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Głowienka-Stodolak M, Bagińska-Drabiuk K, Szubert S, Hennig EE, Horala A, Dąbrowska M, Micek M, Ciebiera M, Zeber-Lubecka N. Human Papillomavirus Infections and the Role Played by Cervical and Cervico-Vaginal Microbiota-Evidence from Next-Generation Sequencing Studies. Cancers (Basel) 2024; 16:399. [PMID: 38254888 PMCID: PMC10814012 DOI: 10.3390/cancers16020399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
This comprehensive review encompasses studies examining changes in the cervical and cervico-vaginal microbiota (CM and CVM) in relation to human papillomavirus (HPV) using next-generation sequencing (NGS) technology. HPV infection remains a prominent global health concern, with a spectrum of manifestations, from benign lesions to life-threatening cervical cancers. The CM and CVM, a unique collection of microorganisms inhabiting the cervix/vagina, has emerged as a critical player in cervical health. Recent research has indicated that disruptions in the CM and CVM, characterized by a decrease in Lactobacillus and the overgrowth of other bacteria, might increase the risk of HPV persistence and the progression of cervical abnormalities. This alteration in the CM or CVM has been linked to a higher likelihood of HPV infection and cervical dysplasia. NGS technology has revolutionized the study of the cervical microbiome, providing insights into microbial diversity, dynamics, and taxonomic classifications. Bacterial 16S rRNA gene sequencing, has proven invaluable in characterizing the cervical microbiome, shedding light on its role in HPV infections and paving the way for more tailored strategies to combat cervical diseases. NGS-based studies offer personalized insights into an individual's cervical microbiome. This knowledge holds promise for the development of novel diagnostic tools, targeted therapies, and preventive interventions for cervix-related conditions, including cervical cancer.
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Affiliation(s)
- Maria Głowienka-Stodolak
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781Warsaw, Poland; (M.G.-S.); (K.B.-D.); (E.E.H.); (M.D.)
| | - Katarzyna Bagińska-Drabiuk
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781Warsaw, Poland; (M.G.-S.); (K.B.-D.); (E.E.H.); (M.D.)
| | - Sebastian Szubert
- Division of Gynaecological Oncology, Department of Gynaecology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (S.S.); (A.H.)
| | - Ewa E. Hennig
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781Warsaw, Poland; (M.G.-S.); (K.B.-D.); (E.E.H.); (M.D.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
| | - Agnieszka Horala
- Division of Gynaecological Oncology, Department of Gynaecology, Poznan University of Medical Sciences, 61-701 Poznan, Poland; (S.S.); (A.H.)
| | - Michalina Dąbrowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781Warsaw, Poland; (M.G.-S.); (K.B.-D.); (E.E.H.); (M.D.)
| | - Martyna Micek
- Second Department of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, 00-189 Warsaw, Poland; (M.M.); (M.C.)
- Warsaw Institute of Women’s Health, 00-189 Warsaw, Poland
| | - Michał Ciebiera
- Second Department of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, 00-189 Warsaw, Poland; (M.M.); (M.C.)
- Warsaw Institute of Women’s Health, 00-189 Warsaw, Poland
| | - Natalia Zeber-Lubecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781Warsaw, Poland; (M.G.-S.); (K.B.-D.); (E.E.H.); (M.D.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland
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Gryaznova M, Kozarenko O, Smirnova Y, Burakova I, Syromyatnikov M, Maslov A, Lebedeva O. Cervical and Vaginal Microbiomes in Early Miscarriages and Ongoing Pregnancy with and without Dydrogesterone Usage. Int J Mol Sci 2023; 24:13836. [PMID: 37762139 PMCID: PMC10531357 DOI: 10.3390/ijms241813836] [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: 08/11/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Emerging evidence suggests that the reproductive tract microbiota is a key modulator of local inflammatory and immune pathways throughout pregnancy and may subsequently impact pregnancy outcomes. In this study, our objective was to analyze the cervical and vaginal microbiomes during early pregnancy among three groups: women with healthy ongoing pregnancies, women undergoing dydrogesterone treatment, and those who experienced miscarriages. The experiment involved 51 women at 8-11 weeks of gestation. The microbiome was examined using 16S rRNA sequencing on the Ion Torrent PGM platform. Across all groups, Lactobacillus iners was predominant, suggesting that the vaginal community type CST III is common among the majority of participants. Notably, our data highlighted the significant roles of Gardnerella vaginalis and Mycoplasma girerdii in the pathogenesis of early miscarriage. Conversely, L. iners and Bifidobacterium longum have a protective effect in early pregnancy. Moreover, dydrogesterone intake appeared to influence notable differences between the cervical and vaginal microbiomes. Overall, our study enhanced our understanding of the cervical and vaginal microbiome composition in the eastern European population during early pregnancy.
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Affiliation(s)
- Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
| | - Olesya Kozarenko
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
- Antenatal Care Department, Yakovlevo Central District Hospital, 309070 Stroitel, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
| | - Inna Burakova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
| | - Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Alexander Maslov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Olga Lebedeva
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; (M.G.); (O.K.); (Y.S.); (I.B.); (M.S.); (A.M.)
- Department of Obstetrics and Gynecology, Belgorod State National University, 308015 Belgorod, Russia
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Doroftei B, Ilie OD, Armeanu T, Stoian IL, Anton N, Babici RG, Ilea C. A Narrative Review Discussing the Obstetric Repercussions Due to Alterations of Personalized Bacterial Sites Developed within the Vagina, Cervix, and Endometrium. J Clin Med 2023; 12:5069. [PMID: 37568471 PMCID: PMC10419759 DOI: 10.3390/jcm12155069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND The reproductive tract microbiota that evolved as an integrative component has been studied intensively in the last decade. As a result, novel research, clinical opportunities, and perspectives have been derived following the close investigation of this microecological environment. This has paved the way for an update to and improvement of the management strategies and therapeutic approaches. However, obscurities, contradictions, and controversies arise regarding the ascension route from the vagina to the endometrium via the cervix, with finality in adverse obstetric outcomes. METHODS Starting from these considerations, we aimed to gather all existing data and information from four major academic databases (PubMed, ISI Web of Knowledge, Scopus, and ScienceDirect) published in the last 13 years (2010-2023) using a controlled vocabulary and dedicated terminology to enhance the coverage, identification, and sorting of potentially eligible studies. RESULTS Despite the high number of returned entries (n = 804), only a slight percentage (2.73%) of all manuscripts were deemed eligible following two rounds of evaluation. Cumulatively, a low level of Lactobacillus spp. and of other core microbiota members is mandatory, with a possible eubiosis-to-dysbiosis transition leading to an impairment of metabolic and endocrine network homeostasis. This transposes into a change in the pro-inflammatory landscape and activation of signaling pathways due to activity exerted by the bacterial lipopolysaccharides (LPSs)/endotoxins that further reflect a high risk of miscarriage in various stages. While the presence of some pathogenic entities may be suggestive of an adverse obstetric predisposition, there are still pros and cons of the role of specific strains, as only the vagina and cervix have been targeted as opposed to the endometrium, which recently started to be viewed as the key player in the vagina-cervix-endometrium route. Consequently, based on an individual's profile, diet, and regime, antibiotics and probiotics might be practical or not. CONCLUSIONS Resident bacteria have a dual facet and are beneficial for women's health, but, at the same time, relaying on the abundance, richness, and evenness that are definitory indexes standing as intermediaries of a miscarriage.
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Affiliation(s)
- Bogdan Doroftei
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, University Street No. 16, 700115 Iasi, Romania
- Clinical Hospital of Obstetrics and Gynecology “Cuza Voda”, Cuza Voda Street No. 34, 700038 Iasi, Romania
- Origyn Fertility Center, Palace Street No. 3C, 700032 Iasi, Romania
| | | | - Theodora Armeanu
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, University Street No. 16, 700115 Iasi, Romania
- Clinical Hospital of Obstetrics and Gynecology “Cuza Voda”, Cuza Voda Street No. 34, 700038 Iasi, Romania
- Origyn Fertility Center, Palace Street No. 3C, 700032 Iasi, Romania
| | - Irina-Liviana Stoian
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, University Street No. 16, 700115 Iasi, Romania
| | - Nicoleta Anton
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, University Street No. 16, 700115 Iasi, Romania
| | - Ramona-Geanina Babici
- Department of Genetics, University of Medicine and Pharmacy “Grigore T. Popa”, University Street No. 16, 700115 Iasi, Romania
| | - Ciprian Ilea
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, University Street No. 16, 700115 Iasi, Romania
- Clinical Hospital of Obstetrics and Gynecology “Cuza Voda”, Cuza Voda Street No. 34, 700038 Iasi, Romania
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Amorín de Hegedüs R, Conesa A, Foster JS. Integration of multi-omics data to elucidate keystone unknown taxa within microbialite-forming ecosystems. Front Microbiol 2023; 14:1174685. [PMID: 37577445 PMCID: PMC10416242 DOI: 10.3389/fmicb.2023.1174685] [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: 02/26/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
Microbes continually shape Earth's biochemical and physical landscapes by inhabiting diverse metabolic niches. Despite the important role microbes play in ecosystem functioning, most microbial species remain unknown highlighting a gap in our understanding of structured complex ecosystems. To elucidate the relevance of these unknown taxa, often referred to as "microbial dark matter," the integration of multiple high throughput sequencing technologies was used to evaluate the co-occurrence and connectivity of all microbes within the community. Since there are no standard methodologies for multi-omics integration of microbiome data, we evaluated the abundance of "microbial dark matter" in microbialite-forming communities using different types meta-omic datasets: amplicon, metagenomic, and metatranscriptomic sequencing previously generated for this ecosystem. Our goal was to compare the community structure and abundances of unknown taxa within the different data types rather than to perform a functional characterization of the data. Metagenomic and metatranscriptomic data were input into SortMeRNA to extract 16S rRNA gene reads. The output, as well as amplicon sequences, were processed through QIIME2 for taxonomy analysis. The R package mdmnets was utilized to build co-occurrence networks. Most hubs presented unknown classifications, even at the phyla level. Comparisons of the highest scoring hubs of each data type using sequence similarity networks allowed the identification of the most relevant hubs within the microbialite-forming communities. This work highlights the importance of unknown taxa in community structure and proposes that ecosystem network construction can be used on several types of data to identify keystone taxa and their potential function within microbial ecosystems.
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Affiliation(s)
- Rocío Amorín de Hegedüs
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Department of Microbiology and Cell Sciences, Space Life Sciences Lab, University of Florida, Merritt Island, FL, United States
| | - Ana Conesa
- Spanish National Research Council, Institute for Integrative Systems Biology, Valencia, Spain
| | - Jamie S. Foster
- Department of Microbiology and Cell Sciences, Space Life Sciences Lab, University of Florida, Merritt Island, FL, United States
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Wadapurkar RM, Sivaram A, Vyas R. Computational studies reveal co-occurrence of two mutations in IL7R gene of high-grade serous carcinoma patients. J Biomol Struct Dyn 2022; 40:13310-13324. [PMID: 34657565 DOI: 10.1080/07391102.2021.1987326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Major cause of mortality in ovarian cancer can be attributed to a lack of specific and sensitive biomarkers for diagnosis and prognosis of the disease. Uncovering the mutations in genes involved in crucial oncogenic pathways is a key step in discovery and development of novel biomarkers. Whole exome sequencing (WES) is a powerful method for the detection of cancer driver mutations. The present work focuses on identifying functionally damaging mutations in patients with high-grade serous ovarian carcinoma (HGSC) through computational analysis of WES. In this study, WES data of HGSC patients was retrieved from the genomic literature available in sequence read archive, the variants were identified and comprehensive structural and functional analysis was performed. Interestingly, I66T and V138I mutations were found to be co-occurring in the IL7R gene in four out of five HGSC patient samples investigated in this study. The V138I mutation was located in the fibronectin type-3 domain and computationally assessed to be causing disruptive effects on the structure and dynamics of IL7R protein. This mutation was found to be co-occurring with the neutral I66T mutation in the same domain which compensated the disruptive effects of V138I variant. These comprehensive studies point to a hitherto unexplored significant role of the IL7R gene in ovarian carcinoma. It is envisaged that the work will lay the foundation for the development of a novel biomarker with potential application in molecular profiling and in estimation of the disease prognosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rucha M Wadapurkar
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Aruna Sivaram
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
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Shabayek S, Abdellah AM, Salah M, Ramadan M, Fahmy N. Alterations of the vaginal microbiome in healthy pregnant women positive for group B Streptococcus colonization during the third trimester. BMC Microbiol 2022; 22:313. [PMID: 36544085 PMCID: PMC9769055 DOI: 10.1186/s12866-022-02730-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Streptococcus agalactiae or group B Streptococcus (GBS) asymptomatically colonizes the genitourinary tracts of up to 30% of pregnant women. Globally, GBS is an important cause of neonatal morbidity and mortality. GBS has recently been linked to adverse pregnancy outcomes. The potential interactions between GBS and the vaginal microbiome composition remain poorly understood. In addition, little is known about the vaginal microbiota of pregnant Egyptian women. RESULTS Using V3-V4 16S rRNA next-generation sequencing, we examined the vaginal microbiome in GBS culture-positive pregnant women (22) and GBS culture-negative pregnant women (22) during the third trimester in Ismailia, Egypt. According to the alpha-diversity indices, the vaginal microbiome of pregnant GBS culture-positive women was significantly more diverse and less homogenous. The composition of the vaginal microbiome differed significantly based on beta-diversity between GBS culture-positive and culture-negative women. The phylum Firmicutes and the family Lactobacillaceae were significantly more abundant in GBS-negative colonizers. In contrast, the phyla Actinobacteria, Tenericutes, and Proteobacteria and the families Bifidobacteriaceae, Mycoplasmataceae, Streptococcaceae, Corynebacteriaceae, Staphylococcaceae, and Peptostreptococcaceae were significantly more abundant in GBS culture-positive colonizers. On the genus and species levels, Lactobacillus was the only genus detected with significantly higher relative abundance in GBS culture-negative status (88%), and L. iners was the significantly most abundant species. Conversely, GBS-positive carriers exhibited a significant decrease in Lactobacillus abundance (56%). In GBS-positive colonizers, the relative abundance of the genera Ureaplasma, Gardnerella, Streptococcus, Corynebacterium, Staphylococcus, and Peptostreptococcus and the species Peptostreptococcus anaerobius was significantly higher. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to the metabolism of cofactors and vitamins, phosphatidylinositol signaling system, peroxisome, host immune system pathways, and host endocrine system were exclusively enriched among GBS culture-positive microbial communities. However, lipid metabolism KEGG pathways, nucleotide metabolism, xenobiotics biodegradation and metabolism, genetic information processing pathways associated with translation, replication, and repair, and human diseases (Staphylococcus aureus infection) were exclusively enriched in GBS culture-negative communities. CONCLUSIONS Understanding how perturbations of the vaginal microbiome contribute to pregnancy complications may result in the development of alternative, targeted prevention strategies to prevent maternal GBS colonization. We hypothesized associations between inferred microbial function and GBS status that would need to be confirmed in larger cohorts.
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Affiliation(s)
- Sarah Shabayek
- grid.33003.330000 0000 9889 5690Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Asmaa M. Abdellah
- grid.33003.330000 0000 9889 5690Department of Obstetrics and Gynecology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Mohammed Salah
- grid.440879.60000 0004 0578 4430Department of Microbiology and Immunology, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Mohammed Ramadan
- grid.411303.40000 0001 2155 6022Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
| | - Nora Fahmy
- grid.33003.330000 0000 9889 5690Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
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Li M, Huang Z, Tao Z, Meng Y, Wen J, Zhang Q, Liu Y, Shang M, Wang Y, Wang Y, Chen R, Wang X, Cao Y, Zhang L, Liao Q. The role of upper and lower genital tract microbiota alterations in term chorionamnionitis: A prospective study. Front Microbiol 2022; 13:1069254. [PMID: 36605507 PMCID: PMC9808057 DOI: 10.3389/fmicb.2022.1069254] [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: 10/13/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
Objective This study aimed to compare the dynamics of lower and upper genital tract microbiota in normal term pregnancy, histological chorioamnionitis (HCA), and clinical chorioamnionitis (CCA) patients to provide a reference for the diagnosis and treatment of chorioamnionitis (CAM) patients. Methods We prospectively collected vaginal and cervical secretions, as well as placenta tissues, fetal membranes, and amniotic fluid from normal-term pregnant women, HCA and CCA patients. Then, we performed genomic DNA extraction and PCR amplification for all samples. The eligible samples were analyzed by 16S ribosomal RNA (16S rRNA) sequencing. Additionally, all placenta tissues were histopathologically examined, and neonatal pharyngeal swabs and placenta tissues from the HCA and CCA groups were subjected to microbial culture. Results A total of 85 term pregnant women were enrolled in this study, including 34 in the normal group (N), 37 in the HCA group, and 14 in the CCA group. A total of 171 qualified samples were analyzed by 16S rRNA sequencing. The results suggested that the cervical microbiota was highly similar to the vaginal microbiota in normal term parturients, with Lactobacillus as the dominant bacterium. Moreover, there was no difference in the alpha and beta diversity of vaginal microbiota between the N, HCA, and CCA groups at the genus level. Besides, no significant differences were detected in cervical microbiome among the three groups. Regarding intrauterine microorganisms, the N and HCA groups had similar microbial composition but were different from the CCA group. No microbe was detected in the placental tissue of normal term parturients, while some microorganisms were found in the intrauterine amniotic fluid and fetal membrane samples. Regardless of cultivation or 16S rRNA sequencing, an extremely low microbial positive rate was detected in HCA and CCA intrauterine samples. Compared to the normal group, Lactobacillus was significantly reduced in the CCA group intrauterine, and Ureaplasma and Enterococcus increased with no statistically significant. Conclusion The N, HCA and CCA groups had similar composition of vaginal and cervical microflora. Some normal-term pregnant women can harbor non-pathogenic microbiota in the uterine cavity. Sterile inflammation is more frequent than microbial-associated inflammation in term HCA and CCA parturients.
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Affiliation(s)
- Meng Li
- School of Clinical Medicine, Tsinghua University, Beijing, China,Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Zhenyu Huang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Zhi Tao
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yiting Meng
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Jia Wen
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Qiongqiong Zhang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Ying Liu
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Mengyuan Shang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Ying Wang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yufeng Wang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Rui Chen
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Xiaoqian Wang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yang Cao
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Lei Zhang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China,*Correspondence: Lei Zhang, ; Qinping Liao,
| | - Qinping Liao
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China,*Correspondence: Lei Zhang, ; Qinping Liao,
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Gryaznova M, Lebedeva O, Kozarenko O, Smirnova Y, Burakova I, Syromyatnikov M, Maslov A, Popov V. Lower Genital Tract Microbiome in Early Pregnancy in the Eastern European Population. Microorganisms 2022; 10:microorganisms10122368. [PMID: 36557621 PMCID: PMC9785265 DOI: 10.3390/microorganisms10122368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/16/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND It is known that the features of the cervicovaginal microbiome can depend on ethnicity, which might be caused by genetic factors, as well as differences in diet and lifestyle. There is no research on the cervicovaginal microbiome of Eastern European women during early pregnancy. METHODS We evaluated the cervical and cervicovaginal microbiome of women with first-trimester pregnancy (n = 22), further delivered at term, using the 16S rRNA sequencing method. RESULTS The predominant bacterial species in both groups was Lactobacillus iners, followed by Prevotella copri, Ileibacterium valens, Gardnerella vaginalis and Muribaculum intestinale in the cervical samples, and Gardnerella vaginalis, Prevotella copri, Bifidobacterium longum, Ileibacterium valens and Muribaculum intestinale in the cervicovaginal samples. The cervical microbiome had higher alpha diversity; a higher abundance of Muribaculum intestinale, Aquabacterium parvum and Methyloversatilis universalis; and a lower abundance of Psychrobacillus psychrodurans. CONCLUSIONS The Lactobacillus iners-dominated microbiome (CST III) was the predominant type of cervical and cervicovaginal microbiome in early pregnancy in the majority of the women. The presence of soil and animal bacteria in the cervicovaginal microbiome can be explained by the rural origin of patients.
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Affiliation(s)
- Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Olga Lebedeva
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Obstetrics and Gynecology, Belgorod State National University, 308015 Belgorod, Russia
- Correspondence: ; Tel.: +7-951-158-97-99
| | - Olesya Kozarenko
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Antenatal Care Department, Yakovlevo Central District Hospital, 309070 Stroitel, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Inna Burakova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Alexander Maslov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Vasily Popov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
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9
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Le N, Cregger M, Fazleabas A, Braundmeier-Fleming A. Effects of endometriosis on immunity and mucosal microbial community dynamics in female olive baboons. Sci Rep 2022; 12:1590. [PMID: 35102185 PMCID: PMC8803974 DOI: 10.1038/s41598-022-05499-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Endometriosis is defined as the growth of endometrial tissue in ectopic locations, and is associated with altered immune and microbial phenotypes. It is unclear if these changes are the result of the disease or may be causative. We induced endometriosis in non-human primates (Papio Anubis) to test our hypothesis that the growth of endometriotic lesions results in alterations in immune and microbial dynamics that may advance disease progression. Baboon samples were collected pre-inoculation (prior to disease induction), at 3, 6, 9, and 15 months after disease induction. Tolerant regulatory T-cells (Tregs) and inflammatory T-helper 17 (Th17) cells were identified in peripheral blood and within the eutopic/ectopic endometrial tissues. Microbiome communities were identified in fecal/urine samples. The induction of endometriosis decreased peripheral Tregs cells while Th17 cells increased at all post-induction collections, thus reducing the Tregs:Th17 cells ratio, indicating systemic inflammation. Microbiome diversity and abundance were altered at each sample site after disease induction. Thus, induction of endometriosis in baboons caused an immune shift toward an inflammatory profile and altered mucosal microbial profiles, which may drive inflammation through production of inflammatory mediators. Immune and microbial profiling may lead to innovative diagnostic tools and novel therapies for endometriosis treatment.
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Affiliation(s)
- Nhung Le
- Department of Obstetrics and Gynecology, Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA
| | | | | | - Andrea Braundmeier-Fleming
- Department of Obstetrics and Gynecology, Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, 62702, USA.
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10
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Le N, Cregger M, Brown V, Loret de Mola J, Bremer P, Nguyen L, Groesch K, Wilson T, Diaz-Sylvester P, Braundmeier-Fleming A. Association of microbial dynamics with urinary estrogens and estrogen metabolites in patients with endometriosis. PLoS One 2021; 16:e0261362. [PMID: 34914785 PMCID: PMC8675749 DOI: 10.1371/journal.pone.0261362] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/29/2021] [Indexed: 01/04/2023] Open
Abstract
Endometriosis is an estrogen dependent gynecological disease associated with altered microbial phenotypes. The association among endogenous estrogen, estrogen metabolites, and microbial dynamics on disease pathogenesis has not been fully investigated. Here, we identified estrogen metabolites as well as microbial phenotypes in non-diseased patients (n = 9) and those with pathologically confirmed endometriosis (P-EOSIS, n = 20), on day of surgery (DOS) and ~1–3 weeks post-surgical intervention (PSI). Then, we examined the effects of surgical intervention with or without hormonal therapy (OCPs) on estrogen and microbial profiles of both study groups. For estrogen metabolism analysis, liquid chromatography/tandem mass spectrometry was used to quantify urinary estrogens. The microbiome data assessment was performed with Next generation sequencing to V4 region of 16S rRNA. Surgical intervention and hormonal therapy altered gastrointestinal (GI), urogenital (UG) microbiomes, urinary estrogen and estrogen metabolite levels in P-EOSIS. At DOS, 17β-estradiol was enhanced in P-EOSIS treated with OCPs. At PSI, 16-keto-17β-estradiol was increased in P-EOSIS not receiving OCPs while 2-hydroxyestradiol and 2-hydroxyestrone were decreased in P-EOSIS receiving OCPs. GI bacterial α-diversity was greater for controls and P-EOSIS that did not receive OCPs. P-EOSIS not utilizing OCPs exhibited a decrease in UG bacterial α-diversity and differences in dominant taxa, while P-EOSIS utilizing OCPs had an increase in UG bacterial α-diversity. P-EOSIS had a strong positive correlation between the GI/UG bacteria species and the concentrations of urinary estrogen and its metabolites. These results indicate an association between microbial dysbiosis and altered urinary estrogens in P-EOSIS, which may impact disease progression.
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Affiliation(s)
- Nhung Le
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
| | - Melissa Cregger
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Veronica Brown
- Division of Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Julio Loret de Mola
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
- Department of Obstetrics and Gynecology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
| | - Pamela Bremer
- Department of Obstetrics and Gynecology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
| | - Lyn Nguyen
- Department of Obstetrics and Gynecology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
| | - Kathleen Groesch
- Department of Obstetrics and Gynecology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
- Center for Clinical Research, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
| | - Teresa Wilson
- Department of Obstetrics and Gynecology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
- Center for Clinical Research, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
| | - Paula Diaz-Sylvester
- Department of Obstetrics and Gynecology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
- Center for Clinical Research, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
| | - Andrea Braundmeier-Fleming
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
- Department of Obstetrics and Gynecology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America
- * E-mail:
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11
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Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. Funct Integr Genomics 2021; 22:3-26. [PMID: 34657989 DOI: 10.1007/s10142-021-00810-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/25/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
Abstract
This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of genomes, emphasizes some tools, and concludes by celebrating the richness of the ecosystem populated by the "metagenome."
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12
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Wolf EA, Rettig HC, Lupatsii M, Schlüter B, Schäfer K, Friedrich D, Graspeuntner S, Rupp J. Culturomics Approaches Expand the Diagnostic Accuracy for Sexually Transmitted Infections. Int J Mol Sci 2021; 22:ijms221910815. [PMID: 34639153 PMCID: PMC8509341 DOI: 10.3390/ijms221910815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023] Open
Abstract
Sexually transmitted infections (STIs) are a major health concern with clinical manifestations being acknowledged to cause severe reproductive impairment. Research in infectious diseases has been centered around the known major pathogens for decades. However, we have just begun to understand that the microbiota of the female genital tract is of particular importance for disease initiation, infection progression, and pathological outcome. Thus, we are now aware that many poorly described, partially not yet known, or cultured bacteria may pave the way for an infection and/or contribute to disease severity. While sequencing-based methods are an important step in diagnosing STIs, culture-based methods are still the gold-standard method in diagnostic routine, providing the opportunity to distinguish phenotypic traits of bacteria. However, current diagnostic culture routines suffer from several limitations reducing the content of information about vaginal microbiota. A detailed characterization of microbiota-associated factors is needed to assess the impact of single-bacterial isolates from the vaginal community on vaginal health and the containment of STIs. Here we provide current concepts to enable modern culture routines and create new ideas to improve diagnostic approaches with a conjunct usage of bioinformatics. We aim to enable scientists and physicians alike to overcome long-accepted limitations in culturing bacteria of interest to the human health. Eventually, this may improve the quality of culture-based diagnostics, facilitate a research interface, and lead to a broader understanding of the role of vaginal microbiota in reproductive health and STIs.
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Affiliation(s)
- Ellinor Anna Wolf
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Britta Schlüter
- Department of Gynecology and Obstetrics, University Medical Center Schleswig-Holstein, 23538 Lübeck, Germany;
| | - Kathrin Schäfer
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Dirk Friedrich
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
- Correspondence:
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13
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Flaviani F, Hezelgrave NL, Kanno T, Prosdocimi EM, Chin-Smith E, Ridout AE, von Maydell DK, Mistry V, Wade WG, Shennan AH, Dimitrakopoulou K, Seed PT, Mason AJ, Tribe RM. Cervicovaginal microbiota and metabolome predict preterm birth risk in an ethnically diverse cohort. JCI Insight 2021; 6:e149257. [PMID: 34255744 PMCID: PMC8410012 DOI: 10.1172/jci.insight.149257] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The syndrome of spontaneous preterm birth (sPTB) presents a challenge to mechanistic understanding, effective risk stratification, and clinical management. Individual associations between sPTB, self-reported ethnic ancestry, vaginal microbiota, metabolome, and innate immune response are known but not fully understood, and knowledge has yet to impact clinical practice. Here, we used multi–data type integration and composite statistical models to gain insight into sPTB risk by exploring the cervicovaginal environment of an ethnically heterogenous pregnant population (n = 346 women; n = 60 sPTB < 37 weeks’ gestation, including n = 27 sPTB < 34 weeks). Analysis of cervicovaginal samples (10–15+6 weeks) identified potentially novel interactions between risk of sPTB and microbiota, metabolite, and maternal host defense molecules. Statistical modeling identified a composite of metabolites (leucine, tyrosine, aspartate, lactate, betaine, acetate, and Ca2+) associated with risk of sPTB < 37 weeks (AUC 0.752). A combination of glucose, aspartate, Ca2+, Lactobacillus crispatus, and L. acidophilus relative abundance identified risk of early sPTB < 34 weeks (AUC 0.758), improved by stratification by ethnicity (AUC 0.835). Increased relative abundance of L. acidophilus appeared protective against sPTB < 34 weeks. By using cervicovaginal fluid samples, we demonstrate the potential of multi–data type integration for developing composite models toward understanding the contribution of the vaginal environment to risk of sPTB.
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Affiliation(s)
- Flavia Flaviani
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine.,Translational Bioinformatics Platform, NIHR Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust
| | - Natasha L Hezelgrave
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine
| | - Tokuwa Kanno
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine.,Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, and
| | - Erica M Prosdocimi
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Evonne Chin-Smith
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine
| | - Alexandra E Ridout
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine
| | - Djuna K von Maydell
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, and
| | - Vikash Mistry
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine
| | - William G Wade
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Andrew H Shennan
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine
| | - Konstantina Dimitrakopoulou
- Translational Bioinformatics Platform, NIHR Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust
| | - Paul T Seed
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine
| | - A James Mason
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, and
| | - Rachel M Tribe
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine
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14
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Vasundhara D, Raju VN, Hemalatha R, Nagpal R, Kumar M. Vaginal & gut microbiota diversity in pregnant women with bacterial vaginosis & effect of oral probiotics: An exploratory study. Indian J Med Res 2021; 153:492-502. [PMID: 34380796 PMCID: PMC8354056 DOI: 10.4103/ijmr.ijmr_350_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Background & objectives: The vaginal microbiota undergoes subtle changes during pregnancy and may affect several aspects of pregnancy outcomes. There has been no comprehensive study characterizing the gestational vaginal and gut microbiota and the dynamics of the microbiota with oral probiotics among Indian women. Hence, the study was aimed to explore the microbiota of pregnant women with normal microbiota and bacterial vaginosis (BV) environments and the effect of oral probiotics on the microbiota and the BV status in these women. Methods: Using high-throughput Illumina-MiSeq sequencing approach, the 16S rRNA gene amplicons were analyzed and the vaginal and gut microbiota of pregnant women with and without BV and pre- and post-probiotics (Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14) intervention for a month was characterized. Results: The study revealed a compositional difference in the vaginal and gut microbiota between BV and healthy pregnant women. The vaginal microbiota of healthy women was characteristically predominated by Lactobacillus helveticus, followed by L. iners and L. gasseri; in contrast, women positive for BV harboured higher α-diversity and had lower abundance of L. helveticus. Similarly, Prevotella copri, a gut microbe, associated with normal environment was detected in the vaginal samples of all pregnant women without BV, it remained undetected in women with the infection, while all women with BV had Gardnerella vaginalis, which decreased significantly with probiotic treatment. Gut microbiota also revealed dominant abundance of P. copri in healthy women, whereas it was significantly lower in women with BV. The bacterial clade, P. copri abundance increased from 9.17 to 16.49 per cent in the probiotic group and reduced from 7.75 to 4.84 per cent in the placebo group. Interpretation & conclusions: This study showed gestational vaginal and gut microbiota differences in normal and BV environments. With probiotic treatment, the dynamics of L. helveticus and P. copri hint towards a possible role of probiotics in modulating the vaginal microbiota.
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Affiliation(s)
- Donugama Vasundhara
- Department of Clinical Epidemiology, ICMR-National Institute of Nutrition, Hyderabad, Telangana, India
| | - Vankudavath Naik Raju
- Nutrition Information, Communication & Health Education (NICHE), ICMR-National Institute of Nutrition, Hyderabad, Telangana, India
| | | | - Ravinder Nagpal
- Department of Internal Medicine-Molecular Medicine; Department of Microbiology & Immunology, Wake Forest, School of Medicine, Winston-Salem, NC, United States
| | - Manoj Kumar
- Department of Microbiology, ICMR-National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
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15
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Brown SE, Robinson CK, Shardell MD, Holm JB, Ravel J, Ghanem KG, Brotman RM. Assessing the Concordance Between Urogenital and Vaginal Microbiota: Can Urine Specimens Be Used as a Proxy for Vaginal Samples? Front Cell Infect Microbiol 2021; 11:671413. [PMID: 34268137 PMCID: PMC8276069 DOI: 10.3389/fcimb.2021.671413] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/28/2021] [Indexed: 01/04/2023] Open
Abstract
Background The vaginal microbiota play a key role in defense against reproductive tract infections; however, many population-based women's health studies do not collect vaginal samples. Molecular examinations of urine samples have revealed common vaginal bacteria. We sought to assess the extent that community state type assignments of archived random-catch and clean-catch urine samples agreed with the paired vaginal samples in both reproductive-age and peri/post-menopausal women. Results Using archived samples, we evaluated the microbiota concordance among women in three studies: two with paired mid-vaginal/random-catch urine (N=91 reproductive-age participants and N=13 peri/post-menopausal participants), and one with paired mid-vaginal/clean-catch urine (N=99 reproductive-age participants). Microbiota composition was characterized by sequencing amplicons of the 16S rRNA gene V3-V4 regions and assigned to community state types. Similarity of paired samples was gauged using agreement of community state types and Yue-Clayton θ indices. Analysis of Composition of Microbiomes II indicated which taxa were differently relatively abundant in paired vaginal and urine samples. In reproductive-age women, random-catch and clean-catch urines were 89.0% and 86.9% concordant on five community state types with paired mid-vaginal swabs, and Kappa statistics indicated almost perfect agreement (κrandom-catch=.85, κclean-catch=.81, p<0.0001). A small number of pairs of samples were discordant (23/190, 12%), and discordant pairs tended to be between samples classified to L. iners-dominated and/or low-Lactobacillus states. Concordance and agreement remained similar when dichotomizing the microbiota to Lactobacillus-dominated versus low-Lactobacillus microbiota, as well as when evaluating separately the three subtypes of the low-Lactobacillus community state type IV. Median similarity of paired urine/vaginal samples was high (θrandom-catch=.85, θclean-catch=.88), and a comparison of the random-catch and clean-catch similarity scores showed no significant difference (p=.80). Concordance and similarity were lower for peri/post-menopausal women, but agreement remained substantial (76.9% concordant, κrandom-catch= 0.64, θrandom-catch=.62). Taxonomic-level analysis confirmed these findings. Conclusions Random-catch and clean-catch urine samples showed substantial agreement on bacterial composition to paired mid-vaginal samples, indicating that the genitourinary microbiota may be a reliable proxy for assessing the overall composition of the vaginal microbiota via community state types. This data suggests that urine samples can, with proper interpretation, be utilized as a surrogate for developing preliminary data and hypothesis-generating studies.
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Affiliation(s)
- Sarah E. Brown
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Courtney K. Robinson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Michelle D. Shardell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Johanna B. Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Khalil G. Ghanem
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rebecca M. Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, United States,*Correspondence: Rebecca M. Brotman,
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16
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Darwish N, Shao J, Schreier LL, Proszkowiec-Weglarz M. Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca. Sci Rep 2021; 11:11848. [PMID: 34088939 PMCID: PMC8178357 DOI: 10.1038/s41598-021-91387-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/26/2021] [Indexed: 01/12/2023] Open
Abstract
We evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting different variable regions of the 16S rRNA gene were employed. DNA sequences were analyzed using open-source platform QIIME2 and the Greengenes database. PICRUSt2 was used to determine the predicted function of bacterial communities. Changes in bacterial relative abundance due to 16S primers were determined by GLMs. The average PCR amplicon size ranged from 315 bp (V3) to 769 bp (V4–V6). Alpha- and beta-diversity, taxonomic composition, and predicted functions were significantly affected by the primer choice. Beta diversity analysis based on Unweighted UniFrac distance matrix showed separation of microbiota with four different clusters of bacterial communities. Based on the alpha- and beta-diversity and taxonomic composition, variable regions V1–V3(1) and (2), and V3–V4 and V3–V5 were in most consensus. Our data strongly suggest that selection of particular sets of the 16S rRNA primers can impact microbiota analysis and interpretation of results in chicken as was shown previously for humans and other animal species.
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Affiliation(s)
- Nadia Darwish
- Agricultural Research Service, NEA, Animal Biosciences and Biotechnology Laboratory, United States Department of Agriculture, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA.,Agricultural Research Service, Northeast Area, Statistic Group, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Jonathan Shao
- Agricultural Research Service, Northeast Area, Statistic Group, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Lori L Schreier
- Agricultural Research Service, NEA, Animal Biosciences and Biotechnology Laboratory, United States Department of Agriculture, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA
| | - Monika Proszkowiec-Weglarz
- Agricultural Research Service, NEA, Animal Biosciences and Biotechnology Laboratory, United States Department of Agriculture, 10300 Baltimore Avenue, B-200, Rm. 100B, BARC-East, Beltsville, MD, 20705, USA.
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17
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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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18
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Zhao E, Zhang W, Geng B, You B, Wang W, Li X. Intestinal dysbacteriosis leads to kidney stone disease. Mol Med Rep 2020; 23:180. [PMID: 33655334 PMCID: PMC7809898 DOI: 10.3892/mmr.2020.11819] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 11/27/2020] [Indexed: 01/04/2023] Open
Abstract
The formation and physicochemical properties of kidney stones (KSs) are closely associated with diet. In view of the differences in ethnicity and dietary composition between Chinese and Western populations, the present study aimed to investigate the association between intestinal dysbacteriosis and KSs in China. The current study examined the differences in intestinal microbes between the KS disease (KSD) and the healthy control (HLT) groups, and statistically significant differences based on 16s rRNA gene amplicons were identified using a Student's t-test or one-way ANOVA. In addition, the calcium oxalate KS (COKS), uric acid KS (UAKS) and carbonate apatite KS(CCKS) groups were compared with a non-parametric statistical test. Determination of bacterial abundance was performed via the analysis of 16s rRNA marker gene sequences using next-generation sequencing. Firmicutes (F) and Bacteroides (B) levels were significantly higher in the KSD group compared with the HLT group (B/F=0.67 vs. 0.08; P<0.001), as were the overall levels of B (6.19-fold higher compared with the HLT group; 22.2 vs. 3.6%; P<0.001). The Prevotella-9 abundance levels in the KSD group were 4.65-fold higher compared with those in the HLT group (8.8 vs. 1.9%; P<0.001). The levels of Blautia and Lachnoclostridium were significantly decreased in the KSD group (13.3 vs. 6.0%; and 5.0 vs. 7.9%; both P<0.05). Moreover, Prevotella-9 levels were higher in non-calciferous KSs (UAKS) compared with calciferous KSs (COKS and CCKS). Therefore, the findings of the present study indicated a key association between specific KS components and intestinal flora, providing a theoretical basis for new treatment methods for KSs. Moreover, differences and interactions between these bacteria could initially predict specific types of urolithiasis.
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Affiliation(s)
- Enyang Zhao
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Wenfu Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Bo Geng
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Bosen You
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Wanhui Wang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Xuedong Li
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
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19
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Sirichoat A, Sankuntaw N, Engchanil C, Buppasiri P, Faksri K, Namwat W, Chantratita W, Lulitanond V. Comparison of different hypervariable regions of 16S rRNA for taxonomic profiling of vaginal microbiota using next-generation sequencing. Arch Microbiol 2020; 203:1159-1166. [PMID: 33221964 DOI: 10.1007/s00203-020-02114-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/15/2020] [Accepted: 11/01/2020] [Indexed: 12/20/2022]
Abstract
The exploration of vaginal microbiota by using next-generation sequencing (NGS) of 16S ribosomal RNA (rRNA) gene is widely used. Up to now, different hypervariable regions have been selected to study vaginal microbiota by NGS and there is no standard method for analysis. The study aimed to characterize vaginal microbiota from clinical samples using NGS targeting the 16S rRNA gene and to determine the performance of individual and concatenated hypervariable region sequences to generate the taxonomic profiles of the vaginal microbiota. Fifty-one vaginal DNA samples were subjected to 16S rRNA gene NGS based on the Ion Torrent PGM platform with the use of two primer sets spanning seven hypervariable regions of the 16S rRNA gene. Our analysis revealed that the predominant bacterial genera were Lactobacillus, Gardnerella and Atopobium, which accounted for 78%, 14% and 2%, respectively, of sequences from all vaginal bacterial genera. At the species level, Lactobacillus iners, Gardnerella vaginalis and Atopobium vaginae accounted for 72%, 10% and 6%, respectively, of the bacterial cells present. Analyses using the V3 region generally indicated the highest bacterial diversity followed by the V6-V7 and V4 regions, while the V9 region gave the lowest bacterial resolution. NGS based on the 16S rRNA gene can give comprehensive estimates of the diversity of vaginal bacterial communities. Selection of sequences from appropriate hypervariable regions is necessary to provide reliable information on bacterial community diversity.
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Affiliation(s)
- Auttawit Sirichoat
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nipaporn Sankuntaw
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, 12120, Thailand
| | - Chulapan Engchanil
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Pranom Buppasiri
- Department of Obstetrics and Gynecology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kiatichai Faksri
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Wises Namwat
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Wasun Chantratita
- Medical Genome Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Viraphong Lulitanond
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
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20
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Stern JM, Burk RD, Asplin J, Krieger NS, Suadicani SO, Wang Y, Usyk M, Lee JA, Chen L, Becker J, Chan M, Bushinsky DA. Kidney stone formation and the gut microbiome are altered by antibiotics in genetic hypercalciuric stone-forming rats. Urolithiasis 2020; 49:185-193. [PMID: 33161469 DOI: 10.1007/s00240-020-01223-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
Antibiotics can alter the gut microbiome (GMB), which may be associated with stone disease. We sought to determine the effect that antibiotics have on the GMB, urine ion excretion and stone formation in genetic hypercalciuric stone-forming (GHS) rats. 116th generation GHS rats were fed a fixed amount of a normal calcium (1.2%) and phosphate (0.65%) diet, and divided into three groups (n = 10): control (CTL) diet, or supplemented with ciprofloxacin (Cipro, 5 mg/day) or Bactrim (250 mg/day). Urine and fecal pellets were collected over 6, 12 and 18 weeks. Fecal DNA was amplified across the 16S rRNA V4 region. At 18 weeks, kidney stone formation was visualized by Faxitron and blindly assessed by three investigators. After 18 weeks, urine calcium and oxalate decreased with Bactrim compared to CTL and Cipro. Urine pH increased with Bactrim compared to CTL and Cipro. Urine citrate increased with Cipro compared to CTL and decreased by half with Bactrim. Calcification increased with Bactrim compared to CTL and Cipro. Increased microbial diversity correlated with decreased urinary oxalate in all animals (R = - 0.46, p = 0.006). A potential microbial network emerged as significantly associated with shifts in urinary pH. Bactrim and Cipro differentially altered the GMB of GHS rats. The Bactrim group experienced a decrease in urine calcium, increased CaP supersaturation and increased calcification. The GMB is likely a contributing factor to changes in urine chemistry, supersaturation and stone risk. Further investigation is required to fully understand the association between antibiotics, the GMB and kidney stone formation.
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Affiliation(s)
- Joshua M Stern
- Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, New York, NY, 10461, USA.
| | - Robert D Burk
- Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, New York, NY, 10461, USA
| | - John Asplin
- Litholink, Laboratory Corporation of America® Holdings, Chicago, IL, USA
| | | | - Sylvia O Suadicani
- Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, New York, NY, 10461, USA
| | - Yi Wang
- Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, New York, NY, 10461, USA
| | - Mykhaylo Usyk
- Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, New York, NY, 10461, USA
| | - Justin A Lee
- Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, New York, NY, 10461, USA
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21
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Vargas-Robles D, Morales N, Rodríguez I, Nieves T, Godoy-Vitorino F, Alcaraz LD, Pérez ME, Ravel J, Forney LJ, Domínguez-Bello MG. Changes in the vaginal microbiota across a gradient of urbanization. Sci Rep 2020; 10:12487. [PMID: 32719372 PMCID: PMC7385657 DOI: 10.1038/s41598-020-69111-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 06/17/2020] [Indexed: 12/27/2022] Open
Abstract
The vaginal microbiota of healthy women typically has low diversity, which increases after perturbations. Among these, lifestyle associated with certain sexual and antimicrobial practices may be associated with higher diversity. To test this hypothesis, we characterized the vaginal microbiota in the cervicovaginal and introital sites in sexually active Amerindians (N = 82) spanning urbanization, and in urban mestizos (N = 29), in the Venezuelan Amazonas. HPV status was also considered. Sampling was performed in an urban gradient from remote villages to a town, and women were individually classified by the degree of urbanization (low, medium, and high). Amerindian cervicovaginal and introital microbiota diversity were not associated with major changes in urbanization or ethnicity. There was a non-significant trend of increased diversity with urbanization, with a few taxa found overrepresented in urban Amerindians (Brevibacterium linens and Peptoniphilus lacrimalis) or mestizos (Mobiluncus mulieris and Prevotella sp.). Among all women, cervicovaginal and introital samples clustered, respectively, in four and two community state types (CSTs), where most profiles were dominated by Lactobacillus iners, Gardnerella vaginalis or were highly diverse profiles. HPV status did not associate with microbial diversity. In conclusion, no association was found between urban level and the vaginal microbiome in Amerindian women, and little difference was found between ethnicities. L. iners and high diversity profiles, associated with vaginal health outcomes, prevail in these populations.
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Affiliation(s)
- Daniela Vargas-Robles
- Department of Biology, University of Puerto Rico, San Juan, PR, USA.,Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, MPPS, Puerto Ayacucho, Venezuela
| | - Natalia Morales
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, MPPS, Puerto Ayacucho, Venezuela
| | - Iveth Rodríguez
- Ministerio del Poder Popular Para La Salud, Caracas, Venezuela
| | - Tahidid Nieves
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, MPPS, Puerto Ayacucho, Venezuela
| | - Filipa Godoy-Vitorino
- Department of Microbiology & Medical Zoology, School of Medicine, University of Puerto Rico, San Juan, PR, USA
| | - Luis David Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María-Eglée Pérez
- Department of Mathematics, University of Puerto Rico, San Juan, PR, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - Larry J Forney
- Department of Biological Sciences and the Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | - María Gloria Domínguez-Bello
- Department of Medicine, New York University School of Medicine, New York, USA. .,Departments of Biochemistry and Microbiology and of Anthropology, Rutgers University, New Brunswick, USA.
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22
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Koedooder R, Mackens S, Budding A, Fares D, Blockeel C, Laven J, Schoenmakers S. Identification and evaluation of the microbiome in the female and male reproductive tracts. Hum Reprod Update 2020; 25:298-325. [PMID: 30938752 DOI: 10.1093/humupd/dmy048] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/16/2018] [Accepted: 01/16/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The existence of an extensive microbiome in and on the human body has increasingly dominated the scientific literature during the last decade. A shift from culture-dependent to culture-independent identification of microbes has occurred since the emergence of next-generation sequencing (NGS) techniques, whole genome shotgun and metagenomic sequencing. These sequencing analyses have revealed the presence of a rich diversity of microbes in most exposed surfaces of the human body, such as throughout the reproductive tract. The results of microbiota analyses are influenced by the technical specifications of the applied methods of analyses. Therefore, it is difficult to correctly compare and interpret the results of different studies of the same anatomical niche. OBJECTIVES AND RATIONALE The aim of this narrative review is to provide an overview of the currently used techniques and the reported microbiota compositions in the different anatomical parts of the female and male reproductive tracts since the introduction of NGS in 2005. This is crucial to understand and determine the interactions and roles of the different microbes necessary for successful reproduction. SEARCH METHODS A search in Embase, Medline Ovid, Web of science, Cochrane and Google scholar was conducted. The search was limited to English language and studies published between January 2005 and April 2018. Included articles needed to be original microbiome research related to the reproductive tracts. OUTCOMES The review provides an extensive up-to-date overview of current microbiome research in the field of human reproductive medicine. The possibility of drawing general conclusions is limited due to diversity in the execution of analytical steps in microbiome research, such as local protocols, sampling methods, primers used, sequencing techniques and bioinformatic pipelines, making it difficult to compare and interpret results of the available studies. Although some microbiota are associated with reproductive success and a good pregnancy outcome, it is still unknown whether a causal link exists. More research is needed to further explore the possible clinical implications and therapeutic interventions. WIDER IMPLICATIONS For the field of reproductive medicine, determination of what is a favourable reproductive tract microbiome will provide insight into the mechanisms of both unsuccessful and successful human reproduction. To increase pregnancy chances with live birth and to reduce reproduction-related health costs, future research could focus on postponing treatment or conception in case of the presence of unfavourable microbiota and on the development of therapeutic interventions, such as microbial therapeutics and lifestyle adaptations.
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Affiliation(s)
- Rivka Koedooder
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynaecology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Shari Mackens
- Centre for Reproductive Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101-1090, Brussels, Belgium
| | - Andries Budding
- Department of Medical Microbiology and Infection Control, Amsterdam UMC-location VUmc, Amsterdam, The Netherlands
| | - Damiat Fares
- Division of Obstetrics and Prenatal Diagnosis, Department of Obstetrics and Gynaecology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Christophe Blockeel
- Centre for Reproductive Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101-1090, Brussels, Belgium
| | - Joop Laven
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynaecology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Sam Schoenmakers
- Division of Obstetrics and Prenatal Diagnosis, Department of Obstetrics and Gynaecology, Erasmus University Medical Centre, Rotterdam, The Netherlands
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23
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Chorna N, Godoy-Vitorino F. A Protocol for the Multi-Omic Integration of Cervical Microbiota and Urine Metabolomics to Understand Human Papillomavirus (HPV)-Driven Dysbiosis. Biomedicines 2020; 8:biomedicines8040081. [PMID: 32276347 PMCID: PMC7235793 DOI: 10.3390/biomedicines8040081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022] Open
Abstract
The multi-omic integration of microbiota data with metabolomics has gained popularity. This protocol is based on a human multi-omics study, integrating cervicovaginal microbiota, HPV status and neoplasia, with urinary metabolites. Indeed, to understand the biology of the infections and to develop adequate interventions for cervical cancer prevention, studies are needed to characterize in detail the cervical microbiota and understand the systemic metabolome. This article is a detailed protocol for the multi-omic integration of cervical microbiota and urine metabolome to shed light on the systemic effects of cervical dysbioses associated with Human Papillomavirus (HPV) infections. This methods article suggests detailed sample collection and laboratory processes of metabolomics, DNA extraction for microbiota, HPV typing, and the bioinformatic analyses of the data, both to characterize the metabolome, the microbiota, and joint multi-omic analyses, useful for the development of new point-of-care diagnostic tests based on these approaches.
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Affiliation(s)
- Nataliya Chorna
- Department of Biochemistry, UPR School of Medicine, 00921 San Juan, Puerto Rico;
| | - Filipa Godoy-Vitorino
- Department of Microbiology & Medical Zoology, UPR School of Medicine, 00921 San Juan, Puerto Rico
- Correspondence: ; Tel.: +1-787-758-2525 (ext. 2096)
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24
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Onywera H, Meiring TL. Comparative analyses of Ion Torrent V4 and Illumina V3-V4 16S rRNA gene metabarcoding methods for characterization of cervical microbiota: taxonomic and functional profiling. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00278] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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25
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Mechanistic insights into the action of probiotics against bacterial vaginosis and its mediated preterm birth: An overview. Microb Pathog 2020; 141:104029. [PMID: 32014462 DOI: 10.1016/j.micpath.2020.104029] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/29/2020] [Indexed: 02/07/2023]
Abstract
The human body is a reservoir of numerous micro-creatures; whose role is substantial and indispensable in the overall development of human beings. The advances in omic approaches have offered powerful means to decipher the core microbiome and metabolome diversities in a specific organ system. The establishment of lactobacilli in the female reproductive tract is thought to be a paramount prerequisite that maintains homeostatic conditions for a sustainable and healthy pregnancy. Nevertheless, a plethora of such Lactobacillus strains of vaginal source revealed probiotic phenotypes. The plummeting in the occurrence of lactobacilli in the vaginal ecosystem is associated with several adverse pregnancy outcomes (APOs). One such pathological condition is "Bacterial Vaginosis" (BV), a pathogen dominated gynecological threat. In this scenario, the ascending traffic of notorious Gram-negative/variable BV pathogens to the uterus is one of the proposed pathways that give rise to inflammation-related APOs like preterm birth. Since antibiotic resistance is aggravating among urogenital pathogens, the probiotics intervention remains one of the alternative biotherapeutic strategies to overcome BV and its associated APOs. Perhaps, the increased inclination towards the safer and natural biotherapeutic strategies rather than pharmaceutical drugs for maintaining gestational and reproductive health resulted in the use of probiotics in pregnancy diets. In this context, the current review is an attempt to highlight the microbiome and metabolites signatures of BV and non-BV vaginal ecosystem, inflammation or infection-related preterm birth, host-microbial interactions, role and effectiveness of probiotics to fight against aforesaid diseased conditions.
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26
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Mei C, Yang W, Wei X, Wu K, Huang D. The Unique Microbiome and Innate Immunity During Pregnancy. Front Immunol 2019; 10:2886. [PMID: 31921149 PMCID: PMC6929482 DOI: 10.3389/fimmu.2019.02886] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/25/2019] [Indexed: 12/26/2022] Open
Abstract
A successful pregnancy depends on not only the tolerance of the fetal immune system by the mother but also resistance against the threat of hazardous microorganisms. Infection with pathogenic microorganisms during pregnancy may lead to premature delivery, miscarriage, growth restriction, neonatal morbidity, and other adverse outcomes. Moreover, the host also has an intact immune system to avoid these adverse outcomes. It is important to note the presence of normal bacteria in the maternal reproductive tract and the principal role of the maternal-placental-fetal interaction in antimicrobial immunity. Previous studies mainly focused on maternal infection during pregnancy. However, this review summarizes the new views on the study of the maternal microbiome and expounds the innate immune defense mechanism of the maternal vagina and decidua as well as how cytotrophoblasts and syncytiotrophoblasts recognize and kill bacteria in the placenta. Fetal immune systems, thought to be weak, also exhibit an immune defense function that is indispensable for maintaining the safety of the fetus. The skin, lungs, and intestines of the fetus during pregnancy constitute the main immune barriers. These findings will provide a new understanding of the effects of normal microbial flora and how the host resists harmful microbes during pregnancy. We believe that it may also contribute to the reference on the clinical prevention and treatment of gestational infection to avoid adverse pregnancy outcomes.
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Affiliation(s)
- Chunlei Mei
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weina Yang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Wei
- Second Affiliated Hospital of Jinlin University, Changchun, China
| | - Kejia Wu
- Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Donghui Huang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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27
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Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D, Meiring TL. Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study. PeerJ 2019; 7:e7488. [PMID: 31435492 PMCID: PMC6698374 DOI: 10.7717/peerj.7488] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/16/2019] [Indexed: 01/07/2023] Open
Abstract
Background Lactobacillus spp. are common bacteria in the cervical and vaginal microbiota (CVM) and are thought to represent a “healthy” cervicovaginal state. Several studies have found an independent association between ethnicity/race and cervical and vaginal microbiota (CVM) composition. Women of sub-Saharan African descent appear to be significantly more likely to have non-Lactobacillus-dominated CVM compared to women of European descent. The factors contributing to these differences remain to be fully elucidated. The CVM of Black South African women and factors influencing their CVM remain understudied. In this study, we characterized the cervical microbiota of reproductive-age South African women and assessed the associations of these microbiota with participants’ metadata. Methods The cervical microbiota from cervical DNA of 62 reproductive-age women were profiled by Ion Torrent sequencing the V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) gene and analyzed with the Quantitative Insights Into Microbial Ecology (QIIME), UPARSE, and metagenomeSeq tools. Associations between cervical microbiota and participants’ metadata were assessed using GraphPad Prism, R packages and an in-house script. Results The cervical microbiota clustered into three distinct community state types (CSTs): Lactobacillus iners-dominated cervical microbiota (CST I (38.7%, 24/62)), unclassified Lactobacillus-dominated cervical microbiota (CST II (4.8%, 3/62)), and diverse cervical microbiota (CST III (56.5%, 35/62)) with an array of heterogeneous bacteria, predominantly the bacterial vaginosis (BV)-associated Gardnerella, Prevotella, Sneathia, and Shuttleworthia. CST III was associated with BV (p = 0.001). Women in CST I were more likely to be on hormonal contraception, especially progestin-based, compared to women in CST III (odds ratio: 5.2 (95% CI [1.6–17.2]); p = 0.005). Women on hormonal contraception had a significantly lower alpha (Shannon indices: 0.9 (0.2–1.9) versus 2.3 (0.6–2.3); p = 0.025) and beta (permutational multivariate analysis of variance (PERMANOVA) pseudo-F statistic =4.31, p = 0.019) diversity compared to non-users. There was no significant difference in the alpha (Shannon indices: 1.0 (0.3–2.2) versus 1.9 (0.3–2.2); p = 0.483) and beta (PERMANOVA pseudo-F statistic = 0.89, p = 0.373) diversity in women with versus without human papillomavirus infection. Conclusions The majority of Black women in our study had non-Lactobacillus-dominated cervical microbiota. Additional studies are needed to examine whether such microbiota represent abnormal, intermediate or variant states of health. Lastly, the association of hormonal contraception with L. iners dominance requires further in-depth research to confirm this association, determine its biological mechanism and whether it has a beneficial effect on the cervicovaginal health.
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Affiliation(s)
- Harris Onywera
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa.,Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Anna-Lise Williamson
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa.,Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa.,SAMRC Gynaecological Cancer Research Centre, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Zizipho Z A Mbulawa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa.,Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa.,SAMRC Gynaecological Cancer Research Centre, University of Cape Town, Cape Town, Western Cape, South Africa.,Center for HIV & STIs, National Institute for Communicable Diseases, National Health Laboratory Service, University of Cape Town, Johannesburg, Gauteng, South Africa
| | - David Coetzee
- Center for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Tracy L Meiring
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa.,Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
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28
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Norenhag J, Du J, Olovsson M, Verstraelen H, Engstrand L, Brusselaers N. The vaginal microbiota, human papillomavirus and cervical dysplasia: a systematic review and network meta-analysis. BJOG 2019; 127:171-180. [PMID: 31237400 DOI: 10.1111/1471-0528.15854] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2019] [Indexed: 01/18/2023]
Abstract
BACKGROUND Persistent infection with high-risk human papillomavirus can lead to cervical dysplasia and cancer. Recent studies have suggested associations between the composition of the vaginal microbiota, infection with human papillomavirus (HPV) and progression to cervical dysplasia and cancer. OBJECTIVE To assess how specific cervico-vaginal microbiota compositions are associated with HPV infection, cervical dysplasia and cancer, we conducted a systematic review and network meta-analysis (registered in PROSPERO: CRD42018112862). SEARCH STRATEGY PubMed, Web of science, Embase and Cochrane database. SELECTION CRITERIA All original studies describing at least two community state types of bacteria (CST), based on molecular techniques enabling identification of bacteria, and reporting the association with HPV infection, cervical dysplasia and/or cervical cancer. DATA COLLECTION AND ANALYSIS For the meta-analysis, a network map was constructed to provide an overview of the network relationships and to assess how many studies provided direct evidence for the different vaginal microbiota compositions and HPV, cervical dysplasia or cancer. Thereafter, the consistency of the model was assessed, and forest plots were constructed to pool and summarise the available evidence, presenting odds ratios and 95% confidence intervals. MAIN RESULTS Vaginal microbiota dominated by non-Lactobacilli species or Lactobacillus iners were associated with three to five times higher odds of any prevalent HPV and two to three times higher for high-risk HPV and dysplasia/cervical cancer compared with Lactobacillus crispatus. CONCLUSIONS These findings suggest an association between certain bacterial community types of the vaginal microbiota and HPV infection and HPV-related disease. This may be useful for guiding treatment options or serve as biomarkers for HPV-related disease. TWEETABLE ABSTRACT This network meta-analysis suggests an association between different vaginal bacterial community types and the risk of HPV.
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Affiliation(s)
- J Norenhag
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - J Du
- Department of Microbiology, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska Hospital, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - M Olovsson
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - H Verstraelen
- Department of Obstetrics & Gynaecology, Ghent University Hospital 0P4, Ghent University, Ghent, Belgium
| | - L Engstrand
- Department of Microbiology, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska Hospital, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - N Brusselaers
- Department of Microbiology, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska Hospital, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
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29
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Winters AD, Romero R, Gervasi MT, Gomez-Lopez N, Tran MR, Garcia-Flores V, Pacora P, Jung E, Hassan SS, Hsu CD, Theis KR. Does the endometrial cavity have a molecular microbial signature? Sci Rep 2019; 9:9905. [PMID: 31289304 PMCID: PMC6616349 DOI: 10.1038/s41598-019-46173-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/21/2019] [Indexed: 01/15/2023] Open
Abstract
Recent molecular studies concluded that the endometrium has a resident microbiota dominated by Lactobacillus spp. and is therefore similar to that of the vagina. These findings were largely derived from endometrial samples obtained through a transcervical catheter and thus prone to contamination. Herein, we investigated the molecular microbial profiles of mid-endometrial samples obtained through hysterectomy and compared them with those of the cervix, vagina, rectum, oral cavity, and controls for background DNA contamination. Microbial profiles were examined through 16S rRNA gene qPCR and sequencing. Universal bacterial qPCR of total 16S rDNA revealed a bacterial load exceeding that of background DNA controls in the endometrium of 60% (15/25) of the study subjects. Bacterial profiles of the endometrium differed from those of the oral cavity, rectum, vagina, and background DNA controls, but not of the cervix. The bacterial profiles of the endometrium and cervix were dominated by Acinetobacter, Pseudomonas, Cloacibacterium, and Comamonadaceae. Both 16S rRNA gene sequencing and Lactobacillus species-specific (L. iners & L crispatus) qPCR showed that Lactobacillus was rare in the endometrium. In conclusion, if there is a microbiota in the middle endometrium, it is not dominated by Lactobacillus as was previously concluded, yet further investigation using culture and microscopy is necessary.
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Affiliation(s)
- Andrew D Winters
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Perinatal Research Initiative in Maternal, Perinatal and Child Health, Wayne State University School of Medicine, Detroit, Michigan, USA.,Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, Detroit, Michigan, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, Detroit, Michigan, USA. .,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA. .,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA. .,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA. .,Detroit Medical Center, Detroit, Michigan, USA.
| | - Maria Teresa Gervasi
- Department of Women's and Children's Health, University Hospital of Padua, Padua, Italy
| | - Nardhy Gomez-Lopez
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Perinatal Research Initiative in Maternal, Perinatal and Child Health, Wayne State University School of Medicine, Detroit, Michigan, USA.,Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Maria Rosa Tran
- Department of Women's and Children's Health, University Hospital of Padua, Padua, Italy
| | - Valeria Garcia-Flores
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Percy Pacora
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Eunjung Jung
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Sonia S Hassan
- Perinatal Research Initiative in Maternal, Perinatal and Child Health, Wayne State University School of Medicine, Detroit, Michigan, USA.,Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Chaur-Dong Hsu
- Perinatal Research Initiative in Maternal, Perinatal and Child Health, Wayne State University School of Medicine, Detroit, Michigan, USA.,Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Kevin R Theis
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA. .,Perinatal Research Initiative in Maternal, Perinatal and Child Health, Wayne State University School of Medicine, Detroit, Michigan, USA. .,Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, Detroit, Michigan, USA.
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30
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Godoy-Vitorino F. Human microbial ecology and the rising new medicine. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:342. [PMID: 31475212 DOI: 10.21037/atm.2019.06.56] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The first life forms on earth were Prokaryotic, and the evolution of all Eukaryotic life occurred with the help of bacteria. Animal-associated microbiota also includes members of the archaea, fungi, protists, and viruses. The genomes of this host-associated microbial life are called the microbiome. Across the mammalian tree, microbiomes guarantee the development of immunity, physiology, and resistance to pathogens. In humans, all surfaces and cavities are colonized by a microbiome, maintained by a careful balance between the host response and its colonizers-thus humans are considered now supraorganisms. These microbiomes supply essential ecosystem services that benefit health through homeostasis, and the loss of the indigenous microbiota leads to dysbiosis, which can have significant consequences to disease. This educational review aims to describe the importance of human microbial ecology, explain the ecological terms applied to the study of the human microbiome, developments within the cutting-edge microbiome field, and implications to diagnostic and treatment.
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Affiliation(s)
- Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, PR, USA
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31
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Roldán Ahumada JA, Avendaño Garrido ML. A Commentary on Diversity Measures UniFrac in Very Small Sample Size. Evol Bioinform Online 2019; 15:1176934319843515. [PMID: 31040637 PMCID: PMC6482663 DOI: 10.1177/1176934319843515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 03/20/2019] [Indexed: 01/24/2023] Open
Abstract
In phylogenetic, the diversity measures as UniFrac, weighted UniFrac, and normalized weighted UniFrac are used to estimate the closeness between two samples of genetic material sequences. These measures are widely used in microbiology to compare microbial communities. Furthermore, when the sample size is large enough, very good results have been obtained experimentally. However, some authors do not suggest using them when the sample size is very small. Recently, it has been mentioned that the weighted UniFrac measure can be seen as the Kantorovich-Rubinstein metric between the corresponding empirical distributions of samples of genetic material. Also, it is well known that the Kantorovich-Rubinstein metric complies the metric definition. However, one of the main reasons to establish it is that the sample size is large enough. The goal of this article is to prove that the diversity measures UniFrac are not metrics when the sample size is very small, which justifies why it must not be used in that case, but yes the Kantorovich-Rubinstein metric.
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32
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Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D, Meiring TL. The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection. PAPILLOMAVIRUS RESEARCH 2019; 7:154-163. [PMID: 30986570 PMCID: PMC6475661 DOI: 10.1016/j.pvr.2019.04.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/02/2019] [Accepted: 04/06/2019] [Indexed: 12/14/2022]
Abstract
In this study we examined potential associations of HPV infection with the cervical microbiota. Cervical samples were collected from 87 HIV-seronegative reproductive-age Black South African women. Microbiota were characterized by Illumina sequencing of the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. Thirty seven (42.5%) and 30 (34.5%) of the women had prevalent HPV and high-risk (HR)-HPV, respectively. Only 23 women (26.4%) had cervical microbiota dominated by a single Lactobacillus species (L. crispatus (2/87 (2.3%)), L. jensenii (2/87 (2.3%)), and L. iners (19/87 (21.8%)). The majority of the women (56/87 (64.4%)) had diverse cervical microbiota consisting of mainly bacterial vaginosis-associated bacteria. The remaining women (8/87 (9.2%)) had microbiota dominated by Aerococcus, Streptococcus, Chlamydia or Corynebacterium. Women with HR-HPV had significantly higher relative abundances of Aerococcaceae, Pseudomonadaceae and Bifidobacteriaceae compared to those with low-risk (LR)-HPV or no HPV-infection (LDA score >2.0, p < 0.05, q < 0.2). Gardnerella, Sneathia, and Atopobium were also found at greater relative abundances in HR-HPV-infected women compared to those with low-risk (LR)-HPV or no HPV-infection (LDA score >2.0, p < 0.05), although the difference was not significant after FDR-adjustment (q > 0.2). Further investigations of the bacterial taxa significantly enriched in HR-HPV-infected women are warranted. Majority of participants (74%) had cervical microbiota not dominated by Lactobacillus. Lactobacillus was not enriched in HPV-negative women compared to HPV-positive women. There was no correlation between cervical microbiota diversity and HPV infection.
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Affiliation(s)
- Harris Onywera
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Anna-Lise Williamson
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa; SAMRC Gynaecological Cancer Research Centre, University of Cape Town, Cape Town, South Africa
| | - Zizipho Z A Mbulawa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa; SAMRC Gynaecological Cancer Research Centre, University of Cape Town, Cape Town, South Africa; Center for HIV & STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - David Coetzee
- Center for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Tracy L Meiring
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa.
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33
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Goldsmith DB, Pratte ZA, Kellogg CA, Snader SE, Sharp KH. Stability of temperate coral Astrangia poculata microbiome is reflected across different sequencing methodologies. AIMS Microbiol 2019; 5:62-76. [PMID: 31384703 PMCID: PMC6646935 DOI: 10.3934/microbiol.2019.1.62] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/21/2019] [Indexed: 02/01/2023] Open
Abstract
The microbiome of the temperate coral Astrangia poculata was first described in 2017 using next-generation Illumina sequencing to examine the coral's bacterial and archaeal associates across seasons and among hosts of differing symbiotic status. To assess the impact of methodology on the detectable diversity of the coral's microbiome, we obtained near full-length Sanger sequences from clone libraries constructed from a subset of the same A. poculata samples. Eight samples were analyzed: two sets of paired symbiotic (brown) and aposymbiotic (white) colonies collected in the fall (September) and two sets collected in the spring (April). Analysis of the Sanger sequences revealed that the microbiome of A. poculata exhibited a high level of richness; 806 OTUs were identified among 1390 bacterial sequences. While the Illumina study revealed that A. poculata's microbial communities did not significantly vary according to symbiotic state, but did vary by season, Sanger sequencing did not expose seasonal or symbiotic differences in the microbiomes. Proteobacteria dominated the microbiome, forming the majority (55% to 80%) of classifiable bacteria in every sample, and the five bacterial classes with the highest mean relative portion (5% to 35%) were the same as those determined by prior Illumina sequencing. Sanger sequencing also captured the same core taxa previously identified by next-generation sequencing. Alignment of all sequences and construction of a phylogenetic tree revealed that both sequencing methods provided similar portrayals of the phylogenetic diversity within A. poculata's bacterial associates. Consistent with previous findings, the results demonstrated that the Astrangia microbiome is stable notwithstanding the choice of sequencing method and the far fewer sequences generated by clone libraries (46 to 326 sequences per sample) compared to next-generation sequencing (3634 to 48481 sequences per sample). Moreover, the near-full length 16S rRNA sequences produced by this study are presented as a resource for the community studying this model system since they provide necessary information for designing primers and probes to further our understanding of this coral's microbiome.
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Affiliation(s)
- Dawn B Goldsmith
- St. Petersburg Coastal and Marine Science Center, U.S. Geological Survey, St. Petersburg, FL 33701, USA
| | - Zoe A Pratte
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Christina A Kellogg
- St. Petersburg Coastal and Marine Science Center, U.S. Geological Survey, St. Petersburg, FL 33701, USA
| | - Sara E Snader
- Cherokee Nation Technologies, contracted to U.S. Geological Survey, St. Petersburg, FL 33701, USA
| | - Koty H Sharp
- Department of Biology, Marine Biology and Environmental Science, Roger Williams University, Bristol, RI 02809, USA
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34
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Rosenbaum J, Usyk M, Chen Z, Zolnik CP, Jones HE, Waldron L, Dowd JB, Thorpe LE, Burk RD. Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota. Sci Rep 2019; 9:1531. [PMID: 30728424 PMCID: PMC6365504 DOI: 10.1038/s41598-018-38049-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
The objective of this study was to evaluate the most effective method of DNA extraction of oral mouthwash samples for use in microbiome studies that utilize next generation sequencing (NGS). Eight enzymatic and mechanical DNA extraction methods were tested. Extracted DNA was amplified using barcoded primers targeting the V6 variable region of the bacterial 16S rRNA gene and the ITS1 region of the fungal ribosomal gene cluster and sequenced using the Illumina NGS platform. Sequenced reads were analyzed using QIIME and R. The eight methods yielded significantly different quantities of DNA (p < 0.001), with the phenol-chloroform extraction method producing the highest total yield. There were no significant differences in observed bacterial or fungal Shannon diversity (p = 0.64, p = 0.93 respectively) by extraction method. Bray-Curtis beta-diversity did not demonstrate statistically significant differences between the eight extraction methods based on bacterial (R2 = 0.086, p = 1.00) and fungal (R2 = 0.039, p = 1.00) assays. No differences were seen between methods with or without bead-beating. These data indicate that choice of DNA extraction method affect total DNA recovery without significantly affecting the observed microbiome.
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MESH Headings
- Biodiversity
- DNA Barcoding, Taxonomic
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Fungal/analysis
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- DNA, Ribosomal Spacer/analysis
- DNA, Ribosomal Spacer/genetics
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Microbiota
- Mouth/microbiology
- Mycobiome
- Pilot Projects
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
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Affiliation(s)
- Jennifer Rosenbaum
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zigui Chen
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Christine P Zolnik
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Biology, Long Island University, Brooklyn, NY, USA
| | - Heidi E Jones
- CUNY Graduate School of Public Health and Health Policy, New York, NY, USA
| | - Levi Waldron
- CUNY Graduate School of Public Health and Health Policy, New York, NY, USA
| | - Jennifer B Dowd
- CUNY Graduate School of Public Health and Health Policy, New York, NY, USA
- Department of Global Health and Social Medicine, King's College London, London, UK
| | - Lorna E Thorpe
- CUNY Graduate School of Public Health and Health Policy, New York, NY, USA
- NYU School of Medicine, Department of Population Health, New York, NY, USA
| | - Robert D Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Departments of Obstetrics & Gynecology and Women's Health, Epidemiology and Population Health, and Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
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35
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Stern JM, Urban‐Maldonado M, Usyk M, Granja I, Schoenfeld D, Davies KP, Agalliu I, Asplin J, Burk R, Suadicani SO. Fecal transplant modifies urine chemistry risk factors for urinary stone disease. Physiol Rep 2019; 7:e14012. [PMID: 30789675 PMCID: PMC6383111 DOI: 10.14814/phy2.14012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/01/2019] [Accepted: 02/03/2019] [Indexed: 01/04/2023] Open
Abstract
Urinary stone disease (USD) is a major health concern. There is a need for new treatment modalities. Recently, our group provided evidence for an association between the GMB composition and USD. The accessibility of the Gut Microbiome (GMB) makes it an attractive target for investigation and therefore, in these studies we have evaluated the extent to which the whole gut microbial community in fecal transplants can affect urinary stone risk parameters in an animal model. Fresh fecal pellets were collected from Zucker lean rats, homogenized in PBS (100 mg/mL), filtered through a 70 μm strainer and then orally gavaged into C57BL/6NTac germ-free mice. Twenty-four hours urine collections and GMB analysis were performed over time for 1 month. Kidney and gut tissue were harvested from transplanted mice for western blot analysis of expression levels of the Slc26a6 transporter involved in oxalate balance. Urinary calcium decreased after fecal transplant by 55% (P < 0.001). Urinary oxalate levels were on average 24% lower than baseline levels (P < 0.001). Clostridiaceae family was negatively correlated with urinary oxalate at 4 weeks after transplant (r = -0.83, P < 0.01). There was a 0.6 unit average increase in urinary pH from a baseline of 5.85 (SE ± 0.028) to 6.49 (SE ± 0.04) (P < 0.001) after transplant. There was a concomitant 29% increase in gastrointestinal alkali absorption (P < 0.001) 4-weeks after fecal transplant. Slc26a6 expression increased by 90% in the cecum after transplant. Our results suggest that the gut microbiome may impact metabolism, alters urinary chemistry, and thereby may influence USD; the accessibility of the GMB can potentially be leveraged for therapeutic interventions.
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Affiliation(s)
- Joshua M. Stern
- Department of UrologyAlbert Einstein College of MedicineBronxNew York
| | | | - Mykhaylo Usyk
- Department of MicrobiologyAlbert Einstein College of MedicineBronxNew York
| | | | - Daniel Schoenfeld
- Department of UrologyAlbert Einstein College of MedicineBronxNew York
| | - Kelvin P. Davies
- Department of UrologyAlbert Einstein College of MedicineBronxNew York
| | - Ilir Agalliu
- Department of EpidemiologyAlbert Einstein College of MedicineBronxNew York
| | | | - Robert Burk
- Department of MicrobiologyAlbert Einstein College of MedicineBronxNew York
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36
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Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG, Blaser MJ. Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population. Front Microbiol 2018; 9:2533. [PMID: 30405584 PMCID: PMC6208322 DOI: 10.3389/fmicb.2018.02533] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/04/2018] [Indexed: 01/28/2023] Open
Abstract
The human cervicovaginal microbiota resides at an interface between the host and the environment and may affect susceptibility to disease. Puerto Rican women have high human papillomavirus (HPV) infection and cervical cancer rates. We hypothesized that the population structure of the cervicovaginal bacterial and fungal biota changed with cervical squamous intraepithelial lesions and HPV infections. DNA was extracted from cervix, introitus, and anal sites of 62 patients attending high-risk San Juan clinics. The 16S rRNA V4 region and ITS-2 fungal regions were amplified and sequenced using Illumina technology. HPV genotyping was determined by reverse hybridization with the HPV SPF10-LiPA25 kit. HPV prevalence was 84% of which ∼44% subjects were infected with high-risk HPV, ∼35% were co-infected with as many as 9 HPV types and ∼5% were infected with exclusively low-risk HPV types. HPV diversity did not change with cervical dysplasia. Cervical bacteria were more diverse in patients with CIN3 pre-cancerous lesions. We found enrichment of Atopobium vaginae and Gardnerella vaginalis in patients with CIN3 lesions. We found no significant bacterial biomarkers associated with HPV infections. Fungal diversity was significantly higher in cervical samples with high-risk HPV and introitus samples of patients with Atypical Squamous Cells of Undetermined Significance (ASCUS). Fungal biomarker signatures for vagina and cervix include Sporidiobolaceae and Sacharomyces for ASCUS, and Malassezia for high-risk HPV infections. Our combined data suggests that specific cervicovaginal bacterial and fungal populations are related to the host epithelial microenvironment, and could play roles in cervical dysplasia.
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Affiliation(s)
- Filipa Godoy-Vitorino
- Microbiome Lab, Department of Microbiology and Medical Zoology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, United States
- Microbial Ecology and Genomics Laboratory, Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, PR, United States
| | - Josefina Romaguera
- Department of Obstetrics and Gynecology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, United States
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Daniela Vargas-Robles
- Department of Biology, University of Puerto Rico, San Juan, PR, Puerto Rico
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, MPPS, Puerto Ayacucho, Venezuela
| | - Gilmary Ortiz-Morales
- Microbial Ecology and Genomics Laboratory, Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, PR, United States
| | - Frances Vázquez-Sánchez
- Microbial Ecology and Genomics Laboratory, Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, PR, United States
| | | | - Manuel de la Garza-Casillas
- Microbial Ecology and Genomics Laboratory, Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, PR, United States
| | - Magaly Martinez-Ferrer
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
- Department of Pharmaceutical Sciences, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, United States
| | | | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology and of Anthropology, Rutgers University, New Brunswick, NJ, United States
| | - Martin J. Blaser
- Department of Medicine and Department of Microbiology, School of Medicine, New York University, New York, NY, United States
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Chen Z, Yeoh YK, Hui M, Wong PY, Chan MCW, Ip M, Yu J, Burk RD, Chan FKL, Chan PKS. Diversity of macaque microbiota compared to the human counterparts. Sci Rep 2018; 8:15573. [PMID: 30349024 PMCID: PMC6197227 DOI: 10.1038/s41598-018-33950-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 10/10/2018] [Indexed: 02/08/2023] Open
Abstract
Studies on the microbial communities in non-human primate hosts provide unique insights in both evolution and function of microbes related to human health and diseases. Using 16S rRNA gene amplicon profiling, we examined the oral, anal and vaginal microbiota in a group of non-captive rhesus macaques (N = 116) and compared the compositions with the healthy communities from Human Microbiome Project. The macaque microbiota was dominated by Bacteroidetes, Firmicutes and Proteobacteria; however, there were marked differences in phylotypes enriched across body sites indicative of strong niche specialization. Compared to human gut microbiota where Bacteroides predominately enriched, the surveyed macaque anal community exhibited increased abundance of Prevotella. In contrast to the conserved human vaginal microbiota extremely dominated by Lactobacillus, the macaque vaginal microbial composition was highly diverse while lactobacilli were rare. A constant decrease of the vaginal microbiota diversity was observed among macaque samples from juvenile, adult without tubectomy, and adult with tubectomy, with the most notable distinction being the enrichment of Halomonas in juvenile and Saccharofermentans in contracepted adults. Both macaque and human oral microbiota were colonized with three most common oral bacterial genera: Streptococcus, Haemophilus and Veillonella, and shared relatively conserved communities to each other. A number of bacteria related to human pathogens were consistently detected in macaques. The findings delineate the range of structure and diversity of microbial communities in a wild macaque population, and enable the application of macaque as an animal model for future characterization of microbes in transmission, genomics and function.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Mamie Hui
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Po Yee Wong
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Martin C W Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Robert D Burk
- Departments of Pediatrics, Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics, Gynecology and Woman's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Francis K L Chan
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China. .,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.
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Murenzi G, Dusingize JC, Rurangwa T, Sinayobye JD, Munyaneza A, Murangwa A, Zawadi T, Hebert T, Mugenzi P, Adedimeji A, Mutesa L, Anastos K, Castle PE. Protocol for the study of cervical cancer screening technologies in HIV-infected women living in Rwanda. BMJ Open 2018; 8:e020432. [PMID: 30082342 PMCID: PMC6078254 DOI: 10.1136/bmjopen-2017-020432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 06/19/2018] [Accepted: 06/22/2018] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The optimal method(s) for screening HIV-infected women, especially for those living in sub-Saharan Africa, for cervical precancer and early cancer has yet to be established. METHODS AND ANALYSIS A convenience sample of >5000 Rwandan women, ages 30-54 years and living with HIV infection, is being consented and enroled into a cross-sectional study of cervical cancer screening strategies. Participants are completing an administered short risk factor questionnaire and being screened for high-risk human papillomavirus (hrHPV) using the Xpert HPV assay (Cepheid, Sunnyvale, California, USA), unaided visual inspection after acetic acid (VIA) and aided VIA using the Enhanced Visual Assessment (EVA) system (Mobile ODT, Tel Aviv, Israel). Women positive for hrHPV and/or by unaided VIA undergo colposcopy, which includes the collection of two cervical specimens prior to undergoing a four-quadrant microbiopsy protocol. The colposcopy-collected specimens are being tested by dual immunocytochemical staining for p16INK4a and Ki-67 (CINtec PLUS Cytology, Ventana, Tucson, Arizona, USA) and for E6 or E7 oncoprotein for 8 hrHPV genotypes (HPV16, 18, 31, 33, 35, 45, 52 and 58) using the next-generation AV Avantage hrHPV E6/E7 test (Arbor Vita Corporation, Freemont, California, USA). Women with a local pathology diagnosis of cervical intraepithelial neoplasia grade 2 (CIN2) or more severe (CIN2+) or pathology review diagnosis of CIN grade three or more severe (CIN3+) will receive treatment. Clinical performance and cost-effectiveness (eg, sensitivity, specificity and predictive values) of different screening strategies and algorithms will be evaluated. ETHICS AND DISSEMINATION The protocol was approved by local and institutional review boards for human subjects research. At the completion of the study, results will be disseminated to the scientific community through peer-reviewed publication and to the Rwandan stakeholders through an external advisory panel.
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Affiliation(s)
| | | | | | | | | | | | | | - Tiffany Hebert
- Albert Einstein College of Medicine, Bronx, New York, USA
| | | | | | - Leon Mutesa
- Rwanda Military Hospital, Kigali, Rwanda
- University of Rwanda, Kigali, Rwanda
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Crucitti T, Hardy L, van de Wijgert J, Agaba S, Buyze J, Kestelyn E, Delvaux T, Mwambarangwe L, De Baetselier I, Jespers V. Contraceptive rings promote vaginal lactobacilli in a high bacterial vaginosis prevalence population: A randomised, open-label longitudinal study in Rwandan women. PLoS One 2018; 13:e0201003. [PMID: 30036385 PMCID: PMC6056036 DOI: 10.1371/journal.pone.0201003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 07/04/2018] [Indexed: 12/12/2022] Open
Abstract
Background Hormonal contraception has been associated with a reduced risk of vaginal dysbiosis, which in turn has been associated with reduced prevalence of sexually transmitted infections (STIs), including HIV. Vaginal rings are used or developed as delivery systems for contraceptive hormones and antimicrobial drugs for STI and HIV prevention or treatment. We hypothesized that a contraceptive vaginal ring (CVR) containing oestrogen enhances a lactobacilli-dominated vaginal microbial community despite biomass accumulation on the CVR’s surface. Methods We enrolled 120 women for 12 weeks in an open-label NuvaRing® study at Rinda Ubuzima, Kigali, Rwanda. Vaginal and ring microbiota were assessed at baseline and each ring removal visit by Gram stain Nugent scoring (vaginal only), quantitative PCR for Lactobacillus species, Gardnerella vaginalis and Atopobium vaginae, and fluorescent in situ hybridization to visualize cell-adherent bacteria. Ring biomass was measured by crystal violet staining. Results Bacterial vaginosis (BV) prevalence was 48% at baseline. The mean Nugent score decreased significantly with ring use. The presence and mean log10 concentrations of Lactobacillus species in vaginal secretions increased significantly whereas those of G. vaginalis and presence of A. vaginae decreased significantly. Biomass accumulated on the CVRs with a species composition mirroring the vaginal microbiota. This ring biomass composition and optical density after crystal violet staining did not change significantly over time. Conclusions NuvaRing® promoted lactobacilli-dominated vaginal microbial communities in a population with high baseline BV prevalence despite the fact that biomass accumulated on the rings.
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Affiliation(s)
- Tania Crucitti
- Institute of Tropical Medicine, Antwerp, Belgium
- * E-mail:
| | | | | | | | | | - Evelyne Kestelyn
- University of Liverpool, Liverpool, United Kingdom
- Rinda Ubuzima, Kigali, Rwanda
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Nilyanimit P, Chansaenroj J, Poomipak W, Praianantathavorn K, Payungporn S, Poovorawan Y. Comparison of Four Human Papillomavirus Genotyping Methods: Next-generation Sequencing, INNO-LiPA, Electrochemical DNA Chip, and Nested-PCR. Ann Lab Med 2018; 38:139-146. [PMID: 29214758 PMCID: PMC5736673 DOI: 10.3343/alm.2018.38.2.139] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/09/2017] [Accepted: 11/02/2017] [Indexed: 11/19/2022] Open
Abstract
Background Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies. Methods Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS). Results Seven HPV genotypes (16, 18, 31, 33, 45, 56, and 58) were identified by all four methods. Nineteen HPV genotypes were detected by NGS, but not by nested-PCR, INNO-LiPA, or electrochemical DNA chip. Conclusions Although NGS is relatively expensive and complex, it may serve as a sensitive HPV genotyping method. Because of its highly sensitive detection of multiple HPV genotypes, NGS may serve as an alternative for diagnostic HPV genotyping in certain situations.
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Affiliation(s)
- Pornjarim Nilyanimit
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok
| | - Jira Chansaenroj
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok
| | - Witthaya Poomipak
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok
| | | | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok.
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Zhang C, Liu Y, Gao W, Pan Y, Gao Y, Shen J, Xiong H. The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia. Cancer Med 2018; 7:2172-2179. [PMID: 29608253 PMCID: PMC5943479 DOI: 10.1002/cam4.1471] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/19/2018] [Accepted: 03/06/2018] [Indexed: 12/31/2022] Open
Abstract
Cervical microbiota composition is associated with cervical HPV infection and CIN severity. Previous studies only assessed the total association between cervical microbiota and HPV infections or CINs, and yet no study reported the direct and indirect associations between cervical microbiota and CINs mediated by HPV infection, respectively. The aim of this study was to investigate the direct and indirect associations between microbiotas and CIN severity. Cervical microbiota of 126 women with CIN 1− (normal cytology and CIN 1) and 40 with CIN 2+ (CIN 2 and CIN 3) were analyzed using Illumina sequencing based on the 16S rRNA gene. HPV was detected using a highly sensitive PCR primer set (SPF1/GP6+). Indirect effects of Pseudomonas stutzeri, Bacteroides fragilis, Lactobacillus delbrueckii, Atopobium vaginae, and Streptococcus agalactiae mediated by HPV infection on CIN status were observed. The directions of the direct and the indirect associations between CIN status and Ps. stutzeri were opposite. The directions of the direct and the indirect associations between CIN status and A. vaginae were the same. B. fragilis, L. delbrueckii, and S. agalactiae only had indirect association with CIN status. In summary, our study provided suggestive evidence that some microbial populations could have direct or indirect effects mediated by affecting HPV infection on CIN progression. Besides HPV infection, microbial community composition possibly plays a role in cervical carcinogenesis.
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Affiliation(s)
- Chaoting Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Ying Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Weijiao Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gynecologic Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Yaqi Pan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Yunong Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gynecologic Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jing Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Core Laboratory, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Hongchao Xiong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
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Huang X, Li C, Li F, Zhao J, Wan X, Wang K. Cervicovaginal microbiota composition correlates with the acquisition of high-risk human papillomavirus types. Int J Cancer 2018; 143:621-634. [PMID: 29479697 DOI: 10.1002/ijc.31342] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/05/2018] [Accepted: 02/08/2018] [Indexed: 12/29/2022]
Abstract
High-risk (hr) human papillomavirus (HPV) infection is closely associated with the clinical conditions of both squamous intraepithelial lesions (SILs) and cervical carcinoma. However, it remains unclear what factors determine the type of hrHPV infection. Here, we have comprehensively investigated the bacterial composition of the cervicovaginal microbiota of 280 women infected with one type of hrHPV (HPV 16, 52 or 58) by the pyrosequencing of barcoded 16S rRNA genes. Differential microbiota composition was observed among various SIL groups and within the subgroups of each group. This result showed that it is not the microbiota diversity or the common microbiota, but rather agents that are specific to each SIL that might have a positive influence on the acquisition of hrHPV types, independent of abundance. Specifically, a composition of Oribacterium, Lachnobacterium and Thermus in the cervicovaginal microbiota is more likely to be associated with HPV 16, while a composition of Motilibacter in the cervicovaginal microbiota is more likely to be associated with HPV 52, and a composition of Litorilinea and Paludibaculum with a concomitant paucity of L. iners in the cervicovaginal microbiota is more likely to be associated with HPV 58. Furthermore, functional predictions regarding infectious diseases and cancer-related genes disclosed significant differences (p < 0.01) among the different (sub)groups. Our study provides an elucidation of the relationship between the composition of the cervicovaginal microbiota and the type of hrHPV acquired.
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Affiliation(s)
- Xiaojie Huang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Chao Li
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Fang Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Junwei Zhao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Xiaoping Wan
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Kai Wang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
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High Prevalence of Leptotrichia amnionii, Atopobium vaginae, Sneathia sanguinegens, and Factor 1 Microbes and Association of Spontaneous Abortion among Korean Women. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5435089. [PMID: 29479540 PMCID: PMC5745682 DOI: 10.1155/2017/5435089] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/09/2017] [Accepted: 10/22/2017] [Indexed: 01/01/2023]
Abstract
Objective. The purpose of this study was to (i) determine the cervical microbial composition in different abortion samples and to (ii) investigate the correlation between spontaneous abortion and cervical microbes in Korean women. Methods. We collected cervical swabs from women who had never undergone abortion (N = 36), had spontaneous abortion (N = 23), and had undergone induced abortion (N = 88) and subjected those samples to 16S rRNA pyrosequencing. Further, factor analysis and correlation between cervical microbiota and spontaneous abortion were evaluated by logistic regression analysis. Results. In spontaneous abortion women, 16 S rRNA gene sequences showed significant increases in Atopobium vaginae, Megasphaera spp., Gardnerella vaginalis, Leptotrichia amnionii, and Sneathia sanguinegens compared to women in nonabortion group. In multivariate logistic regression analysis, A. vaginae (OD = 11.27; 95% = 1.57–81), L. amnionii (OD = 11.47; 95% = 1.22–107.94), S. sanguinegens (OD = 6.89; 95% = 1.07–44.33), and factor 1 microbes (OD = 16.4; 95% = 1.88–42.5) were strongly associated with spontaneous abortion. Conclusions. This study showed a high prevalence of L. amnionii, A. vaginae, S. sanguinegens, and factor 1 microbes in spontaneous abortion and association with spontaneous abortion in Korean women.
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Del Vecchio F, Mastroiaco V, Di Marco A, Compagnoni C, Capece D, Zazzeroni F, Capalbo C, Alesse E, Tessitore A. Next-generation sequencing: recent applications to the analysis of colorectal cancer. J Transl Med 2017; 15:246. [PMID: 29221448 PMCID: PMC5723063 DOI: 10.1186/s12967-017-1353-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023] Open
Abstract
Since the establishment of the Sanger sequencing method, scientists around the world focused their efforts to progress in the field to produce the utmost technology. The introduction of next-generation sequencing (NGS) represents a revolutionary step and promises to lead to massive improvements in our understanding on the role of nucleic acids functions. Cancer research began to use this innovative and highly performing method, and interesting results started to appear in colorectal cancer (CRC) analysis. Several studies produced high-quality data in terms of mutation discovery, especially about actionable or less frequently mutated genes, epigenetics, transcriptomics. Analysis of results is unveiling relevant perspectives aiding to evaluate the response to therapies. Novel evidences have been presented also in other directions such as gut microbiota or CRC circulating tumor cells. However, despite its unquestioned potential, NGS poses some issues calling for additional studies. This review intends to offer a view of the state of the art of NGS applications to CRC through examination of the most important technologies and discussion of recent published results.
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Affiliation(s)
- Filippo Del Vecchio
- Division of Cancer Sciences, University of Southampton, Southampton, Hampshire, SO16 6YD UK
| | - Valentina Mastroiaco
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Antinisca Di Marco
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Daria Capece
- Department of Medicine, Centre for Cell Signaling and Inflammation, Imperial College London, London, W12 0NN UK
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, La Sapienza University, Rome, 00161 Italy
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
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Avilés-Jiménez F, Yu G, Torres-Poveda K, Madrid-Marina V, Torres J. On the Search to Elucidate the Role of Microbiota in the Genesis of Cancer: The Cases of Gastrointestinal and Cervical Cancer. Arch Med Res 2017; 48:754-765. [DOI: 10.1016/j.arcmed.2017.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/15/2017] [Indexed: 02/08/2023]
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Goldman DL, Chen Z, Shankar V, Tyberg M, Vicencio A, Burk R. Lower airway microbiota and mycobiota in children with severe asthma. J Allergy Clin Immunol 2017; 141:808-811.e7. [PMID: 29031597 DOI: 10.1016/j.jaci.2017.09.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/31/2017] [Accepted: 09/13/2017] [Indexed: 12/16/2022]
Affiliation(s)
- David L Goldman
- Department of Pediatrics, Children's Hospital at Montefiore, Bronx, NY; Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY.
| | - Zigui Chen
- Department of Microbiology, Chinese University of Hong Kong, Hong Kong, China
| | - Viswanathan Shankar
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
| | - Michael Tyberg
- Department of Pediatrics, Children's Hospital at Montefiore, Bronx, NY
| | - Alfin Vicencio
- Department of Pediatrics, the Cohen's Children Medical Center, Queens, NY
| | - Robert Burk
- Department of Pediatrics, Children's Hospital at Montefiore, Bronx, NY; Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
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Hugerth LW, Andersson AF. Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing. Front Microbiol 2017; 8:1561. [PMID: 28928718 PMCID: PMC5591341 DOI: 10.3389/fmicb.2017.01561] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 08/02/2017] [Indexed: 12/20/2022] Open
Abstract
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.
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Affiliation(s)
- Luisa W Hugerth
- Department of Molecular, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska InstitutetSolna, Sweden.,Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
| | - Anders F Andersson
- Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
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García-Velasco JA, Menabrito M, Catalán IB. What fertility specialists should know about the vaginal microbiome: a review. Reprod Biomed Online 2017; 35:103-112. [DOI: 10.1016/j.rbmo.2017.04.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/12/2022]
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Abstract
Accurate knowledge of the composition and ecology of the vaginal microbial environment in healthy women is necessary for understanding lactobacilli-dominated normal microbiota and the mechanisms by which it reduces disease risk. The vagina and its microbiota form a balanced ecosystem; any movement outside the normal range for this ecosystem of obligate and/or facultative microbes, termed dysbacteriosis, can lead to infection and disease. This review summarizes recent research on the vaginal ecosystem, the Lactobacillus species that dominate it, and the means by which they suppress the growth, development, and/or proliferation of pathogenic microbial species. Lactobacilli colonization is believed to be beneficial since it prevents other microorganisms from colonizing the vaginal epithelium via competitive adhesion, interactions with the local immunity and plasminogen-plasmin system, and the production of lactic acid, hydrogen peroxide, and antibacterial substances. In addition, lactobacilli also constitute an important part of the urogenital tract microbiota and the lactobacilli-dominated vaginal microbiome is a major determinant for female urogenital health.
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Affiliation(s)
- S Kovachev
- a Department of General and Oncogynecology , Military Medical Academy , Sofia , Bulgaria
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50
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Demkin VV, Koshechkin SI. Characterization of vaginal Lactobacillus species by rplK -based multiplex qPCR in Russian women. Anaerobe 2017; 47:1-7. [PMID: 28315382 DOI: 10.1016/j.anaerobe.2017.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/27/2017] [Accepted: 03/08/2017] [Indexed: 11/25/2022]
Abstract
We describe a multiplex qPCR assay for identification and quantitative assessment of a set of vaginal Lactobacillus species, including L. acidophilus, L. crispatus, L. gasseri, L. helveticus, L. iners, and L. jensenii. The assay extends the previously developed qPCR method for Lactobacillus detection and total quantification based on targeting the rplK gene. Both assays use only single pair of primers and a set of probes combined in three reactions, comprising a vaginal Lactobacillus diagnostic assay panel. The utility of the diagnostic panel was evaluated by analyzing of vaginal swab specimens from 145 patients with different status of vaginal health. Most frequently, only one Lactobacillus species was dominant (68,9%), mostly L. crispatus (18,6%) or L. iners (33,1%), but two or three Lactobacillus species were also being simultaneously detected (24,9%). The diagnostic panel will facilitate investigations of the role of Lactobacillus species in the health of the female reproductive system and promote studies of variability of the vaginal microbiota.
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Affiliation(s)
- Vladimir V Demkin
- Laboratory of Molecular Diagnostics, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow 123182, Russia.
| | - Stanislav I Koshechkin
- Laboratory of Molecular Diagnostics, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow 123182, Russia
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