Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Bacterial Genomes ◽

Significant Interest ◽

Physiological Information ◽

Rrna Gene Sequencing ◽

16S rRNA gene sequencing has engendered significant interest in studying microbial communities. There has been tension between trying to classify 16S rRNA gene sequences to increasingly lower taxonomic levels and the reality that those levels were defined using more sequence and physiological information than is available from a fragment of the 16S rRNA gene.

Highly Distinct Microbial Communities in Elevated Strings and Submerged Flarks in the Boreal Aapa-Type Mire

Microorganisms ◽

10.3390/microorganisms10010170 ◽

2022 ◽

Vol 10 (1) ◽

pp. 170

Author(s):

Andrey L. Rakitin ◽

Shahjahon Begmatov ◽

Alexey V. Beletsky ◽

Dmitriy A. Philippov ◽

Vitaly V. Kadnikov ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Raised Bogs ◽

European North ◽

Rrna Gene Sequencing ◽

Surface Peat

Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. In this paper, we characterized microbial diversity patterns in the surface peat layers of the neighboring string and flark structures located within the mire site in the Vologda region of European North Russia, using 16S rRNA gene sequencing. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks.

Diversity of bacterial communities on the facial skin of different age-group Thai males

PeerJ ◽

10.7717/peerj.4084 ◽

2017 ◽

Vol 5 ◽

pp. e4084 ◽

Cited By ~ 11

Author(s):

Alisa Wilantho ◽

Pamornya Deekaew ◽

Chutika Srisuttiyakorn ◽

Sissades Tongsima ◽

Naraporn Somboonna

Keyword(s):

Young Adults ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

Rrna Gene ◽

Skin Microbiome ◽

The Us ◽

Rrna Gene Sequencing ◽

BackgroundSkin microbiome varies from person to person due to a combination of various factors, including age, biogeography, sex, cosmetics and genetics. Many skin disorders appear to be related to the resident microflora, yet databases of facial skin microbiome of many biogeographies, including Thai, are limited.MethodsMetagenomics derived B-RISA and 16S rRNA gene sequencing was utilized to identify the culture-independent bacterial diversity on Thai male faces (cheek and forehead areas). Skin samples were categorized (grouped) into (i) normal (teenage.hea) and (ii) acne-prone (teenage.acn) young adults, and normal (iii) middle-aged (middle.hea) and (iv) elderly (elderly.hea) adults.ResultsThe 16S rRNA gene sequencing was successful as the sequencing depth had an estimated >98% genus coverage of the true community. The major diversity was found between the young and elderly adults in both cheek and forehead areas, followed by that between normal and acne young adults. Detection of representative characteristics indicated that bacteria from the order Rhizobiales, generaSphingomonasandPseudoalteromonas, distinguished theelderly.heamicrobiota, along the clinical features of wrinkles and pores. Prediction of the metabolic potential revealed reduced metabolic pathways involved in replication and repair, nucleotide metabolism and genetic translation in theelderly.heacompared with that in theteenage.hea. For young adults, some unique compositions such as abundance ofPropionibacterium acnesandStaphylococcus epidermidis, with a minor diversity between normal and acne skins, were detected. The metabolic potentials of the acne vs. normal young adults showed thatteenage.acnwas low in many cellular processes (e.g., cell motility and environmental adaptation), but high in carbohydrate metabolism, which could support acne growth. Moreover, comparison with the age-matched males from the US (Boulder, Colorado) to gain insight into the diversity across national biogeography, revealed differences in the distribution pattern of species, although common bacteria were present in both biogeographical samples. Furthermore, B-RISA served as a crosscheck result to the 16S rRNA gene sequencing (i.e., differences between teenage and elderly microbiota).ConclusionsThis study revealed and compared the microbial diversity on different aged Thai male faces, and included analyses for representing the bacterial flora, the clinical skin characteristics, and comparison with the US age-matched. The results represent the first skin microbiota of Thai males, and helps the design of a large-scale skin microbiome study of Thais. The findings of the diversity among ages, skin type and national biogeography supported the importance of these traits in the skin microbiome and in developing a safe and sustainable treatment for acne and aging skin diseases.

Chemotaxis Away from 4-Chloro-2-nitrophenol, 4-Nitrophenol, and 2,6-Dichloro-4-nitrophenol byBacillus subtilisPA-2

Journal of Chemistry ◽

10.1155/2015/296231 ◽

2015 ◽

Vol 2015 ◽

pp. 1-4 ◽

Cited By ~ 2

Author(s):

Pankaj Kumar Arora ◽

Mi-Jeong Jeong ◽

Hanhong Bae

Keyword(s):

Bacillus Subtilis ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

Rrna Gene ◽

Rrna Gene Sequencing ◽

The 16S Rrna Gene ◽

Drop Plate ◽

Chemotactic Behavior

Bacterial strain PA-2 exhibits chemotaxis away from 4-chloro-2-nitrophenol, 4-nitrophenol, and 2,6-dichloro-4-nitrophenol. This strain was identified asBacillus subtilison the basis of the 16S rRNA gene sequencing. The drop plate assay and the chemical-in-plug method were used to demonstrate negative chemotactic behavior of strain PA-2. The growth studies showed that strain PA-2 did not utilize 4-chloro-2-nitrophenol, 4-nitrophenol, and 2,6-dichloro-4-nitrophenol as its sole sources of carbon and energy. This is the first report of negative chemotaxis of 4-chloro-2-nitrophenol, 4-nitrophenol, and 2,6-dichloro-4-nitrophenol by any bacterium.

LACK OF EVIDENCE FOR A VIABLE MICROBIOTA IN MURINE AMNIOTIC FLUID

10.1101/2021.08.10.455893 ◽

2021 ◽

Author(s):

Andrew D. Winters ◽

Roberto Romero ◽

Jonathan M Greenberg ◽

Jose Galaz ◽

Zachary D Shaffer ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Amniotic Fluid ◽

16S Rdna ◽

Late Gestation ◽

Rrna Gene ◽

Rrna Gene Sequencing ◽

The existence of an amniotic fluid microbiota (i.e., a viable microbial community) in mammals is controversial. Its existence would require a fundamental reconsideration of the role of intra-amniotic microbes in fetal development and pregnancy outcomes. In this study, we determined whether the amniotic fluid of mice harbors a microbiota in late gestation. Bacterial profiles of amniotic fluids located proximally or distally to the cervix were characterized through quantitative real-time PCR, 16S rRNA gene sequencing, and culture (N=21 mice). These profiles were compared to those of technical controls for background DNA contamination. The load of 16S rDNA in the amniotic fluid exceeded that in controls. Additionally, the 16S rDNA profiles of the amniotic fluid differed from those of controls, with Corynebacterium tuberculostearicum being differentially more abundant in amniotic fluid profiles; however, this bacterium was not cultured. Of the 42 total bacterial cultures of amniotic fluids, only one yielded bacterial growth – Lactobacillus murinus. The 16S rRNA gene of this common murine-associated bacterium was not detected in any amniotic fluid sample, suggesting it did not originate from the amniotic fluid. No differences in 16S rDNA load, 16S rDNA profile, or bacterial culture were observed between amniotic fluids located proximal and distal to the cervix. Collectively, these data show that, although there is a modest DNA signal of bacteria in murine amniotic fluid, there is no evidence that this signal represents a viable microbiota. These findings refute the proposed role of amniotic fluid as a source of microorganisms for in utero colonization.

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis

Scientific Reports ◽

10.1038/s41598-020-73403-7 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Sidney P. Walker ◽

Maurice Barrett ◽

Glenn Hogan ◽

Yensi Flores Bueso ◽

Marcus J. Claesson ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Communities ◽

Gene Sequencing ◽

Rrna Gene ◽

Sample Type ◽

Human Dna ◽

Rrna Gene Sequencing ◽

Abstract The targeted sequencing of the 16S rRNA gene is one of the most frequently employed techniques in the field of microbial ecology, with the bacterial communities of a wide variety of niches in the human body have been characterised in this way. This is performed by targeting one or more hypervariable (V) regions within the 16S rRNA gene in order to produce an amplicon suitable in size for next generation sequencing. To date, all technical research has focused on the ability of different V regions to accurately resolve the composition of bacterial communities. We present here an underreported artefact associated with 16S rRNA gene sequencing, namely the off-target amplification of human DNA. By analysing 16S rRNA gene sequencing data from a selection of human sites we highlighted samples susceptible to this off-target amplification when using the popular primer pair targeting the V3–V4 region of the gene. The most severely affected sample type identified (breast tumour samples) were then re-analysed using the V1–V2 primer set, showing considerable reduction in off target amplification. Our data indicate that human biopsy samples should preferably be amplified using primers targeting the V1–V2 region. It is shown here that these primers result in on average 80% less human genome aligning reads, allowing for more statistically significant analysis of the bacterial communities residing in these samples.

Archaeal diversity in permafrost deposits of Bunger Hills Oasis and King George Island (Antarctica) according to the 16S rRNA gene sequencing

Microbiology ◽

10.1134/s0026261714040092 ◽

2014 ◽

Vol 83 (4) ◽

pp. 398-406 ◽

Cited By ~ 8

Author(s):

E. S. Karaevskaya ◽

L. S. Demchenko ◽

N. E. Demidov ◽

E. M. Rivkina ◽

S. A. Bulat ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

Rrna Gene ◽

Archaeal Diversity ◽

King George Island ◽

Rrna Gene Sequencing ◽

Intravaginal microbial flora by the 16S rRNA gene sequencing

American Journal of Obstetrics and Gynecology ◽

10.1016/j.ajog.2011.04.018 ◽

2011 ◽

Vol 205 (3) ◽

pp. 235.e1-235.e9 ◽

Cited By ~ 24

Author(s):

Kazuaki Yoshimura ◽

Nobuo Morotomi ◽

Kazumasa Fukuda ◽

Masahiro Nakano ◽

Masamichi Kashimura ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

Microbial Flora ◽

Rrna Gene ◽

Rrna Gene Sequencing ◽

Evaluation of the airway microbiome in nontuberculous mycobacteria disease

European Respiratory Journal ◽

10.1183/13993003.00810-2018 ◽

2018 ◽

Vol 52 (4) ◽

pp. 1800810 ◽

Cited By ~ 22

Author(s):

Imran Sulaiman ◽

Benjamin G. Wu ◽

Yonghua Li ◽

Adrienne S. Scott ◽

Patrick Malecha ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Potential Role ◽

Lower Airway ◽

Rrna Gene ◽

Airway Microbiome ◽

Rrna Gene Sequencing ◽

Culture Positive ◽

Aspiration is associated with nontuberculous mycobacterial (NTM) pulmonary disease and airway dysbiosis is associated with increased inflammation. We examined whether NTM disease was associated with a distinct airway microbiota and immune profile.297 oral wash and induced sputum samples were collected from 106 participants with respiratory symptoms and imaging abnormalities compatible with NTM. Lower airway samples were obtained in 20 participants undergoing bronchoscopy. 16S rRNA gene and nested mycobacteriome sequencing approaches characterised microbiota composition. In addition, inflammatory profiles of lower airway samples were examined.The prevalence of NTM+cultures was 58%. Few changes were noted in microbiota characteristics or composition in oral wash and sputum samples among groups. Among NTM+samples, 27% of the lower airway samples were enriched withMycobacterium. A mycobacteriome approach identifiedMycobacteriumin a greater percentage of samples, including some nonpathogenic strains. In NTM+lower airway samples, taxa identified as oral commensals were associated with increased inflammatory biomarkers.The 16S rRNA gene sequencing approach is not sensitive in identifying NTM among airway samples that are culture-positive. However, associations between lower airway inflammation and microbiota signatures suggest a potential role for these microbes in the inflammatory process in NTM disease.

FIRST ANALYSIS FROM UK IBD TWIN BIOBANK; 16S RRNA GENE SEQUENCING IDENTIFIES REDUCED DIVERSITY IN ACTIVE IBD AND TAXA ASSOCIATED WITH ACTIVE DISEASE PHENOTYPE TO LEVEL OF SPECIES

10.26226/morressier.59a6b347d462b80290b54eec ◽

2017 ◽

Author(s):

Marcus Harbord

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

Rrna Gene ◽

Disease Phenotype ◽

Rrna Gene Sequencing ◽

Active Disease

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

Current Chemical Biology ◽

10.2174/2212796812666180718114432 ◽

2019 ◽

Vol 13 (1) ◽

pp. 90-101

Author(s):

Sanju Kumari ◽

Utkarshini Sharma ◽

Rohit Krishna ◽

Kanak Sinha ◽

Santosh Kumar

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Molecular Characterization ◽

Biochemical Characterization ◽

Evolutionary Relationship ◽

Gene Sequencing ◽

Cellulase Activity ◽

Rrna Gene ◽

Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 µmol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.