scholarly journals A Deeper Look into the Biodiversity of the Extremely Acidic Copahue volcano-Río Agrio System in Neuquén, Argentina

2019 ◽  
Vol 8 (1) ◽  
pp. 58 ◽  
Author(s):  
Germán Lopez Bedogni ◽  
Francisco L. Massello ◽  
Alejandra Giaveno ◽  
Edgardo Rubén Donati ◽  
María Sofía Urbieta
Keyword(s):  
Extreme Environment ◽  
Low Ph ◽  
Rrna Gene ◽  
Prokaryotic Community ◽  
Operational Taxonomic Units ◽  
Acidic River ◽  
First Time ◽  
The 16S Rrna Gene ◽  
Generation Sequencing ◽  
Autochthonous Species

The Copahue volcano-Río Agrio system, on Patagonia Argentina, comprises the naturally acidic river Río Agrio, that runs from a few meters down the Copahue volcano crater to more than 40 km maintaining low pH waters, and the acidic lagoon that sporadically forms on the crater of the volcano, which is studied for the first time in this work. We used next-generation sequencing of the 16S rRNA gene of the entire prokaryotic community to study the biodiversity of this poorly explored extreme environment. The correlation of the operational taxonomic units (OTUs)s presence with physicochemical variables showed that the system contains three distinct environments: the crater lagoon, the Upper Río Agrio, and the Salto del Agrio waterfall, a point located approximately 12 km down the origin of the river, after it emerges from the Caviahue lake. The prokaryotic community of the Copahue Volcano-Río Agrio system is mainly formed by acidic bacteria and archaea, such as Acidithiobacillus, Ferroplasma, and Leptospirillum, which have been isolated from similar environments around the world. These results support the idea of a ubiquitous acidic biodiversity; however, this highly interesting extreme environment also has apparently autochthonous species such as Sulfuriferula, Acidianus copahuensis, and strains of Acidibacillus and Alicyclobacillus.

scholarly journals Co-occurrence patterns among prokaryotes across an age gradient in pit mud of Chinese strong-flavor liquor

2020 ◽  
Vol 66 (9) ◽  
pp. 495-504
Author(s):  
Yan Zheng ◽  
Xiaolong Hu ◽  
Zhongjun Jia ◽  
Paul L.E. Bodelier ◽  
Zhiying Guo ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Prokaryotic Community ◽  
16S Rrna Gene Analysis ◽  
Pit Mud ◽  
Niche Competition ◽  
Occurrence Patterns ◽  
The 16S Rrna Gene

It is widely believed that the quality and characteristics of Chinese strong-flavor liquor (CSFL) are closely related to the age of the pit mud; CSFL produced from older pit mud tastes better. This study aimed to investigate the alteration and interaction of prokaryotic communities across an age gradient in pit mud. Prokaryotic microbes in different-aged pit mud (1, 6, and 10 years old) were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. Analysis of the 16S rRNA gene indicated that the prokaryotic community was significantly altered with pit mud age. There was a significant increase in the genera Methanosarcina, Methanobacterium, and Aminobacterium with increased age of pit mud, while the genus Lactobacillus showed a significant decreasing trend. Network analysis demonstrated that both synergetic co-occurrence and niche competition were dominated by 68 prokaryotic genera. These genera formed 10 hubs of co-occurrence patterns, mainly under the phyla Firmicutes, Euryarchaeota, and Bacteroidetes, playing important roles on ecosystem stability of the pit mud. Environmental variables (pH, NH4+, available P, available K, and Ca2+) correlated significantly with prokaryotic community assembly. The interaction of prokaryotic communities in the pit mud ecosystem and the relationship among prokaryotic communities and environmental factors contribute to the higher quality of the pit mud in older fermentation pits.

Variation in the microbiome of the spider mite Tetranychus truncatus with sex, instar and endosymbiont infection

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Yu-Xi Zhu ◽  
Zhang-Rong Song ◽  
Shi-Mei Huo ◽  
Kun Yang ◽  
Xiao-Yue Hong
Keyword(s):  
Spider Mite ◽  
Potential Role ◽  
Developmental Stages ◽  
Spider Mites ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Operational Taxonomic Units ◽  
Dominant Bacteria ◽  
The 16S Rrna Gene

ABSTRACT Most arthropod-associated bacterial communities play a crucial role in host functional traits, whose structure could be dominated by endosymbionts. The spider mite Tetranychus truncatus is a notorious agricultural pest harboring various endosymbionts, yet the effects of endosymbionts on spider mite microbiota remain largely unknown. Here, using deep sequencing of the 16S rRNA gene, we characterized the microbiota of male and female T. truncatus with different endosymbionts (Wolbachia and Spiroplasma) across different developmental stages. Although the spider mite microbiota composition varied across the different developmental stages, Proteobacteria were the most dominant bacteria harbored in all samples. Positive relationships among related operational taxonomic units dominated the significant coassociation networks among bacteria. Moreover, the spider mites coinfected with Wolbachia and Spiroplasma had a significantly higher daily fecundity and juvenile survival rate than the singly infected or uninfected spider mites. The possible function of spider-mite associated bacteria was discussed. Our results highlight the dynamics of spider mite microbiotas across different life stages, and the potential role of endosymbionts in shaping the microbiota of spider mites and improving host fitness.

scholarly journals Amplification of the V5 – V8 region of the 16S rRNA gene effectively speciates medically important genital tract Lactobacillus species in the upper female genital tract

2019 ◽  
Author(s):  
Jessica L. O’Callaghan ◽  
Dana Willner ◽  
Melissa Buttini ◽  
Flavia Huygens ◽  
Elise S. Pelzer
Keyword(s):  
Next Generation Sequencing ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Genital Tract ◽  
Rrna Gene ◽  
Next Generation ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
The 16S Rrna Gene ◽  
Generation Sequencing

ABSTRACTBackgroundThe endometrial cavity is an upper genital tract site largely heralded as sterile, however, advances in culture-independent, next generation sequencing technology have revealed that this site harbours a rich microbial community which includes multiple Lactobacillus species. These bacteria are considered to be the most common non-pathogenic genital tract commensals. Next-generation sequencing of the female lower genital tract has revealed significant variation amongst microbial community composition with respect to Lactobacillus sp. in samples collected from healthy and diseased women. The aim of this study was to evaluate the ability of the 16S rRNA gene to characterize genital tract lactobacilli to species-level taxonomy.MethodsSamples were interrogated for the presence of microbial DNA using two-step next generation sequencing technology to exploit the V5–V8 regions of the 16S rRNA gene and compared to standard speciation using qPCR.ResultsThe V5-V8 region of the 16S rRNA gene has sufficient sequence variation within frequently encountered genital tract lactobacilli to allow accurate determination of relative abundance within the community, and speciation for several key community members without completing additional experimentation.ConclusionsNext-generation sequencing of clinical genital tract isolates is an effective method for high throughput identification to species-level of key Lactobacillus sp.IMPORTANCEHuman microbiome experiments, including the low biomass organs such as the upper genital tract, require the development of consensus protocols to ensure accurate comparison between such studies and our data forms an important foundation for future protocols.This paper provides evidence to support the selection of the V5-V8 regions of the 16S rRNA gene improved Lactobacillus speciation using next generation sequencing technology. The choice of variable region for broad-range amplification in microbiome studies is important due to preferential primer binding associated with some genera based on nucleotide sequence patterns. By utilising the V5-V8 region, multiple species of Lactobacillus can be characterised with relative confidence.

Untapped sponge microbiomes: structure specificity at host order and family levels

2019 ◽  
Vol 95 (9) ◽  
Author(s):  
Qi Yang ◽  
Christopher M M Franco ◽  
Hou-Wen Lin ◽  
Wei Zhang
Keyword(s):  
Species Level ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Class Level ◽  
Microbial Resources ◽  
Host Phylogeny ◽  
Shared Otus ◽  
Primer Sets ◽  
The 16S Rrna Gene ◽  
Unique Otus

ABSTRACT Sponges are complex holobionts in which the structure of the microbiome has seldom been characterized above the host species level. The hypothesis tested in this study is that the structure of the sponge microbiomes is specific to the host at the order and family levels. This was done by using 33 sponge species belonging to 19 families representing five orders. A combination of three primer sets covering the V1-V8 regions of the 16S rRNA gene provided a more comprehensive coverage of the microbiomes. Both the diversity and structure of sponge microbiomes were demonstrated to be highly specific to the host phylogeny at the order and family levels. There are always dominant operational taxonomic units (OTUs) (relative abundance >1%) shared between microbial communities of sponges within the same family or order, but these shared OTUs showed high levels of dissimilarity between different sponge families and orders. The unique OTUs for a particular sponge family or order could be regarded as their ‘signature identity’. 70%–87% of these unique OTUs (class level) are unaffiliated and represent a vast resource of untapped microbiota. This study contributes to a deeper understanding on the concept of host-specificity of sponge microbiomes and highlights a hidden reservoir of sponge-associated microbial resources.

scholarly journals Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
César Ruiz ◽  
Marcela Villegas-Plazas ◽  
Olivier P Thomas ◽  
Howard Junca ◽  
Thierry Pérez
Keyword(s):  
Extreme Environments ◽  
Amplicon Sequencing ◽  
Sponge Species ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
16S Amplicon Sequencing ◽  
Ecological Success ◽  
Specific Community ◽  
First Time ◽  
The 16S Rrna Gene

ABSTRACT The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.

scholarly journals Molecular and serological detection of Ehrlichia canis in naturally exposed dogs in Iran: an analysis on associated risk factors

2014 ◽  
Vol 23 (1) ◽  
pp. 16-22 ◽  
Author(s):  
Nadi Maazi ◽  
Abdolali Malmasi ◽  
Parviz Shayan ◽  
Seyed Mahdi Nassiri ◽  
Taghi Zahraei Salehi ◽  
...  
Keyword(s):  
Risk Factors ◽  
Rural Areas ◽  
Ehrlichia Canis ◽  
Rrna Gene ◽  
Igg Antibodies ◽  
Serological Detection ◽  
Blood Samples ◽  
Associated Risk Factors ◽  
First Time ◽  
The 16S Rrna Gene

The general aim of this study, which was conducted for the first time in Iran, was to evaluate the seroprevalence and geographical distribution of Ehrlichia canis in a dog population in Iran, followed by molecular confirmation using PCR and sequencing. Blood samples were collected from 240 dogs in different areas of Alborz and Tehran Provinces and initially analyzed using the immunofluorescent antibody (IFA) test to detect anti-Ehrlichia canis IgG antibodies. Subsequently, nested PCR was performed based on a fragment of the 16S rRNA gene of E. canis on serologically positive samples. The results showed that 40/240 dogs (16.6%) presented anti-Ehrlichia canis IgG antibodies and that nine of the blood samples from the 40 seropositive dogs (22.5%) contained E. canis DNA, which was confirmed by sequencing. The seroprevalence of E. canis tended to be higher in purebred, one to three-year-old male dogs living in the Plain zone, in rural areas; however, this difference was not statistically significant.

scholarly journals Bacterial diversity in the saliva of patients with different oral hygiene indexes

2012 ◽  
Vol 23 (4) ◽  
pp. 409-416 ◽  
Author(s):  
Juliana Vianna Pereira ◽  
Luciana Leomil ◽  
Fabíola Rodrigues-Albuquerque ◽  
José Odair Pereira ◽  
Spartaco Astolfi-Filho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Oral Hygiene ◽  
Dental Plaque ◽  
High Index ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Gene Libraries ◽  
The 16S Rrna Gene

The objective of the present study was to evaluate the bacterial diversity in the saliva of patients with different oral hygiene indexes using of two 16S rRNA gene libraries. Each library was composed of samples from patients with different averages of the differentiated Silness-Löe biofilm index: the first library (A) with an index between 1.0 and 3.0 (considered a high index) and the second library (B) between 0 and 0.5 (considered a low index). Saliva DNA was extracted and the 16S rRNA gene was amplified and cloned. The obtained sequences were compared with those stored at NCBI and RDP GenBank. The saliva of patients with high index presented five known genera - Streptococcus, Granulicatella, Gemella, Veillonella and Peptostreptococcus - and 33.3% of nonculturable bacteria grouped into 23 operational taxonomic units (OTUs). The saliva of patients with low index differed significantly from the first library (p=0.000) and was composed of 42 OTUs distributed into 11 known genera - Streptococcus, Granulicatella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces - including 24.87% of nonculturable bacteria. It was possible to conclude that there is greater bacterial diversity in the saliva of patients with low dental plaque in relation to patients with high dental plaque.

scholarly journals Isolation and Identification ofAcholeplasmasp. from the Mud Crab,Scylla serrata

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Ji-Gang Chen ◽  
Dan Lou ◽  
Ji-Fang Yang
Keyword(s):  
Cell Wall ◽  
Scylla Serrata ◽  
Rrna Gene ◽  
Mud Crab ◽  
Isolation And Identification ◽  
A Cell ◽  
First Time ◽  
The 16S Rrna Gene ◽  
Ferment Glucose ◽  
Mud Crabs

For the first time, a mollicute-like organism (MLO) was cultured from moribund mud crabs (Scylla serrata) during an outbreak of clearwater disease in Zhejiang Province, China. The MLO displayed a fried-egg colony morphology in culture, did not possess a cell wall, and was not retained by 0.45 μm and 0.2 μm filters. It was able to ferment glucose, sucrose, lactose, and maltose, but it did not utilize arginine and urea. The MLO grew in the absence of bovine serum and was not susceptible to digitonin. Sequence analysis of the 16S rRNA gene revealed that this MLO had 99% identity withAcholeplasma laidlawiiPG-8A, which indicates that the organism isolated from mud crabs is a member of the genusAcholeplasma.

scholarly journals Molecular Survey and Genetic Diversity of Hemoplasmas in Rodents from Chile

2020 ◽  
Vol 8 (10) ◽  
pp. 1493
Author(s):  
Amir Salvador Alabí ◽  
Gustavo Monti ◽  
Carola Otth ◽  
Paulina Sepulveda-García ◽  
Melissa Sánchez-Hidalgo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Wild Rodents ◽  
High Identity ◽  
Low Diversity ◽  
Hemotrophic Mycoplasma ◽  
First Time ◽  
The 16S Rrna Gene

Even though hemotrophic mycoplasma (hemoplasma) infections are well documented in a wide variety of hosts worldwide, there is a gap in the knowledge aobut hemoplasmas in rodents. This study aimed to molecularly survey and investigate the genetic diversity of hemoplasmas in rodents from Chile. Synanthropic and wild rodents (n = 74) were captured in the southern province of Valdivia (Corral, Valdivia, Riñihue, and Reumén localities). Spleen samples were submitted to a conventional PCR for hemotrophic Mycoplasma spp. targeting the 16S rRNA gene (800 bp), followed by sequencing, phylogenetic, and genetic diversity analyses. The overall occurrence of hemotrophic mycoplasmas in rodents from Valdivia was 24.5% (18/74) [95% CI (14.5; 34.1)]. Hemoplasmas were detected in Mus musculus (1/4), Rattus norvegicus (1/16), Abrothrix longipilis (7/13), A. olivaceo (6/8), and Oligoryzomys longicaudatus (3/10). The nucleotide polymorphism analysis of the targeted 16S rRNA region showed low diversity, with two genotypes and a high identity to the variants detected in wild rodents from Brazil. Hemoplasmas are described for the first time in rodents from Chile with a moderate occurrence and low 16S rDNA genetic diversity within the sampled rodent population. The detected hemoplasma genotypes were specific to rodents and were not shared with other mammals.

scholarly journals Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing

2022 ◽  
Vol 4 (1) ◽  
Author(s):  
Edna Chiang ◽  
Courtney L. Deblois ◽  
Hannah V. Carey ◽  
Garret Suen
Keyword(s):  
16S Rrna ◽  
Beta Diversity ◽  
Current Knowledge ◽  
Winter Season ◽  
Ground Squirrels ◽  
Rrna Gene ◽  
Active Season ◽  
Operational Taxonomic Units ◽  
The 16S Rrna Gene

Abstract Background Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota’s role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring. Results Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. Conclusions This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.

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