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International Journal of Molecular... Apr 2023Since the first description of a commensal seminal microbiome using sequencing, less than a decade ago, interest in the composition of this microbiome and its...
Since the first description of a commensal seminal microbiome using sequencing, less than a decade ago, interest in the composition of this microbiome and its relationship with fertility has been growing. Articles using next-generation sequencing techniques agree on the identification of the most abundant bacterial phyla. However, at the genus level, there is still no consensus on which bacteria are most abundant in human seminal plasma. This discrepancy may be due to methodological variability such as sample collection, bacterial DNA extraction methodology, which hypervariable regions of gene have been amplified, or bioinformatic analysis. In the present work, seminal microbiota of 14 control samples and 42 samples of idiopathic infertile patients were characterized based on full-length sequencing of the gene using MinION platform from Oxford Nanopore. These same samples had been analyzed previously using Illumina's MiSeq sequencing platform. Comparison between the results obtained with the two platforms has been used to analyze the impact of sequencing method on the study of the seminal microbiome's composition. Seminal microbiota observed with MinION were mainly composed of the phyla , , and , with the most abundant genera being , , , , , , , , and . This composition was similar to that found by the Illumina platform, since these 10 most abundant genera were also among the most abundant genera detected by the Nanopore platform. In both cases, the top 10 genera represented more than 70% of the classified reads. However, relative abundance of each bacterium did not correlate between these two platforms, with intraindividual variations of up to 50 percentage points in some cases. Results suggest that the effect of the sequencing platform on the characterization of seminal microbiota is not very large at the phylum level, with slightly variances in and , but presents differences at the genus level. These differences could alter the composition and diversity of bacterial profiles or posterior analyses. This indicates the importance of conducting multi-platform studies to better characterize seminal microbioma.
Topics: Humans; RNA, Ribosomal, 16S; Microbiota; Bacteria; Firmicutes; Proteobacteria; Actinobacteria; High-Throughput Nucleotide Sequencing; Clostridiales
PubMed: 37175573
DOI: 10.3390/ijms24097867 -
The Journals of Gerontology. Series A,... Jun 2020Emerging links between gut microbiota and diseases of aging point to possible shared immune, metabolic, and cellular damage mechanisms, operating long before diseases...
Emerging links between gut microbiota and diseases of aging point to possible shared immune, metabolic, and cellular damage mechanisms, operating long before diseases manifest. We conducted 16S rRNA sequencing of fecal samples collected from a subsample (n = 668) of Add Health Wave V, a nationally representative longitudinal study of adults aged 32-42. An overlapping subsample (n = 345) included whole-blood RNA-seq. We examined associations between fecal taxonomic abundances and dried blood spot-based markers of lipid and glucose homeostasis and C-reactive protein (measured in Wave IV), as well as gene expression markers of inflammation, cellular damage, immune cell composition, and transcriptomic age (measured in Wave V), using Bayesian hierarchical models adjusted for potential confounders. We additionally estimated a co-abundance network between inflammation-related genes and bacterial taxa using penalized Gaussian graphical models. Strong and consistent microbiota associations emerged for HbA1c, glucose, C-reactive protein, and principal components of genes upregulated in inflammation, DNA repair, and reactive oxygen species, with Streptococcus infantis, Pseudomonas spp., and Peptoniphilus as major players for each. This pattern was largely echoed (though attenuated) for immunological cell composition gene sets, and only Serratia varied meaningfully by transcriptomic age. Network co-abundance indicated relationships between Prevotella sp., Bacteroides sp., and Ruminococcus sp. and gut immune/metabolic regulatory activity, and Ruminococcus sp, Dialister, and Butyrivibrio crossotus with balance between Th1 and Th2 inflammation. In conclusion, many common associations between microbiota and major physiologic aging mechanisms are evident in early-mid adulthood and suggest avenues for early detection and prevention of accelerated aging.
Topics: Adolescent; Adult; Age Factors; Aging; Bayes Theorem; Biomarkers; Feces; Female; Gastrointestinal Microbiome; Humans; Inflammation; Longitudinal Studies; Male; Young Adult
PubMed: 32421783
DOI: 10.1093/gerona/glaa122 -
Annals of Laboratory Medicine Jul 2022
Topics: Abscess; Craniofacial Abnormalities; Firmicutes; Humans
PubMed: 35177572
DOI: 10.3343/alm.2022.42.4.488 -
Gut Microbes 2021To investigate the relationship between intestinal microbiota and SARS-CoV-2-mediated pathogenicity in a United States, majority African American cohort. We...
To investigate the relationship between intestinal microbiota and SARS-CoV-2-mediated pathogenicity in a United States, majority African American cohort. We prospectively collected fecal samples from 50 SARS-CoV-2 infected patients, 9 SARS-CoV-2 recovered patients, and 34 uninfected subjects seen by the hospital with unrelated respiratory medical conditions (controls). 16S rRNA sequencing and qPCR analysis was performed on fecal DNA/RNA. The fecal microbial composition was found to be significantly different between SARS-CoV-2 patients and controls (PERMANOVA FDR- = .004), independent of antibiotic exposure. and were identified as the three most significantly enriched genera in COVID-19 patients compared to controls. Actively infected patients were also found to have a different gut microbiota than recovered patients (PERMANOVA FDR- = .003), and the most enriched genus in infected patients was , with and being enriched in the recovered patients. No difference in microbial community structure between recovered patients and uninfected controls was observed, nor a difference in alpha diversity between the three groups. 24 of the 50 COVID-19 patients (48%) tested positive via RT-qPCR for fecal SARS-CoV-2 RNA. A significant difference in gut microbial composition between SARS-CoV-2 positive and negative samples was observed, with and being enriched in the positive cohort. No significant associations between microbiome composition and disease severity was found. The intestinal microbiota is sensitive to the presence of SARS-CoV-2, with increased relative abundance of genera () associated with gastrointestinal (GI) disease. Further studies are needed to investigate the functional impact of SARS-CoV-2 on GI health.
Topics: Aged; Bacteria; COVID-19; Cohort Studies; Feces; Female; Gastrointestinal Microbiome; Humans; Male; Middle Aged; RNA, Ribosomal, 16S; RNA, Viral; SARS-CoV-2; Severity of Illness Index; United States
PubMed: 34100340
DOI: 10.1080/19490976.2021.1926840 -
New Microbes and New Infections May 2018Strain EL1 was isolated from a sinus sample of an 85-year-old man with chronic refractory sinusitis complicating ethmoidal adenocarcinoma. We studied its phenotypic and...
Strain EL1 was isolated from a sinus sample of an 85-year-old man with chronic refractory sinusitis complicating ethmoidal adenocarcinoma. We studied its phenotypic and genomic characteristics. This is a Gram stain-positive, anaerobic and microaerophilic coccus. Cells are catalase negative, nonmotile and non-spore forming. The major fatty acids are saturated hexadecanoic acid (34%), unsaturated 9-octadecenoic acid (32%) and 9.12-octadecadienoic acid (21%). The 1.86 Mb long genome exhibits a 29.9% G+C content and contains 1750 protein-coding and 43 RNA genes. On the basis of these data, we propose the creation of the new human-associated bacterial species sp. nov.
PubMed: 29707211
DOI: 10.1016/j.nmni.2018.02.007 -
Cureus Apr 2023Postpartum infectious complications can present with a wide range of nonspecific symptoms. Herein, we describe a complicated late postpartum presentation of recurrent...
Postpartum infectious complications can present with a wide range of nonspecific symptoms. Herein, we describe a complicated late postpartum presentation of recurrent fever following a cesarean delivery complicated by chorioamnionitis. Following discharge, the patient experienced cyclical fever and was treated with antipyretics as an outpatient. The patient continued to experience symptoms and reported to the hospital for further evaluation. Initially thought to be septic pelvic thrombophlebitis, the patient was trialed on clindamycin and gentamycin without resolution of symptoms. After extensive evaluation, the fevers were found to be the result of an infected periuterine hematoma and a concomitant subcapsular inferior hepatic abscess. Bacterial cultures isolated two rare anaerobic organisms: and Source control was achieved by drainage of the two abscesses followed by antibiotic treatment with ertapenem and metronidazole, and the patient recovered successfully. This is the first reported case, to the authors' knowledge, of this complicated postpartum picture due to these anaerobic organisms.
PubMed: 37168151
DOI: 10.7759/cureus.37293 -
Scientific Reports Oct 2019Methamphetamine (MA) use is a major public health problem in the United States, especially among people living with HIV (PLWH). Many MA-induced neurotoxic effects are...
Methamphetamine (MA) use is a major public health problem in the United States, especially among people living with HIV (PLWH). Many MA-induced neurotoxic effects are mediated by inflammation and gut microbiota may play a role in this process, yet the effects of MA on the microbiome have not been adequately explored. Therefore, we performed 16S rRNA gene sequencing on rectal swab samples from 381 men who have sex with men, 48% of whom were PLWH and 41% of whom used MA. We compared microbiome composition between MA users and non-users while testing for potential interactions with HIV and controlling for numerous confounders using inverse probability of treatment weighting. We found that MA use explained significant variation in overall composition (R = 0.005, p = 0.008) and was associated with elevated Finegoldia, Parvimonas, Peptoniphilus, and Porphyromonas and reduced Butyricicoccus and Faecalibacterium, among others. Genera including Actinomyces and Streptobacillus interacted with HIV status, such that they were increased in HIV+ MA users. Finegoldia and Peptoniphilus increased with increasing frequency of MA use, among others. In summary, MA use was associated with a microbial imbalance favoring pro-inflammatory bacteria, including some with neuroactive potential and others that have previously been associated with poor HIV outcomes.
Topics: Adult; Bacteria; Drug Users; Gastrointestinal Microbiome; HIV Infections; Homosexuality, Male; Humans; Male; Methamphetamine; Sexual and Gender Minorities; Young Adult
PubMed: 31619731
DOI: 10.1038/s41598-019-51142-8 -
Frontiers in Cellular and Infection... 2024We assessed the anti-chlamydial activity of fresh vaginal secretions, deciphering the microbial and metabolic components able to counteract viability.
INTRODUCTION
We assessed the anti-chlamydial activity of fresh vaginal secretions, deciphering the microbial and metabolic components able to counteract viability.
METHODS
Forty vaginal samples were collected from a group of reproductive-aged women and their anti-chlamydial activity was evaluated by inhibition experiments. Each sample underwent 16S rRNA metabarcoding sequencing to determine the bacterial composition, as well as H-NMR spectroscopy to detect and quantify the presence of vaginal metabolites.
RESULTS
Samples characterized by a high anti-chlamydial activity were enriched in , especially and , while not-active samples exhibited a significant reduction of lactobacilli, along with higher relative abundances of and . showed an opposite behavior compared to , being more prevalent in not-active vaginal samples. Higher concentrations of several amino acids (i.e., isoleucine, leucine, and aspartate; positively correlated to the abundance of and ) lactate, and 4-aminobutyrate were the most significant metabolic fingerprints of highly active samples. Acetate and formate concentrations, on the other hand, were related to the abundances of a group of anaerobic opportunistic bacteria (including and ). Finally, glucose, correlated to and genera, emerged as a key molecule of the vaginal environment: indeed, the anti-chlamydial effect of vaginal fluids decreased as glucose concentrations increased.
DISCUSSION
These findings could pave the way for novel strategies in the prevention and treatment of chlamydial urogenital infections, such as lactobacilli probiotic formulations or lactobacilli-derived postbiotics.
Topics: Female; Humans; Vagina; RNA, Ribosomal, 16S; Lactobacillus; Chlamydia trachomatis; Adult; Streptococcus; Young Adult; Lactobacillus crispatus; Chlamydia Infections
PubMed: 38912205
DOI: 10.3389/fcimb.2024.1403782 -
International Journal of Molecular... Feb 2023Functional or compositional perturbations of the microbiome can occur at different sites, of the body and this dysbiosis has been linked to various diseases. Changes in...
Functional or compositional perturbations of the microbiome can occur at different sites, of the body and this dysbiosis has been linked to various diseases. Changes in the nasopharyngeal microbiome are associated to patient's susceptibility to multiple viral infections, supporting the idea that the nasopharynx may be playing an important role in health and disease. Most studies on the nasopharyngeal microbiome have focused on a specific period in the lifespan, such as infancy or the old age, or have other limitations such as low sample size. Therefore, detailed studies analyzing the age- and sex-associated changes in the nasopharyngeal microbiome of healthy people across their whole life are essential to understand the relevance of the nasopharynx in the pathogenesis of multiple diseases, particularly viral infections. One hundred twenty nasopharyngeal samples from healthy subjects of all ages and both sexes were analyzed by 16S rRNA sequencing. Nasopharyngeal bacterial alpha diversity did not vary in any case between age or sex groups. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the predominant phyla in all the age groups, with several sex-associated. , , , , , , , , , , and were the only 11 bacterial genera that presented significant age-associated differences. Other bacterial genera such as , , , , , , , , , , and appeared in the population with a very high frequency, suggesting that their presence might be biologically relevant. Therefore, in contrast to other anatomical areas such as the gut, bacterial diversity in the nasopharynx of healthy subjects remains stable and resistant to perturbations throughout the whole life and in both sexes. Age-associated abundance changes were observed at phylum, family, and genus levels, as well as several sex-associated changes probably due to the different levels of sex hormones present in both sexes at certain ages. Our results provide a complete and valuable dataset that will be useful for future research aiming for studying the relationship between changes in the nasopharyngeal microbiome and susceptibility to or severity of multiple diseases.
Topics: Male; Female; Humans; RNA, Ribosomal, 16S; Genes, rRNA; Nasopharynx; Microbiota; Bacteria; Aging; Virus Diseases
PubMed: 36835535
DOI: 10.3390/ijms24044127 -
APMIS : Acta Pathologica,... Aug 2019Necrotizing soft tissue infections (NSTIs) are associated with high morbidity and mortality and are increasing in incidence. Proper identification of the microbial...
Necrotizing soft tissue infections (NSTIs) are associated with high morbidity and mortality and are increasing in incidence. Proper identification of the microbial causes of NSTIs is a crucial step in diagnosis and treatment, but the majority of data collected are culture based, which is biased against fastidious organisms, including obligate anaerobes. The goal of this study was to address this gap in knowledge by characterizing NSTI microbial communities through molecular diagnostics. We performed 16S rRNA sequencing on human NSTI samples and identified five genera most commonly found in NSTIs (Prevotella, Bacteroides, Peptoniphilus, Porphyromonas, and Enterococcus). We found that a >70% contribution of obligate anaerobes to the bacterial population distribution was associated with NSTI mortality, and that NSTI samples, from both survivors and non-survivors, had an increased relative abundance of gram negative bacteria compared to those of abscess patients. Based on our data, we conclude that obligate anaerobes are abundant in NSTIs and a high relative abundance of anaerobes is associated with a worse outcome. We recommend increasing anaerobe antibiotic coverage during the treatment of NSTIs even when anaerobes are not found by traditional clinical microbiology methods, and especially when there is a clinical suspicion for anaerobe involvement.
Topics: Adult; Bacteria, Anaerobic; DNA, Ribosomal; Female; Humans; Male; Metagenomics; Middle Aged; RNA, Ribosomal, 16S; Soft Tissue Infections; Young Adult
PubMed: 31127652
DOI: 10.1111/apm.12969