High Diversity of Bacterial Communities in Developmental Stages of Bactrocera carambolae (Insecta: Tephritidae) Revealed by Illumina MiSeq Sequencing of 16S rRNA Gene

Abstract Hyalomma dromedarii is an important blood-feeding ectoparasite that affects the health of camels. We assessed the profile of bacterial communities associated with H. dromedarii collected from camels in the eastern part of the UAE in 2010 and 2019. A total of 100 partially engorged female ticks were taken from tick samples collected from camels (n = 100; 50/year) and subjected to DNA extraction and sequencing. The 16S rRNA gene was amplified from genomic DNA and sequenced using Illumina MiSeq platform to elucidate the bacterial communities. Principle Coordinates Analysis (PCoA) was conducted to determine patterns of diversity in bacterial communities. In 2010 and 2019, we obtained 899,574 and 781,452 read counts and these formed 371 and 191 operational taxonomic units (OTUs, clustered at 97% similarity), respectively. In both years, twenty-five bacterial families with high relative abundance were detected and the following were the most common: Moraxellaceae, Enterobacteriaceae, Staphylococcaceae, Bacillaceae, Corynebacteriaceae, Flavobacteriaceae, Francisellaceae, Muribaculaceae, Neisseriaceae, and Pseudomonadaceae. Francisellaceae and Enterobacteriaceae coexist in H. dromedarii and we suggest that they thrive under similar conditions and microbial interactions inside the host. Comparisons of diversity indicated that microbial communities differed in terms of richness and evenness between 2010 and 2019, with higher richness but lower evenness in communities in 2010. Principle coordinates analyses showed clear clusters separating microbial communities in 2010 and 2019. The differences in communities suggested that the repertoire of microbial communities have shifted. In particular, the significant increase in dominance of Francisella and the presence of bacterial families containing pathogenic genera shows that H. dromedarii poses a serious health risk to camels and people who interact with them. Thus, it may be wise to introduce active surveillance of key genera that constitute a health hazard in the livestock industry to protect livestock and people.

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A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes

Scientific Reports ◽

10.1038/s41598-020-59771-0 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 5

Author(s):

Anders B. Nygaard ◽

Hege S. Tunsjø ◽

Roger Meisal ◽

Colin Charnock

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Illumina Miseq ◽

Rrna Gene ◽

Preliminary Study ◽

Rrna Gene Sequencing ◽

Building Dust

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Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

LWT ◽

10.1016/j.lwt.2021.111579 ◽

2021 ◽

Vol 147 ◽

pp. 111579

Author(s):

Creciana M. Endres ◽

Ícaro Maia S. Castro ◽

Laura D. Trevisol ◽

Juliana M. Severo ◽

Michele B. Mann ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Molecular Characterization ◽

Bacterial Communities ◽

Rrna Gene

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Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts

Applied and Environmental Microbiology ◽

10.1128/aem.05285-11 ◽

2011 ◽

Vol 77 (20) ◽

pp. 7207-7216 ◽

Cited By ~ 76

Author(s):

Naomi F. Montalvo ◽

Russell T. Hill

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Communities ◽

Sponge Species ◽

Rrna Gene ◽

Gene Sequences ◽

Associated Bacteria ◽

Content Type ◽

Key Species ◽

Sponge Associated Bacteria

ABSTRACTThe giant barrel spongesXestospongiamutaandXestospongiatestudinariaare ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences fromX.mutaandX.testudinariashowed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the twoXestospongiaspecies, as well as sequences found also in other sponge species and are dominated by three bacterial groups,Chloroflexi,Acidobacteria, andActinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the twoXestospongiaspecies, and also with the genusXestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts.

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Epipelic cyanobacterial diversity in Pinang River basin, Malaysia, revealed by 16S-based metagenomic approach

Algologia ◽

10.15407/alg31.01.093 ◽

2021 ◽

Vol 31 (1) ◽

pp. 93-113

Author(s):

A.R. Nur Fadzliana ◽

◽

W.O. Wan Maznah ◽

S.A.M. Nor ◽

Choon Pin Foong ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

River Basin ◽

Sequence Data ◽

Diversity Index ◽

Saline Water ◽

Illumina Miseq ◽

Rrna Gene ◽

Cyanobacterial Community ◽

Upstream Station

Cyanobacteria are the most widespread group of photosynthetic prokaryotes. They are primary producers in a wide variety of habitats and are able to thrive in harsh environments, including polluted waters; therefore, this study was conducted to explore the cyanobacterial populations inhabiting river tributaries with different levels of pollution. Sediment samples (epipelon) were collected from selected tributaries of the Pinang River basin. Air Terjun (T1) and Air Itam rivers (T2) represent the upper streams of Pinang River basin, while Dondang (T3) and Jelutong rivers (T4) are located at in the middle of the river basin. The Pinang River (T5) is located near the estuary and is subjected to saline water intrusion during high tides. Cyanobacterial community was determined by identifying the taxa via 16S rRNA gene amplicon sequence data. 16S rRNA gene amplicons generated from collected samples were sequenced using illumina Miseq, with the targeted V3 and V4 regions yielding approximately 1 mln reads per sample. Synechococcus, Phormidium, Arthronema and Leptolyngbya were found in all samples. Shannon-Weiner diversity index was highest (H’ = 1.867) at the clean upstream station (T1), while the moderately polluted stream (T3) recorded the lowest diversity (H’ = 0.399), and relatively polluted stations (T4 and T5) recorded fairly high values of H’. This study provides insights into the cyanobacterial community structure in Pinang River basin via cultivation-independent techniques using 16S rRNA gene amplicon sequence. Occurrence of some morphospecies at specific locations showed that the cyanobacterial communities are quite distinct and have specific ecological demands. Some species which were ubiquitous might be able to tolerate varied environmental conditions.

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Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding

Frontiers in Microbiology ◽

10.3389/fmicb.2020.604964 ◽

2020 ◽

Vol 11 ◽

Author(s):

Pasquale Alibrandi ◽

Sylvia Schnell ◽

Silvia Perotto ◽

Massimiliano Cardinale

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Host Plant ◽

Bacterial Communities ◽

Reproductive Organs ◽

Distribution Model ◽

Rrna Gene ◽

Orchid Species ◽

Core Microbiota

The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.

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A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq

PeerJ ◽

10.7717/peerj.2492 ◽

2016 ◽

Vol 4 ◽

pp. e2492 ◽

Cited By ~ 29

Author(s):

Catherine M. Burke ◽

Aaron E. Darling

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

High Throughput ◽

Single Molecule ◽

Illumina Miseq ◽

Full Length ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Bacterial Taxonomy

BackgroundThe bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision.ResultsWe describe a method for sequencing near full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform and test it using DNA from human skin swab samples. Proof of principle of the approach is demonstrated, with the generation of 1,604 sequences greater than 1,300 nt from a single Nano MiSeq run, with accuracy estimated to be 100-fold higher than standard Illumina reads. The reads were chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection.ConclusionsThis method could be scaled up to generate many thousands of sequences per MiSeq run and could be applied to other sequencing platforms. This has great potential for populating databases with high quality, near full-length 16S rRNA gene sequences from under-represented taxa and environments and facilitates analyses of microbial communities at higher resolution.

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