Influence of intramuscular depot-medroxyprogesterone acetate initiation on vaginal microbiota in the postpartum period

Abstract Background The vaginal microbiome plays a key role in women’s reproductive health. Use of exogenous hormones, such as intramuscular depot-medroxyprogesterone acetate (DMPA-IM), may alter the composition of vaginal bacterial community. Methods Vaginal swabs were collected from postpartum Kenyan women initiating DMPA-IM or non-hormonal contraception (non-HC). Bacterial vaginosis was assessed by Nugent score (Nugent-BV) and bacterial community composition was evaluated using broad-range 16S rRNA gene PCR with high-throughput sequencing. Changes in Nugent score, alpha diversity (Shannon diversity index), and total bacterial load between contraceptive groups from enrollment to three-months post-initiation were estimated using multivariable linear mixed effects regression. Results Among 54 HIV-negative women, 33 choosing DMPA-IM and 21 choosing non-HC, Nugent-BV was more common among DMPA-IM users at enrollment. At follow-up, Nugent score had decreased significantly among DMPA-IM users (Δ=-1.89 (95%CI:-3.53, -0.25; p=0.02) while alpha diversity remained stable (Δ=0.03, 95%CI:-0.24, 0.30; p=0.83). Conversely, Nugent score remained relatively stable among non-HC users (Δ=-0.73, 95%CI:-2.18, 0.73; p=0.33) while alpha diversity decreased (Δ=-0.34, 95%CI:-0.67, -0.001; p=0.05). Total bacterial load decreased slightly in DMPA-IM users and increased slightly among non-HC users, resulting in a significant difference in change between the contraceptive groups (difference=-0.64 log10 gene copies/swab, 95%CI:-1.19, -0.08; p=0.02). While significant changes in Nugent score and alpha diversity were observed within contraceptive groups, changes between groups were not significantly different. Conclusions Postpartum vaginal bacterial diversity did not change in DMPA-IM users despite a reduction in Nugent-BV, but decreased significantly among women using non-HC. Choice of contraception may influence Lactobacillus recovery in postpartum women.

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Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing

PeerJ ◽

10.7717/peerj.6684 ◽

2019 ◽

Vol 7 ◽

pp. e6684 ◽

Cited By ~ 4

Author(s):

Siyu Han ◽

Yu Guan ◽

Hailong Dou ◽

Haitao Yang ◽

Meng Yao ◽

...

Keyword(s):

Bacterial Community ◽

Gut Microbiota ◽

High Throughput ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Panthera Pardus ◽

Invasive Approach ◽

Fecal Samples ◽

Significant Difference

The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.

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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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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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16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya

PLoS ONE ◽

10.1371/journal.pone.0248485 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248485

Author(s):

Edith M. Muwawa ◽

Chinedu C. Obieze ◽

Huxley M. Makonde ◽

Joyce M. Jefwa ◽

James H. P. Kahindi ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Community Structure ◽

Bacterial Community Composition ◽

Geographical Location ◽

Alpha Diversity ◽

Rrna Gene ◽

Chemical Parameters ◽

Mangrove Species ◽

Gazi Bay

Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.

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Different Soil Salinity Imparts Clear Alteration In Rhizospheric Bacterial Community Dynamics In Rice And Peanut.

10.21203/rs.3.rs-646600/v1 ◽

2021 ◽

Author(s):

Md Majharul Islam ◽

Rajarshi Bhattacharya ◽

Biraj Sarkar ◽

Pulak Kumar Maiti ◽

Shouvik Mahanty ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Host Plant ◽

High Throughput Sequencing ◽

Community Dynamics ◽

Bacterial Community Composition ◽

Chemical Properties ◽

Alpha Diversity ◽

Rhizospheric Soil ◽

Bacterial Community Dynamics

Abstract The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in overall health of the host-plant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community-dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence-analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community-structure is related to both the adjoining soil characters and the type of the hosts.

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

Journal of Animal Science ◽

10.1093/jas/skaa178 ◽

2020 ◽

Vol 98 (6) ◽

Cited By ~ 1

Author(s):

Riley D Messman ◽

Zully E Contreras-Correa ◽

Henry A Paz ◽

George Perry ◽

Caleb O Lemley

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Artificial Insemination ◽

Beta Diversity ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Species Level ◽

Rrna Gene ◽

Microbial Composition ◽

Vaginal Tract

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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Cadmium Exposure-Sedum alfrediiPlanting Interactions Shape the Bacterial Community in the Hyperaccumulator Plant Rhizosphere

Applied and Environmental Microbiology ◽

10.1128/aem.02797-17 ◽

2018 ◽

Vol 84 (12) ◽

pp. e02797-17 ◽

Cited By ~ 15

Author(s):

Dandi Hou ◽

Zhi Lin ◽

Runze Wang ◽

Jun Ge ◽

Shuai Wei ◽

...

Keyword(s):

Bacterial Community ◽

Contaminated Soils ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Sedum Alfredii ◽

Cd Stress ◽

Metal Hyperaccumulation ◽

Content Type

ABSTRACTRhizospheric bacteria play important roles in plant tolerance and activation of heavy metals. Understanding the bacterial rhizobiome of hyperaccumulators may contribute to the development of optimized phytoextraction for metal-polluted soils. We used 16S rRNA gene amplicon sequencing to investigate the rhizospheric bacterial communities of the cadmium (Cd) hyperaccumulating ecotype (HE)Sedum alfrediiin comparison to its nonhyperaccumulating ecotype (NHE). Both planting of two ecotypes ofS. alfrediiand elevated Cd levels significantly decreased bacterial alpha-diversity and altered bacterial community structure in soils. The HE rhizosphere harbored a unique bacterial community differing from those in its bulk soil and NHE counterparts. Several key taxa fromActinobacteria,Bacteroidetes, and TM7 were especially abundant in HE rhizospheres under high Cd stress. The actinobacterial genusStreptomyceswas responsible for the majority of the divergence of bacterial community composition between the HE rhizosphere and other soil samples. In the HE rhizosphere, the abundance ofStreptomyceswas 3.31- to 16.45-fold higher than that in other samples under high Cd stress. These results suggested that both the presence of the hyperaccumulatorS. alfrediiand Cd exposure select for a specialized rhizosphere bacterial community during phytoextraction of Cd-contaminated soils and that key taxa, such as the species affiliated with the genusStreptomyces, may play an important role in metal hyperaccumulation.IMPORTANCESedum alfrediiis a well-known Cd hyperaccumulator native to China. Its potential for extracting Cd relies not only on its powerful uptake, translocation, and tolerance for Cd but also on processes underground (especially rhizosphere microbes) that facilitate root uptake and tolerance of the metal. In this study, a high-throughput sequencing approach was applied to gain insight into the soil-plant-microbe interactions that may influence Cd accumulation in the hyperaccumulatorS. alfredii. Here, we report the investigation of rhizosphere bacterial communities ofS. alfrediiin phytoremediation of different levels of Cd contamination in soils. Moreover, some key taxa in its rhizosphere identified in the study, such as the species affiliated with genusStreptomyces, may shed new light on the involvement of bacteria in phytoextraction of contaminated soils and provide new materials for phytoremediation optimization.

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Cyprus Sausages’ Bacterial Community Identification Through Metataxonomic Sequencing: Evaluation of the Impact of Different DNA Extraction Protocols on the Sausages’ Microbial Diversity Representation

Frontiers in Microbiology ◽

10.3389/fmicb.2021.662957 ◽

2021 ◽

Vol 12 ◽

Author(s):

Eleni Kamilari ◽

Marina Efthymiou ◽

Dimitrios A. Anagnostopoulos ◽

Dimitrios Tsaltas

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Dna Extraction ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Additional Tool ◽

Principal Coordinates ◽

The Impact

Cyprus traditional sausages from the Troodos mountainous region of Pitsilia gained the protected geographical indication (PGI) designation from the European Committee (EU 2020/C 203/06). Still, we lack authentication protocols for the distinction of “Pitsilia” from industrially produced Cyprus sausages. Microbial activity is an essential contributor to traditional sausages’ sensorial characteristics, but whether the microbial patterns might be associated with the area of production is unclear. In the present research, we applied high-throughput sequencing (HTS) to provide a linkage between the area of production and Cyprus sausages’ bacterial diversity. To strengthen our findings, we used three different DNA extraction commercial kits: (i) the DNeasy PowerFood Microbial Kit (QIAGEN); (ii) the NucleoSpin Food Kit (MACHEREY-NAGEL); and (iii) the blackPREP Food DNA I Kit (Analytik Jena), in which we applied three different microbial cell wall lysis modifications. The modifications included heat treatment, bead beating, and enzymatic treatment. Results regarding metagenomic sequencing were evaluated in terms of number of reads, alpha diversity indexes, and taxonomic composition. The efficacy of each method of DNA isolation was assessed quantitatively based on the extracted DNA yield and the obtained copy number of (a) the 16S rRNA gene, (b) the internal transcribed spacer (ITS) region, and (c) three Gram-positive bacteria that belong to the genera Latilactobacillus (formerly Lactobacillus), Bacillus, and Enterococcus via absolute quantification using qPCR. Compared with some examined industrial sausages, Pitsilia sausages had significantly higher bacterial alpha diversity (Shannon and Simpson indexes). Principal coordinates analysis separated the total bacterial community composition (beta diversity) of the three Pitsilia sausages from the industrial sausages, with the exception of one industrial sausage produced in Pitsilia, according to the manufacturer. Although the eight sausages shared the abundant bacterial taxa based on 16S rDNA HTS, we observed differences associated with bacterial diversity representation and specific genera. The findings indicate that the microbial communities may be used as an additional tool for identifying of the authenticity of Cypriot sausages.

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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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Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds

Microorganisms ◽

10.3390/microorganisms8020311 ◽

2020 ◽

Vol 8 (2) ◽

pp. 311

Author(s):

Xin Tai ◽

Rui Li ◽

Bao Zhang ◽

Hao Yu ◽

Xiao Kong ◽

...

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Community Composition ◽

Community Assembly ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Sediment Samples ◽

Pollution Levels ◽

Water And Sediment

Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little is known about their effects on the succession of microbial communities in different pollution levels rural ponds. Also, the processes that govern bacterial communities in polluted ponds are poorly understood. In this study, the microbial communities in water and sediment from the ponds were investigated by using the 16S rRNA gene high-throughput sequencing technology. Meanwhile, we used null model analyses based on a taxonomic and phylogenetic metrics approach to test the microbial community assembly processes. Pollution levels were found to significantly alter the community composition and diversity of bacteria. In the sediment samples, the bacterial diversity indices decreased with increasing pollutant levels. Between-community analysis revealed that community assembly processes among water and sediment samples stochastic ratio both gradually decreased with the increased pollution levels, indicating a potential deterministic environmental filtering that is elicited by pollution. Our results identified assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for contaminated freshwater systems.

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