scholarly journals Vaginal microbiome and serum metabolite differences in late gestation commercial sows at risk for pelvic organ prolapse

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zoë E. Kiefer ◽  
Lucas R. Koester ◽  
Lucas Showman ◽  
Jamie M. Studer ◽  
Amanda L. Chipman ◽  
...  
Keyword(s):  
Pelvic Organ Prolapse ◽  
16S Rrna Gene Sequencing ◽  
Pelvic Organ ◽  
Late Gestation ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Swine Industry ◽  
Vaginal Microflora ◽  
Vaginal Swabs ◽  
Rrna Gene Sequencing

AbstractSow mortality attributable to pelvic organ prolapse (POP) has increased in the U.S. swine industry and continues to worsen. Two main objectives of this study were, (1) to develop a perineal scoring system that can be correlated with POP risk, and (2) identify POP risk-associated biological factors. To assess POP risk during late gestation, sows (n = 213) were scored using a newly developed perineal scoring (PS) system. Sows scored as PS1 (low), PS2 (moderate), or PS3 (high) based on POP risk. Subsequently, 1.5, 0.8, and 23.1% of sows scored PS1, PS2, or PS3, respectively, experienced POP. To identify biomarkers, serum and vaginal swabs were collected from late gestation sows differing in PS. Using GC–MS, 82 serum metabolite differences between PS1 and PS3 animals (P < 0.05) were identified. Vaginal swabs were utilized for 16S rRNA gene sequencing and differences in vaginal microbiomes between PS1 and PS3 animals were detected on a community level (P < 0.01) along with differences in abundances of 89 operational taxonomic units (P < 0.05). Collectively, these data demonstrate that sows with greater POP risk have differential serum metabolites and vaginal microflora. Additionally, an initial and novel characterization of the sow vaginal microbiome was determined.

scholarly journals Optimal protocols for sequence-based characterization of the human vaginal microbiome

2020 ◽  
Author(s):  
Luisa W. Hugerth ◽  
Marcela Pereira ◽  
Yinghua Zha ◽  
Maike Seifert ◽  
Vilde Kaldhusdal ◽  
...  
Keyword(s):  
16S Rrna ◽  
Best Practices ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Wide Range ◽  
Rrna Gene Sequencing ◽  
Good Agreement

AbstractThe vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment, but also to the use of conflicting methodologies to study its microbial composition. Here we systematically assess best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region has the best theoretical properties, but limitations of current sequencing technologies mean that the V3-V4 region performs equally well. Both of these approaches present very good agreement with qPCR quantification of key taxa, provided an appropriate bioinformatic pipeline is used. Shotgun metagenomic sequencing presents an interesting alternative to 16S amplification and sequencing, but it is not without its challenges. We have assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and – use, reference database of vaginal taxa. This strategy performed as well as the best performing previously published strategies. Despite the many advantages of shotgun sequencing none of the shotgun approaches assessed here had as good agreement with the qPCR data as 16S rRNA gene sequencing.ImportanceThe vaginal microbiome has been connected to a wide range of health outcomes, from susceptibility to sexually transmitted infections to gynecological cancers and pregnancy outcomes. This has led to a thriving research environment, but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail for them to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.

scholarly journals Understanding host-microbiota interactions in the commercial piglet around weaning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Saladrigas-García ◽  
M. D’Angelo ◽  
H. L. Ko ◽  
P. Nolis ◽  
Y. Ramayo-Caldas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gut Microbiota ◽  
Metabolic Response ◽  
Negative Impact ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Swine Industry ◽  
Weaning Stress ◽  
Rrna Gene Sequencing ◽  
The Impact

AbstractWeaning is a critical period in the life of pigs with repercussions on their health and welfare and on the economy of the swine industry. This study aimed to assess the effect of the commercial early weaning on gut microbiota, intestinal gene expression and serum metabolomic response via an integrated-omic approach combining 16S rRNA gene sequencing, the OpenArray gene expression technology and 1H-NMR spectroscopy. Fourteen piglets from different litters were sampled for blood, jejunum tissue and caecal content two days before (− 2d), and three days after (+ 3d) weaning. A clearly differential ordination of caecal microbiota was observed. Higher abundances of Roseburia, Ruminococcus, Coprococcus, Dorea and Lachnospira genera in weaned piglets compared to prior to weaning showed the quick microbial changes of the piglets’ gut microbiota. Downregulation of OCLN, CLDN4, MUC2, MUC13, SLC15A1 and SLC13A1 genes, also evidenced the negative impact of weaning on gut barrier and digestive functions. Metabolomic approach pinpointed significant decreases in choline, LDL, triglycerides, fatty acids, alanine and isoleucine and increases in 3-hydroxybutyrate after weaning. Moreover, the correlation between microbiota and metabolome datasets revealed the existence of metabolic clusters interrelated to different bacterial clusters. Our results demonstrate the impact of weaning stress on the piglet and give insights regarding the associations between gut microbiota and the animal gene activity and metabolic response.

289 Serum Trace Minerals in Late Gestation Sows at Variable Risk for Pelvic Organ Prolapse

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 111-112
Author(s):  
Zoe E Kiefer ◽  
Amanda Chipman ◽  
Lucas Showman ◽  
Aileen F Keating ◽  
Jason W Ross
Keyword(s):  
Vitamin E ◽  
Pelvic Organ Prolapse ◽  
Serum Vitamin ◽  
Pelvic Organ ◽  
Serum Copper ◽  
Late Gestation ◽  
Trace Minerals ◽  
Swine Industry ◽  
Serum Factors ◽  
Food And Agriculture

Abstract Within the last decade, pelvic organ prolapse (POP) resulting in sow mortality has become an increasing concern for the U.S. swine industry, contributing approximately 21% of all sow deaths. While little is known regarding the etiology preceding POP in sows, many have proposed an association with vitamin and trace minerals abundance to POP incidence. We tested the hypothesis that sows differing in POP risk would have differences in serum trace minerals and vitamins. A perineal scoring (PS) system (PS1 - presumed low risk; PS2 - presumed moderate risk; and PS3 - presumed high risk) to assess risk for POP during late gestation was used to score 213 individual sows. Blood was collected from sows of two different farms during late gestation (days 105–115) that scored a PS3 (n = 20) and a parity matched sow scored as PS 1 (n = 16). Subsequently, 1.5, 0.8, and 23.1% of sows scored as PS1, PS2, or PS3, respectively, experienced POP. Serum was analyzed at the Iowa State University Veterinary Diagnostic Lab for trace mineral content (Calcium, Copper, Iron, Potassium, Magnesium, Manganese, Molybdenum, Phosphorus, Selenium, and Zinc). Additionally, vitamin E was evaluated in serum via GC-MS. Differences (P &lt; 0.05) in copper, potassium, molybdenum, phosphorus, and selenium was observed between farms. Further a PS x Farm interaction (P = 0.06) was observed for serum copper abundance which across all farms was 12% less (P &lt; 0.04) in PS3 compared to PS1 sows. No impact on serum vitamin E was observed between PS sows. These data demonstrate sows with greater POP risk may have potential differences in serum factors although these data also underscore the importance of measuring vitamin and mineral quantities in a tissue specific manner. This project was supported by the National Pork Board and the Foundation for Food and Agriculture Research.

scholarly journals Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome

mSphere ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Luisa W. Hugerth ◽  
Marcela Pereira ◽  
Yinghua Zha ◽  
Maike Seifert ◽  
Vilde Kaldhusdal ◽  
...  
Keyword(s):  
16S Rrna ◽  
Best Practices ◽  
16S Rrna Gene ◽  
In Silico ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Rrna Gene Sequencing

ABSTRACT The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment but also to the use of conflicting methodologies to study its microbial composition. Here, we systematically assessed best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region performed best in silico, but limitations of current sequencing technologies meant that the V3-V4 region performed equally well. Both approaches presented very good agreement with qPCR quantification of key taxa, provided that an appropriate bioinformatic pipeline was used. Shotgun metagenomic sequencing presents an interesting alternative to 16S rRNA gene amplification and sequencing but requires deeper sequencing and more bioinformatic expertise and infrastructure. We assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and -use reference database of vaginal taxa. This curated database performed as well as the best-performing previously published strategies. Despite the many advantages of shotgun sequencing, none of the shotgun approaches assessed here agreed with the qPCR data as well as the 16S rRNA gene sequencing. IMPORTANCE The vaginal microbiome has been connected to various aspects of host health, including susceptibility to sexually transmitted infections as well as gynecological cancers and pregnancy outcomes. This has led to a thriving research environment but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.

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 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 219 Relationship between host-genetics and the vaginal microbiome in commercial gilts

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 43-44
Author(s):  
Leticia Sanglard ◽  
Stephan Schmitz-Esser ◽  
Kent Gray ◽  
Daniel C L Linhares ◽  
Carl J Yeoman ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Vaginal Swab ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Live Virus ◽  
Abundant Otus ◽  
Host Genetic ◽  
Heritability Estimates ◽  
Rrna Gene Sequencing ◽  
Genetic Contributions

Abstract The objective of this study was to investigate host-genetic contributions to the vaginal microbiome of commercial gilts vaccinated for Porcine Reproductive and Respiratory Syndrome (PRRS). Vaginal swab samples (n = 576) from 308 F1 gilts (183±12 days old) were collected on day 4 (D4) and 52 (D52) post-vaccination with a commercial modified live virus PRRS vaccine. Samples were used to profile the vaginal microbiome by 16S rRNA gene sequencing, with sequences clustered into operational taxonomic units (OTUs) and taxonomically classified. All animals were genotyped for 45,536 SNPs. Arcsine of the square root-transformed OTUs abundance data were analyzed using a linear mixed animal model with age at vaccination as a covariate and animal (random) for estimation of genetic parameters. The same model was used for GWAS for the 100 most abundant OTUs but with addition of genotype of SNPs as a covariate, one at a time. For D4, heritability estimates ranged from &lt; 0.001±0.01(13 OTUs) to 0.60±0.13 (Fusobacterium), with OTUs corresponding to the genera Fusobacterium, Pasteurellaceae, Clostridiales, Prevotellaceae, and Lactobacillus having high estimates (0.41±0.13 to 0.60±0.13). For D52, heritability estimates ranged from &lt; 0.001±0.01 (10 OTUs) to 0.63±0.12 (Terrisporobacter), with OTUs corresponding to Clostridium, Terrisporobacter, Romboutsia, Turicibacter, Phascolarctobacterium, Muribaculaceae, and Ruminococcaceae having high estimates (0.42±0.14 to 0.63±0.12). Forty-six QTLs were significantly (P &lt; 0.00001) associated with OTU across days. Among these, one main QTL on chromosome 12 (20–23Mb), a gene-rich region with previously identified QTL for immune-related traits, was identified for 5 and 6 OTUs on D4 and D52, respectively. These OTUs were mainly of the phyla Proteobacteria and Firmicutes on D4 and D52, respectively. In conclusion, there is evidence of substantial host genetic variation for vaginal microbiome in commercial PRRS-vaccinated gilts, including the identification of many QTLs. Additional research is needed to investigate the genetic relationship between vaginal microbiome, health, and production in pigs.

scholarly journals Vaginal microbiome analysis of healthy women during different periods of gestation

2020 ◽  
Vol 40 (7) ◽  
Author(s):  
Dan Li ◽  
Xin-Zuo Chi ◽  
Lei Zhang ◽  
Rui Chen ◽  
Jing-rong Cao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community Composition ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Lactobacillus Species ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Healthy Women ◽  
Vaginal Microflora ◽  
Uncomplicated Pregnancy

Abstract To assess the vaginal microbiome throughout full-term uncomplicated pregnancy, a longitudinal study was designed for 12 healthy women who had prepared to become pregnant and then delivered at term (38–42 weeks) without complications. The vaginal microbial community was studied at pre-pregnancy, 8–12, 24–28, 37–38 weeks of gestation, and puerperium, using hypervariable tag sequencing of the V3–V4 region of the 16S rRNA gene. Sequencing produced approximately 10 million reads on the Illumina MiSeq. Members of the Firmicutes phyla were prevailing before and during pregnancy periods, and the proportion was quite as Proteobacteria until puerperium. Lactobacillus genus was abundant before and during pregnancy, but post-delivery vaginal microflora variety turned diverse. The species-level analysis revealed that a healthy vaginal microbiome before or during pregnancy was prominently dominated by Lactobacillus crispatus. Furthermore, PCoA analysis revealed for differences in the bacterial community composition between the two levels of Lactobacillus species in pre-pregnancy and pregnancy period (PC1 contribution of 58.46%, PC3 contribution of 8.64%). Based on the taxonomic and PCoA analysis, we found that L. crispatus was dominant in the vaginal microflora of healthy women before or during pregnancy, but at the puerperium, the status changed leading to decreased abundance of protective Lactobacillus species that made vaginal micro-ecological barrier vulnerable to diseases. Additionally, vaginal pH was an important environmental property affecting the vaginal microbial community.

scholarly journals 28 Steroid hormones are differentially abundant in sows with elevated risk for pelvic organ prolapse during late gestation

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 113-113
Author(s):  
Zoe Kiefer ◽  
Amanda Chipman ◽  
Jamie M Studer ◽  
Rafael Dal Forno Gianluppi ◽  
Aileen F Keating ◽  
...  
Keyword(s):  
Pelvic Organ Prolapse ◽  
Complete Blood Count ◽  
Pelvic Organ ◽  
Late Gestation ◽  
C Reactive Protein ◽  
Swine Industry ◽  
Serum Factors ◽  
Reactive Protein ◽  
Food And Agriculture ◽  
Hormone Analysis

Abstract Sow mortality, as the result of pelvic organ prolapse (POP), has increased during recent years in the U.S. swine industry and continues to worsen. The objective of this study was to identify putative biological factors associated with POP risk. We hypothesized sows differing in POP risk would differ in serum factors and steroid hormone profiles. Perineal scores (PS) were assigned to sows (n=2865) during late gestation (days 107-116) to assess POP risk. Sows assigned a PS1 had a presumed low risk of POP while those assigned a PS2 or PS3 had a presumed moderate or high risk of POP, respectively. Subsequently, 1.0, 2.7, and 23.4% of sows scored as PS1, PS2, or PS3, experienced POP, respectively. Blood samples were collected on a subset of sows (n=215) identified as PS3 along with parity-matched PS1 sows at the time of scoring and whole blood was subjected to complete blood count (CBC) analysis. Serum from a subset of these (n=110) samples were also subjected to a 17-panel hormone analysis. Additionally, serum biomarkers of inflammation, C-reactive protein and haptoglobin, were analyzed in PS3 sows that subsequently experienced POP and parity matched PS1 sows that did not experience POP. The CBC analysis revealed a 4.3, 7.8 and 5.9% decrease (P &lt; 0.05) in mean platelet volume, lymphocytes, and monocytes, respectively, in PS3 compared to PS1 sows. Deoxycortisol, androstenedione, androsterone, estrone, β-estradiol, and testosterone were greater (P &lt; 0.05) in PS3 compared to PS1 sows. Circulating haptoglobin was unaffected (P = 0.35) by PS, although C-reactive protein was 24.6% greater (P = 0.02) in PS3 sows. Collectively, serum differences in hormone profiles and biomarkers consistent with inflammation in sows differing in POP risk. This project was supported by the National Pork Board and the Foundation for Food and Agriculture Research.

scholarly journals The Two-Way Interaction between the Molecules That Cause Vaginal Malodour and Lactobacilli: An Opportunity for Probiotics

2021 ◽  
Vol 22 (22) ◽  
pp. 12279
Author(s):  
Scarlett Puebla-Barragan ◽  
Polycronis Paul Akouris ◽  
Kait F. Al ◽  
Charles Carr ◽  
Britney Lamb ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Lactobacillus Species ◽  
Rrna Gene ◽  
Large Numbers ◽  
Vaginal Swabs ◽  
The Media ◽  
Rrna Gene Sequencing

Vaginal malodour is a sign of dysbiosis. The biogenic amines (BAs) cadaverine, putrescine and tyramine are known to be causative compounds. Recent reports suggest these compounds produced by pathogens might have a role beyond causing malodour; namely inhibiting the growth of lactobacilli bacteria that are crucial in the maintenance of vaginal homeostasis. The aim of this study was to identify whether certain lactobacilli strains could reduce BAs and to evaluate how Lactobacillus species were affected by these compounds. Using LC–MS and HPLC-UV, five Lactobacillus crispatus strains were identified as being capable of significantly reducing BAs from the media under in vitro conditions. Through 16S rRNA gene sequencing of vaginal swabs exposed to Bas, cadaverine was found to reduce the relative abundance of lactobacilli. When L. crispatus was exposed to media supplemented with BAs with an HCl adjusted lower pH, its growth was enhanced, demonstrating the relevance of the maintenance of an acidic vaginal environment. If strains are to be developed for probiotic application to alleviate bacterial vaginosis and other conditions affecting large numbers of women worldwide, their ability to adapt to Bas and regulate pH should be part of the experimentation.

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