scholarly journals Comparative analysis of cutaneous bacterial communities of farmed Rana dybowskii after gentamycin bath

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8430
Author(s):  
Jia Bie ◽  
Qing Tong ◽  
Xiaoning Liu ◽  
Xianhao Zhang ◽  
Hongbin Wang
Keyword(s):  
Bacterial Community ◽  
Beta Diversity ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Recovery Period ◽  
Alpha Diversity ◽  
Community Diversity ◽  
Control Group ◽  
Rrna Gene ◽  
Rana Dybowskii

Introduction Pathogenic bacteria limit the success of Rana dybowskii breeding. Gentamicin is used to treat R. dybowskii disease. To understand the effects of gentamicin on the composition and structure of the cutaneous bacterial community of R. dybowskii, three groups (control, gentamicin and recovery) were established in this study. Materials & Methods The V3–V4 hypervariable region of the 16S rRNA gene was analyzed in samples by high-throughput sequencing. Alpha diversity and beta diversity were evaluated to compare the cutaneous bacterial community diversity. Results A total of 1,159,668 valid sequences and 3,132 operational taxonomic units (OTUs) were obtained from these three experimental groups. The number of OTUs obtained in the control group, gentamicin group and recovery group were 2,194, 2,288, and 2,047, respectively, and the number of shared OTUs was 1,313. The alpha diversity of the cutaneous bacterial community was not significantly affected by gentamicin, while beta diversity was significantly affected. Discussion & Conclusions The effect of a gentamicin bath on relative species abundance was greater than the effect on the species composition. The changes in Proteobacteria, Acinetobacter, and Chryseobacterium were significant, and reductions were observed after the recovery period. Six potentially pathogenic genera were detected, including Aeromonas, Citrobacter, Chryseobacterium, Pseudomonas, Staphylococcus, and Streptococcus. Among them, Aeromonas and Chryseobacterium were significantly inhibited by the gentamicin bath. The results of this study provide a theoretical basis for the application of gentamicin in R. dybowskii breeding.

scholarly journals Changes in the Gut Microbiota Diversity of Brown Frogs (Rana Dybowskii) After Local Antimicrobial Therapy

2021 ◽  
Author(s):  
Qing Tong ◽  
Li-Yong Cui ◽  
Jia Bie ◽  
Hong-Bin Wang ◽  
Jian-Tao Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Gut Microbiota ◽  
Pathogenic Bacteria ◽  
Alpha Diversity ◽  
Amphibian Conservation ◽  
Control Group ◽  
Antibiotic Administration ◽  
Functional Composition ◽  
And Control ◽  
Rana Dybowskii

Abstract Background: Amphibians frequently receive an antibiotic bath after feedlot placement to control bacterial diseases. The potential collateral effect of these antibiotics on the frog microbiota is largely unknown. Antibiotics are frequently employed to examine the role of the gut microbiota. Existing research relies mainly on oral antibiotics, but knowledge regarding the effects of antibiotics on the gut microbiota through a bath or local antimicrobial therapies is limited. Results: The gut microbiota of gentamicin, recovered, and control Rana dybowskii groups were compared by Illumina high-throughput sequencing, and the functional profiles were analysed using a phylogenetic investigation of communities by the reconstruction of unobserved states (PICRUSt). Furthermore, the relationship between gut microbiota structures and forecast function compositions was determined. The results showed that the alpha diversity indices were significantly reduced by the gentamicin bath, which significantly changed the composition of the gut microbiota. After 7 days, the gut microbiota was still similar to that during the gentamicin bath. Forty-four indicator species were selected at the genus level, namely, 42 species indicating the control group and 2 species indicating the gentamicin and recovery groups. Potential pathogenic bacteria belonging to Aeromonas, Citrobacter, and Chryseobacterium significantly decreased after the gentamicin bath. The community similarity assays did not show an obvious discrepancy in the functional composition between the gentamicin and control frogs, indicating that the functions of the gut bacterial community were highly redundant. Conclusions: The gentamicin bath significantly reduced the alpha diversity of the gut microbiota of R. dybowskii. Gentamicin significantly changed the structure of the gut microbiota, and the gut microbiotas exhibited weak resilience and did not totally recover after seven days. The gentamicin bath did not change the functional composition of the gut microbiota of R. dybowskii, and there was no significant correlation between the composition of the gut microbiota and the functional composition, illustrating the high intestinal functional redundancy of the frog gut bacterial community. This work offers basic data for upcoming research, including the establishment of the amphibian gut microbiota and local antibiotic administration, and has important implications for aquaculture management and amphibian conservation.

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

2020 ◽  
Vol 98 (6) ◽  
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.

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

2020 ◽  
Author(s):  
Bridget M Whitney ◽  
Sujatha Srinivasan ◽  
Kenneth Tapia ◽  
Eric Munene Muriuki ◽  
Bhavna H Chohan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Medroxyprogesterone Acetate ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Bacterial Load ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Nugent Score ◽  
Depot Medroxyprogesterone Acetate ◽  
Significant Difference

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.

scholarly journals Short-Term Exposure to Sterile Seawater Reduces Bacterial Community Diversity in the Sea Anemone, Exaiptasia diaphana

2021 ◽  
Vol 7 ◽  
Author(s):  
Ashley M. Dungan ◽  
Madeleine J. H. van Oppen ◽  
Linda L. Blackall
Keyword(s):  
Bacterial Community ◽  
Model Organism ◽  
Alpha Diversity ◽  
Low Complexity ◽  
Community Diversity ◽  
Rrna Gene ◽  
Adaptation To Climate Change ◽  
Short Term ◽  
Sterile Seawater ◽  
Short Term Exposure

The global decline of coral reefs heightens the need to understand how corals may persist under changing environmental conditions. Restructuring of the coral-associated bacterial community, either through natural or assisted strategies, has been suggested as a means of adaptation to climate change. A low complexity microbial system would facilitate testing the efficacy of microbial restructuring strategies. We used the model organism for corals, Exaiptasia diaphana, and determined that short-term (3 weeks) exposure to filter-sterilized seawater conditions alone reduced the complexity of the microbiome. Metabarcoding of the V5–V6 region of the bacterial 16S rRNA gene revealed that alpha diversity was approximately halved in anemones reared in filter-sterilized seawater compared to controls reared in unfiltered seawater and that the composition (beta diversity) differed significantly between the two. By reducing the complexity of the E. diaphana microbiome, the development of a system for testing assisted strategies such as probiotics, is more feasible.

scholarly journals Temporal Bacterial Community Diversity in the Nicotiana tabacum Rhizosphere Over Years of Continuous Monocropping

2021 ◽  
Vol 12 ◽  
Author(s):  
Lang Yan ◽  
Wenyou Zhang ◽  
Wangjun Duan ◽  
Yizheng Zhang ◽  
Wen Zheng ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Underlying Mechanism ◽  
Development Stage ◽  
Community Diversity ◽  
Rrna Gene ◽  
Bacterial Community Diversity ◽  
Microbial Network ◽  
Tobacco Production ◽  
Occurrence Patterns

Long-term continuous monocropping negatively influences the physicochemical and biological characteristics of cultivated soil, especially for the economically important crop of flue-cured tobacco that is intolerant to continuous monocropping. The underlying mechanism of soil sickness under continuous monoculture and the temporal dynamic changes over the tobacco life cycle among different monoculture time spans remain poorly characterized. In this study, high-throughput sequencing targeting the 16S rRNA gene phylogenetic marker was performed on 60 soil samples of rhizosphere soil from flue−cured tobacco in the replanting, growth and harvest period across 5, 10, and 20 years of a continuous monocropping system. Bacterial community diversity decreased with the increase in duration of continuous monocropping, and the rhizosphere microbiota was highly dynamic in the harvest period. The random forests algorithm identified 17 taxa as biomarkers and a model was established to correlate root microbiota with continuous monocropping time of flue-cured tobacco. Molecular ecological network analysis elaborated the differences and interactions in bacterial co-occurrence patterns under different monocropping systems. The co-occurrence microbial network was larger in size but there were fewer interactions among microbial communities with the increase in continuous monocropping duration. These results provide insights into the changes of flue−cured tobacco root microbiome diversity in response to continuous monocropping and suggest a model for successional dynamics of the root-associated microbiota over continuous monocropping time and development stage. This study may help elucidate the theoretical basis underlying obstacles to continuous monocropping and could contribute to improving guidance for tobacco production.

scholarly journals P673 Microbial diversity in newly diagnosed treatment naïve Inflammatory Bowel Disease patients

2021 ◽  
Vol 15 (Supplement_1) ◽  
pp. S594-S595
Author(s):  
S Ellul ◽  
P Rausch ◽  
A Pisani ◽  
C Bang ◽  
P Ellul ◽  
...  
Keyword(s):  
Species Richness ◽  
Beta Diversity ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Healthy Controls ◽  
Newly Diagnosed ◽  
Treatment Naïve ◽  
Stool Samples

Abstract Background The role of microbiome with the alteration between commensal and pathogenic bacteria, has been linked to IBD. Meanwhile Escherichia coli Nissle 1917, Lactobacillus rhamnosus GG (LGG) and faecal transplantation are used in IBD. The aim of this study was to prospectively determine faecal microbiota composition of newly diagnosed treatment naïve IBD patients. Methods Patients diagnosed with IBD between January 2018-September 2019 were recruited. Clinical data was collected and patients asked to submit stool samples for microbiome analysis. Stool samples from a control population were recruited and analysed via the bacterial 16s rRNA gene sequencing on illumine MiSeq. Results 100 IBD patients (CD: n=46, UC: n=53 & IBDU: n=1) and 97 controls with specific inclusion and exclusion criteria collected. IBD patients were noted to display reduced average species richness and community evenness compared to healthy controls (Alpha- Diversity) (Figure 1). Beta-diversity between microbial communities of healthy individuals and IBD patients was significantly different, but no observed separation between the two types of IBD was noted (Figure 2). 11 ASVs were abundant in CD patients including: ASV-70 – Lactobacillus gasseri, Klebsiella uncl., Candidatus-saccharibacteria, ASV-157 - Acteroides clarus and ASV 249- Parasutterella uncl. In UC cohort, 10 ASVs were abundant including: ASV 6-Escherichia/Shigella uncl., ASB-41-Sutterella wadsworthensis, ASV 44- Bacteroides faecis and Actinobacteria. An association between UC and ASV 313 (Faecalibacteria) was present. In the microbiome of healthy controls, 20 ASVs were abundant, including: ASV-14 G-Alistipes uncl., ASV 20-(Akkermansia muciniphila),(bacterium belonging to the phylum Verrucomicrobia), ASV 321 (Clostridia uncl.), ASV 96 (Rumminococcaceae uncl.), Alistepes uncl. (ASV 61), Subdoligranulum uncl. (ASV 453) and the unclassifiable bacteria. A higher amount of Verrucomicrobia was present in the healthy group as opposed to the IBD. Conclusion ASV 249- Parasutterella unlc., was indicative of CD associated microbiome through the indicator species analysis. Typical microbiome changes in IBD patients include increased abundance of the pro-inflammatory species with a reduction in anti-inflammatory bacterial species, with a noticeable reduction in alpha and beta diversity. In the local cohort, a particular change in the local α- and β diversity was noted to be present between healthy controls and IBD cohort. This could be a potential way in which targeted therapeutic approaches using specific dosage and durations of probiotic or faecal transplant can be used to alter faecal microbiome using specific bacteria present in healthy controls and with elimination of potentially harmful bacteria in IBD patients. Figure 1: Alpha diversity between different Groups using Chao1 species richness and Simpson 1-D Figure 2: Beta diversity between different groups using Bray-Curtis dissimilarity, Jaccard distance.

scholarly journals Changes in the gut microbiota diversity of brown frogs (Rana dybowskii) after an antibiotic bath

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Qing Tong ◽  
Li-Yong Cui ◽  
Jia Bie ◽  
Xiao-Yun Han ◽  
Zong-Fu Hu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Positive Association ◽  
Diversity Indices ◽  
Control Group ◽  
Functional Composition ◽  
Significant Positive Association ◽  
Collateral Effect

Abstract Background Captive amphibians frequently receive antibiotic baths to control bacterial diseases. The potential collateral effect of these antibiotics on the microbiota of frogs is largely unknown. To date, studies have mainly relied on oral administration to examine the effects of antibiotics on the gut microbiota; in contrast, little is known regarding the effects of bath-applied antibiotics on the gut microbiota. The gut microbiota compositions of the gentamicin, recovery, and control groups were compared by Illumina high-throughput sequencing, and the functional profiles were analysed using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Furthermore, the relationship between the structure and predicted functional composition of the gut microbiota was determined. Results The alpha diversity indices were significantly reduced by the gentamicin bath, illustrating that this treatment significantly changed the composition of the gut microbiota. After 7 days, the gut microbiota of the recovery group was not significantly different from that of the gentamicin group. Forty-four indicator taxa were selected at the genus level, comprising 42 indicators representing the control group and 2 indicators representing the gentamicin and recovery groups. Potential pathogenic bacteria of the genera Aeromonas, Citrobacter, and Chryseobacterium were significantly depleted after the gentamicin bath. There was no significant positive association between the community composition and functional composition of the gut microbiota in the gentamicin or control frogs, indicating that the functional redundancy of the gut bacterial community was high. Conclusions Gentamicin significantly changed the structure of the gut microbiota of R. dybowskii, and the gut microbiota exhibited weak resilience. However, the gentamicin bath did not change the functional composition of the gut microbiota of R. dybowskii, and there was no significant correlation between the structural composition and the functional composition of the gut microbiota.

scholarly journals Assessment of microbial community diversity in lakes of İğneada floodplain forest by metabarcoding approach

2021 ◽  
Vol 4 (4) ◽  
pp. 304-312
Author(s):  
E. Gözde Özbayram ◽  
brahim Halil Miraloğlu ◽  
Bahar İnce
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
Floodplain Forest ◽  
Community Diversity ◽  
Rrna Gene ◽  
Community Patterns ◽  
Biotechnological Potential ◽  
Sequencing Platform ◽  
The Family

This paper aims to contribute to the understanding of bacterial community patterns of the lakes of İğneada Floodplain Forest by metabarcoding approach. Within this scope, surface water samples were collected from three lakes located in the area namely Mert Lake, Hamam Lake, and Saka Lake, and the bacterial diversity was assessed by a high throughput sequencing of the 16S rRNA gene. Chao1 richness and Shannon diversity were higher in Saka Lake indicated a more diverse bacterial community. Proteobacteria was by far the most abundant phyla in all lakes. Although Bacteroidetes and Actinobacteria also dominated the community, their abundances differed in each lake. While the family Burkholderiaceae represented 25% of the bacterial community in Saka Lake, the abundances were 9% and 4% in Hamam Lake and Mert Lake, respectively. This study is one of the first investigations specifically focused on the bacterial communities in three lakes of İğneada Floodplain by next-generation sequencing platform and gave a prescreening of the bacterial diversity. Further studies are required to determine the biotechnological potential of this unique habitat.

scholarly journals Sinus Microbiota in Patients With Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis With Nasal Polyps

2021 ◽  
Vol 11 ◽  
Author(s):  
Tingting Feng ◽  
Ping Miao ◽  
Bin Liu ◽  
Yao Liu ◽  
Ximing Bao ◽  
...  
Keyword(s):  
Chronic Rhinosinusitis ◽  
Nasal Polyps ◽  
Pathogenic Bacteria ◽  
Quantitative Polymerase Chain Reaction ◽  
Bacterial Community Composition ◽  
Community Diversity ◽  
Control Group ◽  
Rrna Gene ◽  
Control Subjects ◽  
Healthy Control

Chronic rhinosinusitis with nasal polyps (CRSwNP) is characterized by Th2-skewed inflammation and increased colonization by Staphylococcus aureus. CRSwNP can be distinguished as eosinophilic (ECRSwNP) and non-eosinophilic (NECRSwNP) by the infiltration of eosinophils. The local microbiota plays an important role in the persistent inflammation of CRSwNP. To evaluate the bacterial community composition on the distinct types of CRSwNP patients, we collected nasal swabs from 16 ECRSwNP patients, 18 NECRSwNP patients, and 39 healthy control subjects. The microbiome structure for all the samples were analyzed by high-throughput 16S rRNA gene sequencing. Concentration of S. aureus was determined using TaqMan quantitative polymerase chain reaction (qPCR) targeting the nuclease (nuc) gene. The result showed significant differences in the sinus microbiome among healthy control subjects and CRSwNP patients. Microbiota community diversity was significantly lower in NECRSwNP samples compared to that of healthy control subjects. Interestingly, the abundance of several pathogenic bacteria was diverse between ECRSwNP and NECRSwNP patients. Although Staphylococcus prevailed in all groups, the abundance of Staphylococcus was significantly higher in the healthy control group than the ECRSwNP group. More importantly, the abundance of S. aureus was much higher in NECRSwNP patients. This study highlights that microbiota composition may contribute to the different clinical types of CRSwNP, inspiring new therapeutic strategies to resolve this chronic inflammation process.

scholarly journals Effect of Xiaoning Liquid on Gut Microbiota in Asthmatic Mice by 16s RDNA High - Throughput Sequencing

2020 ◽  
Author(s):  
Yuanyuan He ◽  
Yating Luo ◽  
Qinwan Huang ◽  
Hongyun Zhou ◽  
Ming Qian ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rdna ◽  
High Throughput ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Control Group ◽  
Rrna Gene ◽  
Budesonide Group ◽  
Abundance And Diversity ◽  
Group Control Group

Abstract Background: To investigate the effects of Xiaoning liquid on gut microbiota in mouse during asthma.Methods: A total of 60 mice were randomly and averagely assigned to healthy control group, control group, budesonide group, and Xiaoning liquid group. The later three groups were used to establish an Ovalbumin (OVA) asthma model. The intestinal bacterial communities were compared among groups using 16S rRNA gene amplification. Analyzing the structure of gut microbiota with OTU analysis, Shannon–Wiener, PCA, PCOA, etc. 16s rDNA high- throughput sequencing. Results: The abundance and diversity of the gut microbiota in asthmatic mice increased, most obviously in the control group. The Bacteroidetes and Firmicutes levels increased in all asthmatic mice. The level of Bacteroides increased most obviously, making Bacteroides a useful marker of gut microbiota changes in asthmatic mice. The levels of Proteobacterium, Deferribacteraceae and Mucispirillum dropped significantly in the Xiaoning liquid group. Conclusions: Xiaoning liquid can reduce the species and numbers of pathogenic bacteria and restored the intestinal microecology of asthmatic mice. Xiaoning liquid has a positive effect on the function of gut microbiota.

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