scholarly journals LACK OF EVIDENCE FOR A VIABLE MICROBIOTA IN MURINE AMNIOTIC FLUID

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 ◽  
16S Rrna Gene Sequencing ◽  
Late Gestation ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
The 16S Rrna Gene

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.

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

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4084 ◽  
Author(s):  
Alisa Wilantho ◽  
Pamornya Deekaew ◽  
Chutika Srisuttiyakorn ◽  
Sissades Tongsima ◽  
Naraporn Somboonna
Keyword(s):  
Young Adults ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
The Us ◽  
Rrna Gene Sequencing ◽  
The 16S Rrna Gene

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.

scholarly journals Cat Scratch Disease: the Rare Role ofAfipia felis

1998 ◽  
Vol 36 (9) ◽  
pp. 2499-2502 ◽  
Author(s):  
Michael Giladi ◽  
Boaz Avidor ◽  
Yehudith Kletter ◽  
Suzy Abulafia ◽  
Leonard N. Slater ◽  
...  
Keyword(s):  
Lymph Node ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bartonella Henselae ◽  
16S Rrna Gene Sequencing ◽  
Fatty Acid Analysis ◽  
Rrna Gene ◽  
Cat Scratch Disease ◽  
Rrna Gene Sequencing

Since its isolation in 1988, Afipia felis has been associated with cat scratch disease (CSD) in only one report and its role in CSD has been questioned. We have cultured A. felisfrom a lymph node of a patient with CSD. 16S rRNA gene sequencing, DNA relatedness studies, fatty acid analysis, and PCR of the A. felis ferredoxin gene showed that the isolate is identical to the previously reported A. felis isolate. To determine the role of A. felis in CSD, PCR of the 16S rRNA gene followed by hybridizations with specific probes were performed with lymph node specimens from CSD patients. All 32 specimens tested positive forBartonella henselae and negative for A. felis. We conclude that A. felis is a rare cause of CSD. Diagnostic tests not conducive to the identification of A. felis might cause the diagnosis of CSD due to A. felis to be missed.

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

2015 ◽  
Vol 2015 ◽  
pp. 1-4 ◽  
Author(s):  
Pankaj Kumar Arora ◽  
Mi-Jeong Jeong ◽  
Hanhong Bae
Keyword(s):  
Bacillus Subtilis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna 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.

scholarly journals Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters

mSphere ◽  
2021 ◽  
Author(s):  
Patrick D. Schloss
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Bacterial Genomes ◽  
Significant Interest ◽  
Physiological Information ◽  
Rrna Gene Sequencing ◽  
The 16S Rrna Gene

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.

scholarly journals The Role of 16S rRNA Gene Sequencing in Confirmation of Suspected Neonatal Sepsis

2015 ◽  
Vol 62 (1) ◽  
pp. 75-80 ◽  
Author(s):  
Somaia El Gawhary ◽  
Mervat El-Anany ◽  
Reem Hassan ◽  
Doaa Ali ◽  
El Qassem El Gameel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Neonatal Sepsis ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

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

2020 ◽  
Vol 10 (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 ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sample Type ◽  
Human Dna ◽  
Rrna Gene Sequencing ◽  
The 16S Rrna Gene

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 ◽  
2014 ◽  
Vol 83 (4) ◽  
pp. 398-406 ◽  
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 ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Archaeal Diversity ◽  
King George Island ◽  
Rrna Gene Sequencing ◽  
The 16S Rrna Gene

scholarly journals New insight into the analysis of amniotic fluid microflora using 16S rRNA gene sequencing

2016 ◽  
Vol 3 (2) ◽  
Author(s):  
Young-Ah You ◽  
Ga-Hyun Son ◽  
Eun Jin Kwon ◽  
Mi Hye Park ◽  
Keun-Young Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Amniotic Fluid ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Insight Into

Intravaginal microbial flora by the 16S rRNA gene sequencing

2011 ◽  
Vol 205 (3) ◽  
pp. 235.e1-235.e9 ◽  
Author(s):  
Kazuaki Yoshimura ◽  
Nobuo Morotomi ◽  
Kazumasa Fukuda ◽  
Masahiro Nakano ◽  
Masamichi Kashimura ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Microbial Flora ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
The 16S Rrna Gene
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