scholarly journals PCR-RFLP Detection and Genogroup Identification of Piscirickettsia salmonis in Field Samples

Pathogens ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 358
Author(s):  
Pamela Aravena ◽  
Rodrigo Pulgar ◽  
Javiera Ortiz-Severín ◽  
Felipe Maza ◽  
Alexis Gaete ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
In Silico Analysis ◽  
Cost Effective ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Bacterial Dna ◽  
Phenotypic Differences ◽  
Field Samples ◽  
Pcr Rflp ◽  
Digestion Pattern

Piscirickettsia salmons, the causative agent of piscirickettsiosis, is genetically divided into two genomic groups, named after the reference strains as LF-89-like or EM-90-like. Phenotypic differences have been detected between the P. salmonis genogroups, including antibiotic susceptibilities, host specificities and pathogenicity. In this study, we aimed to develop a rapid, sensitive and cost-effective assay for the differentiation of the P. salmonis genogroups. Using an in silico analysis of the P. salmonis 16S rDNA digestion patterns, we have designed a genogroup-specific assay based on PCR-restriction fragment length polymorphism (RFLP). An experimental validation was carried out by comparing the restriction patterns of 13 P. salmonis strains and 57 field samples obtained from the tissues of dead or moribund fish. When the bacterial composition of a set of field samples, for which we detected mixtures of bacterial DNA, was analyzed by a high-throughput sequencing of the 16S rRNA gene amplicons, a diversity of taxa could be identified, including pathogenic and commensal bacteria. Despite the presence of mixtures of bacterial DNA, the characteristic digestion pattern of the P. salmonis genogroups could be detected in the field samples without the need of a microbiological culture and bacterial isolation.

scholarly journals The Female Urinary Microbiome: a Comparison of Women with and without Urgency Urinary Incontinence

mBio ◽  
2014 ◽  
Vol 5 (4) ◽  
Author(s):  
Meghan M. Pearce ◽  
Evann E. Hilt ◽  
Amy B. Rosenfeld ◽  
Michael J. Zilliox ◽  
Krystal Thomas-White ◽  
...  
Keyword(s):  
Urinary Incontinence ◽  
Urinary Tract ◽  
High Throughput Sequencing ◽  
Urgency Urinary Incontinence ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Content Type ◽  
Urinary Microbiome ◽  
Live Bacteria ◽  
Tract Infections

ABSTRACTBacterial DNA and live bacteria have been detected in human urine in the absence of clinical infection, challenging the prevailing dogma that urine is normally sterile. Urgency urinary incontinence (UUI) is a poorly understood urinary condition characterized by symptoms that overlap urinary infection, including urinary urgency and increased frequency with urinary incontinence. The recent discovery of the urinary microbiome warrants investigation into whether bacteria contribute to UUI. In this study, we used 16S rRNA gene sequencing to classify bacterial DNA and expanded quantitative urine culture (EQUC) techniques to isolate live bacteria in urine collected by using a transurethral catheter from women with UUI and, in comparison, a cohort without UUI. For these cohorts, we demonstrated that the UUI and non-UUI urinary microbiomes differ by group based on both sequence and culture evidences. Compared to the non-UUI microbiome, sequencing experiments revealed that the UUI microbiome was composed of increasedGardnerellaand decreasedLactobacillus. Nine genera (Actinobaculum,Actinomyces,Aerococcus,Arthrobacter,Corynebacterium,Gardnerella,Oligella,Staphylococcus, andStreptococcus) were more frequently cultured from the UUI cohort. AlthoughLactobacilluswas isolated from both cohorts, distinctions existed at the species level, withLactobacillus gasseridetected more frequently in the UUI cohort andLactobacillus crispatusmost frequently detected in controls. Combined, these data suggest that potentially important differences exist in the urinary microbiomes of women with and without UUI, which have strong implications in prevention, diagnosis, or treatment of UUI.IMPORTANCENew evidence indicates that the human urinary tract contains microbial communities; however, the role of these communities in urinary health remains to be elucidated. Urgency urinary incontinence (UUI) is a highly prevalent yet poorly understood urinary condition characterized by urgency, frequency, and urinary incontinence. Given the significant overlap of UUI symptoms with those of urinary tract infections, it is possible that UUI may have a microbial component. We compared the urinary microbiomes of women affected by UUI to those of a comparison group without UUI, using both high-throughput sequencing and extended culture techniques. We identified statistically significant differences in the frequency and abundance of bacteria present. These differences suggest a potential role for the urinary microbiome in female urinary health.

scholarly journals Identification and Differentiation of Pseudomonas Species in Field Samples Using an rpoD Amplicon Sequencing Methodology

mSystems ◽  
2021 ◽  
Author(s):  
Jonas Greve Lauritsen ◽  
Morten Lindqvist Hansen ◽  
Pernille Kjersgaard Bech ◽  
Lars Jelsbak ◽  
Lone Gram ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Field Samples ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Rrna Gene Sequencing ◽  
Specific Species

A high-throughput sequencing-based method for profiling of Pseudomonas species in soil microbiomes was developed and identified more species than 16S rRNA gene sequencing or cultivation. Pseudomonas species are used as biocontrol organisms and plant growth-promoting agents, and the method will allow tracing of specific species of Pseudomonas as well as enable screening of environmental samples for further isolation and exploitation.

scholarly journals Bacterial composition and inferring function profiles in the biofloc system rearing Litopenaeus vannamei postlarvae at a low salinity

2022 ◽  
Author(s):  
Hai-Hong Huang ◽  
Chao-Yun Li ◽  
Yan-Ju Lei ◽  
Wei-Qi Kuang ◽  
Wan-Sheng Zou ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Litopenaeus Vannamei ◽  
High Throughput Sequencing ◽  
Inorganic Nitrogen ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Low Salinity ◽  
Low Concentrations ◽  
Salinity Condition ◽  
Microbial Dna

This study aimed to investigate the bacterial composition and inferring function profiles in the biofloc system rearing Litopenaeus vannamei postlarvae (PL) at a low salinity condition. PL (~ stage 15) were stocked in four parallel tanks filled in water with a salinity of 5.0‰ at a density of 4000 individuals per m3 for a 28-days culture experiment, during which glucose was added as carbon source with a C:N of 20:1. At the end of experiment, water was sampled from each tank and pooled to extract microbial DNA for high-throughput sequencing of V3-V4 region of 16S rRNA gene. Results showed that the bacterial community at 28 d was dominated by phyla of Proteobacteria (45.8%), Bacteroidetes (21.1%), Planctomycetes (13.5%), Chlamydiae (10.3%) and Firmicutes (6.8%). A proportion of 81% inferring KEGG functions of this bacterial community associated with metabolism. Among functions relating to nitrogen metabolism, 48.5% were involved in the conversion of ammonia to glutamate, but the proportion of those involved in transformation among ammonia, nitrite and nitrate was 18.0% in total, inferring higher protein-synthesis but lower inorganic nitrogen-transformation capacities of the bacterial community. At the same time (28 d), high levels of total nitrogen (231.3±6.0 mg L-1) and biofloc (127.0±63.0 mL L-1), but low concentrations of ammonia (0.04±0.01 mg L-1), nitrite (0.2±0.1 mg L-1) and nitrate (12.9±2.5 mg L-1) were observed. The results supply a novel insight for understanding the function of bacterial community in the biofloc system nursing L. vannamei PL at a low salinity.

P–385 The relationship between systemic oestradiol and vaginal microbiota composition in miscarriage and normal pregnancy

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
H Fourie ◽  
M Al-Memar ◽  
A Smith ◽  
S Ng ◽  
Y Lee ◽  
...  
Keyword(s):  
Early Pregnancy ◽  
Species Level ◽  
Lactobacillus Species ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Bacterial Dna ◽  
Significant Difference ◽  
Eventual Outcome

Abstract Study question Is there an association between serum oestradiol, vaginal microbial composition and pregnancy outcome in the early first trimester? Summary answer In women with a vaginal microbiome deplete of Lactobacillus species at the time of Pregnancy of Uncertain Viability (IPUV), higher serum oestradiol associates with livebirth. What is known already During pregnancy, oestradiol mediates vaginal mucosal properties and increases glycogen deposition in epithelial cells which is thought to support colonisation of Lactobacillus species. Low levels of Lactobacillus associates with adverse outcomes such as miscarriage and preterm birth. The direct relationship between systemic oestradiol and the vaginal microbiome has never been studied in pregnancy. However studies have shown a positive correlation between serum oestrone, vaginal glycogen and Lactobacillus abundance in menopausal women. Study design, size, duration This was a prospective cohort study where one-hundred women were recruited in early pregnancy at the time of IPUV and donated paired blood and vaginal samples. 40 women had an eventual miscarriage, 58 had a livebirth and two pregnancies were terminated. All 100 women donated one paired serum and vaginal sample at this time point, and 22 women with Lactobacillus depletion at the time of IPUV donated further longitudinal vaginal samples. Participants/materials, setting, methods Participants were recruited from an Early Pregnancy Unit and underwent transvaginal ultrasound assessment of their pregnancy. Serum samples were analysed with an immunoassay on a ROCHE COBAS E411 analyser for Oestradiol (pg/ml) and Progesterone (ng/ml). Bacterial DNA was extracted from paired vaginal swabs and sequenced using Illumina MiSeq sequencing of 16S rRNA gene amplicons. Main results and the role of chance Lactobacillus dominance of the vagina was associated with higher serum levels of E2 and progesterone compared to depletion (E2=398pg/ml vs 302pg/ml(p = 0.02), P4=23.1ng/ml vs 17ng/ml(p = 0.02)). E2 and P4 were positively correlated (r = 0.6, p < 0.05). At species level, L. crispatus dominance associated with significantly higher levels of E2 compared to high-diversity communities (468pg/ml vs 302pg/ml(p = 0.03) but no such relationship was observed for P4. Both E2 and P4 levels were lower in women who eventually miscarried. However there was no significant difference in the vaginal bacterial composition at genera or species level at this early gestational age (P = 0.08) regardless of per vaginal bleeding. However in women with Lactobacillus depleted microbiota, livebirth was associated with significantly higher E2 levels compared to women suffering miscarriage (212pg/ml in miscarriage vs 395pg/ml in livebirth, p = 0.003) (OR = 22.4 P = 0.004). In 22 women who had Lactobacillus depletion at the time of IPUV (7 with an eventual outcome of miscarriage, and 15 with an eventual outcome of livebirth), longitudinal vaginal bacterial DNA sequencing was performed. In 7/15 women with livebirth, and higher E2 levels, the microbial composition changed to become more Lactobacillus dominant during pregnancy, whereas in those with miscarriage, only 1/7 changed to become Lactobacillus dominant. Limitations, reasons for caution In this study, serum oestradiol levels were compared to the local vaginal bacterial environment. The ideal would be to study local vaginal oestradiol, glycogen and the bacterial composition. Wider implications of the findings: In contrast to previous studies in menopause where low oestrogen levels associate with the vaginal microbial composition, this study uses the high oestradiol environment of early pregnancy to study the mechanistic relationship between oestradiol and vaginal Lactobacillus abundance. Trial registration number NA

scholarly journals Western Kenyan Anopheles gambiae showing intense permethrin resistance harbour distinct microbiota

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Diana Omoke ◽  
Mathew Kipsum ◽  
Samson Otieno ◽  
Edward Esalimba ◽  
Mili Sheth ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Anopheles Gambiae ◽  
High Throughput Sequencing ◽  
Pyrethroid Resistance ◽  
Sensu Stricto ◽  
Malaria Vector Control ◽  
Rrna Gene ◽  
Vector Surveillance ◽  
Bacterial Composition ◽  
Microbial Analysis

Abstract Background Insecticide resistance poses a growing challenge to malaria vector control in Kenya and around the world. Following evidence of associations between the mosquito microbiota and insecticide resistance, the microbiota of Anopheles gambiae sensu stricto (s.s.) from Tulukuyi village, Bungoma, Kenya, with differing permethrin resistance profiles were comparatively characterized. Methods Using the CDC bottle bioassay, 133 2–3 day-old, virgin, non-blood fed female F1 progeny of field-caught An. gambiae s.s. were exposed to five times (107.5 µg/ml) the discriminating dose of permethrin. Post bioassay, 50 resistant and 50 susceptible mosquitoes were subsequently screened for kdr East and West mutations, and individually processed for microbial analysis using high throughput sequencing targeting the universal bacterial and archaeal 16S rRNA gene. Results 47 % of the samples tested (n = 133) were resistant, and of the 100 selected for further processing, 99 % were positive for kdr East and 1 % for kdr West. Overall, 84 bacterial taxa were detected across all mosquito samples, with 36 of these shared between resistant and susceptible mosquitoes. A total of 20 bacterial taxa were unique to the resistant mosquitoes and 28 were unique to the susceptible mosquitoes. There were significant differences in bacterial composition between resistant and susceptible individuals (PERMANOVA, pseudo-F = 2.33, P = 0.001), with presence of Sphingobacterium, Lysinibacillus and Streptococcus (all known pyrethroid-degrading taxa), and the radiotolerant Rubrobacter, being significantly associated with resistant mosquitoes. On the other hand, the presence of Myxococcus, was significantly associated with susceptible mosquitoes. Conclusions This is the first report of distinct microbiota in An. gambiae s.s. associated with intense pyrethroid resistance. The findings highlight differentially abundant bacterial taxa between resistant and susceptible mosquitoes, and further suggest a microbe-mediated mechanism of insecticide resistance in mosquitoes. These results also indicate fixation of the kdr East mutation in this mosquito population, precluding further analysis of its associations with the mosquito microbiota, but presenting the hypothesis that any microbe-mediated mechanism of insecticide resistance would be likely of a metabolic nature. Overall, this study lays initial groundwork for understanding microbe-mediated mechanisms of insecticide resistance in African mosquito vectors of malaria, and potentially identifying novel microbial markers of insecticide resistance that could supplement existing vector surveillance tools.

scholarly journals Effects of a Bioprocessed Soybean Meal Ingredient on the Intestinal Microbiota of Hybrid Striped Bass, Morone chrysops x M. saxatilis

2021 ◽  
Vol 9 (5) ◽  
pp. 1032
Author(s):  
Emily Celeste Fowler ◽  
Prakash Poudel ◽  
Brandon White ◽  
Benoit St-Pierre ◽  
Michael Brown
Keyword(s):  
Striped Bass ◽  
Soybean Meal ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Hybrid Striped Bass ◽  
Bacterial Composition ◽  
Morone Chrysops ◽  
Fish Diets ◽  
Significant Difference

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1–V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass.

scholarly journals Western Kenyan Anopheles gambiae s.s. showing intense permethrin resistance harbor distinct microbiota

2020 ◽  
Author(s):  
Diana Omoke ◽  
Mathew Kipsum ◽  
Samson Otieno ◽  
Edward Esalimba ◽  
Mili Sheth ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
High Throughput Sequencing ◽  
Pyrethroid Resistance ◽  
Malaria Vectors ◽  
Malaria Vector Control ◽  
Rrna Gene ◽  
Vector Surveillance ◽  
Anopheles Gambiae S.S ◽  
Bacterial Composition ◽  
Microbial Analysis

AbstractBackgroundInsecticide resistance poses a growing challenge to malaria vector control in Kenya and around the world. Following evidence of associations between the mosquito microbiota and insecticide resistance, we comparatively characterized the microbiota of An. gambiae s.s. from Tulukuyi village, Bungoma, Kenya, with differing permethrin resistance profiles.MethodsUsing the CDC bottle bioassay, 133 2-3 day-old, virgin, non-blood fed female F1 progeny of field-caught An. gambiae s.s. were exposed to five times (107.5μg/ml) the discriminating dose of permethrin. Post bioassay, 50 resistant and 50 susceptible mosquitoes were subsequently screened for kdr East and West mutations, and individually processed for microbial analysis using high throughput sequencing targeting the universal bacterial and archaeal 16S rRNA gene.Results47% of the samples tested (n=133) were resistant, and of the 100 selected for further processing, 99% were positive for kdr East and 1% for kdr West. Overall, 84 bacterial taxa were detected across all mosquito samples, with 36 of these shared between resistant and susceptible mosquitoes. A total of 20 were unique to the resistant mosquitoes and 28 were unique to the susceptible mosquitoes. There were significant differences in bacterial composition between resistant and susceptible individuals (F=2.33, P=0.001), with presence of Sphingobacterium, Lysinibacillus and Streptococcus (all known pyrethroid-degrading taxa), and the radiotolerant Rubrobacter, being significantly associated with resistant mosquitoes. On the other hand, the presence of Myxococcus, was significantly associated with susceptible mosquitoes.ConclusionThis is the first report of distinct microbiota in An. gambiae s.s. associated with intense pyrethroid resistance. The findings highlight differentially abundant bacterial taxa between resistant and susceptible mosquitoes, and further suggest a microbe-mediated mechanism of insecticide resistance in mosquitoes. Our results also indicate fixation of the kdr East mutation in this mosquito population, precluding further analysis of its associations with the mosquito microbiota, but presenting the hypothesis that any microbe-mediated mechanism of insecticide resistance would be likely of a metabolic nature. Overall, this study lays initial groundwork for understanding microbe-mediated mechanisms of insecticide resistance in African malaria vectors, and potentially identifying novel microbial markers of insecticide resistance that could supplement existing vector surveillance tools.

scholarly journals In Silico Analysis of PKS and NRPS Gene Clusters in Arisostatin- and Kosinostatin-Producers and Description of Micromonospora okii sp. nov.

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1447
Author(s):  
Hisayuki Komaki ◽  
Natsuko Ichikawa ◽  
Akira Hosoyama ◽  
Moriyuki Hamada ◽  
Yasuhiro Igarashi
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Sequence Similarity ◽  
In Silico Analysis ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Rrna Gene ◽  
Type I ◽  
Phenotypic Differences ◽  
Polyketide Synthase Gene

Micromonospora sp. TP-A0316 and Micromonospora sp. TP-A0468 are producers of arisostatin and kosinostatin, respectively. Micromonospora sp. TP-A0316 showed a 16S rRNA gene sequence similarity of 100% to Micromonosporaoryzae CP2R9-1T whereas Micromonospora sp. TP-A0468 showed a 99.3% similarity to Micromonospora haikouensis 232617T. A phylogenetic analysis based on gyrB sequences suggested that Micromonospora sp. TP-A0316 is closely related to Micromonospora oryzae whereas Micromonospora TP-A0468 is an independent genomospecies. As Micromonospora sp. TP-A0468 showed some phenotypic differences to its closely related species, it was classified as a novel species, for which the name Micromonospora okii sp. nov. is proposed. The type strain is TP-A0468T (= NBRC 110461T). Micromonospora sp. TP-A0316 and M. okii TP-A0468T were both found to harbor 15 gene clusters for secondary metabolites such as polyketides and nonribosomal peptides in their genomes. Arisostatin-biosynthetic gene cluster (BGC) of Micromonospora sp. TP-A0316 closely resembled tetrocarcin A-BGC of Micromonospora chalcea NRRL 11289. A large type-I polyketide synthase gene cluster was present in each genome of Micromonospora sp. TP-A0316 and M. okii TP-A0468T. It was an ortholog of quinolidomicin-BGC of M. chalcea AK-AN57 and widely distributed in the genus Micromonospora.

scholarly journals Investigation of the Potential Effects of Host Genetics and Probiotic Treatment on the Gut Bacterial Community Composition of Aquaculture-raised Pacific Whiteleg Shrimp, Litopenaeus vannamei

2019 ◽  
Vol 7 (8) ◽  
pp. 217 ◽  
Author(s):  
Angela Landsman ◽  
Benoit St-Pierre ◽  
Misael Rosales-Leija ◽  
Michael Brown ◽  
William Gibbons
Keyword(s):  
Litopenaeus Vannamei ◽  
Genetic Background ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Operational Taxonomic Unit ◽  
Rrna Gene ◽  
Genetic Line ◽  
Bacterial Composition ◽  
Probiotic Treatment ◽  
Whiteleg Shrimp

This study presents the potential effects of the genetic background and use of probiotics on the gut bacterial composition of Pacific whiteleg shrimp (Litopenaeus vannamei) grown in an indoor aquaculture facility. The strains investigated were Shrimp Improvement Systems (SIS, Islamorada, FL, USA), a strain genetically selected for disease resistance, and an Oceanic Institute (OI, Oahu, HI, USA) strain, selected for growth performance. BioWish 3P (BioWish Technologies, Cincinnati, OH, USA) was the selected probiotic. The study consisted of two separate trials, where all shrimp were raised under standard industry conditions and fed the same diet. Shrimp were stocked in 2920 L production tanks at a density of 200/m3 and acclimated for 14 days. After the acclimation period, triplicate tanks were supplemented daily for a duration of 28 days with probiotics, while three other tanks did not receive any treatment (controls). During the 28-day trial period, there was no statistically supported difference (p > 0.05) in either performance or health status as a result of genetic background or probiotic treatment. However, differences in gut bacterial composition, as assessed by high throughput sequencing of amplicons generated from the V1-V3 region of the bacterial 16S rRNA gene, were observed. The relative abundance of five major operational taxonomic units (OTUs) were found to vary significantly across experimental groups (p < 0.05). Notably, operational taxonomic unit (OTU) SD_Shr-00006 was at its highest abundance in d43 SIS samples, with levels greater than d71 samples of the same genetic line or any of the OI shrimp samples. OTUs for SD_Shr-00098 displayed a similar type of profile, but with highest abundance in the OI genetic line and lowest in the SIS shrimp. SD_Shr-00004 showed an opposite profile, with highest abundance in the SIS d71 samples and lowest in the SIS d43 samples. Together, these results suggest that host genetic background can be an important determinant of gut bacterial composition in aquaculture-raised whiteleg shrimp and indicate that development of strategies to manipulate the microbiome of this important seafood will likely need to be customized depending on the genetic line.

Sign in / Sign up

Export Citation Format

Share Document