scholarly journals The Relationship Between the Cervical Microbiome, HIV Status, and Pre-Cancerous Lesions

2018 ◽  
Author(s):  
Cameron Klein ◽  
Daniela Gonzalez ◽  
Crispin Kahesa ◽  
Julius Mwaiselage ◽  
Nirosh Aluthge ◽  
...  
Keyword(s):  
Hypervariable Region ◽  
Alpha Diversity ◽  
Operational Taxonomic Unit ◽  
Sub Saharan Africa ◽  
Hiv Positive ◽  
Rrna Gene ◽  
High Grade ◽  
Cervical Lesions ◽  
Abundant Otus ◽  
Bacterial Richness

AbstractNearly all cervical cancers are causally associated with Human Papillomavirus (HPV). The burden of HPV-associated dysplasias in Sub-Saharan Africa is influenced by HIV. To investigate the role of the bacterial microbiome in cervical dysplasia, cytobrush samples were collected directly from cervical lesions of 144 Tanzanian women. The V4 hypervariable region of the 16S rRNA gene was amplified and deep-sequenced. Alpha diversity metrics; Chao1, PD whole tree, and operational taxonomic Unit (OTU) estimates, displayed significantly higher bacterial richness in HIV positive patients (P = 0.01) than in HIV negative patients. Within HIV positive patients, there was higher bacterial richness in patients with high grade squamous intraepithelial lesions (HSIL; P = 0.13) than those without lesions. The most abundant OTUs associated with high-grade squamous intraepitheilal lesions (HSIL) were Mycoplasmatales, Pseudomonadales, and Staphylococcus. We suggest that a chronic mycoplasma infection of the cervix can contribute to HPV-dependent dysplasia by sustained inflammatory signals.

scholarly journals Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Cameron Klein ◽  
Daniela Gonzalez ◽  
Kandali Samwel ◽  
Crispin Kahesa ◽  
Julius Mwaiselage ◽  
...  
Keyword(s):  
Hiv Positive ◽  
High Grade ◽  
Squamous Intraepithelial Lesions ◽  
Cervical Lesions ◽  
Cervical Cancers ◽  
Bacterial Microbiome ◽  
Bacterial Richness ◽  
Intraepithelial Lesions ◽  
Hiv Negative

ABSTRACT Nearly all cervical cancers are causally associated with human papillomavirus (HPV). The burden of HPV-associated dysplasias in sub-Saharan Africa is influenced by HIV. To investigate the role of the bacterial microbiome in cervical dysplasia, cytobrush samples were collected directly from cervical lesions of 144 Tanzanian women. The V4 hypervariable region of the 16S rRNA gene was amplified and deep sequenced. Alpha diversity metrics (Chao1, PD whole tree, and operational taxonomic unit [OTU] estimates) displayed significantly higher bacterial richness in HIV-positive patients (P = 0.01) than in HIV-negative patients. In HIV-positive patients, there was higher bacterial richness in patients with high-grade squamous intraepithelial lesions (HSIL) (P = 0.13) than those without lesions. The most abundant OTUs associated with high-grade squamous intraepithelial lesions were Mycoplasmatales, Pseudomonadales, and Staphylococcus. We suggest that a chronic mycoplasma infection of the cervix may contribute to HPV-dependent dysplasia by sustained inflammatory signals. IMPORTANCE HPV is known to be the causal agent in the majority of cervical cancers. However, the role of the cervical bacterial microbiome in cervical cancer is not clear. To investigate that possibility, we collected cervical cytobrush samples from 144 Tanzanian women and performed deep sequencing of bacterial 16S rRNA genes. We found that HIV-positive patients had greater bacterial richness (P = 0.01) than HIV-negative patients. We also observed that women with high-grade squamous intraepithelial lesions (HSIL) had greater cervical bacterial diversity than women with cytologically normal cervices. Data from our precise sampling of cervical lesions leads us to propose that Mycoplasma contributes to a cervical microbiome status that promotes HPV-related cervical lesions. These results suggest a greater influence of the bacterial microbiota on the outcome of HPV infection than previously thought.

Effect of rice bran fermented with Saccharomyces cerevisiae and Lactobacillus plantarum on gut microbiome of mice fed high-sucrose diet

2019 ◽  
Vol 10 (7) ◽  
pp. 811-821
Author(s):  
J. Shibayama ◽  
M. Goto ◽  
T. Kuda ◽  
M. Fukunaga ◽  
H. Takahashi ◽  
...  
Keyword(s):  
Bile Acid ◽  
Rice Bran ◽  
Gut Microbiome ◽  
Control Diet ◽  
Alpha Diversity ◽  
Blood Lipid ◽  
Operational Taxonomic Unit ◽  
Rrna Gene ◽  
High Sucrose

To clarify the effect of rice bran (RB) and fermented RB (FRB) in a high-sucrose and low-dietary fibre diet on the gut microbiome, the in vitro bile acid-lowering capacity and caecal microbiota of ICR mice fed with 20% RB or FRB diets for two weeks were determined. The caecal microbiome was analysed by 16S rRNA gene amplicon sequencing. The in vitro bile acid-lowering capacity was high for FRB. In mouse experiments, triacylglycerol and total cholesterol were generally lower with FRB, although the faecal frequency was highest in mice fed with RB. The Shannon-Wiener and Simpson’s indices for alpha-diversity in the microbiome of mice fed with RB and FRB, were higher than mice fed the control diet. At the phylum level in the caecal microbiome, Firmicutes and Bacteroidetes were high with FRB and RB, respectively. At the operational taxonomic unit level, some bacterial groups related to diabetes and gut toxicity, such as Lachnospiraceae and Enterorhabdus mucosicola, were high for RB but not for FRB diets. These results suggest that FRB, rather than RB, intake improve the intestinal environment and blood lipid condition.

scholarly journals PSXIII-29 Farm of origin has a major influence on the colonic microbiome but alterations due to selection for feed efficiency are also evident

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 475-475
Author(s):  
Stafford Vigors ◽  
Torres Sweeney
Keyword(s):  
Feed Efficiency ◽  
Hypervariable Region ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Nutrient Digestibility ◽  
Major Influence ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Selection For

Abstract While the intestinal microbiota is functionally important in nutrient digestibility and animal performance, the role of the microbiome in influencing feed efficiency is not well characterised. The objective of this experiment was to determine the relative influence of feed efficiency and farm of origin on the pig colonic microbiome. Animals were sourced from two geographically distinct locations in Ireland (farm A + B) and evaluated to identify pigs divergent in feed efficiency. The 8 most efficient (LRFI) & 8 least efficient (HRFI) pigs from farm A and 12 LRFI & 12 HRFI pigs from farm B were slaughtered. Colonic digesta was collected for sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene was performed on the Illumina MiSeq. Alpha diversity differed between the farms in this study with pigs from farm A having greater diversity based on Shannon and InvSimpson measures compared to pigs from farm B (P < 0.05). In agreement with this observation, pigs grouped by farm of origin rather than RFI in the beta diversity analysis. However, despite variation between farms, interesting taxonomic differences were identified between RFI groups. Within the phylum Bacteroidetes, the LRFI pigs had increased abundance of two families BS11 (P < 0.05) and a tendency towards increased Bacteroidaceae (P < 0.10) relative to the HRFI group. At genus level, the LRFI pigs had a tendency towards increased Bacteroides and CF231 (P < 0.10). In conclusion, while farm of origin has a substantial influence on microbial diversity in the pig colon, a microbial signature indicative of feed efficiency status was evident.

scholarly journals The Subgingival Microbiome in Patients with Down Syndrome and Periodontitis

2020 ◽  
Vol 9 (8) ◽  
pp. 2482
Author(s):  
Lourdes Nóvoa ◽  
María del Carmen Sánchez ◽  
Juan Blanco ◽  
Jacobo Limeres ◽  
Maigualida Cuenca ◽  
...  
Keyword(s):  
Down Syndrome ◽  
Bacterial Species ◽  
Hypervariable Region ◽  
Alpha Diversity ◽  
Study Groups ◽  
Abundant Species ◽  
Rrna Gene ◽  
Periodontal Pathogens ◽  
Cross Sectional ◽  
The Difference

Objective: To describe the subgingival microbiome of individuals with Down syndrome (DS). Methods: We conducted a cross-sectional observational study that obtained bacterial DNA samples from 50 patients with DS, 25 with periodontitis (PDS) and 25 with a healthy periodontal condition (HDS). The samples were analyzed by sequencing the 16S rRNA gene V3–V4 hypervariable region using the MiSeq System. Taxonomic affiliations were assigned using the naïve Bayesian classifier integrated in QIIME2 plugins. We evaluated the difference in bacteria abundance between the sample groups using Wilcoxon and Kruskal–Wallis tests. We evaluated the alpha diversity of the identified species using the Observed, Chao1metric, ACE and Shannon indices and evaluated beta diversity with principal coordinate analysis (registration code: 2018/510). Results: Twenty-one genera and 39 bacterial species showed a significantly different abundance between the study groups. Among the genera, Porphyromonas, Treponema, Tannerella and Aggregatibacter were more abundant in the PDS group than in the HDS group, as were the less commonly studied Filifactor, Fretibacterium and Desulfobulbus genera. Among the species, Porphyromonas spp. and Tannerella spp. were the most abundant in the PDS group; the most abundant species in the HDS group were Pseudomonas spp., Granulicatella spp. and Gemella spp. Conclusion: Well-recognized periodontal pathogens and newly proposed pathogenic taxa were associated with periodontitis in patients with DS.

scholarly journals Diet induces reproducible alterations in the mouse and human gut microbiome

2019 ◽  
Author(s):  
Jordan E. Bisanz ◽  
Vaibhav Upadhyay ◽  
Jessie A. Turnbaugh ◽  
Kimberly Ly ◽  
Peter J. Turnbaugh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Meta Analysis ◽  
Alpha Diversity ◽  
Operational Taxonomic Unit ◽  
Molecular Testing ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Dietary Interventions

SummaryThe degree to which diet reproducibly alters the human and mouse gut microbiota remains unclear. Here, we focus on the consumption of a high-fat diet (HFD), one of the most frequently studied dietary interventions in mice. We employed a subject-level meta-analysis framework for unbiased collection and analysis of publicly available 16S rRNA gene and metagenomic sequencing data from studies examining HFD in rodent models. In total, we re-analyzed 27 studies, 1101 samples, and 106 million reads mapping to 16S rRNA gene sequences. We report reproducible changes in gut microbial community structure both within and between studies, including a significant increase in the Firmicutes phylum and decrease in the Bacteroidetes phylum; however, reduced alpha diversity is not a consistent feature of HFD. Finer taxonomic analysis revealed that the strongest signal of HFD on microbiota species composition is Lactococcus spp., which we demonstrate is a common dietary contaminant through the molecular testing of dietary ingredients, culturing, microscopy, and germ-free mouse experiments. After in silico removal of Lactococcus spp., we employed machine learning to define a unique operational taxonomic unit (OTU)-based signature capable of predicting the dietary intake of mice and demonstrate that phylogenetic and gene-family transformations of this model are capable of accurately predicting human samples in controlled feeding settings (area under the receiver operator curve = 0.75 and 0.88 respectively). Together, these results demonstrate the utility of microbiome meta-analyses in identifying robust bacterial signals for mechanistic studies and creates a framework for the routine meta-analysis of microbiome studies in preclinical models.

scholarly journals Precancerous Cervical Lesion Among HIV-Positive Women in Sub-Saharan Africa: A Systematic Review and Meta-Analysis

2019 ◽  
Vol 26 (1) ◽  
pp. 107327481984587 ◽  
Author(s):  
Fitsum Weldegebreal ◽  
Teshager Worku
Keyword(s):  
Associated Factors ◽  
Meta Analysis ◽  
Cervical Lesion ◽  
Sub Saharan Africa ◽  
Hiv Positive ◽  
Cervical Lesions ◽  
Hiv Positive Women ◽  
Precancerous Cervical Lesion ◽  
Sub Saharan ◽  
Precancerous Cervical Lesions

In sub-Saharan Africa, cervical cancer is an intersecting epidemic with HIV and it is the second most common cause of cancer-related deaths in women. Therefore, this study was aimed to estimate the current status of the prevalence and associated factors of precancerous cervical lesions among HIV-positive women in sub-Saharan Africa. A systematic literature search was conducted from legitimate electronic databases, including MEDLINE (Ovid), PubMed, EMBASE (Ovid), Emcare (Ovid), CINAHL (EBSCOhost), Web of Science, Scopus, and PopLine and other gray literature including Google, Google Scholar, World Cat, ResearchGate, and Mednar. Data were extracted with a structured format prepared in Microsoft Excel. Each study was evaluated using the Joanna Briggs Institute critical appraisal tool for cross-sectional and cohort studies checklists. Accordingly, medium and high-quality studies were included in the review. Data synthesis and statistical analysis was conducted using OpenMeta and comprehensive meta-analysis version 2 software. The study protocol is registered on PROSPERO with ID: CRD42018114266. The pooled prevalence of precancerous cervical lesion among HIV-positive women in sub-Saharan Africa was 25.6% (95% confidence interval [CI]: 19.4%-31.8%). Having more than 2 lifetime sexual partners (odds ratio [OR]: 4.77; 95% CI: 1.35-16.93), having had a history of sexually transmitted infections (STIs; OR: 1.92; 95% CI: 1.03-3.57), having more than 2 births (OR: 1.84; 95% CI: 1.33-2.53), and CD4 count <200 cells/mm3 (OR: 1.765; 95% CI: 1.23-2.535) were significantly associated with precancerous cervical lesions. The prevalence of precancerous cervical lesion among HIV-positive women was high. One in 4 HIV-infected women suffers from precancerous cervical lesion. Lower CD4 cell count, STIs, multiple sexual partnering, and histories of multiple births and abortions were the foremost contributing factors for this burden. Precancerous cervical lesion could be reduced significantly if preventive and promotive measures are done on the associated factors.

scholarly journals Vaginal microbiota differences associated with pelvic organ prolapse risk during late gestation in commercial sows

2021 ◽  
Author(s):  
Zoë E Kiefer ◽  
Lucas R Koester ◽  
Jamie M Studer ◽  
Amanda L Chipman ◽  
Christine Mainquist-Whigham ◽  
...  
Keyword(s):  
Pelvic Organ Prolapse ◽  
Community Composition ◽  
Alpha Diversity ◽  
Operational Taxonomic Unit ◽  
Pelvic Organ ◽  
Vaginal Microbiota ◽  
Mitigation Strategies ◽  
Late Gestation ◽  
Rrna Gene ◽  
Study Objective

Abstract During the last decade, sow mortality due to pelvic organ prolapse (POP) has increased. To better understand the biology associated with POP, sows were phenotypically assessed and assigned perineal scores (PS) based on presumed POP risk and categorized as PS1 (low), PS2 (moderate), or PS3 (high). The study objective was to identify changes in sow vaginal microbiota that may be associated with POP. The hypothesis is vaginal microbiota differs between sows with variable risk for POP, and changes in microbiota during late gestation exist between sows with differing risk. Of the 2864 sows scored during gestation week 15, 1.0%, 2.7%, and 23.4% of PS1, PS2, and PS3 sows, respectively, subsequently experienced POP. Vaginal swabs subjected to 16S rRNA gene sequencing revealed differences in community composition (Bray-Curtis; P &lt; 0.05) and individual operational taxonomic unit (OTU) comparisons between vaginal microbiota of PS1 and PS3 sows at gestation week 15. Further, differences (P &lt; 0.05) in community composition and OTUs (Q &lt; 0.05) were observed in PS3 sows that either did or did not subsequently experience POP. Differences in community structure (alpha diversity measurements; P &lt; 0.05), composition (P &lt; 0.05) and OTUs (Q &lt; 0.05) were observed in gestation week 12 sows scored PS1 compared to week 15 sows scored PS1 or PS3, suggesting sow vaginal microbiota shifts during late gestation differently as POP risk changes. Collectively, these data demonstrate sows with greater POP risk have unique vaginal microflora, for which a better understanding could aid in development of mitigation strategies.

scholarly journals Distinction between vaginal and cervical microbiota in high-risk human papilloma virus infected women in China

2021 ◽  
Author(s):  
Zhan Zhang ◽  
Ting Li ◽  
Dai Zhang ◽  
Xiaonan Zong ◽  
Huihui Bai ◽  
...  
Keyword(s):  
High Risk ◽  
Human Papilloma Virus ◽  
Female Genital Tract ◽  
Alpha Diversity ◽  
Hpv Infection ◽  
Lower Percentage ◽  
Rrna Gene ◽  
Cervical Lesions ◽  
Papilloma Virus ◽  
Next Generation Sequencing Technology

Abstract Background: High-risk human papilloma virus (hrHPV) is regarded as the main causal factor of cervical precancer and cancer when persistent infection is left untreated. Previous researches have confirmed that the vaginal microbiota was associated with HPV infection and the development of cervical lesions. A very recent study has revealed the microbiota at different parts of the female genital tract was closely related but different from each other. To analyze the distinction between vaginal and cervical microbiota of hrHPV(+) women in China, one hundred subjects were recruited including 20 healthy controls without HPV infection, 32 with other hrHPV(+), 38 with HPV16/18(+) and 10 with cervical carcinoma. Vaginal and cervical microbiota were separately tested through next-generation sequencing technology (NGS) targeting the variable region (V3-V4) of bacterial ribosome 16S rRNA gene. Results: HrHPV(+) subjects tend to be accustomed to vaginal douching (p =0.001), show more frequent usage of sanitary pads (p =0.007), have more sex partners (p =0.047), be more sexually active (p =0.025) and more diversed in ways of contraception (p =0.001). Alpha diversity of cervical microbiota was higher than that of vagina. Cervical microbiota consisted a lower percentage of Firmicutes and a higher percentage of Proteobacteria compared to the vagina at the phylm level. Sphingomonas of α-Proteobacteria was almost below detection limit in the vagina whereas accounted for five to ten percent at hrHPV(-) cervix (P＜0.001) and reversely associated with hrHPV infection (P＜0.05). Pseudomonas of γ-Proteobacteria could hardly be seen in the normal vagina and shared a little bit percentage in the normal cervix, but significantly higher in the HPV16/18 infected (P＜0.001) and cancerous cervix (P＜0.05). BV associated anaerobes like Gardnerella, Prevotella, Atopobium and Sneathia did not exhibit cervical specificity.Conclusions: Cervical microbiota has its uniqueness from that of vagina in bacterial communities presenting a higher proportion of Proteobacteria, of which Pseudomonas is positively while Sphingomonas was negatively associated with hrHPV infection and cervical cancer. It is of great improtance to deeply explore the cervical microbiota of hrHPV infected women.

scholarly journals Feeding Pre-weaned Calves With Waste Milk Containing Antibiotic Residues Is Related to a Higher Incidence of Diarrhea and Alterations in the Fecal Microbiota

2021 ◽  
Vol 8 ◽  
Author(s):  
Martina Penati ◽  
Giulia Sala ◽  
Filippo Biscarini ◽  
Antonio Boccardo ◽  
Valerio Bronzo ◽  
...  
Keyword(s):  
Alpha Diversity ◽  
Operational Taxonomic Unit ◽  
Fecal Microbiota ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
16S Rrna Gene Analysis ◽  
Gastrointestinal Health ◽  
Milk Substitute ◽  
Waste Milk

The cows receiving antibiotics for intra-mammary infection (IMI) produce milk that cannot be marketed. This is considered waste milk (WM), and a convenient option for farmers is using it as calf food. However, adding to the risk of selecting resistant bacteria, residual antibiotics might interfere with the gut microbiome development and influence gastrointestinal health. We assessed the longitudinal effect of unpasteurized WM containing residual cefalexin on calf intestinal health and fecal microbiota in an 8-week trial. After 3 days of colostrum, six calves received WM and six calves received bulk tank milk (BM) for 2 weeks. For the following 6 weeks, all 12 calves received milk substitute and starter feed. Every week for the first 2 weeks and every 2 weeks for the remaining 6 weeks, we subjected all calves to clinical examination and collected rectal swabs for investigating the fecal microbiota composition. Most WM calves had diarrhea episodes in the first 2 weeks of the trial (5/6 WM and 1/6 BM), and their body weight was significantly lower than that of BM calves. Based on 16S rRNA gene analysis, WM calves had a lower fecal microbiota alpha diversity than that in BM calves, with the lowest p-value at Wk4 (p &lt; 0.02), 2 weeks after exposure to WM. The fecal microbiota beta diversity of the two calf groups was also significantly different at Wk4 (p &lt; 0.05). Numerous significant differences were present in the fecal microbiota taxonomy of WM and BM calves in terms of relative normalized operational taxonomic unit (OTU) levels, affecting five phyla, seven classes, eight orders, 19 families, and 47 genera. At the end of the trial, when 6 weeks had passed since exposure to WM, the phyla Bacteroidetes, Firmicutes, and Saccharibacteria were lower, while Chlamydiae were higher in WM calves. Notably, WM calves showed a decrease in beneficial taxa such as Faecalibacterium, with a concomitant increase in potential pathogens such as Campylobacter, Pseudomonas, and Chlamydophila spp. In conclusion, feeding pre-weaned calves with unpasteurized WM containing antibiotics is related to a higher incidence of neonatal diarrhea and leads to significant changes in the fecal microbiota composition, further discouraging this practice in spite of its short-term economic advantages.

scholarly journals Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6440
Author(s):  
Xiaoxiao Sun ◽  
Meiling Wang ◽  
Lin Guo ◽  
Changlong Shu ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Room Temperature ◽  
Quantitative Polymerase Chain Reaction ◽  
Alpha Diversity ◽  
Operational Taxonomic Unit ◽  
Rrna Gene ◽  
Guanidine Thiocyanate ◽  
Sample Collection ◽  
Thiocyanate Solution ◽  
Health And Development

The interactions between rhizosphere microorganisms and plants are important for the health and development of crops. Analysis of plant rhizosphere bacterial compositions, particularly of those with resistance to biotic/abiotic stresses, may improve their applications in sustainable agriculture. Large-scale rhizosphere samplings in the field are usually required; however, such samples, cannot be immediately frozen. We found that the storage of samples at room temperature for 2 days leads to a considerable reduction in the operational taxonomic unit (OTU) number and the indices of bacterial alpha-diversity of rhizosphere communities. In this study, in order to overcome these problems, we established a method using guanidine thiocyanate (GTC) solution for the preservation of rhizosphere samples after their collection. This method allowed the maintenance of the samples for at least 1 day at room temperature prior to their cryopreservation and was shown to be compatible with conventional DNA isolation protocols. Illumina sequencing of V3 and V4 hypervariable regions of the 16S rRNA gene was used to assess the feasibility and reliability of this method, and no significant differences were observed in the number of OTUs and in the Chao and Shannon indices between samples stored at −70 °C and those stored in GTC solution. Moreover, the representation of Pseudomonas spp. in samples stored in GTC solution was not significantly different from that in samples stored at −70 °C, as determined by real-time quantitative polymerase chain reaction (p > 0.05). Both types of samples were shown to cluster together according to principal coordinate analysis. Furthermore, GTC solution did not affect the bacterial taxon profiles at different storage periods compared with those observed when storing the samples below −70 °C. Even incubation of thawed samples (frozen at −70 °C) for 15 min at room temperature induced minor changes in the bacterial composition. Taken together, our results demonstrated that GTC solution may provide a reliable alternative for the preservation of rhizosphere samples in the field.

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