scholarly journals Insight Into Microbial Community Aerosols Associated With Electronic Waste Handling Facilities by Culture-Dependent and Culture-Independent Methods

2021 ◽  
Vol 9 ◽  
Author(s):  
Yimin Pan ◽  
Qiaoqiao Ren ◽  
Pei Chen ◽  
Jiguo Wu ◽  
Zhendong Wu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Southern China ◽  
Electronic Waste ◽  
Transfer Station ◽  
Culture Independent ◽  
Waste Transfer ◽  
Waste Handling ◽  
First Time ◽  
Culture Dependent

Airborne microorganisms in the waste associated environments are more active and complex compared to other places. However, the diversity and structure of airborne bacteria in waste-associated environments are still not clearly understood. The purpose of this study was to assess airborne bacterial community in electronic waste dismantling site and a waste transfer station based on culture-dependent and culture-independent methods. A total of 229 isolates were obtained from four airborne sites collected from residential area, electronic industrial park, and office area in or near an electronic waste dismantling site and a waste transfer station in Southern China in the morning, afternoon, and evening. Most of the isolates were isolated from air for the first time and 14 potentially novel species were identified by Sanger sequencing. Bacterial communities in waste-associated bioaerosols were predominated by Proteobacteria and Bacteroidetes. Abundant genera (>1%) included Paracaedibacteraceae (uncultured EF667926), Ralstonia, Chroococcidiopsis, Chitinophagaceae (uncultured FN428761), Sphingobium, and Heliimonas. One-third of the species in these genera were uncultured approximately. Differences community structure existed in airborne bacterial diversity among different sampling sites. These results showed that waste-associated environments have unique bacterial diversity. Further studies on such environments could provide new insights into bacterial community.

scholarly journals Assessment of bacterial diversity in breast milk using culture-dependent and culture-independent approaches

2013 ◽  
Vol 110 (7) ◽  
pp. 1253-1262 ◽  
Author(s):  
Ted Jost ◽  
Christophe Lacroix ◽  
Christian Braegger ◽  
Christophe Chassard
Keyword(s):  
Breast Milk ◽  
Bacterial Diversity ◽  
Relative Abundance ◽  
Sanger Sequencing ◽  
454 Pyrosequencing ◽  
State Of The Art ◽  
Culture Independent ◽  
Colonic Health ◽  
First Time ◽  
Culture Dependent

Initial neonatal gut colonisation is a crucial stage for developing a healthy physiology, beneficially influenced by breast-feeding. Breast milk has been shown not only to provide nutrients and bioactive/immunological compounds, but also commensal bacteria, including gut-associated anaerobic Bifidobacterium spp. The aim of the present study was to investigate bacterial diversity in breast milk, with emphasis on identifying gut-associated obligate anaerobes. Breast milk collected from seven mothers at three sampling points (days 3–6, 9–14 and 25–30 postpartum) was analysed by combined culture-dependent and state-of-the-art, culture-independent methods (Sanger sequencing and 454-pyrosequencing). In addition to the predominance of facultative anaerobes such as Staphylococcus, Streptococcus and Propionibacterium (>90 % of isolated strains and 23·7 % relative abundance using pyrosequencing), significant populations of obligate anaerobes, including Bifidobacterium and Veillonella, were detected using pyrosequencing and confirmed by the isolation of viable strains (3·4 % of isolates and 1·4 % relative abundance). Pyrosequencing also revealed the presence of DNA of multiple major gut-associated obligate anaerobes (6·2 % relative abundance) such as Bacteroides and, for the first time, several members of the Clostridia, including butyrate producers, such as Faecalibacterium and Roseburia, which are important for colonic health. The present study suggests that breast milk may be a major source of bacterial diversity to the neonatal gut, including gut-associated obligate anaerobes, and may thus significantly influence gut colonisation and maturation of the immune system.

scholarly journals The bacterial community of the lone star tick (Amblyomma americanum)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
L. Paulina Maldonado-Ruiz ◽  
Saraswoti Neupane ◽  
Yoonseong Park ◽  
Ludek Zurek
Keyword(s):  
Bacterial Community ◽  
Amblyomma Americanum ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
Core Microbiome ◽  
Lone Star Tick ◽  
Animal Pathogens ◽  
Wide Range ◽  
Culture Independent ◽  
Culture Dependent

Abstract Background The lone star tick (Amblyomma americanum), an important vector of a wide range of human and animal pathogens, is very common throughout the East and Midwest of the USA. Ticks are known to carry non-pathogenic bacteria that may play a role in their vector competence for pathogens. Several previous studies using the high throughput sequencing (HTS) technologies reported the commensal bacteria in a tick midgut as abundant and diverse. In contrast, in our preliminary survey of the field collected adult lone star ticks, we found the number of culturable/viable bacteria very low. Methods We aimed to analyze the bacterial community of A. americanum by a parallel culture-dependent and a culture-independent approach applied to individual ticks. Results We analyzed 94 adult females collected in eastern Kansas and found that 60.8% of ticks had no culturable bacteria and the remaining ticks carried only 67.7 ± 42.8 colony-forming units (CFUs)/tick representing 26 genera. HTS of the 16S rRNA gene resulted in a total of 32 operational taxonomic units (OTUs) with the dominant endosymbiotic genera Coxiella and Rickettsia (> 95%). Remaining OTUs with very low abundance were typical soil bacterial taxa indicating their environmental origin. Conclusions No correlation was found between the CFU abundance and the relative abundance from the culture-independent approach. This suggests that many culturable taxa detected by HTS but not by culture-dependent method were not viable or were not in their culturable state. Overall, our HTS results show that the midgut bacterial community of A. americanum is very poor without a core microbiome and the majority of bacteria are endosymbiotic.

scholarly journals A Culture-Independent and Culture-Dependent Study of the Bacterial Community from the Bedrock Soil Interface

2015 ◽  
Vol 05 (13) ◽  
pp. 842-857 ◽  
Author(s):  
Karen Olsson-Francis ◽  
Carl P. Boardman ◽  
Victoria K. Pearson ◽  
Paul F. Schofield ◽  
Anna Oliver ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Culture Independent ◽  
Soil Interface ◽  
Culture Dependent

Bacterial diversity analysis in Kazakh fermented milks Shubat and Ayran by combining culture-dependent and culture-independent methods

LWT ◽  
2021 ◽  
Vol 141 ◽  
pp. 110877
Author(s):  
Sagyman Zhadyra ◽  
Xiao Han ◽  
Bakytzhan B. Anapiyayev ◽  
Fei Tao ◽  
Ping Xu
Keyword(s):  
Bacterial Diversity ◽  
Diversity Analysis ◽  
Culture Independent ◽  
Culture Dependent

scholarly journals To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12035
Author(s):  
Ankit Hinsu ◽  
Ashvin Dumadiya ◽  
Anjali Joshi ◽  
Rohitkumar Kotadiya ◽  
Kavan Andharia ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Similar Nature ◽  
Soil Diversity ◽  
16S Sequencing ◽  
Culture Independent ◽  
The Media ◽  
Ngs Data ◽  
Culture Dependent

Background Sequencing driven metagenomics studies have been instrumental in various aspects of microbiology including identification of newer taxa. While this culture-independent approach has its own merits and demerits, several studies have focussed on comparing it with traditional culture-dependent (CD) approach. However, most of these comparative studies rely on Sanger sequencing of complete 16S rRNA gene from pure culture colonies to determine the culturable bacterial diversity. This approach undercounts culturable diversity as only fewer isolates are selected, sequenced, and identified. Methods In this study, we have used an Illumina based partial 16S sequencing to identify all the microbes growing on the media and directly comparing with its culture-independent (CI) counterpart. Eight different media were used to target different organisms from soil. Diversity on these media were compared with their CI counterpart. The NGS data was analysed using DADA2 to provide more resolution to the data. Results In line with studies of similar nature, current study presented higher bacterial diversity in CI approach. However, the current study reflected that a greater number of sequence variants were missed out in CI approach as compared to number of sequence variants shared with CD approach. We observed around 322 (5.98%) ASVs (Amplicon Sequence Variants) exclusively present in CD samples while, 234 (4.35%) ASVs were shared between both approaches. Most of these 322 CD exclusive ASVs were classified as Enterobacteriaceae family and Bacillus genus, with several ASVs annotated at the species level as well, and these organisms are more commonly observed in soil and were also detected in CI approach. Furthermore, 22 genera were exclusively detected in CD samples, most of which were reported from soil and water.

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