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Frontiers in Microbiology 2021Accumulated evidence shows that complex microbial communities resides in the healthy human urinary tract and can change in urological disorders. However, there lacks a...
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 , , , , , and , 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 , , , or . , , and 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.
PubMed: 34489882
DOI: 10.3389/fmicb.2021.673969 -
The Journal of Allergy and Clinical... Apr 2021Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the respiratory virus responsible for the ongoing...
BACKGROUND
Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the respiratory virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic, and the upper respiratory tract (URT) microbiome.
OBJECTIVE
We sought to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults and to examine the association of SARS-CoV-2 viral load with the URT microbiome during COVID-19.
METHODS
We characterized the URT microbiome using 16S ribosomal RNA sequencing in 59 adults (38 with confirmed, symptomatic, mild to moderate COVID-19 and 21 asymptomatic, uninfected controls). In those with COVID-19, we measured SARS-CoV-2 viral load using quantitative reverse transcription PCR. We then examined the association of SARS-CoV-2 infection status and its viral load with the ⍺-diversity, β-diversity, and abundance of bacterial taxa of the URT microbiome. Our main models were all adjusted for age and sex.
RESULTS
The observed species index was significantly higher in SARS-CoV-2-infected than in -uninfected adults (β linear regression coefficient = 7.53; 95% CI, 0.17-14.89; P = .045). In differential abundance testing, 9 amplicon sequence variants were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified amplicon sequence variant being more abundant in those with SARS-CoV-2 infection and in those with high viral load during COVID-19, whereas Corynebacterium unclassified, Staphylococcus haemolyticus, Prevotella disiens, and 2 Corynebacterium_1 unclassified amplicon sequence variants were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19.
CONCLUSIONS
Our findings suggest complex associations between SARS-CoV-2 and the URT microbiome in adults. Future studies are needed to examine how these viral-bacterial interactions can impact the clinical progression, severity, and recovery of COVID-19.
Topics: Adult; Biodiversity; COVID-19; Case-Control Studies; Female; Host Microbial Interactions; Humans; Male; Microbiota; Middle Aged; Pandemics; RNA, Ribosomal, 16S; Respiratory System; SARS-CoV-2; Species Specificity; Viral Load
PubMed: 33577896
DOI: 10.1016/j.jaci.2021.02.001 -
Frontiers in Cellular and Infection... 2021Gram-positive anaerobic cocci (GPAC) are a commensal part of human flora but are also opportunistic pathogens. This is possibly the first study to report a case of...
Gram-positive anaerobic cocci (GPAC) are a commensal part of human flora but are also opportunistic pathogens. This is possibly the first study to report a case of bacteremia in an abdominal aortic aneurysm (AAA) patient. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) failed to identify the isolate and molecular analysis confirmed it as . A comprehensive literature review revealed that is an emergent pathogen. This study serves as a reminder for practicing clinicians to include anaerobic blood cultures as part of their blood culture procedures; this is particularly important situations with a high level of suspicion of infection factors in some noninfectious diseases, as mentioned in this publication. Clinical microbiologists should be aware that the pathogenic potential of GPAC can be greatly underestimated leading to incorrect diagnosis on using only one method for pathogen identification. Upgradation and correction of the MALDI-TOF MS databases is recommended to provide reliable and rapid identification of GPAC at species level in medical diagnostic microbiology laboratories.
Topics: Aortic Aneurysm; Blood Culture; Firmicutes; Gram-Positive Cocci; Humans; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 35004343
DOI: 10.3389/fcimb.2021.755225 -
PLoS Neglected Tropical Diseases May 2019Triatomine vectors transmit Trypanosoma cruzi, the etiological agent of Chagas disease in humans. Transmission to humans typically occurs when contaminated triatomine...
Triatomine vectors transmit Trypanosoma cruzi, the etiological agent of Chagas disease in humans. Transmission to humans typically occurs when contaminated triatomine feces come in contact with the bite site or mucosal membranes. In the Southern Cone of South America, where the highest burden of disease exists, Triatoma infestans is the principal vector for T. cruzi. Recent studies of other vector-borne illnesses have shown that arthropod microbiota influences the ability of infectious agents to colonize the insect vector and transmit to the human host. This has garnered attention as a potential control strategy against T. cruzi, as vector control is the main tool of Chagas disease prevention. Here we characterized the microbiota in T. infestans feces of both wild-caught and laboratory-reared insects and examined the relationship between microbial composition and T. cruzi infection using highly sensitive high-throughput sequencing technology to sequence the V3-V4 region of the 16S ribosomal RNA gene on the MiSeq Illumina platform. We collected 59 wild (9 with T. cruzi infection) and 10 lab-reared T. infestans (4 with T. cruzi infection) from the endemic area of Arequipa, Perú. Wild T. infestans had greater hindgut bacterial diversity than laboratory-reared bugs. Microbiota of lab insects comprised a subset of those identified in their wild counterparts, with 96 of the total 124 genera also observed in laboratory-reared insects. Among wild insects, variation in bacterial composition was observed, but time and location of collection and development stage did not explain this variation. T. cruzi infection in lab insects did not affect α- or β-diversity; however, we did find that the β-diversity of wild insects differed if they were infected with T. cruzi and identified 10 specific taxa that had significantly different relative abundances in infected vs. uninfected wild T. infestans (Bosea, Mesorhizobium, Dietzia, and Cupriavidus were underrepresented in infected bugs; Sporosarcina, an unclassified genus of Porphyromonadaceae, Nestenrenkonia, Alkalibacterium, Peptoniphilus, Marinilactibacillus were overrepresented in infected bugs). Our findings suggest that T. cruzi infection is associated with the microbiota of T. infestans and that inferring the microbiota of wild T. infestans may not be possible through sampling of T. infestans reared in the insectary.
Topics: Animals; Bacteria; Chagas Disease; DNA, Bacterial; Feces; Gastrointestinal Tract; Humans; Insect Vectors; Laboratories; Microbiota; Phylogeny; RNA, Ribosomal, 16S; Triatoma; Trypanosoma cruzi
PubMed: 31059501
DOI: 10.1371/journal.pntd.0007383 -
Frontiers in Immunology 2022Young men who have sex with men (YMSM) represent a particularly high-risk group for HIV acquisition in the US, despite similarly reported rates of sexual activity as...
Young men who have sex with men (YMSM) represent a particularly high-risk group for HIV acquisition in the US, despite similarly reported rates of sexual activity as older, adult MSM (AMSM). Increased rates of HIV infection among YMSM compared to AMSM could be partially attributable to differences within the rectal mucosal (RM) immune environment associated with earlier sexual debut and less lifetime exposure to receptive anal intercourse. Using an explant HIV challenge model, we found that rectal tissues from YMSM supported higher levels of p24 at peak viral replication timepoints compared to AMSM. Among YMSM, the RM was characterized by increased CD4+ T cell proliferation, as well as lower frequencies of tissue resident CD8+ T cells and pro-inflammatory cytokine producing CD4+ and CD8+ T cells. In addition, the microbiome composition of YMSM was enriched for anaerobic taxa that have previously been associated with HIV acquisition risk, including , and . These distinct immunologic and microbiome characteristics were found to be associated with higher HIV replication following challenge of rectal explants, suggesting the RM microenvironment of YMSM may be uniquely conducive to HIV infection.
Topics: Adult; Male; Humans; Homosexuality, Male; HIV Infections; Sexual and Gender Minorities; Sexual Behavior; Mucous Membrane
PubMed: 36341414
DOI: 10.3389/fimmu.2022.972170 -
Cureus Jun 2023Mastitis and breast abscesses are most common in lactating women but can also be observed in non-lactating women, adolescent girls, and neonates. However, breast...
A Case of Pediatric Breast Abscess Caused by Rarely Observed Bacteria in a Three-Year-Old Boy With an Inverted Nipple: Peptoniphilus harei, Actinotignum sanguinis, and Porphyromonas somerae.
Mastitis and breast abscesses are most common in lactating women but can also be observed in non-lactating women, adolescent girls, and neonates. However, breast abscesses are extremely rare in young boys. Herein, we report the case of a three-year-old boy with a swollen and painful right nipple, later diagnosed with a breast abscess. In this case, we suspected that the patient's inverted nipple was the possible site of the infection. To our best knowledge, this is the first case report of breast abscess in a young boy after the neonatal period. Although is the most common pathogen, our patient showed three rare bacteria, namely, , , and , in the culture of the aspirated pus. Furthermore, this case study is the first report of a breast abscess caused by .
PubMed: 37519494
DOI: 10.7759/cureus.41011 -
Standards in Genomic Sciences Dec 2012Peptoniphilus grossensis strain ph5(T) sp. nov., is the type strain of Peptoniphilus grossensis sp. nov., a new species within the Peptoniphilus genus. This strain,...
Peptoniphilus grossensis strain ph5(T) sp. nov., is the type strain of Peptoniphilus grossensis sp. nov., a new species within the Peptoniphilus genus. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. P. grossensis strain ph5 is a Gram-positive obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,101,866-bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 33.9% and contains 2,041 protein-coding and 29 RNA genes, including 3 rRNA genes.
PubMed: 23408485
DOI: 10.4056/sigs.3076460 -
AIDS (London, England) Apr 2019We employed a high-dimensional covariate adjustment method in microbiome analysis to better control for behavioural and clinical confounders, and in doing so examine the...
OBJECTIVE
We employed a high-dimensional covariate adjustment method in microbiome analysis to better control for behavioural and clinical confounders, and in doing so examine the effects of HIV on the rectal microbiome.
DESIGN
Three hundred and eighty-three MSM were grouped into four HIV viremia categories: HIV negative (n = 200), HIV-positive undetectable (HIV RNA < 20 copies/ml; n = 66), HIV-positive suppressed (RNA 20-200 copies/ml; n = 72) and HIV-positive viremic (RNA > 200 copies/ml; n = 45).
METHODS
We performed 16S rRNA gene sequencing on rectal swab samples and used inverse probability of treatment-weighted marginal structural models to examine differences in microbial composition by HIV viremia category.
RESULTS
HIV viremia explained a significant amount of variability in microbial composition in both unadjusted and covariate-adjusted analyses (R = 0.011, P = 0.02). Alterations in bacterial taxa were more apparent with increasing viremia. Relative to the HIV-negative group, HIV-positive undetectable participants showed depletions in Brachyspira, Campylobacter and Parasutterella, while suppressed participants demonstrated depletions in Barnesiella, Brachyspira and Helicobacter. The microbial signature of viremic men was most distinct, showing enrichment in inflammatory genera Peptoniphilus, Porphyromonas and Prevotella and depletion of Bacteroides, Brachyspira and Faecalibacterium, among others.
CONCLUSION
Our study shows that, after accounting for the influence of multiple confounding factors, HIV is associated with dysbiosis in the gastrointestinal microbiome in a dose-dependent manner. This analytic approach may allow for better identification of true microbial associations by limiting the effects of confounding, and thus improve comparability across future studies.
Topics: Adult; Dysbiosis; Gastrointestinal Microbiome; HIV Infections; Homosexuality, Male; Humans; Male; Microbiota; RNA, Ribosomal, 16S; Rectum; Sequence Analysis, RNA; Unsafe Sex; Viremia
PubMed: 30649052
DOI: 10.1097/QAD.0000000000002132 -
PloS One Jan 2010Circumcision is associated with significant reductions in HIV, HSV-2 and HPV infections among men and significant reductions in bacterial vaginosis among their female...
BACKGROUND
Circumcision is associated with significant reductions in HIV, HSV-2 and HPV infections among men and significant reductions in bacterial vaginosis among their female partners.
METHODOLOGY/PRINCIPAL FINDINGS
We assessed the penile (coronal sulci) microbiota in 12 HIV-negative Ugandan men before and after circumcision. Microbiota were characterized using sequence-tagged 16S rRNA gene pyrosequencing targeting the V3-V4 hypervariable regions. Taxonomic classification was performed using the RDP Naïve Bayesian Classifier. Among the 42 unique bacterial families identified, Pseudomonadaceae and Oxalobactericeae were the most abundant irrespective of circumcision status. Circumcision was associated with a significant change in the overall microbiota (PerMANOVA p = 0.007) and with a significant decrease in putative anaerobic bacterial families (Wilcoxon Signed-Rank test p = 0.014). Specifically, two families-Clostridiales Family XI (p = 0.006) and Prevotellaceae (p = 0.006)-were uniquely abundant before circumcision. Within these families we identified a number of anaerobic genera previously associated with bacterial vaginosis including: Anaerococcus spp., Finegoldia spp., Peptoniphilus spp., and Prevotella spp.
CONCLUSIONS/SIGNIFICANCE
The anoxic microenvironment of the subpreputial space may support pro-inflammatory anaerobes that can activate Langerhans cells to present HIV to CD4 cells in draining lymph nodes. Thus, the reduction in putative anaerobic bacteria after circumcision may play a role in protection from HIV and other sexually transmitted diseases.
Topics: Bacteria, Anaerobic; Bayes Theorem; Circumcision, Male; Humans; Male; Penis; RNA, Bacterial; RNA, Ribosomal, 16S; Species Specificity
PubMed: 20066050
DOI: 10.1371/journal.pone.0008422 -
BMJ Case Reports Dec 2019Our case report describes a patient with a common presenting complaint yet an uncommon infection. Our patient presented with a fluctuant breast mass diagnosed as a...
Our case report describes a patient with a common presenting complaint yet an uncommon infection. Our patient presented with a fluctuant breast mass diagnosed as a breast abscess. An aspirate sample was sent for culture and sensitivities, which revealed the presence of and the anaerobe She was therefore prescribed several weeks of amoxicillin and metronidazole, and made a full recovery. There are only three case reports describing as a causative organism for breast abscess, one of which had also occurred in our department. One case also showed the additional presence of Our findings reveal a growing need for increasing clinician awareness of and the importance of aspirate sample culture and sensitivity.
Topics: Abscess; Actinomycetaceae; Adult; Amoxicillin; Anti-Bacterial Agents; Breast Diseases; Female; Firmicutes; Humans; Metronidazole
PubMed: 31796455
DOI: 10.1136/bcr-2019-231194