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Moraes JGN, Gull T, Ericsson AC, Poock SE, Caldeira MO, Lucy MC. Establishment of the uterine microbiome following artificial insemination in virgin heifers. Front Microbiol 2024; 15:1385505. [PMID: 38903779 PMCID: PMC11188424 DOI: 10.3389/fmicb.2024.1385505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction The concept of a sterile uterus was challenged by recent studies that have described the microbiome of the virgin and pregnant uterus for species including humans and cattle. We designed two studies that tested whether the microbiome is introduced into the uterus when the virgin heifer is first inseminated and whether the origin of the microbiome is the vagina/cervix. Methods The uterine microbiome was measured immediately before and after an artificial insemination (AI; Study 1; n = 7 AI and n = 6 control) and 14 d after insemination (Study 2; n = 12 AI and n = 12 control) in AI and non-AI (control) Holstein heifers. A third study (Study 3; n = 5 Holstein heifers) that included additional negative controls was subsequently conducted to support the presence of a unique microbiome within the uterus despite the low microbial biomass and regardless of insemination. Traditional bacteriological culture was performed in addition to 16S rRNA gene sequencing on the same samples to determine whether there were viable organisms in addition to those detected based on DNA sequencing (16S rRNA gene sequence). Results and discussion Inseminating a heifer did not lead to a large change in the microbiome when assessed by traditional methods of bacterial culture or metataxonomic (16S rRNA gene) sequencing (results of Studies 1 and 2). Very few bacteria were cultured from the body or horn of the uterus regardless of whether an AI was or was not (negative control) performed. The cultured bacterial genera (e.g., Bacillus, Corynebacterium, Cutibacterium, Micrococcus, Staphylococcus, and Streptococcus) were typical of those found in the soil, environment, skin, mucous membranes, and urogenital tract of animals. Metataxonomic sequencing of 16S rRNA gene generated a large number of amplicon sequence variants (ASV), but these larger datasets that were based on DNA sequencing did not consistently demonstrate an effect of AI on the abundance of ASVs across all uterine locations compared with the external surface of the tract (e.g., perimetrium; positive control samples for environment contamination during slaughter and collection). Major genera identified by 16S rRNA gene sequencing overlapped with those identified with bacterial culture and included Cutibacterium, Staphylococcus, and Streptococcus.
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Affiliation(s)
- Joao G. N. Moraes
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Tamara Gull
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Aaron C. Ericsson
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Scott E. Poock
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Monica O. Caldeira
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Matthew C. Lucy
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
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Moraes JGN, Gull T, Ericsson AC, Poock SE, Caldeira MO, Lucy MC. The microbiome of the pregnant uterus in Holstein dairy heifers and cows assessed by bacterial culture and 16S ribosomal RNA gene sequencing. Front Microbiol 2024; 15:1385497. [PMID: 38812678 PMCID: PMC11134370 DOI: 10.3389/fmicb.2024.1385497] [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: 02/12/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction The possibility that there is a resident and stable commensal microbiome within the pregnant uterus has been supported and refuted by a series of recent studies. One element of most of the initial studies was that they were based primarily on 16S rRNA gene sequencing from bacteria. To account for this limitation, the current study performed both bacterial culture and 16S rRNA gene sequencing in a side-by-side manner (e.g., same tissues isolated from the same animal). Methods The uteruses of 10 mid-pregnant (156 ± 5 d of gestation) Holstein heifers and cows were collected following slaughter. The external surface of the reproductive tract (positive control for contamination during tissue collection) as well as tissues within the pregnant uterus (placentome, inter-cotyledonary placenta, inter-caruncular endometrium, amnionic fluid, allantoic fluid, fetal abomasum content, and fetal meconium) were sampled for bacterial culture and 16S rRNA gene sequencing. Results There were 87 unique bacterial species cultured from the external surface of the pregnant reproductive tract (contamination control) and 12 bacterial species cultured from pregnancy tissues. Six out of 10 cattle (60%) exhibited bacterial growth in at least one location within the pregnant uterus. For the metataxonomic results (16S rRNA gene sequencing), a low targeted microbial biomass was identified. Analyses of the detected amplicon sequence variants (ASV) revealed that there were: (1) genera that were prevalent on both the external surface and within the pregnant uterus; (2) genera that were prevalent on the external surface but either not detected or had very low prevalence within the pregnant uterus; and (3) genera that were either not detected or had low prevalence on the external surface but found with relatively high prevalence within the pregnant uterus. Conclusion There are a small number of viable bacteria in the pregnant uterus. The 16S rRNA gene sequencing detected a microbial community within the pregnant uterus but with a low biomass. These results are consistent with recent studies of the pregnant bovine uterus and leave open the question of whether there is adequate microbial mass to significantly affect the biology of the normal healthy bovine pregnancy.
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Affiliation(s)
- Joao G. N. Moraes
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Tamara Gull
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Aaron C. Ericsson
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Scott E. Poock
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Monica O. Caldeira
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Matthew C. Lucy
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
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Yu B, Liu C, Proll SC, Manhardt E, Liang S, Srinivasan S, Swisher E, Fredricks DN. Identification of fallopian tube microbiota and its association with ovarian cancer. eLife 2024; 12:RP89830. [PMID: 38451065 PMCID: PMC10942644 DOI: 10.7554/elife.89830] [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] [Indexed: 03/08/2024] Open
Abstract
Investigating the human fallopian tube (FT) microbiota has significant implications for understanding the pathogenesis of ovarian cancer (OC). In this large prospective study, we collected swabs intraoperatively from the FT and other surgical sites as controls to profile the microbiota in the FT and to assess its relationship with OC. Eighty-one OC and 106 non-cancer patients were enrolled and 1001 swabs were processed for 16S rRNA gene PCR and sequencing. We identified 84 bacterial species that may represent the FT microbiota and found a clear shift in the microbiota of the OC patients when compared to the non-cancer patients. Of the top 20 species that were most prevalent in the FT of OC patients, 60% were bacteria that predominantly reside in the gastrointestinal tract, while 30% normally reside in the mouth. Serous carcinoma had higher prevalence of almost all 84 FT bacterial species compared to the other OC subtypes. The clear shift in the FT microbiota in OC patients establishes the scientific foundation for future investigation into the role of these bacteria in the pathogenesis of OC.
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Affiliation(s)
- Bo Yu
- Department of Obstetrics and GynecologyStanfordUnited States
- Stanford Maternal & Child Health Research Institute, Stanford University School of MedicineStanfordUnited States
| | - Congzhou Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Sean C Proll
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Enna Manhardt
- Department of Obstetrics and Gynecology, University of WashingtonSeattleUnited States
| | - Shuying Liang
- Department of Obstetrics and Gynecology, University of WashingtonSeattleUnited States
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Elizabeth Swisher
- Department of Obstetrics and Gynecology, University of WashingtonSeattleUnited States
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer CenterSeattleUnited States
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Gao X, Louwers YV, Laven JSE, Schoenmakers S. Clinical Relevance of Vaginal and Endometrial Microbiome Investigation in Women with Repeated Implantation Failure and Recurrent Pregnancy Loss. Int J Mol Sci 2024; 25:622. [PMID: 38203793 PMCID: PMC10779912 DOI: 10.3390/ijms25010622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Recent studies have investigated if and how the vaginal and endometrial microbiome might affect endometrial receptivity and reproductive health. Although there is no consensus on the existence of a core uterine microbiome yet, evidence shows that the dominance of Lactobacillus spp. in the female reproductive tract is generally associated with eubiosis and improved chances of successful implantation and an ongoing pregnancy. Conversely, vaginal and endometrial dysbiosis can cause local inflammation and an increase of pro-inflammatory cytokines, compromising the integrity and receptivity of the endometrial mucosa and potentially hampering successful embryonic implantation. This review provides a critical appraisal of the influence of the vaginal and endometrial microbiome as parts of the female reproductive tract on fertility outcomes, focusing on repeated implantation failure (RIF) and recurrent pregnancy loss (RPL). It seems that RIF as well as RPL are both associated with an increase in microbiome diversity and a loss of Lactobacillus dominance in the lower female reproductive system.
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Affiliation(s)
- Xushan Gao
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Yvonne V. Louwers
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Joop S. E. Laven
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Sam Schoenmakers
- Division of Obstetrics and Fetal Medicine, Department of Obstetrics and Gynecology, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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Çömlekcioğlu U, Jezierska S, Opsomer G, Pascottini OB. Uterine microbial ecology and disease in cattle: A review. Theriogenology 2024; 213:66-78. [PMID: 37804686 DOI: 10.1016/j.theriogenology.2023.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/09/2023]
Abstract
Due to the critical contribution of the uterine-associated microbiota in reproductive health, physiology, and performance, culture-independent methods have been increasingly employed to unravel key aspects of microbial ecology in the uterus of cattle. Nowadays, we know that bacterial diversity is crucial to maintain uterine health, however, there is still no consensus on the exact composition of a healthy uterine microbiota (or eubiosis). Generally, loss of bacterial diversity (or dysbiosis) contributes to the development of uterine infections, associated with increased relative abundances of Bacteroides, Fusobacterium, Trueperella, and Porphyromonas. Uterine infections are highly prevalent and gravely influence the profitability of cattle operations, animal welfare, and public health. Thus, understanding the dynamics of uterine microbial ecology is essential to develop effective strategies focused on preventing and mitigating the adverse effects of uterine dysbiosis as well as assisting in the process of restoring the core, healthy uterine microbiota. The aim of this review is to summarize research conducted in the microbial ecology of bovine uteri. We discuss the origin of the uterine microflora of healthy cows and the factors influencing its composition. In addition, we review the biology of specific pathogens that are known to increase in abundance during the occurrence of uterine disease. Lastly, we provide an overview of the bacterial biofilm in the bovine endometrium, and we briefly summarize the rationale for the use of probiotics to prevent uterine disease in cattle.
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Affiliation(s)
- Uğur Çömlekcioğlu
- Department of Biology, Osmaniye Korkut Ata University, 8000, Osmaniye, Turkiye; Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, 9820, Merelbeke, Belgium.
| | | | - Geert Opsomer
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Osvaldo Bogado Pascottini
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, 9820, Merelbeke, Belgium.
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Yu B, Liu C, Proll S, Mannhardt E, Liang S, Srinivasan S, Swisher E, Fredricks DN. Identification of fallopian tube microbiota and its association with ovarian cancer: a prospective study of intraoperative swab collections from 187 patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.28.23291999. [PMID: 37425928 PMCID: PMC10327289 DOI: 10.1101/2023.06.28.23291999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Investigating the human fallopian tube (FT) microbiota has significant implications for understanding the pathogenesis of ovarian cancer (OC). In this large prospective study, we collected swabs intraoperatively from the FT and other surgical sites as controls to profile the microbiota in the FT and to assess its relationship with OC. 81 OC and 106 non-cancer patients were enrolled and 1001 swabs were processed for 16S rRNA gene PCR and sequencing. We identified 84 bacterial species that may represent the FT microbiota and found a clear shift in the microbiota of the OC patients when compared to the non-cancer patients. Of the top 20 species that were most prevalent in the FT of OC patients, 60% were bacteria that predominantly reside in the gastrointestinal tract, while 30% normally reside in the mouth. Serous carcinoma had higher prevalence of almost all 84 FT bacterial species compared to the other OC subtypes. The clear shift in the FT microbiota in OC patients establishes the scientific foundation for future investigation into the role of these bacteria in the pathogenesis of ovarian cancer. .
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Brouns F, Van Haaps A, Keszthelyi D, Venema K, Bongers M, Maas J, Mijatovic V. Diet associations in endometriosis: a critical narrative assessment with special reference to gluten. Front Nutr 2023; 10:1166929. [PMID: 37731404 PMCID: PMC10507348 DOI: 10.3389/fnut.2023.1166929] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
Endometriosis is characterized by the presence of endometrium-like tissue outside the uterus. The etiology remains largely unknown. Despite adequate treatment, patients can still experience symptoms or side effects resulting in therapy incompliance and in self-management strategies such as dietary measures is increasing. A gluten free diet is thought to be contributory in reducing endometriosis-related pain, thereby optimizing quality of life. However, data is conflicting and currently provides no evidence for causality. This narrative review aims to put the effect of dietary self-management strategies on endometriosis in a balanced perspective, especially the effect of gluten and a gluten free diet. Several studies have found a strong overlap in symptoms, metabolic and immune responses associated with endometriosis and those associated with celiac disease, ulcerative colitis, Crohn's disease, irritable bowel syndrome and non-celiac wheat sensitivity. However, it remains unclear whether these diseases and/or disorders are causal to an increased risk of endometriosis. Some studies have found a positive effect on the risk of endometriosis, endometriosis-related symptoms and quality of life (QoL) when women either avoided certain nutrients or foods, or applied a specific nutrient supplementation. This includes the avoidance of red meat and omega-3, an increasing intake of foods rich in anti-oxidants, micronutrients and dietary fibers (e.g., fruit, vegetables) and the appliance of a gluten free diet. However, data from the available studies were generally graded of low quality and it was noted that placebo and/or nocebo effects influenced the reported positive effects. In addition, such effects were no longer seen when adjusting for confounders such as overweight, when a translation was made from in vitro to in vivo, or when the nutrients were not supplemented as isolated sources but as part of a mixed daily diet. Finally, some studies showed that long-term adherence to a gluten free diet is often associated with an impaired diet quality and nutrient intake, leading to negative health outcomes and reduced QoL. Concluding, scientific evidence on the efficacy of dietary interventions on well-defined clinical endpoints of endometriosis is lacking and recommending a gluten free diet to women solely diagnosed with endometriosis should therefore not be advised.
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Affiliation(s)
- Fred Brouns
- Department of Human Biology, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Annelotte Van Haaps
- Endometriosis Center, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, Netherlands
| | - Daniel Keszthelyi
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University, Maastricht, Netherlands
| | - Marlies Bongers
- Department of Obstetrics and Gynecology, Máxima Medical Center, Veldhoven, Netherlands
- Grow-School of Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| | - Jacques Maas
- Grow-School of Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
- Department of Obstetrics and Gynaecology MUMC+, Maastricht, Netherlands
| | - Velja Mijatovic
- Endometriosis Center, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam, Netherlands
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Menon R, Khanipov K, Radnaa E, Ganguly E, Bento GFC, Urrabaz-Garza R, Kammala AK, Yaklic J, Pyles R, Golovko G, Tantengco OAG. Amplification of microbial DNA from bacterial extracellular vesicles from human placenta. Front Microbiol 2023; 14:1213234. [PMID: 37520380 PMCID: PMC10374210 DOI: 10.3389/fmicb.2023.1213234] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction The placenta is essential for fetal growth and survival and maintaining a successful pregnancy. The sterility of the placenta has been challenged recently; however, the presence of a placental microbiome has been controversial. We tested the hypothesis that the bacterial extracellular vesicles (BEVs) from Gram-negative bacteria as an alternate source of microbial DNA, regardless of the existence of a microbial community in the placenta. Methods Placentae from the term, not in labor Cesareans deliveries, were used for this study, and placental specimens were sampled randomly from the fetal side. We developed a protocol for the isolation of BEVs from human tissues and this is the first study to isolate the BEVs from human tissue and characterize them. Results The median size of BEVs was 130-140 nm, and the mean concentration was 1.8-5.5 × 1010 BEVs/g of the wet placenta. BEVs are spherical and contain LPS and ompA. Western blots further confirmed ompA but not human EVs markers ALIX confirming the purity of preparations. Taxonomic abundance profiles showed BEV sequence reads above the levels of the negative controls (all reagent controls). In contrast, the sequence reads in the same placenta were substantially low, indicating nothing beyond contamination (low biomass). Alpha-diversity showed the number of detected genera was significantly higher in the BEVs than placenta, suggesting BEVs as a likely source of microbial DNA. Beta-diversity further showed significant overlap in the microbiome between BEV and the placenta, confirming that BEVs in the placenta are likely a source of microbial DNA in the placenta. Uptake studies localized BEVs in maternal (decidual) and placental cells (cytotrophoblast), confirming their ability to enter these cells. Lastly, BEVs significantly increased inflammatory cytokine production in THP-1 macrophages in a high-dose group but not in the placental or decidual cells. Conclusion We conclude that the BEVs are normal constituents during pregnancy and likely reach the placenta through hematogenous spread from maternal body sites that harbor microbiome. Their presence may result in a low-grade localized inflammation to prime an antigen response in the placenta; however, insufficient to cause a fetal inflammatory response and adverse pregnancy events. This study suggests that BEVs can confound placental microbiome studies, but their low biomass in the placenta is unlikely to have any immunologic impact.
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Affiliation(s)
- Ramkumar Menon
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Enkhtuya Radnaa
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Esha Ganguly
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Giovana Fernanda Cosi Bento
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Rheanna Urrabaz-Garza
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Ananth Kumar Kammala
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Jerome Yaklic
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Richard Pyles
- Department of Pediatrics, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - George Golovko
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Ourlad Alzeus G. Tantengco
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
- Department of Physiology, College of Medicine, University of the Philippines Manila, Manila, Philippines
- Department of Biology, College of Science, De La Salle University, Manila, Philippines
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Hugon AM, Golos TG. Non-human primate models for understanding the impact of the microbiome on pregnancy and the female reproductive tract†. Biol Reprod 2023; 109:1-16. [PMID: 37040316 PMCID: PMC10344604 DOI: 10.1093/biolre/ioad042] [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: 11/28/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
The microbiome has been shown, or implicated to be involved, in multiple facets of human health and disease, including not only gastrointestinal health but also metabolism, immunity, and neurology. Although the predominant focus of microbiome research has been on the gut, other microbial communities such as the vaginal or cervical microbiome are likely involved in physiological homeostasis. Emerging studies also aim to understand the role of different microbial niches, such as the endometrial or placental microbial communities, on the physiology and pathophysiology of reproduction, including their impact on reproductive success and the etiology of adverse pregnancy outcomes (APOs). The study of the microbiome during pregnancy, specifically how changes in maternal microbial communities can lead to dysfunction and disease, can advance the understanding of reproductive health and the etiology of APOs. In this review, we will discuss the current state of non-human primate (NHP) reproductive microbiome research, highlight the progress with NHP models of reproduction, and the diagnostic potential of microbial alterations in a clinical setting to promote pregnancy health. NHP reproductive biology studies have the potential to expand the knowledge and understanding of female reproductive tract microbial communities and host-microbe or microbe-microbe interactions associated with reproductive health through sequencing and analysis. Furthermore, in this review, we aim to demonstrate that macaques are uniquely suited as high-fidelity models of human female reproductive pathology.
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Affiliation(s)
- Anna Marie Hugon
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thaddeus G Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, USA
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Canha-Gouveia A, Pérez-Prieto I, Rodríguez CM, Escamez T, Leonés-Baños I, Salas-Espejo E, Prieto-Sánchez MT, Sánchez-Ferrer ML, Coy P, Altmäe S. The female upper reproductive tract harbors endogenous microbial profiles. Front Endocrinol (Lausanne) 2023; 14:1096050. [PMID: 37415669 PMCID: PMC10321600 DOI: 10.3389/fendo.2023.1096050] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/26/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction The female reproductive tract harbours unique microbial communities (known as microbiota) which have been associated with reproductive functions in health and disease. While endometrial microbiome studies have shown that the uterus possesses higher bacterial diversity and richness compared to the vagina, the knowledge regarding the composition of the Fallopian tubes (FT) is lacking, especially in fertile women without any underlying conditions. Methods To address this gap, our study included 19 patients who underwent abdominal hysterectomy for benign uterine pathology, and 5 women who underwent tubal ligation as a permanent contraceptive method at Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA). We analyzed the microbiome of samples collected from the FT and endometrium using 16S rRNA gene sequencing. Results Our findings revealed distinct microbiome profiles in the endometrial and FT samples, indicating that the upper reproductive tract harbors an endogenous microbiome. However, these two sites also shared some similarities, with 69% of the detected taxa Being common to both. Interestingly, we identified seventeen bacterial taxa exclusively present in the FT samples, including the genera Enhydrobacter, Granulicatella, Haemophilus, Rhizobium, Alistipes, and Paracoccus, among others. On the other hand, 10 bacterial taxa were only found in the endometrium, including the genera Klebsiella, Olsenella, Oscillibacter and Veillonella (FDR <0.05). Furthermore, our study highlighted the influence of the endometrial collection method on the findings. Samples obtained transcervically showed a dominance of the genus Lactobacillus, which may indicate potential vaginal contamination. In contrast, uterine samples obtained through hysterescopy revealed higher abundance of the genera Acinetobacter, Arthrobacter, Coprococcus, Methylobacterium, Prevotella, Roseburia, Staphylococcus, and Streptococcus. Discussion Although the upper reproductive tract appears to have a low microbial biomass, our results suggest that the endometrial and FT microbiome is unique to each individual. In fact, samples obtained from the same individual showed more microbial similarity between the endometrium and FT compared to samples from different women. Understanding the composition of the female upper reproductive microbiome provides valuable insights into the natural microenvironment where processes such as oocyte fertilization, embryo development and implantation occur. This knowledge can improve in vitro fertilization and embryo culture conditions for the treatment of infertility.
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Affiliation(s)
- Analuce Canha-Gouveia
- Department of Physiology, Faculty of Veterinary, University of Murcia, Murcia, Spain
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital "Virgen de la Arrixaca", Murcia, Spain
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Spain
| | - Inmaculada Pérez-Prieto
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Carmen Martínez Rodríguez
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital "Virgen de la Arrixaca", Murcia, Spain
- Genomics Unit, Biomedical Research Institute of Murcia (IMIB)-Arrixaca, Murcia, Spain
| | - Teresa Escamez
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital "Virgen de la Arrixaca", Murcia, Spain
- BiobancMur-Nodo 1, Biomedical Research Institute of Murcia (IMIB)-Arrixaca, Murcia, Spain
- Spanish Biobank Platform, Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Irene Leonés-Baños
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Spain
| | - Eduardo Salas-Espejo
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Spain
| | - Maria Teresa Prieto-Sánchez
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital "Virgen de la Arrixaca", Murcia, Spain
- Department of Obstetrics & Gynecology, “Virgen de la Arrixaca” University Clinical Hospital, Murcia, Spain
| | - Maria Luisa Sánchez-Ferrer
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital "Virgen de la Arrixaca", Murcia, Spain
- Department of Obstetrics & Gynecology, “Virgen de la Arrixaca” University Clinical Hospital, Murcia, Spain
| | - Pilar Coy
- Department of Physiology, Faculty of Veterinary, University of Murcia, Murcia, Spain
- Biomedical Research Institute of Murcia (IMIB-Arrixaca), University Clinical Hospital "Virgen de la Arrixaca", Murcia, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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11
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Zuber A, Peric A, Pluchino N, Baud D, Stojanov M. Human Male Genital Tract Microbiota. Int J Mol Sci 2023; 24:ijms24086939. [PMID: 37108103 PMCID: PMC10139050 DOI: 10.3390/ijms24086939] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The human body is vastly colonised by microorganisms, whose impact on health is increasingly recognised. The human genital tract hosts a diverse microbiota, and an increasing number of studies on the male genital tract microbiota suggest that bacteria have a role in male infertility and pathological conditions, such as prostate cancer. Nevertheless, this research field remains understudied. The study of bacterial colonisation of the male genital tract is highly impacted by the invasive nature of sampling and the low abundance of the microbiota. Therefore, most studies relied on the analysis of semen microbiota to describe the colonisation of the male genital tract (MGT), which was thought to be sterile. The aim of this narrative review is to present the results of studies that used next-generation sequencing (NGS) to profile the bacterial colonisation patterns of different male genital tract anatomical compartments and critically highlight their findings and their weaknesses. Moreover, we identified potential research axes that may be crucial for our understanding of the male genital tract microbiota and its impact on male infertility and pathophysiology.
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Affiliation(s)
- Arnaud Zuber
- Materno-fetal and Obstetrics Research Unit, Department Woman-Mother-Child, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Adriana Peric
- 360° Fertility Center Zurich, 8702 Zollikon, Switzerland
| | - Nicola Pluchino
- Fertility Medicine and Gynaecological Endocrinology Unit, Department Woman-Mother-Child, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - David Baud
- Materno-fetal and Obstetrics Research Unit, Department Woman-Mother-Child, Lausanne University Hospital, 1011 Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, 1011 Lausanne, Switzerland
| | - Milos Stojanov
- Materno-fetal and Obstetrics Research Unit, Department Woman-Mother-Child, Lausanne University Hospital, 1011 Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, 1011 Lausanne, Switzerland
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12
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Panzer JJ, Romero R, Greenberg JM, Winters AD, Galaz J, Gomez-Lopez N, Theis KR. Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets. BMC Microbiol 2023; 23:76. [PMID: 36934229 PMCID: PMC10024458 DOI: 10.1186/s12866-023-02764-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/10/2023] [Indexed: 03/20/2023] Open
Abstract
The existence of a placental microbiota is debated. The human placenta has historically been considered sterile and microbial colonization was associated with adverse pregnancy outcomes. Yet, recent DNA sequencing investigations reported a microbiota in typical human term placentas. However, this detected microbiota could represent background DNA or delivery-associated contamination. Using fifteen publicly available 16S rRNA gene datasets, existing data were uniformly re-analyzed with DADA2 to maximize comparability. While Amplicon Sequence Variants (ASVs) identified as Lactobacillus, a typical vaginal bacterium, were highly abundant and prevalent across studies, this prevalence disappeared after applying likely DNA contaminant removal to placentas from term cesarean deliveries. A six-study sub-analysis targeting the 16S rRNA gene V4 hypervariable region demonstrated that bacterial profiles of placental samples and technical controls share principal bacterial ASVs and that placental samples clustered primarily by study origin and mode of delivery. Contemporary DNA-based evidence does not support the existence of a placental microbiota.ImportanceEarly-gestational microbial influences on human development are unclear. By applying DNA sequencing technologies to placental tissue, bacterial DNA signals were observed, leading some to conclude that a live bacterial placental microbiome exists in typical term pregnancy. However, the low-biomass nature of the proposed microbiome and high sensitivity of current DNA sequencing technologies indicate that the signal may alternatively derive from environmental or delivery-associated bacterial DNA contamination. Here we address these alternatives with a re-analysis of 16S rRNA gene sequencing data from 15 publicly available placental datasets. After identical DADA2 pipeline processing of the raw data, subanalyses were performed to control for mode of delivery and environmental DNA contamination. Both environment and mode of delivery profoundly influenced the bacterial DNA signal from term-delivered placentas. Aside from these contamination-associated signals, consistency was lacking across studies. Thus, placentas delivered at term are unlikely to be the original source of observed bacterial DNA signals.
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Affiliation(s)
- Jonathan J Panzer
- Pregnancy 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, Detroit, MI, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Roberto Romero
- Pregnancy 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, Detroit, MI, 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.
| | - Jonathan M Greenberg
- Pregnancy 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, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Andrew D Winters
- Pregnancy 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, Detroit, MI, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jose Galaz
- Pregnancy 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, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Nardhy Gomez-Lopez
- Pregnancy 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, Detroit, MI, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Kevin R Theis
- Pregnancy 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, Detroit, MI, USA.
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA.
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA.
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13
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Lietaer L, Pascottini OB, Lacoere T, Kerckhof FM, Martens A, Van de Wiele T, Opsomer G. Studying the pre-implantation uterine microbiota in cattle using transabdominal laparoscopic low-volume lavage: Aiming for zero-contamination. J Microbiol Methods 2023; 205:106664. [PMID: 36587901 DOI: 10.1016/j.mimet.2022.106664] [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: 11/23/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Recent studies have suggested that bacteria associated with the female reproductive tract - the uterine microbiota - may be important for reproductive health and pregnancy success. Therefore, uterine microbiome research gained much interest in the last few years. However, it is challenging to study late postpartum uterine samples, since they hold a low microbial biomass. Next-generation sequencing techniques are very sensitive for microbial identification, but they cannot make a distinction between actual microbiota and contaminant bacteria or their DNA. Our aim was to test a new method to sample the bovine uterine lumen in vivo, while minimizing the risk of cross-contamination. In order to evaluate this method, we performed a descriptive assessment of the microbial composition of the obtained samples. Transabdominal, laparoscopic sampling of the uterine lumen was conducted in five Holstein-Friesian cows. Uterine fluid from the uterine horns was collected by low-volume lavage. DNA from the samples was extracted using two different DNA extraction methods, and negative controls (sampling blank controls and DNA extraction blank controls) were included. Bacteria were identified using 16S rRNA gene amplicon sequencing. In this proof-of-concept study, no evidence for authentically present uterine microbiota could be found. During laparoscopic sampling, some practical challenges were encountered, and the reliability of low-volume-lavage for the collection of a low microbial biomass could be questioned. By comparing two DNA extraction methods, a significant contamination background could be noticed originating from the DNA extraction kits.
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Affiliation(s)
- Leen Lietaer
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Osvaldo Bogado Pascottini
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium; Department of Veterinary Sciences, Laboratory of Veterinary Physiology and Biochemistry, University of Antwerp, Wilrijk, Belgium.
| | - Tim Lacoere
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology, and Technology (CMET), Ghent University, Ghent, Belgium
| | - Frederiek-Maarten Kerckhof
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology, and Technology (CMET), Ghent University, Ghent, Belgium
| | - Ann Martens
- Department of Large Animal Surgery, Anesthesia and Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Tom Van de Wiele
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology, and Technology (CMET), Ghent University, Ghent, Belgium
| | - Geert Opsomer
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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14
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Miao B, Liu Y, Yang R, Feng X, Liu F, Cao P, Dai Q, Ping W, Liu Y, Fu Q. Assessment of contaminants associated with gold-standard ancient DNA protocols. Sci Bull (Beijing) 2023; 68:5-9. [PMID: 36610858 DOI: 10.1016/j.scib.2022.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Bo Miao
- College of Life Sciences, Northwest University, Xi'an 710069, China; Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yalin Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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15
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Liu Y, Elworth RAL, Jochum MD, Aagaard KM, Treangen TJ. De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee. Nat Commun 2022; 13:6799. [PMID: 36357382 PMCID: PMC9649624 DOI: 10.1038/s41467-022-34409-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 10/25/2022] [Indexed: 11/12/2022] Open
Abstract
Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low-biomass environments. Contamination from DNA extraction kits or sampling lab environments leaves taxonomic "bread crumbs" across multiple distinct sample types. Here we describe Squeegee, a de novo contamination detection tool that is based upon this principle, allowing the detection of microbial contaminants when negative controls are unavailable. On the low-biomass samples, we compare Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers putative contaminants. We analyze samples of varying biomass from the Human Microbiome Project and identify likely, previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision and thus represents a computational approach for contaminant detection when negative controls are unavailable.
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Affiliation(s)
- Yunxi Liu
- Rice University, Department of Computer Science, Houston, TX, 77005, USA
| | - R A Leo Elworth
- Rice University, Department of Computer Science, Houston, TX, 77005, USA
| | - Michael D Jochum
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
| | - Kjersti M Aagaard
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
| | - Todd J Treangen
- Rice University, Department of Computer Science, Houston, TX, 77005, USA.
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16
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Salmeri N, Carbone IF, Cavoretto PI, Farina A, Morano D. Epigenetics Beyond Fetal Growth Restriction: A Comprehensive Overview. Mol Diagn Ther 2022; 26:607-626. [PMID: 36028645 DOI: 10.1007/s40291-022-00611-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2022] [Indexed: 12/30/2022]
Abstract
Fetal growth restriction is a pathological condition occurring when the fetus does not reach the genetically determined growth potential. The etiology of fetal growth restriction is expected to be multifactorial and include fetal, maternal, and placental factors, the latter being the most frequent cause of isolated fetal growth restriction. Severe fetal growth restriction has been related to both an increased risk of perinatal morbidity and mortality, and also a greater susceptibility to developing diseases (especially cardio-metabolic and neurological disorders) later in life. In the last decade, emerging evidence has supported the hypothesis of the Developmental Origin of Health and Disease, which states that individual developmental 'programming' takes place via a delicate fine tuning of fetal genetic and epigenetic marks in response to a large variety of 'stressor' exposures during pregnancy. As the placenta is the maternal-fetal interface, it has a crucial role in fetal programming, such that any perturbation altering placental function interferes with both in-utero fetal growth and also with the adult life phenotype. Several epigenetic mechanisms have been highlighted in modulating the dynamic placental epigenome, including alterations in DNA methylation status, post-translational modification of histones, and non-coding RNAs. This review aims to provide a comprehensive and critical overview of the available literature on the epigenetic background of fetal growth restriction. A targeted research strategy was performed using PubMed, MEDLINE, Embase, and The Cochrane Library up to January 2022. A detailed and fully referenced synthesis of available literature following the Scale for the Assessment of Narrative Review Articles guidelines is provided. A variety of epigenetic marks predominantly interfering with placental development, function, and metabolism were found to be potentially associated with fetal growth restriction. Available evidence on the role of environmental exposures in shaping the placental epigenome and the fetal phenotype were also critically discussed. Because of the highly dynamic crosstalk between epigenetic mechanisms and the extra level of complexity in interpreting the final placental transcriptome, a full comprehension of these phenomenon is still lacking and advances in multi-omics approaches are urgently needed. Elucidating the role of epigenetics in the developmental origins of health and disease represents a new challenge for the coming years, with the goal of providing early interventions and prevention strategies and, hopefully, new treatment opportunities.
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Affiliation(s)
- Noemi Salmeri
- Gynecology/Obstetrics Unit, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Ilma Floriana Carbone
- Unit of Obstetrics, Department of Woman, Child and Neonate, Mangiagalli Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo Ivo Cavoretto
- Gynecology/Obstetrics Unit, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Antonio Farina
- Division of Obstetrics and Prenatal Medicine, Department of Medicine and Surgery (DIMEC), IRCCS Sant'Orsola-Malpighi Hospital, University of Bologna, 40138, Bologna, Italy.
| | - Danila Morano
- Department of Morphology, Surgery and Experimental Medicine, Section of Obstetrics and Gynecology, Azienda Ospedaliero-Universitaria S. Anna, University of Ferrara, Cona, Ferrara, Italy
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17
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Chen P, Jia L, Zhou Y, Guo Y, Fang C, Li T. Interaction between endometrial microbiota and host gene regulation in recurrent implantation failure. J Assist Reprod Genet 2022; 39:2169-2178. [PMID: 35881269 PMCID: PMC9474991 DOI: 10.1007/s10815-022-02573-2] [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: 05/11/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
AIM To learn about the interaction between endometrial microbiota and host gene regulation in recurrent implantation failure. METHODS The endometrial microbiota of 111 patients (RIF, 75; CON, 36) was analyzed by using 16 s rRNA sequencing technology. Transcriptome sequencing analysis of the endometrial of 60 patients was performed by using high-throughput sequencing. RESULTS We found that the structure and composition of endometrium microbiota community of RIF patients were significantly different from those in control group. The abnormality of microbial structure and composition might interfere with the implantation of embryos by affecting the immune adaptation of the endometrium and the formation of endometrial blood vessels. CONCLUSIONS Our research described the host-microbe interaction in RIF. The structure and composition of endometrium microbiota community of RIF patients were significantly different from those in CON group. The abnormality of microbial structure and composition might interfere with the implantation of embryos by affecting the immune adaptation of the endometrium and the formation of endometrial blood vessels.
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Affiliation(s)
- Peigen Chen
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Lei Jia
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Yi Zhou
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Yingchun Guo
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Cong Fang
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
| | - Tingting Li
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
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18
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Peuranpää P, Holster T, Saqib S, Kalliala I, Tiitinen A, Salonen A, Hautamäki H. Female reproductive tract microbiota and recurrent pregnancy loss: a nested case-control study. Reprod Biomed Online 2022; 45:1021-1031. [DOI: 10.1016/j.rbmo.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 06/02/2022] [Accepted: 06/10/2022] [Indexed: 11/24/2022]
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19
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Microbiome as a predictor of implantation. Curr Opin Obstet Gynecol 2022; 34:122-132. [PMID: 35645010 DOI: 10.1097/gco.0000000000000782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Review the latest research on the female urogenital microbiome as a predictor of successful implantation. RECENT FINDINGS Lactobacillus crispatus seems to be beneficial species in a healthy female genital tract, although the presence of anaerobic bacteria and their impact has yet to be determined. The vaginal microbiome is associated with assisted reproductive technology (ART) outcome in terms of successful implantation and pregnancy. Approaches restoring a dysbiotic vaginal microbiome seem promising. It is questionable if a unique endometrial microbiome exists, given the low bacterial biomass, the invasiveness of endometrial sampling, and its associated high contamination risk. Future studies should focus on the whole microbiome using proteomics and metabolomics, as well as the virome to get a more holistic understanding of its role in reproduction. SUMMARY The vaginal and endometrial compartments are being studied to determine a healthy and unhealthy microbiome composition. Defining a healthy composition could provide insight into physiological processes related to the success of embryo implantation. The vaginal microbiome is easily accessible and its composition can be reliably assessed and can be associated with ART outcome. The existence of an endometrial or uterine microbiome is still debated, due to the combination of low biomass and unavoidable high risk of contamination during sampling.
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20
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Reschini M, Benaglia L, Ceriotti F, Borroni R, Ferrari S, Castiglioni M, Guarneri D, Porcaro L, Vigano' P, Somigliana E, Uceda Renteria S. Endometrial microbiome: sampling, assessment, and possible impact on embryo implantation. Sci Rep 2022; 12:8467. [PMID: 35589752 PMCID: PMC9120179 DOI: 10.1038/s41598-022-12095-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/05/2022] [Indexed: 11/08/2022] Open
Abstract
There is growing interest on the potential clinical relevance of the endometrial microbiome. However, insufficient attention has been given to the methodology of sampling. To minimize contamination, we advocate the use of the double-lumen catheters commonly employed for the embryo transfer. Endometrial fluid samples obtained from 53 women scheduled for IVF were studied for microbiome characterization. Control samples from the vagina of these same women were concomitantly obtained. Samples were analysed by V3-V4-V6 regions of 16S rRNA gene sequencing with Next Generation Sequencing technique. Endometrial Lactobacillus-dominant cases were uncommon compared to previous evidence, being observed in only 4 (8%) women. Taxonomy markedly differed between the endometrial and vaginal microbiomes composition. The most common bacterial genera coincided in only 4 (8%) women. The comparison between women who did and did not subsequently become pregnant failed to identify any microorganism associated with the success of the procedure. However, the endometrial biodiversity resulted higher among pregnant women. Shannon's Equitability index in pregnant and non pregnant women was 0.76 [0.57-0.87] and 0.55 [0.51-0.64], respectively (p = 0.002). In conclusion, the use of embryo transfer catheters for testing the endometrial microbiome is promising. The scant concordance with vaginal samples supports the validity of this approach. Moreover, our study highlighted a possible beneficial role of a higher biodiversity on endometrial receptivity.
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Affiliation(s)
- Marco Reschini
- Infertility Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via M. Fanti, 6, 20122, Milan, Italy.
| | - Laura Benaglia
- Infertility Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via M. Fanti, 6, 20122, Milan, Italy
| | - Ferruccio Ceriotti
- Dept of Clinical Sciences and Community Health, Università Degli Studi Di Milano, Milan, Italy
- Virology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Raffaella Borroni
- Infertility Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via M. Fanti, 6, 20122, Milan, Italy
| | - Stefania Ferrari
- Infertility Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via M. Fanti, 6, 20122, Milan, Italy
| | - Marta Castiglioni
- Infertility Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via M. Fanti, 6, 20122, Milan, Italy
- Dept of Clinical Sciences and Community Health, Università Degli Studi Di Milano, Milan, Italy
| | - Davide Guarneri
- Virology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luigi Porcaro
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paola Vigano'
- Infertility Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via M. Fanti, 6, 20122, Milan, Italy
| | - Edgardo Somigliana
- Infertility Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via M. Fanti, 6, 20122, Milan, Italy
- Dept of Clinical Sciences and Community Health, Università Degli Studi Di Milano, Milan, Italy
| | - Sara Uceda Renteria
- Virology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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21
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Wang Y, Wang X, Zhu M, Ge L, Liu X, Su K, Chen Z, Zhao W. The Interplay Between Cervicovaginal Microbial Dysbiosis and Cervicovaginal Immunity. Front Immunol 2022; 13:857299. [PMID: 35359942 PMCID: PMC8960256 DOI: 10.3389/fimmu.2022.857299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/21/2022] [Indexed: 12/02/2022] Open
Abstract
The cervicovaginal microbiota plays a key role in the health and reproductive outcomes of women. In reality epidemiological studies have demonstrated that there is an association between the structure of cervicovaginal microbiota and reproductive health, although key mechanistic questions regarding these effects remain unanswered and understanding the interplay between the immune system and the structure of the cervicovaginal microbiota. Here, we review existing literature relating to the potential mechanisms underlying the interaction between vaginal microbes and the immune system; we also describe the composition and function of the microbiome and explain the mechanisms underlying the interactions between these microbial communities and various aspects of the immune system. Finally, we also discuss the diseases that are caused by disorders of the reproductive tract and how the immune system is involved. Finally, based on the data presented in this review, the future perspectives in research directions and therapeutic opportunities are explored.
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Affiliation(s)
- Ya Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Xiaoli Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Meiling Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Li Ge
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Xiaochen Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Kaikai Su
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Zhengzheng Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Weidong Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
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22
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Hockney R, Orr CH, Waring GJ, Christiaens I, Taylor G, Cummings SP, Robson SC, Nelson A. Formalin-Fixed Paraffin-Embedded (FFPE) samples are not a beneficial replacement for frozen tissues in fetal membrane microbiota research. PLoS One 2022; 17:e0265441. [PMID: 35298530 PMCID: PMC8929612 DOI: 10.1371/journal.pone.0265441] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Formalin-Fixed Paraffin-Embedded (FFPE) tissues are routinely collected, archived, and used for clinical diagnosis, including maternal and neonatal health. Applying FFPE samples to microbiota research would be beneficial to reduce preparation, storage and costs associated with limited available frozen samples. This research aims to understand if FFPE fetal membrane samples are comparable to frozen tissues, which are the current gold standard for DNA microbiota analysis. Extracted DNA from nine matched paired patients were sequenced by Illumina sequencing of the V4 16S rRNA gene region. This included duplicate frozen amnion and chorion fetal membrane rolls or FFPE combined amniochorionic samples. Negative controls of surrounding wax blocks and DNA extraction reagents were processed alongside samples using identical methods. DNA quality and quantity was assessed by NanoDrop, agarose gel electrophoresis and Bioanalyzer. Decontam and SourceTracker were integrated into microbiota analysis to identify the presence of contaminating sources. The bacterial profile and nine genera differed between FFPE and frozen fetal membranes. There were no differences in bacterial profiles between FFPE samples and corresponding wax negative controls, with 49% of bacteria in FFPE fetal membrane samples matched to the source origin of paraffin wax, and 40% originating from DNA extraction reagent sources. FFPE samples displayed high fragmentation and low quantity of extracted DNA compared to frozen samples. The microbiota of FFPE fetal membrane samples is influenced by processing methods, with the inability to differentiate between the microbiota of the tissue sample and the surrounding wax block. Illumina sequencing results of FFPE and frozen fetal membrane samples should not be compared using the methods employed here. Variation could be influenced by limitations including storage time, DNA extraction and purification methods. To utilise FFPE fetal membrane samples in microbiota research then contamination prevention and detection methods must be included into optimised and standardised protocols, with recommendations presented here.
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Affiliation(s)
- Rochelle Hockney
- School of Health, Leeds Beckett University, Leeds, United Kingdom
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
- * E-mail:
| | - Caroline H. Orr
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Gareth J. Waring
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Inge Christiaens
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Gillian Taylor
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Stephen P. Cummings
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Stephen C. Robson
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
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23
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Plesniarski A, Siddik AB, Su RC. The Microbiome as a Key Regulator of Female Genital Tract Barrier Function. Front Cell Infect Microbiol 2022; 11:790627. [PMID: 34976864 PMCID: PMC8719631 DOI: 10.3389/fcimb.2021.790627] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
The microbiome, the collection of microbial species at a site or compartment, has been an underappreciated realm of human health up until the last decade. Mounting evidence suggests the microbiome has a critical role in regulating the female genital tract (FGT) mucosa's function as a barrier against sexually transmitted infections (STIs) and pathogens. In this review, we provide the most recent experimental systems and studies for analyzing the interplay between the microbiome and host cells and soluble factors with an influence on barrier function. Key components, such as microbial diversity, soluble factors secreted by host and microbe, as well as host immune system, all contribute to both the physical and immunologic aspects of the FGT mucosal barrier. Current gaps in what is known about the effects of the microbiome on FGT mucosal barrier function are compared and contrasted with the literature of the gut and respiratory mucosa. This review article presents evidence supporting that the vaginal microbiome, directly and indirectly, contributes to how well the FGT protects against infection.
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Affiliation(s)
- Andrew Plesniarski
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Abu Bakar Siddik
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Ruey-Chyi Su
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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Zakis DR, Paulissen E, Kornete L, Kaan AMM, Nicu EA, Zaura E. The evidence for placental microbiome and its composition in healthy pregnancies: A systematic review. J Reprod Immunol 2021; 149:103455. [PMID: 34883392 DOI: 10.1016/j.jri.2021.103455] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/11/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
Abstract
OBJECTIVE To assess the available scientific evidence regarding the placental microbial composition of a healthy pregnancy, the quality of this evidence, and the potential relation between placental and oral microbiome. MATERIALS AND METHODS Data sources: MEDLINE and EMBASE up to August 1, 2019. STUDY ELIGIBILITY CRITERIA Human subjects; healthy women; term deliveries; healthy normal birth weight; assessment of microorganisms (bacteria) in placental tissue; full research papers in English. The quality of the included studies was assessed by a modified Joanna Briggs Institute checklist for analytical cross-sectional studies. RESULTS 57 studies passed the inclusion criteria. Of these, 33 had a high risk of quality bias (e.g., insufficient infection control, lack of negative controls, poor description of the healthy cases). The remaining 24 studies had a low (N = 12) to moderate (N = 12) risk of bias and were selected for in-depth analysis. Of these 24 studies, 22 reported microorganisms in placental tissues, where Lactobacillus (11 studies), Ureaplasma (7), Fusobacterium (7), Staphylococcus (7), Prevotella (6) and Streptococcus (6) were among the most frequently identified genera. Methylobacterium (4), Propionibacterium (3), Pseudomonas (3) and Escherichia (2), among others, although frequently reported in placental samples, were often reported as contaminants in studies that used negative controls. CONCLUSIONS The results support the existence of a low biomass placental microbiota in healthy pregnancies. Some of the microbial taxa found in the placenta might have an oral origin. The high risk of quality bias for the majority of the included studies indicates that the results of individual papers should be interpreted with caution.
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Affiliation(s)
- Davis R Zakis
- Department of Conservative Dentistry and Oral Health, Faculty of Dentistry, Rīga Stradiņš University, Latvia; Department of Cariology, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, the Netherlands
| | - Eva Paulissen
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, the Netherlands
| | - Liga Kornete
- Faculty of Medicine, Rīga Stradiņš University, Latvia
| | - A M Marije Kaan
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, the Netherlands
| | - Elena A Nicu
- Department of Periodontology, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, the Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, the Netherlands.
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25
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Reply to Over-celling fetal microbial exposure. Cell 2021; 184:5842-5844. [PMID: 34822780 DOI: 10.1016/j.cell.2021.10.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 11/22/2022]
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26
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Punzón-Jiménez P, Labarta E. The impact of the female genital tract microbiome in women health and reproduction: a review. J Assist Reprod Genet 2021; 38:2519-2541. [PMID: 34110573 PMCID: PMC8581090 DOI: 10.1007/s10815-021-02247-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The aim of this review is to gather the available research focusing on female genital tract (FGT) microbiome. Research question focuses in decipher which is the role of FGT microbiota in eubiosis, assisted reproduction techniques (ARTs), and gynaecological disorders, and how microbiome could be utilised to improve reproduction outcomes and to treat fertility issues. METHODS PubMed was searched for articles in English from January 2004 to April 2021 for "genital tract microbiota and reproduction", "endometrial microbiome", "microbiome and reproduction" and "microbiota and infertility". Manual search of the references within the resulting articles was performed. RESULTS Current knowledge confirms predominance of Lactobacillus species, both in vagina and endometrium, whereas higher variability of species is both found in fallopian tubes and ovaries. Microbial signature linked to different disorders such endometriosis, bacterial vaginosis, and gynaecological cancers are described. Broadly, low variability of species and Lactobacillus abundance within the FGT is associated with better reproductive and ART outcomes. CONCLUSION Further research regarding FGT microbiome configuration needs to be done in order to establish a more precise link between microbiota and eubiosis or dysbiosis. Detection of bacterial species related with poor reproductive outcomes, infertility or gynaecological diseases could shape new tools for their diagnosis and treatment, as well as resources to assess the pregnancy prognosis based on endometrial microbiota. Data available suggest future research protocols should be standardised, and it needs to include the interplay among microbiome, virome and mycobiome, and the effect of antibiotics or probiotics on the microbiome shifts.
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Affiliation(s)
- Paula Punzón-Jiménez
- IVI Global Education, Edificio Bipolo, Hospital Universitario La Fe, Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain.
- Department of Pediatrics, Obstetrics and Gynaecology, Universitat de València, Av. Blasco Ibáñez, 15, 46010, Valencia, Spain.
| | - Elena Labarta
- IVIRMA Valencia, Plaza de la Policía Local, 3, 46015, Valencia, Spain
- IVI Foundation - IIS La Fe, Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain
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Chen W, Wei K, He X, Wei J, Yang L, Li L, Chen T, Tan B. Identification of Uterine Microbiota in Infertile Women Receiving in vitro Fertilization With and Without Chronic Endometritis. Front Cell Dev Biol 2021; 9:693267. [PMID: 34485281 PMCID: PMC8409574 DOI: 10.3389/fcell.2021.693267] [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: 04/10/2021] [Accepted: 07/21/2021] [Indexed: 01/13/2023] Open
Abstract
In vitro fertilization (IVF) is an important assisted reproductive technology in treating infertility, whose failure rate is still high. Studies suggested that uterine microbiota are related to women’s reproductive diseases and persisting intrauterine bacterial infectious conditions, such as chronic endometritis (CE), impairing the pregnant processes. However, the relationship between uterine microbiota and IVF outcomes is still an open question. In the present study, 94 patients diagnosed with infertility were enrolled and were divided into CE (E group, n = 25) and non-CE (NE group, n = 69) groups depending on the hysteroscopy and immunohistochemistry. Subsequently, E (Ep, n = 8 and Enp, n = 17) and NE (NEp, n = 41 and NEnp, n = 28) groups were divided into pregnancy and non-pregnancy groups depending on the IVF outcomes, respectively. The uterine fluids were collected and microbial profiles were examined through the V4 region of 16S rRNA gene high-throughput sequencing. The results demonstrated that patients with CE had significantly lower clinical pregnancy rate compared with the non-CE patients (32 vs. 58.42%, p = 0.0014). The relative abundances of Proteobacteria and Acidobacteria were higher in the non-CE group, whereas high abundances of Actinobacteria and Fusobacteria were observed in the CE group at the phylum level. At the genus level, high relative abundances of Gardnerella were observed in the CE group and non-pregnancy groups, which significantly referred to the negative IVF outcome. In conclusion, CE may be a key factor for the negative outcome after IVF, of which the uterine microbiota plays a pivotal role, and the microbial diversity in uterine may serve as a biomarker to forecast the success of IVF outcome.
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Affiliation(s)
- Weijun Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,The Reproductive Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Kehong Wei
- Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Xia He
- Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Jing Wei
- School of Life Sciences, Nanchang University, Nanchang, China
| | - Lijuan Yang
- The Reproductive Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Lin Li
- The Reproductive Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Tingtao Chen
- Institute of Translational Medicine, Nanchang University, Nanchang, China
| | - Buzhen Tan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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28
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Molina NM, Plaza-Díaz J, Vilchez-Vargas R, Sola-Leyva A, Vargas E, Mendoza-Tesarik R, Galán-Lázaro M, Mendoza-Ladrón de Guevara N, Tesarik J, Altmäe S. Assessing the testicular sperm microbiome: a low-biomass site with abundant contamination. Reprod Biomed Online 2021; 43:523-531. [PMID: 34344601 DOI: 10.1016/j.rbmo.2021.06.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/19/2021] [Accepted: 06/22/2021] [Indexed: 12/31/2022]
Abstract
RESEARCH QUESTION The semen harbours a diverse range of microorganisms. The origin of the seminal microbes, however, has not yet been established. Do testicular spermatozoa harbour microbes and could they potentially contribute to the seminal microbiome composition? DESIGN The study included 24 samples, comprising a total of 307 testicular maturing spermatozoa. A high-throughput sequencing method targeting V3 and V4 regions of 16S rRNA gene was applied. A series of negative controls together with stringent in-silico decontamination methods were analysed. RESULTS Between 50 and 70% of all the detected bacterial reads accounted for contamination in the testicular sperm samples. After stringent decontamination, Blautia (P = 0.04), Cellulosibacter (P = 0.02), Clostridium XIVa (P = 0.01), Clostridium XIVb (P = 0.04), Clostridium XVIII (P = 0.02), Collinsella (P = 0.005), Prevotella (P = 0.04), Prolixibacter (P = 0.02), Robinsoniella (P = 0.04), and Wandonia (P = 0.04) genera demonstrated statistically significant abundance among immature spermatozoa. CONCLUSIONS Our results indicate that the human testicle harbours potential bacterial signature, though in a low-biomass, and could contribute to the seminal microbiome composition. Further, applying stringent decontamination methods is crucial for analysing microbiome in low-biomass site.
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Affiliation(s)
- Nerea M Molina
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Sciences, Granada 18071, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Julio Plaza-Díaz
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain; University of Granada, Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Granada 18071, Spain; Institute of Nutrition and Food Technology (INYTA), 'José Mataix Verdú' Biomedical Research Centre (CIBM), University of Granada, Granada 18016, Spain; Children's Hospital of Eastern Ontario Research Institute, Ottawa ON K1H 8L1, Canada
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto von Guericke University Hospital Magdeburg, Magdeburg 39120, Germany
| | - Alberto Sola-Leyva
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Sciences, Granada 18071, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Eva Vargas
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Jaen 23071, Spain
| | | | - Maribel Galán-Lázaro
- MARGen Clinic, Molecular Assisted Reproduction and Genetics, Granada 18006, Spain
| | | | - Jan Tesarik
- MARGen Clinic, Molecular Assisted Reproduction and Genetics, Granada 18006, Spain
| | - Signe Altmäe
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Sciences, Granada 18071, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain; Competence Centre on Health Technologies, Tartu 50410, Estonia.
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Abstract
PURPOSE OF THE REVIEW In recent years there has been significant progress in the study of endometrial microbiota. This line of investigation has not been free of controversy and discussion. It is a key for clinicians involved to remain updated with the most recent findings in microbiome and its clinical implications to be able to offer patients all possible treatments. RECENT FINDINGS The existence of endometrial microbiota now seems undisputed. Current lines of work are centered on dysbiosis and its connection to other pathologies. It is in the field of assisted reproductive technology where this research plays an even more crucial role. In this case, we are focusing our attention toward the study of ectopic pregnancies, searching for similarities in their etiopathogenesis and alterations in the endometrial microbiota. SUMMARY Ectopic pregnancy has great repercussions for patients and for the healthcare system. We must continue researching to offer patients techniques and behaviors that can prevent it. The increase in its incidence makes ectopic pregnancy an entity that we must study.
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30
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Sola-Leyva A, Andrés-León E, Molina NM, Terron-Camero LC, Plaza-Díaz J, Sáez-Lara MJ, Gonzalvo MC, Sánchez R, Ruíz S, Martínez L, Altmäe S. Mapping the entire functionally active endometrial microbiota. Hum Reprod 2021; 36:1021-1031. [PMID: 33598714 DOI: 10.1093/humrep/deaa372] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/11/2020] [Indexed: 12/13/2022] Open
Abstract
STUDY QUESTION Does endometrium harbour functionally active microorganisms and whether the microbial composition differs between proliferative and mid-secretory phases? SUMMARY ANSWER Endometrium harbours functionally alive microorganisms including bacteria, viruses, archaea and fungi whose composition and metabolic functions change along the menstrual cycle. WHAT IS KNOWN ALREADY Resident microbes in the endometrium have been detected, where microbial dysfunction has been associated with reproductive health and disease. Nevertheless, the core microorganismal composition in healthy endometrium is not determined and whether the identified bacterial DNA sequences refer to alive/functionally active microbes is not clear. Furthermore, whether there are cyclical changes in the microbial composition remains an open issue. STUDY DESIGN, SIZE, DURATION RNA sequencing (RNAseq) data from 14 endometrial paired samples from healthy women, 7 samples from the mid-secretory phase and 7 samples from the consecutive proliferative phase were analysed for the microbial RNA sequences. PARTICIPANTS/MATERIALS, SETTING, METHODS The raw RNAseq data were converted into FASTQ format using SRA Toolkit. The unmapped reads to human sequences were aligned to the reference database Kraken2 and visualised with Krona software. Menstrual phase taxonomic differences were performed by R package metagenomeSeq. The functional analysis of endometrial microbiota was obtained with HUMANn2 and the comparison between menstrual phases was conducted by one-way ANOVA. Human RNAseq analysis was performed using miARma-Seq and the functional enrichment analysis was carried out using gene set enrichment analysis (GSEA; HumanCyc). The integration of metabolic pathways between host and microbes was investigated. The developed method of active microbiota mapping was validated in independent sample set. MAIN RESULTS AND THE ROLE OF CHANCE With the novel metatranscriptomic approach, we mapped the entire alive microbiota composing of >5300 microorganisms within the endometrium of healthy women. Microbes such as bacteria, fungi, viruses and archaea were identified. The validation of three independent endometrial samples from different ethnicity confirmed the findings. Significant differences in the microbial abundances in the mid-secretory vs. proliferative phases were detected with possible metabolic activity in the host-microbiota crosstalk in receptive phase endometrium, specifically in the prostanoid biosynthesis pathway and L-tryptophan metabolism. LARGE SCALE DATA The raw RNAseq data used in the current study are available at GEO GSE86491 and at BioProject PRJNA379542. LIMITATIONS, REASONS FOR CAUTION These pioneering results should be confirmed in a bigger sample size. WIDER IMPLICATIONS OF THE FINDINGS Our study confirms the presence of active microbes, bacteria, fungi, viruses and archaea in the healthy human endometrium with implications in receptive phase endometrial functions, meaning that microbial dysfunction could impair the metabolic pathways important for endometrial receptivity. The results of this study contribute to the better understanding of endometrial microbiota composition in healthy women and its possible role in endometrial functions. In addition, our novel methodological pipeline for analysing alive microbes with transcriptional and metabolic activities could serve to inspire new analysis approaches in reproductive medicine. STUDY FUNDING/COMPETING INTERESTS This work is supported by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER): grants RYC-2016-21199 and ENDORE SAF2017-87526-R; FEDER/Junta de Andalucía-Consejería de Economía y Conocimiento: MENDO (B-CTS-500-UGR18) and by the University of Granada Plan Propio de Investigación 2016 - Excellence actions: Unit of Excellence on Exercise and Health (UCEES) (SOMM17/6107/UGR). A.S.-L. and N.M.M. are funded by the Spanish Ministry of Science, Innovation and Universities (PRE2018-0854409 and FPU19/01638). S.A. has received honoraria for lectures from Merck. The funder had no role in this study.
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Affiliation(s)
- Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Eduardo Andrés-León
- Unidad de Bioinformática, Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada 18016, Spain
| | - Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Laura Carmen Terron-Camero
- Unidad de Bioinformática, Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada 18016, Spain
| | - Julio Plaza-Díaz
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada 18071, Spain.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - María José Sáez-Lara
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Institute of Nutrition and Food Technology (INYTA), "José Mataix Verdú" Biomedical Research Centre (CIBM), University of Granada, Armilla, Granada 18016, Spain
| | - María Carmen Gonzalvo
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Unidad Reproducción, UGC Laboratorio clínico y UGC Obstetricia y Ginecología. Hospital Universitario Virgen de las Nieves, Granada 18014, Spain
| | - Rocío Sánchez
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Unidad Reproducción, UGC Laboratorio clínico y UGC Obstetricia y Ginecología. Hospital Universitario Virgen de las Nieves, Granada 18014, Spain
| | - Susana Ruíz
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Unidad Reproducción, UGC Laboratorio clínico y UGC Obstetricia y Ginecología. Hospital Universitario Virgen de las Nieves, Granada 18014, Spain
| | - Luís Martínez
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Unidad Reproducción, UGC Laboratorio clínico y UGC Obstetricia y Ginecología. Hospital Universitario Virgen de las Nieves, Granada 18014, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Competence Centre on Health Technologies, Tartu 50411, Estonia
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Neckovic A, van Oorschot RAH, Szkuta B, Durdle A. Identifying background microbiomes in an evidence recovery laboratory: A preliminary study. Sci Justice 2021; 61:280-290. [PMID: 33985676 DOI: 10.1016/j.scijus.2021.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/08/2020] [Accepted: 01/03/2021] [Indexed: 01/16/2023]
Abstract
16S rRNA profiling of bacterial communities may have forensic utility in the identification or association of individuals involved with criminal activities. Microbial profiling of evidence may, in the future, be performed within environments currently utilised for human DNA recovery, such as a forensic biology laboratory. It would be important to establish the background microbiome of such an environment to determine the potential presence of human or environmental microbial signatures to assist forensic scientists in the appropriate interpretation of target microbial communities. This study sampled various surfaces of an Evidence Recovery Laboratory (ERL) on three occasions including (a) before a monthly deep-clean, (b) immediately following the deep-clean, and (c) immediately after the laboratory's use by a single participant for the purposes of routine item examinations. Microbial profiles were also generated for the involved participant and researcher for comparison purposes. Additionally, human nuclear DNA was profiled for each of the samples collected, using standard forensic profiling techniques, to provide a prospective link to the presence or absence of a background microbial signature within the ERL after its use. Taxonomic distributions across ERL samples revealed no consistent signature of any of the items sampled over time, however, major phyla noted within all ERL samples across the three timepoints were consistent with those found in human skin microbiomes. PCoA plots based on the Unweighted Unifrac metric revealed some clustering between participant microbial reference samples and surfaces of the ERL after use, suggesting that despite a lack of direct contact, and adherence to standard operating procedures (SOPs) suitable for human DNA recovery, microbiomes may be deposited into a forensic setting over time. The reference samples collected from the involved participant and researcher generated full STR profiles. Human DNA was observed to varying degrees in samples taken from the ERL across each of the sampling timepoints. There was no correlation observed between samples that contained or did not contain detectable quantities of human nuclear DNA and microbial profile outputs.
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Affiliation(s)
- Ana Neckovic
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia.
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, Macleod, Australia; School of Molecular Sciences, La Trobe University, Bundoora, Australia
| | - Bianca Szkuta
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, Macleod, Australia
| | - Annalisa Durdle
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
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Lietaer L, Bogado Pascottini O, Hernandez-Sanabria E, Kerckhof FM, Lacoere T, Boon N, Vlaminck L, Opsomer G, Van de Wiele T. Low microbial biomass within the reproductive tract of mid-lactation dairy cows: A study approach. J Dairy Sci 2021; 104:6159-6174. [PMID: 33685679 DOI: 10.3168/jds.2020-19554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
The microbiome from the reproductive tract is being investigated for its putative effect on fertility, embryo development, and health status of the human or animal host postpartum. Besides the presence of a vaginal microbiome, recent studies have claimed the existence and putative role of the uterine microbiome. Yet, the extremely low bacterial numbers and high eukaryotic/prokaryotic DNA ratio make this a highly challenging environment to study with next-generation sequencing (NGS) techniques. Here, we describe the methodological challenges that are typically encountered when performing an accurate analysis of low microbial biomass samples, illustrated by data of our own observational study. In terms of the research question, we compared the microbial composition throughout different parts of the reproductive tract of clinically healthy, mid-lactation Holstein-Friesian cows. Samples were collected from 5 dairy cows immediately after killing. Swabs were taken from the vagina, and from 4 pre-established locations of the uterine endometrium. In addition to the conventional DNA extraction blank controls, sterile swabs rubbed over disinfected disposable gloves and the disinfected surface of the uterus (tunica serosa) before incision were taken as sampling controls. The DNA extraction, DNA quantification, quantitative PCR of the 16S rRNA genes, and 16S rRNA gene sequencing were performed. In terms of NGS data analysis, we performed prevalence-based filtering of putative contaminant operational taxonomic units (OTU) using the decontam R package. Although the bacterial composition differed between the vagina and uterus, no differences in bacterial community structure (α and β diversity) were found among the different locations in the uterus. At phylum level, uterine samples had a greater relative abundance of Proteobacteria, and a lesser relative abundance of Firmicutes than vaginal samples. The number of shared OTU between vagina and uterus was limited, suggesting the existence of bacterial transmission routes other than the transcervical one to the uterus. The mid-lactation bovine genital tract is a low microbial biomass environment, which makes it difficult to distinguish between its constitutive versus contaminant microbiome. The integration of key controls is therefore strictly necessary to decrease the effect of accidentally introduced contaminant sequences and improve the reliability of results in samples with low microbial biomass.
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Affiliation(s)
- L Lietaer
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - O Bogado Pascottini
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium; Department of Veterinary Sciences, Laboratory of Veterinary Physiology and Biochemistry, University of Antwerp, Wilrijk 2610, Belgium
| | - E Hernandez-Sanabria
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven 3000, Belgium
| | - F-M Kerckhof
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent 9000, Belgium
| | - T Lacoere
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent 9000, Belgium
| | - N Boon
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent 9000, Belgium
| | - L Vlaminck
- Department of Surgery and Anaesthesiology of Domestic Animals, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - G Opsomer
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium.
| | - T Van de Wiele
- Department of Biotechnology, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent 9000, Belgium
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Oberle A, Urban L, Falch-Leis S, Ennemoser C, Nagai Y, Ashikawa K, Ulm PA, Hengstschläger M, Feichtinger M. 16S rRNA long-read nanopore sequencing is feasible and reliable for endometrial microbiome analysis. Reprod Biomed Online 2021; 42:1097-1107. [PMID: 33849786 DOI: 10.1016/j.rbmo.2021.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 01/09/2023]
Abstract
RESEARCH QUESTION Full-length 16S rRNA gene sequencing using nanopore technology is a fast alternative to conventional short-read 16S rRNA gene sequencing with low initial investment costs that has been used for various microbiome studies but has not yet been investigated as an alternative approach for endometrial microbiome analysis. Is in-situ 16S rRNA gene long-read sequencing using portable nanopore sequencing technology feasible and reliable for endometrial microbiome analysis? DESIGN A prospective experimental study based on 33 patients seeking infertility treatment between January and October 2019. A 16S rRNA gene long-read nanopore sequencing protocol for analysing endometrial microbiome samples was established, including negative controls for contamination evaluation and positive controls for bias evaluation. Contamination caused by kit and exterior sources was identified and excluded from the analysis. Endometrial samples from 33 infertile patients were sequenced using the optimized long-read nanopore sequencing protocol and compared with conventional short-read sequencing carried out by external laboratories. RESULTS Of the 33 endometrial patient samples, 23 successfully amplified (69.7%) and their microbiome was assessed using nanopore sequencing. Of those 23 samples, 14 (60.9%) were Lactobacillus-dominated (>80% of reads mapping to Lactobacillus), with 10 samples resulting in more than 90% Lactobacillus reads. Our long-read nanopore sequencing revealed results similar to two conventional short-read sequencing approaches and to long-read sequencing validation carried out in external laboratories. CONCLUSION In this pilot study, 16S rRNA gene long-read nanopore sequencing was established to analyse the endometrial microbiome in situ that could be widely applied owing to its cost efficiency and portable character.
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Affiliation(s)
- Anna Oberle
- Wunschbaby Institut Feichtinger, Lainzerstrasse 6, Vienna 1130, Austria
| | - Lara Urban
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Department of Anatomy, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Stefanie Falch-Leis
- Tyrolpath, Pathologielabor Dr. Obrist Dr. Brunhuber, Hauptplatz 4, Zams 6511, Austria
| | - Chiara Ennemoser
- Tyrolpath, Pathologielabor Dr. Obrist Dr. Brunhuber, Hauptplatz 4, Zams 6511, Austria
| | - Yoko Nagai
- Varinos, Inc., Dai 2 Gotanda Fujikoshi Bldg., 6F 5-23-1 Higashigotanda, Shinagawa-ku Tokyo, Japan
| | - Kyota Ashikawa
- Varinos, Inc., Dai 2 Gotanda Fujikoshi Bldg., 6F 5-23-1 Higashigotanda, Shinagawa-ku Tokyo, Japan
| | - Patricia A Ulm
- Wunschbaby Institut Feichtinger, Lainzerstrasse 6, Vienna 1130, Austria
| | | | - Michael Feichtinger
- Wunschbaby Institut Feichtinger, Lainzerstrasse 6, Vienna 1130, Austria; Department of Oncology - Pathology, Karolinska Institutet, Karolinska vägen, A2:07171 64 Solna Stockholm, Sweden.
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Molina NM, Sola-Leyva A, Haahr T, Aghajanova L, Laudanski P, Castilla JA, Altmäe S. Analysing endometrial microbiome: methodological considerations and recommendations for good practice. Hum Reprod 2021; 36:859-879. [DOI: 10.1093/humrep/deab009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT
There is growing evidence that the upper female genital tract is not sterile, harbouring its own microbial communities. However, the significance and the potential effect of endometrial microorganisms on reproductive functions remain to be fully elucidated. Analysing the endometrial microbiome, the microbes and their genetic material present in the endometrium, is an emerging area of study. The initial studies suggest it is associated with poor reproductive outcomes and with different gynaecological pathologies. Nevertheless, studying a low-biomass microbial niche as is endometrium, the challenge is to conduct well-designed and well-controlled experiments in order to avoid and adjust for the risk of contamination, especially from the lower genital tract. Herein, we aim to highlight methodological considerations and propose good practice recommendations for future endometrial microbiome studies.
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Affiliation(s)
- Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Thor Haahr
- The Fertility Clinic, Skive Regional Hospital, Skive 7800, Denmark
| | - Lusine Aghajanova
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Stanford School of Medicine, Sunnyvale, CA 94087, USA
| | - Piotr Laudanski
- Department of Obstetrics and Gynecology, Medical University of Warsaw, Warsaw 02-015, Poland
| | - Jose Antonio Castilla
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, Granada 18012, Spain
- CEIFER Biobanco—NextClinics, Granada 18004, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
- Competence Centre on Health Technologies, Tartu 50410, Estonia
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35
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Silverstein RB, Mysorekar IU. Group therapy on in utero colonization: seeking common truths and a way forward. MICROBIOME 2021; 9:7. [PMID: 33436100 PMCID: PMC7805186 DOI: 10.1186/s40168-020-00968-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/06/2020] [Indexed: 05/04/2023]
Abstract
The human microbiome refers to the genetic composition of microorganisms in a particular location in the human body. Emerging evidence over the past many years suggests that the microbiome constitute drivers of human fate almost at par with our genome and epigenome. It is now well accepted after decades of disbelief that a broad understanding of human development, health, physiology, and disease requires understanding of the microbiome along with the genome and epigenome. We are learning daily of the interdependent relationships between microbiome/microbiota and immune responses, mood, cancer progression, response to therapies, aging, obesity, antibiotic usage, and overusage and much more. The next frontier in microbiome field is understanding when does this influence begin? Does the human microbiome initiate at the time of birth or are developing human fetuses already primed with microbes and their products in utero. In this commentary, we reflect on evidence gathered thus far on this question and identify the unknown common truths. We present a way forward to continue understanding our microbial colleagues and our interwoven fates.
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Affiliation(s)
- Rachel B Silverstein
- Department of Obstetrics and Gynecology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA
| | - Indira U Mysorekar
- Department of Obstetrics and Gynecology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA.
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA.
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36
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Scott EM, Lewin AC, Leis ML. Current ocular microbiome investigations limit reproducibility and reliability: Critical review and opportunities. Vet Ophthalmol 2020; 24:4-11. [PMID: 33382917 DOI: 10.1111/vop.12854] [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: 09/28/2020] [Revised: 11/13/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022]
Abstract
Enthusiasm for research describing microbial communities using next-generation sequencing (NGS) has outpaced efforts to standardize methodology. Without consistency in the way research is carried out in this field, the comparison of data between studies is near impossible and the utility of results remains limited. This holds true for bacterial microbiome research of the ocular surface, and other sites, in both humans and animals. In addition, the ocular surface remains under-explored when compared to other mucosal sites. Low bacterial biomass samples from the ocular surface lead to further technical challenges. Taken together, two major problems were identified: (1) Normalization of the workflow in studies utilizing NGS to investigate the ocular surface bacteriome is necessary in order to propel the field forward and improve research impact through cross-study comparisons. (2) Current microbiome profiling technology was developed for high bacterial biomass samples (such as feces or soil), posing a challenge for analyses of samples with low bacterial load such as the ocular surface. This article reviews the challenges and limitations currently facing ocular microbiome research and provides recommendations for minimum reporting standards for veterinary ophthalmologists and clinician scientists to limit inter-study variation, improve reproducibility, and ultimately render results from these studies more impactful. The move toward normalization of methodology will expedite and maximize the potential for microbiome research to translate into meaningful discovery and tangible clinical applications.
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Affiliation(s)
- Erin M Scott
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
| | - Andrew C Lewin
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Marina L Leis
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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37
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He Q, Kwok LY, Xi X, Zhong Z, Ma T, Xu H, Meng H, Zhao F, Zhang H. The meconium microbiota shares more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota. Gut Microbes 2020; 12:1794266. [PMID: 32744162 PMCID: PMC7524391 DOI: 10.1080/19490976.2020.1794266] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 02/03/2023] Open
Abstract
The early-life gut microbiota is associated with potential development of diseases in adulthood. The sterile womb paradigm has been challenged by recent reports that revealed the presence of the meconium, amniotic fluid, and placenta microbiome. This study aimed to explore the maternal origin of the microbiota of neonate meconium by using the PacBio single-molecule real-time circular consensus sequencing technology. Such technology could produce high fidelity reads of full-length 16S rRNA genes, improving the sensitivity and specificity of taxonomic profiling. It also reduced the risk of false positives. This study analyzed the full-length 16S rRNA-based microbiota of maternal samples (amniotic fluid, feces, vaginal fluid, saliva) and first-pass meconium of 39 maternal-neonate pairs. Alpha- and beta-diversity analyses revealed sample type-specific microbiota features. Most sample types were dominated by sequences representing different genera (Lactobacillus and Curvibacter in the amniotic fluid and vaginal fluid microbiota; Bacillus and Escherichia/Shigella in the meconium microbiota; Bacteroides and Faecalibacterium in the maternal fecal microbiota; Streptococcus and Prevotella in the maternal saliva microbiota). Moreover, specific operational taxonomic units (OTUs) were identified in all sample types. Dyad analysis revealed common OTUs between the meconium microbiota and microbiota of multiple maternal samples. The meconium microbiota shared more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota. Our results strongly suggested that the meconium microbiota was seeded from multiple maternal body sites, and the amniotic fluid microbiota contributed most to the seeding of the meconium microbiota among the investigated maternal body sites.
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Affiliation(s)
- Qiuwen He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R.C, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs P.R.C., Inner Mongolia Agricultural University, Huhhot, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R.C, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs P.R.C., Inner Mongolia Agricultural University, Huhhot, China
| | - Xiaoxia Xi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R.C, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs P.R.C., Inner Mongolia Agricultural University, Huhhot, China
| | - Zhi Zhong
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R.C, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs P.R.C., Inner Mongolia Agricultural University, Huhhot, China
| | - Teng Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R.C, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs P.R.C., Inner Mongolia Agricultural University, Huhhot, China
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R.C, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs P.R.C., Inner Mongolia Agricultural University, Huhhot, China
| | - Haixia Meng
- Department of Gynecology and Obstetrics, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P.R.C, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs P.R.C., Inner Mongolia Agricultural University, Huhhot, China
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38
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Abstract
The interplay between the commensal microbiota and the mammalian immune system development and function includes multifold interactions in homeostasis and disease. The microbiome plays critical roles in the training and development of major components of the host's innate and adaptive immune system, while the immune system orchestrates the maintenance of key features of host-microbe symbiosis. In a genetically susceptible host, imbalances in microbiota-immunity interactions under defined environmental contexts are believed to contribute to the pathogenesis of a multitude of immune-mediated disorders. Here, we review features of microbiome-immunity crosstalk and their roles in health and disease, while providing examples of molecular mechanisms orchestrating these interactions in the intestine and extra-intestinal organs. We highlight aspects of the current knowledge, challenges and limitations in achieving causal understanding of host immune-microbiome interactions, as well as their impact on immune-mediated diseases, and discuss how these insights may translate towards future development of microbiome-targeted therapeutic interventions.
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39
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Zheng D, Liwinski T, Elinav E. Interaction between microbiota and immunity in health and disease. Cell Res 2020; 30:492-506. [PMID: 32433595 PMCID: PMC7264227 DOI: 10.1038/s41422-020-0332-7] [Citation(s) in RCA: 1534] [Impact Index Per Article: 383.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/20/2020] [Indexed: 02/08/2023] Open
Abstract
The interplay between the commensal microbiota and the mammalian immune system development and function includes multifold interactions in homeostasis and disease. The microbiome plays critical roles in the training and development of major components of the host's innate and adaptive immune system, while the immune system orchestrates the maintenance of key features of host-microbe symbiosis. In a genetically susceptible host, imbalances in microbiota-immunity interactions under defined environmental contexts are believed to contribute to the pathogenesis of a multitude of immune-mediated disorders. Here, we review features of microbiome-immunity crosstalk and their roles in health and disease, while providing examples of molecular mechanisms orchestrating these interactions in the intestine and extra-intestinal organs. We highlight aspects of the current knowledge, challenges and limitations in achieving causal understanding of host immune-microbiome interactions, as well as their impact on immune-mediated diseases, and discuss how these insights may translate towards future development of microbiome-targeted therapeutic interventions.
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Affiliation(s)
- Danping Zheng
- Immunology Department, Weizmann Institute of Science, 234 Herzl Street, 7610001, Rehovot, Israel.,Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Timur Liwinski
- Immunology Department, Weizmann Institute of Science, 234 Herzl Street, 7610001, Rehovot, Israel.,1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, 234 Herzl Street, 7610001, Rehovot, Israel. .,Cancer-Microbiome Division, Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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40
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Theis KR, Romero R, Winters AD, Jobe AH, Gomez-Lopez N. Lack of Evidence for Microbiota in the Placental and Fetal Tissues of Rhesus Macaques. mSphere 2020; 5:e00210-20. [PMID: 32376701 PMCID: PMC7203455 DOI: 10.1128/msphere.00210-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
The prevailing paradigm in obstetrics has been the sterile womb hypothesis. However, some are asserting that the placenta, intra-amniotic environment, and fetus harbor microbial communities. The objective of this study was to determine whether the fetal and placental tissues of rhesus macaques harbor bacterial communities. Fetal, placental, and uterine wall samples were obtained from cesarean deliveries without labor (∼130/166 days gestation). The presence of bacteria in the fetal intestine and placenta was investigated through culture. The bacterial burden and profiles of the placenta, umbilical cord, and fetal brain, heart, liver, and colon were determined through quantitative real-time PCR and DNA sequencing. These data were compared with those of the uterine wall as well as to negative and positive technical controls. Bacterial cultures of fetal and placental tissues yielded only a single colony of Cutibacterium acnes This bacterium was detected at a low relative abundance (0.02%) in the 16S rRNA gene profile of the villous tree sample from which it was cultured, yet it was also identified in 12/29 background technical controls. The bacterial burden and profiles of fetal and placental tissues did not exceed or differ from those of background technical controls. By contrast, the bacterial burden and profiles of positive controls exceeded and differed from those of background controls. Among the macaque samples, distinct microbial signals were limited to the uterine wall. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of bacterial communities in the fetal and placental tissues of rhesus macaques.IMPORTANCE Microbial invasion of the amniotic cavity (i.e., intra-amniotic infection) has been causally linked to pregnancy complications, especially preterm birth. Therefore, if the placenta and the fetus are typically populated by low-biomass microbial communities, current understanding of the role of microbes in reproduction and pregnancy outcomes will need to be fundamentally reconsidered. Could these communities be of benefit by competitively excluding potential pathogens or priming the fetal immune system for the microbial bombardment it will experience upon delivery? If so, what properties (e.g., microbial load and community membership) of these microbial communities preclude versus promote intra-amniotic infection? Given the ramifications of the in utero colonization hypothesis, critical evaluation is required. In this study, using multiple modes of microbiologic inquiry (i.e., culture, quantitative real-time PCR [qPCR], and DNA sequencing) and controlling for potential background DNA contamination, we did not find consistent evidence for microbial communities in the placental and fetal tissues of rhesus macaques.
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Affiliation(s)
- Kevin R Theis
- Department of Biochemistry, Microbiology and Immunology, 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, Maryland, and 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, Maryland, and 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
- Department of Obstetrics and Gynecology, Florida International University, Miami, Florida, USA
| | - Andrew D Winters
- Department of Biochemistry, Microbiology and Immunology, 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, Maryland, and Detroit, Michigan, USA
| | - Alan H Jobe
- Cincinnati Children's Hospital, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
| | - Nardhy Gomez-Lopez
- Department of Biochemistry, Microbiology and Immunology, 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, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
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41
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Molina NM, Sola-Leyva A, Saez-Lara MJ, Plaza-Diaz J, Tubić-Pavlović A, Romero B, Clavero A, Mozas-Moreno J, Fontes J, Altmäe S. New Opportunities for Endometrial Health by Modifying Uterine Microbial Composition: Present or Future? Biomolecules 2020; 10:E593. [PMID: 32290428 PMCID: PMC7226034 DOI: 10.3390/biom10040593] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 02/08/2023] Open
Abstract
Current knowledge suggests that the uterus harbours its own microbiota, where the microbes could influence the uterine functions in health and disease; however, the core uterine microbial composition and the host-microbial relationships remain to be fully elucidated. Different studies are indicating, based on next-generation sequencing techniques, that microbial dysbiosis could be associated with several gynaecological disorders, such as endometriosis, chronic endometritis, dysfunctional menstrual bleeding, endometrial cancer, and infertility. Treatments using antibiotics and probiotics and/or prebiotics for endometrial microbial dysbiosis are being applied. Nevertheless there is no unified protocol for assessing the endometrial dysbiosis and no optimal treatment protocol for the established dysbiosis. With this review we outline the microbes (mostly bacteria) identified in the endometrial microbiome studies, the current treatments offered for bacterial dysbiosis in the clinical setting, and the future possibilities such as pro- and prebiotics and microbial transplants for modifying uterine microbial composition.
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Affiliation(s)
- Nerea M. Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (N.M.M.); (A.S.-L.); (M.J.S.-L.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
| | - Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (N.M.M.); (A.S.-L.); (M.J.S.-L.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
| | - Maria Jose Saez-Lara
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (N.M.M.); (A.S.-L.); (M.J.S.-L.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- “José Mataix Verdú” Institute of Nutrition and Food Technology (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18100 Granada, Spain
| | - Julio Plaza-Diaz
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- “José Mataix Verdú” Institute of Nutrition and Food Technology (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18100 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18011 Granada, Spain
| | | | - Barbara Romero
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Ana Clavero
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Juan Mozas-Moreno
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER Epidemiología y Salud Pública-CIBERESP), 28029 Madrid, Spain
- Departament of Obstetrics and Gynecology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Juan Fontes
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (N.M.M.); (A.S.-L.); (M.J.S.-L.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain; (J.P.-D.); (B.R.); (A.C.); (J.M.-M.); (J.F.)
- Competence Centre on Health Technologies, 50410 Tartu, Estonia
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Abstract
Necrotizing enterocolitis (NEC) is a poorly defined disease that primarily affects preterm infants. There has not been much progress in the prevention or treatment of NEC since it became recognized as a common problem in preterm infants. Reasons for this lack of progress include the likelihood that different diseases are being put under the same moniker of "NEC," similar to using "diabetes" for the different diseases it represents. In order to make progress, better delineation of the phenotypes that present as NEC will be necessary to clearly establish their pathophysiology, find specific and sensitive biomarkers, and establish preventative regimens. In this review, we summarize some of the entities that are being called NEC, discuss the pathophysiology of the most classic form of NEC, and provide an overview of how we might proceed in the future to make progress in this field.
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Affiliation(s)
- Josef Neu
- University of Florida, Gainesville, USA.
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43
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Theis KR, Romero R, Greenberg JM, Winters AD, Garcia-Flores V, Motomura K, Ahmad MM, Galaz J, Arenas-Hernandez M, Gomez-Lopez N. No Consistent Evidence for Microbiota in Murine Placental and Fetal Tissues. mSphere 2020; 5:e00933-19. [PMID: 32102944 PMCID: PMC7045391 DOI: 10.1128/msphere.00933-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/05/2020] [Indexed: 12/26/2022] Open
Abstract
The existence of a placental microbiota and in utero colonization of the fetus have been the subjects of recent debate. The objective of this study was to determine whether the placental and fetal tissues of mice harbor bacterial communities. Bacterial profiles of the placenta and fetal brain, lung, liver, and intestine samples were characterized through culture, quantitative real-time PCR (qPCR), and 16S rRNA gene sequencing. These profiles were compared to those of the maternal mouth, lung, liver, uterus, cervix, vagina, and intestine, as well as to background technical controls. Positive bacterial cultures from placental and fetal tissue samples were rare; of the 165 total bacterial cultures of placental tissue samples from the 11 mice included in this study, only nine yielded at least a single colony, and five of those nine positive cultures came from a single mouse. Cultures of fetal intestinal tissue samples yielded just a single bacterial isolate, Staphylococcus hominis, a common skin bacterium. Bacterial loads of placental and fetal brain, lung, liver, and intestinal tissues were not higher than those of DNA contamination controls and did not yield substantive 16S rRNA gene sequencing libraries. From all placental or fetal tissue samples (n = 51), there was only a single bacterial isolate that came from a fetal brain sample having a bacterial load higher than that of contamination controls and that was identified in sequence-based surveys of at least one of its corresponding maternal samples. Therefore, using multiple modes of microbiological inquiry, there was not consistent evidence of bacterial communities in the placental and fetal tissues of mice.IMPORTANCE The prevailing paradigm in obstetrics has been the sterile womb hypothesis, which posits that fetuses are first colonized by microorganisms during the delivery process. However, some are now suggesting that fetuses are consistently colonized in utero by microorganisms from microbial communities that inhabit the placenta and intra-amniotic environment. Given the established causal role of microbial invasion of the amniotic cavity (i.e., intra-amniotic infection) in pregnancy complications, especially preterm birth, if the in utero colonization hypothesis were true, there are several aspects of current understanding that will need to be reconsidered; these aspects include the magnitude of intra-amniotic microbial load required to cause disease and its potential influence on the ontogeny of the immune system. However, acceptance of the in utero colonization hypothesis is premature. Herein, we do not find consistent evidence for placental and fetal microbiota in mice using culture, qPCR, and DNA sequencing.
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Affiliation(s)
- Kevin R Theis
- Department of Biochemistry, Microbiology and Immunology, 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, 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, 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
- Department of Obstetrics and Gynecology, Florida International University, Miami, Florida, USA
| | - Jonathan M Greenberg
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Andrew D Winters
- Department of Biochemistry, Microbiology and Immunology, 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, Detroit, Michigan, USA
| | - 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, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Kenichiro Motomura
- 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, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Madison M Ahmad
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jose Galaz
- 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, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcia Arenas-Hernandez
- 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, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Nardhy Gomez-Lopez
- Department of Biochemistry, Microbiology and Immunology, 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, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
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O’Callaghan JL, Clifton VL, Prentis P, Ewing A, Miller YD, Pelzer ES. Modulation of Placental Gene Expression in Small-for-Gestational-Age Infants. Genes (Basel) 2020; 11:genes11010080. [PMID: 31936801 PMCID: PMC7017208 DOI: 10.3390/genes11010080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/19/2019] [Accepted: 01/07/2020] [Indexed: 02/08/2023] Open
Abstract
Small-for-gestational-age (SGA) infants are fetuses that have not reached their genetically programmed growth potential. Low birth weight predisposes these infants to an increased risk of developing cardiovascular, metabolic and neurodevelopmental conditions in later life. However, our understanding of how this pathology occurs is currently incomplete. Previous research has focused on understanding the transcriptome, epigenome and bacterial signatures separately. However, we hypothesise that interactions between moderators of gene expression are critical to understanding fetal growth restriction. Through a review of the current literature, we identify that there is evidence of modulated expression/methylation of the placental genome and the presence of bacterial DNA in the placental tissue of SGA infants. We also identify that despite limited evidence of the interactions between the above results, there are promising suggestions of a relationship between bacterial signatures and placental function. This review aims to summarise the current literature concerning fetal growth from multiple avenues and propose a novel relationship between the placental transcriptome, methylome and bacterial signature that, if characterised, may be able to improve our current understanding of the placental response to stress and the aetiology of growth restriction.
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Affiliation(s)
- Jessica L. O’Callaghan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane 4001, Queensland, Australia;
- Institute of Health and Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane 4059, Queensland, Australia
- Correspondence:
| | - Vicki L. Clifton
- Mater Medical Research Institute, University of Queensland, Brisbane 4101, Queensland, Australia; (V.L.C.); (A.E.)
| | - Peter Prentis
- School of Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane 4001, Queensland, Australia;
| | - Adam Ewing
- Mater Medical Research Institute, University of Queensland, Brisbane 4101, Queensland, Australia; (V.L.C.); (A.E.)
| | - Yvette D. Miller
- School of Public Health and Social Work, Faculty of Health, Queensland University of Technology, Brisbane 4059, Queensland, Australia;
| | - Elise S. Pelzer
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane 4001, Queensland, Australia;
- Institute of Health and Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane 4059, Queensland, Australia
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