-
Standards in Genomic Sciences Jul 2012We report the properties of a draft genome sequence of the bacterium Anaerococcus vaginalis strain PH9, a species within the Anaerococcus genus. This strain, whose...
We report the properties of a draft genome sequence of the bacterium Anaerococcus vaginalis strain PH9, a species within the Anaerococcus genus. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. A. vaginalis is an obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,048,125-bp long (one chromosome but no plasmid) and contains 2,095 protein-coding and 38 RNA genes, including three rRNA genes.
PubMed: 23407456
DOI: 10.4056/sigs.2716452 -
Biomedicines Sep 2022Recent advances in next-generation sequencing and metagenomic studies have provided insights into the microbial profile of different body sites. However, research on the...
Recent advances in next-generation sequencing and metagenomic studies have provided insights into the microbial profile of different body sites. However, research on the microbial composition of urine is limited, particularly in children. The goal of this study was to optimize and develop reproducible metagenome and virome protocols using a small volume of urine samples collected from healthy children. We collected midstream urine specimens from 40 healthy children. Using the metagenomics shotgun approach, we tested various protocols. Different microbial roots such as Archaea, Bacteria, Eukaryota, and Viruses were successfully identified using our optimized urine protocol. Our data reflected much variation in the microbial fingerprints of children. Girls had significantly higher levels of Firmicutes, whereas boys had significantly higher levels of Actinobacteria. The genus Anaerococcus dominated the urinary bacteriome of healthy girls, with a significant increase in Anaerococcus prevotii, Anaerococcus vaginalis, and Veillonella parvula (p-value < 0.001) when compared with that of boys. An increased relative abundance of Xylanimonas and Arthrobacter, with a significantly high abundance of Arthrobacter sp. FB24 (p-value 0.0028) and Arthrobacter aurescences (p-value 0.015), was observed in boys. The urinary mycobiome showed a significant rise in the genus Malassezia and Malassezia globose fungus (p-value 0.009) in girls, whereas genus Saccharomyces (p-value 0.009) was significantly high in boys. The beta diversity of the urinary mycobiome was found to differ between different age groups. Boys had significantly more Mastadenovirus and Human mastadenovirus-A in their urinary virome than girls. With increasing age, we noticed an increase in the relative abundance of the order Caudovirales. Our optimized protocols allowed us to identify the unique microbes for each sex by using an adequate volume of urine (3−10 mL) to screen for the bacteriome, mycobiome, and virome profiles in the urine of healthy children. To the best of our knowledge, this is the first study to characterize the metagenomics profiles of urine in a healthy pediatric population.
PubMed: 36289674
DOI: 10.3390/biomedicines10102412 -
Microbiome May 2021Obesity and vaginal microbiome (VMB) dysbiosis are each risk factors for adverse reproductive and oncological health outcomes in women. Here, we investigated the...
BACKGROUND
Obesity and vaginal microbiome (VMB) dysbiosis are each risk factors for adverse reproductive and oncological health outcomes in women. Here, we investigated the relationship between obesity, vaginal bacterial composition, local inflammation and bariatric surgery.
METHODS
Vaginal bacterial composition assessed by high-throughput sequencing of bacterial 16S rRNA genes and local cytokine levels measured using a multiplexed Magnetic Luminex Screening Assay were compared between 67 obese and 42 non-obese women. We further assessed temporal changes in the microbiota and cytokines in a subset of 27 women who underwent bariatric surgery.
RESULTS
The bacterial component of the vaginal microbiota in obese women was characterised by a lower prevalence of a Lactobacillus-dominant VMB and higher prevalence of a high diversity (Lactobacillus spp., and Gardnerella- spp. depleted) VMB, compared with non-obese subjects (p<0.001). Obese women had higher relative abundance of Dialister species (p<0.001), Anaerococcus vaginalis (p=0.021), and Prevotella timonensis (p=0.020) and decreased relative abundance of Lactobacillus crispatus (p=0.014). Local vaginal IL-1β, IL-4, IL-6, IL-8, IFNγ, MIP-1α and TNFα levels were all higher among obese women, however, only IL-1β and IL-8 correlated with VMB species diversity. In a subset of obese women undergoing bariatric surgery, there were no significant overall differences in VMB following surgery; however, 75% of these women remained obese at 6 months. Prior to surgery, there was no relationship between body mass index (BMI) and VMB structure; however, post-surgery women with a Lactobacillus-dominant VMB had a significantly lower BMI than those with a high diversity VMB.
CONCLUSIONS
Obese women have a significantly different vaginal microbiota composition with increased levels of local inflammation compared to non-obese women. Bariatric surgery does not change the VMB; however, those with the greatest weight loss 6-month post-surgery are most likely to have a Lactobacillus-dominant VMB. Video abstract.
Topics: Bariatric Surgery; Female; Firmicutes; Humans; Microbiota; Obesity; Prevotella; RNA, Ribosomal, 16S; Vagina; Weight Loss
PubMed: 34049596
DOI: 10.1186/s40168-021-01011-2 -
Frontiers in Cellular and Infection... 2023Although recent studies have shown that the human microbiome is involved in the pathogenesis of allergic diseases, the impact of microbiota on allergic rhinitis (AR) and...
INTRODUCTION
Although recent studies have shown that the human microbiome is involved in the pathogenesis of allergic diseases, the impact of microbiota on allergic rhinitis (AR) and non-allergic rhinitis (nAR) has not been elucidated. The aim of this study was to investigate the differences in the composition of the nasal flora in patients with AR and nAR and their role in the pathogenesis.
METHOD
From February to September 2022, 35 AR patients and 35 nAR patients admitted to Harbin Medical University's Second Affiliated Hospital, as well as 20 healthy subjects who underwent physical examination during the same period, were subjected to 16SrDNA and metagenomic sequencing of nasal flora.
RESULTS
The microbiota composition of the three groups of study subjects differs significantly. The relative abundance of Vibrio vulnificus and Acinetobacter baumanni in the nasal cavity of AR patients was significantly higher when compared to nAR patients, while the relative abundance of Lactobacillus murinus, Lactobacillus iners, Proteobacteria, Pseudomonadales, and Escherichia coli was lower. In addition, Lactobacillus murinus and Lacttobacillus kunkeei were also negatively correlated with IgE, while Lacttobacillus kunkeei was positively correlated with age. The relative distribution of Faecalibacterium was higher in moderate than in severe AR patients. According to KEGG functional enrichment annotation, ICMT(protein-S-isoprenylcysteine O-methyltransferase,ICMT) is an AR microbiota-specific enzyme that plays a role, while glycan biosynthesis and metabolism are more active in AR microbiota. For AR, the model containing Parabacteroides goldstemii, Sutterella-SP-6FBBBBH3, Pseudoalteromonas luteoviolacea, Lachnospiraceae bacterium-615, and Bacteroides coprocola had the highest the area under the curve (AUC), which was 0.9733(95%CI:0.926-1.000) in the constructed random forest prediction model. The largest AUC for nAR is 0.984(95%CI:0.949-1.000) for the model containing Pseudomonas-SP-LTJR-52, Lachnospiraceae bacterium-615, Prevotella corporis, Anaerococcus vaginalis, and Roseburia inulinivorans.
CONCLUSION
In conclusion, patients with AR and nAR had significantly different microbiota profiles compared to healthy controls. The results suggest that the nasal microbiota may play a key role in the pathogenesis and symptoms of AR and nAR, providing us with new ideas for the treatment of AR and nAR.
Topics: Humans; Male; Female; Young Adult; Adult; Rhinitis, Allergic; Rhinitis; Nasal Cavity; Metagenome; Biodiversity; Microbiota; RNA, Ribosomal, 16S; Bacteria
PubMed: 37180436
DOI: 10.3389/fcimb.2023.1166389 -
PeerJ 2022Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having...
BACKGROUND
Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of species (CST IV). The objective of this study was to characterize the vaginal microbiomes across a more diverse intercontinental group of women ( = 151) of different ethnicities (African American, African Kenyan, Afro-Caribbean, Asian Indonesian and Caucasian German) using 16S rRNA gene sequence analysis to determine their structures and offer a comprehensive description of the non- dominant CSTs and subtypes.
RESULTS
In this study, the bacterial composition of the vaginal microbiomes differed significantly among the ethnic groups. spp. (. and . ) dominated the vaginal microbiomes in African American women (91.8%) compared to European (German, 42.4%), Asian (Indonesian, 45.0%), African (Kenyan, 34.4%) and Afro-Caribbean (26.1%) women. Expanding on CST classification, three subtypes of CST IV (CST IV-A, IV-B and IV-C) ( = 56, 37.1%) and four additional CSTs were described: CST VI -dominant ( = 6, 21.8%); CST VII (-dominant, = 1, 0.66%); CST VIII ( = 9, 5.96%), resembling aerobic vaginitis, was differentiated by a high proportion of taxa such as , and (relative abundance [RA] > 50%) and CST IX ( = 7, 4.64%) dominated by genera other than , or (., and ). Within the vaginal microbiomes, 32 "taxa with high pathogenic potential" (THPP) were identified. Collectively, THPP (mean RA ~5.24%) negatively correlated (r = -0.68, < 2.2e-16) with species but not significantly with / spp. combined (r = -0.13, = 0.1). However, at the individual level, exhibited moderate positive correlations with (r = 0.46, = 2.6e-09) and spp. (r = 0.47, = 1.4e-09).
CONCLUSIONS
These findings while supporting the idea that vaginal microbiomes vary with ethnicity, also suggest that CSTs are more wide-ranging and not exclusive to any particular ethnic group. This study offers additional insight into the structure of the vaginal microbiome and contributes to the description and subcategorization of non-dominated CSTs.
Topics: Female; Humans; Male; RNA, Ribosomal, 16S; Kenya; Vagina; Microbiota; Lactobacillus; Bacteria; Gardnerella
PubMed: 36518275
DOI: 10.7717/peerj.14449 -
Foot & Ankle Orthopaedics Jul 2021Accurate identification of primary pathogens in foot infections remains challenging due to the diverse microbiome. Conventional culture may show false-positive or...
BACKGROUND
Accurate identification of primary pathogens in foot infections remains challenging due to the diverse microbiome. Conventional culture may show false-positive or false-negative growth, leading to ineffective postoperative antibiotic treatment. Next-generation sequencing (NGS) has been explored as an alternative to standard culture in orthopedic infections. NGS is highly sensitive and can detect an entire bacterial genome along with genes conferring antibiotic resistance in a given sample. We investigated the potential use of NGS for accurate identification and quantification of microbes in infected diabetic foot ulcer (DFU). We hypothesize that NGS will aid identification of dominant pathogen and provide a more complete profile of microorganisms in infected DFUs compared to the standard culture method.
METHODS
Data were prospectively collected from 30 infected DFU patients who underwent operative treatment by a fellowship-trained orthopedic foot and ankle surgeon from October 2018 to September 2019. The average age of the patient was 60.4 years. Operative procedures performed were irrigation and debridement (12), toe or ray amputation (13), calcanectomies (4), and below-the-knee amputation (1). Infected bone specimens were obtained intraoperatively and processed for standard culture and NGS. Concordance between the standard culture and NGS was assessed.
RESULTS
In 29 of 30 patients, pathogens were identified by both NGS and culture, with a concordance rate of 70%. In standard culture, (58.6%) was the most common pathogen, followed by coagulase-negative (24.1%), (17.2%), and (17.2%). In NGS, (44.8%) was the most common microorganism followed by (41.4%), and (24.1%). On average, NGS revealed 5.1 (range, 1-11) pathogens in a given sample, whereas culture revealed 2.6 (range, 1-6) pathogens.
CONCLUSION
NGS is an emerging molecular diagnostic method of microbial identification in orthopedic infection. It frequently provides different profiles of microorganisms along with antibiotic-resistant gene information compared to conventional culture in polymicrobial foot infection. Clinical use of NGS for management of foot and ankle infections warrants further investigation.
LEVEL OF EVIDENCE
Level II, diagnostic study.
PubMed: 35097461
DOI: 10.1177/24730114211026933 -
Microbiology (Reading, England) Jul 2003Here, a rapid and reliable two-step multiplex PCR assay for identifying 14 Gram-positive anaerobic cocci (GPAC) species originally classified in the genus... (Comparative Study)
Comparative Study
Rapid identification of Gram-positive anaerobic coccal species originally classified in the genus Peptostreptococcus by multiplex PCR assays using genus- and species-specific primers.
Here, a rapid and reliable two-step multiplex PCR assay for identifying 14 Gram-positive anaerobic cocci (GPAC) species originally classified in the genus Peptostreptococcus (Anaerococcus hydrogenalis, Anaerococcus lactolyticus, Anaerococcus octavius, Anaerococcus prevotii, Anaerococcus tetradius, Anaerococcus vaginalis, Finegoldia magna, Micromonas micros, Peptostreptococcus anaerobius, Peptoniphilus asaccharolyticus, Peptoniphilus harei, Peptoniphilus indolicus, Peptoniphilus ivorii and Peptoniphilus lacrimalis) is reported. Fourteen type strains representing 14 GPAC species were first identified to the genus level by multiplex PCR (multiplex PCR-G). Since three of these genera (Finegoldia, Micromonas and Peptostreptococcus) contain only a single species, F. magna, M. micros and P. anaerobius, respectively, these organisms were identified to the species level directly by using the multiplex PCR-G. Then six species of the genus Anaerococcus (A. hydrogenalis, A. lactolyticus, A. octavius, A. prevotii, A. vaginalis and A. tetradius) were further identified to the species level using multiplex PCR assays (multiplex PCR-Ia and multiplex PCR-Ib). Similarly, five species of the genus Peptoniphilus (Pn. asaccharolyticus, Pn. harei, Pn. indolicus, Pn. ivorii and Pn. lacrimalis) were identified to the species level using multiplex PCR-IIa and multiplex PCR-IIb. The established two-step multiplex PCR identification scheme was applied to the identification of 190 clinical isolates of GPAC species that had been identified previously to the species level by 16S rRNA sequencing and phenotypic tests. The identification obtained from multiplex PCR assays showed 100 % agreement with 16S rDNA sequencing identification, but only 65 % (123/190) agreement with the identification obtained by phenotypic tests. The multiplex PCR scheme established in this study is a simple, rapid and reliable method for the identification of GPAC species. It will permit a more accurate assessment of the role of various GPAC species in infection and of the degree of antimicrobial resistance in each of the group members.
Topics: Base Sequence; DNA Primers; DNA, Bacterial; DNA, Ribosomal; Gram-Positive Cocci; Peptostreptococcus; Polymerase Chain Reaction; RNA, Bacterial; RNA, Ribosomal, 16S; Sensitivity and Specificity; Species Specificity
PubMed: 12855723
DOI: 10.1099/mic.0.26227-0 -
Clinical Microbiology and Infection :... Oct 2007Fluorescent probes targeted at 16S rRNA were designed for Peptostreptococcus anaerobius and Peptostreptococcus stomatis (Pana134), Parvimonas micra (Pamic1435),...
Fluorescent probes targeted at 16S rRNA were designed for Peptostreptococcus anaerobius and Peptostreptococcus stomatis (Pana134), Parvimonas micra (Pamic1435), Finegoldia magna (Fmag1250), Peptoniphilus asaccharolyticus (Pnasa1254), Peptoniphilus ivorii (Pnivo731), Peptoniphilus harei (Pnhar1466), Anaerococcus vaginalis (Avag1280) and Anaerococcus lactolyticus (Alac1438), based on the 16S rRNA sequences of reference strains and 88 randomly chosen clinical isolates. These strains were also used for validation of the probes. Application of the probes to an additional group of 100 clinical isolates revealed that 87% of Gram-positive anaerobic cocci (GPAC) could be identified with this set of probes. The 16S rRNAs of 13 clinical isolates that could not be identified were sequenced. Most of these isolates were GPAC that were not targeted by the probes. No clinical isolates of Pn. asaccharolyticus were encountered. Near full-length sequences were obtained from 71 of 101 (n = 88 + 13) sequenced clinical isolates. Of these, 25 showed <98% similarity with the homologues of the closest established species. The Fmag1250, Pamic1435, Pnhar1466, Pana134, Pnasa1254 and Pnivo731 probes allowed reliable identification and hybridised with all corresponding isolates. The Avag1280 and Alac1438 probes failed to hybridise with two isolates and one isolate, respectively, because of intra-species variation. However, overall, the set of probes yielded fast and reliable identification for the majority of clinical isolates.
Topics: Anaerobiosis; Bacterial Typing Techniques; DNA, Bacterial; DNA, Ribosomal; Fluorescent Dyes; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Humans; Phylogeny; RNA, Ribosomal, 16S; Reference Standards; Sensitivity and Specificity; Sequence Analysis, DNA; Species Specificity
PubMed: 17714522
DOI: 10.1111/j.1469-0691.2007.01803.x