scholarly journals Human Endometrial Microbiota at Term of Normal Pregnancies

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 971 ◽  
Author(s):  
Claudia Leoni ◽  
Oronzo Ceci ◽  
Caterina Manzari ◽  
Bruno Fosso ◽  
Mariateresa Volpicella ◽  
...  
Keyword(s):  
16S Rrna ◽  
Caesarean Delivery ◽  
Bacterial Population ◽  
Hypervariable Region ◽  
Normal Pregnancy ◽  
Endometrial Biopsy ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Caucasian Women ◽  
Elective Caesarean Delivery

The endometrium is a challenging site for metagenomic analysis due to difficulties in obtaining uncontaminated samples and the limited abundance of the bacterial population. Indeed, solid correlations between endometrial physio-pathologic conditions and bacteria compositions have not yet been firmly established. Nevertheless, the study of the endometrial microbiota is of great interest due to the close correlations between microbiota profiles, women’s health, and successful pregnancies. In this study, we decided to tackle the study of the endometrial microbiota through analysis of bacterial population in women subjected to elective caesarean delivery. As a pilot study, a cohort of 19 Caucasian women at full term of normal pregnancy and with a prospection of elective caesarean delivery was enrolled for endometrium sampling at the time of caesarean section. Sampling was carried out by endometrial biopsy soon after the delivery of the newborn and the discharge of the placenta and fetal membranes from the uterus. Bacterial composition was established by a deep metabarcoding next generation sequencing (NGS) procedure addressing the V5–V6 hypervariable region of the 16S rRNA gene. Amplicon sequences were analysed by bioinformatic procedures for denoising and taxonomic classification. The RDP database was used as 16S rRNA reference collection. Metabarcoding analysis showed the presence of a common bacterial composition, including six genera classifiable within the human microbiota (Cutibacterium, Escherichia, Staphylococcus, Acinetobacter, Streptococcus, Corynebacterium), that could be part of the core endometrial microbiota under the specific conditions examined. These results can provide useful information for future studies on the correlations between bacteria and successful pregnancies.

scholarly journals Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Petra Videnska ◽  
Kristyna Smerkova ◽  
Barbora Zwinsova ◽  
Vlad Popovici ◽  
Lenka Micenkova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Isolation ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Illumina Platform ◽  
Gram Positive ◽  
Bacterial Composition ◽  
Rrna Gene Sequencing

Abstract Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up the optimal sampling and DNA isolation procedures is crucial for robustness and reproducibility of the results. We performed a systematic comparison of several sampling and DNA isolation kits, quantified their effect on bacterial gDNA quality and the bacterial composition estimates at all taxonomic levels. Sixteen volunteers tested three sampling kits. All samples were consequently processed by two DNA isolation kits. We found that the choice of both stool sampling and DNA isolation kits have an effect on bacterial composition with respect to Gram-positivity, however the isolation kit had a stronger effect than the sampling kit. The proportion of bacteria affected by isolation and sampling kits was larger at higher taxa levels compared to lower taxa levels. The PowerLyzer PowerSoil DNA Isolation Kit outperformed the QIAamp DNA Stool Mini Kit mainly due to better lysis of Gram-positive bacteria while keeping the values of all the other assessed parameters within a reasonable range. The presented effects need to be taken into account when comparing results across multiple studies or computing ratios between Gram-positive and Gram-negative bacteria.

scholarly journals Isolation, Characterization, and Identification of Bacterial Population from Textile and Tannery Effluents of Bangladesh

2016 ◽  
Vol 29 (2) ◽  
pp. 84-88
Author(s):  
A Hakim ◽  
S Hoque ◽  
SM Ullah
Keyword(s):  
Bacterial Population ◽  
Bacterial Species ◽  
Bacterial Count ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Tannery Effluents ◽  
Bacterial Composition ◽  
Degrading Bacteria ◽  
Diagnostic Characteristics ◽  
Metal Treatment

Ten effluent samples from two different sites located at Hazaribagh tannery belt and Dhaka EPZ, Savar were collected. This study aimed to compare the bacterial composition isolated from tannery and textile effluents and to investigate the occurrence of metal toxicity tolerant and dye degrading bacteria and to select the potential strains for the use in bioremediation. The average bacterial count of HT and DETDE varied in between 3.35×106 and 5.45×106 cfu/mL and 4.8×106 and 7.75×106cfu/mL, respectively. A total of 12 bacterial isolates were characterized as strains of Bacillus, Staphylococcus, and Pseudomonas. A few, however, were re-cultured on other recommended media for verification of diagnostic characteristics. Maximum numbers of bacterial species were isolated from textile effluent. The results showed that a Gram-positive bacillus with a yellow pigment was considered as a major group of the population. Among them three isolates were identified based on alignments of partial sequence of 16S rRNA gene. These are also being used in different wastewater and metal treatment plants all over the world.Bangladesh J Microbiol, Volume 29, Number 2, Dec 2012, pp 84-88

scholarly journals Intestinal Microbiota of Fattening Pigs Offered Non-Fermented and Fermented Liquid Feed with and without the Supplementation of Non-Fermented Coarse Cereals

2020 ◽  
Vol 8 (5) ◽  
pp. 638 ◽  
Author(s):  
Sebastian Bunte ◽  
Richard Grone ◽  
Birgit Keller ◽  
Christoph Keller ◽  
Eric Galvez ◽  
...  
Keyword(s):  
Hypervariable Region ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Liquid Feed ◽  
Faecal Samples ◽  
Genus Lactobacillus ◽  
Miseq Platform ◽  
Small And Large Intestine

Introducing high numbers of lactic acid bacteria into the gastrointestinal tract of pigs via fermented liquid feed (FLF) could have an impact on intestinal bacterial ecosystems. Twenty piglets were allocated into four groups and fed a botanically identical liquid diet that was offered either non-fermented (twice), fully fermented or partially fermented but supplemented with 40% of non-fermented coarse cereals. Microbiota studies were performed on the small and large intestine digesta and faecal samples. A 16S rRNA gene amplification was performed within the hypervariable region V4 and sequenced with the Illumina MiSeq platform. R (version 3.5.2) was used for the statistical analyses. The digesta of the small intestines of pigs fed FLF were dominated by Lactobacillaceae (relative abundance up to 95%). In the colonic contents, the abundance of Lactobacillaceae was significantly higher only in the pigs fed the FLF supplemented with non-fermented coarse cereals. Additionally, the digesta of the small and large intestines as well as in the faeces of the pigs fed the FLF supplemented with non-fermented coarse cereals were significantly enriched for two operational taxonomic units (OTUs) belonging to the genus Lactobacillus and Bifidobacterium. The FLF supplemented with non-fermented coarse cereals had probiotic and prebiotic-like impacts on the intestinal and faecal bacterial composition of pigs.

Quantifying bacterial population dynamics in compost using 16S rRNA gene probes

2004 ◽  
Vol 66 (4) ◽  
pp. 457-463 ◽  
Author(s):  
Patrick D. Schloss ◽  
Anthony G. Hay ◽  
David B. Wilson ◽  
James M. Gossett ◽  
Larry P. Walker
Keyword(s):  
Population Dynamics ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Population ◽  
Rrna Gene ◽  
Gene Probes

scholarly journals Bar-Coded Pyrosequencing of 16S rRNA Gene Amplicons Reveals Changes in Ileal Porcine Bacterial Communities Due to High Dietary Zinc Intake

2010 ◽  
Vol 76 (19) ◽  
pp. 6689-6691 ◽  
Author(s):  
W. Vahjen ◽  
R. Pieper ◽  
J. Zentek
Keyword(s):  
Zinc Oxide ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Rrna Gene ◽  
Dietary Zinc ◽  
Bacterial Composition ◽  
Zinc Intake ◽  
Gram Negative ◽  
Facultative Anaerobic

ABSTRACT Feeding high levels of zinc oxide to piglets significantly increased the relative abundance of ileal Weissella spp., Leuconostoc spp., and Streptococcus spp., reduced the occurrence of Sarcina spp. and Neisseria spp., and led to numerical increases of all Gram-negative facultative anaerobic genera. High dietary zinc oxide intake has a major impact on the porcine ileal bacterial composition.

scholarly journals Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods

Microbiology ◽  
2004 ◽  
Vol 150 (8) ◽  
pp. 2565-2573 ◽  
Author(s):  
Xia Zhou ◽  
Stephen J. Bent ◽  
Maria G. Schneider ◽  
Catherine C. Davis ◽  
Mohammed R. Islam ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Pcr Amplification ◽  
Single Species ◽  
Rrna Gene ◽  
Caucasian Women ◽  
Tract Infections

The normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. Thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the aetiology of these diseases. Common wisdom is that lactobacilli dominate the normal vaginal microflora of post-pubertal women. However, this conclusion is based on methods that require cultivation of microbial populations; an approach that is known to yield a biased and incomplete assessment of microbial community structure. In this study cultivation-independent methods were used to analyse samples collected from the mid-vagina of five normal healthy Caucasian women between the ages of 28 and 44. Total microbial community DNA was isolated following resuspension of microbial cells from vaginal swabs. To identify the constituent numerically dominant populations in each community 16S rRNA gene libraries were prepared following PCR amplification using the 8f and 926r primers. From each library, the DNA sequences of approximately 200 16S rRNA clones were determined and subjected to phylogenetic analyses. The diversity and kinds of organisms that comprise the vaginal microbial community varied among women. Species of Lactobacillus appeared to dominate the communities in four of the five women. However, the community of one woman was dominated by Atopobium sp., whereas a second woman had appreciable numbers of Megasphaera sp., Atopobium sp. and Leptotrichia sp., none of which have previously been shown to be common members of the vaginal ecosystem. Of the women whose communities were dominated by lactobacilli, there were two distinct clusters, each of which consisted of a single species. One class consisted of two women with genetically divergent clones that were related to Lactobacillus crispatus, whereas the second group of two women had clones of Lactobacillus iners that were highly related to a single phylotype. These surprising results suggest that culture-independent methods can provide new insights into the diversity of bacterial species found in the human vagina, and this information could prove to be pivotal in understanding risk factors for various infectious diseases.

scholarly journals Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shoichiro Kameoka ◽  
Daisuke Motooka ◽  
Satoshi Watanabe ◽  
Ryuichi Kubo ◽  
Nicolas Jung ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Analysis Data ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Sequencing Technologies ◽  
Primer Sets ◽  
Microbiome Data

Abstract Background 16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1–V2 (V12) and the standard V3–V4 primer (V34) sets to optimize the gut microbiota analysis protocol. Results QIIME1 and QIIME2 analysis revealed a higher number of unclassified representative sequences in the V34 data than in the V12 data. The comparison of bacterial composition demonstrated that at the phylum level, Actinobacteria and Verrucomicrobia were detected at higher levels with V34 than with V12. Among these phyla, we observed higher relative compositions of Bifidobacterium and Akkermansia with V34. To estimate the actual abundance, we performed quantitative real-time polymerase chain reaction (qPCR) assays for Akkermansia and Bifidobacterium. We found that the abundance of Akkermansia as detected by qPCR was close to that in V12 data, but was markedly lower than that in V34 data. The abundance of Bifidobacterium detected by qPCR was higher than that in V12 and V34 data. Conclusions These results indicate that the bacterial composition derived from the V34 region might differ from the actual abundance for specific gut bacteria. We conclude that the use of the modified V12 primer set is more desirable in the 16S analysis of the Japanese gut microbiota.

scholarly journals Analysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota

2014 ◽  
Vol 80 (14) ◽  
pp. 4301-4312 ◽  
Author(s):  
Emre Aksoy ◽  
Erich L. Telleria ◽  
Richard Echodu ◽  
Yineng Wu ◽  
Loyce M. Okedi ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Hypervariable Region ◽  
Sympatric Species ◽  
Tsetse Fly ◽  
Tsetse Flies ◽  
Rrna Gene ◽  
Low Density ◽  
Content Type

ABSTRACTThe invertebrate microbiome contributes to multiple aspects of host physiology, including nutrient supplementation and immune maturation processes. We identified and compared gut microbial abundance and diversity in natural tsetse flies from Uganda using five genetically distinct populations ofGlossina fuscipes fuscipesand multiple tsetse species (Glossina morsitans morsitans,G. f. fuscipes, andGlossina pallidipes) that occur in sympatry in one location. We used multiple approaches, including deep sequencing of the V4 hypervariable region of the 16S rRNA gene, 16S rRNA gene clone libraries, and bacterium-specific quantitative PCR (qPCR), to investigate the levels and patterns of gut microbial diversity from a total of 151 individuals. Our results show extremely limited diversity in field flies of different tsetse species. The obligate endosymbiontWigglesworthiadominated all samples (>99%), but we also observed wide prevalence of low-densitySodalis(tsetse's commensal endosymbiont) infections (<0.05%). There were also several individuals (22%) with highSodalisdensity, which also carried coinfections withSerratia. Albeit in low density, we noted differences in microbiota composition among the genetically distinctG. f. fuscipesflies and between different sympatric species. Interestingly,Wigglesworthiadensity varied in different species (104to 106normalized genomes), withG. f. fuscipeshaving the highest levels. We describe the factors that may be responsible for the reduced diversity of tsetse's gut microbiota compared to those of other insects. Additionally, we discuss the implications ofWigglesworthiaandSodalisdensity variations as they relate to trypanosome transmission dynamics and vector competence variations associated with different tsetse species.

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