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.

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 Synergy of culture-dependent molecular identification and whole-community metabarcode sequencing for characterizing the microbiota of arable crop residues

2021 ◽  
Author(s):  
Valérie Laval ◽  
Lydie Kerdraon ◽  
Matthieu Barret ◽  
Anne-Lise Liabot ◽  
Coralie Marais ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Crop Residues ◽  
Culture Collection ◽  
Diversity Analysis ◽  
Complementary Information ◽  
Rhizosphere Microflora ◽  
Strain Isolation ◽  
Culture Independent ◽  
Dependent Strain ◽  
Culture Dependent

AbstractThis study is the first to compare culture-dependent (strain isolation plus molecular identification) and culture-independent (whole-community metabarcode sequencing) approaches for characterizing the microbiota of crop residues. We investigated the diversity of fungal and bacterial communities in wheat and oilseed rape residues, using two different culture-dependent strategies to cover the maximum diversity for each kingdom: broad substrate sampling coupled with low-throughput isolation and diversity analysis for fungi, and reduced substrate sampling coupled with high-throughput isolation and diversity analysis for bacteria. The proportion of cultivable microorganisms was neither as low as the ‘1%’ paradigm long associated with the rhizosphere microflora, nor as high as the 50% sometimes reported for the phyllosphere microflora. It was, thus, intermediate between the values for soil and plants. This finding is consistent with residues being considered to constitute an ecotone, at the interface between soil and phyllosphere. Isolation and metabarcoding provided consistent complementary information: they revealed close community profiles, leading to the identification of several common and specific amplicon sequence variants (ASVs). The power of the culture-independent approach was thus confirmed. By contrast the culture-dependent approach was less weak than anticipated. Firstly, it provided complementary information about microbial diversity, with several ASVs not retrieved by metabarcoding being identified after isolation in the community-based culture collection. Secondly, this approach made it possible to preserve and test different taxa either individually or after the creation of synthetic communities, for deciphering the ecological functions of communities beyond merely descriptive aspects.

scholarly journals Physicochemical and Microbial Diversity Analyses of Indian Hot Springs

2021 ◽  
Vol 12 ◽  
Author(s):  
Manik Prabhu Narsing Rao ◽  
Zhou-Yan Dong ◽  
Zhen-Hao Luo ◽  
Meng-Meng Li ◽  
Bing-Bing Liu ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Hot Springs ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Dominant Group ◽  
Thermostable Enzymes ◽  
Culture Independent ◽  
Culture Dependent

In the present study, physicochemical and microbial diversity analyses of seven Indian hot springs were performed. The temperature at the sample sites ranged from 32 to 67°C, and pH remained neutral to slightly alkaline. pH and temperature influenced microbial diversity. Culture-independent microbial diversity analysis suggested bacteria as the dominant group (99.3%) when compared with the archaeal group (0.7%). Alpha diversity analysis showed that microbial richness decreased with the increase of temperature, and beta diversity analysis showed clustering based on location. A total of 131 strains (divided into 12 genera and four phyla) were isolated from the hot spring samples. Incubation temperatures of 37 and 45°C and T5 medium were more suitable for bacterial isolation. Some of the isolated strains shared low 16S rRNA gene sequence similarity, suggesting that they may be novel bacterial candidates. Some strains produced thermostable enzymes. Dominant microbial communities were found to be different depending on the culture-dependent and culture-independent methods. Such differences could be attributed to the fact that most microbes in the studied samples were not cultivable under laboratory conditions. Culture-dependent and culture-independent microbial diversities suggest that these springs not only harbor novel microbial candidates but also produce thermostable enzymes, and hence, appropriate methods should be developed to isolate the uncultivated microbial taxa.

scholarly journals Analysis of the Bacterial Diversity Associated with the Roots of Maize (Zea mays L.) through Culture-Dependent and Culture-Independent Methods

ISRN Ecology ◽  
2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Paola Pereira ◽  
Fernando Ibáñez ◽  
Mónica Rosenblueth ◽  
Miriam Etcheverry ◽  
Esperanza Martínez-Romero
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Zea Mays L ◽  
Culture Collection ◽  
Maize Roots ◽  
Culture Independent ◽  
Internal Transcribed Spacer Sequences ◽  
Gradient Separation ◽  
Culture Dependent ◽  
Its Primers

The present study investigated bacterial diversity associated with the roots of maize through the use of culture-dependent and culture-independent methods. Bacterial 16S–23S rDNA internal transcribed spacer sequences (ITS) primers were used to amplify sequences obtained directly from the root matrix by Percoll gradient separation. This assay showed that γ-Proteobacteria within Enterobacter, Erwinia, Klebsiella, Pseudomonas, and Stenotrophomonas genera were predominant groups. The culturable component of the bacterial community was also assessed, revealing that the predominant group was Firmicutes, mainly of Bacillus genus, while Achromobacter, Lysinibacillus, and Paenibacillus genera were rarely found in association with the roots. Only two genera within γ-Proteobacteria, Enterobacter and Pseudomonas, were found in the culture collection. Differences in richness and diversity between the rhizospheric and endophytic bacterial communities were also evidenced. The spectrum of bacteria naturally associated with maize roots is wide and the magnitude of such diversity will depend on the methods chosen for analysis. The knowledge of this spectrum will facilitate the search of microorganisms capable of exerting antagonism to diverse pathogens or detecting plant growth enhancers.

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