Vaginal bacterial community composition and concentrations of estradiol at the time of artificial insemination in Brangus heifers

Abstract The knowledge surrounding the bovine vaginal microbiota and its implications on fertility and reproductive traits remains incomplete. The objective of the current study was to characterize the bovine vaginal bacterial community and estradiol concentrations at the time of artificial insemination (AI). Brangus heifers (n = 78) underwent a 7-d Co-Synch + controlled internal drug release estrus synchronization protocol. At AI, a double-guarded uterine culture swab was used to sample the anterior vaginal tract. Immediately after swabbing the vaginal tract, blood samples were collected by coccygeal venipuncture to determine concentrations of estradiol. Heifers were retrospectively classified as pregnant (n = 29) vs. nonpregnant (n = 49) between 41 and 57 d post-AI. Additionally, heifers were classified into low (1.1 to 2.5 pg/mL; n = 21), medium (2.6 to 6.7 pg/mL; n = 30), and high (7.2 to 17.6 pg/mL; n = 27) concentration of estradiol. The vaginal bacterial community composition was determined through sequencing of the V4 region from the 16S rRNA gene using the Illumina Miseq platform. Alpha diversity was compared via ANOVA and beta diversity was compared via PERMANOVA. There were no differences in the Shannon diversity index (alpha diversity; P = 0.336) or Bray–Curtis dissimilarity (beta diversity; P = 0.744) of pregnant vs. nonpregnant heifers. Overall, bacterial community composition in heifers with high, medium, or low concentrations of estradiol did not differ (P = 0.512). While no overall compositional differences were observed, species-level differences were present within pregnancy status and estradiol concentration groups. The implications of these species-level differences are unknown, but these differences could alter the vaginal environment thereby influencing fertility and vaginal health. Therefore, species-level changes could provide better insight rather than overall microbial composition in relation to an animal’s reproductive health.

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22 Comparison of vaginal microbiome and concentrations of estradiol at artificial insemination in Brangus heifers

Journal of Animal Science ◽

10.1093/jas/skz397.095 ◽

2020 ◽

Vol 98 (Supplement_2) ◽

pp. 41-42

Author(s):

Riley D Messman ◽

Zully Contreras-Correa ◽

Henry A Paz ◽

George Perry ◽

Caleb O Lemley

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Artificial Insemination ◽

Diversity Index ◽

Bacterial Community Composition ◽

Principal Component ◽

Alpha Diversity ◽

Illumina Miseq ◽

Rrna Gene ◽

Vaginal Microbiome

Abstract The knowledge surrounding the bovine vaginal microbiome and its implications on fertility and reproductive traits remains incomplete. The objective of the current study was to characterize the bovine vaginal microbiome and estradiol concentrations at time of artificial insemination (AI). Brangus heifers (n = 78) underwent a 7-d Co-Synch + CIDR estrus synchronization protocol. At AI, a double guarded uterine culture swab was used to sample the anterior vaginal tract. Blood samples were collected by coccygeal venipuncture to determine concentrations of estradiol. Heifers were retrospectively classified as pregnant (n = 29) versus nonpregnant (n = 49) on day 35. Lastly, heifers were classified into low (1.1 - 2.5 pg/ml; n = 21), medium (2.6 - 6.7 pg/ml; n = 30), and high (7.2 - 17.6 pg/ml; n = 27) concentrations of estradiol. The vaginal bacterial community composition was determined through sequencing of the V4-V5 region from the 16S rRNA gene using the Illumina Miseq platform. ANOVA was used to compare the diversity metrics between treatment groups. PERMANOVA was utilized to determine variation in community structure. There were no statistical differences in the Shannon diversity index (alpha diversity; P = 0.336) or principal component analysis (beta diversity; P = 0.744) of pregnant versus nonpregnant animals. The vaginal microbiome of pregnant and nonpregnant animals was similar with the four most abundant phyla being Tenericutes, Proteobacteria, Fusobacteria, and Firmicutes. Overall bacterial community composition in animals with high, medium, or low concentrations of estradiol did not differ (P = 0.512). These results indicate that concentration of estradiol does not impact vaginal microbiome composition. In conclusion, the composition of the bovine vaginal microbiome, although dynamic, may not be directly linked to an animal’s reproductive ability.

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23 Comparison of vaginal microbiome and concentrations of estradiol at artificial insemination in Brangus heifers

Journal of Animal Science ◽

10.1093/jas/skz397.032 ◽

2020 ◽

Vol 98 (Supplement_2) ◽

pp. 14-15

Author(s):

Riley D Messman ◽

Zully Contreras-Correa ◽

Henry A Paz ◽

George Perry ◽

Caleb O Lemley

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Artificial Insemination ◽

Diversity Index ◽

Bacterial Community Composition ◽

Principal Component ◽

Alpha Diversity ◽

Illumina Miseq ◽

Rrna Gene ◽

Vaginal Microbiome

Abstract The knowledge surrounding the bovine vaginal microbiome and its implications on fertility and reproductive traits remains incomplete. The objective of the current study was to characterize the bovine vaginal microbiome and estradiol concentrations at time of artificial insemination (AI). Brangus heifers (n = 78) underwent a 7-day Co-Synch + CIDR estrus synchronization protocol. At AI, a double guarded uterine culture swab was used to sample the anterior vaginal tract. Blood samples were collected by coccygeal venipuncture to determine concentrations of estradiol. Heifers were retrospectively classified as pregnant (n = 29) versus nonpregnant (n = 49) on day 35. Lastly, heifers were classified into low (1.1 - 2.5 pg/ml; n = 21), medium (2.6 - 6.7 pg/ml; n = 30), and high (7.2 - 17.6 pg/ml; n = 27) concentrations of estradiol. The vaginal bacterial community composition was determined through sequencing of the V4-V5 region from the 16S rRNA gene using the Illumina Miseq platform. ANOVA was used to compare the diversity metrics between treatment groups. PERMANOVA was utilized to determine variation in community structure. There were no statistical differences in the Shannon diversity index (alpha diversity; P = 0.336) or principal component analysis (beta diversity; P = 0.744) of pregnant versus nonpregnant animals. The vaginal microbiome of pregnant and nonpregnant animals was similar with the four most abundant phyla being Tenericutes, Proteobacteria, Fusobacteria, and Firmicutes. Overall bacterial community composition in animals with high, medium, or low concentrations of estradiol did not differ (P = 0.512). These results indicate that concentration of estradiol does not impact vaginal microbiome composition. In conclusion, the composition of the bovine vaginal microbiome, although dynamic, may not be directly linked to an animal’s reproductive ability.

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Impact of enzymatic digestion on bacterial community composition in CF airway samples

PeerJ ◽

10.7717/peerj.3362 ◽

2017 ◽

Vol 5 ◽

pp. e3362 ◽

Cited By ~ 1

Author(s):

Kayla M. Williamson ◽

Brandie D. Wagner ◽

Charles E. Robertson ◽

Emily J. Johnson ◽

Edith T. Zemanick ◽

...

Keyword(s):

Bacterial Community ◽

Dna Extraction ◽

Community Composition ◽

Bacterial Communities ◽

Beta Diversity ◽

Diversity Index ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Enzymatic Digestion ◽

Rrna Gene

BackgroundPrevious studies have demonstrated the importance of DNA extraction methods for molecular detection ofStaphylococcus,an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF.MethodsDNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD.ResultsShannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the generaGemella(p < 0.01),Streptococcus(p < 0.01), andRothia(p < 0.01).Staphylococcus(p < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD:Veillonella(p < 0.01),Granulicatella(p < 0.01),Prevotella(p < 0.01), andGemella(p = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition.DiscussionWe show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection ofStaphylococcusin CF OP samples. The enhanced identification ofStaphylococcus aureusis a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

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Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop

PeerJ ◽

10.7717/peerj.6768 ◽

2019 ◽

Vol 7 ◽

pp. e6768

Author(s):

Matheus A.P. Cipriano ◽

Afnan K.A. Suleiman ◽

Adriana P.D. da Silveira ◽

Janaína B. do Carmo ◽

Eiko E. Kuramae

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

16S Rrna ◽

Community Composition ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Nitrous Oxide Emissions ◽

Rrna Gene ◽

Bacterial Strains ◽

Microbial Composition

The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on16S rRNAsequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar toLysinibacillus, encode fornirKgene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.

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Melatonin-induced Changes in the Bovine Vaginal Microbiota During Maternal Nutrient Restriction in Brangus Heifers

Journal of Animal Science ◽

10.1093/jas/skab096.047 ◽

2021 ◽

Vol 99 (Supplement_2) ◽

pp. 26-27

Author(s):

Riley D Messman ◽

Caleb O Lemley ◽

Zully E Contreras-Correa ◽

Henry A Paz

Keyword(s):

Gestational Age ◽

Artificial Insemination ◽

Beta Diversity ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Vaginal Microbiota ◽

Nutrient Restriction ◽

Rrna Gene ◽

Linear Discriminant ◽

Genus Level

Abstract Altering the composition of the bovine vaginal microbiota has proved challenging; with recent studies deeming the microbiota dynamic due to few overall changes being found. Therefore, the objectives of this study were to determine if gestational age, endogenous progesterone, maternal nutrient restriction, or dietary melatonin altered the composition of the bovine vaginal microbiota. Brangus heifers (n = 29) from timed artificial insemination to d 240 of gestation were used; at d 160 of gestation, heifers were assigned to either an adequate (ADQ; n = 14; 100% NRC requirements) or restricted (RES; n = 15; 60% NRC requirements) nutritional plane and were either supplemented with dietary melatonin (MEL; n = 15) or not supplemented (CON; n = 14). Samples for vaginal microbiota analysis were taken on d 0 (prior to artificial insemination), d 150 (prior to dietary treatments), and d 220 of gestation (60 days post-treatment initiation) using a double guarded culture swab. The vaginal bacterial community composition was determined through sequencing the V4 region of the 16S rRNA gene using the Illumina Miseq platform. Alpha diversity was compared via two-way ANOVA; beta diversity was compared via PERMANOVA. The linear discriminant analysis for effect size (LEfSe) pipeline was utilized for analysis of taxonomic rank differences between bacterial communities. Gestational age, progesterone concentration, and maternal nutritional plane did not alter alpha or beta diversity of the vaginal microbiota. However, gestational age resulted in compositional changes at the order, family, and genus level. Moreover, dietary melatonin supplementation did not alter alpha diversity of the vaginal microbiota but did alter beta diversity (P = 0.02). Specifically, melatonin altered the composition at the genus level and increased the prevalence of aerobic bacteria in the vaginal tract. To date, melatonin is the first hormone associated with altering the composition of the vaginal microbiota.

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Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652031 ◽

2021 ◽

Vol 12 ◽

Author(s):

Matteo Daghio ◽

Francesca Ciucci ◽

Arianna Buccioni ◽

Alice Cappucci ◽

Laura Casarosa ◽

...

Keyword(s):

Bacterial Community ◽

Growth Performance ◽

Community Composition ◽

Lipid Composition ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Daily Weight Gain ◽

Rrna Gene ◽

Rumen Microbiota ◽

Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

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Soil microbes and oxygen influence the changes in bacterial community composition during swine carcass decomposition

10.21203/rs.3.rs-211559/v1 ◽

2021 ◽

Author(s):

Michelle Miguel ◽

Seon Ho Kim ◽

Sang Suk Lee ◽

Yong Il Cho

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

Community Composition ◽

Soil Microbes ◽

Close Association ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Decomposition Process ◽

Metagenomic Sequencing ◽

Unsterilized Soil

Abstract Background Carcass decomposition is influenced by various factors such as temperature, humidity, microorganisms, invertebrates, and scavengers. Soil microbes play a significant role in the decomposition process. In this study, we investigated the changes in the bacterial community during carcass decomposition in soil with an intact microbial community and soil which was sterilized decomposed with and without oxygen access using 16s rRNA metagenomic sequencing. Results Based on the 16S rRNA metagenomic sequencing, a total of 988 operational taxonomic units (OTUs) representing 16 phyla and 533 genera were detected. The bacterial diversity varied across the based on the alpha diversity indices. The bacterial composition in the unsterilized soil – aerobic condition (U_A) and unsterilized soil – anaerobic condition (U_An) set-ups have higher alpha diversity than the other burial set-ups. Beta diversity analysis revealed a close association in the samples according to the burial type and decomposition day. Firmicutes was the dominant phylum across all samples regardless of the burial type and decomposition day. The bacterial community composition changed throughout the decomposition process in all burial set-up. Meanwhile, the genus Bacillus dominated the bacterial community towards the end of decomposition period. Conclusions Our results showed that bacterial community composition changed during carcass decomposition and was affected by the soil and oxygen access, with microorganisms belonging to phylum Firmicutes dominating the community.

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Influence of Sampling Site and other Environmental Factors on the Bacterial Community Composition of Domestic Washing Machines

Microorganisms ◽

10.3390/microorganisms8010030 ◽

2019 ◽

Vol 8 (1) ◽

pp. 30 ◽

Cited By ~ 1

Author(s):

Susanne Jacksch ◽

Dominik Kaiser ◽

Severin Weis ◽

Mirko Weide ◽

Stefan Ratering ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Community Composition ◽

Sampling Site ◽

Alpha Diversity ◽

Growth Conditions ◽

Microbial Colonization ◽

Rrna Gene ◽

Washing Machines ◽

16S Rrna Gene Pyrosequencing ◽

Machine Parts

Modern, mainly sustainability-driven trends, such as low-temperature washing or bleach-free liquid detergents, facilitate microbial survival of the laundry processes. Favourable growth conditions like humidity, warmth and sufficient nutrients also contribute to microbial colonization of washing machines. Such colonization might lead to negatively perceived staining, corrosion of washing machine parts and surfaces, as well as machine and laundry malodour. In this study, we characterized the bacterial community of 13 domestic washing machines at four different sampling sites (detergent drawer, door seal, sump and fibres collected from the washing solution) using 16S rRNA gene pyrosequencing and statistically analysed associations with environmental and user-dependent factors. Across 50 investigated samples, the bacterial community turned out to be significantly site-dependent with the highest alpha diversity found inside the detergent drawer, followed by sump, textile fibres isolated from the washing solution, and door seal. Surprisingly, out of all other investigated factors only the monthly number of wash cycles at temperatures ≥ 60 °C showed a significant influence on the community structure. A higher number of hot wash cycles per month increased microbial diversity, especially inside the detergent drawer. Potential reasons and the hygienic relevance of this finding need to be assessed in future studies.

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Dynamics of the bacterial community in a channel catfish nursery pond with a cage–pond integration system

Canadian Journal of Microbiology ◽

10.1139/cjm-2018-0268 ◽

2018 ◽

Vol 64 (12) ◽

pp. 954-967 ◽

Cited By ~ 2

Author(s):

Liqiang Zhong ◽

Daming Li ◽

Minghua Wang ◽

Xiaohui Chen ◽

Wenji Bian ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Community Composition ◽

Channel Catfish ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Integration System ◽

Nursery Pond ◽

Site Variation

The changes in the bacterial community composition in a channel catfish nursery pond with a cage–pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage–pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.

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