme2.me21006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
IgA nephropathy is one of the leading causes of chronic kidney disease in Japan. Since the origin and mechanisms by which IgA nephropathy develops currently remain unclear, a confirmed disease diagnosis is currently only possible by highly invasive renal biopsy. With the background of the salivary microbiome as a rich source of biomarkers for systemic diseases, we herein primarily aimed to investigate the salivary microbiome as a tool for the non-invasive diagnosis of IgA nephropathy. In a comparison of salivary microbiome profiles using 16S rRNA amplicon sequencing, significant differences were observed in microbial diversity and richness between IgA nephropathy patients and healthy controls. Furthermore, recent studies reported that patients with IgA nephropathy are more likely to develop inflammatory bowel diseases and that chronic inflammation of the tonsils triggered the recurrence of IgA nephropathy. Therefore, we compared the salivary microbiome of IgA nephropathy patients with chronic tonsillitis and ulcerative colitis patients. By combining the genera selected by the random forest algorithm, we were able to distinguish IgA nephropathy from healthy controls with an area under the curve (AUC) of 0.90, from the ulcerative colitis group with AUC of 0.88, and from the chronic tonsillitis group with AUC of 0.70. Additionally, the genus Neisseria was common among the selected genera that facilitated the separation of the IgA nephropathy group from healthy controls and the chronic tonsillitis group. The present results indicate the potential of the salivary microbiome as a biomarker for the non-invasive diagnosis of IgA nephropathy.
Collapse
Affiliation(s)
- Anushka Khasnobish
- Laboratory of Animal Applied Microbiology, Graduate School of Environmental and Life Science, Okayama University
| | - Lena Takayasu
- Department of Human Ecology, School of International Health, Graduate School of Medicine, The University of Tokyo
| | - Ken-Ichi Watanabe
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine
| | - Tien Thi Thuy Nguyen
- Faculty of Engineering and Technology College of Agriculture and Forestry, Hue University
| | - Kensuke Arakawa
- Laboratory of Animal Applied Microbiology, Graduate School of Environmental and Life Science, Okayama University
| | | | - Kensuke Joh
- Department of Pathology, Tohoku University Graduate School of Medicine
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University
| | - Shuhei Hosomi
- Department of Gastroenterology, Osaka City University Graduate School of Medicine
| | - Masahira Hattori
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences
| | - Hidetoshi Morita
- Laboratory of Animal Applied Microbiology, Graduate School of Environmental and Life Science, Okayama University
| |
Collapse
|
27
|
Kondo Y. Construction of a Mutant in Prevotella melaninogenica Using the Conjugation Transfer Method with Escherichia coli. Methods Mol Biol 2021; 2210:33-41. [PMID: 32815125 DOI: 10.1007/978-1-0716-0939-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Prevotella melaninogenica is a bacterium that is resident in the oral cavity and upper respiratory tract and is associated with periodontal disease and aspiration pneumonia. Prevotella mutants are difficult to produce and only few reports have been reported. We examined several methods and many strains and succeeded in producing mutants in Prevotella melaninogenica GAI 07411. In this chapter, we will describe how to create a mutation of a target gene by carrying out conjugation transfer using Escherichia coli S17-1 as a donor and introducing a plasmid into P. melaninogenica.
Collapse
Affiliation(s)
- Yoshio Kondo
- Department of Pediatric Dentistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
| |
Collapse
|
28
|
Garcia-Nuñez M, Garcia-Gonzalez M, Pomares X, Montón C, Millares L, Quero S, Prina E, Asensio O, Bosque M, Capilla S, Cuevas O, Monsó E. The Respiratory Microbiome in Cystic Fibrosis: Compartment Patterns and Clinical Relationships in Early Stage Disease. Front Microbiol 2020; 11:1463. [PMID: 32695090 PMCID: PMC7339930 DOI: 10.3389/fmicb.2020.01463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/04/2020] [Indexed: 11/28/2022] Open
Abstract
We compared the bacterial microbiomes lodged in the bronchial tree, oropharynx and nose of patients with early stage cystic fibrosis (CF) not using chronic antibiotics, determining their relationships with lung function and exacerbation frequency. CF patients were enrolled in a cohort study during stability and were checked regularly over the following 9 months. Upper respiratory samples (sputum [S], oropharyngeal swab [OP] and nasal washing [N]) were collected at the first visit and every 3 months. 16S rRNA gene amplification and sequencing was performed and analyzed with QIIME. Seventeen CF patients were enrolled (16.6 SD 9.6 years). Alpha-diversity of bacterial communities between samples was significantly higher in S than in OP (Shannon index median 4.6 [IQR: 4.1–4.9] vs. 3.7 [IQR: 3-1-4.1], p = 0.003/Chao 1 richness estimator median 97.75 [IQR: 85.1–110.9] vs. 43.9 [IQR: 31.7–59.9], p = 0.003) and beta-diversity analysis also showed significant differences in the microbial composition of both respiratory compartments (Adonis test of Bray Curtis dissimilarity matrix, p = 0.001). Dominant taxa were found at baseline in five patients (29.4%), who showed lower forced expiratory volume in the first second (FEV1%, mean 74.8 [SD 19] vs. 97.2 [SD 17.8], p = 0.035, Student t test). The Staphylococcus genus had low RAs in most samples (median 0.26% [IQR 0.01–0.69%]), but patients with RA > 0.26% of Staphylococcus in bronchial secretions suffered more exacerbations during follow-up (median 2 [IQR 1–2.25] vs. 0 [0–1], p = 0.026. Mann–Whitney U test), due to S. aureus in more than a half of the cases, microorganism that often persists as bronchial colonized in these patients (9/10 [90%] vs. 2/7 [28.6%], p = 0.034, Fisher’s exact test). In conclusion, the bronchial microbiome had significantly higher diversity than the microbial flora lodged in the oropharynx in early stage CF. Although the RA of the Staphylococcus genus was low in bronchial secretions and did not reach a dominance pattern, slight overrepresentations of this genus was associated with higher exacerbation frequencies in these patients.
Collapse
Affiliation(s)
- Marian Garcia-Nuñez
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Miguel Garcia-Gonzalez
- Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain.,Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Xavier Pomares
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Concepción Montón
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Laura Millares
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Infectious and Respiratory Disease Research Group, Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Sara Quero
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Infectious and Respiratory Disease Research Group, Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Elena Prina
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Oscar Asensio
- Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain.,Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Montserrat Bosque
- Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain.,Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Silvia Capilla
- Department of Microbiology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Oscar Cuevas
- Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Eduard Monsó
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Universitat Autonoma de Barcelona, Barcelona, Spain
| |
Collapse
|
29
|
Adhikari B, Kwon YM. Cell density alters bacterial community structure in culture-enriched 16S rRNA gene microbiota profiling. BMC Res Notes 2020; 13:269. [PMID: 32493423 PMCID: PMC7268277 DOI: 10.1186/s13104-020-05113-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/26/2020] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Microbial community profiling using 16S rRNA gene has provided invaluable insights into diverse microbial communities. Recently a few studies have attempted to use 16S rRNA gene microbiota profiling in combination with the conventional culture methods to explore bacterial communities. In this "culture-enriched microbiota profiling" approach, microbes in a sample are cultured on solid media, and the resulting colonies are combined and subjected to 16S rRNA gene microbiota profiling. Here we investigated the effect of cell densities as determined by varying levels of sample dilution on the culture-enriched microbiota profiles using De Man, Rogosa and Sharpe (MRS) agar medium as a model system. RESULTS Cecal samples collected from 10 healthy chickens were serially diluted to 102 fold (M-LOW), 104 fold (M-MEDIUM), and 106 fold (M-HIGH), and the dilutions were plated on MRS agar. 16S rRNA gene profiling showed that the relative abundance of certain genera showed gradual increase (Pediococcus and Enterococcus) or decrease (Lactobacillus and Turicibacter) with higher dilutions, though it was significant only for Pediococcus (p < 0.05). The result indicates that the dilution levels of the samples can alter the resulting microbiota profiles via unknown density-dependent mechanisms and thus should be considered for designing experiments using culture-enriched microbiota profiling.
Collapse
Affiliation(s)
- Bishnu Adhikari
- Department of Poultry Science, College of Agricultural, Food and Life Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Young Min Kwon
- Department of Poultry Science, College of Agricultural, Food and Life Sciences, University of Arkansas, Fayetteville, AR, 72701, USA. .,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
| |
Collapse
|
30
|
Françoise A, Héry-Arnaud G. The Microbiome in Cystic Fibrosis Pulmonary Disease. Genes (Basel) 2020; 11:E536. [PMID: 32403302 PMCID: PMC7288443 DOI: 10.3390/genes11050536] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/20/2020] [Accepted: 05/08/2020] [Indexed: 12/19/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease with mutational changes leading to profound dysbiosis, both pulmonary and intestinal, from a very young age. This dysbiosis plays an important role in clinical manifestations, particularly in the lungs, affected by chronic infection. The range of microbiological tools has recently been enriched by metagenomics based on next-generation sequencing (NGS). Currently applied essentially in a gene-targeted manner, metagenomics has enabled very exhaustive description of bacterial communities in the CF lung niche and, to a lesser extent, the fungi. Aided by progress in bioinformatics, this now makes it possible to envisage shotgun sequencing and opens the door to other areas of the microbial world, the virome, and the archaeome, for which almost everything remains to be described in cystic fibrosis. Paradoxically, applying NGS in microbiology has seen a rebirth of bacterial culture, but in an extended manner (culturomics), which has proved to be a perfectly complementary approach to NGS. Animal models have also proved indispensable for validating microbiome pathophysiological hypotheses. Description of pathological microbiomes and correlation with clinical status and therapeutics (antibiotic therapy, cystic fibrosis transmembrane conductance regulator (CFTR) modulators) revealed the richness of microbiome data, enabling description of predictive and follow-up biomarkers. Although monogenic, CF is a multifactorial disease, and both genotype and microbiome profiles are crucial interconnected factors in disease progression. Microbiome-genome interactions are thus important to decipher.
Collapse
Affiliation(s)
- Alice Françoise
- UMR 1078 GGB, University of Brest, Inserm, EFS, F-29200 Brest, France;
| | - Geneviève Héry-Arnaud
- UMR 1078 GGB, University of Brest, Inserm, EFS, F-29200 Brest, France;
- Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent, 29200 Brest, France
| |
Collapse
|
31
|
Shelomi M, Wu MK, Chen SM, Huang JJ, Burke CG. Microbes Associated With Black Soldier Fly (Diptera: Stratiomiidae) Degradation of Food Waste. ENVIRONMENTAL ENTOMOLOGY 2020; 49:405-411. [PMID: 31904089 DOI: 10.1093/ee/nvz164] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Indexed: 06/10/2023]
Abstract
Black soldier fly (Hermetia illucens L.) larvae are capable of valorizing waste by converting it into insect biomass that can be used as animal feed, leaving undigested residue that can be used as soil enrichment. Evidence is conflicting over whether larvae fed substrate containing pathogenic microbes emerge uncontaminated. Studies also differ on which clades comprise the species' gut microbiome, and on whether and how diet affects these microbes. Using culturing and metabarcoding, the bacterial microbiota of black soldier fly larvae reared on two different kinds of food waste (postproduction soy pulp and postconsumer cafeteria waste) were analyzed, along with the microbes of their substrates. Little to no overlap was found between the wastes, the larvae, and the residues, but the larvae fed different foods had a significant percentage of their microbes in common. The data, in line with other works on this species, suggest the larvae have a conserved microbiota whose components vary geographically.
Collapse
Affiliation(s)
- Matan Shelomi
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Meng-Kun Wu
- Black Soldier Fly Facility, Yi Mi Community College, Chiayi County, Taiwan
| | - Shu-Min Chen
- Black Soldier Fly Facility, Yi Mi Community College, Chiayi County, Taiwan
| | - Jing-Jiun Huang
- Black Soldier Fly Facility, Yi Mi Community College, Chiayi County, Taiwan
| | | |
Collapse
|
32
|
Ditz B, Christenson S, Rossen J, Brightling C, Kerstjens HAM, van den Berge M, Faiz A. Sputum microbiome profiling in COPD: beyond singular pathogen detection. Thorax 2020; 75:338-344. [PMID: 31996401 PMCID: PMC7231454 DOI: 10.1136/thoraxjnl-2019-214168] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/19/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023]
Abstract
Culture-independent microbial sequencing techniques have revealed that the respiratory tract harbours a complex microbiome not detectable by conventional culturing methods. The contribution of the microbiome to chronic obstructive pulmonary disease (COPD) pathobiology and the potential for microbiome-based clinical biomarkers in COPD are still in the early phases of investigation. Sputum is an easily obtainable sample and has provided a wealth of information on COPD pathobiology, and thus has been a preferred sample type for microbiome studies. Although the sputum microbiome likely reflects the respiratory microbiome only in part, there is increasing evidence that microbial community structure and diversity are associated with disease severity and clinical outcomes, both in stable COPD and during the exacerbations. Current evidence has been limited to mainly cross-sectional studies using 16S rRNA gene sequencing, attempting to answer the question 'who is there?' Longitudinal studies using standardised protocols are needed to answer outstanding questions including differences between sputum sampling techniques. Further, with advancing technologies, microbiome studies are shifting beyond the examination of the 16S rRNA gene, to include whole metagenome and metatranscriptome sequencing, as well as metabolome characterisation. Despite being technically more challenging, whole-genome profiling and metabolomics can address the questions 'what can they do?' and 'what are they doing?' This review provides an overview of the basic principles of high-throughput microbiome sequencing techniques, current literature on sputum microbiome profiling in COPD, and a discussion of the associated limitations and future perspectives.
Collapse
Affiliation(s)
- Benedikt Ditz
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Stephanie Christenson
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, the United States
| | - John Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center, University of Groningen, Groningen, the Netherlands
| | - Chris Brightling
- Institute of Lung Health, University of Leicester, Leicester, UK
| | - Huib A M Kerstjens
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alen Faiz
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
33
|
Cummings LA, Hoogestraat DR, Rassoulian-Barrett SL, Rosenthal CA, Salipante SJ, Cookson BT, Hoffman NG. Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture. Sci Rep 2020; 10:5446. [PMID: 32214207 PMCID: PMC7096443 DOI: 10.1038/s41598-020-62424-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/11/2020] [Indexed: 01/19/2023] Open
Abstract
Optimal clinical decision-making depends on identification of clinically relevant organisms present in a sample. Standard microbiological culture may fail to identify unusual or fastidious organisms and can misrepresent relative abundance of sample constituents. Culture-independent methods have improved our ability to deconvolute polymicrobial patient samples. We used next-generation 16S rRNA gene sequencing (NGS16S) to determine how often cultivatable organisms in complex polymicrobial samples are not reported by standard culture. Twenty consecutive bronchoalveolar lavage (BAL) samples were plated to standard and additional media; bacteria were identified by NGS16S analysis of DNA extracted directly from samples or from washed culture plates. 96% of organisms identified were cultivable, but only 21% were reported by standard culture, indicating that standard work-up provides an incomplete assessment of microbial constituents. Direct NGS16S correlated well with standard culture, identifying the same predominant organism in 50% of samples. When predominant organisms differed, NGS16S most often detected anaerobes, whose growth is unsupported by standard culture conditions for this specimen. NGS16S identified more organisms per sample and allowed identification of fastidious organisms, while culture was better at capturing organisms when bacterial load was low, and allowed incidental recovery of non-bacterial pathogens. Molecular and culture-based methods together detect more organisms than either method alone.
Collapse
Affiliation(s)
- Lisa A Cummings
- Departments of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Daniel R Hoogestraat
- Departments of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | | | | | - Stephen J Salipante
- Departments of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Brad T Cookson
- Departments of Laboratory Medicine, University of Washington, Seattle, Washington, USA.,Departments of Microbiology, University of Washington, Seattle, Washington, USA
| | - Noah G Hoffman
- Departments of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
| |
Collapse
|
34
|
The characterization of bacterial communities of oropharynx microbiota in healthy children by combining culture techniques and sequencing of the 16S rRNA gene. Microb Pathog 2020; 143:104115. [PMID: 32135220 DOI: 10.1016/j.micpath.2020.104115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/01/2020] [Accepted: 03/01/2020] [Indexed: 12/28/2022]
Abstract
The high incidence of bacterial respiratory infections has led to a focus on evaluating the human respiratory microbiome. Studies based on culture-based and molecular methods have shown an increase in the bacterial community that includes the bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria in the oropharynx of healthy individuals. Therefore, recognizing this microbial compound and subsequently identifying those carriers of specific pathogens can be of great help in predicting future infections and their control. In this prospective study, we sought to characterize the bacterial communities of the respiratory microbiome in healthy children aged between 3 and 6 years old by combining both cultural techniques and sequencing of the 16S rRNA gene. Seventy-seven oropharynx samples using Dacron swabs were collected from 77 healthy children in the kindergartens of Ilam, Iran. Bacterial identification was performed by phenotypic methods and in house developed PCR-based sequencing (the V1-V9 hypervariable region of the bacterial 16S ribosomal RNA gene). In total, 346 bacterial isolates were characterized based on phenotypic and sequencing-based molecular methods. The 3 most predominant phyla were Firmicutes (74%), Proteobacteria (22%), and Actinobacteria (4%). At the level of the genus, Staphylococci (coagulase-positive and coagulase-negative) and Streptococci were dominant. Also, the most commonly identified potentially pathogenic colonisers were S. aureus (75%), Enterobacteriaceae spp. (40.1%), and A. baumannii (15.6%). The present study identified 3 phyla and 9 family of bacteria in the oropharyngeal microbiome. Remarkably, the presence of potential pathogenic bacteria in the nasopharynx of healthy children can predispose them to infectious diseases, and also frequent exposure to human respiratory bacterial pathogens are further risk factors.
Collapse
|
35
|
Carney SM, Clemente JC, Cox MJ, Dickson RP, Huang YJ, Kitsios GD, Kloepfer KM, Leung JM, LeVan TD, Molyneaux PL, Moore BB, O'Dwyer DN, Segal LN, Garantziotis S. Methods in Lung Microbiome Research. Am J Respir Cell Mol Biol 2020; 62:283-299. [PMID: 31661299 PMCID: PMC7055701 DOI: 10.1165/rcmb.2019-0273tr] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/29/2019] [Indexed: 12/13/2022] Open
Abstract
The lung microbiome is associated with host immune response and health outcomes in experimental models and patient cohorts. Lung microbiome research is increasing in volume and scope; however, there are no established guidelines for study design, conduct, and reporting of lung microbiome studies. Standardized approaches to yield reliable and reproducible data that can be synthesized across studies will ultimately improve the scientific rigor and impact of published work and greatly benefit microbiome research. In this review, we identify and address several key elements of microbiome research: conceptual modeling and hypothesis framing; study design; experimental methodology and pitfalls; data analysis; and reporting considerations. Finally, we explore possible future directions and research opportunities. Our goal is to aid investigators who are interested in this burgeoning research area and hopefully provide the foundation for formulating consensus approaches in lung microbiome research.
Collapse
Affiliation(s)
| | | | | | | | - Yvonne J Huang
- University of Michigan Medical School, Ann Arbor, Michigan
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Kirsten M Kloepfer
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Janice M Leung
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Philip L Molyneaux
- Fibrosis Research Group, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Foundation National Health Service Trust, London, United Kingdom
| | | | | | - Leopoldo N Segal
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, New York; and
| | - Stavros Garantziotis
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| |
Collapse
|
36
|
Whelan FJ, Waddell B, Syed SA, Shekarriz S, Rabin HR, Parkins MD, Surette MG. Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota. Nat Microbiol 2020; 5:379-390. [PMID: 31959969 DOI: 10.1038/s41564-019-0643-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/18/2019] [Indexed: 01/07/2023]
Abstract
Amplicon sequencing (for example, of the 16S rRNA gene) identifies the presence and relative abundance of microbial community members. However, metagenomic sequencing is needed to identify the genetic content and functional potential of a community. Metagenomics is challenging in samples dominated by host DNA, such as those from the skin, tissue and respiratory tract. Here, we combine advances in amplicon and metagenomic sequencing with culture-enriched molecular profiling to study the human microbiota. Using the cystic fibrosis lung as an example, we cultured an average of 82.13% of the operational taxonomic units representing 99.3% of the relative abundance identified in direct sequencing of sputum samples; importantly, culture enrichment identified 63.3% more operational taxonomic units than direct sequencing. We developed the PLate Coverage Algorithm (PLCA) to determine a representative subset of culture plates on which to conduct culture-enriched metagenomics, resulting in the recovery of greater taxonomic diversity-including of low-abundance taxa-with better metagenome-assembled genomes, longer contigs and better functional annotations when compared to culture-independent methods. The PLCA is also applied as a proof of principle to a previously published gut microbiota dataset. Culture-enriched molecular profiling can be used to better understand the role of the human microbiota in health and disease.
Collapse
Affiliation(s)
- Fiona J Whelan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Barbara Waddell
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Saad A Syed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Shahrokh Shekarriz
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Harvey R Rabin
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.,Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.,Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Michael G Surette
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada. .,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada. .,Department of Medicine, McMaster University, Hamilton, Ontario, Canada.
| |
Collapse
|
37
|
Yoo K, Han I, Ko KS, Lee TK, Yoo H, Khan MI, Tiedje JM, Park J. Bacillus-Dominant Airborne Bacterial Communities Identified During Asian Dust Events. MICROBIAL ECOLOGY 2019; 78:677-687. [PMID: 30904989 DOI: 10.1007/s00248-019-01348-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Asian dust (AD) events have received significant attention due to their adverse effects on ecosystems and human health. However, detailed information about airborne pathogens associated with AD events is limited. This study monitored airborne bacterial communities and identified AD-specific bacteria and the potential hazards associated with these bacteria during AD events. Over a 33-month period, 40 air samples were collected under normal atmospheric conditions (non-AD events; n = 34) and during AD events (n = 6). The airborne bacterial communities in the air samples collected during non-AD events (non-AD sample) and AD events (AD sample) were evaluated using both culture-dependent and culture-independent methods. The bacterial diversity increased significantly, along with the 16S rRNA gene copy number, in AD samples (p < 0.05) and was positively correlated with PM10 concentration. High throughput sequencing of the 16S rRNA gene revealed that the relative abundance of the phylum Firmicutes increased substantially in AD samples (44.3 ± 5.0%) compared with non-AD samples (27.8 ± 4.3%). Within the phylum Firmicutes, AD samples included a greater abundance of Bacillus species (almost 23.8%) than non-AD samples (almost 13.3%). Both culture-dependent and culture-independent methods detected common predominant species closely related to Bacillus cereus during AD events. Subsequent multilocus sequence typing (MLST) and enterotoxin gene assays confirmed the presence of virulence factors in B. cereus isolates from AD samples. Furthermore, the abundance of bceT, encoding enterotoxin in B. cereus, was significantly higher in AD samples (p < 0.05). The systematic characterization of airborne bacterial communities in AD samples in this study suggests that B. cereus pose risks to public health.
Collapse
Affiliation(s)
- Keunje Yoo
- Department of Civil and Environmental Engineering, Yonsei University, Yonsei-ro 50, Seodaemun-gu, Seoul, South Korea
| | - Il Han
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju, South Korea
| | - Hyunji Yoo
- Department of Civil and Environmental Engineering, Yonsei University, Yonsei-ro 50, Seodaemun-gu, Seoul, South Korea
| | - Muhammad Imran Khan
- Department of Civil and Environmental Engineering, Yonsei University, Yonsei-ro 50, Seodaemun-gu, Seoul, South Korea
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38040, Pakistan
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Joonhong Park
- Department of Civil and Environmental Engineering, Yonsei University, Yonsei-ro 50, Seodaemun-gu, Seoul, South Korea.
| |
Collapse
|
38
|
Reece E, McClean S, Greally P, Renwick J. The prevalence of Aspergillus fumigatus in early cystic fibrosis disease is underestimated by culture-based diagnostic methods. J Microbiol Methods 2019; 164:105683. [PMID: 31386863 DOI: 10.1016/j.mimet.2019.105683] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 11/28/2022]
Abstract
Aspergillus fumigatus is the most common fungus infecting/colonising people with cystic fibrosis (CF) and can negatively impact clinical status. Diagnostic laboratories rely on culture to detect A. fumigatus which is known to be less sensitive than molecular approaches. Therefore, A. fumigatus colonisation in the CF population may be underestimated. Sputum (n = 60) from 25 children with CF were collected and A. fumigatus was detected using routine culture (CM1), enhanced culture (CM2) and ITS1 qPCR. The prevalence of A. fumigatus in this young CF population was 68% by qPCR and only 16% by CM1. CM1, CM2 and qPCR detected A. fumigatus in 8%, 22% and 53% of samples, respectively. qPCR had a 94.2% and 77.4% increased odds of detecting A. fumigatus over CM1 and CM2, respectively. Molecular methods proved superior for detecting A. fumigatus in CF sputum. A. fumigatus is likely more prevalent in early CF disease than is currently reported.
Collapse
Affiliation(s)
- Emma Reece
- Department of Clinical Microbiology, Trinity College Dublin, Trinity Centre for Health Science, Tallaght University Hospital, Dublin 24, Ireland
| | - Siobhán McClean
- School of Biomolecular and Biomedical Sciences, University College Dublin, Ireland
| | - Peter Greally
- Department of Respiratory Medicine, The National Children's Hospital, Tallaght University Hospital, Dublin 24, Ireland
| | - Julie Renwick
- Department of Clinical Microbiology, Trinity College Dublin, Trinity Centre for Health Science, Tallaght University Hospital, Dublin 24, Ireland.
| |
Collapse
|
39
|
Vandeplassche E, Tavernier S, Coenye T, Crabbé A. Influence of the lung microbiome on antibiotic susceptibility of cystic fibrosis pathogens. Eur Respir Rev 2019; 28:28/152/190041. [PMID: 31285289 PMCID: PMC9488708 DOI: 10.1183/16000617.0041-2019] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022] Open
Abstract
The lungs of patients with cystic fibrosis (CF) are colonised by a microbial community comprised of pathogenic species, such as Pseudomonas aeruginosa and Staphylococcus aureus, and microorganisms that are typically not associated with worse clinical outcomes (considered as commensals). Antibiotics directed at CF pathogens are often not effective and a discrepancy is observed between activity of these agents in vitro and in the patient. This review describes how interspecies interactions within the lung microbiome might influence the outcome of antibiotic treatment targeted at common CF pathogens. Protective mechanisms by members of the microbiome such as antibiotic degradation (indirect pathogenicity), alterations of the cell wall, production of matrix components decreasing antibiotic penetration, and changes in metabolism are discussed. Interspecies interactions that increase bacterial susceptibility are also addressed. Furthermore, we discuss how experimental conditions, such as culture media, oxygen levels, incorporation of host–pathogen interactions, and microbial community composition may influence the outcome of microbial interaction studies related to antibiotic activity. Hereby, the importance to create in vitro conditions reflective of the CF lung microenvironment is highlighted. Understanding the role of the CF lung microbiome in antibiotic efficacy may help find novel therapeutic and diagnostic approaches to better tackle chronic lung infections in this patient population. Interspecies interactions in the lung microbiome may influence the outcome of antibiotic treatment targeted at cystic fibrosis pathogenshttp://bit.ly/2WQp0iQ
Collapse
Affiliation(s)
- Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Sarah Tavernier
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
40
|
A longitudinal characterization of the Non-Cystic Fibrosis Bronchiectasis airway microbiome. Sci Rep 2019; 9:6871. [PMID: 31053725 PMCID: PMC6499777 DOI: 10.1038/s41598-019-42862-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 04/08/2019] [Indexed: 12/30/2022] Open
Abstract
A diverse microbiota exists within the airways of individuals with non-cystic fibrosis bronchiectasis (nCFB). How the lung microbiome evolves over time, and whether changes within the microbiome correlate with future disease progression is not yet known. We assessed the microbial community structure of 133 serial sputa and subsequent disease course of 29 nCFB patients collected over a span of 4–16 years using 16S rRNA paired-end sequencing. Interestingly, no significant shifts in the microbial community of individuals were observed during extended follow-up suggesting the microbiome remains relatively stable over prolonged periods. Samples that were Pseudomonas aeruginosa culture positive displayed markedly different microbial community structures compared to those that were positive for Haemophilus influenzae. Importantly, patients with sputum of lower microbial community diversity were more likely to experience subsequent lung function decline as defined by annual change in ≥−1 FEV1% predicted. Shannon diversity values <1 were more prevalent in patients with FEV1 decline (P = 0.002). However, the relative abundance of particular core microbiota constituents did not associate with risk of decline. Here we present data confirming that the microbiome of nCFB individuals is generally stable, and that microbiome-based measurements may have a prognostic role as biomarkers for nCFB.
Collapse
|
41
|
Sherrard LJ, Einarsson GG, Johnston E, O'Neill K, McIlreavey L, McGrath SJ, Gilpin DF, Downey DG, Reid A, McElvaney NG, Boucher RC, Muhlebach MS, Elborn JS, Tunney MM. Assessment of stability and fluctuations of cultured lower airway bacterial communities in people with cystic fibrosis. J Cyst Fibros 2019; 18:808-816. [PMID: 30905581 DOI: 10.1016/j.jcf.2019.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 01/09/2023]
Abstract
BACKGROUND Routine clinical culture detects a subset of the cystic fibrosis (CF) airways microbiota based on culture-independent (molecular) methods. This study aimed to determine how extended sputum culture of viable bacteria changes over time in relation to clinical status and predicts exacerbations. METHODS Sputa from patients at a baseline stable and up to three subsequent time-points were analysed by extended-quantitative culture; aerobe/anaerobe densities, ecological indexes and community structure were assessed together with clinical outcomes. RESULTS Eighty patients were prospectively recruited. Sputa were successfully collected and cultured at 199/267 (74.5%) study visits. Eighty-two sputa from 25 patients comprised a complete sample-set for longitudinal analyses. Bacterial density, ecological indexes and clinical outcomes were unchanged in 18 patients with three sequential stable visits. Conversely, in 7 patients who had an exacerbation, total bacterial and aerobe densities differed over four study visits (P < .001) with this difference particularly apparent between the baseline visit and completion of acute antibiotic treatment where a decrease in density was observed. Bacterial communities were more similar within than between patients but stable patients had the least variation in community structure over time. Using logistic regression in a further analysis, baseline features in 37 patients without compared to 15 patients with a subsequent exacerbation showed that clinical measures rather than bacterial density or ecological indexes were independent predictors of an exacerbation. CONCLUSIONS Greater fluctuation in the viable bacterial community during treatment of an exacerbation than between stable visits was observed. Extended-quantitative culture did not provide prognostic information of a future exacerbation.
Collapse
Affiliation(s)
- Laura J Sherrard
- Halo Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK.
| | - Gisli G Einarsson
- Halo Research Group, Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Elinor Johnston
- Halo Research Group, Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Katherine O'Neill
- Halo Research Group, Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Leanne McIlreavey
- Halo Research Group, Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Stephanie J McGrath
- Halo Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Deirdre F Gilpin
- Halo Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Damian G Downey
- Halo Research Group, Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK; Belfast Health and Social Care Trust, Belfast, UK
| | | | - Noel G McElvaney
- Respiratory Research Division, Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin, Ireland
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marianne S Muhlebach
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J Stuart Elborn
- Halo Research Group, Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK; Imperial College and Royal Brompton Hospital and Harefield NHS Foundation Trust, London, UK
| | - Michael M Tunney
- Halo Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| |
Collapse
|
42
|
Kiedrowski MR, Bomberger JM. Viral-Bacterial Co-infections in the Cystic Fibrosis Respiratory Tract. Front Immunol 2018; 9:3067. [PMID: 30619379 PMCID: PMC6306490 DOI: 10.3389/fimmu.2018.03067] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/11/2018] [Indexed: 12/15/2022] Open
Abstract
A majority of the morbidity and mortality associated with the genetic disease Cystic Fibrosis (CF) is due to lung disease resulting from chronic respiratory infections. The CF airways become chronically colonized with bacteria in childhood, and over time commensal lung microbes are displaced by bacterial pathogens, leading to a decrease in microbial diversity that correlates with declining patient health. Infection with the pathogen Pseudomonas aeruginosa is a major predictor of morbidity and mortality in CF, with CF individuals often becoming chronically colonized with P. aeruginosa in early adulthood and thereafter having an increased risk of hospitalization. Progression of CF respiratory disease is also influenced by infection with respiratory viruses. Children and adults with CF experience frequent respiratory viral infections with respiratory syncytial virus (RSV), rhinovirus, influenza, parainfluenza, and adenovirus, with RSV and influenza infection linked to the greatest decreases in lung function. Along with directly causing severe respiratory symptoms in CF populations, the impact of respiratory virus infections may be more far-reaching, indirectly promoting bacterial persistence and pathogenesis in the CF respiratory tract. Acquisition of P. aeruginosa in CF patients correlates with seasonal respiratory virus infections, and CF patients colonized with P. aeruginosa experience increased severe exacerbations and declines in lung function during respiratory viral co-infection. In light of such observations, efforts to better understand the impact of viral-bacterial co-infections in the CF airways have been a focus of clinical and basic research in recent years. This review summarizes what has been learned about the interactions between viruses and bacteria in the CF upper and lower respiratory tract and how co-infections impact the health of individuals with CF.
Collapse
Affiliation(s)
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| |
Collapse
|
43
|
Libertucci J, Young VB. The role of the microbiota in infectious diseases. Nat Microbiol 2018; 4:35-45. [PMID: 30546094 DOI: 10.1038/s41564-018-0278-4] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 09/28/2018] [Indexed: 02/07/2023]
Abstract
The human body is colonized by a diverse community of microorganisms collectively referred to as the microbiota. Here, we describe how the human microbiota influences susceptibility to infectious diseases using examples from the respiratory, gastrointestinal and female reproductive tract. We will discuss how interactions between the host, the indigenous microbiota and non-native microorganisms, including bacteria, viruses and fungi, can alter the outcome of infections. This Review Article will highlight the complex mechanisms by which the microbiota mediates colonization resistance, both directly and indirectly, against infectious agents. Strategies for the therapeutic modulation of the microbiota to prevent or treat infectious diseases will be discussed, and we will review potential therapies that directly target the microbiota, including prebiotics, probiotics, synbiotics and faecal microbiota transplantation.
Collapse
Affiliation(s)
- Josie Libertucci
- Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA. .,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
44
|
Wu Y, Klapper I, Stewart PS. Hypoxia arising from concerted oxygen consumption by neutrophils and microorganisms in biofilms. Pathog Dis 2018; 76:4982780. [PMID: 29688319 DOI: 10.1093/femspd/fty043] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/20/2018] [Indexed: 11/14/2022] Open
Abstract
Infections associated with microbial biofilms are often found to involve hypoxic or anoxic conditions within the biofilm or its vicinity. To shed light on the phenomenon of local oxygen depletion, mathematical reaction-diffusion models were derived that integrated the two principal oxygen sinks, microbial respiration and neutrophil consumption. Three simple one-dimensional problems were analyzed approximating biofilm near an air interface as in a dermal wound or mucus layer, biofilm on an implanted medical device, or biofilm aggregates dispersed in mucus or tissue. In all three geometries considered, hypoxia at the biofilm-neutrophil interface or within the biofilm was predicted for a subset of plausible parameter values. The finding that oxygen concentration at the biofilm-neutrophil juncture can be diminished to hypoxic levels is biologically relevant because oxygen depletion will reduce neutrophil killing ability. The finding that hypoxia can readily establish in the interior of the biofilm is biologically relevant because this change will alter microbial metabolism and persistence.
Collapse
Affiliation(s)
- Yilin Wu
- Department of Mathematics, Temple University, Philadelphia, PA 19122, USA
| | - Isaac Klapper
- Department of Mathematics, Temple University, Philadelphia, PA 19122, USA
| | - Philip S Stewart
- Center for Biofilm Engineering and Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717-3980, USA
| |
Collapse
|
45
|
Héry-Arnaud G, Boutin S, Cuthbertson L, Elborn SJ, Tunney MM. The lung and gut microbiome: what has to be taken into consideration for cystic fibrosis? J Cyst Fibros 2018; 18:13-21. [PMID: 30487080 DOI: 10.1016/j.jcf.2018.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/06/2018] [Accepted: 11/11/2018] [Indexed: 12/20/2022]
Abstract
The 15th European Cystic Fibrosis Society (ECFS) Basic Science pre-conference Symposium focused on the topic of the microbiome, asking the question "The lung and gut microbiome: what has to be considered for cystic fibrosis (CF)?" This review gives an overview of the main points raised during the symposium, which dealt with the technical considerations, pathophysiology and clinical implications of the microbiome in CF.
Collapse
Affiliation(s)
- Geneviève Héry-Arnaud
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France; Unité de Bactériologie, Pôle de Biologie-Pathologie, Hôpital La Cavale Blanche, CHRU de Brest, Brest, France.
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | | | - Stuart J Elborn
- National Heart and Lung Institute, Imperial College, London, UK; Halo Research Group, Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Michael M Tunney
- Halo Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| |
Collapse
|
46
|
Katsoulis K, Ismailos G, Kipourou M, Kostikas K. Microbiota and asthma: Clinical implications. Respir Med 2018; 146:28-35. [PMID: 30665515 DOI: 10.1016/j.rmed.2018.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 10/01/2018] [Accepted: 11/20/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Konstantinos Katsoulis
- Pulmonary Department, 424 Army General Hospital, Periferiaki Odos, 56429, Efkarpia, Thessaloniki, Greece
| | - Georgios Ismailos
- Experimental-Research Center ELPEN, ELPEN Pharmaceuticals, Leoforos Marathonos 95, 19009, Pikermi, Attika, Greece
| | - Maria Kipourou
- Pulmonary Department, 424 Army General Hospital, Periferiaki Odos, 56429, Efkarpia, Thessaloniki, Greece.
| | - Konstantinos Kostikas
- 2nd Respiratory Medicine Department, University of Athens Medical School, Attikon Hospital, Athens, Greece
| |
Collapse
|
47
|
Dickson RP. Kudzu and sleeper cells: the varied ecology of respiratory infections. Eur Respir J 2018; 52:52/4/1801607. [PMID: 30361265 DOI: 10.1183/13993003.01607-2018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Dept of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA .,Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI, USA
| |
Collapse
|
48
|
Kondo Y, Sato K, Nagano K, Nishiguchi M, Hoshino T, Fujiwara T, Nakayama K. Involvement of PorK, a component of the type IX secretion system, in Prevotella melaninogenica pathogenicity. Microbiol Immunol 2018; 62:554-566. [PMID: 30028034 DOI: 10.1111/1348-0421.12638] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 12/27/2022]
Abstract
Prevotella melaninogenica is a gram-negative anaerobic commensal bacterium that resides in the human oral cavity and is isolated as a pathogen of suppurative diseases both inside and outside the mouth. However, little is known about the pathogenic factors of P. melaninogenica. The periodontal pathogens Porphyromonas gingivalis and Tanerella forsythia secrete virulence factors such as protease and bacterial cell surface proteins via a type IX secretion system (T9SS) that are involved in pathogenicity. P. melaninogenica also possesses all known orthologs of T9SS. In this study, a P. melaninogenica GAI 07411 mutant deficient in the orthologue of the T9SS-encoding gene, porK, was constructed. Hemagglutination and biofilm formation were decreased in the porK mutant. Furthermore, following growth on skim milk-containing medium, the diameters of the halos surrounding the porK mutant were smaller than those of the wild-type strain, suggesting a decrease in secretion of proteases outside the bacterium. To investigate this in detail, culture supernatants of wild-type and porK mutant strains were purified and compared by two-dimensional electrophoresis. In the mutant strain, fewer spots were detected, indicating fewer secreted proteins. In infection experiments, the mortality rate of mice inoculated with the porK mutant strain was significantly lower than in the wild-type strain. These results suggest that P. melaninogenica secretes potent virulence factors via the T9SS that contribute to its pathogenic ability.
Collapse
Affiliation(s)
- Yoshio Kondo
- Department of Pediatric Dentistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Keiko Sato
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Keiji Nagano
- Department of Microbiology, School of Dentistry, Aichi Gakuin University 1-100 Kusumoto-cho, Chikusa-ku, Nagoya, Aichi 464-8650, Japan
| | - Miyuki Nishiguchi
- Department of Pediatric Dentistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Tomonori Hoshino
- Department of Pediatric Dentistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Taku Fujiwara
- Department of Pediatric Dentistry, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| |
Collapse
|
49
|
van der Does AM, Amatngalim GD, Keijser B, Hiemstra PS, Villenave R. Contribution of Host Defence Proteins and Peptides to Host-Microbiota Interactions in Chronic Inflammatory Lung Diseases. Vaccines (Basel) 2018; 6:vaccines6030049. [PMID: 30060554 PMCID: PMC6161034 DOI: 10.3390/vaccines6030049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/11/2022] Open
Abstract
The respiratory tract harbours a variety of microorganisms, collectively called the respiratory microbiota. Over the past few years, alterations in respiratory and gut microbiota composition have been associated with chronic inflammatory diseases of the lungs. How these changes influence disease development and progression is an active field of investigation. Identifying and understanding host-microbiota interactions and factors contributing to these interactions could promote the development of novel therapeutic strategies aimed at restoring host-microbiota homeostasis. In this review, we discuss recent literature on host-microbiota interactions in the respiratory tract, with a specific focus on the influence of endogenous host defence peptides and proteins (HDPs) on the composition of microbiota populations in vivo and explore possible HDPs-related therapeutic approaches targeting microbiota dysbiosis in chronic inflammatory lung diseases.
Collapse
Affiliation(s)
- Anne M van der Does
- Department of Pulmonology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands.
| | - Gimano D Amatngalim
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3508 AB, The Netherlands.
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht 3508 AB, The Netherlands.
| | - Bart Keijser
- Research Group Microbiology and Systems Biology, TNO (The Netherlands Organization for Applied Scientific Research), Zeist 3704 HE, The Netherlands.
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam (ACTA), University of Amsterdam, Amsterdam 1008 AA, The Netherlands.
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands.
| | | |
Collapse
|
50
|
Faria MMP, Winston BW, Surette MG, Conly JM. Bacterial DNA patterns identified using paired-end Illumina sequencing of 16S rRNA genes from whole blood samples of septic patients in the emergency room and intensive care unit. BMC Microbiol 2018; 18:79. [PMID: 30045694 PMCID: PMC6060528 DOI: 10.1186/s12866-018-1211-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 06/27/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sepsis refers to clinical presentations ranging from mild body dysfunction to multiple organ failure. These clinical symptoms result from a systemic inflammatory response to pathogenic or potentially pathogenic microorganisms present systemically in the bloodstream. Current clinical diagnostics rely on culture enrichment techniques to identify bloodstream infections. However, a positive result is obtained in a minority of cases thereby limiting our knowledge of sepsis microbiology. Previously, a method of saponin treatment of human whole blood combined with a comprehensive bacterial DNA extraction protocol was developed. The results indicated that viable bacteria could be recovered down to 10 CFU/ml using this method. Paired-end Illumina sequencing of the 16S rRNA gene also indicated that the bacterial DNA extraction method enabled recovery of bacterial DNA from spiked blood. This manuscript outlines the application of this method to whole blood samples collected from patients with the clinical presentation of sepsis. RESULTS Blood samples from clinically septic patients were obtained with informed consent. Application of the paired-end Illumina 16S rRNA sequencing to saponin treated blood from intensive care unit (ICU) and emergency department (ED) patients indicated that bacterial DNA was present in whole blood. There were three clusters of bacterial DNA profiles which were distinguished based on the distribution of Streptococcus, Staphylococcus, and Gram-negative DNA. The profiles were examined alongside the patient's clinical data and indicated molecular profiling patterns from blood samples had good concordance with the primary source of infection. CONCLUSIONS Overall this study identified common bacterial DNA profiles in the blood of septic patients which were often associated with the patients' primary source of infection. These results indicated molecular bacterial DNA profiling could be further developed as a tool for clinical diagnostics for bloodstream infections.
Collapse
Affiliation(s)
- Monica Martins Pereira Faria
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB T2N 4N1 Canada
| | - Brent Warren Winston
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB T2N 4N1 Canada
- Foothills Medical Centre, Alberta Health Services, Room AGW5, 1403 29th Street NW, Calgary, AB T2N 2T9 Canada
| | - Michael Gordon Surette
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4K1 Canada
- Department of Medicine and Biochemistry, Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4K1 Canada
- Department of Biomedical Sciences, Faculty of Health Science, McMaster University, Hamilton, ON L8S 4K1 Canada
| | - John Maynard Conly
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB T2N 4N1 Canada
- O’Brien Institute for Public Health, University of Calgary, Calgary, AB T2N 4N1 Canada
- Foothills Medical Centre, Alberta Health Services, Room AGW5, 1403 29th Street NW, Calgary, AB T2N 2T9 Canada
| |
Collapse
|