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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Prete CD, Nocera FP, Piegari G, Palumbo V, Martino LD, Cocchia N, Paciello O, Montano C, Pasolini MP. Use of cytobrush for bacteriological and cytological diagnosis of endometritis in mares. Vet World 2024; 17:398-406. [PMID: 38595673 PMCID: PMC11000473 DOI: 10.14202/vetworld.2024.398-406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/24/2024] [Indexed: 04/11/2024] Open
Abstract
Background and Aim A combined microbial and cytological examination of uterine samples is the main diagnostic method for endometritis in mares. This study aimed to describe a procedure for using the same uterine cytobrush (CB) for both bacteriological and cytological evaluation. Material and Methods The procedure consists of rolling the CB onto a sterilized glass slide immediately after collection and before the transfer into a sterile saline solution. In Experiment 1, a comparison between bacteriological results of the cotton swab (CS) and CB or pellet was made in 10 mares; in Experiment 2, bacteriological and cytological results were compared between different processing methods of CB in 28 mares; in other 6 mares, a CB was processed for cytology only, to investigate the reasons for the low cellularity of the pellet. Results The agreement between culture results from the CB and CS was evaluated, and a comparison between the cytological data obtained by different processing methods of CB was performed. The perfect agreement between the CB and CS microbiological results was found. The described procedure enables useful diagnostic smears for cytology. Moreover, the seeding of both the tip of CB and the saline solution used for the transport produced accurate bacteriological results. Conclusion The protocol described in this study for the use of CB for both cytological and bacteriological analysis could be used for the diagnosis of endometritis. To maximize diagnostic sample quality, cytology slides must be prepared with meticulous care in the field to preserve cellular integrity and minimize artifacts.
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Affiliation(s)
- Chiara Del Prete
- Reproduction Unit, Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Francesca Paola Nocera
- Diagnostic Service of Pathology and Animal Health, Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Giuseppe Piegari
- Diagnostic Service of Pathology and Animal Health, Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Veronica Palumbo
- Regional Reference Center for Urban Veterinary Hygiene (CRIUV), Naples, Italy
| | - Luisa De Martino
- Diagnostic Service of Pathology and Animal Health, Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Natascia Cocchia
- Reproduction Unit, Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Orlando Paciello
- Diagnostic Service of Pathology and Animal Health, Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Chiara Montano
- Surgery Unit, Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Maria Pia Pasolini
- Surgery Unit, Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
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3
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Teh HE, Pung CK, Arasoo VJT, Yap PSX. A Landscape View of the Female Genital Tract Microbiome in Healthy Controls and Women With Reproductive Health Conditions Associated With Ectopic Pregnancy. Br J Biomed Sci 2024; 80:12098. [PMID: 38283642 PMCID: PMC10811206 DOI: 10.3389/bjbs.2023.12098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024]
Abstract
Disruption of the female genital microbiome is associated with several pregnancy complications, including miscarriage, preterm onset of labour, and tubal pregnancy. Ectopic pregnancy is a known cause of maternal morbidity and mortality, but early diagnosis and treatment of ectopic pregnancy remain a challenge. Despite growing established associations between genital microbiome and female reproductive health, few studies have specifically focused on its link with ectopic pregnancy. Therefore, the current review aims to provide a comprehensive account of the female genital microbiome in healthy and fertile women compared to those in ectopic pregnancy and its associated risk factors. The microbial diversity from various sites of the female genital tract was explored for a reliable proxy of female reproductive health in sequencing-based ectopic pregnancy research. Our report confirmed the predominance of Lactobacillus in the vagina and the cervix among healthy women. The relative abundance decreased in the vaginal and cervical microbiome in the disease state. In contrast, there were inconsistent findings on the uterine microbiome across studies. Additionally, we explore a spectrum of opportunities to enhance our understanding of the female genital tract microbiome and reproductive conditions. In conclusion, this study identifies gaps within the field and emphasises the need for visionary solutions in metagenomic tools for the early detection of ectopic pregnancy and other gynaecological diseases.
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Affiliation(s)
| | | | | | - Polly Soo Xi Yap
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
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4
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Sow D, Ndiour CN, Thiam O, Ndiaye M, Diagne PN, Doucouré S, Senghor B, Gaye O, Sokhna C, Faye B. Cytobrush and cotton swab as sampling tools for molecular diagnosis of female genital schistosomiasis in the uterine cervix. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2023; 4:100143. [PMID: 37841305 PMCID: PMC10570942 DOI: 10.1016/j.crpvbd.2023.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/02/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023]
Abstract
Female genital schistosomiasis (FGS) caused by Schistosoma haematobium is a neglected chronic parasitic disease. Diagnosis relies mainly on a colposcopy, which reveals non-specific lesions. This study aimed to assess the performance of two sampling methods for the molecular diagnosis of FGS in the uterine cervix. We conducted a descriptive cross-sectional study in women of reproductive age in Saint Louis, Senegal, who presented for cervical cancer screening. Cotton swab and cytobrush samples were collected from the cervix and examined by real-time PCR. The PCR results obtained using the cotton swabs were compared with those obtained using cytobrush. Of the 189 women recruited, 56 (30%) were found to be positive for S. haematobium infection via real-time PCR. Women aged 40-54 years were predominantly infected (45%) followed by those aged 25-39 years (36%). Numerically more PCR-positive specimens were identified using cytobrush sampling. Of the 89 women who underwent both cytobrush and cotton swab sampling, 27 were PCR-positive in the cytobrush sampling vs 4 in the swab sampling. The mean Ct-value was 31.0 ± 3.8 for cytobrush-based PCR vs 30.0 ± 4.4 for swab-based PCR. The results confirm that real-time PCR can detect Schistosoma haematobium DNA in the uterine cervix. The next step will be to compare PCR with the other diagnostic methods of FGS.
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Affiliation(s)
- Doudou Sow
- Service de Parasitologie-Mycologie, UFR Sciences de la Santé, Université Gaston Berger, BP 234, St Louis, Senegal
| | - Coumba Nar Ndiour
- Service de Parasitologie-Mycologie, UFR Sciences de la Santé, Université Gaston Berger, BP 234, St Louis, Senegal
| | - Ousmane Thiam
- Service de Gynécologie - Obstétrique, UFR Sciences de la Santé, Université Gaston Berger, BP 234, St Louis, Senegal
| | - Magatte Ndiaye
- Service de Parasitologie - Mycologie, FMPO, Université Cheikh Anta Diop, BP 5005, Dakar, Senegal
| | - Pape Ndiole Diagne
- Service de Parasitologie-Mycologie, UFR Sciences de la Santé, Université Gaston Berger, BP 234, St Louis, Senegal
| | | | - Bruno Senghor
- Unité VITROME, Institut de Recherche et de Développement, Dakar, Senegal
| | - Oumar Gaye
- Service de Parasitologie - Mycologie, FMPO, Université Cheikh Anta Diop, BP 5005, Dakar, Senegal
| | - Cheikh Sokhna
- Unité VITROME, Institut de Recherche et de Développement, Dakar, Senegal
| | - Babacar Faye
- Service de Parasitologie - Mycologie, FMPO, Université Cheikh Anta Diop, BP 5005, Dakar, Senegal
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Turner F, Drury J, Hapangama DK, Tempest N. Menstrual Tampons Are Reliable and Acceptable Tools to Self-Collect Vaginal Microbiome Samples. Int J Mol Sci 2023; 24:14121. [PMID: 37762424 PMCID: PMC10531428 DOI: 10.3390/ijms241814121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Many women report embarrassment as the cause for their avoidance of routine gynaecological screening appointments. Methods of self-collection of bio samples would perhaps encourage women to participate in routine screening programs. The vaginal microbiome plays a key role in women's health and reproductive function. Microbial disturbances can result in the loss of lactobacillus dominance, also known as dysbiosis, associated with an increased risk of contracting sexually transmitted infections (STIs), pregnancy complications and infertility. Our primary aim was to determine if vaginal microbiome screening results are comparable between two methods for self-collected sample acquisition: tampons and lower vaginal swabs (LVSs). Secondary aims included the assessment of the effect of pre-analytic storage on the data (to streamline processing), the prevalence of dysbiosis and the acceptability of the tampons to the participants. Statistical analysis revealed no significant difference in the microbiome data, from tampons versus LVSs or fresh versus frozen samples. The prevalence of dysbiosis in this population of healthy volunteers was 42.9%. The questionnaire data revealed that 52.4% of volunteers use tampons every period, and the majority of volunteers rated the tampons as 5 on a 1-5 Likert scale regarding their perceived comfort using tampons. All (100%) of volunteers were happy to provide a tampon as a sample for testing. The findings from this study show that tampons and LVSs were comparable when analysing the vaginal microbiome, with potential superiority of the tampon with regard to patient acceptability. Self-collection of vaginal secretions for gynaecological screening using tampons warrants further research as this could change the screening landscape, ensuring wider participation and increasing efficacy.
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Affiliation(s)
- Florence Turner
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (F.T.); (J.D.); (D.K.H.)
| | - Josephine Drury
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (F.T.); (J.D.); (D.K.H.)
| | - Dharani K. Hapangama
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (F.T.); (J.D.); (D.K.H.)
- Liverpool Women’s NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK
| | - Nicola Tempest
- Centre for Women’s Health Research, Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (F.T.); (J.D.); (D.K.H.)
- Liverpool Women’s NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK
- Hewitt Centre for Reproductive Medicine, Liverpool Women’s NHS Foundation Trust, Liverpool L8 7SS, UK
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6
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Short CES, Quinlan R, Lee YS, Preda VG, Smith A, Marchesi JR, Shattock R, Bennett PR, MacIntyre DA, Taylor GP. Comparative analysis of vaginal microbiota sampling using menstrual cups and high vaginal swabs in pregnant women living with HIV-1 infection. Front Cell Infect Microbiol 2023; 13:1190160. [PMID: 37228662 PMCID: PMC10204588 DOI: 10.3389/fcimb.2023.1190160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Background Menstrual cups (MCs) are increasingly used to collect cervicovaginal secretions to characterise vaginal mucosal immunology, in conjunction with high vaginal swabs (HVS) for metataxonomics, particularly in HIV transmission studies. We hypothesised that both methods of collecting bacterial biomass are equivalent for 16S rRNA gene sequencing. Material and Methods Cervicovaginal fluid (CVF) samples from 16 pregnant women with HIV-1 (PWWH) were included to represent the major vaginal bacterial community state types (CST I-V). Women underwent sampling during the second trimester by liquid amies HVS followed by a MC (Soft disc™) and samples were stored at -80°C. Bacterial cell pellets obtained from swab elution and MC (500 µL, 1 in 10 dilution) were resuspended in 120 µL PBS for DNA extraction. Bacterial 16S rRNA gene sequencing was performed using V1-V2 primers and were analysed using MOTHUR. Paired total DNA, bacterial load, amplicon read counts, diversity matrices and bacterial taxa were compared by sampling method using MicrobiomeAnalyst, SPSS and R. Results The total DNA eluted from one aliquot of diluted CVF from an MC was similar to that of a HVS (993ng and 609ng, p=0.18); the mean bacterial loads were also comparable for both methods (MC: 8.0 log10 16S rRNA gene copies versus HVS: 7.9 log10 16S rRNA gene copies, p=0.27). The mean number of sequence reads generated from MC samples was lower than from HVS (MC: 12730; HVS:14830, p=0.05). The α-diversity metrices were similar for both techniques; MC Species Observed: 41 (range 12-96) versus HVS: 47 (range 16-96), p=0.15; MC Inverse Simpson Index: 1.98 (range 1.0-4.0) versus HVS: 0.48 (range 1.0-4.4), p=0.22). The three most abundant species observed were: Lactobacillus iners, Lactobacillus crispatus and Gardnerella vaginalis. Hierarchical clustering of relative abundance data showed that samples obtained using different techniques in an individual clustered in the same CST group. Conclusion These data demonstrate that despite sampling slightly different areas of the lower genital tract, there was no difference in bacterial load or composition between methods. Both are suitable for characterisation of vaginal microbiota in PWWH. The MC offers advantages, including a higher volume of sample available for DNA extraction and complimentary assays.
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Affiliation(s)
- Charlotte-Eve S. Short
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- St Mary’s Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
- March of Dimes Prematurity Research Centre, Division of the Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, United Kingdom
| | - Rachael Quinlan
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- St Mary’s Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
- March of Dimes Prematurity Research Centre, Division of the Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, United Kingdom
| | - Yun S. Lee
- March of Dimes Prematurity Research Centre, Division of the Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, United Kingdom
| | - Veronica G. Preda
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- St Mary’s Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Ann Smith
- Faculty of Health and Applied Sciences, University West of England, Bristol, United Kingdom
| | - Julian R. Marchesi
- March of Dimes Prematurity Research Centre, Division of the Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, United Kingdom
- Marchesi Laboratory, Department of Metabolism, Digestion, and Reproduction, Division of Digestive Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Robin Shattock
- Section of Immunology of Infection, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Phillip R. Bennett
- St Mary’s Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
- March of Dimes Prematurity Research Centre, Division of the Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, United Kingdom
| | - David A. MacIntyre
- March of Dimes Prematurity Research Centre, Division of the Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, United Kingdom
| | - Graham P. Taylor
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- St Mary’s Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
- March of Dimes Prematurity Research Centre, Division of the Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, United Kingdom
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Moreno E, Ron R, Serrano-Villar S. The microbiota as a modulator of mucosal inflammation and HIV/HPV pathogenesis: From association to causation. Front Immunol 2023; 14:1072655. [PMID: 36756132 PMCID: PMC9900135 DOI: 10.3389/fimmu.2023.1072655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/06/2023] [Indexed: 01/24/2023] Open
Abstract
Although the microbiota has largely been associated with the pathogenesis of viral infections, most studies using omics techniques are correlational and hypothesis-generating. The mechanisms affecting the immune responses to viral infections are still being fully understood. Here we focus on the two most important sexually transmitted persistent viruses, HPV and HIV. Sophisticated omics techniques are boosting our ability to understand microbiota-pathogen-host interactions from a functional perspective by surveying the host and bacterial protein and metabolite production using systems biology approaches. However, while these strategies have allowed describing interaction networks to identify potential novel microbiota-associated biomarkers or therapeutic targets to prevent or treat infectious diseases, the analyses are typically based on highly dimensional datasets -thousands of features in small cohorts of patients-. As a result, we are far from getting to their clinical use. Here we provide a broad overview of how the microbiota influences the immune responses to HIV and HPV disease. Furthermore, we highlight experimental approaches to understand better the microbiota-host-virus interactions that might increase our potential to identify biomarkers and therapeutic agents with clinical applications.
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Affiliation(s)
- Elena Moreno
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá, IRYCIS, Madrid, Spain.,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Ron
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá, IRYCIS, Madrid, Spain.,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá, IRYCIS, Madrid, Spain.,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
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8
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Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M, Ostrowski J. Increased diversity of a cervical microbiome associates with cervical cancer. Front Oncol 2022; 12:1005537. [PMID: 36249017 PMCID: PMC9562559 DOI: 10.3389/fonc.2022.1005537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 12/02/2022] Open
Abstract
The cervical microbiome (CM) is a complex ecosystem that can change in response to gynecological cancers. We aimed to evaluate changes in the CM of patients who underwent chemoradiation (CRT) therapy for locally advanced cervical cancer. Before and after CRT, cervical swab samples were collected from 16 patients with squamous cell carcinoma of the cervix, and 30 healthy women. All samples were subjected to 16s rRNA-Seq analysis. In healthy premenopausal women the CM comprised mostly Lactobacillus (>90%); the CM community in samples from both pre- and postmenopausal pre-treatment cancer patients was heterogeneous, with a low proportion of Lactobacillus in younger cases. On the genus level, 27 and 11 taxa differentiated healthy controls from cancer patients in pre- and postmenopausal age groups, while 31 and 2 genera differentiated pre- and post-radiation samples and pre-radiation and the follow-up samples, respectively. Microbiome diversity was significantly higher in pre-treatment patients than in healthy controls. The results reveal significant alterations in the CM of cervical cancer patients relative to that in healthy controls; these changes were more striking after CRT. However, further research is needed to determine whether alteration of the CM offers new therapeutic options.
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Affiliation(s)
- Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Bogusław Lindner
- Department of Gynaecological Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Ryszard Krynicki
- Department of Gynaecological Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Andrzej Nowakowski
- Department of Cancer Prevention, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Mariusz Bidzinski
- Department of Gynaecological Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- *Correspondence: Jerzy Ostrowski,
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Boetius Hertz F, Holm JB, Pallejá A, Björnsdóttir MK, Mikkelsen LS, Brandsborg E, Frimodt-Møller N. The vaginal microbiome following orally administered probiotic. APMIS 2022; 130:605-611. [PMID: 35801409 PMCID: PMC9540456 DOI: 10.1111/apm.13261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/05/2022] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Here we present a longitudinal shotgun sequencing metagenomics study of 16 healthy, Danish women in the reproductive age. The aim of the study was to investigate whether lactobacilli, orally consumed, had any impact on the vaginal microbiome and its functional potential. MATERIALS AND METHODS The 16 women aged 19-45 years were recruited from Copenhagen, Denmark. One baseline vaginal sample (day 0) and two study samples (day 25-30 and day 55-60, respectively) were sampled. The vaginal samples were analyzed by shotgun metagenomics. RESULTS We detected 26 species in the vaginal microbiota of the 16 women, of which six belonged to the Lactobacillus genus. We observed three vaginal microbiome clusters mainly dominated by Gardnerella vaginalis, Lactobacillus iners or Lactobacillus crispatus. The oral probiotic had no detectable effect on either the composition or the functional potential of the vaginal microbiota. DISCUSSION Most of the study subjects (11 out of 16 women) exhibited only minor changes in the vaginal microbiome during the treatment with probiotics. Any compositional changes could not be associated to the probiotic treatment. Future studies may benefit from an increased number of participants, and administration of the probiotics during conditions with bacterial imbalance (e.g. during/after antibiotic treatment) or the use of different Lactobacillus spp. known to colonize the vagina.
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Affiliation(s)
- Frederik Boetius Hertz
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev, Denmark.,Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark
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10
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Taku O, Onywera H, Mbulawa ZZA, Businge CB, Meiring TL, Williamson AL. Molecular Identification of Cervical Microbes in HIV-Negative and HIV-Positive Women in an African Setting Using a Customized Bacterial Vaginosis Microbial DNA Quantitative PCR (qPCR) Array. Microbiol Spectr 2022; 10:e0222921. [PMID: 35647888 PMCID: PMC9241767 DOI: 10.1128/spectrum.02229-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
Bacterial vaginosis (BV) is a common polymicrobial vaginal disorder that is associated with sexually transmitted infections (STIs), including HIV. Several studies have utilized broad-range 16S rRNA gene PCR assays with sequence analysis to characterize cervicovaginal bacterial communities of women with healthy and diseased conditions. With the high burden of BV and STIs among African women, there is a need for targeted PCR assays that can rapidly determine the true epidemiological profile of key cervical microbes, including BV-associated bacteria, and a need to explore the utility of such assays for microbiological diagnosis of BV. Here, we used a taxon-directed 16S rRNA gene quantitative PCR (qPCR) assay to examine the prevalences and determinants of specific cervical microbes among African women with and without HIV infection. Cervical samples were collected using a cytobrush from 162 women (aged ≥30 years) attending a community-based clinic in Eastern Cape, South Africa. The samples were screened for specific microbes (i.e., STIs, emerging sexually transmitted pathogens [pathobionts], and BV-associated bacteria) using a customized bacterial vaginosis microbial DNA qPCR array. Statistical analyses were performed using GraphPad Prism v6.01. Chi-square/Fisher's exact tests were used to evaluate the determinants associated with specific cervical microbes. Only 145 women had any detectable microbes and were included in the analysis. Lactobacillus iners (62.8%) and specific BV-associated bacteria, namely, Gardnerella vaginalis (58.6%), Atopobium vaginae (40.7%), and the pathobiont Ureaplasma parvum (37.9%), were the most prevalent microbes. Hierarchical clustering analysis revealed that 42.8% of the women (62/145) had a diverse array of heterogeneously distributed bacteria typically linked to BV. Women with detectable Lactobacillus species, specifically Lactobacillus crispatus and Lactobacillus jensenii, and to a lesser extent L. iners, had very low prevalence of BV-associated bacteria. Although the cumulative burden of STIs/pathobionts was 62.8%, Chlamydia trachomatis (3.4%), Neisseria gonorrhoeae (4.8%), and Trichomonas vaginalis (4.8%) were detected at low rates. HIV infection was associated with the presence of STIs/pathobionts (P = 0.022) and L. iners (P = 0.003). Prevalent STIs/pathobionts were associated with having multiple partners in the past 12 months (n ≥ 2, P = 0.015), high number of lifetime sexual partners (n ≥ 3, P = 0.007), vaginal sex in the past month (P = 0.010), and decreasing age of women (P = 0.005). C. trachomatis was associated with increasing age among HIV-positive women (P = 0.016). The pathobiont Ureaplasma urealyticum was inversely associated with age of women in the whole cohort (P = 0.018). The overall prevalence of STIs/pathobionts was high and was associated with HIV infection and sexual behavior. Our study helps us to understand the epidemiological trend of STIs and pathobionts and highlights the need to understand the impact of sexual networks on STI and pathobiont transmission and prevention among women in an African setting. IMPORTANCE Bacterial vaginosis (BV), whose etiology remains a matter of controversy, is a common vaginal disorder among reproductive-age women and can increase the risk for sexually transmitted infections (STIs). African women bear a disproportionately high burden of STIs and BV. Using a targeted quantitative PCR (qPCR) assay, a customized bacterial vaginosis microbial DNA qPCR array, we examined the prevalences and determinants of key cervical microbes, including BV-associated bacteria and emerging sexually transmitted pathogens (pathobionts) among women of African descent aged between 30 and 75 years. High-risk behaviors were associated with a higher prevalence of STIs/pathobionts, suggesting the need to better understand the influence of sexual networks on STI and pathobiont transmission and prevention among women. Our molecular assay is important in the surveillance of BV-associated bacteria, pathobionts, and STIs as well as diagnostic microbiology of BV. Furthermore, our research contributes to a better understanding of the epidemiology of STIs and pathobionts in Africa.
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Affiliation(s)
- Ongeziwe Taku
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Harris Onywera
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Research, Innovations, and Academics Unit, Tunacare Services Health Providers Limited, Nairobi, Kenya
- Research and Innovation, Mount Kenya University, Thika, Kenya
| | - Zizipho Z. A. Mbulawa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- UCT-MRC Gynaecological Cancer Research Centre, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Nelson Mandela Academic Hospital, Mthatha, South Africa
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha, South Africa
| | - Charles B. Businge
- Department of Obstetrics and Gynaecology, Nelson Mandela Academic Hospital, Mthatha, South Africa
- Department of Obstetrics and Gynaecology, Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa
| | - Tracy L. Meiring
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Research and Innovation, Mount Kenya University, Thika, Kenya
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11
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Lee S, You H, Lee S, Lee Y, Kang HG, Sung HJ, Choi J, Hyun S. Individual Identification with Short Tandem Repeat Analysis and Collection of Secondary Information Using Microbiome Analysis. Genes (Basel) 2021; 13:85. [PMID: 35052425 PMCID: PMC8774430 DOI: 10.3390/genes13010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Forensic investigation is important to analyze evidence and facilitate the search for key individuals, such as suspects and victims in a criminal case. The forensic use of genomic DNA has increased with the development of DNA sequencing technology, thereby enabling additional analysis during criminal investigations when additional legal evidence is required. In this study, we used next-generation sequencing to facilitate the generation of complementary data in order to analyze human evidence obtained through short tandem repeat (STR) analysis. We examined the applicability and potential of analyzing microbial genome communities. Microbiological supplementation information was confirmed for two of four failed STR samples. Additionally, the accuracy of the gargle sample was confirmed to be as high as 100% and was highly likely to be classified as a body fluid sample. Our experimental method confirmed that anthropological and microbiological evidence can be obtained by performing two experiments with one extraction. We discuss the advantages and disadvantages of using these techniques, explore prospects in the forensic field, and highlight suggestions for future research.
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Affiliation(s)
- Solip Lee
- Department of Senior Healthcare, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (H.Y.)
| | - Heesang You
- Department of Senior Healthcare, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (H.Y.)
| | - Songhee Lee
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (Y.L.)
| | - Yeongju Lee
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (Y.L.)
| | - Hee-Gyoo Kang
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam 13135, Korea; (H.-G.K.); (H.-J.S.)
| | - Ho-Joong Sung
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam 13135, Korea; (H.-G.K.); (H.-J.S.)
| | - Jiwon Choi
- Forensic DNA Analysis Division, National Forensic Service, Seoul 08636, Korea;
| | - Sunghee Hyun
- Department of Senior Healthcare, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (H.Y.)
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (Y.L.)
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12
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Clinton M, Wyness AJ, Martin SAM, Brierley AS, Ferrier DEK. Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs. BMC Microbiol 2021; 21:313. [PMID: 34758745 PMCID: PMC8579561 DOI: 10.1186/s12866-021-02374-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Background Understanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained from Atlantic salmon (Salmo salar) gills by swabbing versus biopsy excision. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome. Results The microbiome was sampled using swabs and biopsies from fish gills, with identical treatment of samples for 16S next generation Illumina sequencing. Results show a clear divergence in microbial communities obtained through the different sampling strategies, with swabbing consistently isolating a more diverse microbial consortia, and suffering less from the technical issue of host DNA contamination associated with biopsy use. Sequencing results from biopsy-derived extractions, however, hint at the potential for more cryptic localisation of some community members. Conclusions Overall, results demonstrate a divergence in the obtained microbial community when different sampling methodology is used. Swabbing appears a superior method for sampling the microbiota of mucosal surfaces for broad ecological research in fish, whilst biopsies might be best applied in exploration of communities beyond the reach of swabs, such as sub-surface and intracellular microbes, as well as in pathogen diagnosis. Most studies on the external microbial communities of aquatic organisms utilise swabbing for sample collection, likely due to convenience. Much of the ultrastructure of gill tissue in live fish is, however, potentially inaccessible to swabbing, meaning swabbing might fail to capture the full diversity of gill microbiota. This work therefore also provides valuable insight into partitioning of the gill microbiota, informing varied applications of different sampling methods in experimental design for future research. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02374-0.
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Affiliation(s)
- Morag Clinton
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK. .,Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA.
| | - Adam J Wyness
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK.,Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Makhanda (Grahamstown), 6139, South Africa
| | - Samuel A M Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Andrew S Brierley
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - David E K Ferrier
- Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, KY16 8LB, UK.
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13
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Shibata T, Nakagawa M, Coleman HN, Owens SM, Greenfield WW, Sasagawa T, Robeson MS. Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota. PLoS One 2021; 16:e0237556. [PMID: 34460815 PMCID: PMC8404996 DOI: 10.1371/journal.pone.0237556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 ± 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated by Lactobacillus iners.
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Affiliation(s)
- Takeo Shibata
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Department of Obstetrics and Gynecology, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Mayumi Nakagawa
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Hannah N. Coleman
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Sarah M. Owens
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States of America
| | - William W. Greenfield
- Department of Obstetrics and Gynecology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Toshiyuki Sasagawa
- Department of Obstetrics and Gynecology, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Michael S. Robeson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
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14
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Della Vella F, Lauritano D, Pannone G, Del Prete R, Di Stasio D, Contaldo M, Petruzzi M. Prevalence of HPV in patients affected by oral Lichen planus: A prospective study using two different chair-side sampling methods. J Oral Pathol Med 2021; 50:716-722. [PMID: 33501732 DOI: 10.1111/jop.13164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/02/2021] [Accepted: 01/14/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Human Papillomavirus (HPV) role in oral potentially malignant lesions remains unclear. Aims of this study were to evaluate the prevalence of HPV infection in a cohort of patients affected by oral lichen planus, to analyze the genotypes involved, and to compare the performance of two specimen collection methods: brushing and biopsy. METHODS Consecutive patients with oral lichen planus were enrolled. Each patient's clinical and anamnestic data were recorded before he/she underwent brushing and biopsy procedures. The collected samples were analyzed using RT-PCR. Prevalence of HPV infection was evaluated considering cytobrush and biopsy outcomes alone and combined. Correlation between HPV presence and sex, age, smoke, alcohol, kind of lichen planus, Hepatitis C virus, and involved mucosae was analyzed using chi-square test (significance at P < .05). Cohen's k coefficient was employed to compare brushing and biopsy. RESULTS Fifty-two patients affected by oral lichen planus were enrolled. Total HPV prevalence was 17%, when considering only the biopsy and the cytobrush the prevalence was 15% and 6%, respectively. None of the considered variables showed significant correlation with HPV (P > .05). The concordance between the two methods was "fair" (k = .305). CONCLUSIONS The biopsy appears more reliable than cytobrush to detect HPV in course of oral lichen planus. No statistical correlation emerged with the analyzed variables. The most frequently detected genotypes were HPV 6 and 11, while only two cases presented with HPV 16 and 53, known as human oncogenic.
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Affiliation(s)
- Fedora Della Vella
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Dorina Lauritano
- Department of Medicine and Surgery, Centre of Neuroscience Milan, University of Milan-Bicocca, Monza, Italy
| | - Giuseppe Pannone
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Raffaele Del Prete
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Dario Di Stasio
- Multidisciplinary Department of Medical-Surgical and Odontostomatological Specialties, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Contaldo
- Multidisciplinary Department of Medical-Surgical and Odontostomatological Specialties, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Massimo Petruzzi
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", Bari, Italy
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15
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Kawahara R, Fujii T, Kukimoto I, Nomura H, Kawasaki R, Nishio E, Ichikawa R, Tsukamoto T, Iwata A. Changes to the cervicovaginal microbiota and cervical cytokine profile following surgery for cervical intraepithelial neoplasia. Sci Rep 2021; 11:2156. [PMID: 33495564 PMCID: PMC7835242 DOI: 10.1038/s41598-020-80176-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/15/2020] [Indexed: 01/04/2023] Open
Abstract
Persistent HPV infection associated with immune modulation may result in high-grade squamous intraepithelial lesions (CIN)2/3. Currently, there is little information on the cervicovaginal microbiome, local cytokine levels and HPV infection related to CIN. Follow-up of patients after local surgery provides an opportunity to monitor changes in the cervicovaginal environment. Accordingly, we undertook this longitudinal retrospective study to determine associations between HPV genotypes, cervicovaginal microbiome and local cytokine profiles in 41 Japanese patients with CIN. Cervicovaginal microbiota were identified using universal 16S rRNA gene (rDNA) bacterial primers for the V3/4 region by PCR of genomic DNA, followed by MiSeq sequencing. We found that Atopobium vaginae was significantly decreased (p < 0.047), whereas A. ureaplasma (p < 0.022) increased after surgery. Cytokine levels in cervical mucus were measured by multiplexed bead-based immunoassays, revealing that IL-1β (p < 0.006), TNF-α (p < 0.004), MIP-1α (p < 0.045) and eotaxin (p < 0.003) were significantly decreased after surgery. Notably, the level of eotaxin decreased in parallel with HPV clearance after surgery (p < 0.028). Thus, local surgery affected the cervicovaginal microbiome, status of HPV infection and immune response. Changes to the cervicovaginal microbiota and cervical cytokine profile following surgery for cervical intraepithelial neoplasia may be important for understanding the pathogenesis of CIN in future.
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Affiliation(s)
- Rina Kawahara
- Department of Obstetrics and Gynecology, Fujita Health University, School of Medicine, 1-98, Dengakugakubo, Toyoake, Aichi, 470-1192, Japan
| | - Takuma Fujii
- Department of Obstetrics and Gynecology, Fujita Health University, School of Medicine, 1-98, Dengakugakubo, Toyoake, Aichi, 470-1192, Japan.
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1, Gakuen, Musashi-murayama, Tokyo, 208-0011, Japan
| | - Hiroyuki Nomura
- Department of Obstetrics and Gynecology, Fujita Health University, School of Medicine, 1-98, Dengakugakubo, Toyoake, Aichi, 470-1192, Japan
| | - Rie Kawasaki
- Department of Obstetrics and Gynecology, Fujita Health University, School of Medicine, 1-98, Dengakugakubo, Toyoake, Aichi, 470-1192, Japan
| | - Eiji Nishio
- Department of Obstetrics and Gynecology, Fujita Health University, School of Medicine, 1-98, Dengakugakubo, Toyoake, Aichi, 470-1192, Japan
| | - Ryoko Ichikawa
- Department of Obstetrics and Gynecology, Fujita Health University, School of Medicine, 1-98, Dengakugakubo, Toyoake, Aichi, 470-1192, Japan
| | - Tetsuya Tsukamoto
- Department of Pathology, Fujita Health University, School of Medicine, 1-98, Dengakugakubo, Toyoake, Aichi, 470-1192, Japan
| | - Aya Iwata
- Department of Obstetrics and Gynecology, Fujita Health University, School of Medicine, 1-98, Dengakugakubo, Toyoake, Aichi, 470-1192, Japan
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16
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Tsakmaklis A, Vehreschild M, Farowski F, Trommer M, Kohler C, Herter J, Marnitz S. Changes in the cervical microbiota of cervical cancer patients after primary radio-chemotherapy. Int J Gynecol Cancer 2020; 30:1326-1330. [PMID: 32376743 PMCID: PMC7497561 DOI: 10.1136/ijgc-2019-000801] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE Several recent studies have identified a potential interaction between the vaginal microbiota and gynecological cancers, but little is known about the cervical microbiota and its changes during cancer treatment. Therefore, the aim of the study was to evaluate the quantitative and qualitative changes of cervical microbiota in patients undergoing concurrent chemotherapy and radiation treatment for locally advanced cervical cancer. METHODS Cervical cytobrush samples of 15 cervical patients undergoing chemoradiation treatment were collected 1 day before starting external beam radiation therapy and on the day of the last fraction of brachytherapy. After DNA extraction, 16S rRNA amplicon sequencing of the V3-V4 region was performed on the MiSeq platform, followed by data processing and statistical analyses concerning the alpha and beta diversity of 16 samples (7 samples were excluded because of incomplete sample sets). RESULTS The amount of amplicon yield after polymerase chain reaction analysis in post-radiation samples was significantly lower compared with the baseline samples (pre 31.49±24.07 ng/µl; post 1.33±1.94 ng/µl; p=0.007). A comparison of pre-treatment and post-treatment samples did not show significant differences regarding beta diversity (weighted UniFrac). There was no significant difference in alpha diversity, which is used to characterize species diversity within a particular community and takes into account both number and abundance (Shannon Diversity Index pre-treatment samples: 2.167±0.7504 (95% CI 1.54 to 2.79); post-treatment samples: 1.97±0.43 (95% CI 1.61 to 2.33); p=0.38). Interindividual differences in patients could partly explain some variation of the samples (permutational multivariate analysis of variance). CONCLUSION There was a strong reduction in cervical bacterial loads after chemoradiation. Neither alpha nor beta diversity varied significantly when baseline samples were compared with post-treatment samples.
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Affiliation(s)
- Anastasia Tsakmaklis
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Maria Vehreschild
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, University of Cologne, Cologne, Germany.,Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Fedja Farowski
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, University of Cologne, Cologne, Germany.,Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maike Trommer
- Department of Radiation Oncology, CyberKnife and Radiotherapy, University Hospital Cologne, Cologne, Germany
| | - Christhardt Kohler
- Department of Gynecology, University Hospital Cologne, Cologne, Germany.,Department of Special Operative and Oncologic Gynecology, Asklepios-Clinic Hamburg-Altona, Asklepios Hospital Group, Hamburg, Germany
| | - Jan Herter
- Department of Radiation Oncology, CyberKnife and Radiotherapy, University Hospital Cologne, Cologne, Germany
| | - Simone Marnitz
- Department of Radiooncology, Medical Faculty of the University of Cologne, Cologne, Germany
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17
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Della Vella F, Pannone G, Patano A, Ninivaggi R, Del Prete R, Lauritano D, Petruzzi M. Detection of HPV in oral leukoplakia by brushing and biopsy: prospective study in an Italian cohort. Clin Oral Investig 2019; 24:1845-1851. [PMID: 31402398 DOI: 10.1007/s00784-019-03048-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/05/2019] [Indexed: 12/15/2022]
Abstract
AIM The aim of the present study was to evaluate the prevalence of HPV infection in oral leukoplakia, specifying the HPV genotypes eventually involved. We also compared the micro-biopsy and brushing HPV detecting efficacy. MATERIALS AND METHODS Consecutive patients with a presumptive diagnosis of oral leukoplakia were enrolled. Demographical, behavioral data (smoking, alcohol) and lesion features were recorded. Each patient underwent a brushing procedure, performed with a cytobrush rubbed on the lesion, and then a biopsy was performed. The brushing and micro-biopsy specimens were both analyzed with the HPV 28 Anyplex II Seegene RT-PCR. The prevalence of HPV infection was calculated considering the two methods' outcomes separately and then combining both. Cohen's k coefficient was used to assess the agreement between the two methods. RESULTS Sixty-five patients were enrolled with a mean age of 60 years. The HPV infection prevalence was 17%, decreasing to 5% considering the brushing outcomes alone. The most frequently detected genotypes were 6 (12%), 11 (3%), 42 (3%), and 16 (3%). No statistically significant correlation was found between HPV infection and the variables analyzed, except for smoking and the type of mucosa (p < 0.05). The strength of agreement between cytobrush and micro-biopsy was "fair" (k = 0.384). CONCLUSIONS The present study showed a low prevalence of HPV infection in oral leukoplakia. The micro-biopsy appeared to be more reliable than brushing in detecting HPV DNA in oral leukoplakia, but the method invasiveness discourages its employ as a screening tool. The importance of HPV in the etiopathogenesis of oral potentially malignant lesions remains unclear; further studies are needed to establish the HPV role in oral leukoplakia. CLINICAL RELEVANCE HPV involvement in oral leukoplakia and an effective and appropriate detecting technique are still a debated issue. From this study, the restricted use of brushing did not appear sufficient to assess the presence of HPV infection with PCR techniques in samples obtained from oral leukoplakia.
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Affiliation(s)
- Fedora Della Vella
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", Bari, Italy.
| | - Giuseppe Pannone
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Assunta Patano
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Rossella Ninivaggi
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Raffaele Del Prete
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Dorina Lauritano
- Department of Medicine and Surgery
- University of Milan-Bicocca, Monza, Italy
| | - Massimo Petruzzi
- Interdisciplinary Department of Medicine, University of Bari "Aldo Moro", Bari, Italy.
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18
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Mattei V, Murugesan S, Al Hashmi M, Mathew R, James N, Singh P, Kumar M, Lakshmanan AP, Terranegra A, Al Khodor S, Tomei S. Evaluation of Methods for the Extraction of Microbial DNA From Vaginal Swabs Used for Microbiome Studies. Front Cell Infect Microbiol 2019; 9:197. [PMID: 31245304 PMCID: PMC6563847 DOI: 10.3389/fcimb.2019.00197] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 05/22/2019] [Indexed: 12/26/2022] Open
Abstract
Background: The composition of the microbiome in human body sites plays an important role in health. The vaginal environment is colonized by several species of bacteria that have a major influence on reproductive health. The advancement of sequencing technologies has made the assessment of the composition of the microbiota possible through microbial DNA extraction and sequencing. Therefore, it is of a paramount importance to select a sensitive and reproducible DNA extraction method, that facilitates isolation of microbial DNA with a sufficient quantity and purity, from microbial species living in the vaginal environment. Here, we have evaluated four different DNA extraction protocols from self-collected vaginal swabs. Methods: Five healthy female volunteers were enrolled in the study. Each donor was asked to self-collect 4 samples using Copan ESwab. DNA was extracted using Qiagen DNeasy kit and three modified protocols of the MoBio PowerSoil kit ("DNeasy PowerSoil" after acquisition from Qiagen). DNA quantity and integrity was checked through Nanodrop and LabChip GX. DNA was further tested through quantitative real-time PCR (qPCR) and 16S sequencing. Vaginal microbiota diversities were determined using MiSeq-Illumina high-throughput sequencing of bacterial 16S rDNA V1-V3 fingerprint. Sequencing data were analyzed using QIIME pipeline. Results: Qiagen DNeasy protocol resulted in the highest DNA yield as compared to the modified protocols of MoBio Powersoil kit. The size of the DNA extracted using each protocol was ~40 kb. Qiagen DNeasy protocol gave the highest Genomic Quality Score (average ± standard deviation: 4.24 ± 0.36), followed by the different MoBio Powersoil protocols. A substantial variability in microbial DNA abundance was found across the protocols. The vaginal microbiota of the healthy volunteers was dominated by Lactobacillus species. MoBio Powersoil kit provided a significantly higher alpha diversity as compared to the Qiagen DNeasy kit, while beta diversity measures did not reveal any significant cluster changes, except when the Bray-Curtis method was applied. Conclusion: We were able to isolate microbial DNA from the vaginal swabs. Qiagen DNeasy method gave the highest DNA yield and quality but was not optimal in detecting microbial diversity. The modified MoBio PowerSoil protocols showed higher microbial diversities as compared to the standard protocol.
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Affiliation(s)
| | | | | | | | | | - Parul Singh
- Research Branch, Sidra Medicine, Doha, Qatar
| | - Manoj Kumar
- Research Branch, Sidra Medicine, Doha, Qatar
| | | | | | | | - Sara Tomei
- Research Branch, Sidra Medicine, Doha, Qatar
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19
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O'Connell CM, Brochu H, Girardi J, Harrell E, Jones A, Darville T, Seña AC, Peng X. Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis. MICROBIAL CELL 2019; 6:177-183. [PMID: 30854394 PMCID: PMC6402362 DOI: 10.15698/mic2019.03.672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pelvic inflammatory disease (PID) is a female upper genital tract inflammatory disorder that arises after sexually transmitted bacterial infections (STI). Factors modulating risk for reproductive sequelae include co-infection, microbiota, host genetics and physiology. In a pilot study of cervical samples obtained from women at high risk for STIs, we examined the potential for unbiased characterization of host, pathogen and microbiome interactions using whole transcriptome sequencing analysis of ribosomal RNA-depleted total RNAs (Total RNA-Seq). Only samples from women with STI infection contained pathogen-specific sequences (3 to 38% transcriptome coverage). Simultaneously, we identified and quantified their active microbial communities. After integration with host-derived reads from the same data, we detected clustering of host transcriptional profiles that reflected microbiome differences and STI infection. Together, our study suggests that total RNA profiling will advance understanding of the interplay of pathogen, host and microbiota during natural infection and may reveal novel, outcome-relevant biomarkers.
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Affiliation(s)
- Catherine M O'Connell
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hayden Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Jenna Girardi
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Erin Harrell
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Aiden Jones
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Arlene C Seña
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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20
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Afiuni-Zadeh S, Boylan KLM, Jagtap PD, Griffin TJ, Rudney JD, Peterson ML, Skubitz APN. Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome. Sci Rep 2018; 8:10868. [PMID: 30022083 PMCID: PMC6052116 DOI: 10.1038/s41598-018-29092-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/04/2018] [Indexed: 01/30/2023] Open
Abstract
The human cervical-vaginal area contains proteins derived from microorganisms that may prevent or predispose women to gynecological conditions. The liquid Pap test fixative is an unexplored resource for analysis of microbial communities and the microbe-host interaction. Previously, we showed that the residual cell-free fixative from discarded Pap tests of healthy women could be used for mass spectrometry (MS) based proteomic identification of cervical-vaginal proteins. In this study, we reprocessed these MS raw data files for metaproteomic analysis to characterize the microbial community composition and function of microbial proteins in the cervical-vaginal region. This was accomplished by developing a customized protein sequence database encompassing microbes likely present in the vagina. High-mass accuracy data were searched against the protein FASTA database using a two-step search method within the Galaxy for proteomics platform. Data was analyzed by MEGAN6 (MetaGenomeAnalyzer) for phylogenetic and functional characterization. We identified over 300 unique peptides from a variety of bacterial phyla and Candida. Peptides corresponding to proteins involved in carbohydrate metabolism, oxidation-reduction, and transport were identified. By identifying microbial peptides in Pap test supernatants it may be possible to acquire a functional signature of these microbes, as well as detect specific proteins associated with cervical health and disease.
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Affiliation(s)
- Somaieh Afiuni-Zadeh
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Kristin L M Boylan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Center for Mass Spectrometry and Proteomics, University of Minnesota, Minneapolis, MN, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Center for Mass Spectrometry and Proteomics, University of Minnesota, Minneapolis, MN, USA
| | - Joel D Rudney
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | | | - Amy P N Skubitz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
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21
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Pruski P, Lewis HV, Lee YS, Marchesi JR, Bennett PR, Takats Z, MacIntyre DA. Assessment of microbiota:host interactions at the vaginal mucosa interface. Methods 2018; 149:74-84. [PMID: 29705211 DOI: 10.1016/j.ymeth.2018.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/10/2018] [Accepted: 04/22/2018] [Indexed: 12/12/2022] Open
Abstract
There is increasing appreciation of the role that vaginal microbiota play in health and disease throughout a woman's lifespan. This has been driven partly by molecular techniques that enable detailed identification and characterisation of microbial community structures. However, these methods do not enable assessment of the biochemical and immunological interactions between host and vaginal microbiota involved in pathophysiology. This review examines our current knowledge of the relationships that exist between vaginal microbiota and the host at the level of the vaginal mucosal interface. We also consider methodological approaches to microbiomic, immunologic and metabolic profiling that permit assessment of these interactions. Integration of information derived from these platforms brings the potential for biomarker discovery, disease risk stratification and improved understanding of the mechanisms regulating vaginal microbial community dynamics in health and disease.
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Affiliation(s)
- Pamela Pruski
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Holly V Lewis
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK; Queen Charlotte's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London W12 0HS, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Julian R Marchesi
- Department of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Centre for Digestive and Gut Health, Surgery and Cancer, Imperial College London, London W2 1NY, UK
| | - Phillip R Bennett
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK; Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Zoltan Takats
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK.
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22
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Campisciano G, Zanotta N, Licastro D, De Seta F, Comar M. In vivo microbiome and associated immune markers: New insights into the pathogenesis of vaginal dysbiosis. Sci Rep 2018; 8:2307. [PMID: 29396486 PMCID: PMC5797242 DOI: 10.1038/s41598-018-20649-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/23/2018] [Indexed: 02/03/2023] Open
Abstract
The microbiota fulfils a key role in the training and function of the immune system, which contributes to the symbiosis between the host and complex microbial communities. In this study, we characterized the interplay between vaginal bacteria and local immune mediators during dysbiosis in selected women of reproductive age who were grouped according to Nugent’s criteria. The abundance of Gardnerella vaginalis and Bifidobacterium breve was increased in the intermediate dysbiotic status, while the presence of a plethora of non-resident bacteria characterized the group with overt vaginosis. In response to these increases, the anti-inflammatory IL1ra and pro-inflammatory IL2 increased, while the embryo trophic factors FGFβ and GMCSF decreased compared to the healthy milieu. A specific pattern, including IL1α, IL1β, IL8, MIG, MIP1α and RANTES, distinguished the intermediate group from the vaginosis group, while IL5 and IL13, which are secreted by Th2 cells, were significantly associated with the perturbation of the commensals Lactobacilli, Gardnerella and Ureaplasma. Summarizing, we postulate that although the dysbiotic condition triggers a pro-inflammatory process, the presence of a steady state level of Th2 may influence clinical manifestations. These results raise clinically relevant questions regarding the use of vaginal immunological markers as efficacious tools to monitor microbial alterations.
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Affiliation(s)
- Giuseppina Campisciano
- SSD of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Via dell'Istria 65/1, 34137, Trieste, Italy
| | - Nunzia Zanotta
- SSD of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Via dell'Istria 65/1, 34137, Trieste, Italy
| | - Danilo Licastro
- CBM Scrl-Genomics, Area Science Park, Basovizza, 34149, Trieste, Italy
| | - Francesco De Seta
- Medical Sciences Department, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy.,SC of Gynecology - Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Via dell'Istria 65/1, 34137, Trieste, Italy
| | - Manola Comar
- SSD of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Via dell'Istria 65/1, 34137, Trieste, Italy. .,Medical Sciences Department, University of Trieste, Piazzale Europa 1, 34127, Trieste, Italy.
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