Combining culturing and 16S rDNA sequencing to reveal seasonal and room variations of household airborne bacteria and correlative environmental factors in nanjing, southeast china
Abstract:Bioaerosols are ubiquitous in indoor and outdoor environment. 1 They are tiny airborne particles, usually ranging from 0.001 nm to 100 μm, containing pathogenic and non-pathogenic dead or alive microorganisms (bacteria, fungi, and virus). 2,3 Fine bioaerosols tend to suspend for a long time in the air, varying from several minutes and even hours depending on their size. [4][5][6] Exposure to bioaerosols potentially poses adverse health effects, including infectious and respiratory diseases, allergies, and even… Show more
“…For bacterial diversity analysis, the universal primer (343F-5'-TACGGRAGGCAGCAG-3' and 798R-5'-AGGGTATCTAATCCT-3') was used to amplify the V3-V4 hypervariable regions of the bacterial 16S rDNA gene. 13 For fungal diversity analysis, the universal primer (ITS1F-5'-CTTGGTCATTTAGAGGAAGTAA-3' and ITS2-5'-GCTGCGTTCTTCATCGATGC-3') was used to amplify the ITS hypervariable regions. 38 The detailed information of the collected samples has been provided in Table 1.…”
“…29 Zhai et al 30 proposed that the 'inhalable coarse particles' with a diameter of 2.5 to 10 μm and the 'fine particles' smaller than 2.5 μm in diameter can enter the human inner body, 31 while most of the bioaerosols larger than 10 μm will deposit in the upper respiratory tract. 32 Ye et al 13 also revealed that particles <4.7 μm size range could penetrate the lower respiratory tract, such as the trachea, bronchus and alveolus. 13,33 Thus, the identification of factors that could affect the size distribution of bioaerosols in a built environment is important, as many studies have shown.…”
Section: Introductionmentioning
confidence: 99%
“…32 Ye et al 13 also revealed that particles <4.7 μm size range could penetrate the lower respiratory tract, such as the trachea, bronchus and alveolus. 13,33 Thus, the identification of factors that could affect the size distribution of bioaerosols in a built environment is important, as many studies have shown. 30,34 For example, Li et al 3 claimed that the size distribution of airborne bacteria and fungi are associated with indoor sources and human occupancy.…”
Section: Introductionmentioning
confidence: 99%
“…Many studies have investigated distributions of bioaerosols in one type of buildings, such as residences, [13][14][15][16] hospitals, [17][18][19][20] schools, 21,22 office buildings [23][24][25] and libraries. 26,27 The factors influencing bioaerosol concentration have also been explored, such as seasonal changes, 13 different indoor environments, 14 ventilation systems, 17 filtration, 23 the number of occupants. 26,28 In addition, Kadaifciler also found that the deterioration of books can also cause higher fungal activity in a library.…”
The characteristics of airborne bacteria and fungi in different types of buildings are still unclear. This article applied the culturing and next-generation sequencing methods to characterize the airborne bacteria and fungi in five types of buildings during winter in Kunming, China. Results showed that the mean concentrations of fungi in different buildings were similar (approx. 387 ± 388 CFU/m3). The highest culturable bacterial concentration was found in residences, while the lowest was in the library. Lowering relative humidity, PM2.5 concentration and occupant density can reduce the bacterial concentrations. The major bacterial size in residences and in a hospital was 1.1–2.1 μm, while in other buildings was 2.1–3.3 μm. The PM2.5 concentration and occupant activities are key factors that could affect the microorganism size distributions . The community structures of the bacteria in the library and fungi in the hospital showed distinctive differences from the results in other buildings. The community structure of outdoor microorganisms showed great differences between soil and air samples. This study is helpful to give practical implications for assessing microbial characteristics in different types of buildings and provide valuable data for the formulation of indoor bioaerosol standards in China.
“…For bacterial diversity analysis, the universal primer (343F-5'-TACGGRAGGCAGCAG-3' and 798R-5'-AGGGTATCTAATCCT-3') was used to amplify the V3-V4 hypervariable regions of the bacterial 16S rDNA gene. 13 For fungal diversity analysis, the universal primer (ITS1F-5'-CTTGGTCATTTAGAGGAAGTAA-3' and ITS2-5'-GCTGCGTTCTTCATCGATGC-3') was used to amplify the ITS hypervariable regions. 38 The detailed information of the collected samples has been provided in Table 1.…”
“…29 Zhai et al 30 proposed that the 'inhalable coarse particles' with a diameter of 2.5 to 10 μm and the 'fine particles' smaller than 2.5 μm in diameter can enter the human inner body, 31 while most of the bioaerosols larger than 10 μm will deposit in the upper respiratory tract. 32 Ye et al 13 also revealed that particles <4.7 μm size range could penetrate the lower respiratory tract, such as the trachea, bronchus and alveolus. 13,33 Thus, the identification of factors that could affect the size distribution of bioaerosols in a built environment is important, as many studies have shown.…”
Section: Introductionmentioning
confidence: 99%
“…32 Ye et al 13 also revealed that particles <4.7 μm size range could penetrate the lower respiratory tract, such as the trachea, bronchus and alveolus. 13,33 Thus, the identification of factors that could affect the size distribution of bioaerosols in a built environment is important, as many studies have shown. 30,34 For example, Li et al 3 claimed that the size distribution of airborne bacteria and fungi are associated with indoor sources and human occupancy.…”
Section: Introductionmentioning
confidence: 99%
“…Many studies have investigated distributions of bioaerosols in one type of buildings, such as residences, [13][14][15][16] hospitals, [17][18][19][20] schools, 21,22 office buildings [23][24][25] and libraries. 26,27 The factors influencing bioaerosol concentration have also been explored, such as seasonal changes, 13 different indoor environments, 14 ventilation systems, 17 filtration, 23 the number of occupants. 26,28 In addition, Kadaifciler also found that the deterioration of books can also cause higher fungal activity in a library.…”
The characteristics of airborne bacteria and fungi in different types of buildings are still unclear. This article applied the culturing and next-generation sequencing methods to characterize the airborne bacteria and fungi in five types of buildings during winter in Kunming, China. Results showed that the mean concentrations of fungi in different buildings were similar (approx. 387 ± 388 CFU/m3). The highest culturable bacterial concentration was found in residences, while the lowest was in the library. Lowering relative humidity, PM2.5 concentration and occupant density can reduce the bacterial concentrations. The major bacterial size in residences and in a hospital was 1.1–2.1 μm, while in other buildings was 2.1–3.3 μm. The PM2.5 concentration and occupant activities are key factors that could affect the microorganism size distributions . The community structures of the bacteria in the library and fungi in the hospital showed distinctive differences from the results in other buildings. The community structure of outdoor microorganisms showed great differences between soil and air samples. This study is helpful to give practical implications for assessing microbial characteristics in different types of buildings and provide valuable data for the formulation of indoor bioaerosol standards in China.
“…Combined with short-read next-generation sequencing (NGS), 16S rDNA gene amplicon-based metagenomic analysis of bacterial communities is possible and relatively straightforward (1). At present, 16S rDNA sequencing has been widely incorporated in the field of science, including food analysis (2)(3)(4), environmental surveys (5,6), and clinical tests (7)(8)(9)(10).…”
Although polymerase chain reaction (PCR) amplification and sequencing of the 16S rDNA region has been used in a wide range of scientific fields, it does not provide DNA methylation information. We describe a simple add-on method to investigate 5-methylcytosine residues in the bacterial 16S rDNA region from clinical samples or flora. Single-stranded bacterial DNA after bisulfite conversion was preferentially amplified with multiple displacement amplification (MDA) at pH neutral, and the 16S rDNA region was analyzed using nested bisulfite PCR and sequencing. 16S rDNA bisulfite sequencing can provide clinically important bacterial DNA methylation status concurrently with intact 16S rDNA sequence information. We used this approach to identify novel methylation sites and a methyltransferase (M. MmnI) in Morganella morganii. Next, we analyzed bacterial flora from clinical specimens of small amount and identified different methylation motifs among Enterococcus faecalis strains. The method developed here, referred to as "add-on" to the conventional 16S rDNA analysis, is the most clinically used bacterial identification genetic test, which provides additional information that could not be obtained with the conventional method. Since the relationship between drug resistance in bacteria and DNA methylation status has been reported, bacterial epigenetic information would be useful in clinical testing as well. Our analysis suggests that M. MmnI has a promotive effect on erythromycin resistance. 16S rDNA bisulfite PCR and sequencing coupled with MDA at pH neutral is a useful add-on tool for analyzing 16S meta-epigenetics.
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