scholarly journals Characterization of the Genitourinary Microbiome of 1,165 Middle-Aged and Elderly Healthy Individuals

2021 ◽  
Vol 12 ◽  
Author(s):  
Junjie Qin ◽  
Xulian Shi ◽  
Junming Xu ◽  
Simin Yuan ◽  
Bo Zheng ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Healthy Individuals ◽  
Middle Aged ◽  
Healthy Human ◽  
Gender And Age ◽  
Healthy Cohort ◽  
Urological Disorders ◽  
Rrna Gene Sequencing

Accumulated evidence shows that complex microbial communities resides in the healthy human urinary tract and can change in urological disorders. However, there lacks a comprehensive profiling of the genitourinary microbiota in healthy cohort. Here, we performed 16S rRNA gene sequencing of midstream urine specimens from 1,172 middle-aged and elderly healthy individuals. The core microbiota included 6 dominant genera (mean relative abundance >5%), including Prevotella, Streptococcus, Lactobacillus, Gardnerella, Escherichia-Shigella, and Veillonella, and 131 low-abundance genera (0.01–5%), displaying a distinct microbiome profiles to that of host-matched gut microbiota. The composition and diversity of genitourinary microbiome (GM) were distinct between genders and may fluctuate with ages. Several urotypes were identified by the stratification of microbiome profiles, which were mainly dominated by the six most predominant genera. The prevalence of urotypes was disparate between genders, and the male sample additionally harbored other urotypes dominated by Acinetobacter, Corynebacterium, Staphylococcus, or Sphingomonas. Peptoniphilus, Ezakiella, and Porphyromonas were co-occurred and co-abundant, and they may play crucial roles as keystone genera and be associated with increased microbial diversity. Our results delineated the microbial structure and diversity landscape of the GM in healthy middle-aged and elderly adults and provided insights into the influence of gender and age to it.

scholarly journals The Origin of Plasma-Derived Bacterial Extracellular Vesicles in Healthy Individuals and Patients with Inflammatory Bowel Disease: A Pilot Study

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1636
Author(s):  
Emily Jones ◽  
Régis Stentz ◽  
Andrea Telatin ◽  
George M. Savva ◽  
Catherine Booth ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Pilot Study ◽  
16S Rrna ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Healthy Individuals ◽  
Inflammatory Bowel ◽  
Rrna Gene Sequencing ◽  
Blood Microbiota

The gastrointestinal tract harbors the gut microbiota, structural alterations of which (dysbiosis) are linked with an increase in gut permeability (“leaky gut”), enabling luminal antigens and bacterial products such as nanosized bacterial extracellular vesicles (BEVs) to access the circulatory system. Blood-derived BEVs contain various cargoes and may be useful biomarkers for diagnosis and monitoring of disease status and relapse in conditions such as inflammatory bowel disease (IBD). To progress this concept, we developed a rapid, cost-effective protocol to isolate BEV-associated DNA and used 16S rRNA gene sequencing to identify bacterial origins of the blood microbiome of healthy individuals and patients with Crohn’s disease and ulcerative colitis. The 16S rRNA gene sequencing successfully identified the origin of plasma-derived BEV DNA. The analysis showed that the blood microbiota richness, diversity, or composition in IBD, healthy control, and protocol control groups were not significantly distinct, highlighting the issue of ‘kit-ome’ contamination in low-biomass studies. Our pilot study provides the basis for undertaking larger studies to determine the potential use of blood microbiota profiling as a diagnostic aid in IBD.

scholarly journals Characterization of the Spoilage Microbiota of Hake Fillets Packaged Under a Modified Atmosphere (MAP) Rich in CO2 (50% CO2/50% N2) and Stored at Different Temperatures

Foods ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 489 ◽  
Author(s):  
Adriana Antunes-Rohling ◽  
Silvia Calero ◽  
Nabil Halaihel ◽  
Pedro Marquina ◽  
Javier Raso ◽  
...  
Keyword(s):  
Storage Temperature ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Modified Atmosphere ◽  
Modified Atmospheres ◽  
Different Temperatures ◽  
Rrna Gene Sequencing ◽  
Storage Temperatures

The aim of this study was to characterize the spoilage microbiota of hake fillets stored under modified atmospheres (MAP) (50% CO2/50% N2) at different temperatures using high-throughput 16S rRNA gene sequencing and to compare the results with those obtained using traditional microbiology techniques. The results obtained indicate that, as expected, higher storage temperatures lead to shorter shelf-lives (the time of sensory rejection by panelists). Thus, the shelf-life decreased from six days to two days for Batch A when the storage temperature increased from 1 to 7 °C, and from five to two days—when the same increase in storage temperature was compared—for Batch B. In all cases, the trimethylamine (TMA) levels measured at the time of sensory rejection of hake fillets exceeded the recommended threshold of 5 mg/100 g. Photobacterium and Psychrobacter were the most abundant genera at the time of spoilage in all but one of the samples analyzed: Thus, Photobacterium represented between 19% and 46%, and Psychrobacter between 27% and 38% of the total microbiota. They were followed by Moritella, Carnobacterium, Shewanella, and Vibrio, whose relative order varied depending on the sample/batch analyzed. These results highlight the relevance of Photobacterium as a spoiler of hake stored in atmospheres rich in CO2. Further research will be required to elucidate if other microorganisms, such as Psychrobacter, Moritella, or Carnobacterium, also contribute to spoilage of hake when stored under MAP.

scholarly journals Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs

Pathogens ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 638
Author(s):  
Caitlin E. Older ◽  
Aline Rodrigues Hoffmann ◽  
Kathleen Hoover ◽  
Frane Banovic
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
16S Rrna Gene Sequencing ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Bacterial Microbiota ◽  
Starting Point ◽  
Rrna Gene Sequencing ◽  
Antimicrobial Treatments ◽  
Staphylococcus Spp

Although Staphylococcus pseudintermedius is considered the major pathogen associated with superficial canine pyoderma, no study has investigated the entire bacterial community in these lesions with molecular techniques. The objectives of this study were to characterize the bacterial microbiota in two forms of superficial canine pyoderma lesions, superficial bacterial folliculitis (SBF) and epidermal collarette (EC), especially in terms of the staphylococcal community. Swabs from 12 SBF and 9 EC lesions were obtained from eight and six atopic dogs, respectively. Eight samples from the axilla and groin of four healthy dogs served as controls. DNA was extracted for 16S rRNA gene sequencing and quantitative polymerase chain reaction of Staphylococcus spp. and S. pseudintermedius. Healthy skin samples harbored significantly more diverse bacterial communities than pyoderma samples. Healthy samples had communities that were more similar to each other, and were distinct from pyoderma samples. Staphylococcus spp. abundance was increased in pyoderma samples, especially those from EC samples. Although determining species-level identities of staphylococcal sequences revealed many species, S. pseudintermedius was the primary staphylococcal species found in all sample types. As expected, there are many differences in the microbiota when comparing healthy and canine pyoderma lesions samples. These lesions do not seem to be associated with a change in the relative abundance of specific Staphylococcus species, but simply an overall increase in Staphylococcus spp. abundance. The results of this study provide a starting point for future studies investigating how antimicrobial treatments may further change the microbiota associated with these lesions.

Morphological and molecular characterization of cyanobacterial isolates from the mouth of the Amazon River

Phytotaxa ◽  
2019 ◽  
Vol 387 (4) ◽  
pp. 269 ◽  
Author(s):  
ELANE D. CUNHA DE OLIVEIRA ◽  
ALAN C. DA CUNHA ◽  
NATALINA B. DA SILVA ◽  
RAQUEL CASTELO-BRANCO ◽  
JOÃO MORAIS ◽  
...  
Keyword(s):  
River Mouth ◽  
Taxonomic Revision ◽  
16S Rrna Gene Sequencing ◽  
Gene Clusters ◽  
Toxin Production ◽  
Amazon River ◽  
Rrna Gene ◽  
Cyanobacterial Diversity ◽  
Rrna Gene Sequencing

The Amazon region contains a great diversity of species, and the Amazon River basin accounts for almost 20% of all the freshwater in the world. Despite the favorable environmental conditions in this region, little is known about the cyanobacterial diversity of this waterbody, especially at the mouth of the river. In this paper, we used the polyphasic approach to identify 14 cyanobacterial strains isolated in the Amazon River on the inlet site from a drinking water supply located close to the river mouth. The isolated strains were characterized based on morphology, behavior in culture, 16S rRNA gene sequencing, phylogenetic analysis and potential for toxin production. The isolated strains belong to seven different genera, namely, Alkalinema, Cephalothrix, Limnothrix, Leptolyngbya, Phormidium, Pseudanabaena and an unidentified Nostocales taxa that may represent a new genus. Strikingly, there were no new species, nor detection of gene clusters associated with cyanotoxin production. However, the phylogenetic placements of the Amazonian strains of Limnothrix and Pseudanabaena provide new insight into the taxonomy of these genera, reinforcing the need for taxonomic revision.

scholarly journals Longitudinal Characterization of the Tumoral Microbiome during Radiotherapy in HPV-associated Oropharynx Cancer

2020 ◽  
Author(s):  
Houda Bahig ◽  
Clifton D Fuller ◽  
Aparna Mitra ◽  
Travis Solley ◽  
Sweet Ping Ng ◽  
...  
Keyword(s):  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Concurrent Chemotherapy ◽  
Rrna Gene ◽  
Entire Cohort ◽  
Oropharynx Cancer ◽  
History Of ◽  
Rrna Gene Sequencing ◽  
Never Smokers

ABSTRACTPurposeTo describe the baseline and serial tumor microbiome in HPV-associated oropharynx cancer (OPC) over the course of radiotherapy (RT).MethodsPatients with newly diagnosed HPV-associated OPC treated with definitive radiotherapy +/- concurrent chemotherapy were enrolled in this prospective study. Using 16S rRNA gene sequencing, dynamic changes in tumor microbiome during RT were investigated. Surface tumor samples were obtained before RT and at week 1, 3 and 5 of RT. Radiological primary tumor response at mid-treatment was categorized as complete (CR) or partial (PR).ResultsTen patients were enrolled. Mean age was 63 years (range: 51-71). As per AJCC 8th Ed, 50%, 20% and 30% of patients had stage I, II and III, respectively. At 4-weeks, 7 patients had CR and 3 patients had PR; at follow-up imaging post treatment, all patients had CR. Baseline diversity of tumoral and buccal microbiomes was not statistically different. For the entire cohort, alpha diversity was significantly decreased over the course of treatment (p=0.02). There was a significant alteration in the bacterial community within the first week of radiation. Baseline tumor alpha diversity of patients with CR was significantly higher than those with PR (p=0.03). While patients with CR had significant reduction in diversity over the course of radiation (p=0.02), the diversity remained unchanged in patients with PR. Patients with history of smoking had significantly increased abundance of Granulicatella (p=0.04), and Kingella (0.05) and lower abundance of Alloprevotella (p=0.04) compared to never smokers.ConclusionsThe tumor microbiome of HPV-associated OPC exhibits reduced alpha diversity and altered taxa abundance over the course of radiotherapy. The baseline bacterial profiles of smokers vs. non-smokers were inherently different. Baseline tumor alpha diversity of patients with CR was higher than patients with PR, suggesting that the microbiome as a biomarker of radiation response deserves further investigation.

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

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

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

scholarly journals A Potential Bioactive Secondary Metabolites and Antimicrobial Efficacy of Streptomyces thermocarboxydus Strain KSA-2, Isolated from Kali River, Karwar

2020 ◽  
Vol 1 (1) ◽  
pp. 5-13
Author(s):  
Sreenivasa Nayaka ◽  
Muthuraj R. ◽  
Bidhayak Chakraborty ◽  
Meghashyama Prabhakara Bhat ◽  
Pallavi S.S. ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Ftir Spectroscopy ◽  
16S Rrna Gene Sequencing ◽  
Broth Culture ◽  
Rrna Gene ◽  
Vis Spectroscopy ◽  
Bioactive Secondary Metabolites ◽  
Kali River ◽  
Rrna Gene Sequencing

In the present study, an Actinomycetes strain KSA-2 was isolated from freshwater sediment samples of Kali River, Karwar, Karnataka, India. The strain KSA-2 was selected among seven isolates based on primary screening of antimicrobial activity against pathogenic organisms. The morphological physiological and biochemical characterizations were performed, the bioactive secondary metabolites were produced in liquid broth culture and was characterized by UV-Vis. spectroscopy and FTIR spectroscopy. Later, the potent KSA-2 strain was identified by 16S rRNA gene sequencing (1366 bp) and a phylogenetic tree was constructed and the strain KSA-2 was confirmed as Streptomyces thermocarboxydus strain KSA-2. Further, the characterization of methanolic extract by UV-Vis. and FTIR spectroscopy analysis revealed the presence of broad spectrum of antimicrobial and other compounds and alkyl halides, alkenes, sulfoxide, carboxylic acids, alkanes respectively.

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